1. Structure of water and hydrogen bonding:
AP Biology
Unit 1 - Chemistry of Life
● Water: a “universal solvent” due to its ability to dissolve many solutes
● Properties of water:
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram
o cohesion, ability of adhesion, being a “universal solvent”, the solid being
less dense than the liquid, having a high specific heat, and having a high
boiling point (212 degrees Fahrenheit, 100 degrees Celsius), and surface
Key Terms:
tension.
● Solvent: able to dissolve other substances.
● Hydrogen bond: weak chemical bond
● Solute: the minor component in a solution, dissolved in the solvent.
o Formed when partial charges resulting from polar molecules attract/are
● Polar: when electrons are not evenly distributed in a covalent bond
attracted to each other
● Non-Polar: when electrons are evenly distributed in a covalent bond
o Example: cohesion between water molecules are a result of hydrogen
● Cohesion: attraction that occurs between identical molecules
bonds
● Adhesion: attraction that occurs between molecules of different substances.
● Specific heat: the heat needed in order to raise the temperature of the unit mass of
● Water has a high vaporization temperature.
o Evaporative Cooling: when humans sweat, the water absorbs the body’s
a given substance by a given amount (usually one degree).
excess heat and then evaporates, cooling the body
● Density: calculated by dividing the mass of a substance by its volume
● Water molecules form hydrogen bonds between each other, forming a strong
● Heat of Vaporization: The amount of energy needed to change one gram of a
lattice structure. The result is high surface tension.
liquid substance to a gas at constant temperature.
● Water has a bent or V-Shaped figure because of its polarity.
● Macromolecules: A large molecule composed of many smaller molecules
2. Elements of life:
1
2
o "Descent with modification"
● Living system: Open systems that take in raw materials, use certain parts of the
o "Natural Selection" - Those who are the most fit and apt have a higher
system, and then proceed to release waste
chance of survival and passing on the good genes to their offspring.
● Energy: The ability to do work or cause change
● Constant input of energy: necessary to maintain the complicated organization of a
● Darwin’s Observations
o Individuals have a variety of traits in themselves and between themselves,
system.
with many passed on through offspring
● Matter: Anything that has mass and takes up space.
● Examples of Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic acids.
o Competition is unavoidable because offspring are constantly being created
and are in need for resources
● Atoms: matters building blocks or basic units
o Species adapt to have advantage within the population and to have better
● Exchange of matter between the environment and organisms allows organisms to
access to the limited resource pool
grow, reproduce, and retain organization.
● “Edits:
● Carbon: backbone of most, but not all, biological macromolecules.
o "Edit”: metaphor for natural selection; natural selection cuts out or edits
● Nitrogen: A necessary atom in proteins and nucleic Acids, but not in
out the unnecessary or disadvantageous traits, as beings with those traits
carbohydrates and lipids.
are less likely to survive and reproduce
● Taxonomy:
● Common ancestry and natural selection:
o biological branch of study that classifies species, establishes the ordering
o First common ancestor or "prototype”is marked as the beginning of all
of species into groups based on the characteristics they share.
life. All life began from an ancestor, so we are united, but natural selection
● Levels of Taxonomy (most to least inclusive):
has changed life throughout time through adaptation and “edits”
1. Domain -- Dear
2. Kingdom -- King
3. Phylum -- Phillip
4. Class – Came
5. Order – Over
6. Family -- For
7. Genus -- Good
8. Species -- Soup
● Bacteria, Archaea, and Eukarya: Differences
o Bacteria: Prokaryotic
o Archaea: Prokaryotic
o Eukarya: Eukaryotic, 3 groups (Animalia, Fungi, Plantae), includes
protists
3. Introduction to Biological Macromolecules:
● Darwin’s two main ideas:
3
4
● Hierarchy: organizes interacting biological levels of structures
● Polypeptide: a large protein macromolecule whose conjoined amino acids are held
● Monomer: simple compound or molecule that is joined with other molecules to
together by peptide bonds.
produce polymers.
● Primary structure: The first level of a protein structure; linear sequence of amino
acids
● Polymer: large and complex compound that is composed of combined smaller
o Amino (or N-) terminus: The end of the protein chain that has an exposed
compounds, or monomers.
amino group (-NH2).
● Hydrolysis: process where a molecule is split through the addition of water
o Carboxyl (or C-) terminus: The end of the protein chain that has an
● Dehydration synthesis: Condensation reaction where molecules are joined
exposed carboxylic acid group (-COOH).
together by the removal of water
o R group (side chain): Part of amino acid that determines the molecule’s
physical and chemical properties.
4. Properties of Biological Molecules:
▪
● Protein: A three-dimensional polymer made of conjoined amino acids.
● Polysaccharides: complex carbohydrates made of sugar monomers.
● Amino Acids: Building blocks of proteins.
o Examples: Starch, glycogen, cellulose
● Carbohydrate: composed of carbon, hydrogen, and oxygen atoms
● Lipid properties:
o Acts as a major source of short term energy for the body
-Do not form polymers,
o Monosaccharides: Building blocks of carbohydrates.
-Water fearing or hydrophobic
● Lipids (fats):Composed of long carbon chains
-Fatty acids are long non polar hydrocarbon chains with an acid group at the
o Often used in the body through insulation and long term energy (energy
end
storage)
● Saturated fats: A fat that is solid at room temperature; hydrogens are saturated, or
o Fatty acids: chains of carbon that build most lipids.
the carbons are all connected with single bonds
o Glycerol: A three- carbon alcohol that covalently bonds to fatty acids,
o Examples: animal fats, lards, and dairy products.
forming oils and fats (lipids)
● Unsaturated fats: contain at least one double bond resulting in a kink in structure.
● Nucleic acids: contain hydrogen, oxygen, nitrogen, carbon, and phosphorus
o Cannot pack in an organized manner, and thus they are liquid at room
o Nucleotides: Building blocks of nucleic acids.
temperature. these are often found in plants and fish
o Five-Carbon Sugar: part of nucleotides
▪
● Phospholipids: composed of two fatty acids, plus hydrophilic phosphate, and
Deoxyribose: A Five-Carbon sugar that is a component of DNA
glycerol.
nucleotides.
▪
R group properties: Non-polar, polar, acidic, basic, or ionic.
o They play a role in cell membranes
Ribose: A Five-Carbon sugar present in RNA.
o Phosphate: part of of nucleotides, connected to the five-carbon-sugar’s 5’
end
o Nitrogen base: part of a nucleotide. Includes adenine, guanine, cytosine,
5. Structure and Function of Biological Macromolecules:
thymine, or uracil; attached to the five-carbon-sugar’s 1’ end
5
6
● Structure: The directionality and order of subcomponents (monomers) in a
● Nucleic acids: formed through the conjoin of nucleotide monomers
macromolecule (polymer)
● Nucleotides: a nucleic acid monomer, contains 3 parts
o Form = function
o Nitrogenous base, pentose sugar, phosphate group.
● 5’ end and 3’ end: 5’ end – has a 5’ carbon attached to a phosphate. 3’ end – has a
▪
3’ carbon attached to the next nucleotide in the linear chain of DNA or RNA.
Pentose: Ribose (ribonucleotides) or 2-prime-deoxyribose
(deoxyribonucleotides).
● Anti-parallel: Separate strands that run in opposite directions.
▪
● Adenine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
Phosphate: Phosphorous attaches to the nitrogenous base.
● Nucleic acids hold genetic info
thymine in DNA using (two hydrogen bonds).
● Nitrogenous bases: A, C, T, G, U.
● Thymine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
● Complementary bases: A and T, C and G
adenine in DNA (using two hydrogen bonds).
o These will always pair together in DNA structure
● Cytosine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
● Purines: large nitrogenous bases A and G.
guanine in DNA (using three hydrogen bonds).
● Pyrimidines: small nitrogenous bases T, C (U replaces T for RNA)
● Guanine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
cytosine in DNA (using three hydrogen bonds).
● Growing polypeptide chain: Linear chains of amino acids formed by creating
covalent bonds at the carboxyl terminus.
● Primary structure of protein: The amino acid sequence.
● Secondary structure of protein: local folding and twisting of amino acid chains
into elements such as alpha-helices and beta-sheets.
o Alpha-helix: spiral shape
o Beta-sheet: side by side folding of amino acids with each other through
hydrogen bonds
● Tertiary structure of proteins: 3-D structure; formed through hydrophobic and
hydrophilic interactions between far off regions in the polypeptide (not local).
Shape aims to minimize the free energy
o Hydrogen bonds, disulfide bonds, ionic bonds, other interactions
● Quaternary structure of proteins: conjoining of multiple polypeptides.
● Carbohydrate structure: made of linear chains of monomers, connected through
covalent bonds
6. Nucleic Acids:
7
8
● Functions of SER: Biosynthesis of steroids (testis), Drug Detox (liver), Ca
AP Biology
Unit 2 - Cell Structure and Function
pumping ( muscle ), Sequestration
● Golgi Apparatus: Attaches sugar to the protein= glycoproteins. Condenses the
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram
1.
protein and packages them into membrane bound secretion granules. Has 2 facesconcave and forming.
● Lysosomes: Digests waste inside the cell by digesting internal cellular debris
Cell Structure: SubCellular Components:
(autophagy). Created in ER and packaged in Golgi apparatus
● Cell: Smallest unit of living organism.
o Lysosomal Enzyme Deficiencies: Pompe, Tay-Sach, & Danon.
● Membrane: fluid phospholipid bilayer with integrated proteins.
● Peroxisomes: Bounded by a single permeable membrane with a crystalline core.
o The rate at which a molecule diffuses across a lipid bilayer depends on its
Catalase. Breakdown of H2O2 (hydrogen peroxide). Involved in cholesterol
electric charge and size.
biosynthesis.
o Membrane works as a selectively permeable barrier, cel subdivision and
● Mitochondria: Production of ATP, Cell signaling, Cell differentiation, Apoptosis.
compartmentalization
● Mitochondria Structure: 2 concentric membrane-bounded spaces.
● Chemistry of the membrane: consists of lipids, protein and carbohydrate
● Intermediate filaments: Provide mechanical support & strength. Ex: lamina,
● Membrane Structure: Asymmetric and fluid
keratin, desmin, vimentin, neurofilaments.
● Nucleus: eukaryotic membrane-enclosed organelle, acts as the control center for
o Microfilaments (Actin filaments): 2 stranded helical polymers.
cells
▪
o Nuclear envelope: envelopes the nucleus, and is continuous with the
Relate to cell mobility, organelle transport and contraction.
o Myosin filaments: Differ in cell distribution & function: contraction,
membrane of the RER; dotted with ribosomes.
vesicular transport.
o Nuclear Pores: responsible for molecular transport through nuclear
o Microtubules: Widest filaments in the cell. Found in most cells, especially
envelope
near the cell center.
o Fibrous Lamina: inner surface of nuclear membrane.
● Microtubules (Flagella & cilia): Central pair & 9 outer doublet microtubules.
● Fibrous Lamina Function: Maintain nuclear stability, organize chromatin, bind
nuclear pore, complexes and important cellular vents like DNA replication & cell
division
Interaction with ATPase dynein & ATP in the transduction of chemical energy.
● Microtubules (Mitotic Apparatus): Mitotic spindle/ spindle fibers.
● Microtubules: Cytoskeletal. Microtubules are positioned in a way that stiffens or
● Nucleus: DNA and histones.
supports the cytoplasm.
o Euchromatin
● Microtubules (Saltatory Movements): They make these movements that start
o Heterochromatin
abruptly. The mechanism seems to be along microtubules tracts.
● Free ribosomes: synthesize or make cytoplasmic proteins
● Centriole: Non Membrane organelle which exists in pairs in each cell.
● Smooth Endoplasmic Reticulum: Endoplasmic reticulum without attached
Play a role in establishing cell polarity and the spindle during cell division.
ribosomes. Differs from RER both structurally and functionally, in the form of
● Glycogen: Highly branched polymer of D-glucose.
tubes arranged neatly in parallel rows or in a tangle.
1
2
o Function of glycogen: Carbohydrate energy store
○ crossing over (recombination) between homologous chromosomes
○ random separation of homologous chromosomes
● Function of lipid droplets: Storage of triglycerides
● Structure of the biological membrane:
● Distribution of lipid droplets: Adipose (Fat cells), quantity varies with metabolic
○ Globular proteins are suspended and laterally mobile (fluid-mosaic model)
state.
The membrane is asymmetric with carbohydrates located exclusively
● Mitosis & Meiosis Cell Cycle: process of cell division, has stages:
outside of cells.
○ G1: Rapidly synthesize RNA & protein, enlarging their nuclei and
● Lysosome and disease:
cytoplasm from the last cell division.
○ When the cells are lysed or lysosomes fuse with plasma membrane, or
○ G2: Cells with polytene chromosomes & polyploid cells (mammalian liver
lysosomal leak out during phagocytosis, released enzymes harm
cells), remain in this period indefinitely.
surrounding environment
● Chromosome: Highly condensed chromatin.
○ Defective lysosomal genes: The substrate of this particular enzyme
○ Humans have 46
accumulates in the cells, which causes lysis or dysfunction of the cells or
● Mitosis Stages
organs. When lysosomal fusion with phagosome is impaired, the
○ Prophase: Nucleolus disappears as centrioles begin to divide and move to
individual becomes very susceptible to various infectious diseases.
opposite sides of the cell
○ Metaphase: Chromosomes align themselves in a plane called metaphase
plate. Homologous chromosomes do not line up side by side.
○ Anaphase: The centromeres holding the sister chromatids split in half, and
each one is now called a daughter chromosome.
○ Telophase: Process of uncoiling all chromosomes and reforming nuclear
envelopes.
● Meiosis: going from diploid to haploid
○ Synaptonemal complexes: Sites in pairing between 2 homologous
chromosomes.
○ Metaphase 1/Anaphase 1: Same as in mitosis, except that the homologous
chromosomes pair up side by side
○ Metaphase II/ Anaphase II: Each bivalent splits producing 2 sister
chromatids. None of the daughter cells have identical sets of
chromosomes.
○ Down Syndrome: common condition that results from meiotic
abnormalities in humans, trisomy 21
● Genetic diversity:
2.
3
Cell Structure and Function:
4
located in the cytoplasm of animal and protist cells
● Cell: basic unit of all living things
o Mitochondrion: converts food particles (mainly sugars) into usable
● Cell theory:
energy..
o All living organisms are composed of one or more cells.
o Chloroplast: organelle that captures light energy and converts it to
o Cells are the basic unit of structure and organization of all living
chemical energy through photosynthesis
organisms.
o Cell wall: thick, rigid, mesh of fibers that surrounds the outside of the
o Cells come from other living cells, passing down their genetic information
plasma membrane, protects and give support to the plant cell
to their daughter cells.
o Cilia: short, hair-like projections that help in the movement of some cells
● Compound light microscope: microscope composed of two or more lenses and
o Flagellum: long projection that helps in the movement of some cells
uses light to produce a magnified image; can magnify to a maximum of 1000x
● Diffusion: net movement of particles from an area of high concentration to area of
● SEM: produces a 3-D image of the surface of the specimen
lower concentration
● TEM: electron microscope; uses electrons to show contrast of structures
● STM: scanning tunnel microscope; used to scan molecules such as DNA
● Brownian movement: random movement of particles
● Components of the Cell
● Facilitated diffusion: transport proteins allow substances to move across the
plasma membrane without using any energy
o Plasma membrane: boundary of the cell, controls entrance of molecules
● Osmosis: diffusion of water; important in maintaining homeostasis
o Organelles: specialized structures with specific functions
o Isotonic solution: concentration of cell environment the same as on the
o Transport proteins: proteins tunnels that allow substances to get pass the
inside of the cell
plasma membrane
o Hypotonic solution: solution that has a lower concentration of solutes than
o Cytoskeleton: network of fibers that maintain cell shape and provide an
inside the cell; cell will swell
anchor for the organelles; composed of microfilaments and microtubules
o Hypertonic solution: solution that has a higher concentration of solutes
o Cytoplasm: a semi-fluid environment outside the nucleus
than inside the cell; cell will shrink
o Ribosome: organelle; manufactures proteins; made of protein and RNA
● Passive transport: cell transport that does not require a cell to use energy such as
o Nucleolus: within the nucleus where ribosomes are made
diffusion or osmosis
o Endoplasmic reticulum (ER): system of folded sacs and conjoined
● Active transport: cell transport that requires a cell to use energy such as
channels; where proteins and lipids are synthesized
endocytosis or exocytosis
o Golgi apparatus: flattened stack of membranes that modifies and packages
o Endocytosis: process where the cell surrounds a substance and pinches off
proteins into vesicles
inside the cell; requires energy
o Vesicles: sacs that fuse with the plasma membrane to release proteins to
o Exocytosis: secretion of materials at the plasma membrane and removes
the environment outside the cell
substances from the cell; requires energy
o Vacuoles: organelle that acts as a storage center
o Lysosomes: digest excess or worn-out organelles and food particles
o Centrioles: groups of microtubules that function during cell division;
3.
5
Cell Size:
6
(who love water) pass slowly, ex ions
● Small cells are more efficient
○ The surface area to volume ratio limits the size of a cell.
● Aquaporins: facilitate passage of water molecules
○ Cell size is limited because you need a rapid exchange of materials
○ Involved in osmosis
between the environment and the cell for the cell to survive.
● Channel proteins: holds onto passengers and changes shape to take them across
● The plasma/cell membrane is responsible for maintaining homeostasis
● Concentration gradient: substance diffuse from its higher concentration to lower
○ Regulates exchange of all materials
concentration areas
● The greater the distance materials must travel to reach their destinations
● Tonicity: ability of a solution to cause cells to lose or gain water.
(organelles or exit the cell), the slower the rate.
● Osmoregulation: cells with no cell walls need this which is the control of solute
○ The volume of a cell slows the rate of exchange
concentration and water balance
○ For the cell to be most efficient, a large surface area compared to the
○ Turgid/flaccid: healthy state of plants where water intake by osmosis has
volume is needed.
cell wall opposing further intake.
4. Plasma Membranes:
limp
● Phospholipids are amphipathic which means they have a hydrophilic and a
○ Plasmolysis: when plant cell shrivels up and the plant wilts and the
hydrophobic region.
membrane pulls away from cell wall
○ As temperature decreases, phospholipids pack together and solidify.
● ATP: energy molecules often involved in active transport of signal transduction
membranes can be fluid at a lower temp if they have phospholipids with
○ Sodium potassium pump: exchange of Na for K
unsaturated hydrocarbon tails.
○ Membrane potential: voltage (electrical potential energy) across the
● Steroid cholesterol helps resist changes in fluidity
membrane. cytoplasmic is neg to ECM
● Integral proteins penetrate the lipid bilayer
○ Electrochemical gradient: passive transport. chemical and electrical forces
push ions in and out of the cell. ions diffuse down its electrochemical
● Peripheral proteins are loosely bound to membrane
gradient
● Proteins are attached to cytoskeleton and fibers of ECM
○ Electrogenic pump: a transport protein that makes voltage across the
● Transport protein provides a hydrophilic channel and shuttles substances, or
membrane. It helps store energy.
hydrolyzes (chemical breakdown) ATP
● Proton pump: for plants, fungi, bacteria that transports proteins (H+)
● Signal transduction: part of cellular communication
● Cotransport: transport protein that does the downward diffusion of a solute and
○ Cell to cell recognition: glycoproteins recognize other membrane proteins
upward of a 2nd substance against its concentration. H+ helps transport sucrose
○ Intercellular joining: membrane proteins that bind together in gap/tight
● Bulk Transport: transport of large molecules
junctions
○ Exocytosis: fusion of vesicles with the plasma membrane. vesicle
○ Cytoskeleton attaches to ECM: microfilaments non covalently bond to
membrane and membrane fuse. It’s used to export carbohydrates and
membrane proteins for cell shape
proteins
○ Endocytosis: cell takes in molecules to form vesicles from plasma
● Permeability of lipid bilayer: nonpolar molecules cross easily, polar molecules
7
8
membrane
● Small Hydrophobic Molecules: Pass through the membrane through simple
○ Phagocytosis: cell engulfs particle to be digested in food vacuoles
diffusion (Ex: O2, CO2, N2)
○ Pinocytosis: cell gulps extracellular fluid to form infoldings in plasma
● Small Uncharged Polar Molecules: Small enough to slip through the membrane
membrane
(Ex: H2O, glycerol, ethanol)
○ Receptor mediated endocytosis: cell acquires bulk quantities of fluid
● Large Uncharged Polar Molecules: Do not go through the Membrane!! (Ex:
where proteins are exposed to it
Amino Acids, glucose, nucleotides)
● Ions: Do not go through the Membrane!! (Ex: H+, Na+, K+, Cl-, etc.)
6. Mechanisms of Transport:
● Energy in diffusion: does not require energy
○ The rate of diffusion is affected by: presence of a gradient membrane
electrical potential, and pressure difference. It is also affected by the
amount of substance available, and its lipid solubility
● Simple Diffusion (no channel): Occurs FREELY through "openings" of the lipids
of the bilayer.
○ Substances with high lipid solubility
7. Cell Compartmentalization (terms previously covered):
● ER: where proteins, lipids, and molecules are modified.
o Smooth ER: synthesis of lipids, metabolism or carbs. storage for calcium
ions.
o Rough ER: site for translation, processes proteins. send them to be
secreted.
● Golgi apparatus: proteins, lipids and molecules are further modified in the golgi.
material enters the cis side and exits the trans side via vesicles.
● Vesicles: organelles that shuttle between other organelles and the plasma
membrane.
● Free ribosome: ribosomes that are free within the cell.
● Bound ribosomes are attached to the ER. (rough ER)
● Plasma membrane. delivers stuff from outside of the cell to the inside.
● Mitochondria: generate chemical energy needed to power the cell's biochemical
reactions, produced energy is stored in adenosine triphosphate (ATP).
5.
Membrane permeability:
o Cristea: Folds inside the mitochondria.
9
10
o Matrix: Gel-like space in the mitochondria. Where the citric acid cycle
●
takes place.
Endosymbiotic theory: mitochondria and chloroplasts were once free-living
prokaryotic cells that entered a large host cell through endocytosis. Overtime, the
prokaryotes and their hosts evolved together
● Chloroplasts: a plastid that contains chlorophyll and in which photosynthesis
takes place.
●
Prokaryotes:
o Free floating DNA takes a circular form; it does not contain membrane
bound organelles. Includes bacteria and archaea, and are usually small and
always unicellular
●
Eukaryotes:
o Linear DNA inside the membrane bound nucleus, has membrane bound
organelles. Include animal, plant, fungi, and protist cells and can be either
multicellular or unicellular
Sources
● www.khanacdemy.org
8.
Origins of Cell Compartmentalization:
11
12
1.
● Protein phosphatase: enzyme the removes the phosphate group from proteins
o encourages the cascade of reaction during signal transduction
the next protein kinase in a reaction cascade
● Protein kinase: Enzyme that removes the phosphate from ATP and attaches it to
o Common in short distance cell signaling
● Local regulator: type of cell signal that acts locally
in response to the binding of a specific ligand
1
o Ligand-gated ion channel: channel in the plasma membrane that opens
ligands usually have intracellular receptors
o Water soluble ligands require an external receptor, while hydrophobic
binding to the receptor is the onset of signal transduction
● Ligand: a molecule that binds to a very specific receptor in the cell membrane; it’s
muscle and liver cells
● Glycogen: polysaccharide that acts as a storage for glucose; it is common in
materials to pass through
● Gap junction: intercellular junction common between animal cells, allows
signals from the outside to the inside of the cell
● G protein: Binds with GTP and works with a G-protein coupled receptor to relays
o also referred to as adrenaline
o responsible for the onset of the fight or flight reaction
into usable sugar/energy
● Epinephrine: water soluble ligand molecule; signals the cell to convert glycogen
● Apoptosis: can be termed as “cell suicide”, occurs as a result of cell signals
o response - cell responds when the end of the cascade is reached
cascade of reactions
o transduction - original signal from ligand is amplified through a
o reception - ligand binds to receptor
● Stages of Cell Communication:
transcription of specific genes.
● Transcription factor: A regulatory protein that binds to DNA and affects
in the process of male reproductive system development.
● Testosterone: steroid hormone that works as a ligand for multiple signals that aid
extracellular (or intracellular) signal
● Signal transduction: the processes that include how the cell responds an
time
● Amplification: An effect that occurs when the original signal is strengthened by
many domino-effect reactions within signal transduction.
signals, as it is able to trigger numerous signal pathways at the same
o helps cells in their regulation of cell cycle and cell reproductive
signaling
2
● Receptor tyrosine kinase: Another plasma membrane receptor that functions in cell
o Often used to halt a certain signal that has been cascading
kinases in signal transduction
Cell Communication:
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram
AP Biology
Unit 4 - Communication and Cell Cycle
2.
cGMP phosphodiesterase
Ca2+ and K+ channels
Phospholipase-C, -A2 or D
▪
▪
▪
kickstart the cell response
3
and their effect is dependent on the number of hormones/ligands present to
o Nuclear receptors: water-fearing hormones bind to intracellular receptors,
Adenylyl cyclase
▪
transduction. Some common ones are:
activates more enzymes that continue the cascade effect of signal
extracellular receptor causes a conformational change, which in turn
o Extracellular/membrane receptors: binding of hormonal ligand to an
● Major classes of hormone receptors:
o , aldosterone, progestins, vitamin D, estrogens
● Steroid hormones are made from cholesterol
their own secretion or intracellular processes
● Autocrine function: hormone acts back on the cells of their origin to modulate
● Paracrine function: hormonal signals that act on local cells
axon and then into bloodstream to the distant target cells
● Neurocrine function: Hormones transmit the molecular signal from neuron to its
● Endocrine function: produces and sends hormones
common in long-distance communication
● Hormone: chemical substance that acts as a ligand in signal transduction;
Introduction to Signal Transduction:
3.
Phosphatase shuts off pathways
Kinases stimulate pathways
ligand binding.
● Signal Termination: Signal response is terminated quickly by the reversal of the
o Translation: RNA used to make proteins
o Transcription: copies DNA into RNA
and transcription
4
● Gene Expression: gene information is used to produce proteins through translation
leads to protein production, inciting a cellular response.
● Cell signaling leads to a cytoplasmic response or a change in the nucleus that
Tyrosine Kinase Receptor pathways.
o Calcium Ions: a common messenger and relays signals in G-Protein and
works with adenylyl cyclase
o cyclic-AMP: responsible for activating the protein kinase cascade. Often
pass a signal; spread via diffusion.
● Secondary Messengers: Small, non-protein, water-soluble molecules or ions that
from the protein.
● Dephosphorylation: Occurs when phosphatase enzymes remove the phosphates
▪
▪
another signal is sent to prevent phosphorylation of ATP.
o Signals are constantly transduced (translated) into a different form until
o The multiple kinases allow places for control and regulation
the next level of the cascade reaction
o Amplification occurs when a single kinase activates multiple kinases in
amplify the signal received by the binding of ligand
● Transduction: cascades of interactions between protein kinases and ATP that
o Steroids, hormones
hydrophobic ligands
● Intracellular Signals: protein kinases or signal receptors inside the cell that bind to
Signal Transduction:
5.
4.
Insulin: hormone produced to help the body use sugar
●
●
sister chromatids
5
▪
making organelles, proteins, and membranes
G2 phase of interphase: cell finishes growth; prepares to divide by
a full set of DNA
● DNA replicates prior to cell division so each daughter cell gets
S phase of interphase: DNA replicates in preparation for division
G1 of interphase: cells grow after they are "born"
cell cycle and no longer divide
G0 phase of interphase: optional part of interphase where cells exit the
uncoil back into chromatin
o Telophase: centrosomes disassemble, nuclei reform, chromosomes start to
fibers and centrosome
o Anaphase: sister chromatids are pulled to opposite sides of cell by spindle
to opposite poles of cell
6
o Metaphase: Chromosomes line up in the middle of the cell; centrosomes move
centrosomes form and spindle fibers attach to chromosomes
o Prophase: Chromosomes become visible, nuclear envelope dissolves,
● Mitosis: cell division of somatic cells that produces identical daughter cells
▪
▪
▪
Feedback Mechanism: a system in which the products formed by a signal pathway
help regulate and inhibit that pathway
NO division happens here
o 3 phases of interphase: G1 phase, S phase, G2 phase
▪
o Interphase: cells are often in this phase; the longest phase
● Stages of Cell Cycle
signal in one direction activates and amplifies in that direction
Positive Feedback Loop: signal pathways that move away from a set point; a
or close to a set point
● Negative Feedback Loop: similar to homeostasis in which a system aims to stay at
Feedback:
Neurotransmitters: ligand for nerve cells
o Mitotic chromosome: a chromosome that has duplicated, often referred to as
●
o Chromosomes: DNA that is wrapped tightly
between neighboring cells
●
o Chromatin: coiled DNA
Plasmodesma: allow small molecules (including signaling molecules) to flow
● DNA in Cell Division
Helper T lymphocyte (TH): CD4+ cells help in the adaptive characteristic of the
●
●
o Multi-Cellular: growth, repair, replace dying/dead cells
● Parent and daughter cells are identical: DNA, organelles, etc.
Antigen-presenting cell (APC): immune system cells that help in regulation
●
immune system
o Unicellular: to reproduce and have their kind continue on
Pheromone: chemical signal released externally by animals of the same species
● Purpose of Cell Division:
Cell Cycle:
●
Quorum sensing: cellular communication method common in bacteria where
6.
bacteria inform each other of the excess of products in their environment
●
Other Signal Involved in Signal Transduction
7.
progress through the cell cycle, etc.
● Regulatory Proteins: "signals that help the cell know when to duplicate, when to
● Radiation: another cancer therapy that targets cancer cells with radiation
● Chemotherapy: chemical therapy used to treat cancer
● Malignant: cancerous tumor that metastasizes
● Benign: form of cancer that produces tumors, but does not metastasize
● Cancer: cell division that is uncontrolled and unregulated
Regulation of the Cell Cycle:
separates the resulting daughter cells
o Cytokinesis in plant cells: cell plate, which then becomes a cell wall that
o Cytokinesis in animal cells: cleavage furrow
7
Meiosis:
-chromosomes condense
● Prophase I: occupies more than 90% of the time required for meiosis
produces somatic cells by mitosis
● Zygote: result of fertilization; diploid cell
o Ex: the union between egg and sperm
● Fertilization: when two haploid gametes contain to form a diploid cell
(can have different alleles however in the same genes)
1
● Homologous chromosomes: chromosomes with the same length, shape, and genes
cells
● Gamete: haploid cells that have already undergone meiosis; also referred to as sex
● somatic cell: diploid cells that undergo mitosis; also referred to as bodily cells
● Genome: all of the cell’s DNA
order
● Karyotype: display of a cell’s chromosomes, with homologues paired up and in
● Diploid: cell containing two set of chromosomes (2n)
● Haploid: cell containing only one set of chromosome (n)
results from meiosis
● Genetic recombination: the resulting regrouping of genes in an offspring that
● Y chromosome: sex chromosome present only in males
● X chromosome: sex xhromosome; occurs twice in females, and once inmales.
o Line up gene by gene
● Synapsis: the pairing of homologous chromosomes
● Gene: unit of DNA that codes for RNA, proteins, and polypeptides
each other
● Crossing over: homologous chromosomes exchange parts of their chromatids with
1.
Instagram
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
AP Biology
Unit 5- Heredity
fertilization between a random egg and random sperm
● Random fertilization: cause of genetic variation; refers to random process of
2
●
●
●
Meiosis 1
new cells(used only in fertilization)
MEIOSIS: results in the reproduction of chromosomes number by half in the 4
-1 nuclear division
-creates 2 diploid cells
-DNA replicated 1 time
-23 pairs of chromosomes in identical daughter cells
-growth and repair of cell organisms
daughter cells IDENTICAL to the parent cell to make somatic cells(2n)
Comparing Mitosis and Meiosis: MITOSIS: results in the production of 2
the parent
Meiosis ends with four gametes each containing half the genetic complement of
○ Cytokines
○ Telophase
○ Anaphase
○ Metaphase
○ prophase
Meiosis11
○ Cytokinesis
○ Telophase
○ Anaphase
○ Metaphase
○ prophase
Cellular division (Meiosis):
●
○ 2n → n
Nuclear division splits the amount of chromosomes in the parent cell into half
●
●
○ Men: happens in tests
● Variation: difference of expressed alleles in gene pool
○ Women: happens in ovaries
● Chiasmata: point of crossover in homologous chromosomes
Purpose
○ Produce gametes for sexual reproduction
●
Meiosis and Genetic Diversity:
● Asexual reproduction: not involving the fusion of gametes.
2.
● Sexual reproduction: the fusion of gametes
-tetrads and chiasmata
-synapse and crossing over
3
●
○ Randomization
○ Crossing Over
Genetic Diversity:
● 1 nuclear division
● creates 2 diploid cells
● Production of sex cells for sexual
● DNA replicated 1 time
● 2 nuclear division
● Creates 4 haploid cells
● DNA replicates 1 time
reproduction
● To make sex cells(n)
new cells(used only in fertilization)
make somatic cells(2n)
● growth and repair of cell organisms
chromosomes number by half in the 4
● results in the reproduction of
Meiosis
cells IDENTICAL to the parent cell to
● results in the production of 2 daughter
Mitosis
-2 nuclear division
-Creates 4 haploid cells
-DNA replicates 1 time
-23 chromosomes in each 4 genetically different daughter cells
-Production of sex cells for sexual reproduction
-To make sex cells(n)
4
3.
Phenotype: An organism's physical appearance
Sex-linked: genes locatd on sec chromsomes
●
●
●
of one gene.
Mendelian traits are traits that are passed down by dominant and recessive alleles
generations of a family.
Pedigree: A diagram that shows the occurrence of a genetic trait in several
trait.
Carrier: A person who has one recessive allele for a trait but does not have the
Genotype: genetic makeup
●
●
Heterozygous: two different alleles for a trait
●
Homozygous: two identical alleles for a trait
Recessive: inferior allele; masked in the presence of a dominant allele
Dominant: dominating allele
Allele: Different forms of a gene
●
●
●
●
●
Mendelian Genetics:
5
4.
●
●
Multiple Alleles: A gene that has more than two alleles
organs
male; THe individual is genetically male, but has female reproductive
A disorder occurs if this gene is deleted from the Y chromosome of a
o Trisomy X Syndrome: female has an extra X, resulting in XXX
▪
pathway in animals.
o SRY gene: Y linked gene that triggers the male sexual development
o turner syndrome: XO
o klinefelter syndrome: XXY
● Disorders that result from GeneAbnormalities
and attached to a different chromosome
o Translocation: a chromosomal fragment is removed from a chromosome
the chromosome
o Inversion: fragment during crossover is moved in a reverse orientation to
o Duplication: portion of a chromosome is duplicated
o Deletion: one or more nucleotides are deleted or lost
● Genetic Mutations
o Polyploidy: cell genome contains an extra chromosome
genes
o Aneuploidy: cell genome is missing a chromosome
chromosomes do not detach from each other
Polygenic Traits: Characteristics that are influenced by more than one pair of
Pleiotropy: The ability of a single gene to have an effect on multiple expressions
●
● Nondisjunction: error that occurs in cell division in which homologous
unit is equivalent to a 1% recombination frequency
7
o Map units: a unit of measurement of the distance between genes. one map
recombination frequency
in the phenotype
Mitochondrial Inheritance: genes passed through the mother’s side
would have been by chance along
Linkage: Occurs when different traits are inherited together more often that they
●
●
● Linkage map: a map of genes on a chromosome depending on the genes’
neither are expressed fully
Incomplete Dominance: where both dominate, differing alleles are blended;
●
inheritance as a pair
● Recombinant: new combination of inherited gene
Epistasis: when a gene also control the expression of other, independent genes
●
6
Codominance: where both dominant, differing alleles are equally expressed in the
●
phenotype
offspring
X Inactivation: Condensation of X chromosomes into Barr bodies
●
● Genes close enough to each other on the chromosome that result in their constant
of those genes during the process of meiosis affects the phenotype of the resulting
Recombination Frequency: average amount of crossovers
● Chromosome theory of inheritance:chromosomes contain genes, and the behavior
Not determined by the simplicity of dominant versus recessive
Chromosomal inheritance:
●
5.
●
Non-Mendelian Genetics:
1.
●
●
●
○ Mutation: changes that occur in a gene’s DNA sequence
○ Stabilizing selection: where extremes are not favored, but rather
wipes out a less favorable trait
Adaptation: characteristic that a species overtime develops as natural selection
with these traits to have a selective advantage
1
Natural selection: where the environment favors certain traits, allowing organisms
organisms
Relative fitness:how likely an organism is to reproduce in comparison to other
intermediates have the selection advantage.
○ Gene Flow: Mixture of genes between populations
of alleles in the gene pool
2
organisms migrate to an uninhabited area, and thus change the proportions
○ Disruptive selection: both extremes of a variation are favored
○ Directional selection: one extreme of a variation is favored
Types of Selection
●
ecosystem
○ Founder's Effect: genetic drift, but in the case where a certain group of
decrease in population; often a result of disaster or disturbance to the
individuals. (Ex: peppered moths due to pollution)
Heterozygote advantage: more chances of reproductive success for heterozygotes
○ Bottleneck Effect: gene pool of a population changes due to the dramatic
Industrial melanism: event where selection favors darker individuals over lighter
from a single ancestral species
○ Adaptive radiation: An evolutionary pattern in which many species evolve
Evolutionary Trends/Changes
in the population, and wipes out individuals with unfavorable traits
○ Survival of the fittest: natural process that leaves the most fit individuals
Competition:
Over-reproduction: too much offspring
pass on to their offspring
Variation of Traits: the varied alleles and traits that parents have and that they
fit individuals survive
Results in a group of organisms that have traits the environment favors; the most
another time, selection favors the other (happens often with changing seasons)
●
●
●
●
●
Natural Selection:
○ Genetic Drift: gene pool of a population changes due to chance
2.
Oscillating selection: where at one time, selection favors one phenotype, and then
trait.
○ Positive frequency dependent selection: selection favors the more common
trait
○ Negative frequency dependent selection:selection favors the less common
common it is in the population
Frequency dependent selection: a phenotype’s fitness is dependent on how
●
●
●
●
Introduction to Natural Selection:
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram
AP Biology
Unit 7 - Natural Selection
3.
●
different directions
○ Adaptive radiation: a single species or a small group of species evolve in
directions, becoming even more distinguishable from each other overtime
3
What is the Hardy Weinberg equation?
genotypic frequency
5. No natural selection: differential survival and reproduction will alter
4. Random mating
3. No net mutations: no changing alleles in another
4
2. No gene flow: no migration or transfer of alleles with other populations
1. No genetic drift: must have very large population
equilibrium is hardly ever achieved in reality. These five factors are
can be NO "outside factors" that affect allele frequencies. But this
○ For a population to be considered in Hardy-Weinberg equilibrium there
sack)
fertilization have no effect on overall gene pool. (ex: Just mixing marbles in a
● Hardy Weinberg Theorem: shuffling of alleles due to meiosis and random
traits, not the individual itself.
favorable trait survive and reproduce. Thus, the species evolves to have favorable
where individuals with less favorable traits die off, while those with a specific
individuals do not evolve. Evolution occurs in a species or group of organisms
● Natural selection occurs between individuals and their environment, but
○ Very different from Darwin’s theory
passed down
Divergent evolution: when species of a common ancestor evolve in different
maintained and will change to become more beneficial. These traits are then
pressures, not a result of evolutionary origin
body parts will shrink and disappear. More utilized body parts will be
○ Use and Disuse (Lamarckism): in a single organism’s lifetime, its less utilized
function and appearance; result of undergoing similar environmental
○ Analogous structures: structures in unrelated species that are similar in
not because of evolutionary origin
● Jean Baptiste Lamarck
descent with modification
Convergent evolution:unrelated, independent organisms in the same environment
evolve similar traits in relation one another, only because of the environment and
○ Divergent species have a common ancestor, from which they evolved due to
GMOs: Genetically modified organisms
●
on variations in their traits
○ The differential survival and reproduction of individuals in a population based
●
Selective Breeding: artificial selection; breeding is done deliberately and
●
● Charles Darwin
Population Genetics:
○ Adaptation was a product of natural selection
Genetic Engineering: intention and direct manipulation traits in DNA
●
4.
selectively to produce desired traits.
Artificial Selection: Selection brought about by humans (ex: breeding)
●
Artificial Selection:
gradualism vs. punctuated equilibrium...how speciation occurs, etc.
q = freq of recessive allele
selection.
are heterozygous advantage e.g. sickle cell anemia AND frequency dependent
maintain stable frequency in the population. Two mechanisms for preserving this
● Balanced polymorphism is when 2 or more phenotypes of the same locus
discrete differences
In contrast to cline, geographic variation between isolated pops often consist of
in different areas. A graded change in a trait along a geographic axis: cline
● Geographic variations are differences in variation between population subgroups
sudden surges in allele frequencies. The drift is a result of this.
populations, it is clear to see how there would be fluctuations in alleles, and then
even more variation hidden behind carrier organisms (heterozygous). IN smaller
align randomly during meiosis create great variations in resulting offspring, and
5
particular location.
6
animal embryo. Prompts structures to develop into structures appropriate for a
○ Hox Genes = class of homeotic genes that provide positional information in
the phenotypic expression
● Homeotic Genes: Genes that control how body parts are organized and placed in
larger, webbed feet
of allometric growth. e.g. salamanders evolved to vertical climbing developed
example of heterochrony = evolution of morphology that arises by modification
● Evolution of morphology that arises by modification of allometric growth is an
and downward sloping brow
transforms rounded skull of newborn chimp into ape skull with ↑ jaw growth
e.g. fetal skulls of human & chimp are similar, but allometric growth
● Allometric Growth: Proportional growth that helps the body get its specific form.
in gene pool.
● Genetic drift is a direct result of independent assortment. The chromosomes that
periods of apparent stasis punctuated by sudden change in species caused by shift
e.g. via mutation.
● Punctuated equilibrium: Pattern of evolutionary change over time; describes
overlap interbreed but end populations are too distantly related to breed
only way to truly increase genetic diversity is by introducing new traits and alleles
diversity as alleles disappear and reappear overtime in smaller populations. The
● Genetic drift cannot increase genetic diversity, but will actually decrease genetic
immediately adjacent to each other e.g. "ring species" in which populations that
● Parapatric speciation is when ranges do not significantly overlap but are
○ Caused often by genetic drift and natural selection
● Sympatric Speciation - speciate even without a physical barrier
to be evolving even if in H-W eq for all other loci
isolated subpopulations?
flow. If one allele at specific locus is changing from gen to gen, then pop is said
disturbed when population is divided into geographically (physical barrier)
Change occurs constantly through mutation, natural selection, genetic drift, gene
● Allopatric Speciation (means "other - homeland") occurs when gene flow is
of gametes and the proper development of viable zygotes.
● Postzygotic barriers = advance past prezygotic barriers; prevents the proper fusion
changes in frequency of allele in the population from generation to generation.
● Microevolution refers to specific changes in gene pool on the small scale e.g.
● heterozygous individuals: 2pq.
● Prezygotic Barriers = factors that prevent mating between organisms
p+q = 1 (1 = 100%)
p = freq of dominant allele = 1 - q
- think of it as "the big picture", which includes patterns of macroevolution i.e.
- evolution above species level; such as appearance of a pelvis in tetrapods
● What does macroevolution refer to?
p² + 2pq + q² = 1
q = recessive
p = dominant
6.
5.
●
●
DNA/RNA, cells with membranes, membrane bound organelles.
Proven by the observation that organisms have similar life processes: glycolysis,
7
demonstrating descent from a common ancestor
● Homologous Structures: Structures that have anatomical similarities
similarities that may be a result of evolutionary relationships
● DNA sequence alignment: A way of arranging the DNA sequences to identify
species
● Cladogram: A diagram showing the cladistic relationship between different
evolutionary history
● Analogous structures: Structures that have the same use but have different
relationships between species
● Phylogenetic tree: A diagram showing the hypothesized evolutionary
organisms
● Phylogenetics: The study of evolutionary relationships between groups of
shared with any other group
● Monophyletic: descended from a common ancestor or ancestral group that is not
Molecular Homology: Comparing DNA molecules or protein sequence between
organisms to show how closely related they are
● Fossils: The remains of a prehistoric organism in stone or amber
developmental stages
Common Ancestry:
●
● Morphology: The study of the forms of living organisms and the relationships
Embryology: scientific branch that compares/studies embryos and various
●
between their structures
● Speciation: The formation of a new, distinct species through evolution
Embryo: a developing, unborn offspring
herbicides, and even chemotherapy drugs that drive that cycle
Evolution is constant in this never-ending cycle, along with that of pesticides,
Proven with genetic changes and changes in fossils overtime
and the patterns that emerge from such analysis
Biogeography: the study of the past and present geological distribution of species
●
of creature. Older fossils are found deeper than more recent fossils.
Continuing Evolution:
Fossil Record: Can show the changes that occurred over time for a specific type
7.
●
●
●
Evidence of Evolution:
8
9.
8.
○ Even if hybrids are vigorous, they may be sterile
○ Reduced hybrid fertility
Extinction: When an entire species dies out
Mass Extinction: Many species going extinct at once
Background Extinction: The "normal" extinction rate
Biodiversity: extinction leaves empty niches that many species are free to
●
●
●
●
9
interact and impair the hybrid's development or survival in its environment
○ Reduced hybrid viability: Genes of the different parent species may
genus
Hybrid: Offspring from an interspecific cross, normally of parents from the same
Extinction:
●
○ Gametic Isolation: sperm and egg cannot fuse due to their incompatibility
○ Mechanical Isolation: reproductive organs are not compatible for mating
species are effective barriers to mating
○ Behavioral Isolation: Courtship rituals and other behaviors unique to a
○ Temporal Isolation: Species that breed at different times
■ Differentiation of niches
■ Not isolated by physical barriers
■ two species occupy different habitats and meet rarely
○ Habitat Isolation
Intrinsic barriers are isolating mechanisms
●
RNA was most likely the first genetic model
Miller-Urey Experiment: Experiment that replicated conditions from early earth
code, DNA, RNA, Protein. 400 genes that code for same proteins
10
All living things have Right-handed spiral DNA (double helix), Universal genetic
Stromatolites: Fossilized mats of cyanobacteria
LUCA: Last Universal Common Ancestor
Sources: www.khanacademy.org
●
●
●
●
●
Origin of Life on Earth:
pass on their genes in the case of a disaster.
Extrinsic Barriers: Physical barriers (mountains, rivers) are isolating mechanisms
event. Variation is like a safeguard that allows for some individual to survive and
the entire population is vulnerable to complete wipeout by a single disastrous
● Essential for survival. If all individuals in a population had the same set of genes,
Variations in Populations:
speciation
11.
10.
Barriers: Mechanisms preventing interbreeding (gene flow) are central to
○ New species occur due to many of the following factors
Speciation: the origin of new species is at the focal point of evolutionary theory
●
●
●
Speciation:
takeover, giving space for biodiversity and speciation