AP Biology Review Notes
Chapters 2-3
Chemistry and Water
Matter – anything that takes up space and has mass
Element - most common C,H,O,N = 96 % of living things
Compound – two or more elements, H2O, NaCl
Trace elements – required by organisms in very small
quantities
Atoms – protons(+ in nucleus), neutrons (neutral in
nucleus), electrons (- in orbital)
Atomic number – number of protons
Mass number – number of protons and neutrons
Isotopes – different number of neutrons – does not change
charge – different mass number
Bonding
Ionic – give and take
Covalent – share
Hydrogen – only between hydrogen and oxygen ,
nitrogen, etc. Weak – attach, detach, attach, detach
Water
Water is POLAR – (Unequal pull of electrons)
Difference in charges.
Hydrogen is positive and oxygen is negative.
Properties of water:
Cohesion – sticky (to itself). Transpiration (water to
water)
Adhesion – Sticky (to other things) like water to
windshield
Surface tension – water striders walk on water
Specific heat – the amount of energy it takes to raise
the temp. 1 degree Celsius. High Specific Heat!
Moderation of temperature
Evaporative cooling – when water evaporates it takes
heat with it (sweat to cool human body)
Insulation of bodies of water by floating ice – ice is
lighter than liquid water.
Important solvent – something else is dissolved in a
solvent
Solution – solvent and solute (what is being dissolved)
3 hydrogen bonds per water molecule
pH – amount of hydrogen ions(H+) and hydroxide ions
(OH-)
neutral is 7 (pure water)
acid – increase of hydrogen ions, less than 7
base – increase of hydroxide, more than 7
buffer – minimizes changes in pH
Chapter 4
Organic chemistry – has CARBON
Carbohydrates
Lipids
Proteins
Nucleic Acids
Carbon can make 4 bonds(single, double or triple bonds).
Has 4 valence electrons
Isomer – same molecular formula – different arrangement
Hydrocarbon – organic molecules consisting of only carbon
and hydrogen
Functional groups
Hydroxyl (alcohol) C-OH carbon attached to
oxygen attached to hydrogen
Carbonyl
C=O
Carbon double bond
oxygen
If the C=O is in the middle of a carbon chain, it is
called a keytone
If the C=O is at the end – it is an aldehyde
Carboxyl – carbonyl and hydroxyl C=O
OH
Amino – nitrogen bonded to two hydrogen NH2
Phosphate – phosphate PO3
Sulfhydryl SH
Chapter 5
Organic Macromolecules
Macromolecules
1- carbohydrates
2- lipids
3- proteins
4- nucleic acids
Polymer – many monomers put together.
Monomer – one unit
Put monomers together through the process of dehydration
synthesis (take water out, make the bond) – AKA
Condensation reactions
Break polymers apart through the process of hydrolysis
(water breaking, add water to break the bond)
Carbohydrates (1C:2H:1O)
4 calories per gram
Extra carbs eaten get turned into fat (long term storage)
Monosaccharide – one sugar (glucose, fructose, galactose)
Ribose (C5H10O5)
glucose C6H12O6
disaccharide – two sugars
maltose – glucose/glucose
sucrose – glucose/fructose
lactose – glucose/galactose
polysaccharide – up to 1,000 monomers
Functions:
1. Energy storage
Starch is storage in plants
Glycogen is storage in animals (muscle, liver)
2. Structural Support
Cellulose – plant cell walls (undigestable to
humans)
Chitin – exoskeletons of arthropods, and in fungi
Lipids (fats, triglycerides, phospholipids, steroids)
Hydrophobic (fear of water)
Animal functions – insulation and buoyancy in marine
and artic animals. PLASMA MEMBRANES
Triglyceride – glycerol and 3 fatty acid chains (long
chains of carbons)
saturated – no double bonds, solid at room temp,
animal fat – lard butter), animals, cardiovascular
disease
unsaturated – has C=C double bonds, plant, fish,
vegi (liquid at room temp) (corn oil, olive oil)
9 calories per gram
Atherosclerosis – fat build up in arteries
Phospholipid
Glycerol and phosphate and two fatty acid chains
Head region is glycerol and phosphate – hydrophilic
(attracted to water) CELL MEMBRANE
Tail region – one saturate and one unsaturated fatty acid
chain. Hydrophobic
Steroid – four fuzed rings. Many hormones – produced
from cholesterol
Functions:
Energy storage – twice as many calories per gram than
carbs
Protection of vital organs. Insulation
Proteins
C with a carboxyl group, amino group, hydrogen atom and
an R group
Used for structure, signaling, defense
4 calories per gram
50% of cell
Amino acids are the monomers
Amino acid – amino group and carboxyl group. 20
different side chains. (R group)
Dipeptide – two amino acids formed by dehydration
synthesis
Peptide bond – between two amino acids
Polypeptide – many a.a’s
Shape –
Primary – sequence of amino acids
Secondary – interaction of hydrogen bonds, alpha
helix or beta pleated sheet
Teriary – interaction between the secondary structure.
(globular – three dimensional)
Quarternary – two or more polypeptide chains. Multisubunit protein – Examples: hemoglobin, DNA
polymerase, collagen
Denaturation – pH, Salt Concentration, Temp, toxic
compounds
Nucleic Acids
DNA – Deoxyribonucleic acid
RNA – ribonucleic acid
Nucleotide
Nitrogenous base (adenine, thymine, cytosine,
quinine, and uracil)
Pentose sugar (deoxyribose, or ribose)
Phosphate group
DNA
Heredity
Double stranded
RNA
Single stranded
Chapter 6 Cells
Things to know for today:
The differences between prokaryotic and eukaryotic
cells.
The structure and function of organelles found in both
plants and animals.
The structure and function of organelles found in
either plant or animal cells only.
Cytology – study of cells.
Cytoplasm – inside portion of the cell
Cytosol – fluid within cell
Prokaryotes vs. Eukaryotes
Domains Bacteria and Archaea are prokaryotic.
The other domain, Eukarya, which includes kingdoms:
animals, fungi, plants, and protists – are eukaryotic
Prokaryotes: considered first form of life
1. Chromosomes are grouped together in a region
called the nucleoid, but there is no nuclear
membrane. There is no true nucleus.
2. No membrane-bounded organelles are found in
the cytosol. (free Ribosomes are found)
3. Eukaryotic cells are 10-100 times larger than
prokaryotic cells
4. Has a cell wall external to plasma membrane.
Does not contain phospholipids or
transmembrane proteins.
5. Has a capsule – lies outside of cell wall (carb.)
Eukaryotic cells:
1. Have a Nucleus! Chromosomes are found in a
membrane called the nucleus.
2. Many membrane-bound organelles are found in
the cytoplasm.
3. On average, eukaryotes are much larger than
prokaryotes.
Both Animal and Plant Cells
1. Plasma membrane –
Forms the boundary for a cell
Selectively permeable (lets certain things in and
out of the cell)
Made up of phospholipids, proteins and
carbohydrates.
2. Nucleus –
Contains DNA
Larger size – noticeable
Double membrane
Contains pores that control what does in and out
Continuous with Rough ER
Chromatin – complex of DNA and protein in the
nucleus. Chromatin condenses into chromosomes
(during prophase of mitosis/meiosis)
Nucleolus – region in nucleus where ribosomal
RNA is formed.
3. Ribosomes –
Sites of protein synthesis
Have large and small subunits
If “free” floating – proteins made are intended for
inside the cell.
If “bound” (attached to rough endoplasmic
reticulum) proteins made will export the cell or be
used in the cell membrane.
4. Endoplasmic Reticulum (ER)
More than half the total membrane structure in
many cells.
Network of membranes and sacs whose internal
area is called the cisternal space.
Smooth ER (no ribosomes) - synthesis of lipids,
metabolism of carbohydrates, and detoxification of
drugs and poisons.
Rough ER (has ribosomes – appears “rough”) –
proteins are secreted out (leave cell). Proteins go to
Golgi by way of transport vesicles.
5. Golgi Apparatus - like the postal system.
Proteins from the transport vesicles are modified,
store, and shipped.
Consists of flattened sacs of membranes, again
called cisternae, arranged in stacks. Golgi stacks have
polarity –the cis face receives vesicles, whereas the
trans face ships vesicles.
6. Mitochondria - (powerhouse)
Site of cellular respiration (ATP is created)
Enclosed by a double membrane - the inner membrane
has in folds called cristae.
7. Peroxisomes –
single-membrane-bound compartments
transfer hydrogen from compounds to oxygen,
producing hydrogen peroxide (H2O2). Detoxifies
alcohol
Break down fatty acids that get sent to mitochondria
for fuel
8. Cytoskeleton –
Network of protein fibers that run throughout the
cytoplasm.
Provides support, motility, and regulating some
biochemical activities.
Three types of cytoskeleton fibers:
a. Microtubules:
made of the protein tubulin
largest of cytoskeleton fibers
shape and support the cell
serve as tracks along which organelles equipped with
motor molecules can move
separate chromosomes during mitosis and meiosis
(forming the spindle)
structural components of cilia and flagella (found
primarily in animal cells.)
b. Microfilaments:
composed of the protein actin
Much smaller than microtubules
function in smaller scale support
When coupled with the motor molecule myosin,
microfilaments can be involved with movement.
(amoeboid movement, muscle cells)
c. Intermediate filaments:
Slightly larger than microfilaments and smaller than
microtubules.
more permanent fixtures in the cell
important in maintaining the shape of the cell and
fixing the position of certain organelles.
9. Centrosomes –
Region located near the nucleus, from which
microtubules grow (the area is also called the
microtubule organizing center.)
Centrosomes contain centrioles in animal cells.
Animal Cells Only:
Lysosomes –
Membrane-bound sacs of hydrolytic enzymes.
Digests large molecules
Organic monomers are released into the cytosol
(recycled).
Acidic environment for enzymes to work.
If breaks – enzymes can’t work (not acidic enough)
Centrioles
In centrosome, replicate before cell division
cilia and flagella “9+2 pattern”
ultrastructure – nine pairs of microtubules surrounding
a core of two microtubules.
Flagella
microtubule – long and few in number.
Sperm in animals, algae and some plants, unicellular
eukaryotic organisms use for movement
Cilia
Microtubule – shorter and more numerous than
flagella
Move fluid over the surface of the tissue (trachea)
Movement
Extracellular matrix (ECM)
External to plasma membrane
Made of glycoproteins (collagen)
Strengthens tissues and transmits external stimuli in
Intercellular junctions
Tight junctions
Two neighboring cells are fused.
Desmosomes
Fasten adjacent animal cells together
Gap junctions
Provide channels between adjacent animal cells
(ions, sugars and other small molecules can pass).
Plant Cells (bacteria and protists, too)
Central Vacuole
Membrane-bound organelle
Storage and breakdown of wastes
Can take up to 80% of plant cell
Chloroplast
Found in plant and algae cells
Sites of photosynthesis
Cell Wall
Protects
Maintains shape
Cellulose is main component
Plasmodesmata
Channels between adjacent plant cells
Allow for passage of some molecules
Chapter 7
Cell Membranes: Structure and Function
To know:
Why membranes are selectively permeable.
Know the role of phospholipids, proteins, and
carbohydrates in membranes.
How water will move if a cell is placed in an isotonic,
hypertonic, or hypotonic solution.
How electrochemical gradients are formed.
Fluid Mosaic Model
Membrane is selectively permeable (some substances
can cross, others cannot). Membranes are not static.
Phospholipids move laterally but rarely “flip-flop.”
Cholesterol in the membranes makes the membrane less
fluid.
Figure 7.5
Three main components:
Phospholipids: hydrophobic/hydrophilic qualities
(amphipathic) make the membrane selectively permeable.
Hydrophilic molecules cannot enter easily. They need to
pass through the barrier at a transport protein.
Hydrophobic molecules can enter more easily. Nonpolar
molecules (hydrocarbons, carbon dioxide and oxygen) are
hydrophobic.
Proteins: (functions for transport, enzymatic activity,
signal transduction and cell communication).
Figure 7.9
Integral proteins – proteins that are completely
embedded in the membrane. Protein will have hydrophobic
and hydrophilic regions.
Peripheral proteins – proteins that are bound to
the membrane’s surface.
Carbohydrates: useful for cell-to-cell recognition and
in tissue differentiation. (Blood typing)
Aquaporins – transport protein that moves water
across membrane. 3 billion water molecules per protein,
per second.
Passive Transport
Passive transport: Diffusion of a substance across a
membrane with no energy investment.
Substances move from where it is more concentrated to
where it is less concentrated. Diffuse DOWN the
concentration gradient.
Osmosis – movement of water across a selectively
permeable membrane. Movement from hypotonic to
hypertonic solution.
Figure 7.12
Isotonic solution – no net movement of water across the
plasma membrane. Water will move but in equal amounts
both ways. Plant cells will be flaccid in isotonic solutions.
Hypertonic solution – cell will lose water to its
surroundings. Hyper means more. The solution has more
solutes in the water around the cell than inside the cell.
The cell will shrivel and may die. Plasmolyzed cells are
plant cells that lose water.
Hypotonic solution – water will enter the cell faster than it
leaves. Hypo refers to less solutes in solution than in cell.
The cell will swell and may burst. Plant cells will be
turgid, which is normal for plan cells
Figure 7.13
Lab #1 – Diffusion and Osmosis
Facilitated Diffusion – gets polar molecules and ions across
a membrane. Facilitated diffusion uses a channel, or
binding to move substances across a membrane.
Figure 7.15
Active Transport
Active transport uses energy to move solutes against their
gradients.
Movement from where a molecule is less concentration to
the side where they are more concentrated.
Requires energy – usually ATP
Sodium-Potassium Pump – example of active transport
Figure 7.16
Figure 7.17
Co-Transport – an ATP pump that transports a specific
solute, indirectly drives the active transport of other
substances.
Figure 7.19
Bulk Transport
Large molecules are moved across the cell membrane
through exocytosis and endocytosis.
Exocytosis – vesicles from inside the cell fuse with the cell
membrane and are expelled out.
Endocytosis – cell takes in macromolecules
Phagocytosis – “cellular eating” occurs when the cell
engulfs (reaches out and grabs) particles and brings it into
the cell.
Pinocytosis – “cellular drinking” occurs when the
plasma membrane moves in toward the inside taking with it
particles.
Receptor-mediated endocytosis – is a specific process
that the cell uses to bring in specific molecules. Substances
(called ligands) bind to receptors on the surface of the cell
and once bound, a vesicle will form to bring it inside.
Figure 7.20
Chapter 8 - Metabolism
Metabolism
Metabolism – total chemical reactions in an organism.
Catabolic pathway – release of energy by the breakdown of
complex molecules to simpler ones. (break down food
during digestion)
Anabolic pathway – consume energy to build complex
molecules from simpler ones (physical exercise builds
muscles).
Energy – capacity to do work
Kinetic energy – energy of motion
Potential energy – energy as a result of its position or
structure.
Chemical energy – form of potential energy – energy of
molecular bonds.
Thermodynamics (energy transformation)
1st law – energy can be transferred and transformed
but it cannot be created or destroyed.
2nd law – every energy transfer increases entropy
(amount of disorder or randomness in the universe).
Free-energy
Free energy is the part of a system’s energy that is able to
do work.
Exergonic reaction – energy is released
Endergonic reaction – requires energy to happen
Figure 8.6
ATP powers cellular work
Energy coupling – the use of an exergonic process to drive
an endergonic one.
ATP
adenosine triphosphate.
Made up of: nitrogenous base, adenine; ribose and three
phosphate groups.
When the phosphate group is hydrolyzed – energy is
released.
ADP – adenosine diphosphate results with the release of
the phosphate group (exergonic reaction) to power
endergonic work.
Enzymes
Catalysts are substances that can change the rate of a
reaction without being altered in the process.
Enzymes are macromolecules that are biological catalysts.
Most enzymes are proteins.
Figure 8.15
Activation energy is the amount of energy it takes to start a
reaction.
Enzymes speed up reactions by lowering the activation
energy.
Active site is the part of the enzyme that binds to the
substrate.
Products are converted from the substrate.
Enzymes have three dimensional shapes that can be
affected by changes in pH and temperature.
Figure 8.17
Lab #2 – Enzyme Lab
Many enzymes require cofactors to function properly.
Cofactors include zinc, iron, and copper. If a co-factor is
organic it is called a coenzyme. Vitamins are coenzymes.
Competitive inhibitors are reversible inhibitors that
compete with the substrate for the active site on the
enzyme.
Noncompetitive inhibitors impede enzyme activity by
binding to another part of the enzyme. This causes the
enzyme to change its shape and will make the active site
nonfunctional.
Figure 8.19
toothpickase
Regulation of enzymes
Allosteric site – place on an enzyme other than the active
site.
Allosteric site binding can either speed up or slow down.
Feedback inhibition exists when the end product of an
enzymatic pathway will switch off its pathway by binding
to the allosteric site of the enzyme.
Figure 8.22
Chapter 9 - Cellular Respiration
Catabolic Pathways
Fermentation – partial degradation of sugars that occurs
without the use of oxygen
Cellular respiration or aerobic respiration – break down of
sugars in the presence of oxygen.
Sugar + Oxygen makes Carbon Dioxide + water
ATP
+
C6H12O6 + 6O2 makes
ATP
+
6CO2
+
6H2O
The exergonic release of energy from glucose is used to
phosphorylate ADP to ATP.
Cellular respiration is considered an oxidation-reduction
reaction or (redox).
Oxidation – loss of one or more electrons from a
reactant.
Reduction – gain of one or more electrons.
Figure 9.2
Figure 9.6
Glycolysis
Occurs in the cytosol
Break down glucose to form 2 pyruvate molecules
6 carbon glucose – changes into 2, 3 carbon pyruvate.
ATP is consumed (2 ATP used)
4 ATP are formed – (only Net 2 ATP)
2 NADH’s are produced (used in electron transport)
Water is formed.
Figure 9.8
Transition Step
Pyruvate moves into the mitochondria matrix (all the way
inside – very center) (uses a transport protein)
One carbon comes of each pyruvate (in the form of CO2)
1 NADH is created for each pyruvate (2 total).
A Coenzyme is attached to create acetyl CoA (has two
carbons).
Figure 9.10
Citric acid cycle
Receives two acetyl CoA molecules per glucose.
Add one acetyl CoA per cycle.
Per cycle you get 2CO2, 3NADH, 1FADH2 and 1 ATP –
so double that because you have two acetyl CoA.
By the end of the citric acid cycle – all of the carbons in
glucose have been released as CO2 (which you exhale).
Glucose is gone and only 4 ATP’s have been formed.
Energy is in electron carriers, NADH and FADH2.
Figure 9.12
Oxidative phosphorylation, electron
transport chain and chemiosmosis.
Location: inner membrane of the mitochondria.
Three trans membrane proteins that pump hydrogen out of
the matrix.
There are two carrier molecules that transport electrons
between hydrogen pumps.
There are thousands of electron transport chains in the
inner mitochondrial membrane.
Electrons are donated by the electron carriers (NADH and
FADH2) they travel down the membrane (chain) giving
off energy that the proteins use to pump protons (H+)
across the membrane (hyperconcentrating it).
Oxygen is the final electron acceptor to form water.
When oxygen is not available no hydrogen ions are
pumped and no ATP is produced.
The hydrogen ions flow back down their gradient through a
channel in the transmembrane protein known as ATP
synthase. (Chemiosmosis)
ATP synthase harnesses the proton motive force to
combine (phosphorylate) ADP to form ATP.
Oxidative phosphorylation is the term used because oxygen
is necessary to work and because ADP is phosphorylated.
Oxidative phosphorylation produces 32 to 34 ATP per
glucose to give a grand total in cellular respiration of 36-38
ATP.
Figure 9.16
Figure 9.17
Fermentation
Anaerobic condition – no oxygen.
Glycolysis only!
NAD+ is necessary to keep process going.
Alcohol fermentation – pyruvate is converted to ethanol to
create more NAD+.
Lactic acid fermentation – pyruvate is reduced, NAD+ is
formed and lactate is formed as a waste product.
Facultative anaerobes – organisms that can make ATP by
aerobic respiration if oxygen is present but that can switch
to fermentation under anaerobic conditions.
Figure 9.18