AP Biology Exam Review Part I: Biochemistry, Cells and Transport
2A3: Organisms must exchange matter with the environment to grow, reproduce, and maintain organization.
2B1: Cell Membranes are selectively permeable due to their structures.
2B2: Growth and dynamic homeostasis are maintained by the constant movement of molecules across membranes.
2B3: Eukaryotic cells maintain internal membranes that partition the cell into specialized regions.
4A1: The subcomponents of biological molecules and their sequence determine the properties of that molecule.
4A3: The structure and function of subcellular components, and their interactions, provide essential cellular processes.
4C1: Variation in molecular units provides cells with a wider range of function.
A.
Chemistry of Life
CHNOPS- most common elements in all living matter
1.
2.
Bonds- ionic (transfer electrons), covalent (sharing- polar/unequal sharing and non-polar/equal
sharing), hydrogen (weak bonds between hydrogen and negatively charged items), hydrophobic
interactions (how non-polar compounds congregate together- lipids)
3.
pH
a.
b.
c.
4.
acid-base/ 0-14, # of H ions determines scale; logarithmic- pH 3 = 10-3 = 1/1000
blood- 7.4, stomach- 2, small intestine- 8; enzymes are specific to pH
buffers such as bicarbonate handle slight pH swing
Water properties- polarity, cohesion(attraction to other water molecules), adhesion (attraction
to other charged compounds) low density when frozen, versatile solvent, high heat of
fusion/vaporization; surface tension
5. Organic molecules (monomers are simplest form of all; monomers join together via
dehydration synthesis- loss of water- to make polymers; polymers are broken down via
hydrolysis- input of water.)
a. Carbohydrates- CHO 1:2:1 ratio, monomer= monosaccharides, 2=disaccharides, 3 or more=
polysaccharides
b. Used for energy (cell respiration)
c. Examples
(1) glucose- immediate energy to make ATP
(2) starch- stored energy in plants
(3) glycogen- stored energy in animals (stored in liver)
(4) cellulose- plant cell wall
d. Lipids – C, H, O (not a 1:2:1 ratio) *P only in phospholipids
(1) fats, waxes, oils and sterols
(2) Saturated fats have single bonds between carbons, unsaturated fats have at least one
double bond between carbons (kinky); plants make polyunsaturated; animals make
monounsaturated
(3) Phospholipids make up cell membranes (double layer) and are amphipathic- hydrophilic
and hydrophobic
(4) uses- in all membranes, sex hormones, & corticoids; stored energy, protection,
insulation, myelin sheath of nerves
e. Proteins- C, H, O, N (may have other elements in R group)
(1) Monomer- amino acids (20 total types), 2=dipeptide, 3 or more= polypeptide
(2) Parts of amino acid= carboxyl group (COOH) on one end, amino group on the other end
(NH2), central carbon and variable R group (can be hydrophobic or hydrophilic) which
determines chemical properties.
(3) Protein Folding- shape determines function; primary= a.a. chain; secondary= beta
pleated sheet or alpha helix( hydrogen bonds); tertiary=globular; folds in on itself
(disulfide bridges, hydrogen bonds, hydrophobic interactions; ionic bonding);
quartenary= more than one polypeptide.
(4) Uses- protein carriers in cell membrane, antibodies, hemoglobin, enzymes, most
hormones, muscle (actin and myosin)
f. Nucleic acids(1) Monomer= nucleotide, 2 = dinucleotide, 2 or more polynucleotide
(2) Nucleotide made up of sugar, phosphate and base
(3) Used to store genetic information
(4) DNA is double stranded, has deoxyribose, A, G, C, T
(5) RNA is single stranded, has ribose, A, G, C, U
(6) mRNA- copies genetic message; rRNA- attaches mRNA and makes up ribosomes (most
common);tRNA- carries amino acids;DNA- carries genetic code
B. Cells
1. Prokaryotic (Bacteria)
Eukaryotic (all other living things)
no membrane-bound organelles
m.b.o, ex. Chloroplasts and nucleus
no nucleus(single; circular DNA)
multiple linear DNA
free ribosomes and cell wall
histones on DNA
2. Cell organelles
a. Nucleus- holds DNA and nucleolus(where ribosomal subunits are made)
b. Mitochondria- double membrane; outer is smooth and inside is folded with enzymes to
make ATP (site of cellular respiration (glucose breakdown)
c. Ribosome- site of translation- protein synthesis; made of rRNA and protein
d. E.R.- connected to nucleus; allows for reactions, membranous; smooth= lipids;
rough=proteins
e. Golgi complex- packaging in membrane and signals for export
f. Cytoskeleton: Microfilaments- contractile protein, gives shape, movement within cell;
Microtubules- centrioles, cilia, flagella, spindle fibers
g. vacuoles/vesicles- water and solutes; large and central in plants
h. ANIMAL
 Lysosomes- contain enzymes; used for intracellular digestion and apoptosis
 Centrioles- used in cell division
 Peroxisomes- contain enzymes to break down H2O2

Extra Cellular Matrix (ECM)- collection of proteins and glycoproteins on outside of
cell membrane; MHC
i.
PLANT
 Chloroplast- double membrane; site of photosynthesis (glucose synthesis)
 Cell wall- middle lamella- pectin; primary cell wall- cellulose; secondary cell walllignin
j. Cell junctions- plasmodesmata (between plant cells); gap junctions (between animal cells);
tight junctions (stitched animal cells); anchoring junctions (riveted together animals cells)
k. Endosymbiont theory- all eukaryotic cells came from bacterial cells that lived together;
proof= all chloroplasts and mitochondria have own DNA and are autonomous
3. Cell membrane (separates the internal environment of cell from external environment).
a. Phospholipid bilayer (selectively permeable; amphipathic)
b. Fluid mosaic model (in motion; proteins, cholesterol, glycoproteins and glycolipids among
phospholipids). Membrane is hydrophilic on inside and outside, hydrophobic within
membrane
c. Simple diffusion- from high to low concentration- small and uncharged move freely through
phospholipids ex. CO2, O2 (passive; no energy;no protein carrier)
d. Facilitated diffusion- large or charged from high to low, passive; with protein carrier: ex.
glucose, K+,
e. Active transport- from low to high concentration; uses ATP; uses a protein
f. Endocytosis- phagocytosis (solid) and pinocytosis (liquid); membrane surrounds and forms
vesicles; receptor mediated endocytosis has receptors on surface
g. Exocytosis- release of material using vesicles fusing with membrane
h. Osmosis- diffusion of water using a selectively permeable membrane; passive; no proteins
i. Water potential= pressure potential plus pressure potential; water moves from high water
potential to low water potential; solutes always lower water potential; pressure can
increase or decrease depending on if it is negative or positive.
j. Plant cells have pressure related to cell wall and vacuole; turgor pressure
k. Hypertonic (high solute), hypotonic (low solute), and isotonic solutions(equal
concentration)
l. Plasmolysis (plant cells; membrane pull away from cell wall); crenation (animal cell shrivels)
--------------------------------------------------------------------------------------------------------------------------------------AP Investigation 4: Diffusion and Osmosis
Part I- Diffusion in Agar Cubes
Overview: Various size cubes of phenolphthalein agar were placed in NaOH and then diffusion rates were
calculated.
IV- Size of cube
DV- percent diffusion
Equations: Volume = L x W x H, volume diffused = total volume – volume not pink, % diffusion = Volume
diffused /total volume x 100, surface area of a cube = L x W x # of sides, surface area/volume ratio.
Part II- Osmosis in Living Cells (Potatoes)
Overview: Potato cylinders placed in sucrose (sugar) solutions and massed before and after to get percent
change in mass.
Determined by graphing percent changes in mass
versus molarity of solution
IV- Sucrose solutions (varying molarities)
DV- percent change in mass
Equations:
,
Part III- Design Your Own Experiment (Dialysis Bags)
Overview: Students were provided with dialysis bags, colored sucrose solutions of unknown molarities, and
basic lab equipment to use to design an experiment on how to determine the molarities of the colored
solutions.
IV- unknown molarities
DV- for most groups it was percent change in mass
Equations: (final mass-initial mass)/ initial mass
-------------------------------------------------------------------------------------------------------------------------------------------------Biochemistry:
amino acid
amphipathic
carbohydrate
carbon
denaturation
disaccharide
ester bond
fibrous protein
globular protein
glycosydic bond
hydrogen bond
ion
lipid
macromolecule
monomer
monosaccharide
nitrogen
non-polar molecule
nucleic acid
nucleotide
organic molecule
peptide bond
phospholipid
polar molecule
polymer
protein
water
Cells:
active transport
amphipathic
apoptosis
aquaporin
carrier protein
cell wall
centrioles
channel protein
chloroplast
concentration gradient
cytoplasm
cytoskeleton
diffusion
electron microscope
endocytosis
endoplasmic reticulum
glycolipid
glycoprotein
Golgi apparatus
hypertonic
hypotonic
ion pump
isotonic
ligand
light microscope
lysosome
magnification
membrane
mitochondrion
nuclear envelope
nuclear pore
phospholipid
pinocytosis
plasma membrane
plasmolysis
prokaryotic cell
resolution
ribosome
rough ER
selectively permeable
smooth ER
exocytosis
eukaryotic cell
facilitated diffusion
flagella
fluid mosaic model
nucleus
organelles
osmosis
passive transport
phagocytosis
surface area:volume ratio
transmembrane protein
turgor
vacuole
-------------------------------------------------------------------------------------------------------------------------------------------------Questions and Practice
1. How do the unique chemical and physical properties of water make life on earth possible?
2. What is the role of carbon in the diversity of life?
3. How do cells synthesize and breakdown macromolecules?
4. How do structures of biological molecules account for their function (carbs, proteins, lipids, DNA)?
5. What are the similarities and differences between prokaryotic and eukaryotic cells?
6. What the evolutionary relationships between prokaryotic and eukaryotic cells?
7. How does compartmentalization organize a cell’s functions?
8. How are the structures of the various subcellular organelles related to their functions?
9. How do organelles function together in cellular processes?
10. What is the current model of molecular architecture of membranes?
11. How do variations in this structure account for functional differences among membranes?
12. How does the structure of membranes provide for transport and recognition?
13. What are various mechanisms by which substances can cross the membrane?
14. In osmosis and diffusion lab, how was osmosis measured in both living and artificial?
15. What was the IV in the dialysis bag part of the lab? DV? Control? Controlled variables?
16. What was the IV in the potato part of the lab? DV? Control? Controlled variables?
17. Draw concept map showing the connections between the following terms: Atom, Compound,
Carbohydrate, Lipid, Protein, Nucleic Acid, Organelles, Nucleus, Mitochondria, Cell membrane, Golgi
Apparatus, ER, prokaryotic cell, eukaryotic cell
AP Biology Review Part 2: Energy Conversions & Enzymes and Cell Cycle and Cell Communication
2A1: All living system require constant input of free energy.
2A2: Organisms capture free energy and store free energy for use in biological processes.
3A2: In eukaryotes, heritable information is passed to the next generation via processes that include the cell cycle and mitosis or
meiosis plus fertilization.
3B2: A variety of intercellular and intracellular signal transmissions mediate gene expression.
3D1: Cell communication processes share common features that reflect a shared evolutionary history.
3D2: Cells communicate with each other through direct contact with other cells or from a distance via chemical signaling.
3D3: Signal transduction pathways link signal reception with cellular response.
3D4: Changes in signal transduction pathways can alter cellular response.
4B1: Interactions between molecules affect their structure and function
6.
a.
b.
c.
d.
7.
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
Energy
Organisms use free energy for organization, growth and reproduction. Loss of order or free energy flow
results in death.
More free energy (ex. Food) than needed will be stored for growth (roots, glycogen, fat, etc.).
Matter and energy are not created but change form (1st law of thermo; ex. Sun energy to bond energy
in glucose) and entropy is increasing in disorganization of energy (i.e. heat released by cell respiration).
More organized or built up compounds have more free energy and less entropy (i.e. glucose) and less
organized have less free energy and more entropy (i.e. carbon dioxide).
Reactions can be coupled to maintain a system, ex. Photosynthesis and cell respiration
Enzymes
Biological catalysts (made of protein) that speed up rate of chemical reactions by lowering activation
energy required for reaction to occur
Enzyme has active site (exposed R groups) where reaction occurs
Enzymes can break down substance (catabolic reaction) or build up substances (anabolic)
Enzyme/substrate complex is formed
Substrate is what enzyme acts on
Rate is determined by collisions between substrate and enzyme
Ends in –ase, named after substrate often
Enzyme is specific to substrate; the substrate must be complementary to the surface properties (shape
and charge) of the active site (which is made up of R groups with specific chemistry, i.e. hydrophobic).
Enzyme rate is affected by:

pH (optimal for each enzyme),

temperature (optimal for each enzyme but in general increased temp means increased
collisions so rate goes up initially; too much heat can denature enzyme), enzyme concentration
(more enzyme faster rate or vice versa)

substrate concentration (more substrate faster rate; vmax is fastest enzyme can work when
saturated)
Inhibition-competitive inhibition (something competes for active site; can be overcome with more
substrate)
Non-competitive inhibition- attaches at allosteric site and changes shape of enzyme so it is not
functional; can not be overcome with more substrate
Coenzymes (organic; NAD and vitamin B etc.) and cofactors (inorganic; zinc, magnesium etc.) interact
with enzymes to put them into the right structure to do work.
8.
Energy Transformations
ATP- adenosine triphosphate- energy molecule for cells (recyclable)
A. Photosynthesis 6CO2 + 6H2O C6H12O6 + 6O2
Photosynthetic organisms capture free energy present in sunlight and use water and carbon dioxide to make
carbon products and free oxygen.
Light-dependent reactions- photophosphorylation
(1)
Photosystems I and II (chlorophyll and proteins) are embedded in the internal membranes of
chloroplasts (thylakoids of the grana). They pass electrons through an electron transport chain (ETC).
When electrons are passed they allow hydrogen ions (protons) across the thykaloid membrane. The
formation of the proton gradient powers the process of ATP synthesis to add a phosphate ADP to ATP
(chemiosmosis).
(2)
Electrons are passed to NADP+ to make NADPH (electron carrier)
(3)
H2O is used and O2 released as by-product
(4)
Red and blue light works best (green is reflected typically)
(5)
Pigments= chlorophyll a and b; accessory pigments
(6)
Energy converted from sun into chemical energy of ATP and NADPH to be used in building of sugar
(Calvin Cycle)
Light-independent reactions- Calvin Cycle
(1)
carbon fixation occurs
(2)
occurs in stroma of chloroplasts
(3)
ATP and NADPH are used; rubisco is enzyme that fixes carbon (not picky and will fix O 2 toophotorespiration; “the ho”)
Evolution of Photosynthesis
(1)
Photosynthesis first evolved in prokaryotic organisms; (bacterial) photosynthesis was responsible for
the production of an oxygenated atmosphere
(2)
C4 photosynthesis- crabgrass, corn, drought resistance, uses new enzyme- PEP carboxylase which is
specific for just CO2 and CAM- Crassulacean Acid metabolism used in dry climates, ex. Cacti stomates
are closed during day and open at night
B. Cellular respiration C6H12O6 + 6O26CO2 + 6H2O
Makes ATP for cell use; uses glucose and oxygen makes waste products of carbon dioxide and water; occurs in
mitochondria; NADH is electron carrier used
Glycolysis
(1)
occurs in cytoplasm; anaerobic
(2)
rearranges the bonds in glucose molecules, releasing free energy to form ATP from ADP resulting in the
production of pyruvate.
Kreb’s cycle
(1)
occurs in mitochondrial matrix
(2)
also called the citric acid cycle
(3)
occurs twice (one for each acetyl co-a)
(4)
Pyruvate is oxidized further and carbon dioxide is released ; ATP is synthesized from ADP and inorganic
phosphate via substrate level phosphorylation and electrons are captured by coenzymes (NAD+ and
FAD).
(5)
(6)
NADH and FADH2 carry them to the electron transport chain.
The electron transport chain captures in a process similar to light dependent reactions to make ATP.
At end 38 ATP made per glucose molecule- could be 36 if it cost ATP to get in mitochondria; some of
the energy in bonds is lost as heat (not completely efficient but since it occurs in several reactions with
enzymes it is more efficient than one combustion)
Anaerobic Fermentation
(1)
No oxygen; cell only goes through glycolysis followed by fermentation
(2)
Fermentation recycles NAD needed to restart glycolysis
(3)
alcohol fermentation ex. yeast cells- glucose  ethyl alcohol + CO2+ NAD
(4)
lactic acid fermentation ex. muscle cells- glucose  lactic acid + NAD
(5)
Fermentation does not make ATP but glycolysis does- 2ATP; very inefficient; sufficient for
microorganisms
9.
a.
b.
c.
d.
e.
f.
g.
h.
i.
j.
k.
l.
m.
o.
10.
a.
b.
Cell cycle
Reason for division- as cells increase in volume, the surface area decreases and demand for material
resources increases which limits cell size
Smaller cells have a more favorable surface area-to-volume ratio for exchange of materials with the
environment (diffusion, etc.). High SA:V ratio is favorable. Ex. 6:1 is better than 6:5
Cell cycle switches between interphase and cell division.
Interphase has three phases: growth (G1), synthesis of DNA (S) and preparation for mitosis (G2).
During mitosis duplicated chromosomes line up in center with spindle fibers attached to help pull them
apart. Duplicated chromosomes are pulled apart by spindle fibers.
Cytokinesis-division of cytoplasm and reformation of cell membrane. Animal cell- pinches in (cleavage)
using microfilaments; plant cell- form cell plate reforms cell wall (golgi deposits material).
The cell cycle is directed by internal controls or checkpoints. Internal (enzymes and promoting factors)
and external signals (growth factors) provide stop and- go signs at the checkpoints. Ex. Mitosispromoting factor (MPF); Platelet-derived growth factor (PDGF); p53 gene products
Cancer results from disruptions in cell cycle control (too much division, defective tumor suppressor
genes, overactive genes) which are a result of DNA damage to proto-oncogenes (regulatory
genes)which make products like cyclins and cyclin-dependent kinases.
Cells spend different amounts of time in interphase or division. Nondividing cells may exit the cell
cycle; or hold at a particular stage in the cell cycle.
Mitosis is used for growth and repair in animals; plants use mitosis to make gametes and for growth or
repair.
Mitosis usually begins with 1 cell, makes 2 identical cells or clones; maintains chromosome number;
1n1n or 2n2n.
Meiosis (occurs after interphase) takes diploid cells and reduces the chromosome number to haploid.
2n1n.
During meiosis, homologous chromosomes are paired (one from mom and one from dad) and line up
in the center of the cell randomly. The homologues are pulled apart and separated in meiosis I. A
second division occurs in which the duplicated chromosomes are pulled apart.
Variation occurs in gametes during “crossing over,” and fertilization because of all possible
combinations.
Cell to Cell Communication
Cells receive or send inhibitory or stimulatory signals from other cells, organisms or the environment.
In single-celled organisms it is response to its environment. Ex. quorum sensing,
d.
e.
f.
g.
h.
i.
j.
k.
In multicellular organisms, signal transduction pathways coordinate the activities within individual
cells. Ex. Epinephrine stimulation of glycogen breakdown in mammals
Cells communicate by cell-to-cell contact. Ex Immune cells interact by cell-cell contact, antigenpresenting cells (APCs), helper T-cells and killer T cells or plasmodesmata between plant cells that allow
material to be transported from cell to cell.
Cells communicate over short distances by using local regulators that target cells in the vicinity of the
emitting cell. Ex. Neurotransmitters, plant immune response
Signals released by one cell type can travel long distances to target cells of another cell type. Ex.
Hormones.
A receptor protein recognizes signal molecules, causing the receptor protein’s shape to change,
which initiates transduction of the signal. Ex. G-protein linked receptors, ligand-gated ion channels,
tyrosine kinase receptors.
Signal transduction is the process by which a signal is converted to a cellular response. Signaling
cascades relay signals from receptors to cell targets, often amplifying the incoming signals, with the
result of appropriate responses by the cell.
Second messengers are often essential to the function of the cascade. Ex. cyclic AMP calcium ions
(Ca2+), and inositol triphosphate (IP3)
Many signal transduction pathways include: Protein modifications or phosphorylation cascades in
which a series of protein kinases add a phosphate group to the next protein in the cascade sequence.
------------------------------------------------------------------------------------------------------------------------------------------------AP Lab Investigation 5 Photosynthesis
Overview: Spinach cut out disks were placed in two different syringes (bicarbonate and without) and those
photosynthetic rate was calculated by measuring the number that floated over time. Students
then designed their own experiment to see what factors affected photosynthesis.
IV: presence of bicarbonate
DV: number of disks floating
Equations: ET50 = the point at which 50% of the leaf disks are floating (the median or ET 50, the Estimated Time
it takes 50% of the disks to float), inverse relationship between rate and ET50 so we graphed 1/ET50 in this lab.
AP Lab Investigation 6 Cell Respiration
Overview: Germinating and non-germinating seeds (peas) were placed in different temperature water baths
and cell respiration rate was determined based on oxygen consumption. Design your own experiment to
determine what other factors affect cell respiration (type of seed, age of seed, etc.)
IV: germinating or non-germinating and temperature
DV: O2 consumption
*volume was controlled with glass beads, CO2 gas was controlled with KOH, temperature was controlled with
water bath
Equations: dY/dt or product formed (dY) over time interval (dt)
AP Lab Investigation 7 Cell Cycle
Part I: Mitosis
Overview: Two treatment groups of plant root tips were compared, one group was treated with lectin
(increases cell division) and the other was a control group that had not been treated with lectin (we used cards
for these). Chi-square analysis was used to determine if there was a significant difference between the two
groups.
IV: Lectin
DV: Rate of Division
Equations:
, x2 value is compared to chart under .05 probability and correct degrees of
freedom (number of groups -1). Numbers at critical value or above reject null hypothesis.
Part II: Meiosis
Overview: Spores of a fungus were evaluated for crossing over and cross over rates were calculated. Also
karyotypes were evaluated for cancer and genetic diseases as a result of cross over mistakes.
Equations: # of crossover/total number of spores = % cross over, % cross over /2 = map units
AP Lab Investigation 13 Enzymes
Overview: Rate of decomposition (breakdown) of hydrogen peroxide by the enzyme peroxidase was measured
by measuring the amount of O2 gas produced in the reaction. An indicator called guaiacol was used to detect
oxygen by changing a darker color which was measured by a colorimeter (measures transmittance of light
through a sample). Designing your own experiment to determine what other factors affect enzyme reaction
(light, temperature, pH or concentrations).
IV: Time
DV: color change (indicates oxygen production)
Equations: rate dY/dt (change in transmittance of light over change in time)
------------------------------------------------------------------------------------------------------------------------------------------------Cell Division:
anaphase
cancer
cell cycle
cellular differentiation
cell division
centrioles
chromosome
crossing over
crossover frequency
cyclin-dependent kinase
cytokinesis
differentiation
diploid (2N)
DNA replication
fertilization
gamete
haploid (1N)
homologous chromosomes
independent assortment
interphase
maternal chromosome
meiosis
metaphase
mitosis
nuclear division
p53
paternal chromosome
potency
prophase
recombination
sex chromosome
somatic cell
specialized cell
synapsis
telophase
Communication
communication
cyclic AMP (cAMP)
G-protein linked receptor
phosphorylation cascade
protein kinase
quorum sensing
receptor
second messenger
signal cascade
signal transduction
signal transduction pathway
Cell Energy
absorption spectrum
accessory pigment
acetyl coA
action spectrum
activation energy
active site
anabolism
anaerobic metabolism
allosteric regulation
ATP
autotroph
Calvin cycle
catabolism
catalyst
cellular respiration
chemiosmosis
chemoautotroph
chlorophyll
chloroplast
citric acid cycle
coenzyme
cofactor
compartmentalization
consumer
cyclic electron flow
denaturation
electron transport chain
entropy
endergonic reaction
enzyme
exergonic reaction
feedback inhibition
fermentation
glycolysis
heterotroph
induced fit model
light dependent reactions
light independent reactions
metabolic pathway
mitochondrion
NAD
NADP
negative feedback
non-cyclic electron flow
oxidative phosphorylation
photolysis
photosynthesis
positive feedback
ribulose bisphosphate
substrate-level phosphorylation
thylakoid membrane
Questions and Practice
18. How do the laws of thermodynamics relate to the biochemical processes that provide energy to living systems?
19. How do enzymes regulate the rate of chemical reactions?
20. How does the specificity of an enzyme depend on its structure?
21. How is the activity of an enzyme regulated?
22. How does the cell cycle assure genetic continuity?
23. How does mitosis allow for the even distribution of genetic information to new cells?
24. What are the mechanisms of cytokinesis?
25. How is the cell cycle regulated?
26. How can aberrations in the cell cycle lead to tumor formation?
27. Why is meiosis important in heredity?
28. How is meiosis related to gametogenesis?
29. What are the similarities and differences between gametogenesis in animals and plants?
30. What is the role of ATP in coupling the cell’s anabolic and catabolic processes?
31. How does chemiosmosis function in bioenergetics?
32. How are organic molecules broken down by catabolic pathways?
33. What is the role of oxygen in energy-yielding pathways?
34. How do cells generate ATP in the absence of oxygen?
35. How does photosynthesis convert light energy into chemical energy?
36. How are the chemical products of the light-trapping reactions coupled to the synthesis of carbohydrates?
37. What kinds of photosynthetic adaptations have evolved in response to different environmental conditions?
38. What interactions exist between photosynthesis and cellular respiration?
39. How was photosynthetic rate measured in the photosynthesis lab?
40. What was the IV in the photosynthesis lab? DV? Control? Controlled variables?
41. How was respiration rate measured in respiration lab?
42. What was the IV in the lab? DV? Control? Controlled variables?
43. Make a concept map to relate the following terms: high free energy, low free energy, entropy,
enzymes, photosynthesis, light dependent reaction, light independent reaction, cell respiration,
glycolysis, krebs, etc, and fermentation.
44. Make a concept map to relate the following terms: cell cycle, interphase, growth, dna replication,
mitosis, meiosis, homologous chromosomes, separation of chromosomes, cancer, checkpoints,
regulatory proteins.
45. Make a concept map to relate the following terms: unicellular, multicellular, local regulators, long
distance regulation, contact, receptor, signal transduction, enzyme cascade, response
AP Biology Review Part 3: Genetics & DNA and Protein Synthesis
3A1- DNA, and in some cases RNA, is the primary source of heritable information
3A3: The chromosomal basis of inheritance provides an understanding of the pattern of passage (transmission) of genes from
parents to offspring.
3A4: The inheritance pattern of many traits cannot be explained by simple Mendelian genetics.
3C1: Changes in genotype can result in changes in phenotype.
1.
A.
1.
2.
3.
DNA (genetic info is passed down through DNA and RNA)
Discovery
Avery-MacLeod- Marty- 1944 isolated DNA from Griffith’s transformation experiment
Hershey-Chase- 1952 elegant experiment with virus and bacteria showing DNA was injected not protein
Watson, Crick, Wilkins, and Franklin- 1953 W and C published work showing structure of DNA (used
Wilkins and Franklins work to do so)
B.
1.
2.
3.
4.
Structure of DNA
Deoxyribose nucleic acid
Double helix (two twisted stsrands) made of nucleotides (monomers)
Nucleotide = phosphate + 5C deoxyribose sugar + nitrogen base
Antiparallel strands- one runs 3’ to 5’ the other runs 5’ to 3’,sides of phosphates and sugars (backbone),
rungs of paired bases with hydrogen bonds in between
Purines (adenine,guanine; double rings) pair with Pyrimidines (cytosine, uracil, thymine; single ring)
A - T- double H bond
C – G- triple H bond
a.
b.
c.
C.
1.
2.
3.
2.
a.
b.
c.
Location
In eukaryotes DNA is found in nucleus on multiple linear chromosomes (a chromosome IS a strand of
DNA with proteins etc. associated).
In prokaryotes DNA is not in a nucleus and is usually a single circular chromosome
Prokaryotes, viruses, and eukaryotes (yeast) can contain plasmids (small extra-chromosomal DNA that is
double stranded DNA)
DNA replication
Process of making exact copies of DNA (i.e. for mitosis or meiosis)
Process is semi conservative (original strand is copied)
Steps
1. Enzyme (helicase) unzip strands by breaking hydrogen bonds
2. “Spare” nucleotides are added bidirectionally to bond complementarily with use of DNA
polymerases (DNA pol)
3. DNA pol only can add to the 3’ to 5’ side and new DNA is made in the 5’ to 3’direction
4. Replication bubbles open up and a replication fork is created because bubble is in half and it
has one side 3/5 and one 5/3
5. RNA primers must be laid down to start process (RNA primase makes primers)
6. Leading strand makes DNA continuously (3/5)
7. Lagging strand makes DNA discontinuously (5/3), Okazaki fragments
8. Lagging strand requires enzyme (ligase) to fuse fragments
3.
a.
b.
c.
d.
e.
f.
g.
RNA
Ribonucleic acid
Single stranded, different sugar called ribose, different base called uracil INSTEAD of thymine
Base pair rules in RNA, A-U and C-G
messenger RNA or mRNA carries information from DNA to the ribosome
transfer RNA or tRNA bind amino acids and are used in translation at ribosome
ribosomal RNA or rRNA are part of ribosomes that have catalytic function
RNAi are molucules that are used for regulation of gene expression (turn on or off)
4.
a.
b.
c.
d.
e.
f.
g.
h.
Transcription
making mRNA in nucleus
enzyme RNA pol reads the DNA in 3’ to 5’ direction and synthesizes complementary mRNA
Ex. 3’ to 5’ DNA is ATG CAT then the 5’ to 3’ mRNA made will be UAC GUA
Steps
TATA Box where RNA pol binds and begins
Transcription Factors (proteins that enhance transcription and help RNA pol into correct shape)
Elongation (adding of RNA nucleotides- does not stay attached to DNA)
Termination, ends when RNA pol reaches a termination sequence
5.
a.
b.
c.
d.
e.
f.
mRNA editing
introns are excised (cut out)
exons are left and spliced together using spliceosomes (snRNP’s)
add polyA tail to 3’
add GTP cap to 5’
each 3 are called a codon
go to ribosome (free or in RER)
6.
a.
Translation
mRNA code is read and matched with tRNA (brings amino acids) to construct a polypeptide using the
ribosome
Ex. mRNA codon is AAA then tRNA anticodon will be UUU and will have a corresponding amino acid for
that codon of mRNA
Initiation: 5’ end of mRNA attaches to small ribosome, tRNA with anticodon UAC attaches to start
codon AUG ; large ribosomal subunit binds and tRNA is in P site
Elongation: new tRNA enters A site; peptide bond forms when a.a. is transferred from tRNA in P site to
A site; translocation occurs and tRNA in A site moves to P
Termination: Ribosome encounters stop codon (UAA, UAG, UGA)
If in ER then: polypeptide is released into ER, then to Golgi complex, vesicle to cell membrane, then
exocytosis (may be given signals for exit/destination)
Free ribosomes typically make products for the cell and are not exported
b.
c.
d.
e.
f.
g.
7.
a.
b.
c.
d.
e.
Mutations
any change of DNA sequence, can be inheritable if it is in egg or sperm
point mutations- one nucleotide error; substitutions (i.e. A instead of G)
frame shift mutations- one or more bases deleted or inserted
silent mutations can occur, i.e. substitution codes for same a.a. or deletion/insertion is of three
nucleotides
Missense mutation- means that new letter codes for a new amino acid, i.e. sickle cell; can be extensive
with frameshift mutations
f.
8.
A.
B.
Nonsense mutation- means that a stop codon is coded for too early and results in short polypeptide
1. Single gene mutations in humans caused by DNA mutations
a. PKU- recessive; phenylketonuria, enzyme deficiency
b. Sickle cell- recessive; primarily of African descent, carriers resistant to malaria
c. Cystic fibrosis- recessive; primarily of European descent, protein in channel misshaped; thick
mucus
d. Huntington’s- dominant; nervous disorder at age 40 or so; fatal
Heredity
Mendel’s Laws (remember he laid groundwork for genetics but these rules can all be broken looking at
chromosome theory and molecular genetics)
1. Law of Dominance- one allele will be expressed over another (ex. Aa – if big A is purple it will be seen
over little a which is white)
2. Law of Segregation- alleles pairs separate from each other during meiosis
3. Law of Independent Assortment- alleles assort independently during meiosis IF they are on separate
chromosomes (i.e. AaBb can make gametes AB, Ab, aB or ab)
4. Terms to know
5. dominant
6. recessive
7. genotype
8. phenotype
9. allele
10. homozygous
11. heterozygous
12. testcross
Probability,Patterns and Exceptions to Mendel’s Rules
1. product rule- multiply chance of one event happening by the chance of another event happening to get
the chance of both events occurring together
2. Inheritance patterns
3. autosomal vs. sex-linked (on the X or Y chromosome)
4. monohybrid cross; one trait; 3:1 (Aa x Aa); 1:1 (Aa x aa) or 4:1 (AA x_), (aa x aa)
5. dihybrid cross; 9:3:3:1 genotype (AaBb x AaBb) or test cross 1:1:1:1(AaBb x aabb)
6. Thomas Hunt Morgan- fruit flies, X- linked traits
a. male- heterozygous XY; Y chromosome is very small in mammals and fruit flies with few genes
b. female- homozygous XX
c. not for all living things sometime sex is determined by haploid/diploid or temperature or it is
reversed in birds, moths, butterflies (XX is boy)
d. single gene mutations on X chromosome cause disease such as hemophilia or colorblindness
e. sex limited traits are dependent on sex of individual like milk production or male patterned
baldness
7. incomplete dominance- red X white  pink; both protein product are expressed and blended
8. codominance- red x white  red and white; both protein products are equally expressed ex.AB blood
types
9. multiple alleles- blood types- ABO
10. epistasis- one gene affects expression of another
11. linked genes- genes on same chromosome that are inherited together (can be unlinked by crossing
over); recombination frequency calculated by recombinants/total; used for chromosome mapping;
genes further apart cross over more often
12. gene/environment- phenotypes affect by environment, Siamese cat, flower color with soil pH, seasonal
color in arctic animals, human height and weight
13. polygenic- continuous variation, many genes affect one trait- height, color
14. Chloroplasts and mitochondria (come from egg in mammals)are randomly assorted in cell division so
they do not follow Mendelian rules.
C.
Human Genetics
1. karyotype- 22 pair autosomes & 1 pair sex chromosomes + 46 total chromosomes
2. Chromosomal Mutations (occur during gamete formation- usually denovo)
2. deletion, inversion, addition of genes as a result of crossing over mistakes, ex. Prader Willi
3. chromosomal number abnormalities
a. nondisjunction- failure of chromosomes to separate at anaphase of meiosis
b. monosomy- 45 chromosomes- Turner’s- XO
c. trisomy- Down’s- trisomy 21; Kleinfelters- XXY
4. amniocentesis- for prenatal diagnosis
-------------------------------------------------------------------------------------------------------------------------------------------------Fruit Fly Lab (Not an AP Investigation)
Overview: Three crosses were performed by different groups (one trait, two trait and sexlinked) by allowing F1
fruit flies to mate and then counting F2 generation. Chi Square analysis was used to determine if offspring
were as expected.
IV: Fruit flies
DV: Traits in Offspring
Equations: See Chi-Square Analysis
Laws of Probability
If A and B are mutually exclusive, then P (A or B) = P(A) + P(B)
If A and B are independent, then P (A and B) = P(A) x P(B)
-------------------------------------------------------------------------------------------------------------------------------------------------DNA
amino acids
genetic code
Okazaki fragments
anticodon
helicase
protein
base-pairing rules
hydrogen bonding
replication fork
cell differentiation
inducible genes
repressor
coding strand
introns
RNA (mRNA, rRNA, tRNA
codon
lagging strand
RNAi
DNA
leading strand
start codon/stop codon
DNA ligase
micro RNA (miRNA)
template strand
DNA polymerase
mutation
transcription
DNA replication
nucleic acids
transcription factors
exons
nucleotides
translation
Genetics
allele
heterozygous
Punnett square
autosome
homozygous
pure-breeding (aka
back cross
incomplete dominance
true-breeding)
cline
independent assortment
recessive
codominance
lethal allele
segregation
continuous variation
linkage
selfing
cross
monohybrid cross
sex chromosome
dihybrid cross
multiple alleles
sex-limited traits
discontinuous variation
non-disjunction
sex linked gene
dominant
non-nuclear inheritance
test cross
F1/F2 Generation
pedigree analyisis
trait
genetic counseling
phenotype
genomic imprinting
phenotypic plasticity
genotype
polygenetic inheritance
--------------------------------------------------------------------------------------------------------------------------------------Questions and Practice
1.
How is genetic information organized in the eukaryotic chromosome?
2.
How does this organization contribute to both continuity of and variability in the genetic information?
3.
How did Mendel’s work lay the foundation of modern genetics?
4.
What are the principal patterns of inheritance?
5.
How do the structures of nucleic acids relate to their functions of information storage and protein
synthesis?
6.
What are the similarities and differences between prokaryotic and eukaryotic genomes?
7.
What is one way genetic information can be altered?
8.
What problems can it cause?
9.
What are the differences and similarities between protein synthesis in prokaryotes and eukaryotes?
10.
Draw a picture to show the relationship between chromosome, DNA, gene, allele, nucleotide, base, and
a trait.