[2018] DAT Bootcamp Biology Notes (1)

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Table of Contents
Chapter 1: Molecules and Fundamentals of Biology
Chapter 2: Cells and Organelles
Chapter 3: Cellular Energy
Chapter 4: Photosynthesis
Chapter 5: Cell Division
Chapter 6: Molecular Genetics
Chapter 7: Heredity
Chapter 8: Microscopy & Lab Techniques
Chapter 9: Diversity of Life
Chapter 10: Plants
Chapter 11.1: Circulatory System
Chapter 11.2: Respiratory System
Chapter 11.3: Human Immune System
Chapter 11.4: Nervous System
Chapter 11.5: Muscular System
Chapter 11.6: Skeletal System
Chapter 11.7: Endocrine System
Chapter 11.8: Digestive System
Chapter 11.9: Excretory System
Chapter 11.10: Integumentary System
Chapter 12: Reproduction and Developmental Biology
Chapter 13: Evolution
Chapter 14: Ecology
Chapter 15: Animal Behavior
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Chapter 1: Molecules and Fundamentals of
Table of Contents
Biological Chemistry
Nucleic Acids
Biological Hypothesis and Theories
Biological Chemistry
Basic terminology:
Matter - anything that takes up space and has
Element - a pure substance that has specific
physical/chemical properties, can’t be broken
down into a simpler substance.
Atom - smallest unit of matter that still retains
the chemical properties of the element.
Molecule - two or more atoms joined together.
Intramolecular forces - attractive forces that
hold atoms within a molecule.
Intermolecular forces - forces that exist
between molecules and affect physical
properties of the substance.
Monomers - single molecules that can
potentially polymerize.
Polymers - substances made up of many
monomers joined together.
Ribose - five carbon monosaccharide.
Fructose - six carbon monosaccharide.
Glucose - six carbon monosaccharide.
Glucose and fructose are isomers of each
other (same chemical formula, different
arrangement of atoms).
Disaccharides contain two monosaccharides
joined together by a glycosidic bond. It is the
result of a dehydration (condensation) reaction,
where a water molecule leaves and a covalent
bond forms. A hydrolysis reaction is the opposite,
through which the covalent bond is broken by the
addition of water.
Sucrose - glucose + fructose disaccharide.
Lactose - galactose + glucose disaccharide.
Maltose - glucose + glucose disaccharide.
Polysaccharides contain many monosaccharides
connected by glycosidic bonds into a long polymer.
Starch - energy storage for plants and is an
alpha (α) bonded polysaccharide. Linear
starch is called amylose, while the branched
form is amylopectin.
Glycogen - energy storage for humans and is
an alpha (α) bonded polysaccharide. Much
more branching than starch.
Carbohydrates contain carbon, hydrogen, and
oxygen atoms (CHO). They can come in the form
of monosaccharides, disaccharides, and
Monosaccharides are carbohydrate monomers
with empirical formula of (CH2O)n. “n” represent
the number of carbons.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=30131154
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Cellulose - structural component in plant cell
walls, and is a beta (β) bonded polysaccharide.
Linear strands packed rigidly in parallel.
Chitin - structural component in fungi cell walls
and insect exoskeletons. It is a beta (β)
bonded polysaccharide with nitrogen added
to each monomer.
Proteins contain carbon, hydrogen, oxygen, and
nitrogen atoms (CHON). These atoms combine to
form amino acids, which link together to build
polypeptides (or proteins).
Amino acids (a.a.) are the monomers of proteins
with the structure shown below:
Adapted from: https://commons.wikimedia.org/w/index.php?curid=41348719
There are twenty different kinds of amino acids,
each with a different “R-group”.
Polypeptides are polymers of amino acids and are
joined by peptide bonds through dehydration
(condensation) reactions, and hydrolysis
reactions break these bonds.
The N-terminus (amino terminus) of a
polypeptide is the side that ends with the last
amino acid’s amino group.
Protein structure:
1. Primary structure - sequence of a.a..
2. Secondary structure - intermolecular forces
between the polypeptide backbone (not
R-groups) due to hydrogen bonding. Forms
α-helices or β-pleated sheets.
3. Tertiary structure - three dimensional
structure due to interactions between R-groups.
Can create hydrophobic or hydrophilic
spaces based on the R-groups. Disulfide
bonds are created by covalent bonding
between the R-groups of two cysteine a.a.’s
(sulfur-sulfur bond).
4. Quaternary structure - multiple polypeptide
chains come together to form one protein.
Proteins can also be classified based on structure
as fibrous, globular, or intermediate. When
looking at protein composition, they can be simple
(amino acids only) or conjugated (amino acids +
other components).
Protein denaturation describes the loss of
protein function and higher order structures. Only
the primary structure is unaffected. Some reasons
a protein will denature is a result of high or low
temperatures, pH changes, and salt
concentrations. As an example, cooking an egg in
high heat will disrupt the intermolecular forces in
the egg’s proteins, causing it to coagulate.
Protein functions:
The C-terminus (carboxyl terminus) of a
polypeptide is the side that ends with the last
amino acid’s carboxyl group.
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Catalysts increase reaction rates by lowering the
activation energy of a reaction. The transition
state is the unstable intermediate between the
reactants and the products, Catalysts reduce the
energy of the transition state. Catalysts do not shift
a chemical reaction and they do not affect
Enzymes act as biological catalysts by binding to
substrates (reactants) and converting them into
Enzymes bind to substrates at an active site,
which is specific for the substrate that it acts
upon. Most enzymes are proteins.
The specificity constant measures how
efficient an enzyme is at binding to the
substrate and converting it to a product.
The induced fit theory describes how the
active site molds itself and changes shape to fit
the substrate when it binds. The outdated
theory was the “lock and key” model.
A ribozyme is an RNA molecule that can act
as an enzyme (a non-protein enzyme).
A cofactor is a non-protein molecule that helps
enzymes perform reactions. A coenzyme is an
organic cofactor such as vitamins. Inorganic
cofactors are usually metal ions.
Holoenzymes are enzymes that are bound to
their cofactors while apoenzymes are enzymes
that are not bound to their cofactors.
Prosthetic groups are cofactors that are
tightly or covalently bound to their enzymes.
Protein enzymes are susceptible to
denaturation. They require optimal
temperatures and pH for function.
An enzyme kinetics plot can be used to visualize
how inhibitors affect enzymes. Below are a few
terms used to describe the plot:
1. The x-axis represents substrate
concentration [X] while the y-axis represents
reaction rate or velocity (V).
2. Vmax is the maximum reaction velocity.
3. Michaelis Constant (KM) is the substrate
concentration [X] at which the velocity (V) is
50% of the maximum reaction velocity
4. Saturation occurs when all active sites are
occupied, so the rate of reaction does not
increase anymore despite increasing substrate
concentration (graph plateaus).
Competitive inhibition → KM increases, while Vmax
stays the same
Noncompetitive inhibition → KM stays the same,
while Vmax decreases
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49924777
Competitive inhibition occurs when a
competitive inhibitor competes directly with the
substrate for active site binding. The rate of
enzyme action can be increased by adding more
Noncompetitive inhibition occurs when the
noncompetitive inhibitor binds to an allosteric
site (location on enzyme that is different from the
active site), modifying the active site. In
noncompetitive inhibition, the rate of enzyme
action cannot be increased by adding more
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Lipids contain carbon, hydrogen, and oxygen
atoms (CHO), like carbohydrates. However, they
have long hydrocarbon tails, making them very
Triacylglycerol (triglyceride) is a lipid molecule
with a glycerol backbone (three carbons and
three hydroxyl groups) and three fatty acids (long
hydrocarbon tails). Glycerol and the three fatty
acids are connected by ester linkages.
Saturated fatty acids have no double bonds and
as a result pack tightly (solid at room temperature).
Unsaturated fatty acids have double bonds. They
can be divided into monounsaturated fatty acids
(one double bond) and polyunsaturated fatty
acids (two or more double bonds).
Cholesterol is also a lipid molecule that is a
component of the cell membranes and is
amphipathic. It is the most common precursor to
steroid hormones (lipids that have four
hydrocarbon rings). Cholesterol is also the starting
material for vitamin D and bile acids.
Factors that influence membrane fluidity:
1. Temperature - ↑ temperatures increase fluidity
while ↓ temperatures decrease it.
2. Cholesterol - holds membrane together at
high temperatures and keeps membrane fluid
at low temperatures.
3. Degrees of unsaturation - saturated fatty
acids pack more tightly than unsaturated fatty
acids, which have double bonds that may
introduce kinks.
Lipoproteins allow the transport of lipid
molecules in the bloodstream due to an outer coat
of phospholipids, cholesterol, and proteins.
Cis-unsaturated fatty acids have kinks that cause
the hydrocarbon tails to bend. As a result, they do
not pack tightly.
Trans-unsaturated fatty acids have straighter
hydrocarbon tails, so they pack tightly.
Phospholipids are lipid molecules that have a
glycerol backbone, one phosphate group, and
two fatty acids. The phosphate group is polar
while the fatty acids are nonpolar. As a result, they
are amphipathic (hydrophobic and hydrophilic).
Furthermore, they spontaneously assemble into a
lipid bilayer.
Low-density lipoproteins (LDLs) - low protein
density and deliver cholesterol to peripheral
tissues. “Bad cholesterol” and vessel blockage
can occur (heart disease).
High-density lipoproteins (HDLs) - high
protein density and take cholesterol away from
peripheral tissues. “Good cholesterol”
because they deliver cholesterol to the liver to
make bile (reduces blood lipid levels).
Waxes are simple lipids that have long fatty acids
connected to monohydroxy alcohols (contain a
single hydroxyl group) through ester linkages. Used
mainly as hydrophobic protective coatings.
Carotenoids are lipid derivatives containing long
carbon chains with conjugated double bonds and
six-membered rings at each end. They function
mainly as pigments.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=1828495 and
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Nucleic Acids
Nucleic acids contain carbon, hydrogen, oxygen,
nitrogen, and phosphorus atoms (CHONP). They
contain nucleotide monomers that build into DNA
(deoxyribonucleic acid) and RNA (ribonucleic
acid) polymers.
Nucleosides contain a five-carbon sugar and a
nitrogenous base while nucleotides also contain a
phosphate group. Deoxyribose sugars (in DNA)
contain a hydrogen at the 2’ carbon while ribose
five-carbon sugars (in RNA) contain a hydroxyl
group at the 2’ carbon.
Adenine (A), thymine (T), cytosine (C), and
guanine (G) are the nucleotides in DNA. The
uracil (U) nucleotide replaces T in RNA.
A and G are purines (two rings), while C, U, and T
are pyrimidines (one ring).
PUR As Gold = PURines are Adenine and Guanine
CUT the PY = Cytosine, Uracil, and Thymine are
Phosphodiester bonds connect the phosphate
group of one nucleotide (at the 5’ carbon) to the
hydroxyl group of another nucleotide (at the 3’
carbon). A series of phosphodiester bonds create
the sugar-phosphate backbone, with a 5’ end
(free phosphate) and a 3’ end (free hydroxyl).
Nucleic acid polymerization proceeds as
nucleoside triphosphates are added to the 3’ end of
the sugar-phosphate backbone.
Fundamentals of Biology
Modern cell theory:
1. All lifeforms have one or more cells.
2. The cell is the basic structural, functional, and
organizational unit of life.
3. All cells come from other cells (cell division).
4. Genetic information is stored and passed down
through DNA.
5. An organism’s activity is dependent on the total
activity of its independent cells.
6. Metabolism and biochemistry (energy flow)
occurs within cells,
7. All cells have the same chemical composition
within organisms of similar species.
The central dogma of genetics states that
information is passed from DNA → RNA →
proteins. There are a few exceptions (eg. reverse
transcriptase and prions).
The RNA world hypothesis states that RNA
dominated Earth’s primordial soup before there
was life. RNA developed self-replicating
mechanisms and later could catalyze reactions
such as protein synthesis to make more complex
macromolecules. Since RNA is reactive and
unstable, DNA later became a better way of reliably
storing genetic information.
DNA is an antiparallel double helix, in which two
complementary strands with opposite
directionalities (positioning of 5’ ends and 3’ ends)
twist around each other. Furthermore, A can only
H-bond to T (two hydrogen bonds) and G can only
H-bond to C (three hydrogen bonds). RNA is
single stranded after being copied from DNA
during transcription. In RNA, U binds to A, replacing
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Chapter 2: Cells and Organelles
Table of Contents
Cell Membrane
Crossing Cell Membranes
Extracellular Matrix
Cellular Tonicity and Cell Circulation
Peripheral membrane proteins are found on the
outside of the bilayer, and they may or may not be
amphipathic. Below are some possible functions:
Cell Membrane
Cell membranes hold cellular contents and are
mainly made up of phospholipids, cholesterol,
and proteins:
1. Phospholipids - glycerol backbone, one
phosphate group (hydrophilic), and two fatty
acid tails (hydrophobic). Amphipathic
because the molecules have both polar and
nonpolar parts, allowing them to form a lipid
bilayer in an aqueous environment.
Receptor - trigger secondary responses within
the cell for signaling.
Adhesion - attaches cells to other things (eg.
other cells) and act as anchors for the
Cellular recognition - proteins which have
carbohydrate chains (glycoproteins). Used by
cells to recognize other cells.
The fluid mosaic model describes how the
components that make up the cell membrane can
move freely within the membrane (“fluid”).
Furthermore, the cell membrane contains many
different kinds of structures (“mosaic”).
The fluidity of the cell membrane can be affected
Temperature - ↑ temperatures increase fluidity
while ↓ temperatures decrease it.
Cholesterol - holds membrane together at
high temperatures and keeps membrane fluid
at low temperatures.
Degrees of unsaturation - saturated fatty
acids pack more tightly than unsaturated fatty
acids, which have double bonds that may
introduce kinks. Trans-unsaturated fatty acids
pack more tightly than cis-unsaturated fatty
acids (which have a more severe kink).
2. Cholesterol - has four fused hydrocarbon
rings and is a precursor to steroid hormones.
Also amphipathic and helps regulate
membrane fluidity.
3. Membrane proteins - are either integral or
peripheral membrane proteins.
Integral (transmembrane) proteins traverse the
entire bilayer, so they must be amphipathic. Their
nonpolar parts lie in the middle of the bilayer while
their polar ends extend out into the aqueous
environment. Usually assist in cell signaling or
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49923679
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Crossing Cell Membranes
Cells must regulate the traveling of substances
across the cell membrane. 3 types of transport
across the cell membrane:
1. Simple diffusion - flow of small, uncharged,
nonpolar substances (eg. O2 and CO2) across
the cell membrane down their concentration
gradient (high to low) without using energy.
● Osmosis is a type of simple diffusion that
involves water molecules (water is polar,
but is small enough to cross the
2. Facilitated transport - integral proteins allow
larger, hydrophobic molecules to cross the cell
● These proteins can be uniporters (single
substance, single direction), symporters
(two substances, same direction), or
antiporters (two substances, opposite
● Also, they can also be classified as channel
proteins (open tunnel that faces both sides
of bilayer) and carrier proteins (binds to
molecule on one side and changes shape to
bring it to the other side).
● Passive diffusion is a type of facilitated
transport that is performed by channel
proteins, bringing molecules down their
concentration gradient without energy
use (similar to simple diffusion, but a
protein channel is used). Examples include
porins for hydrophilic molecules and ion
channels for ions.
3. Active transport - substances travel against
their concentration gradient and require the
consumption of energy by carrier proteins.
● Primary active transport uses ATP
hydrolysis to pump molecules against their
concentration gradient. For example, the
sodium-potassium (Na+/K+) pump
establishes membrane potential (discussed
in later chapters).
Secondary active transport uses free
energy released when other molecules
flow down their concentration gradient
(gradient established by primary active
transport) to pump the molecule of interest
across the membrane.
Cytosis refers to the bulk transport of large,
hydrophilic molecules within the cytoplasm and
requires energy (active transport mechanism).
Endocytosis involves the cell membrane wrapping
around an extracellular substance, internalizing it
into the cell via a vesicle or vacuole. Below are
different forms of endocytosis:
Phagocytosis - cellular eating around solid
Pinocytosis - cellular drinking around
dissolved materials (liquids).
Receptor-mediated endocytosis - requires
the binding of dissolved molecules to
peripheral membrane receptor proteins,
which initiates endocytosis.
Exocytosis is the opposite of endocytosis, releasing
material to the extracellular environment through
vesicle secretion.
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Parts of the nucleus:
Adapted from: https://commons.wikimedia.org/w/indeg.php?curid=20664784
Organelles are cellular compartments enclosed by
phospholipid bilayers (membrane bound). They
are located within the cytosol (aqueous
intracellular fluid) and together make up the
cytoplasm (cytosol + organelles).
Only eukaryotic cells contain membrane bound
organelles. Prokaryotes do not, but they have
other adaptations such as keeping their genetic
material in a region called the nucleoid (more on
this in later chapters).
The nucleus primarily functions to protect and
house DNA. DNA replication and transcription
(DNA → mRNA) occurs here.
The nucleoplasm is the cytoplasm of the
The nuclear envelope is the membrane of the
nucleus. It contains two phospholipid bilayers
(one inner, one outer) with a perinuclear
space in the middle.
Nuclear pores are holes in the nuclear
envelope that allow molecules to travel in and
out of the nucleus.
The nuclear lamina provides structural
support to the nucleus, as well as regulating
DNA and cell division.
The nucleolus is a dense area that is
responsible for making rRNA, and producing
ribosomal subunits (rRNA + proteins).
Ribosomes are not organelles but work as small
factories that carry out translation (mRNA →
protein). They are composed of ribosomal
Eukaryotic ribosomal subunits (60S and 40S)
assemble in the nucleoplasm and form the
complete ribosome in the cytosol (80S).
Prokaryotic ribosomal subunits (50S and 30S)
assemble in the nucleoid and form the complete
ribosome in the cytosol (70S).
Free-floating ribosomes make proteins that
function in the cytosol while ribosomes embedded
in the rough endoplasmic reticulum (rough ER)
make proteins that are sent out of the cell or to the
cell membrane.
The rough endoplasmic reticulum (rough ER) is
continuous with the outer membrane of the
nuclear envelope and is “rough” because it is
embedded with ribosomes. Proteins synthesized
by the embedded ribosomes are sent into the
lumen (inside of the rough ER) for modifications
(eg. glycosylation). Afterwards, they are either sent
out of the cell or become part of the cell membrane.
The smooth endoplasmic reticulum (smooth ER)
is not continuous with other membranes. Its main
function is to synthesize lipids, produce steroid
hormones, and detoxify cells.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=6197500
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The Golgi apparatus is made up of cisternae
(flattened sacs) that modify and package
substances. Vesicles come from the ER and reach
the cis face (side closest to ER) of the Golgi
apparatus. Vesicles leave the Golgi apparatus from
the trans face (side closest to cell membrane).
Mitochondria are the powerhouses of the cell,
producing ATP for energy use through cellular
respiration (chapter 3).
Lysosomes are membrane-bound organelles that
break down substances (hydrolysis) taken in
through endocytosis. Lysosomes contain acidic
digestive enzymes that function at a low pH. They
also carry out autophagy (the breakdown of the
cell’s own machinery for recycling) and apoptosis
(programmed cell death).
Centrosomes are organelles found in animal cells
containing a pair of centrioles. They act as
microtubule organizing centers (MTOCs) during
cell division (chapter 5).
Transport vacuoles - transport materials
between organelles.
Food vacuoles - temporarily hold endocytosed
food and later fuse with lysosomes.
Central vacuoles - very large in plants and
have a specialized membrane called the
tonoplast (helps maintain cell rigidity by
exerting turgor). Function in storage and
material breakdown).
Storage vacuoles - store starches, pigments,
and toxic substances.
Contractile vacuoles - found in single-celled
organisms and works to actively pump out
excess water.
The endomembrane system is a group of
organelles and membranes that work together to
modify, package, and transport proteins and
lipids that are entering or exiting a cell. It includes
the nucleus, rough and smooth ERs, Golgi
apparatus, lysosomes, vacuoles, and cell
Peroxisomes perform hydrolysis, and break down
stored fatty acids and help with detoxification.
These processes generate hydrogen peroxide,
which is toxic since it can produce reactive
oxygen species (ROS). ROS damage cells through
free radicals. Peroxisomes contain an enzyme
called catalase, which quickly breaks down this
hydrogen peroxide into water and oxygen.
Chloroplasts are found in plants and some
protists.They carry out photosynthesis (chapter 4).
The cytoskeleton provides structure and function
within the cytoplasm.
Microfilaments are the smallest, and are
composed of a double helix of two actin filaments.
They are mainly involved in cell movement and
can quickly assemble, and disassemble. Below are
some of their functions:
1. Cyclosis (cytoplasmic streaming) - ‘stirring of
the cytoplasm’; organelles and vesicles travel
on microfilament “tracks”.
2. Cleavage furrow - during cell division, actin
microfilaments form contractile rings that split
the cell.
3. Muscle contraction - actin microfilaments
have directionality, allowing myosin motor
proteins to pull on them for muscle
Intermediate filaments are between
microfilaments and microtubules in size. They are
more stable than microfilaments and mainly help
with structural support. For example, keratin is
an important intermediate filament protein in skin,
hair, and nails. Lamins are a type of intermediate
filament which helps make up the nuclear lamina,
a network of fibrous intermediate filaments which
support the nucleus.
Microtubules are the largest in size and give
structural integrity to cells. They are hollow and
have walls made of tubulin protein dimers.
Microtubules also have functions in cell division,
cilia, and flagella.
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Microtubule Organizing Centers (MTOCs) are
present in eukaryotic cells and organize
microtubule extension.
Centrioles are hollow cylinders made of nine
triplets of microtubules (9x3 array). Centrosomes
contain a pair of centrioles oriented at 90 degree
angles to one-another. They replicate during the S
phase of the cell cycle so that each daughter cell
after cell division has one centrosome.
Cilia and flagella have nine doublets of
microtubules with two singles in the center (9+2
array). They are produced by a basal body, which
is initially formed by the mother centriole (older
centriole after S phase replication).
Extracellular Matrix
The extracellular matrix (ECM) provides
mechanical support between cells.
ECM components:
Proteoglycan - type of glycoprotein that have a
high proportion of carbohydrates.
Collagen - most common structural protein and
organized into collagen fibrils (fibers of
glycosylated collagen secreted by fibroblasts).
Integrin - transmembrane protein that
facilitates ECM adhesion and signals to cells
how to respond to the extracellular
environment (growth, apoptosis, etc.).
Fibronectin - protein that connects integrin to
ECM and helps with signal transduction.
Laminin - behaves similarly to fibronectin.
They influence cell differentiation, adhesion,
and movement. It is a major component of the
basal lamina (a layer of the ECM secreted by
epithelial cells).
Cell walls are carbohydrate-based structures that
act like a substitute ECM because they provide
structural support to cells that either do not have,
or have a minimal ECM. They are present in plants
(cellulose), fungi (chitin), bacteria
(peptidoglycan), and archaea.
The glycocalyx is a glycolipid/glycoprotein coat
found mainly on bacterial and animal epithelial
cells. Helps with adhesion, protection, and cell
Cell-matrix junctions (connect ECM →
1. Focal adhesions - ECM connects via integrins
to actin microfilaments inside the cell.
2. Hemidesmosomes - ECM connects via
integrins to intermediate filaments inside the
Cell-cell junctions (connect adjacent cells):
1. Tight junctions - form water-tight seals
between cells to ensure substances pass
through cells and not between them.
2. Desmosomes - provide support against
mechanical stress. Connects neighboring cells
via intermediate filaments.
3. Adherens junctions - similar in structure and
function to desmosomes, but connects
neighboring cells via actin microfilaments.
4. Gap junctions - allow passage of ions and
small molecules between cells.
Plant cells contain a few unique cell junctions:
1. Middle lamina - sticky cement similar in
function to tight junctions.
2. Plasmodesmata - tunnels with tubes between
plant cells. Allows cytosol fluids to freely travel
between plant cells.
Cellular Tonicity and Cell Circulation
Isotonic solutions have the same solute
concentration as the cells placed in them.
Hypertonic solutions have a higher solute
concentration than the cells placed in them,
causing water to leave the cell (cell shrivels).
Hypotonic solutions have a lower solute
concentration than the cells place in them, causing
water to enter the cell (cell swells up). Lysis is the
bursting of a cell when too much water enters.
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Chapter 3: Cellular Energy
Table of Contents
Adenosine Triphosphate
Aerobic Cellular Respiration
ATP Yield of Aerobic Cellular Respiration
Alternative Sources of Energy Generation
Metabolism refers to all the metabolic pathways
(series of chemical reactions) that are happening in
a given organism. Catabolic processes involve
breaking down larger molecules for energy while
anabolic processes involve using energy to build
larger macromolecules.
Reaction coupling is the process of powering an
energy-requiring reaction with an energy-releasing
one. It allows an unfavorable reaction to be
powered by a favorable reaction, making the net
Gibbs free energy negative (-ΔG = exergonic =
releases energy + spontaneous).
Mitochondria are organelles that produce ATP
through cellular respiration (catabolic process).
They have an outer membrane and an inner
membrane with many infoldings called cristae.
The intermembrane space is located between the
outer and inner membranes while the
mitochondrial matrix is located within the inner
To break down carbohydrates for energy, cells
either utilize aerobic cellular respiration
(consumes oxygen, more energy produced) or
anaerobic cellular respiration (no oxygen
needed, but less energy produced).
Adenosine Triphosphate
Adenosine triphosphate (ATP) is an RNA
nucleoside triphosphate. It contains an adenine
nitrogenous base linked to a ribose sugar (RNA
nucleoside part), and three phosphate groups
connected to the sugar (triphosphate part).
ATP is used as the cellular energy currency
because of high energy bonds between the
phosphate groups. These bonds release energy
upon hydrolysis (breaking bonds).
The endosymbiotic theory states that aerobic
bacteria were internalized as mitochondria while
the photosynthetic bacteria became chloroplasts.
Some evidence for this includes size similarities
and the fact that mitochondria and chloroplasts
contain their own circular DNA and ribosomes.
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Aerobic Cellular Respiration
Aerobic cellular respiration is performed to
phosphorylate ADP into ATP, by breaking down
glucose and moving electrons around (oxidation
and reduction reactions). Aerobic cellular
respiration involves 4 catabolic processes:
1. Glycolysis
2. Pyruvate manipulations
3. Krebs cycle
4. Oxidative phosphorylation
Because 2 ATP are used up in the energy
investment phase and 4 ATP are produced in the
energy payoff phase, a net of 2 ATP is produced
within glycolysis.
1. Glycolysis
Glucose → 2 ATP + 2 NADH + 2 pyruvate
Glycolysis takes place in the cytosol and does not
require oxygen, so it is also used in fermentation.
Substrate-level phosphorylation is the process
used to generate ATP in glycolysis, transferring a
phosphate group to ADP directly from a
phosphorylated compound.
Glycolysis has an energy investment phase and
an energy payoff phase:
1. Hexokinase uses one ATP to phosphorylate
glucose into glucose-6-phosphate, which
cannot leave the cell (it becomes trapped by
the phosphorylation).
2. Isomerase modifies glucose-6-phosphate into
3. Phosphofructokinase uses a second ATP to
phosphorylate fructose-6-phosphate into
4. Fructose-1,6-bisphosphate is broken into
dihydroxyacetone phosphate (DHAP) and
glyceraldehyde-3-phosphate (G3P), which
are in equilibrium with one another.
5. G3P proceeds to the energy payoff phase so
DHAP is constantly converted into G3P to
maintain equilibrium. Thus, 1 glucose molecule
will produce 2 G3P that continue into the next
6. G3P undergoes a series of redox reactions to
produce 4 ATP through
substrate-level-phosphorylation, 2 pyruvate
and 2 NADH.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=53712885
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2. Pyruvate manipulations
2 pyruvate → 2 CO2 + 2 NADH + 2 acetyl-CoA
Pyruvate dehydrogenase is an enzyme that
carries out the pyruvate manipulation steps below:
1. Decarboxylation - Pyruvate molecules (3
carbon molecule) move from the cytosol into
the mitochondrial matrix (stays in the cytosol
for prokaryotes), where they undergo
decarboxylation, producing 1 CO2 and one two
carbon molecule per pyruvate.
2. Oxidation - The two-carbon molecule is
converted into an acetyl group, giving
electrons to NAD+ to convert it into NADH.
3. Coenzyme A (CoA) - CoA binds to the acetyl
group, producing acetyl-CoA.
3. Krebs cycle
2 acetyl-CoA → 4 CO2 + 6 NADH + 2 FADH2 + 2
The Krebs cycle is also known as the citric acid
cycle or the tricarboxylic acid (TCA) cycle. Like
pyruvate manipulations, it also occurs in the
mitochondrial matrix and the cytosol for
1. Acetyl-CoA joins oxaloacetate (four-carbon)
to form citrate (six-carbon).
2. Citrate undergoes rearrangements producing
2 CO2 and 2 NADH.
3. After the loss of two CO2, the resulting
four-carbon molecule produces 1 GTP through
substrate-level phosphorylation.
4. The molecule will now transfer electrons to 1
FAD+, which is reduced into 1 FADH2.
5. Lastly, the molecule is converted back into
oxaloacetate and also gives electrons to
produce 1 NADH.
6. Two acetyl-CoA molecules produces 4 CO2 + 6
NADH + 2 FADH2 + 2 GTP.
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4. Oxidative phosphorylation
Electron carriers (NADH + FADH2) + O2 → ATP +
The electron transport chain (ETC) and
chemiosmosis (ions moving down electrochemical
gradient) work together to produce ATP in
oxidative phosphorylation. Oxygen acts as a final
electron acceptor and gets reduced into water.
ETC goal: Regenerate electron carriers and create
an electrochemical gradient to power ATP
The mitochondrial inner membrane is the ETC for
eukaryotes while the cell membrane is the ETC for
Four protein complexes I-IV are responsible for
moving electrons through a series of
oxidation-reduction (redox) reactions in the
ETC. As the series of redox reactions occurs,
protons are pumped from the mitochondrial matrix
to the intermembrane space, forming an
electrochemical gradient. This is the reason the
intermembrane space is highly acidic.
NADH is more effective and drops electrons off
directly at complex-I, regenerating NAD+.
FADH2 drops electrons off at the second protein
complex-II, regenerating FAD+. However, this
results in less pumping of protons due to the
bypassing of complex-I.
Adapted from: https://commons.wikimedia.org/w/indeg.php?curid=49924811
ATP Yield of Aerobic Cellular Respiration
Aerobic respiration is exergonic, with a ΔG = -686
The estimate is around 4 protons for 1 ATP.
NADH produces 3 ATP (NADH from glycolysis
produces less)*
*The 2 NADH from glycolysis produce 4-6 ATP
because a varying amount of ATP must be used to
shuttle these NADH from the cytosol to the
mitochondrial matrix. However, prokaryotes do
not need to shuttle their NADH, so they will
produce 6 ATP.
FADH2 produces 2 ATP.
Chemiosmosis goal: Use the proton
electrochemical gradient (proton-motive force) to
synthesize ATP.
ATP synthase is a channel protein that provides a
hydrophilic tunnel to allow protons to flow down
their electrochemical gradient (from the
intermembrane space back to the mitochondrial
matrix). The spontaneous movement of protons
generates energy that is used to convert ADP + Pi
into ATP, a condensation reaction that is
endergonic (requires energy +nonspontaneous =
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Fermentation is an anaerobic pathway (no
oxygen) that only relies on glycolysis by
converting the produced pyruvate into different
molecules in order to oxidize NADH back to NAD+.
Regenerating NAD+ means glycolysis can continue
to make ATP. Fermentation occurs within the
cytosol. The two most common types of
fermentation are lactic acid fermentation and
alcohol fermentation.
2. Alcohol Fermentation
Alcohol fermentation uses the 2 NADH from
glycolysis to convert the 2 pyruvate into 2 ethanol.
Thus, NADH is oxidized back to NAD+ so that
glycolysis may continue. However, this process has
an extra step that first involves the
decarboxylation of pyruvate into acetaldehyde,
which is only then reduced by NADH into ethanol.
1. Lactic acid fermentation
Lactic acid fermentation uses the 2 NADH from
glycolysis to reduces the 2 pyruvate into 2 lactic
acid. Thus, NADH is oxidized back to NAD+ so that
glycolysis may continue. This happens frequently
in muscle cells and occurs continuously in red blood
cells, which do not have mitochondria for aerobic
The Cori cycle is used to help convert lactate back
into glucose once oxygen is available again. It
transports the lactate to liver cells, where it be
oxidized back into pyruvate. Pyruvate can then be
used to form glucose, which can be used for more
ideal energy generation.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=17301493
Types of organisms based on ability to grow in
Obligate aerobes - only perform aerobic
respiration, so they need the presence of
oxygen to survive.
Obligate anaerobes - only undergo anaerobic
respiration or fermentation, and oxygen is
poison to them.
Facultative anaerobes - can do aerobic
respiration, anaerobic respiration, or
fermentation, but prefers aerobic respiration
because it generates the most ATP.
Microaerophiles - only perform aerobic
respiration, but high amounts of oxygen are
harmful to them.
Aerotolerant organisms - only undergo
anaerobic respiration or fermentation, but
oxygen is not poisonous to them.
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Alternative Sources of Energy Generation
Molecules other than glucose such as other types
of carbohydrates, fats, and proteins can enter
cellular respiration at various stages for energy
1. Other carbohydrates mostly enter during
glycolysis. Glycogenolysis describes the release of
glucose-6-phosphate from glycogen, a highly
branched polysaccharide of glucose. Disaccharides
can undergo hydrolysis to release two
carbohydrate monomers, which can enter
Chylomicrons are lipoprotein transport structures
formed by the fusing of triglycerides with proteins,
phospholipids, and cholesterol. They leave
enterocytes and enter lacteals, small lymphatic
vessels that take fats to the rest of the body.
Low-density lipoproteins (LDLs) - low density of
proteins, considered unhealthy because they
transport cholesterol to the peripheral tissues,
where it can cause vessel blockage.
High-density lipoproteins (HDLs) - high density
of proteins, considered healthy because they bring
cholesterol to the liver to make bile.
When a glycerol molecule travels to the liver, it
can undergo a conversion to enter glycolysis or
make new glucose via gluconeogenesis at the liver.
Carbohydrates are the preferred energy source
since they are easily catabolized and are high yield
(4 kcal/gram).
Glycogenesis refers to the reverse process - the
conversion of glucose into glycogen to be stored in
the liver when energy and fuel is sufficient.
2. Fats are mostly present in the body as
triglycerides. Lipases are required to first digest
fats into free fatty acids and alcohols through a
process called lipolysis. These digested pieces
then can be absorbed by enterocytes in the small
intestine and reform triglycerides.
Adipocytes are cells that store fat (triglycerides)
and have hormone sensitive lipase enzymes to
help release triglycerides back into circulation as
lipoproteins or as free fatty acids bound by a
protein called albumin.
Free fatty acids undergo beta-oxidation to be
converted into acetyl-CoA. Beta-oxidation
requires an initial investment of ATP, but then is
continuously cleaved to yield two-carbon
acetyl-CoA molecules (which can be used in the
Krebs cycle for ATP generation) and electron
carriers (NADH + FADH2 - produces more ATP).
3. Proteins are the least desirable energy source
because the processes to get them into cellular
respiration take considerable energy and proteins
are needed for many essential functions in the
They are broken down into amino acids, which
must first undergo oxidative deamination
(removal of NH3) before being shuttled to various
parts of cellular respiration.
Ammonia (NH3) is toxic, so it must be converted
into uric acid or urea depending on the species
and excreted from the body. For example, humans
convert ammonia into into urea, which is excreted
as urine.
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Chapter 4: Photosynthesis
Table of Contents
Objective of Photosynthesis
Photosynthesis and Cellular Respiration
Leaf Anatomy
Light Dependent Reactions of
The Calvin Cycle
Alternative Photosynthetic Pathways
Anoxygenic Photosynthesis
Heterotrophs must get energy from the food they
eat, while autotrophs can make their own food.
Photoautotrophs take light energy and convert it to
chemical energy using photosynthesis.
Photosynthesis creates chemical energy that is
transferred through food-chains, reduces
atmospheric carbon dioxide, and releases oxygen.
Photosynthesis and Cellular Respiration
Photosynthesis and cellular respiration are reverse
processes in terms of their overall reaction:
Photosynthesis is non-spontaneous and
endergonic, producing glucose after an input of
solar energy.
Cellular respiration is spontaneous and exergonic,
breaking down glucose to generate energy in the
form of ATP.
Photons (light energy) are used to synthesize
sugars (glucose) in photosynthesis.
Carbon fixation is the process by which inorganic
carbon (CO2) is converted into an organic molecule
(glucose). Photosynthesis takes electrons released
from photolysis (splitting water molecules) and
excites them using solar energy. These excited
electrons are then used to power carbon fixation.
Adapted from: https://www.flickr.com/photos/[email protected]/10187194256
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Leaf Anatomy
Epidermis - an outer layer of cells that provides
protection and prevents water loss.
Palisade mesophyll cells - right below upper
epidermis, has many chloroplasts and this is where
most photosynthesis occurs.
Spongy mesophyll cells - bottom of the leaf,
where the leaf has a lot of spaces for gas
movement. Has some chloroplasts for moderate
amounts of photosynthesis.
Stomata - pores underneath the leaf for gas to
enter and exit.
Guard cells - surround stomata and control their
Chloroplasts are organelles found in plants and
photosynthetic algae but not in cyanobacteria.
They are similar to mitochondria and contain the
structures listed below (outermost to innermost).
Parts of a Chloroplast
Light Dependent Reactions of Photosynthesis
The light dependent reactions take place in the
thylakoid membrane and harness light energy to
produce ATP and NADPH (an electron carrier) for
later use in the Calvin cycle (ATP generated here is
not used to power the cell - it is consumed in the
Calvin cycle).
Photosystems contain special pigments such as
chlorophyll and carotenoids that absorb photons.
The reaction center is a special pair of chlorophyll
molecules in the center of these proteins.
Photosystem II (P680) and Photosystem I (P700)
are used in photosynthesis.
Non-cyclic photophosphorylation is carried out
by the light dependent reactions. Below are the
important steps of this process:
1. Water is split (photolysis), passing electrons
to photosystem II and releasing protons into the
thylakoid lumen.
2. Photons excite electrons in the reaction
center of photosystem II, passing the
electrons to a primary electron acceptor.
3. The primary electron acceptor sends the
excited electrons to the electron transport
chain (ETC). During the redox reactions within
the ETC, protons are pumped from the stroma
to the thylakoid lumen. The electrons are
then deposited into photosystem I.
4. Photons excite pigments now in photosystem
I, energizing the electrons in the reaction center
to be passed to another primary electron
5. The electrons are sent to a short electron
transport chain that terminates with NADP+
reductase, an enzyme then reduces NADP+
into NADPH using electrons and protons.
6. The accumulation of protons in the thylakoid
lumen generates an electrochemical gradient
that is used to produce ATP using an ATP
synthase (chemiosmosis), as H+ moves from
the thylakoid lumen back into the stroma.
Cyclic photophosphorylation happens when
photosystem I passes its electrons back to the
first ETC instead of the second ETC. This causes
more proton pumping and more ATP production,
while no NADPH is generated.
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The Calvin Cycle
The Calvin cycle is also known as the light
independent reactions because it does not
directly use light energy, but can only occur if the
light dependent reactions are providing ATP and
The Calvin cycle takes place in the chloroplast
stroma of plant mesophyll cells. It fixes carbon
dioxide that enters stomata.
1. Carbon fixation - carbon dioxide combines
with five-carbon ribulose-1,5-bisphosphate
(RuBP) to form six-carbon molecules, which
quickly break down into three-carbon
phosphoglycerates (PGA). This reaction is
catalyzed by RuBisCo.
2. Reduction - PGA is phosphorylated by ATP and
subsequently reduced by NADPH to form
glyceraldehyde-3-phosphate (G3P).
3. Regeneration - Most of the G3P is converted
back to RuBP.
4. Carbohydrate synthesis - some of the G3P is
used to make glucose.
6 CO2 + 18 ATP + 12 NADPH + H+ →
18 ADP + 18 Pi +12 NADP+ + 1 glucose
RuBisCo, in addition to fixing carbon dioxide into
RuBP, can also cause oxygen to bind to RuBP in a
process called photorespiration.
Photorespiration occurs in the stroma,
producing a two-carbon molecule
phosphoglycolate that is shuttled to
peroxisomes and mitochondria for conversion
into PGA. However, fixed carbon is lost as carbon
dioxide in the process. Overall, there is a net loss
of fixed carbon atoms and no new glucose would
be made.
Alternative Photosynthetic Pathways
C3 photosynthesis - normal photosynthesis, where
three-carbon PGA is produced.
C4 photosynthesis - produces four-carbon
oxaloacetate, occurs in plants living in hot
environments. Spatial isolation of carbon dioxide
to prevent photorespiration. Below are the
important steps:
1. PEP carboxylase fixes CO2 into a three carbon
PEP molecule, producing oxaloacetate, which
is converted into malate in the mesophyll cell.
2. Malate is transferred to bundle sheath cells,
which have lower concentrations of oxygen.
3. Malate is decarboxylated to release CO2,
spatially isolating where CO2 is fixed by
RuBisCo. The only drawback is that pyruvate
is also produced and needs to be shuttled back
to mesophyll cells using ATP energy.
4. Pyruvate is converted back into PEP.
CAM photosynthesis - uses temporal isolation
of carbon dioxide to prevent photorespiration in
hot environments. Below are the important steps:
1. During the day, stomata are closed to prevent
transpiration (evaporation of water from
2. During the night, stomata are open to let
carbon dioxide in. Just like in C4
photosynthesis, PEP carboxylase fixes CO2
into PEP, producing oxaloacetate and
afterwards malate. However, malate is stored
in vacuoles instead of being shuttled to
bundle sheath cells.
3. During the next day, the stomata are closed
again and malate is converted back into
oxaloacetate, which releases CO2 and PEP.
Thus, CO2 accumulates in the leaf for use in the
Calvin cycle through temporal isolation.
Also called C2 photosynthesis, since two-carbon
phosphoglycolate is produced.
Hot and dry - stomata closed to minimize water
loss, oxygen accumulates inside leaf while carbon
dioxide is used up. RuBisCo binds oxygen and
photorespiration occurs.
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Chapter 5: Cell Division
Table of Contents
Key Terms
The Cell Cycle
Components of Interphase
Microtubule Organizing Centers
Components of the M Phase
Cell Cycle Regulation
Binary Fission
Chromosome and Chromatid Numbers
During Mitosis and Meiosis
Summary Chart
Part of cell theory states that all cells arise from
pre-existing cells through cell division.
Key Terms
Genome - all the DNA in a cell.
Chromosomes - separate DNA molecules that
make up the entire genome.
Homologous chromosome pairs - two
different versions of the same chromosome
number. One from mother and one from
Karyokinesis - division of the nucleus.
Cytokinesis - physical division of the
cytoplasm and cell membrane.
Parent cell- one parent cell produces two
daughter cells after division.
Ploidy - describes the number of chromosome
sets found in the body. Humans are diploid
because they contain two sets of
chromosomes (46 chromosomes, 23 pairs),
one from each parent. However, they also
have haploid cells (gametes) that only contain
one chromosome set (23 chromosomes).
Sex chromosomes - one pair in the human
body and determine sex.
Autosomes - 22 pairs in the human body and
are nonsex chromosomes.
Gametes - haploid cells (sperm and eggs).
Germ cells - diploid cells that divide by meiosis
to produce gametes.
Gametocyte - eukaryotic germ cells that can
either divide to form more gametocytes or
produce gametes.
Somatic cells - body cells excluding the
gametes. Diploid in humans.
Adapted from https://commons.wikimedia.org/wiki/File:Meiosis_Overview_new.svg
Sister chromatids - identical, attached copies
of a single chromosome, forming dyads.
Dyads - replicated chromosomes containing
two sister chromatids that look like an “X”.
Centromeres - regions of DNA that connect
sister chromatids in a dyad.
Kinetochores - proteins on the sides of
centromeres that help microtubules pull sister
chromatids apart during cell division.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=13308417
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The Cell Cycle
The cell cycle is divided into interphase (G1, G0, S,
and G2) and the M phase. 90% of the cell cycle
happens during interphase. M phase is where
karyokinesis and cytokinesis occur.
DAT Mnemonic for the cell cycle:
Go = Gap Phase 1 (G1) of interphase
Sam = Synthesis Phase (S) of interphase
Go = Gap Phase 2 (G2) of interphase
Make = Mitosis of the M phase
Cake = Cytokinesis of the M phase
Components of Interphase
1. Gap phase 1 (G1) - cell grows in preparation
for cell division. Also checks for favorable
conditions. If favorable, cell will enter S phase. If
unfavorable, cell will enter G0 phase.
a. G0 phase - cells still carry out their
functions but halt in the cell cycle. Cells
that do not divide are stuck here.
2. Synthesis phase (S) - cell replicates its genome
here and moves to G2 phase when completed.
Centrosome also duplicates.
3. Gap phase 2 (G2) - cell continues to grow and
prepare for cell division by checking DNA for
any errors after replication. Also checks for
mitosis promoting factor (MPF), which needs
to be in adequate amounts for cell cycle
continuation. Organelles are replicated here.
Microtubule Organizing Centers
Microtubule Organizing Centers (MTOCs) are
present in eukaryotic cells and organize
microtubule extension, which are made of the
protein tubulin. Specifically, they are responsible
for forming the spindle apparatus, which guides
chromosomes during karyokinesis.
Centrosomes are organelles found in animal cells
containing a pair of centrioles. They act as
microtubule organizing centers (MTOCs).
Microtubules in the spindle apparatus:
1. Kinetochore microtubules - extend from
centrosomes and attach to kinetochores on
2. Astral microtubules - extend from
centrosomes to cell membrane to orient the
spindle apparatus.
3. Polar microtubules - extend from the two
centrosomes and connect with each other.
Pushes centrosomes to opposite ends of the
Centrioles are hollow cylinders made of nine
triplets of microtubules (9x3 array). Centrosomes
are located near the nucleus and contain a pair of
centrioles oriented at 90 degree angles to
one-another (attached to each other by
interconnecting fibers). They replicate during the
S phase of the cell cycle so that each daughter cell
after cell division has one centrosome.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=4008957
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The pericentriolar material surrounds the
centrioles and is responsible for microtubules
nucleation (anchoring tubulin to start microtubule
Cilia and flagella have nine doublets of
microtubules with two singles in the center (9+2
array). They are produced by a basal body, which
is initially formed by the mother centriole (older
centriole after S phase replication) attaching itself to
the cell membrane.
Cytokinesis is the physical separation of the
cytoplasm and cell membrane into two daughter
In animal cells, cytokinesis begins in late anaphase
with the formation of a cleavage furrow. The
cleavage furrow is a contractile ring of actin
microfilaments and myosin motors that pinches the
cell into two.
Components of the M phase
The M-phase is the stage in the cell cycle where
karyokinesis and cytokinesis occurs. Mitosis is a
type of karyokinesis (nuclear division) that involves
a diploid parent cell dividing into two diploid
daughter cells.
Four phases of mitosis:
1. Prophase - chromatin condenses into
chromosomes (X-shaped dyads). The
nucleolus and nuclear envelope disappear.
Spindle apparatus forms.
2. Metaphase - the spindle apparatus guides
the chromosomes to the metaphase plate
(midpoint of cell) in single file.
3. Anaphase - kinetochore microtubules
shorten to pull sister chromatids apart. Now,
the sister chromatids are considered separate
chromosomes. Chromosome number
4. Telophase - chromosomes have segregated
and nuclear membranes reform. In addition,
nucleoli reappear and chromosomes
decondense into chromatin.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49926273
In plant cells, cytokinesis begins in telophase with
the formation of a cell plate. The cell plate is
created by vesicles from the Golgi apparatus and
ends up producing the middle lamella (cements
plant cells together).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49926273
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Cell Cycle Regulation
The cell cycle influences cell division through
limitations to growth and regulations to prevent
cancerous growth.
Functional limitations:
Surface to volume ratio (S/V) - cell division
occurs when volume is too large because cells
rely on the surface area of their cell
membrane for transport of material. Decrease
in S/V leads to division.
Genome to volume ratio (G/V) - cell division
occurs when volume is too large for cells to
support with its limited genome. Decrease in
G/V leads to division.
Binary Fission
Mitosis is used to increase the number of cells in
an organism, whereas binary fission is used by
archaea, bacteria, and certain organelles to
During binary fission, organisms will replicate
their genome while cell division is happening (no S
phase for DNA replication). Also, there is no spindle
Cell specific regulations:
Cell specific checkpoints - G0 phase (checks
for favorable conditions to grow), and end of
G2 (checks accuracy of DNA replication and
MPF levels), and M checkpoint (during
metaphase, checks for chromosomal
attachment to spindle fibers).
Cyclin-dependent kinases (CDKs) phosphorylate certain substrates to signal cell
cycle progression. Activated by cyclin, a
protein that cycles through stages of synthesis
and degradation.
Growth factors - bind to receptors in the
plasma membrane to signal for cell division.
Density dependent inhibition - halting cell
division when density of cells is high.
Anchorage dependence - dividing only when
attached to an external surface.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=327384
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Meiosis produces four haploid daughter cells from
one diploid parent cell. It does this by repeating the
steps of karyokinesis twice. Meiosis can be divided
into meiosis I (homologous chromosomes
separate) and meiosis II (sister chromatids
Meiosis I (reductional division) produces two
haploid daughter cells through separation of
homologous chromosomes.
1. Prophase I - chromatin condenses into
chromosomes (X-shaped dyads). Also
nucleolus and nuclear envelope will
disappear. Homologous chromosomes pair
up and crossing over occurs.
● Synapsis - the pairing up of homologous
chromosomes to form tetrads (aka
● Synaptonemal complex - protein
structure that forms between
homologous chromosomes during
● Tetrads (bivalents) - pair of two
homologous chromosomes each with
two sister chromatids.
● Chiasmata - where chromatids
physically crossover during synapsis,
causing genetic recombination.
● Genetic recombination - exchange
of DNA between chromosomes to
produce genetically diverse offspring.
2. Metaphase I - tetrads randomly line up
double file on metaphase plate, also
contributes to genetic diversity.
3. Anaphase I - kinetochore microtubules
shorten to separate homologous
chromosomes from each other. Will not
begin unless at least one chiasmata has
formed within each tetrad.
4. Telophase and Cytokinesis I - after
tetrads have been pulled to opposite
poles, nuclear membranes reform. In
addition, nucleoli reappear and
chromosomes decondense into
chromatin. Cleavage furrow formed in
animal cells and cell plate formed in plant
Meiosis II is very similar to mitosis because sister
chromatids are separated. Two haploid cells divide
into four haploid daughter cells.
1. Prophase II - chromatin condenses into
chromosomes (X-shaped dyads). Also
nucleolus and nuclear envelope will disappear.
Spindle apparatus forms. No crossing over.
2. Metaphase II - chromosomes line up single
file at the metaphase plate just like in mitosis.
3. Anaphase II - kinetochore microtubules
shorten to pull sister chromatids apart. Sister
chromatids become separate chromosomes
and chromosome number doubles.
4. Telophase and Cytokinesis II - nuclear
membranes reform, nucleoli reappear, and
chromosomes decondense into chromatin.
Four haploid daughter cells are produced in
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49630204
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Chromosome and Chromatid Numbers During
Mitosis and Meiosis
(Click here for a deeper breakdown)
During the S phase of the cell cycle, a human’s 46
chromosomes are duplicated. Afterwards, there
are still 46 chromosomes but also 92 chromatids.
They line up in metaphase individually as shown
For meiosis I, a human goes through the same
DNA replication in S phase as mitosis that results
in 46 chromosomes and 92 chromatids.
However, during metaphase the chromosomes
double up as shown below:
During anaphase of meiosis I, homologous
chromosomes split up. This results in the same
total numbers - 46 chromosomes and 92
chromatids. Each cell will have 23 chromosomes
and 46 chromatids.
During anaphase of mitosis, sister chromatids
split. This produces 92 separate chromosomes,
which are also counted as 92 chromatids. Each
separated cell will have 46 chromosomes (46
chromatids). These cells are diploid.
Meiosis II is very similar to mitosis and involves
chromosomes lining up individually in metaphase.
During anaphase, sister chromatids are
separated, resulting in 23 chromosomes (23
chromatids) in each daughter cell. These cells are
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Chapter 6: Molecular Genetics
Table of Contents
Genetic Building Blocks
DNA Organization
DNA Replication
Prokaryotic Transcriptional Control
Eukaryotic Transcriptional Control
Eukaryotic Post-Transcriptional
Gene Mutations
Molecular Genetics of Viruses
Molecular Genetics of Bacteria
Genetic Building Blocks
Nucleotide - ribose sugar, nitrogenous base, and
phosphate group.
A binds to T (two hydrogen bonds)
G binds to C (three hydrogen bonds)
Nucleoside - ribose sugar and nitrogenous base.
DNA is a polymer of nucleotides that have
hydrogen on the ribose sugar’s 2’ carbon. RNA is a
polymer of nucleotides that have hydroxyl group
on the ribose sugar’s 2’ carbon. This is the reason
DNA is called deoxyribonucleic acid, while RNA is
called ribonucleic acid.
Purines are double-ringed nitrogenous bases
adenine and guanine.
Pyrimidines are single-ringed nitrogenous bases
cytosine, thymine, and uracil.
A binds to U (two hydrogen bonds)
G binds to C (three hydrogen bonds)
Since G-C bonds have more hydrogen bonds, a
higher temperature is needed to break DNA
strands with a larger proportion of G-C bonds.
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DNA Organization
Nucleosomes are complexes of DNA wrapped
around histone proteins. Each nucleosome has
nine histones total. The central core contains two
of each histone H2A, H2B, H3 and H4. On the
outside, a single histone H1 holds the DNA in
Chromatin refers to the overall packaging of DNA
and histones. Below are two types of chromatin:
1. Euchromatin - nucleosomes are “loosely
packed”, so DNA is readily accessible for
2. Heterochromatin - nucleosomes are “tightly
packed”, so DNA is mostly inactive.
Histones are positively charged while DNA is
negatively charged, allowing proper binding.
Acetylation of histones removes positive charges,
relaxing DNA-histone attractions and allowing for
more transcription to happen.
Deacetylation of histones increases positive
charges, tightening DNA-histone attractions and
decreasing transcription.
Methylation of histones adds methyl groups to
reduce transcription by covering up DNA.
DNA replication
An origin of replication is required to initiate DNA
replication, where the DNA strands first separate.
Organisms with circular DNA such as bacteria
have a single origin of replication while organisms
with linear DNA such as humans have multiple
origins of replication.
DNA undergoes semiconservative replication,
where each new double helix produced by
replication has one “new” strand and one “old”
DNA is antiparallel, meaning that the 5’ end
(terminal phosphate group) of one strand is
always next to the 3’ end (terminal hydroxyl
group) of the other strand and vice versa.
Steps of DNA replication:
1. Initiation - creating origins of replication at
A-T rich segments of DNA because A-T bonds
only have two hydrogen bonds.
2. Elongation - producing new DNA strands using
different types of enzymes.
● Helicase unzips DNA by breaking hydrogen
bonds between strands, creating the
replication fork.
● Single-strand binding proteins bind to
uncoiled DNA strands, preventing
● Topoisomerase nicks the DNA double
helix ahead of helicase to relieve built-up
● DNA polymerase adds free nucleoside
triphosphates to 3’ ends.
● Primase places RNA primers at the origin
of replication to create 3’ ends for
nucleotide addition.
● Sliding clamp proteins hold DNA
polymerase onto the template strand.
● The leading strand is produced
continuously because it has a 3’ end that
faces the replication fork.
● The lagging strand is produced
discontinuously because its 3’ end is facing
away from the replication fork. Thus, many
RNA primers are needed to produce short
DNA fragments called Okazaki fragments.
● A different DNA polymerase replaces RNA
primers with DNA.
● DNA ligase glues separated fragments of
DNA together.
3. Termination - replication fork cannot
continue, ending DNA replication.
● Telomeres are noncoding, repeated
nucleotide sequences at the ends of linear
chromosomes. They are necessary in
eukaryotes because when the replication
fork reaches the end of a chromosome, a
small segment of DNA from the telomere is
not replicated and lost (no RNA primer to
help produce another Okazaki fragment).
● Telomerase is an enzyme that extends
telomeres to prevent DNA loss.
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To review, the G1/S checkpoint regulates cell cycle
transition from the G1 phase into the S phase,
checking for favorable conditions to grow. If
unfavorable, the cell will remain in G0 phase and
will not enter the S phase for DNA replication.
Specifically, DNA undergoes transcription to
produce single-stranded messenger RNA (mRNA).
Steps of transcription:
1. Initiation - a promoter sequence (aka
promoter) next to the gene attracts RNA
polymerase to transcribe the gene.
2. Elongation - transcription bubble forms and
RNA polymerase travels in the 3’ → 5’ direction
on the template strand. However, it extends
RNA in the 5’ → 3’ direction.
3. Termination - a termination sequence (aka
terminator) signals to RNA polymerase to
stop transcribing the gene.
Genes are instructions within DNA that code for
proteins. However, they must first be transcribed
into RNA before being translated into proteins.
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Prokaryotic Transcriptional Control
In prokaryotes, transcription occurs in the cytosol.
RNA polymerase opens up DNA, forming a
transcription bubble.
Before transcription can occur, a sigma factor
combines with prokaryotic core RNA
polymerase to form RNA polymerase
holoenzyme, giving it the ability to target specific
DNA promoter regions.
An operon is a group of genes that is controlled by
one promoter, functioning as a single unit. The
operator region is present near the operon’s
promoter and binds activator/repressor
proteins to regulate the promoter.
The lac operon is an inducible operon (must be
induced to become active). LacZ, lacY, and lacA
are the three genes contained within the lac
operon that encode proteins required for lactose
metabolism. The lac operon will only be induced
when glucose is not available as an energy source,
so lactose must be used.
The lac repressor protein is the first way that the
lac operon is controlled. This protein is encoded by
an entirely separate gene called lacI, which is
constitutively expressed (always on). Thus, the
lac repressor protein is always bound to the
operator, blocking transcription. However, when
lactose is present it is converted to allolactose.
Allolactose binds directly to the repressor and
removes it from the operator, allowing
transcription to occur.
Another operon employed by prokaryotes is the
trp operon, which is responsible for producing the
amino acid tryptophan. It is known as a
repressible operon because it codes for
tryptophan synthetase and is always active
unless the presence of tryptophan in the
environment represses the operon.
Tryptophan binds to the trp repressor protein,
which then attaches to the operator on the trp
operon to prevent tryptophan production. Thus,
this is the first level of trp operon regulation. When
tryptophan is not present in the environment, the
trp operon will undergo transcription because the
trp repressor protein will be inactive.
cAMP levels and catabolite activator protein
(CAP) are the second level of lac operon regulation.
cAMP levels are inversely related to glucose levels,
so when glucose is low, cAMP is high. cAMP binds
to catabolite activator protein (CAP), which then
attaches near the lac operon promoter to help
attract RNA polymerase, promoting transcription.
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Eukaryotic Transcriptional Control
Unlike in prokaryotes, eukaryotic transcription
occurs in the nucleus and uses RNA polymerase
II to transcribe most genes.
Transcription factors are needed in eukaryotes
to help RNA polymerase bind to promoters. The
TATA box is a sequence in many promoters that
transcription factors can recognize and bind to.
Enhancers are DNA sites that activator
proteins can bind to and help increase
transcription of a gene.
Silencers are DNA sites that repressor
proteins can bind to and decrease transcription
of a gene.
Eukaryotic Post-Transcriptional Modifications
Post-transcriptional modification describes the
conversion of pre-mRNA into processed mRNA,
which leaves the nucleus. Below are the three
main types of post-transcriptional modification:
1. 5’ capping - 7-methylguanosine cap is added
to the 5’ end of the mRNA during elongation,
protecting the mRNA from degradation.
2. Polyadenylation of the 3’ end - addition of
the poly A tail to prevent degradation.
3. Splicing out introns - introns are
interruptions in DNA between protein coding
DNA called exons. Splicing refers to removing
introns from pre-mRNA using spliceosomes.
“Splice signals” are present within introns,
signaling to the spliceosome where to cut.
snRNAs (small nuclear RNA) and proteins make
up the functional part of a spliceosome and are
collectively referred to snRNPs (small nuclear
RiboNucleic Protein).
Alternative splicing describes a single pre-mRNA
having various possible spliced mRNA products.
Thus, the same pre-mRNA can produce many
different proteins.
Enhancers and silencers can be far upstream or
downstream from the gene, so DNA from these
sites are thought to loop around to colocalize with
RNA polymerase.
The poly A signal is located within the terminator
sequence and stimulates polyadenylation
(addition of adenine nucleotides to the 3’ end of
the mRNA).
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Ribosomes and tRNA (transfer RNA) are
important players in translation, the process of
converting mRNA into protein products.
Ribosomes are made up of one small and one
large subunit as described below:
Ribosomal binding sites for tRNA:
1. A site - A for aminoacyl-tRNA, which first
enters at this site.
2. P site - P for peptidyl-tRNA, which carries the
growing polypeptide.
3. E site - E for exit site. The tRNA from the P site
is sent here and released from the ribosome.
Eukaryotes - small (40S) and large (60S)
subunits form a 80S ribosome. They are
composed of rRNA (ribosomal RNA) and
proteins, which are assembled together in the
Prokaryotes - small (30S) and large (50S)
subunits form a 70S ribosome. They are also
composed of rRNA and proteins, but are
assembled together in the nucleoid.
A codon is a group of three mRNA bases (A, U, G,
or C) that code for an amino acid or terminate
translation. There are 64 codon combinations
total but only 20 amino acids, so degeneracy is
present (multiple codons code for the same amino
Memorize these codons →
Start codon: AUG (methionine)
Stop codons: UAA, UAG, UGA (end translation, do
not code for any amino acid)
The ribosome catalyzes the formation of a peptide
bond between the polypeptide in the P site and
the newly added amino acid in the A site.
Afterwards, the polypeptide is transferred to the A
site’s tRNA and the ribosome shifts one codon
down the mRNA. The A site will now be empty and
ready to accept another aminoacyl-tRNA. The tRNA
from the P site will be transferred to the E site and
will leave the ribosome.
An anticodon is a group of three tRNA bases (A, U,
G, or C) that base pairs with a codon. Each tRNA
carries an amino acid to be added to the growing
Aminoacyl-tRNA refers to a tRNA bound to an
amino acid.
Aminoacyl-tRNA synthetase is the enzyme that
attaches an amino acid to a specific tRNA using the
energy from ATP.
Adapted from:
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A DNA mutation is a heritable change in the
DNA nucleotide sequence that can be passed
down to daughter cells.
Three main types of DNA mutations:
1. Base substitutions (point mutations) one nucleotide is replaced by another.
Below are various effects they may have:
● Silent mutations - no change in
amino acid sequence. Due to “third
base wobble”, mutations in the DNA
sequence that affect the third base of
a codon can still result in the same
amino acid being added to the
protein. Relies on the degeneracy
(redundancy) of translation.
● Missense mutations - single change in
amino acid sequence. Can either be
conservative (mutated amino acid similar
to unmutated) or non-conservative
(mutated amino acid different from
● Nonsense mutations - single change in
amino acid sequence that results in a stop
codon. Results in early termination of
2. Insertions - adding nucleotides into the DNA
sequence - can shift reading frame.
3. Deletions - removing nucleotides from the
DNA sequence - can shift reading frame.
Factors that contribute to DNA mutations:
DNA polymerase errors during DNA
Loss of DNA during meiosis crossing over.
Chemical damage from drugs.
Factors that prevent DNA mutations:
DNA polymerase proofreading by DNA
Mismatch repair machinery that checks
uncaught errors.
Nucleotide excision repair that cuts out
damaged DNA and replaces it with correct
DNA using complementary base pairing.
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Molecular Genetic of Viruses
Viruses are not living because they must infect
living cells to multiply.
The capsid is a viral protein coat that is made of
subunits called capsomeres. Some viruses also
have a phospholipid envelope that they pick up
from the host cell membrane.
Two viral life cycle types:
1. Lysogenic cycle - virus is considered dormant
because it inserts its own genome into the
host’s genome and does not harm the host.
Each time the host genome undergoes
replication, so does the viral genome.
2. Lytic cycle - virus takes over host to replicate
and does harm the host. The viral particles
produced can lyse the host cell to find other
hosts to infect.
Molecular Genetics of Bacteria
Bacteria are asexual and divide by binary fission,
so they only receive genes from one parent cell
and do not increase genetic diversity through
Instead, they must increase genetic diversity
through horizontal gene transfer, which
describes the transfer of genes between individual
organisms. Below are the three methods of
horizontal gene transfer:
1. Conjugation - bacteria use a cytoplasmic
bridge called a pili to copy and transfer a
special plasmid known as the F plasmid
(fertility factor). If a bacteria contains an F
plasmid, it is referred to as F+. If not, it is
referred to as F-. To review, plasmids are
circular DNA pieces that are independent from
a bacteria’s single circular chromosome.
2. Transformation - bacteria take up extracellular
DNA. Bacteria are referred to as competent if
they can perform transformation.
Electroporation is the process of using
electrical impulses to force bacteria to become
3. Transduction - viruses transfer bacterial DNA
between different bacterial hosts. This occurs
when a bacteriophage enters the lysogenic
cycle in its host and carries bacterial DNA
along with its own genome upon re-entering
the lytic cycle.
It is important to note that viruses can switch
between the lysogenic and lytic cycles. For example,
favorable conditions can stimulate a virus in the
lysogenic cycle to replicate and enter to lytic cycle.
Retroviruses (eg. HIV) have an RNA genome that
infects host cells. They contain an enzyme called
reverse transcriptase, which converts their RNA
into cDNA (complementary DNA). The cDNA can
integrate into the host genome and enter the
lysogenic cycle.
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Chapter 7: Heredity
Table of Contents
Key Heredity Terms
Patterns of Inheritance
Gene Defects
Mendel’s Laws
Nondisjunction and Aneuploidies
Pedigree Analysis
Creating Genetic Diversity
Gene Linkage
Hemizygous - only one allele is present. For
example, men only have one X and one Y
chromosome (not homologous), which contain
hemizygous genes.
Penetrance - proportion of individuals who
have the phenotype associated with a specific
allele. Can be complete penetrance or
incomplete penetrance. As shown below, Bb
individuals all have brown eyes only when
there is complete penetrance.
Heredity is the passing of traits from parents to
offspring. These traits can be passed down
sexually (mating in animals) or asexually (binary
fission in bacteria).
Key Heredity Terms
Genome - all the DNA within a cell.
Gene - sequence of DNA that codes for a trait.
Locus - location of a gene on a chromosome.
Plural is gene loci.
Allele - one variation of a gene.
Wild-type allele - normal allele that is most
common in nature. Can turn into a mutant
Mutation - heritable change in DNA.
Genotype - genetic composition of an organism.
Phenotype - observable traits that result from
the genotype.
Dominant alleles - mask the expression of
recessive alleles. Typically represented by
uppercase letters (“A”).
Recessive alleles - only show up in phenotype
if dominant alleles are not present. Typically
represented by lowercase letters (“a”).
Homologous pairs - two different copies of
the same chromosome in a diploid organism.
One from each parent. Each copy is very
similar, except for minor nucleotide variations
that generate unique alleles.
Heterozygous - one dominant allele and one
recessive allele in its homologous pair.
Homozygous - same allele in both homologs.
Can be homozygous dominant or
homozygous recessive.
Expressivity - describes the degree of a certain
phenotype such as hair length or height
despite having the same genotype.
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Patterns of Inheritance
Incomplete dominance is the situation where
one allele is not completely expressed over its paired
allele. The heterozygous will have an
intermediate state. (Ex. red x white = pink).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=45105028
Codominance is the situation where the
heterozygous will express both alleles. (Ex. red x
white = red + white spots).
Multiple alleles describes when there are more
allele options than just two. (Ex. ABO blood typing
- A, B, O alleles).
Epistasis is when one gene affects the expression
of a different gene. (Ex. baldness gene covers up
the genes for hair color).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=30382414
Pleiotropy describes when one gene is
responsible for many traits. (Ex. cystic fibrosis,
disease with many symptoms caused by a single
Polygenic inheritance when many genes are
responsible for one trait. This gives the trait
continuous variation. (Ex. height, a single trait
affected by many genes).
The image below displays both pleiotropy and
polygenic inheritance:
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Gene Defects
Haploinsufficiency occurs when one copy of the
gene is lost or nonfunctional and the remaining
copy is not sufficient for a normal phenotype.
Haplosufficiency describes when the remaining
copy of the gene is sufficient for a normal
Proto-oncogenes are genes that can become
oncogenes (cancer-causing genes) due to
gain-of-function mutations. Gain-of-function
mutations cause too much protein to be made or
production of an over-active protein. Cancerous
growth occurs as a result because
proto-oncogenes are normally involved in cell cycle
Proto-oncogenes follow the one hit hypothesis,
which states that a gain-of-function mutation in
one copy of the gene turns it into a oncogene.
Tumor-suppressor genes are genes that become
cancerous as a result of loss-of-function
mutations because they are normally needed to
suppress cancerous growth.
Tumor-suppressor genes follow the two hit
hypothesis, which states that a loss-of-function
mutation in both copies of the gene are needed to
make it cancer-causing. Thus, tumor-suppressor
genes are haplosufficient.
Null alleles come from mutations that cause the
alleles to lack normal function. Tumor-suppressor
genes have null alleles when they become
p53 is an important tumor-suppressor gene
that is known as the guardian of the cell. It is
upregulated to prevent cells from becoming
p21 is another tumor-suppressor gene that
inhibits phosphorylation activity in order to
decrease rampant cell division.
Retinoblastoma gene (RB) is a
tumor-suppressor gene that codes for a
retinoblastoma protein, which prevents
excessive cell growth during interphase.
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Mendel’s Laws
Gregor Mendel studied genetics and proposed
three laws:
1. Law of dominance - dominant alleles mask
the expression of recessive alleles. Mendel
studied plant height to come to this conclusion.
3. Law of independent assortment homologous chromosomes line up
independently during metaphase I of meiosis
so that alleles separate randomly (increases
genetic variability). Metaphase II is different,
during which sister chromatids are pulled apart
instead. The law of independent assortment
can produce 223 options (23 homologous
chromosome pairs split).
Under the law of independent assortment, if we
consider a 6 chromosome diploid organism
(haploid number is 3), the 6 chromosomes could
assort with:
Trial 1: All paternal on one side, all maternal on
the other:
Resulting in daughter cells that look like this:
Trial 2: However, they also could randomly align
like this:
2. Law of segregation - homologous gene copies
separate during meiosis (specifically anaphase
I). Thus, Aa individuals will produce gametes
with “A” or “a” alleles.
Resulting in daughter cells that look like this:
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Nondisjunction and Aneuploidies
Nondisjunction is the improper segregation of
chromosome pairs during anaphase and produces
daughter cells with an incorrect number of
3. Single nondisjunction of sister chromatids
during mitosis
46 chromosomes in diploid parent cell
47, 45 chromosomes in diploid daughter cells
1. Single nondisjunction of homologous
chromosomes during meiosis I
46 chromosomes in diploid parent cell
24, 24, 22, 22 chromosomes in haploid daughter
Adapted from: https://commons.wikimedia.org/w/index.php?curid=26233546
2. Single nondisjunction of sister chromatids
during meiosis II
46 chromosomes in diploid parent cell
24, 22, 23, 23 chromosomes in haploid daughter
Aneuploidy refers to an abnormal number of
chromosomes in the daughter cells. After
fertilization, trisomy (3 chromosomes copies) or
monosomy (1 chromosome copies) can occur.
Down syndrome is a trisomy of chromosome #21
(each diploid cell has 47 chromosomes total).
Turner syndrome is a monosomy of the X
chromosome in females (each diploid cell has 45
chromosomes total). Individuals have physical
abnormalities and sterility.
Klinefelter’s syndrome is a trisomy of the sex
chromosomes in males, giving them XXY (each
diploid cell has 47 chromosomes total). Individuals
usually have disorders in intellectual, physical, and
reproductive development.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=26233546
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A cross refers to when two organisms are mated
to produce offspring.
A test-cross pairs an individual of unknown
genotype with one that is homozygous recessive. By
looking at the offspring from a test-cross, we can
determine the unknown genotype.
True-breeding organisms are homozygous for all
the traits of interest.
The F1 generation (aka filial 1 hybrid) is the first
generation cross between true-breeding parents
with different alleles. The offspring are all
The F2 generation (aka filial 2 hybrid) is the
second generation cross between the heterozygous
offspring from the F1 generation. This is where
Mendel’s three laws can be studied.
If these two generations are studied under
monohybrid crosses, then only a single gene is
examined. In the F2 generation, the genotype ratio
(AA:Aa:aa) should be (1:2:1) and the phenotype
ratio (dominant:recessive) should be (3:1).
On the other hand, a dihybrid cross examines the
inheritance of two genes on separate
chromosomes. Although the genotype ratio is
complex in the F2 generation, just remember that
the phenotype ratio (both dominant:one
dominant one recessive:one dominant one
recessive:both recessive) should be (9:3:3:1).
Punnett squares are used to visualize these
crosses but are too complex for dihybrid cross.
Thus, one-gene cross ratios can be used to solve
these questions faster. Below are the single allele
crosses you should memorize:
1. Homozygous x homozygous = 1/1 AA or
1/1 Aa or 1/1 aa
2. Homozygous x heterozygous = ½ AA (or
aa) and ½ Aa
3. Heterozygous x heterozygous = ¼ AA, ½
Aa, ¼ aa
Multiple-locus crosses can then be solved using
these single alleles cross. As shown below, RrYy
individuals are crossed with each other. The Rr
single cross probabilities can be multiplied with
the Yy single cross probabilities to get the dihybrid
offspring probabilities shown on the right.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=6070182
Adapted from: https://commons.wikimedia.org/w/index.php?curid=49926348
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Pedigree Analysis
Creating Genetic Diversity
Pedigree charts are used to track traits over many
generations to see how they are inherited. Females
are circles while males are squares. Furthermore,
unaffected individuals are unshaded while
affected individuals are shaded.
Crossing over also creates genetic diversity and
occurs during prophase I of meiosis. Homologous
chromosomes join together to form tetrads (aka
bivalents) and exchange genetic material at points
referred to as chiasmas. Afterwards, genetically
unique chromatids are produced as a result of
crossing over.
The pedigree chart shown above has affected
individuals depicted red and unaffected individuals
depicted blue.
Given that the “affected” trait is autosomal
dominant, we can use this chart to solve for the
genotype of the affected male in the third
The logic goes like this → Since the male is affected,
we know that he can be heterozygous or
homozygous dominant. However, since his father
is unaffected, the male could not have received an
“affected” allele from his father. Thus, this
individual must be heterozygous. The single
dominant allele came from his mother.
Recombinant gametes describe the gametes that
receive the genetically unique chromatids (new
combination of alleles), while non-recombinant
gametes refer to the gametes that receive
parental chromatids (alleles match parental).
These kinds of questions are frequently asked by
the DAT, so practice them and use clues from
parents/offspring to find the answers!
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Gene linkage
Linked genes are found close together on the same
chromosome. By looking at recombination
frequencies, we can deduce the relative distance
between these genes.
One map unit is defined as the chromosomal
distance that would allow 0.01 crossover events
per generation. 20 map units would mean 0.2
crossover events occur between the two genes per
generation, or 20% chance of recombination.
Recombination frequencies of less than 50%
mean that the two genes are linked. A random
assortment of unlinked genes have 50%
recombinant progeny.
Genomic imprinting refers to genes that are
expressed depending on parental origin and are
influenced by epigenetic factors. These genes are
different from sex-linked traits because they can
come from autosomal chromosomes (non-sex
chromosomes) as well.
X-inactivation is the process by which one of a
female’s X chromosomes is inactivated, forming a
Barr body and preventing excess transcription.
However, a female carrier may become an
affected individual for a disease if her unaffected
X chromosome with a normal wild-type allele is
inactivated, leaving behind a recessive allele that is
not covered up.
Linkage maps can be drawn out using map units
to infer the distance between genes on a
A haplotype is a group of genes that are usually
inherited together because they are located in
close proximity to each other.
Sex-linked traits come from genes located on the
sex chromosomes. Most sex-linked disorders have
X-chromosome linkage. Below are three types of
sex-linked traits:
1. X-linked dominant - dominant inheritance on
the X chromosome. Any offspring (male or
female) that receive the affected allele will end
up with the disorder.
2. X-linked recessive - recessive inheritance on
the X chromosome. For males, only one
affected allele is needed to cause the disorder.
For females, two affected alleles are needed to
cause the disorder because females have two
X chromosomes.
3. Y-linked - inheritance on the Y chromosome.
Can only be passed from father to son. Will
always be expressed whether it is dominant or
recessive because males only have one Y
Epigenetics does not involve modifying the
genetic code, but instead the regulation of when
genes are expressed. Epigenetic changes are
heritable. Below are some examples of
epigenetic changes:
DNA methylation - causes gene suppression
through the addition of methyl groups,
recruiting methyl-binding proteins (MBDs) and
preventing transcription factors from binding.
Histone acetylation - causes gene activation
and formation of euchromatin (easily
accessible DNA).
Histone de-acetylation - causes gene
suppression and formation of
heterochromatin (hard to access DNA).
Histone methylation - causes gene
suppression and formation of
heterochromatin (hard to access DNA).
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Chapter 8: Microscopy & Lab Techniques
Types of Optical Microscopes
Table of Contents
● Overview of Microscopy
● Types of Optical Microscopes
● Types of Electron Microscopes
● Cellular Biological Lab Techniques
● Biological Laboratory Techniques for
Nucleic Acids and Proteins
● Genomics
● Miscellaneous Biological Laboratory
Techniques that are Important for the DAT
1. Stereo microscopes (dissection microscopes):
low magnification to view surface of an object.
2. Compound microscopes: have multiple lenses
to view simple, one-cell thick, live cells. Without
fixing and staining, it has poor contrast.
3. Bright field microscopes: compound
microscopes with a bright light.
4. Phase contrast microscopes: can view thin
samples with live cells. Light is refracted
through an annular ring creating a phase shift,
leading to high contrast. Large phase shifts can
lead to a halo effect (can be reduced with
phase plates or thinner samples).
5. Fluorescence microscopy: fluorophores
(fluorescent chemicals) are used to visualize
different parts of the cell. A dichroic filter is
used which allows certain wavelengths of light
to be reflected and others to pass through.
Distortions or artifacts decrease the resolution.
6. Confocal laser scanning microscopy:
visualizes fluorescent objects. Can be used
without fluorescence tagging. Artifacts are
reduced by focusing a beam of UV light onto the
sample. This reduces intensity so samples must
be illuminated longer.
7. Dark field microscopy: increases contrast
between sample and the field around it to
allow visualization of unstained live cells. Only
scattered light is viewed - allows the sample to
be viewed against a black background.
Overview of Microscopy
Before microscopy, we must first fix and stain
1. Fixation: getting cells to ‘stick’ to the slide and
preserving them in their most life-like state.
There are 2 types: heat fixation and chemical
fixation. During heat fixation cells are placed
on top of the slide and then the underside of
the slide is run over a bunsen burner. This
heats the cells, preserving and sticking them to
the slide.
2. Staining adds color to cells, making cell
structures easier to visualize. Staining often kills
the cells.
General Types of Microscopy:
1. Optical microscopy: cells are viewed directly.
Light shines on a sample and is magnified via
lenses. Can observe living cells.
2. Electron microscopy:
cells are viewed indirectly
via computer after being
bombarded with electrons
which pass through
magnetic fields in a
vacuum. Can be used to
view smaller objects but
cells must be fixed,
stained (metal coated) and
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Types of Electron Microscopes
1. Scanning electron microscopy (SEM): high
resolution 3D images of the surface of a
dehydrated sample.
Cellular Biological Lab Techniques
Techniques to count cells:
1. Hemocytometers (counting chambers):
gridded slide under microscope. Can count
cells in a known area and extrapolate for full
volume of sample.
2. Colony Forming Units (CFUs): estimates
number of cells plated on growth medium
assuming that one cell gives rise to one colony.
3. Automated cell counting includes electrical
resistance (counting cells by observing flow of
electricity) and flow cytometry (cells in narrow
tube detected by laser).
Cell fractionation separates cell contents by
centrifugation. Centrifuge spins contents to
separate them by mass, density, and/or shape. More
dense particles collect at the bottom (pellet) and
less dense particles remain as supernatant liquid
on top.
2. Cryo-scanning electron microscopy
(cryo-SEM): type of SEM where sample is
frozen in liquid nitrogen instead of dehydrated.
Costly and produces artifacts.
3. Transmission electron microscopy (TEM):
high resolution 2D images of the sample’s
internal structures.
Differential centrifugation: cells are first split
open to release contents (homogenization).
Multiple cycles where supernatant is removed
and spun again allowing for fractionation
(isolation) of each organelle.
4. Electron tomography: not a type of
microscopy. Sandwiches TEM images to create
a 3D image of sample’s internal structure.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=37665969
Density centrifugation: one cycle where
organelles are separated by density into layers.
○ From most dense to least dense: nuclei >
mitochondria/chloroplast > ER fragments >
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Biological Laboratory Techniques for Nucleic
Acids and Proteins
1. Karyotyping: observing chromosomes under
light microscope during metaphase. Can be
used to diagnose conditions involving
chromosomal aberrations, breakages,
aneuploidies (e.g. Down’s syndrome or trisomy
2. DNA sequencing: sequencing nucleotides in
fragments of DNA. 2 methods are dideoxy
chain termination or Sanger sequencing
(older) and next generation sequencing
(newer). Can sequence complete genomes
piece by piece. In humans single nucleotide
polymorphisms (SNPs) serve as markers for
disease causing genes.
● Recombinant DNA is produced when
restriction enzymes cut DNA at
palindromic sequences generating sticky
ends (have unpaired nucleotides) or blunt
ends (have paired nucleotides).
Restriction fragment length
polymorphisms (RFLPs) are unique
lengths of DNA from restriction enzymes,
allows for comparison between individuals.
Analyzes non-coding DNA (coding DNA is
highly conserved).
3. DNA fingerprinting: identifies individuals
through unique aspects of DNA such as RFLPs
and short tandem repeats (STR’s). Used in
paternity and forensic cases.
4. Polymerase Chain Reaction (PCR): automated
process creating millions of copies of DNA in 3
Denaturation (~95 °C): heating separates
DNA into single strands.
Primer annealing (~65 °C): DNA primers
hybridize with single strands.
Elongation (~70 °C): nucleotides are added
to the 3’ end of DNA using Taq
5. Bacterial cloning: cloning eukaryotic gene
products in prokaryotic cells. Used to produce
● Protocol: Processed mRNA for eukaryotic
gene is isolated then treated with reverse
transcriptase to make cDNA → cDNA
incorporated into plasmid (transfer
vector) using reverse transcriptase and
DNA ligase → vector taken up by
competent bacterial cells (can undergo
transformation; made competent using
electroporation or heat shock) and undergo
transformation → gene of interest is
found using antibiotic resistance
(antibiotic resistant gene attached to target
gene) or color change (vectors containing
genes making cells blue) methods.
6. Gel electrophoresis: separates DNA
fragments by charge and size. An electric field is
applied to agarose gel (top = negative cathode,
bottom = positive anode). Smaller fragments
travel further from top of gel.
7. Southern blotting: identifies fragments of
known DNA sequence in a large population of
DNA. Electrophoresed DNA separated into
single strands and identified via complementary
DNA probe.
8. Northern blotting: identifying fragments of
known RNA using an RNA probe.
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9. Western blotting: quantifies amount of target
protein in a sample using sodium dodecyl
sulfate polyacrylamide gel electrophoresis or
SDS PAGE (proteins denatured and given
negative charge proportional to their mass).
Treated with primary antibody (binds to
target protein) and secondary antibody
(attached to indicator and binds to primary
Mnemonic: SNOW DROP
10. Enzyme-Linked Immunosorbent Assay
(ELISA): determines if a person has a specific
antigen. Important to diagnose diseases (e.g.
HIV). Antibodies are placed on a microtiter
plate and with antigens and change color.
11. Pulse chase experiments: useful for studying
gene expression and the fate of proteins by
viewing how a protein moves through a cell.
During the pulse phase amino acids are
radioactively labeled and then incorporated
into proteins. The chase phase prevents
radioactively labelled protein production.
Using simple staining, the radioactive proteins
can be tracked.
Genomics is the study of all genes present in an
organism’s genome and how they interact.
1. A genomic library stores the DNA of an
organism’s genome. DNA fragments are
incorporated into plasmids and can be
screened for by using antibiotic resistance and
color changing techniques. They are then
cloned via bacterial cloning.
2. DNA microarrays contain thousands of DNA
probes that bind to complementary DNA
fragments, allowing researchers to see which
genes are expressed.
● Protocol: isolate a cell and remove mRNA
(active transcription) → synthesize cDNA
from mRNA using reverse transcriptase →
hybridize cDNA with DNA probes →
examine microarray for fluorescence →
compare microarray with the sequenced
3. Transgenic animals are models used to
identify the function of a gene. A gene is taken
from one organism and inserted into another.
Can be used for mass medication production
(e.g. clotting factors for hemophiliacs). This
process is labor intensive.
4. Reproductive cloning: producing a genetic
copy of an organism from a somatic cell. A
multipotent cell must be converted to a
totipotent cell. E.g. Dolly the sheep.
● Totipotent cells: can differentiate into an
entire organism (including extraembryonic
membranes). E.g. zygote → morula.
● Pluripotent cells: can differentiate into
the three germ layers (endoderm,
mesoderm, ectoderm). Cannot give rise to
extraembryonic membranes.
● Multipotent cells: can give rise to some of
the three germ layers - not all.
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Miscellaneous Biological Laboratory
Techniques that are Important for the DAT
1. Chromatography: separating components of
a heterogeneous sample using differential
solubility. The sample is dissolved in the solvent
(mobile phase) and placed in an apparatus
containing the stationary phase. The mobile
phase climbs up the stationary phase and the
different components ascend to different
3. Fluorescence Lifetime Imaging Microscopy
(FLIM): provides a quantitative measure of the
concentration of various ions, molecules, and gases
in a cell. Cell is irradiated with light and fluorescence
lifetime is measured.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=1175699
2. Fluorescence Recovery After
Photobleaching (FRAP): quantitative measure
of how and where biomolecules move in a live
● Protocol: baseline fluorescence is
measured → area of the sample is
photobleached → photobleached molecules
are replaced by unbleached molecules
overtime due to cell dynamics → area
gradually recovers fluorescence.
3. Knockout mice: selected gene is ‘knocked out’
and changes between knockout and wild type
are observed.
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Chapter 9: Diversity of Life
Table of Contents
● Taxonomy
● Prokaryotes
● Eukaryotes
(Click here to see our taxonomy video miniseries)
(Click here to download our taxonomy cheat sheet)
Taxonomy is the science of classifying organisms.
Gram Positive Bacteria:
● stain dark purple.
● thick peptidoglycan layer in cell wall.
● no outer membrane.
● very minor periplasm (outside plasma
● No lipopolysaccharide (LPS - an
endotoxin released when bacteria is
● Secrete exotoxins.
● Contain teichoic acids (polysaccharide
connecting peptidoglycan layer and plasma
membrane for rigidity and structure).
Gram Negative Bacteria:
● Stain pink (due to counterstain).
● Thin peptidoglycan layer in cell wall.
● Contains periplasm between inner and outer
● Outer membrane present.
● LPS present (in outer membrane).
● Secrete exotoxins.
● No teichoic acids.
Eubacteria vs. Archaea
King Phillip Came Over For Great Soup.
The 6 kingdoms are: Archaea, Eubacteria,
Protista, Fungi, Plantae, Animalia.
Prokaryotes: organisms that do not have
membrane bound nuclei and tend to not have
membrane bound organelles. E.g. Eubacteria and
Eubacteria: Gram Positive vs. Gram Negative
Gram positive bacteria have a thick peptidoglycan
layer in their cell wall; whereas gram negative
bacteria have a thin peptidoglycan layer and a
second outer membrane. Both are covered by a
capsule (a virulence factor protecting the
bacteria from drying out).
● Contain cell walls.
● 70S ribosomes.
● DNA is organized in circular plasmids
(horizontal gene transfer via pilli).
● Flagellum for movement.
● Reproduce via binary fission.
Cell wall contains
peptidoglycan; lipids
bound via
Cell wall lacks
peptidoglycan; lipids
bound via
Ribosome has unique
Ribosome has unique
DNA lacks introns and
Contain introns, some
have histones.
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Eukaryotes: organisms whose cells contain
membrane bound nuclei and organelles. E.g.
Protista, Fungi, Plantae, and Animalia.
Protists: kingdom of (mostly unicellular)
eukaryotic organisms.
1. Fungus-like protists: unlike fungi, no cell wall
made of chitin. Can move via cilia or flagella
(e.g. slime molds). Are saprophytic and feed
via phagocytosis. Reproduce via asexual
reproduction and sporulation (resist
environmental conditions).
2. Plant-like (algae-like) protists: among the
most important primary producers.
Dinoflagellates, diatoms, and euglenoids are
unicellular, photosynthetic autotrophs,
reproduce asexually, and are found in aquatic
● Dinoflagellates: responsible for red tide
(toxins build up, O2 in water is depleted),
have two flagella (find food in absence of
light), and are heterotrophic (parasitic).
3. Animal-like protists: known as protozoa,
have food vacuoles. Include amoeba and
paramecium. Heterotrophic (move via flagella
and cilia) and often parasitic pathogens.
Fungi are heterotrophic saprophytes.
1. Nonfilamentous fungi (e.g. yeast) are
unicellular, reproduce asexually by budding, and
are facultative anaerobes.
2. Filamentous fungi (e.g. molds) are
multicellular, multinucleate (form hyphae),
reproduce sexually, and are aerobic.
Hyphae are long, branching filaments that extend
out to form a network of fungi (mycelium).
Mycelium can either grow with septate hyphae
(have septas dividing hyphae in different sections)
or with coenocytic hyphae (one long continuous
multinucleated cell; cytokinesis does not occur
during cell division).
Under favorable environments, fungi reproduce
asexually by producing a haploid spore producing
structure which produces haploid spores that grow
via mitosis. In unfavorable environments, fungi
reproduce sexually producing genetically different
offspring with greater chance of survival. Two
hyphae fuse their cytoplasm (plasmogamy)
creating a single fused cell with 2 haploid
pronuclei which fuse (karyogamy) to produce a
single diploid cell. The diploid cell produces a spore
producing structure that produces spores via
Lichens are symbiotic autotrophs where a fungi
is paired with either algae or cyanobacteria. Fungi
protect the cyanobacteria / algae and provide it
with water and nutrients while algae /
cyanobacteria photosynthesize, producing food for
the fungi.
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Animals are eukaryotic, diploid, multicellular
heterotrophic aerobes.
Animals can be distinguished based on the
presence of a coelom (cavity). In coelomates
mesoderm surrounds the coelom on all sides
whereas in acoelomates it does not, and in
pseudocoelomates the coelom is partially
surrounded. The pseudocoelom is a
hydroskeleton (fluid pressure providing structural
support) that helps with motility.
● E.g. Sponge
● Body symmetry: Asymmetrical
● Tissue organization: Parazoa (no true tissues)
● Circulatory system: None (diffusion)
● Nervous system: None
● Respiratory system: None (diffusion)
● Digestive system: Intracellular digestion via
amoebocytes (totipotent cells contribute to
structure, digestion, regeneration, move via
General characteristics: sessile (non-motile),
suspension feeders, aquatic habitats, earliest
animals, reproduce asexually (budding) or sexually
(hermaphrodites - has male and female sex
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● E.g: hydra, jellyfish, sea anemone, coral.
● Body symmetry: Radial (around central axis).
● Tissue organization: Diploblasts (two cellular
layers: endo- and ectoderm), true tissues
● Circulatory system: None (diffusion).
● Nervous system: Nerve net (neurons spread
apart), no brain.
● Respiratory system: None (diffusion).
● Digestive system: gastrovascular cavity (one
opening, two way digestion, acts as hydrostatic
skeleton to aid movement).
General Characteristics: Aquatic habitats, some
have nematocysts (cells shooting poisonous
barbs), some have life cycles that switch from
polyp (non-motile, reproduce asexually) to medusa
(motile, reproduce sexually) forms.
● E.g. Flatworms, trematoda, flukes, tapeworm,
● Body symmetry: Bilateral (right and left
halves, axis at sagittal plane) with
cephalization (central nervous system - brain).
● Tissue organization: Triploblasts (three germ
layers), eumetazoa.
● Circulatory system: None (diffusion).
● Nervous system: Two nerve cords (dense
nerve bundle running along length of
invertebrates), anterior centralized ganglia
(brain), some planarians have eyespots.
● Respiratory system: None (diffusion).
● Digestive system: Gastrovascular cavity
(except tapeworms - absorb food).
● Excretory system: Protonephridia (bundles
of flame cells - involved in osmoregulation).
General Characteristics: reproduce sexually
(hermaphrodites) or asexually (regeneration), mainly
aquatic habitats, parasitic lifestyles, most primitive
of triploblasts, has organs.
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● E.g. Round worm, hook worm, trichinella, C.
elegans, ascarcis.
● Body symmetry: Bilateral.
● Tissue organization: Triploblasts, eumetazoa.
● Circulatory system: None (diffusion).
● Nervous system: Nerve cord and ring
(surrounds esophagus).
● Respiratory system: None (diffusion).
● Digestive system: Alimentary canal (passage
between mouth and anus).
General Characteristics: Some have cuticle
(prevents degradation by host digestive system),
longitudinal muscles (no circular muscles),
parasitic, not segmented.
● Key names: Rotifers.
● Body symmetry: Bilateral.
● Tissue organization: Triploblasts, eumetazoa.
● Circulatory system: None (diffusion).
● Nervous system: Cerebral ganglia (brain) with
nerves extending through body.
● Respiratory system: None (diffusion).
● Digestive system: Alimentary canal, mouth
and anus.
● Excretory system: Protonephridia and flame
General Characteristics: Not truly segmented,
can reproduce sexually or parthenogenetically,
mostly freshwater environments. Draw food and
water into mouth by beating cilia.
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● E.g. Earthworm, leech.
● Body symmetry: Bilateral.
● Tissue organization: Triploblasts, eumetazoa.
● Circulatory system: Closed circulatory
system (blood pumped through vessels by
heart), multiple pairs of aortic arches, distinct
arteries and veins.
● Nervous system: Ventral nerve cord, anterior
ganglia (brain).
● Respiratory system: None (diffusion).
● Digestive system: Alimentary canal, mouth
and anus.
● Excretory system: Most have metanephridia
(excretory glands for osmoregulation. Tubes of
cilia move fluid emptying into coelom, ducts
bring fluid to exterior).
● Embryonic development: Protostome
(blastopore forms mouth).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=8062105
General Characteristics: Segmented bodies,
coelom is divided by septa, sexual (hermaphrodites)
and asexual (regeneration) reproduction,
longitudinal and circular muscles.
● E.g. Clam, snail, slug, squid, octopus,
cephalopod, gastropod.
● Body symmetry: Bilateral.
● Tissue organization: Triploblasts, eumetazoa.
● Circulatory system: Mainly open; hemocoel
(spaces inside an organism where blood freely
flows around organs).
● Nervous system: Ventral nerve cords and
● Respiratory system: Gills.
● Digestive system: Complete (alimentary
canal and accessory glands), mouth and anus,
radula (tongues covered in tiny teeth - unique
to mollusks).
● Excretory system: Nephridia (pairs of
osmoregulatory ‘kidneys’ in invertebrates).
● Embryonic development: Protostome
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Arthropoda (all):
● Body symmetry: Bilateral.
● Tissue organization: Triploblasts, eumetazoa.
● Circulatory system: open, hemolymph
(equivalent to blood).
● Nervous system: Fused ganglia (masses of
nerve tissue), ventral nerve cord.
● Digestive system: one-way digestion, some
have salivary glands.
● Embryonic development: Protostome.
1. Arthropoda (Insecta):
● E.g. ant, grasshopper.
● Respiratory system: Spiracles (small
openings on exoskeleton where air enters)
branch into tracheal tubes (site of gas
● Excretory system: Malpighian tubules
(small tubes on abdomen, help with uric
acid excretion).
General Characteristics: Exoskeleton of chitin,
jointed appendages, three pairs of legs, more
species than any other phylum combined,
metamorphosis (distinct stages, altered
appearance as insect matures).
Arthropoda (Insecta):
Arthropoda (Arachnida):
2. Arthropoda (Arachnida):
● E.g. spider, scorpion.
● Respiratory system: trachea or book
lungs (sheets of vascularized tissue on
either side to increase surface area).
● Excretory system: Malpighian tubules and
/ or coxal glands.
General Characteristics: Exoskeleton, jointed
appendages, four pairs of legs, terrestrial habitats.
3. Arthropoda (Crustacea):
● E.g. lobster, crayfish, crab.
● Respiratory system: some have gills.
● Excretory system: Green glands (aquatic),
malpighian tubules (terrestrial).
Arthropoda (Crustacea):
General Characteristics: Exoskeleton, jointed
appendages, aquatic and terrestrial habitats.
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● E.g. Starfish, sea urchin, sea cucumber.
● Body symmetry: Bilateral (larvae), five fold
radial (adult).
● Tissue Organization: Triploblasts, eumetazoa.
● Circulatory system: open, no heart.
● Nervous System: Nerve ring and radial
● Respiratory system: None (diffusion).
● Digestive system: Complete, mouth and anus.
● Excretory system: None (diffusion).
● Embryonic Development: Deuterostome
(blastopore forms anus).
General Characteristics: Spiny, central disk
(central portion from which arms radiate, contains
mouth, anus and opening for water to enter for
water vascular system), tube feet (suction cups for
walking and obtaining food), sexual or asexual
reproduction, closest related major phyla to
Chordates (Most important for DAT):
● E.g. Vertebrates.
● Body Symmetry: Bilateral.
● Tissue Organization: Triploblasts, eumetazoa.
● Embryonic Development: Deuterostome.
Adapted from: https://commons.wikimedia.org/wiki/File:Figure_29_01_04.jpg
Shared Traits of all Chordates:
1. Notochord: cartilaginous rod derived from
mesoderm. Forms the primitive axis and
supports the body during embryonic
development. Lost in most chordates, and
replaced by bone.
2. Dorsal Hollow Nerve Cord: forms spinal cord basis of nervous system and brain.
3. Pharyngeal Gill Slits: forms pharynx, gills,
other feeding structures. Provides channel
from pharynx to other structures. In humans
forms Eustachian tubes and other head and
neck structures.
4. Muscular post-anal tail: lost during
embryonic development in humans and many
other chordates.
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Types of Chordates:
1. Lancelets (also known as Amphioxus):
● Subphylum: Cephalochordata.
● Circulatory system: Closed circulatory
system, lacks heart, contains contractile
blood vessels.
● Respiratory system: Gills.
● General characteristics: Keep all the
same developmental characteristics as
other chordates, but lack vertebrae.
Commonly used to study the origin of
2. Tunicates (also known as Urochordata):
● Subphylum: Tunicata.
● Circulatory system: Both closed and open
circulatory systems.
● Respiratory system: Gills.
● General characteristics: Sessile, filter
feeders, hermaphroditic, sexual and
asexual (budding) reproduction. Benthic
habitats (bottom of a body of water),
notochord in larvae.
3. Fish (Jawless):
● E.g agnatha, lamprey, hagfish.
● Subphylum: Vertebrata.
● Circulatory system: Two chambered
● Respiratory system: Gills, countercurrent
● General characteristics: Notochord in
larvae and adult, cartilaginous skeleton.
4. Fish (Cartilaginous):
● E.g. Shark.
● Subphylum: Fish (Cartilaginous).
● Circulatory system: Two chambered
● Respiratory system: Gills.
● General characteristics: Jaws and teeth,
reduced notochord with cartilaginous
5. Fish (Bony):
● E.g. Salmon, halibut.
● Subphylum: Vertebrata.
● Circulatory system: Two chambered
● Respiratory system: Gills.
● General characteristics: scales, bony
6. Amphibia:
● E.g. Frog, toad, salamander, newt
● Subphylum: Vertebrata
● Circulatory system: Three chambered
● Respiratory system: Gills (juvenile), Lungs
● General characteristics: No scales.
Undergo metamorphosis. Tadpoles
(aquatic) have tails, no legs. Adults
(terrestrial) two pairs of legs, no tail.
7. Mammalia (Monotremes):
● E.g. Duckbill platypus, spiny anteater.
● Subphylum: Vertebrata.
● Circulatory system: Four chambered
● Respiratory system: Lungs.
● General characteristics: Warm blooded
(homeothermic), feed young with milk,
leathery eggs, mammary glands with many
openings (no nipples).
8. Mammalia (Marsupials):
● E.g. Kangaroo, opossum.
● Subphylum: Vertebrata.
● Circulatory system: Four chambered
● Respiratory system: Lungs.
● General characteristics: Homeotherms,
feed young with milk.
9. Mammalia (Placental):
● E.g. Bat, whale, mouse, human.
● Subphylum: Vertebrata.
● Circulatory system: Four chambered
● Respiratory system: Lungs.
● General characteristics: homeotherms,
placenta supports fetus.
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10. Reptilia:
● E.g. Turtle, snake, crocodile, alligator.
● Subphylum: Vertebrata.
● Circulatory system: Three chambered
heart (exception: crocodiles and alligators
= four chambered heart).
● Respiratory system: Lungs.
● General characteristics: Mainly
terrestrial, leathery eggs, internal
fertilization, cold blooded
11. Birds:
● E.g. Eagle, blue jay.
● Subphylum: Vertebrata.
● Circulatory system: Four chambered
● Respiratory system: Lungs.
● General characteristics: homeotherms,
eggs in shells.
Prokaryotes vs. Eukaryotes
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Chapter 10: Plants
Table of Contents:
● The Seed and Germination
● Primary vs. Secondary Growth
● Plant Tissues
● Leaf Structures
● Movement of Water
● Movement of Food
● Plant Hormones
● Alternation of Generations
● Homosporous vs. Heterosporous Plants
● Bryophytes
● Tracheophytes
● Flower Structures
● Angiosperms: Monocots vs. Dicots
● Nitrogen Fixation
The Seed and Germination
1. Seed coat: hard outer layer that covers and
protects the seed.
2. Endosperm: storage material, provides the
embryo with nutrients.
3. Embryo: consists of 4 parts ● Radicle: first to emerge, develops into root,
anchors the plant into soil.
● Hypocotyl: bottom region of young shoot.
● Plumule: develops into leaves.
● Epicotyl: top region (shoot tip).
Primary vs. Secondary Growth
Plant growth takes place via mitosis at meristems.
Primary growth is vertical growth occurring at
apical meristems (located at tips of roots and
shoots). Occurs before secondary growth.
Root Growth: root cap covers roots protecting the
apical meristem. The root tip has three zones:
● Zone of division: where apical meristem cells
are located and divide.
● Zone of elongation: above apical meristem,
cells absorb water and elongate.
● Zone of maturation: cells differentiate to
specific plant tissues.
Secondary growth is horizontal growth occurring
at lateral meristems (vascular cambium and
cork cambium). Only occurs in woody plants.
Vascular cambium is a ring of meristematic tissue
located between primary xylem (closer to center)
and primary phloem (closer to outer edge). Cell
produced inside ring of vascular cambium become
secondary xylem (forms wood along with pith)
and cells outside become secondary phloem
(forms bark with cork and cork cambium). New
xylem is produced every year (forming growth
rings) whereas new phloem replaces old phloem.
Cork cambium is a ring of meristematic tissue
located outside the phloem. Produces cork, the
outermost protective layer.
Germination: the sprouting of a seedling from a
previously dormant state when environmental
conditions are favorable. Water is the most
important condition. The seed absorbs water
(imbibition) which breaks the seed coat and
initiates growth.
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Plant Tissues
Leaf Structures
1. Ground tissue: provides structural support,
makes up most of plant’s mass.
● Parenchyma: filler tissue, makes up bulk of
plant, thin cell walls.
● Collenchyma: extra support (e.g. in areas
of active growth), irregular cell walls.
● Sclerenchyma: provides main structural
support, thick cell walls.
2. Vascular tissue: transports materials from a
source to a sink (source to sink theory). The
stele is formed by xylem, phloem, and the
pith (made of parenchyma) in the center of the
plant for transport.
● Phloem: transports sugars from leaves
(source) to roots and other areas (sink).
Made of sieve cells (long cells, lacking
organelles, connected to form a tunnel for
transport) and companion cells
(connected to sieve cells, contain organelles
for metabolic functions).
● Xylem: transports water from roots
(source) to leaves (sink) and provides
structural support. Made up of tracheids
(long and thin, water travels through pits in
their tapered ends) and vessel elements
(short and stout, water travels via
perforations in cell walls).
3. Dermal tissue: outer layer of the plant.
Provides protection and regulation.
● Epidermis: covered by cuticle (waxy layer)
which limits water evaporation.
● Root hairs: increase surface area of roots
for greater nutrient and water uptake.
Leaves are covered by an epidermal layer,
covered by a waxy cuticle. Stomata in the lower
epidermis open and close, allowing for gas
exchange. Water influx to the guard cells makes
them turgid, opening the stomata. Stomata are
open when CO2 concentration is low (allows for CO2
intake and photosynthesis) and closed when CO2
concentrations are high and when temperatures
are high (prevents water loss via transpiration). A
balance must exist between opening stomata for
food production via photosynthesis and closing
stomata to prevent water loss (desiccation).
Water uptake in the roots occurs via the
symplastic pathway (inside the cell’s cytoplasm)
or the apoplastic pathway (outside the cell
through cell walls). The Casparian strip (made of
fat and wax) is an impenetrable substance in the
cell walls of the roots. It forces water coming from
the cell walls into the cytoplasm for filtering before
entering the rest of the plant.
Between the upper and lower epidermis is the
● Palisade mesophyll: closer to upper
epidermis, tightly packed cells that carry out
● Spongy mesophyll: closer to lower epidermis,
loosely-packed allowing for gas exchange.
Bundle sheath cells surround and protect the
vascular bundle.
Adapted from:
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Movement of Water
1. Cohesion-tension theory: transpiration, the
driving force causes water to evaporate from
the stomata and leads to a transpirational
pull. This cohesive force (between similar
substances, e.g. the water molecules) pulls the
water column upward.
2. Capillary action: an adhesive force (between
dissimilar substances) due to attraction
between water and xylem vessels causing
water to climb upwards.
3. Root pressure: builds up in roots producing
an osmotic gradient which drives water from
soil into the roots.
3. Cytokinins: regulate cell differentiation and
division with auxins. Can prevent aging.
4. Gibberellins: stem and shoot elongation,
elimination of dormancy of a seed, flowering,
fruit production, leaf and fruit death.
5. Abscisic Acid: functions during stress.
Promotes dormant seeds, closes stomata
(drought), inhibits growth.
Alternation of Generations
Alternation between diploid and haploid.
Movement of Food
Pressure flow hypothesis: source cells produce
sugar and load it into phloem → increased sugar
concentration creates a gradient pulling water into
phloem → turgor pressure in phloem increases
resulting in bulk flow movement of sugar from
leaves down to roots.
Plant Hormones
1. Ethylene: gas that increases fruit ripening.
2. Auxins: cause cell growth. Work with
cytokinins. Responsible for plant tropisms
(growth in certain direction). Auxin
concentrated on one side of stem leads to
asymmetric growth.
● Phototropism: growth towards light.
● Gravitropism: growth away from pull of
● Thigmotropism: growth in response to
contact (e.g. vine growing up a wall)
Two haploid gametes fuse producing diploid
zygote → zygote becomes sporophyte via mitosis
→ in their sporangia, sporophyte undergoes
meiosis to produce haploid spores → spore
becomes gametophyte via mitosis →
gametophyte produces gametes → cycle repeats.
Homosporous vs. Heterosporous Plants
Homosporous plants: bisexual gametophyte,
produces one type of spore.
Heterosporous plants: produce two types of
spores; microspores (male) and megaspores
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Nonvascular plants (e.g. mosses, hornworts,
liverworts) therefore are small and short. Found in
moist habitats and grow horizontally to remain close
to water and nutrients. Contain rhizoids (hair-like
projections) which aid in water absorption and
minor anchorage.
Majority of life cycle spent in gametophyte stage
and have a reduced sporophyte which depends
upon and is attached to the gametophyte.
not-flagellated and is dispersed in seeds
by wind.
Angiosperms: Most abundant plant.
Flower-bearing and produce fruit (plant
ovary, protects seeds). Sperm is
not-flagellated and is dispersed by wind
or animals often as pollen. Can exhibit
double fertilization (female gamete
fertilized by two male sperm).
Flower Structures
1. Petals: attract animals to achieve pollination.
2. Stamen: male plant sex organ. Composed of
anther (site of microspore formation) and
filament (supports anther).
● Microspore undergoes mitosis to form
generative cell (contains sperm) and tube
cell which combine to form pollen.
3. Pistil: female plant sex organ. Composed of
stigma (top), style (tube leading to ovary), and
ovary (contains ovule or egg).
Vascular, grow vertically and tall and have a root
system for anchorage. Spend most of life cycle in
sporophyte stage.
1. Seedless tracheophytes: (lycophytes and
pterophytes, e.g. club moss, quillworts, fern,
horsetail). Mostly heterosporous with
flagellated sperm.
2. Seed-bearing tracheophytes (all
● Gymnosperms: The first seeded plants.
Seed not protected. E.g. conifers such as
firs, spruce, pine, redwood. Sperm is
Pollen lands on stigma → tube cell elongates down
style forming pollen tube → generative cell travels
down pollen tube to ovary → splits forming two
sperm cells (double fertilization)
● One sperm cell meets ovule forming the
seed or embryo. Ovary develops into fruit
which is eaten by animals and deposited in
a new location (gene migration).
● The other sperm cell combines with ovule’s
polar nuclei forming endosperm.
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Angiosperms: Monocots vs. Dicots
Cotyledons: first leaves to appear on seedling.
Contain nutrients from seed to feed growing
Single cotyledon
Two cotyledon
Long narrow leaf
Broad leaf
Parallel veins
Network of veins
Vascular bundles
Vascular bundles in a
Floral parts in
multiples of 3
Floral parts in
multiples of 4 or 5
Nitrogen Fixation
Plants have a symbiotic relationship with
nitrogen-fixing bacteria. Bacteria fix nitrogen to a
usable form for plants and plants produce food for
bacteria via photosynthesis.
1. Nitrogen fixing bacteria (in root nodules of
legumes) fix atmospheric nitrogen (N2) to
ammonia (NH3) and ammonium (NH4+).
2. Nitrifying bacteria convert ammonia and
ammonium to nitrites (NO2-) and then to nitrates
3. Nitrates are taken up by plants (assimilation of
nitrogen) and incorporated into amino acids
and chlorophyll. Animals (consumers) acquire
nitrogen by eating plants (producers).
4. Detritus of dead decaying plants and animals
provides soil with nitrates.
5. Denitrifying bacteria: convert nitrates back to
atmospheric nitrogen
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Chapter 11: Anatomy and Physiology
Chapter 11.1: Circulatory System…………………………………………..………………………….....65
Chapter 11.2: Respiratory System………………………………………………………………………...70
Chapter 11.3: Human Immune System………………………………………………………………...76
Chapter 11.4: Nervous System……………………………………………………………………………..80
Chapter 11.5: Muscular System…………………………………………………………………………....86
Chapter 11.6: Skeletal System……………………………………………………………………………...89
Chapter 11.7: Endocrine System…………………………………………………………………………..92
Chapter 11.8: Digestive System…………………………………………………………………………….97
Chapter 11.9: Excretory System…………………………………………………………………………….100
Chapter 11.10: Integumentary System………………………………………………………………....102
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Chapter 11.1: Circulatory System
Human Heart
Table of Contents
Invertebrate Circulation
Vertebrate Circulation
Human Heart
Cardiac Cycle
Heart Function Measurements
Blood Vessels
Blood and Blood Types
Fetal Circulation
The Lymphatic System
Invertebrate Circulation
1. No circulatory system – use simple diffusion
to distribute nutrients. Includes bacteria,
protista, fungi, invertebrate animals.
2. Open circulatory system – pump fluid called
hemolymph into sinuses or hemocoel.
Includes some mollusca, arthropoda,
3. Closed circulatory system – Use a pumping
heart to move blood through vessels. Includes
annelida (earthworms)
Vertebrate Circulation
Most chordates (eukaryotic vertebrate within
kingdom Animalia) have a closed circulatory
2 chamber hearts (atrium and ventricle) – fish.
Deoxygenated blood fills the heart and is pumped
deoxygenated to the gills for oxygen exchange.
3 chamber hearts (2 atriums and 1 ventricle) –
amphibians and reptiles. Poikilothermic chordates.
Alligators and crocodiles are exceptions, they have
4 chamber hearts.
4 chamber hearts (2 atriums and 2 ventricles) –
bird and humans. Homeothermic chordates.
Flow of blood through heart
1. Right atrium – Deoxygenated blood is returned
here from the upper superior vena cava and
the lower inferior vena cava. Blood passes
through the right atrioventricular valve (AV
valve, or tricuspid valve) to the right
ventricle. AV valve is attached to papillary
muscles, which contract to close the AV valves
and prevent backflow of blood.
2. Right ventricle – Pumps deoxygenated blood
through the pulmonary semilunar valve to the
pulmonary artery. Blood enters pulmonary
circulation. When the ventricle contracts, the AV
valve is closed and the pulmonary semilunar
valve is open. When the ventricle relaxes, the
AV valve is open to refill the ventricle, and the
pulmonary semilunar valve closes to prevent
the backflow of blood.
3. Left atrium – Oxygenated blood is returned
here from the lungs from the pulmonary vein.
Blood passes through the left AV valve (or
bicuspid, or mitral valve) to the left ventricle.
Left ventricle – Most muscular chamber of
the heart. Pumps oxygenated blood into the
aorta and systemic circulation.
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Pulmonary circulation moves deoxygenated
blood from heart to the lungs and back in order
for it to become oxygenated. Pathway:
Right atrium → tricuspid valve →
right ventricle → pulmonary semilunar valve →
pulmonary arteries → lung → pulmonary veins → left
Systemic circulation moves oxygenated blood
from the heart throughout the body. Pathway:
Left atrium → bicuspid / mitral valve → left
ventricle → aortic semilunar valve → aorta → body
→ vena cava → right atrium
Human Cardiac Cycle
The heart needs to contract and relax rhythmically
in order to pump blood throughout the body.
Cardiomyocytes (heart muscle cells) have a
property of automaticity, which means they are
self-excitable and able to initiate an action
potential without an external nerve.
Systole occurs right after the ventricles eject their
blood into the arteries they connect to. Therefore,
it is the phase of the cardiac cycle where blood
pressure is highest in the arteries.
Diastole occurs right after the atria contract to fill
the ventricles. The myocardium is completely
relaxed at this point. Diastole is the phase of the
cardiac cycle where blood pressure is lowest in the
The cardiac cycle:
1. The SA node (pacemaker) is located in the
upper wall of the right atrium and usually
initiates the cardiac cycle. It has the greatest
automaticity and is most likely to reach
threshold to stimulate a heartbeat. It sends a
signal to contract both atria to send blood to
the ventricles. It also sends a signal to the AV
node to initiate contraction too.
2. The AV node is located in the lower wall of the
right atrium. The function of the AV node is to
add a brief delay between the contraction of
the atria and the contraction of the ventricles.
It also sends a signal to the bundle of His,
located in the interventricular septum
between the ventricles. The bundle of His
carries the signal to the Purkinje fibers which
contract the ventricles.
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Heart Sounds
The heartbeat sound is described as “lub-dub”.
Lub – The atria are relaxed, while the
ventricles are contracting. The noise
comes from the AV valves snapping shut
as the ventricles contract.
Dub – The atria are contracting, while the
ventricles are relaxing. The noise comes
from the semilunar valves snapping
Systole happens between the lub-dub sounds.
Diastole occurs between the dub and next lub
Signal Transduction
The heart has intercalated discs that connect
adjacent heart cells (cardiomyocytes). Intercalated
discs are made of desmosomes and gap junctions
and function to transmit the signal to contract in a
coordinated, rhythmic fashion.
Measuring the Cardiac Cycle
Heart Function Measurements
Heart rate (HR) is how fast the heart beats.
Tachycardia is greater than 100 beats per minute,
bradycardia is less than 60 beats per minute
Stroke volume (SV) is the volume of blood
pumped from the heart with each beat. Stroke
volume is calculated by subtracting end-systolic
volume and end-diastolic volume.
Cardiac output (CO) is the stroke volume
multiplied by the heart rate. This tells us the
volume of blood being pumped by the heart in 1
CO = HR x SV
Total peripheral resistance (TPR) is the total
amount of resistance that blood faces when
flowing through the vasculature of the body.
Vasoconstriction increases TPR, while vasodilation
decreases TPR.
Systolic blood pressure is the highest pressure in
your arteries when your ventricles contract. This is
the top number in a blood pressure reading.
120/80 → 120 mmHg is the systolic
Diastolic blood pressure is the pressure in your
arteries while the heart is relaxing between beats.
This is the bottom number in a blood pressure
120/80 → 80 mmHg is the diastolic
Mean arterial pressure (MAP) is the average
arterial pressure during one complete cardiac
cycle. It is calculated by multiplying your cardiac
output by your total peripheral resistance.
P wave – atria depolarization
Q wave – depolarization through interventricular
R wave – ventricular depolarization
S wave – completion of ventricular depolarization
MAP = (HR x SV) x TPR
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Blood Vessels
Components of Blood
1. Plasma contains water, proteins, nutrients,
hormones, and makes up most of the blood
volume. Makes up ~55% of blood volume.
2. White blood cells (leukocytes) are our
immune cells and defend against infection. The
most common white blood cell is the
Vessels transport blood to and from the heart in a
closed circulatory system. Arteries move blood
away from the heart, while veins move blood
toward the heart.
Arteries are where blood pressure is the highest
due to the hydrostatic pressure from the heart.
They branch off into smaller arteries called
arterioles. This is where we see the greatest drop
off of blood pressure. Arterioles branch further
into capillaries, which are vessels that are 1 cell
thick and diffuse gas and nutrients to the
interstitial fluid.
Capillaries also collect waste and CO2 and enter a
venule, which then connects to a vein, which
brings the blood back to the heart. Blood moves
back to the heart by a series of valves within the
veins that prevents backflow of blood. Skeletal
muscles squeeze the veins to push the blood
forward, it is not the pumping of the heart that
moves blood through the veins.
3. Platelets (thrombocytes) are cell fragments
that do not have a nucleus, they are
responsible for clotting. Large bone marrow
cells called megakaryocytes are the precursor
to platelets. Platelets release factors that help
convert fibrinogen into fibrin, which creates a
‘net’ to stop bleeding. Many of the clotting
factors are synthesized with Vitamin K, a
deficiency in Vitamin K will lead to increased
Leukocytes and thrombocytes make up <1% of
blood volume.
Red blood cells (erythrocytes) are
responsible for transporting oxygen attached
to hemoglobin. Mature red blood cells are
anucleate (they don’t have a nucleus) in order
to maximize the amount of space they have to
carry hemoglobin and oxygen. Makes up ~45%
of blood volume.
Veins contain more blood by volume than arteries
and have the lowest blood pressure of all vessels.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=3986752
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Blood Types
Red blood cells (erythrocytes) have antigens on
their surface. These antigens are little sugars and
proteins that mark our blood as a certain type.
Blood types are described as follows.
1. Type A blood – has ‘A’ antigen
2. Type B blood – has ‘B’ antigen
3. Type AB blood – has both ‘A’ and ‘B’ antigens.
4. Type O blood – has neither ‘A’ or ‘B’ antigens.
In addition to blood type A and B, your body also
has another surface protein called the Rhesus
factor (Rh). You either have Rh (+) or you don’t
have Rh (-). If a donor is Rh(+) , they cannot donate
to someone who is Rh(-), because the donor has
antigens on the surface of the blood cell.
A universal donor (blood donor who can donate
to anyone) is O (-). O blood type has neither A nor
B surface antigens, and O (-) blood also does not
have an Rh surface antigen. This means there are
no blood cell surface antigens that would stimulate
immune clearance by someone receiving the O (-)
A universal acceptor is AB (+). Because an AB (+)
person has both A and B cell surface antigens, as
well as an Rh surface antigen, they can receive any
blood type and not mount an immune response.
Any blood cell surface antigen they receive would
be something their blood cells already have.
Fetal Circulation
A fetus gets the oxygen and nutrients it needs
from the placenta through the umbilical cord,
which gets its oxygen from its mother. Because the
fetus gets its oxygen through the placenta, the
blood in its heart does not need to go to the
pulmonary system – it is not exposed to air.
Instead, the oxygenated blood in the right atrium
goes directly to the left atrium through a hole in
the heart called foramen ovale.
There is no mixing of the mother’s blood and fetus’
blood in the placenta, the placenta provides an
exchange of gas and nutrients across a barrier.
Erythroblastosis Fetalis
A concept occasionally tested is if the mother has
Rh (-) blood type and the fetus is Rh (+) blood type.
The issue is during labor, the fetal Rh (+) blood will
enter the mother’s system, and she will develop
anti-Rh antibodies. This will not pose a problem
in the first pregnancy, but if the mother becomes
pregnant again with another Rh (+) fetus, the
mother’s anti-Rh antibodies will attack the fetus,
because antibodies are small enough to cross the
placental barrier.
Lymphatic System
Nutrient and gas exchange occurs at the level of
the capillaries. Hydrostatic pressure pushes fluid
out of the capillaries on the arterial end into
interstitial space. Osmotic pressure brings fluid
back into the capillaries at the venule end.
However, not all the fluid is reabsorbed from the
interstitial space into the venule.
Lymphatic capillaries collect the remaining fluid,
called lymph, consisting of interstitial fluid,
bacteria, fats, and proteins. The lymphatic
capillaries merge together to form larger vessels
that travel to the heart. Along the way, the lymph is
filtered through lymph nodes, which are centers
for the immune response system to eliminate
infections. Lymph vessels have no pressure like
veins, and the fluid moves back towards the heart
due to the constriction of skeletal muscle and
backflow of fluid is prevented with a system of
valves, similar to veins.
The waste and carbon dioxide from the fetus is
removed from right ventricle to the umbilical cord.
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Chapter 11.2: Respiratory System
Table of Contents
Respiration in Plants
Respiration in Animalia Species
Human Lungs
Gas Exchange
The Oxygen Dissociation Curve
Respiration in Animalia Species
1. Cnidaria are small invertebrates that use
simple diffusion for respiration due to the lack
of a circulatory system. Almost all cells must be
in direct contact with the environment.
Environment must be moist for diffusion to
Respiration: the exchange of gases between the
outside environment and the inside of an
Respiration in Plants
Autotrophs produce their own food through
photosynthesis, releasing oxygen and making
Cellular respiration is also performed by plants
after photosynthesis, using up oxygen and
carbohydrates to produce energy.
Stomata (in leaves and green stems) and lenticels
(in woody stems) are pores found in plants that
allow gas exchange to occur.
2. Annelida are roundworms that also use
simple diffusion for respiration but have a
closed circulatory system. They use a slimy
mucus to facilitate the transport of oxygen
into their closed circulatory system.
3. Arthropoda are invertebrates such as
insects and crustaceans that have an open
circulatory system with hemolymph, a fluid
similar to blood. Gas exchange happens
mainly through the tracheal system for
insects and the book lungs for arachnids,
not the hemolymph.
4. Fish are a part of the phylum Chordata and
have a closed circulatory system with blood
to transport gas. Fish have gills with a large
surface area for gas exchange and use
countercurrent exchange to efficiently
absorb oxygen and remove carbon dioxide
from their blood.
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Human Lungs
Lungs are located in the thoracic cavity and
covered by the rib cage. The left lung has two lobes
and is smaller than the right lung, which has three
Adapted from: https://commons.wikimedia.org/w/index.php?curid=5140582
The pleura covers the lungs and is dual layered
membrane composed of the parietal layer (outer
layer) and the visceral layer (inner layer).
The pleural space is a fluid-filled space in between
the parietal and visceral layers. This space is at a
lower pressure than the atmosphere, and creates
the intrapleural pressure.
1. Inspiration or inhalation involves the
contraction of the diaphragm (pulls lungs
downwards) and the external intercostal
muscles (expands the rib cage). These
contractions cause the pressure of the
intrapleural space to decrease and the volume
of the lungs to increase, bringing air into the
2. Expiration or exhalation involves the
relaxation of the diaphragm and the external
intercostal muscles, bringing
the lungs back up and closing
up the rib cage through
elastic recoil. This causes the
pressure of the intrapleural
space to increase and the
volume of the lungs to
decrease, driving air out of the
lungs. The internal
intercostal muscles can also
contract during a more
forced expiration, closing the
rib cage even more.
Lung Volumes
Tidal volume is the volume of air that moves
through the lungs between a normal inhalation
and exhalation.
Inspiratory reserve volume is the maximum
volume of air that can be inhaled further after a
normal inhalation is already taken in.
Expiratory reserve volume is the maximum
volume of air that can be exhaled further after a
normal exhalation is already released.
Residual volume is the minimum amount of air
that needs to be present in the lungs to prevent
Functional residual capacity is the entire volume
of air still present in the lungs after a normal
exhalation. It is also the sum of the expiratory
reserve volume and the residual volume.
Vital capacity is the maximum amount of air that
can be exhaled after a maximum inhalation. It is
the sum of the inspiratory reserve volume, tidal
volume, and expiratory reserve volume.
Total lung capacity is the sum of the vital
capacity and the residual volume: it is that
maximum volume the lungs could possibly hold at
any given time.
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Pathways of Air
1. The nasal cavity contains goblet cells
(secrete mucus) and ciliated epithelial cells
(move mucus and trapped debris) that work
in tandem with each other.
2. The pharynx is at the beginning of the throat
after the nasal cavity. Under the control of the
epiglottis, it diverts air and food into the
larynx and the esophagus.
3. The larynx receives air and contains the
voice box. The upper respiratory tract
refers to the nasal cavity, pharynx, and
larynx. On the other hand, the esophagus
receives food and connects to the stomach.
4. The trachea is below the larynx and has
reinforced cartilage along with ciliated
epithelial cells to filter air.
5. Next are the two main left and right bronchi,
which end up branching into smaller
bronchioles and eventually into alveoli. The
lower respiratory tract refers to the
trachea, bronchi, bronchioles, and alveoli.
Alveoli contain type 1 epithelial cells
(structural support) and type 2 epithelial cells
(produce surfactant). Surfactant is a
substance that prevent the lungs from
collapsing by reducing surface tension.
Oxygen: Air → Blood → Tissues
Carbon Dioxide: Tissues → Blood → Air
Erythrocytes (red blood cells) contain
hemoglobin. Hemoglobin is tetrameric and has
a heme cofactor in each of its four subunits.
Heme cofactors are organic molecules that
contain iron atoms, which bind oxygen. Thus,
each hemoglobin can carry up to four oxygen
Oxyhemoglobin (HbO2) transports most of the
oxygen traveling in the blood.
Cooperativity describes the process by which
the binding of one oxygen molecule to
hemoglobin makes it easier for others to bind
due to changes in the shape of the hemoglobin
polypeptide. This also works in reverse, allowing
efficient unloading of oxygen in body tissues.
Carboxyhemoglobin (HbCO) is produced when
carbon monoxide outcompetes oxygen for
hemoglobin binding. Carbon monoxide poisoning
occurs as a result because oxygen can no longer
be transported efficiently.
Carbaminohemoglobin (HbCO2) is a form of
hemoglobin that transports carbon dioxide.
However, carbon dioxide is much more soluble in
blood than oxygen, so most of the carbon
dioxide is dissolved in blood as bicarbonate
anion (HCO3).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=10296586
Overall Pathway of Air
Nasal Cavity → Pharynx → Larynx → Trachea →
Bronchi → Bronchioles → Alveoli
Differences in partial pressure allow gases to flow
from areas of high pressure to low pressure
through simple diffusion. This is required for
external respiration (gas exchange between
inspired air and lung alveolar capillaries) and
internal respiration (gas exchange between
blood and tissues).
Reduced hemoglobin (H+Hb) is produced by H+
ions binding to hemoglobin, outcompeting
oxygen and lowering oxygen binding affinity (less
HbO2). On the other hand, carbon dioxide
binding affinity is increased (more HbCO2).
Myoglobin is a single peptide with one heme
cofactor. It has a much higher affinity for oxygen
than oxyhemoglobin and is found within cardiac
and skeletal muscle cells to bring oxygen in. Also,
myoglobin has a hyperbolic oxygen dissociation
curve because it does not undergo cooperativity
(hemoglobin’s curve is sigmoidal).
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Oxygen Dissociation Curve
The oxygen dissociation curve reveals the
relationship between the saturation of hemoglobin
with oxygen in the blood and the partial pressure
of oxygen. Certain conditions will shift this curve
either left or right.
A right shifted curve corresponds to a lowered
affinity for oxygen in hemoglobin. Below are the
main reasons for a right shifted curve.
(H+Hb) has a lowered affinity for binding
oxygen, resulting in less HbO2.
● High partial pressure of carbon dioxide:
more carbon dioxide is converted to
bicarbonate anions (HCO3) and protons (H+),
which lower oxygen binding affinity through
decreased pH.
● 2,3-diphosphoglycerate (2,3-DPG) aka
2,3-bisphosphoglycerate (2,3-BPG):
accumulates in cells that undergo anaerobic
respiration as a result of the loss of oxygen.
This compound decreases oxygen binding
affinity so more oxygen is released from
hemoglobin to fuel aerobic respiration.
● Increased body temperature: correlates to
more cellular respiration, which uses up
oxygen and produces more carbon dioxide.
Thus, hemoglobin will need to unload more
oxygen for tissues to use and have decreased
oxygen binding affinity.
A left shifted curve corresponds to an increased
affinity for oxygen in hemoglobin. Below are the
main reasons for a left shifted curve.
● Increased pH (more basic): fewer protons (H+)
to produce reduced hemoglobin (H+Hb), so
more oxyhemoglobin (HbO2) remains.
● Low partial pressure of carbon dioxide: less
carbon dioxide is converted to bicarbonate
anions (HCO3) and protons (H+), leading to
increased oxygen binding affinity through
increased pH.
● Fetal hemoglobin: binds oxygen better than
adult hemoglobin to give oxygen to the fetus.
● Decreased body temperature: less cellular
respiration, so hemoglobin isn’t influenced to
unload more oxygen and has an increased
oxygen binding affinity.
DAT Mnemonic: CADET, face Right!
CADET = Carbon dioxide, Acid,
2,3-Diphosphoglycerate, Exercise and
CADET Increase → Right shifted curve
Decreased pH : a lowered pH means a higher
number of protons (H+), which produces
reduced hemoglobin. Reduced hemoglobin
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Changes in Hemoglobin Affinity
Bohr effect - hemoglobin has decreased oxygen
affinity when carbon dioxide is high. Carbon
dioxide is converted to bicarbonate anions and
protons, which produce reduced hemoglobin
Haldane effect - hemoglobin has increased
carbon dioxide affinity when oxygen is low. As a
result of low oxygen, reduced hemoglobin
(H+Hb) levels are higher and have a greater
affinity for carbon dioxide.
Gas Exchange in Tissues
Gas Exchange in Lungs
1. Blood travels to the lungs through bulk flow
2. Since most of the carbon dioxide is present in
the blood plasma as bicarbonate ions
(HCO3-), the bicarbonate ions re-enter
erythrocytes at the lungs and chloride ions
leave through the reverse chloride shift.
3. The bicarbonate buffer system equation
proceeds in the reverse direction, producing
carbon dioxide and water. The carbon
dioxide exits into the alveoli as gas while
oxygen enters the blood, forming
The bicarbonate buffering system can be
described by the equation below and is catalyzed
by carbonic anhydrase in both directions based
on concentrations. Carbonic anhydrase is an
enzyme present in red blood cells.
CO2 + H2O ↔ H2CO3 ↔ HCO3- + H+
Carbonic acid (H2CO3)
Bicarbonate anion (HCO3–)
1. In erythrocytes (red blood cells) in the
systemic circulation, the partial pressure of
carbon dioxide is low. As a result, carbon
dioxide continuously diffuses in from the
tissues, and is converted into bicarbonate
and protons. Bicarbonate is able to diffuse
out of the cell, however, protons (H+) cannot
leave. As some bicarbonate diffuses out, this
creates a positive charge within the
erythrocyte, and chloride ions (Cl-) must
diffuse into the blood cell to cancel out the
positive charge of the protons. This process
is known as the chloride shift.
2. Influx of protons causes the pH to decrease
within the erythrocyte, resulting in the
conversion of oxyhemoglobin into reduced
hemoglobin. Reduced hemoglobin has lower
affinity for O2, leading to release of oxygen
which diffuses to the tissues.
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Breathing Pace
The medulla oblongata is located in the brain
and controls the diaphragm to regulate
respiratory rate. Central chemoreceptors and
peripheral chemoreceptors signal to the medulla.
Central chemoreceptors are located in the
medulla oblongata and contained within the
blood brain barrier. Since carbonic anhydrase is
present in the cerebrospinal fluid, carbon dioxide
is converted into bicarbonate ions and protons
here. However, protons cannot exit through the
blood brain barrier. As carbon dioxide
accumulates, acidity increases and is directly
sensed by central chemoreceptors, which signal
to the medulla oblongata to increase breathing
Peripheral chemoreceptors surround the aortic
arch and carotid arteries. These peripheral
chemoreceptors directly sense oxygen, carbon
dioxide, and proton levels to signal to the medulla
oblongata. When carbon dioxide is high and
oxygen is low, peripheral chemoreceptors signal to
the medulla oblongata to increase breathing rate.
Rate of Breathing
Respiratory acidosis - lowered blood pH occurs
due to inadequate breathing (hypoventilation)
Respiratory alkalosis - increased blood pH
occurs due to rapid breathing
Metabolic acidosis (lowered blood pH) and
metabolic alkalosis (increased blood pH) occur as
a result of imbalances in carbon dioxide, oxygen,
or proton levels.
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Chapter 11.3: Human Immune System
Table of Contents
Innate Immunity: Overview
Innate Immunity: Inflammatory Responses
Innate Immunity: Immune Cells and
Innate Immunity: Complement System
Adaptive Immunity: Overview
Adaptive Immunity: B cells
Adaptive Immunity: T cells
Passive vs. Active Immunity
Innate Immunity: Inflammatory Responses
Mast cells are a type of leukocyte responsible for
the first part of the inflammatory response known
as rally signaling:
1. Mast cells sit in the tissue in preparation
for injury
2. If there is an injury, mast cells will release
histamine, which dilates blood vessels
3. This increases blood flow and makes
vessels more permeable to let immune cells
into the tissues
Pathogens: harmful microorganisms that causes
Leukocytes: white blood cells.
Lymphocytes: white blood cells found mainly in
the lymphatic organs (T cells, B cells, natural killer
cells) and originate from the bone marrow.
However, T cells mature in thymus while B cells
mature in the bone marrow.
Innate Immunity: Overview
The innate immune system is the first line of
defense and is known as a nonspecific immune
response (generalized).
The outer walls are the first layer of innate
Skin - consists of a thick epidermis, dermis,
and hypodermis. Also mucous membrane
to trap pathogens and lysozyme to break
down bacterial cell walls. Has sebaceous
glands to secrete oil (sebum) as a barrier.
Sebum also has antimicrobial properties.
Cilia - hair-like projections in the respiratory
tract that sweep away debris and pathogens.
Stomach acid - gastric acid that kills microbes
due to low pH.
Symbiotic bacteria - outcompete pathogenic
bacteria and fungi.
If these barriers are penetrated, the rest of the
immune system will kick in.
Adapted from
Five signs of inflammation:
DAT Mnemonic:
Inflammatory response → SLIPR
Loss of function
Increased heat
1. Swelling - permeable capillaries result in fluids
leaking into tissues.
2. Loss of function - body part with
inflammation becomes less usable.
3. Increased heat - increased blood flow results
in a higher temperature.
4. Pain - throbbing pain caused by swelling,
which puts continuous pressure on nerve
5. Redness - increased blood flow causes
redness of skin.
A fever can also occur from the inflammatory
response but is controlled by the brain and causes
a systemic response to kill pathogens with higher
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Innate Immunity: Immune Cells and Molecules
Diapedesis is the process by which cells move
from the capillaries to tissues in order to fight
Chemotaxis is the method by which cells move
in response to a chemical signal. Immune cells
use chemotaxis to move to the tissues.
DAT Mnemonic:
Five main types of leukocytes from highest to
lowest in quantity → Never Let Monkeys Eat
1. Neutrophils - phagocytes in innate immunity
and make up over half of all leukocytes.
2. Lymphocytes - B cells, T cells, and natural
killer cells. B and T cells are part of adaptive
immunity and must be activated. Natural
killer (NK) cells are part of innate immunity
and attack virally-infected cells + cancerous
cells. NK cells use perforin (create holes) and
granzyme (stimulate apoptosis) to lyse cells.
3. Macrophages/Monocytes - phagocytes in
innate immunity. Monocytes are the
immature form in blood vessels and
macrophages are the mature form after
diapedesis. Can also act as antigen-presenting
cells to activate adaptive immunity.
4. Eosinophils - part of innate immunity and
have granules that can be released to kill
pathogens, especially parasites.
5. Basophils - least numerous leukocyte and
also contain granules with histamine
(vasodilation) and heparin (an anticoagulant
to prevent blood clotting). Very similar to
mast cells, except basophils circulate as
mature cells while mast cells circulate as
immature cells.
Dendritic cells are also part of innate immunity
and scan tissues using pinocytosis (cell drinking)
and phagocytosis (cell eating). They act as
antigen-presenting cells like macrophages,
migrating to the lymph nodes to activate
adaptive immunity.
Interferons are secreted by virally-infected cells
and bind to non-infected cells to prepare them for
a virus attack. Also, interferons help activate
dendritic cells.
Innate Immunity: Complement System
The complement system is a group of
approximately 30 proteins that aid immune cells
in fighting pathogens. These proteins turn on
each other through the complement cascade,
which amplifies the complement effects by
releasing cytokines.
Complement protein actions:
Tags antigens for phagocytosis in a process
called opsonization
Amplifies inflammatory response Eg. binds to
mast cells for increase histamine release
Forms a membrane attack complex (MAC),
which pokes holes in pathogens and lyses
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Adaptive Immunity: Overview
The adaptive immune system is a specific
immune response (targets specific antigens).
An antigen is an immunogenic foreign molecule
and is the target of the immune response. The
epitope is the important part of the antigen that
is recognized by the immune cell.
Adaptive Immunity: B cells
B cells control antibody-mediated immunity
(humoral immunity) by managing the
production and release of antibodies. They can
also act as antigen-presenting cells.
B cell receptors (BCRs) are located on B cells
and bind to antigen epitopes either free-floating
or on APCs. Each B cell has a unique BCR.
The clonal selection model describes the
development of one type of BCR for every B cell.
Through clonal expansion, these B cells divide
into either plasma cells (antibody-secreting cells)
or memory B cells (to be activated later in case
of another attack).
The immune system recognizes self proteins from
non-self proteins using the major
histocompatibility complex (MHC), which is
found on the surface of cells. Thus, foreign
antigens and foreign MHC will be identified as
enemies by the immune system.
Antibodies (immunoglobulins) are structurally
identical to BCRs but freely circulate in blood and
lymph. They can tag antigens for phagocytosis,
neutralize the antigen by coating it, or activate the
complement system. Antibodies contain light
chains and heavy chains linked by disulphide
bonds. In addition, the variable region
recognizes different antigens while the constant
region is the same for antibodies within the
same class.
MHC Class I is a surface molecule present on all
nucleated cells, and each genetically different
individual will have a different MHC I molecule.
Organ transplants that have different MHC I may
lead to failure and rejection, so
immunosuppressants are given to transplant
patients. Also, autoimmune diseases occur when
the immune system attacks self MHC I.
MHC Class II is a surface molecule present on
antigen-presenting cells (dendritic cells,
macrophages) and is used to present foreign
antigens to activate immune cells.
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DAT Mnemonic:
Classes of Antibodies → Me And Eve Don’t Go
1. IgM - present in a pentameric form and is the
largest antibody. The first antibody to be
produced and activates the complement
2. IgA - present in a dimeric form and found
most abundantly in bodily secretions.
Newborns receive passive immunity
through breast milk containing IgA. Also, IgA
mainly binds pathogens externally, outside
of circulation.
3. IgE - monomer that is present on basophils
and mast cells as antigen receptors. When
bound to an allergen, triggers histamine
release and an allergic reaction.
4. IgD - monomer that we have very little
information about. Only small amounts are
5. IgG - monomer that is the most abundant
antibody in circulation. Also the only antibody
that can cross the placenta to give fetus
passive immunity. Helps complement
system to cause opsonization (tags antigens
and subsequent phagocytosis).
Adaptive Immunity: T cells
T cells control cell-mediated immunity by
directly acting on cells instead of sending
antibodies out.
T cell receptors (TCRs) are unique just like BCRs,
binding only to one type of antigen per T cell.
Thus, T cells also undergo clonal selection just
like B cells.
T cells must to bind to antigens presented on
APCs (antigen-presenting cells) to be activated.
There are two ways antigens may be presented
to T cells:
1. MHC I Presentation: T cells differentiate into
CD8 T cells (cytotoxic T cells), which directly
kill infected cells through perforin (poke holes)
and granzymes (cause apoptosis). However, T
cells are different from natural killer cells
because they are more specific and require
antigen presentation.
2. MHC II Presentation: T cells differentiate into
CD4 T cells (helper T cells), which release
cytokines to boost both innate immunity and
adaptive immunity. These cytokines help attract
innate immune cells and increase proliferation
of other T and B cells.
Active vs. Passive Immunity
Memory B cells survive for a long time and lay
dormant until reactivated by the same antigen
that triggered the original clonal expansion.
They are the key to vaccinations because
vaccines cause memory B cell production for
later reactivation. After reactivation, memory B
cells cause massive antibody production.
Passive immunity refers to the immunity one
organism gains from receiving the antibodies
from another organism already has that
immunity. For example, a fetus gains passive
immunity through the placenta (IgG) while a
newborn gains passive immunity through breast
milk (IgA). The fetus and newborn are referred
to as immuno-naive because they do not yet
have their own active immunity.
Active immunity refers to the immunity an
organism gains from being infected once already
by a pathogen. A vaccination introduces the
antigen or pathogen in a deactivated state to
stimulate active immunity, which is referred to as
artificial immunity in this case and induces
memory B and T cell formation.
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Chapter 11.4: Nervous System
Action Potentials
Table of Contents
The Neuron
Action Potentials
Synaptic Transmission
Glial Cells
Central vs. Peripheral Nervous System
Central Nervous System
Peripheral Nervous System: Somatic vs.
Autonomic Nervous System
Autonomic Nervous System: Sympathetic
vs. Parasympathetic Nervous System
Special Senses
The Neuron
The neuron is the most basic unit of the nervous
system. It has three parts: the soma (cell body),
dendrites (extensions that receive signals), and
the axon (sends signals out).
The Axon:
Axon hillock - area where the axon is
connected to the cell body. Responsible for the
summation of graded potentials.
Myelin sheath - fatty insulation of the axon
that speeds up action potential propagation by
stopping ion exchange. The myelin sheath is
formed by oligodendrocytes (in central
nervous system) and Schwann cells (in
peripheral nervous system).
Nodes of Ranvier - gaps between myelin
sheath where ion exchange occurs. Propagation
of the the action potential occurs here,
jumping from gap to gap (node to node) in a
process called saltatory conduction.
Steps of an action potential:
1. At resting potential, the membrane potential
of the neuron is around -70mV and is
maintained by Na+/K+ ATPases, which pump
three Na+ ions out and two K+ ions in powered
by hydrolysis of one ATP. K+ leak channels are
also present and help maintain resting
potential through passive K+ leakage.
2. When a stimulus causes threshold potential
to be reached (around -55mV in neurons),
voltage-gated Na+ channels open up, letting
Na+ inresulting in depolarization of the
neuron (reaches a peak of around +30mV to
3. Next is repolarization of the neuron due to
the opening of voltage-gated K+ channels,
letting K+ out. This causes the membrane
potential to become less positive since positive
ions are leaving.
4. When the membrane potential becomes even
more negative than the normal resting
potential, this is known as hyperpolarization.
This results in a refractory period being
established, during which another action
potential cannot be fired because the
membrane potential is very negative.
5. The membrane potential returns to normal
resting potential through the pumping of
Na+/K+ ATPases and K+ leak channels.
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An absolute refractory period refers to the
period after the initiation of the action potential
during which another action potential cannot be
fired no matter how powerful the stimulus is. It is
due to the inactivation of voltage-gated Na+
channels after they open.
An inhibitory postsynaptic potential (IPSP) is a
graded potential that is a hyperpolarizes the
membrane. Inhibitory neurotransmitters cause K+
ion gates to open and let K+ ions flow out of the
cell. Another IPSP types allows influx of Cl-,
allowing negative Cl- ions in.
The relative refractory period refers to the
period after the action potential fires during which
a stronger than normal stimulus could cause
another action potential to be fired.
Synaptic Transmission
The synapse is the space between two
neurons. The presynaptic neuron sends the
signal and releases neurotransmitters into the
synapse, while the postsynaptic neuron
receives the signal by interacting with the
released neurotransmitters.
Steps of synaptic transmission:
1. Action potential reaches the end of the
presynaptic axon, causing voltage gated
calcium channels to open and letting Ca2+
ions into the neuron.
2. The Ca2+ ions cause synaptic vesicles to fuse
and undergo exocytosis, releasing
neurotransmitters into the synapse.
3. The neurotransmitters (described in the table
on the next page) bind to ligand-gated ion
channels on the postsynaptic neuron,
producing graded potentials (depolarizations
or hyperpolarizations of the membrane).
4. These graded potentials summate at the axon
hillock and an action will fire if the summation
of graded potentials is higher than the
threshold potential of neurons.
An excitatory postsynaptic potential (EPSP) is a
graded potential that depolarizes the membrane.
In an EPSP, excitatory neurotransmitters cause Na+
ion gates to open and let Na+ ions flow into the cell.
Glial cells
Glial cells are non-neuronal cells in the nervous
system that help support and surround neurons.
They are divided into microglial cells and
macroglial cells.
Microglial cells are macrophages that protect the
central nervous system (CNS).
Macroglial cells have many subtypes:
Astrocytes are the most abundant glial cell
and form the blood-brain barrier. They also
help recycle neurotransmitters and provide
blood supply to the CNS neurons.
Schwann cells form the myelin sheath in the
peripheral nervous system (PNS).
Oligodendrocytes form the myelin sheath in
the central nervous system (CNS).
Satellite cells have the same functions as
astrocytes but instead help PNS neurons.
Ependymal cells produce cerebrospinal fluid
(CSF), which cushions the CNS.
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Neurotransmitters and their functions
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Central vs. Peripheral Nervous System
The central nervous system (CNS) is composed
of the brain and spinal cord.
The peripheral nervous system (PNS) is
composed of nerves branching off the CNS.
Central Nervous System
In embryonic development, we consider the
forebrain, midbrain, and hindbrain:
The developed brain cortex is divided into four
main lobes.
The brainstem is composed of the midbrain
(relays senses to other parts of brain), pons (relays
messages from cerebellum to forebrain), and
medulla oblongata (heart and breathing rate,
blood pressure, toxin sensing) and connects the
cerebrum/cerebellum to the spinal cord.
The thalamus is known as the “relay center” of the
brain and is located between the cerebrum and
the midbrain.
The limbic system is next to the thalamus and is
composed of the hypothalamus, hippocampus,
and amygdala (details below). It is responsible for
emotion, memory, learning, and motivation.
Finally, the spinal cord is nervous tissue in the
part of the central nervous system and connects
the brain to the body. Sensory (afferent)
neurons send signals to the spinal cord and
subsequently the brain through dorsal roots.
Motor (efferent) neurons send signals back out
to the muscles through ventral roots.
The meninges protect the CNS and have three
layers called the dura mater, arachnoid, and pia
DAT Mnemonic for outermost to innermost
meninges → DAP = dura → arachnoid → pia
Somatic vs. Autonomic Nervous System
The peripheral nervous system is divided into
the somatic nervous system (voluntary motor
action and sensory input) and the autonomic
nervous system (involuntary).
The cerebellum is located underneath the
occipital lobe and is responsible for the
coordination of movement.
Different types of sensory (afferent) neurons in
the peripheral nervous system are responsible for
receiving input from stimuli, including
mechanoreceptors (mechanical stimuli),
nociceptors (pain stimuli), thermoreceptors
(temperature-related stimuli), chemoreceptors
(chemical stimuli), and electromagnetic receptors
(light, electricity, and magnetic stimuli).
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Autonomic Nervous System: Sympathetic vs.
Parasympathetic Nervous System
The autonomic nervous system can be further
divided into the sympathetic nervous system
(fight or flight) and the parasympathetic nervous
system (rest and digest).
Sympathetic nervous system effects:
Release of sugar into blood for energy.
Increase in heart rate for oxygen delivery to
brain and muscles.
Dilation of bronchi and bronchioles to allow
more oxygen into lungs.
Dilation of the pupil to give the brain more
visual information.
Parasympathetic nervous system effects
(through vagus nerve):
Relaxation of muscles.
Decrease in heart rate.
Maintenance of homeostasis.
Increase in gastrointestinal activity.
A ganglion is defined as a cluster of nerve bodies
in the peripheral nervous system. The autonomic
nervous system’s neurons are either
preganglionic or postganglionic. The
preganglionic neuron comes from the central
nervous system and synapses with the
postganglionic neuron at the ganglion.
Sympathetic nervous system → short
preganglionic nerves and long postganglionic
nerves (ganglia far from effector organs)
Parasympathetic nervous system → long
preganglionic nerves and short postganglionic
nerves (ganglia close to effector organs)
Sympathetic nervous system → uses
acetylcholine (Ach) for preganglionic nerves and
norepinephrine (NE)/epinephrine (E) for
postganglionic nerves. The parasympathetic
nervous system also can stimulate the adrenal
medulla to release NE/E into the blood.
Parasympathetic nervous system → uses
acetylcholine (Ach) for both preganglionic and
postganglionic nerves.
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Special Senses
The outer ear takes in sound waves, and the
tympanic membrane transfer the sound from
outer ear to middle ear.
The middle ear is composed of three bony
ossicles → the malleus, incus, & stapes. The
ossicles transfer vibrations through the middle
ear and amplify the signal.
The stapes transfers the vibrations from the
middle to the inner ear via the oval window.
The cochlea uses fluid and hairs to convert the
mechanical signal into a neuronal signal,
known as transduction.
The round window is a membrane covered
opening between the middle ear and the inner
ear, similar to the oval window. It helps the
fluid expand and vibrate.
The semicircular canals has fluid and hairs
just like the cochlea but gives information
about the person’s movement. It is also the
reason we get dizzy.
Cornea - transparent; focuses light and
protects the eye.
Iris - controls the size of the pupil.
Pupil - controls how much light enters
Lens - focuses images on retina.
Retina - back of the eye that has
photoreceptors (rods + cones).
Fovea - highest concentration of
photoreceptors in the retina and responsible
for high acuity vision.
Amacrine and bipolar cells take information
from rods and cones, transmitting the
information to ganglion cells of the optic
nerve fibers.
Optic nerve - bundle of axons that transmit
visual information to the brain.
Optic disk - the blind spot of the eye, where
the optic nerve passes through to reach the
Sclera - protective connective tissue that
surrounds the eye, the “white part” of eye.
Choroid - vascular connective tissue.
Five taste receptor cells, sensing salty,
sweet, bitter, sour, and umami.
Taste information is sent to to the thalamus
and subsequently the gustatory cortex.
Contains olfactory receptor cells that sense
molecules and send signals to the olfactory
cortex, which gives us the perception of smell.
These signals also integrate in the thalamus
and orbitofrontal cortex for smell sensation.
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Chapter 11.5: Muscular System
Table of Contents
Types of Muscle
Skeletal Muscle Anatomy
Sliding Filament Theory of Muscle
Motor Units
Twitch Contractions
Muscle Fiber Types
Degrees of Muscle Contraction
How Muscles Work Together to Create
Skeletal Muscle Anatomy
Skeletal muscle is composed of many bundles
within bundles.
Muscle → Muscle fascicles → Muscle fibers
(muscle cells) → Myofibrils (contractile protein)
The sarcolemma, is the muscle fiber’s cellular
membrane, and protects each muscle fiber.
The sarcoplasm is the cytoplasm of the muscle
fiber and holds the myofibrils.
Types of Muscle
There are three types of muscles: smooth
muscle, cardiac muscle, and skeletal muscle.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=30015037
Striated means the muscle contains sarcomeres.
Smooth muscle therefore lack sarcomeres,
whereas cardiac and skeletal muscle contain them.
Cardiac muscle contains intercalated discs,
which are made of desmosomes (hold cells
together) and gap junctions (connect the
cytoplasm of cells together to allow ion exchange
and electrical impulse propagation).
Sliding Filament Theory of Muscle Contraction
All muscles always contract (pull) across a joint
to move body parts, they never push.
Sarcomeres inside of myofibrils are the functional
unit of muscle fibers and shorten to cause muscle
Myofilaments are contained within sarcomeres,
divided into thin actin filaments and thick
myosin filaments. These filaments slide past
each other to shorten sarcomeres through the
sliding filament model of muscle contraction.
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Stimulation of a muscle contraction:
1. Action potential propagation reaches the end
of a motor neuron’s axon.
2. Acetylcholine is released as a
neurotransmitter between the presynaptic
motor neuron and postsynaptic skeletal muscle
fiber at the neuromuscular junction.
3. Acetylcholine binds to ligand gated sodium
channels, causing sodium to enter the cell,
which creates graded potentials on the
muscle fibers.
4. The graded potentials trigger opening of
voltage gated sodium channels, which may
produce action potentials on the muscle if the
stimulus is large enough.
Cross bridge cycling:
1. Initiation: Calcium ions expose the
myosin-binding-sites on actin.
2. A cocked back, high energy myosin head
(containing ADP and Pi) forms a cross bridge
with the actin.
3. The myosin head contracts and the power
stroke occurs, bringing the myosin head back
to a low energy state and releasing ADP and
Pi. As a result, the sarcomere shortens.
4. A new ATP molecule binds to myosin, causing
detachment of the myosin head from the
actin filament.
5. The myosin head is an ATPase, and it
hydrolyzes the ATP into ADP and Pi. This
causes the myosin head to re-enter a cocked
back, high energy state. (Return to Step 2 if
calcium ions present).
6. Termination: Neuronal signaling from motor
neurons ends. The sarcoplasmic reticulum
pumps calcium back into itself, and troponin
brings tropomyosin back to cover
myosin-binding-sites on actin.
Rigor mortis occurs in dead animals when there is
no ATP available to release myosin from the actin.
The Sarcomere
Adapted from:
The sarcolemma is the cell membrane of striated
muscle and contains T-tubules, invaginations that
quicken action potential propagation on the
The sarcoplasmic reticulum is the
endoplasmic reticulum of muscle fibers that
releases stored calcium ions into the
sarcoplasm through voltage gated calcium
channels when triggered by the depolarization
of the muscle cell.
The calcium ions then bind to troponin, which
removes tropomyosin from the
myosin-binding-sites on actin, allowing myosin
to interact with actin and cause sarcomere
shortening, via sliding filaments.
The Z lines are the ends of the sarcomeres. Thin
actin filaments branch from the Z lines towards
the middle of the sarcomere.
The M lines are the midpoints of the sarcomeres.
Thick myosin filaments branch from the M lines
towards the ends of the sarcomere.
The I band is the area in the sarcomere where only
actin is present. (Mnemonic: “I” is a thin letter,
representing thin actin filaments)
The A band is the area in the sarcomere where
actin and myosin overlap.
The H zone is the area in the sarcomere where
only myosin is present. (Mnemonic: “H” is a thick
letter, representing thick myosin filaments)
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Degrees of Muscle Contraction
Summation is the process by which twitches add
up to create a larger overall contraction.
There are two types of summation:
Adapted from: https://commons.wikimedia.org/w/index.php?curid=7921353
Motor Units
Motor units make up muscles and a single motor
unit refers to all the muscle fibers innervated by a
single neuron.
1. Wave summation (temporal summation) depolarizing a motor unit again during the
relaxation phase. Can cause tetanus, which is
when the muscle fibers cannot be further
stimulated due to a lack of relaxation.
Twitches blend together during tetany,
eventually causing fatigue (loss of muscle
Small motor units include only a few muscle
fibers (precision movement) while large motor
units include many muscle fibers that are
innervated by a single neuron (powerful
Twitch Contractions
A twitch contraction is the contraction of a
muscle fiber through motor unit stimulation.
Each twitch has the same size and duration.
Twitch contractions also follow the all-or-none
principle, which states that a depolarization will
cause all the muscle fibers to twitch if it is above
threshold potential but will not cause any
twitching if the depolarization is below threshold
Three phases of a twitch:
1. Latent: action potential spreads over
sarcolemma and T-tubules, signaling to
sarcoplasmic reticulum to release calcium.
2. Contraction: formation of cross bridges as a
result of calcium ions binding to troponin. H
zones shrink and muscle tension increases.
3. Relaxation: calcium is pumped back into the
sarcoplasmic reticulum, ending cross bridge
cycling and decreasing muscle tension.
Adapted from: https://commons.wikimedia.org/w/index.php?curid=30015045
2. Motor unit summation - different motor
units are stimulated at different times to
produce the intended amount of muscle
contraction. This is also known as the size
principle of motor unit recruitment
because smaller motor units are stimulated
first before larger motor units come in to
Weak and involuntary twitches in small motor
unit groups contribute to maintaining muscle
tone (muscle tonus). Fatigue is never reached
because different motor units are stimulated at
different times.
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Chapter 11.6: Skeletal System
Table of Contents
Types of Skeletons
Types of Bones and their Structure
Bone Remodeling
Embryonic Ossification
Connective Tissues and Joints
Types of Skeletons
An exoskeleton is an external skeleton. Many
invertebrates and all arthropods possess
Vertebrates contain an endoskeleton on the
inside. An endoskeleton can be divided into the
axial skeleton (core bones) and the
appendicular skeleton (appendages).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=27796930
Types of Bones and their Structure
Types of bones in the endoskeleton:
1. Long bones - made of cortical bone
(compact) and pockets of cancellous bone
(spongy). Important features include the
epiphysis, diaphysis, medullary cavity,
metaphysis, and epiphyseal plate.
● Epiphysis - end of a long bone that forms
joints with other bones and contains red
bone marrow for hematopoiesis (blood
cell synthesis).
● Diaphysis - long hollow shaft in center of
● Medullary cavity - located within the
diaphysis and contains red and yellow
bone marrow (area of fat storage).
● Metaphysis - similar to epiphyses and
found between the medullary cavity and
epiphyseal plates.
● Epiphyseal plate - “growth “plate” located
between epiphysis and metaphysis. Made
out of hyaline cartilage and works to
lengthen the diaphysis through growth and
2. Short bones - as wide as they are long and
mainly provide support (eg. parts of the
3. Flat bones - mainly provide protection (eg.
4. Sesamoid bones - found within tendons to
help muscles pull (eg. kneecap).
5. Irregular bones - irregularly shaped (eg.
Cortical bone is the dense outer layer of bone that
supports the weight of our bodies. It is composed
of many microstructures:
Osteons - cortical bone’s functional unit,
composed of tiny multi-layered cylinders.
Also known as haversian systems because
they contain a haversian canal in their center.
Haversian canals - ‘tubes’ that contain blood
vessels for nutrient supply.
Lamellae - layers of the osteon.
Lacunae - small spaces between lamellae that
hold bone cells and interconnect through
Canaliculi - small channels that connect
lacunae and the haversian canal.
Volkmann’s canals - connect haversian canals
to the periosteum, which provides nutrients.
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Cancellous bone is the spongy inner layer of bone
that soaks up red bone marrow via a web of
trabeculae (web of connective tissue that
supports cancellous bone).
Mechanisms involved in bone remodeling:
Bone Remodeling
Bone remodeling involves the constant back and
forth between ossification (bone formation) and
resorption (bone loss).
Types of cells involved in bone remodeling:
Parathyroid hormone - increases blood
calcium levels by stimulating osteoclasts and
depressing osteoblasts. Secreted by the
parathyroid gland.
Vitamin D - increases blood calcium levels by
raising osteoclast activity and intestinal calcium
absorption. Activated by parathyroid hormone,
but provides negative feedback on PTH
Calcitonin - decreases blood calcium levels by
depressing osteoclasts, allowing osteoblasts to
build bone without competition. Secreted by
the thyroid gland.
Osteoid is the organic component of bone
containing many proteins such as collagen (gives
bone tensile strength).
Hydroxyapatite is the inorganic mineral
component of bone that gives the bone density
and strength.
Osteoprogenitors - immature precursor cells
that differentiate into osteoblasts.
Osteoblasts - build bone by secreting
proteins and utilizing blood calcium. They
mature into osteocytes after getting trapped
inside the bone matrix they create.
Osteocytes - live in lacunae in osteons to
maintain bone.
Osteoclasts - eat and resorb bone, bringing
calcium back into the blood. Derived from
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Embryonic Ossification
Connective Tissue and Joints
Two types of embryonic ossification:
Types of connective tissue:
1. Intramembranous ossification - bone is
created directly within fibrous membrane,
mainly for flat bones. Osteoblasts start by
secreting osteoid, which hardens and houses
osteocytes. Eventually, cortical bone is
2. Endochondral ossification - bone is created
indirectly through a cartilage model, mainly
for long bones. The cartilage model calcifies
during fetal development, creating
ossification centers that help form the
features of long bones.
1. Fibrous connective tissue has a matrix made
up of fibers.
● Tendons - connect muscle to bone.
● Ligaments - connect bone to bone.
● Periosteum - membrane that covers
cortical bone with an outer fibrous layer
(vascularized) and an inner/cambium
layer (collagen for attachment to cortical
● Endosteum - membrane located between
cortical and cancellous bone.
2. Cartilage is avascular (lacks blood vessels)
and is not innervated (as opposed to bone
which is highly vascular and innervated).
Chondroblasts build cartilage by secreting
collagen and elastin.
● Hyaline cartilage - slightly flexible and
important in providing support and
stability to joints.
● Fibrous cartilage - high rigidity and resists
tension, found in intervertebral discs and
knee meniscus.
● Elastic cartilage - highly flexible and found
in ears and epiglottis.
3. Joints are vascularized and innervated. They
are found between bone. Below are types of
● Synarthroses - dense, fibrous joints that do
not move.
● Amphiarthroses - cartilaginous joints that
partially move.
● Diarthroses - synovial joints that fully
move. Typically contain hyaline cartilage.
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Chapter 11.7: Endocrine System
Table of Contents
Hypothalamus and Pituitary
Thyroid and Parathyroid
Adrenal Gland
Testes and Ovaries
Feedback Loops
Hormones can be secreted in the following ways:
Endocrine - through the bloodstream.
Exocrine - through ducts.
Paracrine - to neighboring cells.
Autocrine - onto the same cell that is secreting
the hormone.
There are three types of hormones: peptide
hormones, steroid hormones, and amino-acid
derived hormones.
1. Peptide hormones (protein hormones):
Synthesis - produced in the rough ER and made
of amino acids connected by peptide bonds.
Action - binds to cell surface receptors because
they cannot pass freely through the cell
membrane as a result of being water-soluble
(and not lipid-soluble). The process of hormone
function is an indirect stimulation. The two
ways the signal can be received is through
intracellular secondary messengers or
ligand-gated ion channels.
G protein coupled receptors (GPCRs) are cell
surface receptors that can initiate a secondary
messenger response after binding to a peptide
hormone extracellularly. A G protein is coupled
to the receptor and dissociates into subunits
(alpha (α), beta (β) and gamma (γ)) after
activation. These subunits then act upon
intracellular second messengers to propagate
the signal.
Receptor tyrosine kinases (RTKs) are another
cell surface receptor that dimerizes and initiates
second messenger responses upon binding to a
peptide hormone (eg. insulin). The intracellular
domains of RTKs cross-phosphorylate each
other and initiate second messenger signaling
within the cell.
The second messenger system of peptide
hormone signaling allows for quick and
immediate physiological changes.
Ligand-gated ion channels change shape upon
binding to peptide hormones, allowing ions to flow
across the cell membrane. No second messengers
are involved.
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2. Steroid hormones:
3. Amino-acid derived hormones:
Synthesis - produced in the smooth ER and made
up of a fused 4-ring structure.
Can have properties that are similar to both
peptide hormones and steroid hormones.
Synthesis - produced in rough ER and cytosol.
Mainly derived from the amino acid tyrosine.
Examples - all hormones produced by the
adrenal medulla (epinephrine and
norepinephrine, which are water-soluble). Also
includes T3 and T4 (lipid-soluble).
Examples - all hormones produced by the adrenal
cortex (glucocorticoids, mineralocorticoids,
androgenic steroids) and reproductive organs
(progesterone, testosterone, estrogen).
Action - requires a protein carrier to travel
through the bloodstream due to being lipophilic.
Freely crosses the cell membrane, and binds to
receptors either in the cytoplasm or the nucleus to
form molecule-receptor complexes that bind to
DNA, and influence gene transcription. This
process is direct stimulation.
Steroid hormones cause slow and gradual
physiological changes.
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Hypothalamus and Pituitary
The hypothalamus coordinates the body’s
internal environment and maintains homeostasis.
Hypothalamic-inhibiting hormones are released
by the hypothalamus to inhibit the release of other
hormones by the anterior pituitary.
The pituitary gland (hypophysis) is under the
hypothalamus and is composed of two lobes the anterior pituitary and posterior pituitary.
The anterior pituitary then produces its own
hormones, classified as tropic hormones and
direct hormones.
1. Posterior pituitary:
Tropic hormones target other endocrine glands
for further hormone release. Important
examples released from the anterior pituitary:
Known as the neurohypophysis because it is
made of neuronal tissue. It is a direct neuronal
extension of the hypothalamus.
Two hormones are stored and released by the
posterior pituitary (and are produced by the
1. Anti-diuretic hormone (ADH aka
vasopressin) - decreases urination by
increasing water retention. Targets nephrons,
increasing the number of aquaporins for
water reuptake.
2. Oxytocin - causes uterine contractions during
child labor and the release of milk during
breastfeeding (mammary gland).
2. Anterior pituitary:
Known as the adenohypophysis, it is made of
glandular tissue, and produces its own hormones.
It is connected to the hypothalamus through a
hypophyseal portal system, which allows for
quick diffusion of hormones through a portal
vein. Hypothalamic-releasing hormones are
released by the hypothalamus to stimulate the
anterior pituitary to release other hormones.
GnRH (gonadotropin-releasing hormone)
- causes release of luteinizing hormone
(LH) and follicle stimulating hormone
TRH (thyrotropin-releasing hormone) causes release of thyroid stimulating
hormone (TSH).
CRH (corticotropin-releasing hormone) causes release of adrenocorticotropic
hormone (ACTH).
GRH (growth hormone-releasing hormone)
- causes release of growth hormone (GH).
FSH (follicle stimulating hormone) - follicle
growth (females) and sperm maturation
(males) in the gonads.
LH (luteinizing hormone) - stimulates
ovulation, corpus luteum formation (females),
and testosterone production (males) in the
ACTH (adrenocorticotropic hormone) stimulates release of glucocorticoids from the
adrenal gland to fight stress.
TSH (thyroid stimulating hormone) - stimulates
T3 and T4 production by the thyroid gland to
increase metabolism.
Direct hormones target organs directly for effects.
Important examples released from the anterior
Prolactin - stimulates mammary gland
development and increases milk production
after childbirth.
Growth Hormone (somatotropin) - stimulates
body cells to grow and divide.
Finally, the pineal gland in the brain produces
melatonin, which regulates circadian rhythm.
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Thyroid and Parathyroid
The thyroid gland is the largest endocrine organ
and is located in front of the trachea.
The pancreas is a gland that contains exocrine
and endocrine tissue.
Three main hormones of the thyroid:
The exocrine tissue secretes digestive enzymes
through the pancreatic duct into the small
The endocrine tissue (the islets of Langerhans)
secretes glucagon, insulin and somatostatin.
These three hormones are each secreted by a
different cell type as listed below:
1. Triiodothyronine (T3) - released in response
to TSH and increases metabolism in the
body. Has a negative feedback effect on
TSH secretion.
2. Thyroxine (T4) - performs the same actions
as T3 above. However, T4 has one more
iodine and gets converted into T3 upon cell
uptake. It is much less potent than T3 but is
more stable in the blood.
3. Calcitonin - secreted by the parafollicular
cells to decrease blood calcium levels.
Stimulates osteoblasts to use up blood
calcium to build bone and inhibits
osteoclasts. Also decreases calcium uptake in
intestines and kidneys.
Hypothyroidism describes the under-secretion
of T3 and T4, resulting in reduced levels of
metabolism in the body.
1. Alpha (α) cells - secrete glucagon in response
to low blood glucose levels. Glucagon raises
glucose levels by stimulating the liver and fat
tissue to release their glucose storages.
2. Beta (β) cells - secrete insulin in response to
high blood glucose levels. Insulin lowers
glucose levels by stimulating the liver,
muscle, and fat tissue to store glucose.
3. Delta (δ) cells - secrete somatostatin, which
inhibits growth hormone. It also inhibits the
secretion of glucagon and insulin.
Hyperthyroidism describes the over-secretion of
T3 and T4, resulting in increased levels of
metabolism in the body.
Both hypothyroidism and hyperthyroidism can
lead to goiter (physical enlargement of the
thyroid gland). Hypothyroidism causes
over-secretion of TRH to compensate for low T3
and T4, enlarging the thyroid gland, while
hyperthyroidism itself results from a
hyperactive thyroid gland.
The parathyroid gland secretes parathyroid
hormone (PTH) which perform the opposite
effects of calcitonin. It stimulates osteoclasts and
decreases calcium uptake. Parathyroid hormone
increases blood calcium levels.
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Adrenal Gland
Our body has two adrenal glands. Each adrenal
gland has an outer cortex and an inner medulla.
They mainly help the body deal with stress.
Testes and Ovaries
After stimulation by LH and FSH from the anterior
pituitary, the ovaries produce progesterone and
estrogen while the testes produce androgens
such as testosterone.
Adrenal cortex:
Deals with longer term stress
Stimulated by secretion of ACTH from the
anterior pituitary.
Releases steroid hormones.
Produces glucocorticoids (i.e. cortisol) to
raise blood glucose levels for immediate fuel
during periods of long-term stress. However,
this also lowers our immune response.
Produces mineralocorticoids (i.e.
aldosterone) to increase blood volume and
blood pressure by raising reabsorption of
Na+. Water passively gets reabsorbed with
Na+ due to osmosis.
Produces a small amount of male sex
hormones (androgens).
Adrenal medulla:
Deals with short-term stress.
Stimulated by sympathetic nervous system.
Releases amino-acid derived hormones.
Produces catecholamines (epinephrine and
norepinephrine) to initiate “fight or flight”
response by increasing heart rate and the
breakdown of glucose. Also increases blood
flow to brain/muscles and air flow to lungs.
LH - during menstrual cycle, the LH surge
causes ovulation. This results in a corpus
luteum, which produces progesterone and
FSH - stimulates follicle growth in ovaries,
which results in the increased production of
progesterone and estrogen.
LH - triggers testosterone production by
Leydig cells.
FSH - stimulates sperm maturation.
Feedback Loops
Hormonal control relies on feedback systems,
which fall under positive and negative feedback
1. Positive feedback - the change causes the
amplification of itself, forming a loop that
continues to intensify. You can think of it as
promoting exponential growth.
2. Negative feedback - the change causes the
inhibition of itself, forming a loop that
prevents hormone overproduction. You can
think of it as promoting stability in the body.
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Chapter 11.8: Digestive System
Table of Contents:
● Digestion in Humans
● Mouth, Pharynx, Esophagus
● Stomach
● Small Intestine
● Liver
● Large Intestine
● Summary: Digestive Hormones & Enzymes
Digestion is the process of breaking down large
food into smaller substances for absorption by
the body.
● Intracellular digestion = within cells (eg:
amoeba pseudopods bring food inside
its single cell for digestion)
● Extracellular digestion = outside of cells
(eg: humans digest food then brings
nutrients into its cell for further
Digestion in Humans
The digestive tract has two openings: mouth and
Mouth, Pharynx, Esophagus
Mechanical (chewing) and chemical (salivary
amylase) digestion begin in the mouth. Salivary
amylase in saliva breaks down starch into
maltose (glucose + glucose). Saliva also lubricates
the food creating a bolus.
Upon swallowing, food enters the pharynx
(common to digestive and respiratory systems) which
separates to form the trachea and the esophagus.
The epiglottis blocks the opening to the trachea,
preventing choking.
Food continues to the esophagus (tubular
structure guiding food to stomach). The bolus is
pushed down via peristalsis (rhythmic waves of
contraction). The upper third of the esophagus
consists of skeletal muscle, the lower third
consists of smooth muscle, and the middle third
is a mixture of the two.
Food enters the stomach via the cardiac
sphincter (ring of muscles) where mechanical
(churning of food) and chemical (enzymatic
breakdown of protein and fat) digestion occur.
The stomach lining is filled with gastric pits
leading to gastric glands (multiple cell types).
Mucous cells produce mucus which lubricates and
protects the lining from the acid.
Food entry causes the stomach to distend,
signaling G cells to release gastrin, a hormone
with two functions:
Adapted from:
1. Mechanical Digestion = physical breakdown
of food
2. Chemical Digestion = chemical breakdown
of food, using enzymes.
1. Stimulates parietal cells to release
extremely acidic gastric juice (pH= 2; high
HCl concentration).
2. Stimulates chief cells to secrete gastric
lipase (breaks down fats to fatty acids +
glycerol) and pepsinogen (a zymogen an inactive enzyme precursors) which is
activated to pepsin in acid. Pepsin cleaves
peptide bonds (proteins → amino acids).
Chyme (acidic, semi-digested food) exists to the
small intestine via the pyloric sphincter.
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Small Intestine
Responsible for 90% of digestion and nutrient
absorption. Consists of 3 parts: duodenum
(digestion), jejunum and ileum (absorption) remember DJ Eye (D > J > I).
Inside the villus, nutrients (glucose and amino
acids) are absorbed into blood capillaries and fats
(fatty acids and glycerol) into lacteals.
Goblet cells secrete mucus to protect the
epithelial lining from acidic chyme. Chyme also
triggers the release of secretin (a hormone),
stimulating the pancreas to release basic
bicarbonate ions (HCO3-) into the duodenum via
the pancreatic duct.
Cholecystokinin (CCK) released by the small
intestine: slows gastric emptying, stimulates
pancreas to release digestive enzymes and
gallbladder to release bile into the duodenum.
Accessory organs in the digestive system include
the pancreas, liver, and gallbladder.
Bile (emulsifies fats) is produced by the liver and
stored and concentrated by the gallbladder.
The pancreas secretes HCO3- (neutralization),
pancreatic amylase (starch → maltose) and
proteases (proteins → amino acids). The
pancreatic proteases are trypsin and
chymotrypsin, which are initially released as
zymogens (trypsinogen and chymotrypsinogen).
Enteropeptidase in the duodenum converts
trypsinogen to trypsin which then converts
chymotrypsinogen to chymotrypsin.
Food is moved via peristalsis to the jejunum
and ileum for absorption. Villi (finger-like
projections which increase surface area), made
of enterocytes are lined with microvilli. Villi and
microvilli increase surface area and absorption
efficiency. Crypts (invagintions in the intestinal
wall) contain cells that secrete enzymes and
produce new lining epithelial cells
Adapted from:
In addition to bile production, the liver is
involved in many processes.
1. Blood Maintenance
● Stores blood.
● Filters and detoxifies blood coming
from the digestive system via the hepatic
portal system.
● Destroys erythrocytes and bacteria.
Kupffer cells (phagocytes) eat bacteria
and break down hemoglobin in red
blood cells (red) to bilirubin (yellow) for
secretion in the bile.
2. Glucose Metabolism
● Glycogenesis - converts excess glucose
into glycogen for storage in the liver
(after meals).
● Glycogenolysis - breaks down glycogen to
glucose for bodily use (between meals).
● Gluconeogenesis - converts glycerol and
amino acids into glucose when glycogen
stores are depleted.
3. Protein Metabolism
● Synthesizes plasma proteins from amino
acids (albumin and blood clotting
● Converts ammonia (dangerous byproduct
of protein metabolism) to urea (safer) for
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Large Intestine
Summary: Digestive Hormones & Enzymes
Water and mineral absorption occur at the
cecum (small pouch). The appendix (projection
in the cecum) is a vestigial structure with
negligible immune function and can become
inflamed (appendicitis). In the colon water
absorption is completed, hardening feces. The
feces is stored in the rectum and expelled
through the anus.
The large intestine has 3 functions:
1. Water absorption.
2. Mineral absorption (salts).
3. Vitamin production and absorption: in a
mutualistic relationship, bacteria produce
vitamins B and K (absorbed), metabolize
bile acid, and ferment fiber.
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Chapter 11.9: Excretory System
Table of Contents:
● The Kidney
● The Nephron
● Filtration
● Reabsorption
● Secretion
● Excretion
● Hormones in Excretory System
● General Pathway
Excretion is the filtering out of metabolic wastes
from the body’s fluids and eliminating them as
The Kidney
Humans have two kidneys. Each kidney consists
of a cortex (outer portion where blood enters
the kidney), a medulla (middle portion), and a
pelvis (inner portion where filtrate exits the
Filtration occurs in cortex at the renal corpuscle
which consists of the glomerulus and the
Bowman’s capsule. Blood enters from the
afferent arteriole into the glomerulus which acts
as a sieve. Podocytes from the Bowman’s
capsule surround the glomerulus to form
fenestrations allowing small substances (water
and solutes) to be filtered into the Bowman’s
capsule while larger substances (proteins and
blood cells) remain in the blood. The glomerulus
exits the Bowman’s capsule via the efferent
arteriole which goes on to form the peritubular
Adapted from: https://commons.wikimedia.org/wiki/File:Kidney_Cross_Section.png
The Nephron
A nephron is the single, functional unit of a kidney.
There are four main processes that occur in the
1. Filtration
2. Reabsorption
3. Secretion
4. Excretion
Throughout the nephron, water and solutes that
the body needs are reabsorbed from the filtrate
back into the blood.
The loop of Henle descends into the medulla
and has selective permeability. It is surrounded
by the vasa recta (capillaries running parallel to
the loop of Henle). Water is reabsorbed into the
blood as the filtrate travels down the descending
limb (filtrate becomes more concentrated) and
solutes are reabsorbed as the filtrate travels up
the ascending limb (filtrate becomes less
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Angiotensin II has many effects in the
body. The most important are:
Secretion is the transfer of solutions from the
blood vasculature directly into the nephron tubule
filtrate. This occurs at the distal convoluted
tubule and the proximal convoluted tubule.
The filtrate (now urine) travels from the
nephrons to the collecting duct which leads to
the renal pelvis and then to the ureter.
The ureter connects the kidney to the bladder
where urine is stored. When the signal is received,
urine is excreted from the bladder and the body
via the urethra.
1. Parathyroid Hormone (PTH) = more
blood calcium. Stimulates calcium
reabsorption in the tubules, and indirect
stimulation of osteoclasts (more bone
2. Calcitonin: less blood calcium (calcitonin
tones down calcium). Inhibits calcium
reabsorption in the tubules, inhibits
osteoclasts (less bone breakdown)
3. Renin Angiotensin Aldosterone
Juxtaglomerular cells can detect
changes in blood pressure and sodium
levels. When blood pressure or blood
sodium is low, these cells release renin.
Renin is an enzyme which acts on
angiotensinogen to activate it to the
form angiotensin I. Another enzyme
called Angiotensin Converting Enzyme
(ACE) acts on angiotensin I to convert it to
angiotensin II. Angiotensin II is the active
It stimulates additional aldosterone
release from the adrenal gland cortex
(so aldosterone levels increase).
It increases Na+ reabsorption from
the proximal tubule (and water will
follow the salt).
It is a potent systemic
vasoconstrictor: causing vessels to
constrict, thereby increasing total
peripheral resistance (TPR).
It makes the individual more thirsty:
so they drink more and increase their
blood liquid volume (increasing TPR).
Aldosterone: is a mineralocorticoid
produced by the adrenal cortex. It
increases salt and water reabsorption and
potassium secretion in the distal tubules
and collecting ducts
Antidiuretic Hormone (aka ADH or
vasopressin). Released from the posterior
pituitary upon stimulation from the
hypothalamus. Causes aquaporins to
insert into the collecting duct of the
nephron and increases water reabsorption
Atrial natriuretic peptide (ANP) is
produced by atrial cells in response to atria
distension by an increased blood volume
and pressure. ANP will reduce the blood
volume and blood pressure. It
accomplishes this by: Increasing the
glomerular filtration rate (GFR); decreasing
sodium reabsorption and increasing
sodium excretion; inhibiting renin and the
renin-angiotensin-aldosterone system
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Chapter 11.10: Integumentary System
Table of Contents:
● Epidermis
● Dermis
● Hair
● Glands
● Hypodermis
Located just below the epidermis, it supports and
epidermis and cushions against injury. It contains
2 layers: the papillary dermis (more superficial
and thin, high surface area) and the reticular
dermis (deeper and thick, made of dense
irregular connective tissue).
The integumentary system has 3 layers:
epidermis, dermis, and hypodermis. It has a
role in homeostasis, vitamin D production, and
protection from pathogens.
The most superficial layer of the skin and
contains keratinocytes. The epidermis protects
against dehydration, UV radiation, and
pathogens. The layers of the epidermis from
superficial to deep are:
Corneocytes (dead
keratinocytes) form the
outermost, protective layer.
Dead keratinocytes that are not
yet fully differentiated into
corneocytes. *It’s present in
palms and soles.
Keratinocytes secrete lamellar
bodies to form a water-barrier.
Important for strength
(desmosomes) and immunity
(Langerhans cells).
Precursor keratinocyte stem
cells proliferate here. This is also
where light touch sensation
(Merkel cells) and melanin
synthesis (melanocytes) occurs.
Hair: made of keratin, generated from hair
follicles, stands up via erector pili muscles, and
offers sun and hypothermia protection.
1. Sudoriferous (Sweat) glands consist of:
a. Eccrine glands (sweat glands)
located on the entire body surface
and are important in
b. Apocrine glands are located at
specific sites and secrete into a
hair follicle. They produce earwax
(ceruminous) or milk
2. Sebaceous glands are located over the
entire body except at the palms of hands
and soles of feet. They secrete sebum
(oils + wax) into a hair follicle
The deepest layer containing larger nerves and
blood vessels. Made of loose connective tissue
and adipose (fat) tissue. Its main function is fat
Come Let’s Get Some Beers
Corneum Lucidum Granulosum Spinosum Basale
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Chapter 12: Reproduction and Developmental
Table of Contents
● Asexual Reproduction
● Human Reproduction
● Male Anatomy and Spermatogenesis
● Hormones in Males
● Female Anatomy and Oogenesis
● Hormones in Females
● Menstrual Cycle
● Hormone Feedback Loops
● Fertilization
● Cleavage, Morula, Blastula
● Gastrulation
● Organogenesis
● Extraembryonic Development
● Important Animal Embryonic Models
● Factors Influencing Development
Asexual Reproduction
1. Binary Fission: Unicellular organisms
(prokaryotes and the mitochondria and
chloroplasts of eukaryotes). DNA is replicated,
migrates to opposite ends of cell. Septum
forms in the middle and separates, creating
two separate cells.
2. Budding: bud (outgrowth) forms on organism.
DNA replicated and deposited into bud which
buds off, eg. hydra, yeast.
3. Regeneration or fragmentation: piece of
organism breaks off. Can regenerate broken
piece or sometimes a new organism can
grow from a fragment, eg. hydra, flatworms.
4. Parthenogenesis: unfertilized egg develops
to a viable organism, eg. Honeybees exhibit
haplodiploidy (males haploid, females
Human Reproduction
Sexual reproduction: joining of two gametes
(male sperm and female egg) to create offspring.
Germ cells (male spermatogonia, female oogonia)
produce gametes via meiosis.
Male Anatomy and Spermatogenesis
Spermatogonia undergo two meiotic divisions
to become spermatids and differentiate into
1. Seminiferous tubules of testes = site of
spermatogenesis (sperm production) and
● Sertoli cells: activated by follicle
stimulating hormone (FSH). Surround and
nourish sperm. Produce inhibin (inhibits
FSH - negative feedback).
● Spermatogenic cells: produce
2. Sperm (not yet mature) transported via
peristalsis to epididymis (duct around testes)
for maturation and storage.
3. Sperm moves through vas deferens (group
of tubules) to ejaculatory duct (where vas
deferens meets seminal vesicles) which
propels sperm into urethra and leads to
ejaculation out of penis as semen (sperm +
accessory gland secretions).
Mnemonic (SEVEn UP): Seminiferous tubules →
Epididymis → Vas Deferens → Ejaculatory Duct →
Urethra → Penis.
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Sperm Structure:
● Head: contains nucleus and acrosome
● Midpiece: mitochondria (ATP production).
● Tail: long flagellum (microtubules) to
propel sperm.
Accessory Glands:
1. Seminal Vesicles: secrete fructose (nutrients
to produce ATP), viscous mucus (cleans and
lubricates urethra), and prostaglandins
(causes urethral contractions which propels
2. Prostate Gland: alkaline secretions (basic) to
counteract uterine acidity.
3. Bulbourethral Glands: viscous mucus (cleans
and lubricates urethra).
Hormones in Males
1. Follicle Stimulating Hormone (FSH):
stimulates sperm development in seminiferous
2. Luteinizing Hormone (LH): stimulates Leydig
cells to produce testosterone.
3. Testosterone: matures sperm, gives rise to
male secondary sex characteristics.
Female Anatomy and Oogenesis
Uterus: muscular, vascular organ. Provides
ideal environment for fertilized egg to
implant and develop. 3 layers: perimetrium
(outer), myometrium (middle, smooth
muscle), endometrium (inner epithelial, lined
by mucous membranes).
Cervix: narrow opening of uterus leading to
Vagina: opens to external environment (where
sperm enters and birth occurs).
1. Many oogonia produced, majority die via
apoptosis, small fraction remain and
differentiate to primary oocytes (begin
meiosis but arrested in prophase I until
2. At puberty: one egg per month ovulates,
completing meiosis I, producing large
secondary oocyte (arrested in meiosis II
during metaphase II) and a polar body.
3. If fertilization occurs: meiosis II is completed.
4. At the end of meiosis II: 2-3 polar bodies
(non-viable) and 1 oocyte (viable, contains
majority of cytoplasm and nutrients for fetus)
are produced.
Hormones in Females
1. Follicle Stimulating Hormone (FSH):
stimulates follicles in ovary to develop as well
produce estrogen and progesterone.
2. Luteinizing Hormone (LH): stimulates
ovulation of egg, corpus luteum formation,
which produces estrogen and progesterone.
3. Estrogen and Progesterone: menstrual cycle
and reproduction, give rise to female secondary
sex characteristics.
Adapted from:
Ovary: produces eggs (singular: ovum; plural:
ova) which travel through the oviduct (or
fallopian tube) to the uterus.
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Menstrual Cycle
1. Follicular Phase: hypothalamus releases
Gonadotropin Releasing Hormone (GnRH)
→ anterior pituitary releases LH and FSH →
FSH binds to the ovaries and induces follicles
to develop → developing follicles release
estrogen → endometrium thickens → rapid
LH spike → ovulation.
2. Ovulation: Ovulation (egg is released from
Graafian follicle) → fimbriae on oviduct
catches egg, cilia sweep egg into oviduct →
egg travels down oviduct (awaiting sperm
3. Luteal Phase: follicle develops into the
corpus luteum (maintained by FSH and LH)
→ corpus luteum produces progesterone
and some estrogen → uterine lining thickens
(prepares for implantation).
4. If No Implantation Occurs: LH and FSH
levels drop (due to hypothalamus and
pituitary inhibition by increased progesterone
and estrogen) → corpus luteum can no longer
be maintained → progesterone and
estrogen levels drop (hypothalamus and
pituitary are not inhibited anymore) →
endometrium sloughs off (menstruation) →
cycle repeats.
5. If Implantation Occurs: outer layer of
placenta produces Human Chorionic
Gonadotropin (HCG) → maintains corpus
luteum → progesterone and estrogen levels
maintained → endometrium remains (no
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Hormone Feedback Loops
Positive feedback loops stimulate a pathway to
increase production.
● Lactation: Infant suckling increases
prolactin production which causes
lactation (milk production) and further
increases infant suckling. Oxytocin
releases milk (milk let down reflex).
● Childbirth: Oxytocin induces
contractions which push the baby out of
the womb. The baby pushes against a
nerve in the cervix signaling the
hypothalamus and pituitary to release
more oxytocin.
Negative feedback loops inhibit a pathway to
decrease production.
● The hypothalamus releases GnRH
causing the pituitary to release FSH and
LH which increase testosterone levels.
High testosterone levels inhibit the
hypothalamus from releasing GnRH,
lowering FSH and LH and testosterone.
● The same occurs with estrogen and
progesterone in the menstrual cycle.
Fertilization is the joining of a haploid sperm and
a haploid egg to form a diploid zygote.
Sperm: head (with acrosome at its tip), midpiece
(contains mitochondria), tail.
Egg: Outermost layer, corona radiata (jelly coat,
made of follicular cells), nourishes developing egg.
Underneath is the vitelline layer (zona pellucida
in mammals), made of glycoproteins. Plasma
membrane is under the zona pellucida.
1. Capacitation: the final maturation step for
sperm prior to fertilization. Triggered by
secretions in uterine wall. Destabilizes sperm
plasma membrane proteins and lipids
resulting in:
● Preparation of sperm tip for acrosomal
● Increased calcium permeability causing a
hyperactive state (flagella beats harder,
sperm swims faster).
2. Acrosomal reaction: recognition process
between sperm and egg before fusion.
Ensures same-species fertilization. Sperm
goes through the corona radiata to reach
zona pellucida. Actin from sperm binds to
ZP3 protein of egg’s zona pellucida (mutual
recognition). Membranes of sperm head and
acrosome fuse, releasing hydrolytic
acrosomal enzymes to digest zona pellucida
and allow sperm to fuse with plasma
membrane of egg (fertilization).
Adapted from:
3. Polyspermy Block: prevents polyploidy by
inhibiting polyspermy (multiple sperms
penetrating egg).
● Fast block occurs first when sodium ions
diffuse into the egg, depolarizing its
membrane and prevents sperm binding.
● Slow block: gradual, long-lasting occurs
second. Calcium ions released in egg
stimulate cortical reaction (exocytosis of
cortical granules). Cortical granules
make zona pellucida impenetrable and
stimulate proteases to separate zona
pellucida from plasma membrane.
4. Completion of Meiosis II for the Secondary
Oocyte: During meiosis II, the egg is arrested
in metaphase. After penetration, meiosis in
the secondary oocyte continues creating a
haploid oocyte and producing a second
polar body.
5. Zygote formation:
● Monozygotic twins: identical twins. One
zygote splits. Two embryos with identical
genetic material.
● Dizygotic twins: fraternal twins. Two
separate eggs fertilized by two separate
sperms. Two zygotes with different
genetic material.
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Cleavage, Morula, Blastula
Cleavage is rapid cell division without changing
the total mass of cells. The subsequently smaller
cells resulting from cleavage called blastomeres.
1. Axis of Cleavage.
● Radial Cleavage: cells aligned in vertical
axis (eg. deuterostomes).
● Spiral Cleavage: misaligned cells, deviate
from axis (eg. protostomes).
2. Fate of Cells.
● Determinate Cleavage: blastomeres
have decided fate.
● Indeterminate Cleavage: blastomeres
do not have pre-set fate.
3. Evenness of Embryo Division.
● Holoblastic Cleavage: throughout entire
embryo, evenly divides embryo, in
animals with little yolk (eg. humans, sea
○ Exception: Frogs have lots of yolk
and also undergo holoblastic
cleavage that is uneven (exhibit
● Meroblastic Cleavage: partial cleavage,
embryo not evenly divided, in animals
with lots of yolk (eg. birds, fish, reptiles).
Exhibits polarity with animal pole
(active cleavage) and vegetal pole
(mainly yolk, negligible division).
Embryogenesis in Mammals
Morula (ball of blastomeres): forms at 12-16 cell
Blastula stage (hollow cavity): forms at 128 cell
stage. Blastocoel is hollow, fluid filled centre.
Blastocyst stage: cells of blastula divide and
differentiate to form:
1. Trophoblast (outer ring of cells)
● Forms extraembryonic membranes
(amnion, yolk sac, chorion, allantois) support embryo.
● Implants embryo in uterus.
● Produces HCG (maintains corpus luteum
and endometrium).
2. Inner Cell Mass (ICM) forms embryo.
Differentiates into two layers (bilaminar
● Hypoblast: partially contributes to yolk
sac, remainder degenerates via apoptosis.
● Epiblast: contributes to main embryo.
Cells thicken to form primitive streak
which defines left-right and top-bottom
axes and is crucial for gastrulation to
Fertilization occurs in the oviduct, cleavage
occurs as fertilized egg travels to uterus. At
uterus, fertilized egg is at blastocyst stage. To
implant in uterine wall, blastocyst undergoes
zona hatching. Trophoblasts replace zona
pellucida and implantation can occur.
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Gastrulation is the formation of a trilaminar
embryo. Epiblast cells invaginate inwards through
primitive streak forming three germ layers:
endoderm, mesoderm, ectoderm. Embryo is
now at gastrula stage.
Organogenesis: formation of new organs.
Neurulation is nervous system development:
1. Notochord stimulates ectoderm to thicken,
forming the neural plate.
2. Neural plate folds onto itself forming the
neural fold / neural groove.
3. Neural fold continues to fold, forming a
hollow tube (neural tube).
● Some cells roll off forming neural crest
cells (migrate to form teeth, bones, skin
pigmentation, etc.).
As cells invaginate they create an opening called
the blastopore which forms the archenteron
(center cavity becomes
digestive tract).
1. Ectoderm (outer germ layer) forms:
● CNS (brain and spinal cord) and PNS.
● Sensory parts of ear, eye, and nose.
● Epidermis layer of skin, hair, and nails.
● Mammary and sweat glands.
● Pigmentation cells.
● Enamel of teeth..
● Adrenal medulla.
2. Mesoderm (middle germ layer) forms:
● Bone and skeleton.
● Muscles.
● Cardiovascular system.
● Gonads.
● Adrenal cortex.
● Spleen.
● Notochord (induces spinal cord formation
from ectoderm).
3. Endoderm (inner germ layer) forms:
● Epithelial lining of digestive respiratory,
and excretory systems.
● PLTT (Pancreas, liver, Thyroid and
parathyroid. Thymus).
4. Neural tube differentiates into CNS.
Mesoderm cells (somites) form two masses
alongside notochord. Become vertebrae and
skeletal muscles associated with axial skeleton.
Stem cells are undifferentiated cells with
potential (potency) to become many types of
● Totipotent stem cells can become any cell
(eg. zygote, blastomeres of morula).
● Pluripotent stem cells can become any of of
the 3 germ layers (eg. ICM cells → embryonic
stem cells).
● Multipotent stem cells can only differentiate
to a few cell types of a specific tissue type (eg.
hematopoietic stem cell → many blood cells).
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Extraembryonic Development
Development of structures outside the embryo
(derived from the trophoblast layer). Provide
protection and nourishment to fetus.
Placental mammals have internal pregnancies
while egg-laying animals such as reptiles, birds,
and monotremes (egg-laying mammals) lay eggs.
Marsupials are mammals that carry their babies
in a pouch.
1. Amnion: innermost layer, membrane around
embryo secretes amniotic fluid (water
cushion, protecting embryo).
● Amniotes (reptiles, mammals, birds)
have an amnion, anamniotes
(amphibians, fish) do not (surrounding
water serves as cushion).
2. Chorion: outermost layer.
● Placental mammals: forms fetal half of
the placenta (platform for exchange of
gases, nutrients, and waste).
● Egg-laying animals: membrane for gas
exchange just underneath egg shell.
3. Allantois: sac that buds off of the
archenteron. Stores waste for disposal.
● Placental mammals: transports waste to
placenta, becomes the umbilical cord,
and in adults forms urinary bladder.
● Egg-laying animals: initially stores uric
acid, later fuses with chorion (helps with
gas exchange).
4. Yolk Sac: contains yolk (intraembryonic,
provides nutrients).
● Placental mammals: transient function
until placenta develops. First site of blood
cell formation.
● Egg-laying animals: sole player in providing
Important Animal Embryonic Models
Frog Embryo
Lots of yolk, Uneven holoblastic cleavage with
animal pole (darker colour) and vegetal pole
(paler). Gray crescent is opposite to the site of
sperm entry. Forms due to cytoplasm rotation
causing mixing from the two poles. Any cell from
the first cleavage that receives a bit of the gray
crescent can become a full frog embryo. Frog
embryos have no primitive streak. Instead,
gastrulation begins at the dorsal lip of
blastopore (forms at site of gray crescent).
Chick Embryo
Model for all egg-laying animals. Embryo has no
direct connection to mother and needs large
yolk for nutrients. Chalaza connects yolk to ends
of shell (allows nutrient distribution to entire
embryo). Chicks have a primitive streak.
Blastodisc (analogous to ICM in mammals) is
flattened resulting in an elongated blastopore
upon gastrulation at primitive streak.
Factors Influencing Development
1. Embryonic Induction:
● Organizers secrete chemicals that
influence what neighboring cells become
in the future (eg. dorsal lip of blastopore
in frogs).
2. Homeotic genes:
● Master controller turning different gene
expressions on / off. Homeobox is a
common sequence containing homeotic
genes homologous across organisms
(~180 nucleotides). Crucial in animal
3. Egg Cytoplasm Determinant:
● If egg cytoplasm is unevenly distributed
(creating animal and vegetal poles), an
axis is created, influencing how embryo
divides during cleavage.
4. Apoptosis:
● Programmed cell death important for
normal development of fetus (eg.
removing webbing between fingers) and
adults (preventing cancer).
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Chapter 13: Evolution
Table of Contents:
● Evidence of Evolution
● Theory of Evolution
● Natural Selection
● Gene Equilibrium
● Microevolution
● Macroevolution
● Origins of Life
Evolution is the gradual development and
change of heritable traits (allele frequencies) in
populations over successive generations.
Evolution increases biodiversity.
Evidence of Evolution
1. Paleontology is the study of fossils through
actual remains of the animal or their traces
(ichnofossils). We can see the transition
through time by comparing deepest (oldest)
fossils to shallowest (youngest).
2. Looking at biogeography evidence, we can
see the spread of different species around
the world, both similarities and how they are
3. Embryology allows us to see embryological
similarities and differences between early
stages of related organisms. Eg. all chordates
have a gill slit during development.
4. Comparative Anatomy compares different
body parts of different animals:
● Homologous structures: may or may not
perform the same function but have a
common ancestor. eg. forearm of bird and
● Analogous structures: same function, do
not have a common ancestor. eg. bird
and bat wings.
● Vestigial structures: serve no purpose
but are homologous to functional
structures in other organisms eg. human
appendix and cow cecum.
5. Biochemical methods allow for DNA
sequence comparisons. Can see conserved
DNA sequences (higher similarity = higher
relatedness) and common conserved
pathways (eg. Krebs cycle). .
Theory of Evolution
1. Cuvier proposed catastrophism.
Catastrophes lead to mass extinctions of
species in those areas. The different
populations in different areas were shaped
by what catastrophes had occurred, and
what random organisms survived and then
populated that area.
2. Lamarck proposed:
● Use and disuse: used body parts will
develop and unused ones are weakened,
leading to evolution.
● Inheritance of acquired traits: traits
acquired through use and disuse are
passed onto offspring (eg. giraffe
stretching neck will cause its neck to
develop, and produce long necked
offspring). This is incorrect - acquired
characteristics are generally not heritable.
3. Darwin - theory of natural selection.
Natural Selection
Natural selection is the gradual, non-random
process where allele frequencies change as a
result of environmental interaction. Survival of
the fittest occurs as individuals with greatest
fitness (ability to survive and produce viable
and fertile offspring) have greatest success, and
pass on more DNA to future generations
compared to less fit parents. Leads to the
evolution of the population (not individuals).
Requirements for Natural Selection
1. Demand for resources exceeds supply:
results in competition for survival (fittest
survive to pass on genes).
2. Difference in levels of fitness due to variation
in traits: differentiate ability to compete and
survive (eg. black peppered moths favored
over white moths during Industrial
3. Variation in traits must be geneticallyinfluenced (heritable) to be passed onto
4. Variation in traits must be significant for
reproduction and/or survival: genes
improving reproductive success / survival are
favored and increase over generations and
vice versa.
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Types of Natural Selection
Adapted from: https://commons.wikimedia.org/wiki/File:Selection_Types_Chart.png
1. Stabilizing Selection: mainstream (average)
is favored (eg. birth weight). Diagram is
standard bell curve.
2. Directional Selection: one extreme favored
(eg. longest giraffe neck allows access to the
most leaves).
3. Disruptive Selection: rare traits favored,
mainstream is not. (eg. snails living in low
and high vegetation areas).
Other Types of Selection
Sexual Selection: non-random mating between
males and females. Females favor high quality
offspring, males prefer high quantity of partners
to increase their number of offspring.
Note: traits selected for may be favorable for
reproduction but not for survival.
Artificial Selection: carried out by humans to
selectively breed for specific traits (eg. dog
Gene Equilibrium (No Evolution)
The Hardy-Weinberg formula calculates genetic
frequency during genetic equilibrium (no
change in gene frequencies). If both equations
hold true, the population is under
Hardy-Weinberg equilibrium.
The requirements for Hardy-Weinberg
equilibrium are:
(Mnemonic: Large, Random, M&M)
Large population: minimizes genetic drift.
Random mating
No mutation
No natural selection
No migration (gene flow): population must
be isolated.
When conditions not met, evolution occurs.
Microevolution is the process when gene
frequencies change within a population over
generations (favorable genes increase,
unfavorable decrease).
Factors Causing Microevolution
1. Genetic Drift: allele frequencies change by
chance. Larger effects on small populations.
● Bottleneck effect: smaller gene pool,
some alleles may be lost (eg. disaster
killing majority of population).
● Founder effect: some individuals migrate
away from the population.
2. Non-random Mating: sexual selection,
outbreeding, inbreeding.
3. Mutations: can be dormant until
environmental change allows it to flourish.
4. Natural Selection: no luck involved
5. Gene Flow: migration (non-random) moving
alleles between population leading to
variation through mixing.
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Sources of Genetic Variation
1. Mutation: must not be fatal.
2. Sexual Reproduction: crossing over,
independent assortment and random joining
of gametes.
3. Balanced Polymorphism: maintains a
variety of phenotypes within a population.
● Heterozygote advantage (eg. sickle Cell
● Minority Advantage: rare phenotypes
offer higher fitness. Cycle between high
and low frequency. (eg. advantageous
against hunters’ search images).
● Hybrid Advantage: Two strains of
organisms produce more superior
● Neutral Variations: may become
beneficial if environment changes.
4. Polyploidy: plants have multiple copies of
alleles introducing more variety and
preserving different alleles. Can also mask
effects of a harmful recessive allele.
Macroevolution is long-term and occurs at a
level at or higher than species. Species are
reproductively isolated (via prezygotic and
postzygotic isolating mechanisms) resulting in a
lack of gene flow between species.
2. Postzygotic Isolation: backup in case hybrid
zygote forms.
● Hybrid Mortality: hybrid zygote
not-viable (often due to different
chromosome numbers).
● Hybrid Sterility: hybrid zygote sterile.
● Hybrid F2 Breakdown: offspring of
hybrids have decreased fitness.
1. Prezygotic Isolation prevents fertilization
from occuring between species.
● Habitat Isolation: occupying different
● Temporal Isolation: reproducing at
different times/seasons.
● Behavioral Isolation: different courtship
● Mechanical Isolation: male and female
genitalia are not compatible.
● Gamete Isolation: gametes do not
recognize / fertilize each other (eg. zona
pellucida on mammalian oocytes).
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Speciation is how species form starting with
reproductive isolation which leads to
interruption of gene flow between populations
who gradually develop into two species.
1. Allopatric Speciation: due to a geographical
● Adaptive Radiation: occurs when many
species arise from one ancestor as they
adapt differently to their environments.
2. Sympatric Speciation: occurs without a
geographical barrier.
● Balanced Polymorphism: different
phenotypes are isolated within the same
● Polyploidy: in plants results from
nondisjunction during meiosis. (eg. Two
3n organisms - usually sterile - meet and
are reproductively compatible).
● Hybridization: some hybrids are more fit
than purebreds.
Patterns of Evolution
1. Divergent Evolution: diverge from common
2. Convergent Evolution (Homoplasy):
unrelated species adapt to similar
environments becoming more alike
(analogous structures).
3. Parallel Evolution: diverge from common
ancestor but undergo similar changes.
4. Coevolution: two species impart selective
pressure on each other.
● Camouflage (cryptic coloration): match
appearance to environment to avoid
● Aposematic Coloration (warning
coloration): vibrant coloration in
poisonous animals to warn predators.
● Mimicry: evolving to resemble another
species. In Batesian mimicry a
non-harmful animal resembles a harmful
one. In Mullerian mimicry, two
poisonous animals resemble each other to
warn their predator.
Phylogenetic Trees
Theories of Macroevolution:
1. Phyletic gradualism: evolution happened
gradually via accumulation of small
intermediary changes. Not likely to be true (not
supported by fossil evidence).
2. Punctuated equilibrium: short spurts of
evolutionary changes during periods of stasis
(supported by fossil evidence).
A Phylogenetic tree is a branched diagram that
shows inferred evolutionary relationships
between different taxa. A clade is a cluster with
an ancestor and all its descendants.
Parsimony means the simpler the explanation
the better. Trees minimizing evolutionary
reversals, convergent evolution and parallel
evolution are preferred.
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Origins of LIfe
● Big Bang: ~ 14 billion years ago.
● Earth: ~ 4.5 billion years ago.
● Prokaryotes: ~ 3.5 billion years ago.
● Eukaryotes: ~ 2 billion years ago.
Earth’s current atmosphere:
● Nitrogen gas (most common) = 78%.
● Oxygen gas = 21%.
● Argon gas = 0.9%.
● Trace amounts of CO2, methane, ozone.
Primordial Earth:
1. Earth’s primordial atmosphere consisted of
inorganic compounds and no oxygen - it was a
reducing environment.
2. Earth cooled down, gases condensed
forming the primordial sea.
3. Simple compounds became more complex,
organic compounds formed.
4. Organic monomers became polymers
forming protenoids (behave like proteins).
5. Protobionts arose: precursors to cells. Had
microsomes (membrane-like) and proteinoids.
6. Heterotrophic prokaryotes form.
7. Autotrophic prokaryotes form (eg.
cyanobacteria - can photosynthesize).
● Important: The development of
autotrophs led to the production oxygen
- and its accumulation (oxidizing
environment forms).
8. Oxygen accumulates, reacts with UV forming
ozone layer which blocks UV. This terminates
abiotic chemical evolution.
9. Primitive eukaryotes form
● Endosymbiotic theory:
membrane-bound organelles
(mitochondria, chloroplasts), once
free-living, were phagocytosed by other
prokaryotes and lived in symbiosis with
them, as organelles.
10. More complex eukaryotes and multicellular
organisms come about.
Organic “Soup” Theory: proposed by Oparin
and Haldane. They believed that oxygen is too
reactive for organic chemicals to be produced in
primordial atmosphere, and therefore oxygen
must have been lacking in the primordial
atmosphere. Strong energy (eg. lightning, volcanic
heat, UV radiation) drove reactions that formed
organic compounds.
Miller-Urey Experiment: mimicked reducing
environment proposed by Oparin and Haldane.
Set up a flask containing inorganic compounds but
no oxygen (CH4, NH3, H2, H2O) connected it to
another flask with electrodes (simulates lightning)
and heated it up (simulates high temperatures).
Organic compounds (amino acids, organic acids,
but no complete nucleic acids) were formed.
Supports the Organic “Soup” Theory.
Adapted from:
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Chapter 14: Ecology
Table of Contents:
● Ecological Niche
● Speciation
● Biological Interactions
● Ecosystem Ecology
● Population Ecology
● Ecological Succession
● Biomes
Key Terms
● Abiotic factors: nonliving elements of an
ecosystem (eg. temperature, water, light).
● Biotic factors: living elements of an
ecosystem (eg. plants, animals, etc.).
● Species: a group that can interbreed and have
viable, fertile offspring.
● Population: a specific species living in a
specific location.
● Habitat: the type of place where a specific
organism lives. Includes other organisms
(biotic) and physical aspects (abiotic).
● Ecological community: all populations in a
given area.
● Ecosystem: all the organisms in an ecological
community (biotic), and the abiotic factors
interacting within it.
● Biosphere: all ecosystems on Earth, their
interactions with each other and the
lithosphere, geosphere, hydrosphere,
● Density dependent factors depend on
population density (eg. disease, resource
● Density independent factors do not depend
on population density (eg. climate, weather).
Gause’s Law (competitive exclusion principle):
Two species cannot occupy the same niche and
maintain population levels: one will outcompete
the other. Resource partitioning allows species
to coexist.
Biological Interactions
In competition, (short-term interaction) 2 species
compete for the same resources.
Intraspecific competition occurs between
members of the same species (eg. two rabbits
competing for carrots).
Exploitation competition is indirect. Occurs
when resources are depleted. (eg. cheetahs
deplete gazelle population, affecting lions).
Apparent competition occurs when one
predator preys on two species.
Ecological Niche
An organism’s niche is the biotic and abiotic
resources it uses. Its realized niche is where it
truly lives and its fundamental niche is the full
range of environmental conditions where it could
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Symbiosis (living together) is a close, long-term
interaction between two organisms (symbionts).
Mutualism (+/+): both organisms benefit (eg.
oxpecker bird eating ticks off rhino).
Commensalism (+/0): one organism benefits
and the other is unaffected. (eg. jackal eating
tiger’s leftovers).
Parasitism (+/-): one organism benefits at the
other’s expense. (eg. tapeworm in human
gastrointestinal tract).
Ecosystem Ecology
Food chain: linear depiction of what eats
what (eg. carrot → rabbit → fox → lion).
Food web: expanded food chain depicting
interconnections between food chains.
Trophic level: an organism’s position within
a food chain or food web.
Autotroph: produces organic compounds
from abiotic factors (sunlight, water, CO2,
Heterotroph: must ingest organic
compounds to generate energy & survive.
Predation: relationship between predator
(hunter) and prey (hunted - plant or animal).
Herbivore: plant eater.
Carnivore: meat eater.
Omnivore: plant and meat eater.
Scavengers (carnivores or herbivores)
decompose other dead animals (or plants). eg.
vultures, some beetles. Saprophytes (plants,
fungi, microorganisms) are decomposers that
consume dead or decaying organic material, and
work with scavengers in organic recycling. Fungi
(most important decomposers) and some
bacteria decompose organisms, forming
detritus (feces and decomposing matter).
Detritivores (worms and slugs), consume
detritus, exposing more organic material for
Primary producers, at the lowest trophic level,
are autotrophs undergoing energy production
(eg. photosynthesis) to generate the biomass of an
ecosystem. Consumers (higher trophic levels) eat
producers or other consumers.
Primary consumers (often herbivores) are just
above producers. Secondary consumers
(carnivores) prey on primary consumers and
tertiary consumers prey on secondary
consumers. An apex predator is at the top of
the chain (tertiary consumer or higher).
Only ~10% of energy stored in a trophic level is
converted to organic tissue in the next trophic
level as energy transfer is inefficient between
trophic levels.
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Population Ecology
Population dynamics explores how populations
change in space and time and how they
interaction with their environment.
Biotic potential: a species’ ability to undergo
its highest population growth (highest births,
lowest deaths) when conditions are ideal.
Carrying capacity: the maximum population
size an ecosystem can sustain.
r/K selection theory
K-selected species: long gestation period, few,
large offspring, long time to mature, significant
parental investment, high survival to reproductive
age (eg. humans, large mammals). Demonstrated
by a type I survivorship curve.
R-selected species: abundant, small offspring,
mature quickly, no parental investment, many do
not survive to reproductive age (eg. bacteria,
insects, species with free swimming larvae).
Demonstrated by a type III survivorship curve.
In a type II survivorship curve, survival
probability is constant regardless of age (eg.
hydra, some birds & small mammals, lizards).
Ecological Succession
Ecological succession is the predictable process
where an ecological community develops and
changes over time. Occurs in a new habitat or
after a disturbance.
Primary succession occurs after a large
disturbance in an area that has never supported
life. Begins with a pioneer species (eg. lichen,
fungi, algae).
The order of organisms colonizing is:
pioneer species → thin soil → vascular plants
(grasses, shrubs) → larger plants (trees) →
Eventually a climax community results. A steady
state is reached and a balance of species is
Secondary succession occurs on terrain that has
supported life previously, and has had destruction
following a disturbance (eg. flood, fire). Follows a
similar pattern as primary succession but begins
with grasses & shrubs.
A keystone species maintains ecological balance
despite low abundance (eg. keystone predator
hunts other animals and prevents
Aquatic Biomes:
Largest of Earth’s biomes (~75% of Earth’s
surface). Photosynthetic algae contribute most of
Earth’s atmospheric O2.
Divided into freshwater biomes (~3%) and
saltwater biomes (~97%). Estuaries are areas
where freshwater meets saltwater.
Layers of the ocean are divided based on the
amount of sunlight received:
Euphotic zone: Strong irradiance allows for
plant survival and photosynthesis. Closest to
surface. The littoral zone is the area of the
euphotic zone where sunlight penetrates all
the way to the ocean floor.
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Disphotic zone: semi-irradiated with sun (not
sufficient for plants). Bioluminescent
species produce light here.
Aphotic zone: no light or photosynthetic
species. Some bioluminescent species. Select
fish can survive off of dead matter
descending to the ocean floor.
Terrestrial Biomes:
Land based (non-aquatic) biomes. Summarized in
the chart.
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Chapter 15: Animal Behavior
Table of Contents:
● Types of Animal Behaviors
● Animal Movements
● Communication
● Social Behavior
● Mating
Ethology: the study of animal behaviors, which
are inherited (innate), or learned.
Types of Animal Behaviors
Learned Behaviors
Learned behaviors increase an animal’s fitness,
allowing it to adapt to unexpected events.
1. Classical conditioning: pairing a neutral
stimulus (elicits no physiological response) to an
unconditioned stimulus (naturally elicits a
physiological response - unconditioned
response). This conditions the unconditioned
response to be mentally paired with a neutral
stimulus (becomes a conditioned stimulus)
resulting in a conditioned response.
Inherited Behaviors:
1. Instincts: innate behaviors occurring without
thought. eg: a baby suckling on a presented
mother’s nipple.
2. Reflexes are involuntary rapid responses to a
stimulus. Reflex arcs are controlled by a neural
circuit. There are 2 types:
1. Simple reflexes are most rapid. An
afferent sensory neuron travels from
stimulus to central nervous system and
synapses on efferent motor neurons
which travel from central nervous system
to muscle.
2. Complex reflexes are slower because
peripheral nerves are separated by an
3. Fixed Action Patterns: hardwired actions
initiated by a specific stimulus (releaser or sign
stimuli). Once initiated, will continue to
completion even if the stimulus is removed during
the behavior. Leads to predictable and
appropriate behaviors that do not need to be
learned. (ex: goose rolling egg back into nest,
male insects attacking red bellied males).
Adapted from: https://commons.wikimedia.org/w/index.php?curid=32037734
Stimulus generalization: a conditioned
animal responds to stimuli not identical to
the original conditioned stimulus. The more a
stimulus differs from the original conditioned
stimulus, the smaller the conditioned
response (stimulus generalization
Stimulus discrimination: differentiation
between a conditioned stimulus and other
similar, but different, non-conditioned stimuli.
4. Imprinting: an innate way that animals learn
behaviors that will never be forgotten. Occurs
during the critical period or critical imprinting
stage (eg: ducklings treating a moving object as
their mother & following it).
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Learned Behaviors (continued)
2. Operant conditioning: learning to associate a
behavior with a reward (increases behavior) or a
punishment (decreases behavior).
B.F. Skinner: Skinner box for experiments
Allows coordination of social behaviors with
other animals (finding shelter, food, mates, &
avoiding predation).
1. Visual: associated with aggressive (eg: wolves
baring teeth) and submissive behaviors (eg:
wolves lowering tail). Another example is
courtship/mating rituals.
2. Auditory: communication via sounds.
Beneficial at night and over long distances.
3. Associative Learning: learning that two things
are connected to each other. Increases stimulus
response efficiency. Can be forgotten (extinction)
or remembered via re-association (recovery)
● Spatial learning: associating a response with
a specific location.
● Sensitization: as stimulus occurs more often,
behavioral response increases.
● Habituation: decreasing behavioral response
in response to repetitive meaningless
stimulus. If stimulus is absent for some time,
spontaneous recovery of the behavior can
● Observational learning: learning by
watching another animal perform the same
behavior. Animal learns without
reinforcement and increases efficiency.
● Insight: learning in a new situation. No
reinforcement required.
Animal Movements
1. Kinesis: changing speed in random directions no target (Favourable environment → reduce
speed; Unfavourable environment → increase
speed). eg: flatworm escaping when exposed to
2. Taxis: movement with a specific direction,
towards (positive taxis) or away (negative taxis)
from a stimulus. Light stimulus = phototaxis;
chemical stimulus = chemotaxis.
3. Migration: long-distance movement from one
area to another due to instinct, often seasonal.
3. Tactile: communication via touch (eg: wolves
greeting by licking muzzles).
4. Chemical: communication via chemicals.
Releaser pheromones (immediate, reversible
behaviors) and primer pheromones (long term
Social Behavior
Allows interaction for companionship, finding
food, protection, and mating.
Cooperation: grouping together to better
achieve a goal (eg: coordinated hunting).
Agonistic behaviors: competing for food,
territory, or mates. Include: threats, aggression
(often detrimental to both parties), and
submission. Appeasement behavior (a threat
by one animal causes other animal’s submission)
avoids aggression (prevents injuries).
Dominance Hierarchy = pecking order. Alpha
male = top ranked male.
Territoriality: behaviors used to protect an
animal’s territory or safe space (eg: employing
watchers and defenders and using pheromones
to scare off others).
Search images: abbreviating what food looks like
to quickly locate abundant and safe food without
much thought.
Altruistic behaviors: sacrifices made for
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Inclusive fitness = sum of animal’s direct
(genes animal passes on) and indirect (genes
passed on by relatives) fitness. Increased by
indirect fitness (kin selection).
Monogamy = one mating partner at once.
Polygamy = multiple partners at once.
Polygyny = one male multiple females.
Polyandry = one female multiple males.
Semelparity = mate once in lifetime (multiple
offspring, low survival, harsh conditions, no
parental care).
Iteroparity = mate many times in lifetime
(one offspring, high survival, dependable
environment, parental care).
Reciprocal altruism: sacrifices made for
unrelated animals of same species in
anticipation of a future reward (‘I help your
family, you later help mine’).
Herds, flocks, schools, packs provide greater
power and protection.
Sexual selection: how males and females differ
in mating behavior to maximize fitness.
● Females contribute a lot of energy in mating
(maximize fitness with focus on high quality
mates and offspring), while males contribute
little energy (maximize fitness with focus on
quantity of offspring).
● Female choice increases attractive traits in
● Male competition rewards strongest males
with more mating opportunities.
● Sexual dimorphism: males and females of
same species look different (eg. males larger
than females).
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