REVIEW : BIOCHEMISTRY
A. Top “10” — If you learned anything from this unit, you should have learned:
1. All living matter made up of CHONPS
2. Bonds
a. covalent bonds are strong
b. hydrogen bonds are weak
c. polar molecules vs. non-polar molecules
d. reaction with water (cytoplasm & extracellular solution) vs. cell membrane
3. Reactions of life
a. dehydration synthesis
• releases water
• synthesis: builds covalent bonds
• anabolic, endergonic
b. hydrolysis
• uses water
• digestion: break covalent bonds
• catabolic, exergonic
4. Water
a. polar molecule leads to special properties
• cohesion, adhesion, high specific heat, less dense as solid
5. Macromolecules
a. carbohydrates
• sugar monomer
• energy, structure (cell wall, chitin)
b. lipids
• phospholipids (cell membrane)
• energy storage
• steroid hormones
c. proteins (amino acids)
• amino acid monomer
• 4 levels of structure
• bonding at each level: covalent, H bonds, hydrophobic interactions, van der Waals
forces, ionic bonds, disulfide bridges
• many functions!: enzymes, structure, regulatory molecules
d. nucleic acids
• nucleotide monomers
• information storage
6. Enzyme function
a. proteins & RNA
b. bind to substrate
c. speed rate of reactions: reduce activation energy
d. induced fit (lock & key)
e. affected by temperature, pH, salinity, concentration of substrate & enzyme
B. Labs
1. Enzyme Catalysis
Be sure to review the procedures and the conclusions, and understand:
a. Factors that affect enzyme function
b. How to set up a similar experiment
c. Controls vs. Experimental
REVIEW : CELLS & CELL DIVISION
A. Top “10” — If you learned anything from this unit, you should have learned:
1. Prokaryotes vs. eukaryotes
 No internal membranes vs. membrane-bound organelles
2. Cell structures & the functions they perform
a. Controlling internal environment
 cell membrane, membrane proteins & cell receptors
 movement across membrane: diffusion, facilitated diffusion, osmosis, active transport
 hypertonic, hypotonic, isotonic solutions
b. Protein production
 nucleus & DNA
 ribosomes
 ER & vesicles
 Golgi apparatus & vesicles
c. Energy production
 mitochondria, chloroplasts
d. Cell reproduction
 nucleus & DNA
 centrioles & spindle fibers
e. Digestion
 lysosomes & vesicle, vacuoles
f. Cell connections
 connecting junctions: plasmodesmata & gap junctions
3. Cell division
a. Cell cycle
 interphase; mitosis: prophase, metaphase, anaphase, telophase; cytokinesis
 G0, G1, S, G2
b. Produces genetically identical clones
c. Replication
 DNA polymerase (I & III), leading strand, lagging strand, helicase, single-stranded binding proteins,
ligase, primase, RNA primer, Okazaki fragments, telomeres
d. Regulation
 G1/S & G2/M checkpoints, cdKs, cyclins, growth factors
 cancers are caused by loss of cell cycle control
 p53, proto-oncogenes, tumor suppressor genes
B. Labs
1. Diffusion & Osmosis
Be sure to review the procedures and the conclusions, and understand:
a. Factors that affect movement of water across a membrane
b. How water & solutes will move across a membrane under different osmotic conditions
c. How to measure osmotic concentration of an unknown tissue or solution using solutions of known
concentrations
2. Cell Division
Be sure to review the procedures and the conclusions, and understand:
a. Replication
b. How chromosomes are distributed during mitosis
c. The products of mitosis
C. Sample Free Response Questions
1. The following experiment was designed to test whether different concentration gradients affect the rate of
diffusion. In this experiment, four solutions (0% NaCl, 1% NaCl, 5% NaCl, and 10% NaCl) were tested under
identical conditions. Fifteen milliliters (mL) of 0% NaCl were
put into a bag formed of dialysis tubing that is permeable to Na+,
Cl–, and water. The same was done for each NaCl solution. Each
bag was submerged in a separate beaker containing 300 mL of
distilled water. The concentration of NaCl in mg/L in the water
outside the bag was measured at 40-second intervals. The results
from the 5% bag are shown in the table
2. Membranes are essential components of all cells.
a. Identify THREE macromolecules that are components of the plasma membrane in a eukaryotic cell and
discuss the structure and function of each.
b. Explain how membranes participate in THREE of the following biological processes.
 muscle contraction
 fertilization of an egg
 chemiosmotic production of ATP
 intercellular signaling
3. A major distinction between prokaryotes and eukaryotes is the presence of membrane bound organelles in
eukaryotes.
a. Describe the structure and function of TWO eukaryotic membrane-bound organelles other than the nucleus.
b. Prokaryotic and eukaryotic cells have some non-membrane-bound components in common. Describe the
function of TWO of the following and discuss how each differs in prokaryotes and eukaryotes.
 DNA
 cell wall
 ribosomes
c. Explain the endosymbiotic theory of the origin of eukaryotic cell and discuss an example
of evidence supporting this theory.
REVIEW: METABOLISM — RESPIRATION & PHOTOSYNTHESIS
A. Top “10” — If you learned anything from this unit, you should have learned:
1. Energy production through chemiosmosis
a. pumping of H+ ions onto one side of a membrane through protein pumps in an Electron Transport Chain
(ETC)
b. flow of H+ ions across a membrane down the concentration gradient through ATP synthase
2. Coupled reactions get the work done
a. oxidation & reduction
b. ETC & pumping of H+ (protons)
3. Respiration
a. mitochondria
 ETC in inner membrane: cristae increase surface area
 H+ ion concentrated in intermembrane space & flows into matrix through ATP synthase
 oxidative phosphorylation: O2 final electron acceptor + NAH/FADH to donate electron
 Kreb’s cycle produces electron carriers: NADH, FADH
 high ATP production (~36 ATP)
b. anaerobic: glycolysis, fermentation
 low ATP production (~2 ATP)
4. Photosynthesis
a. chloroplasts
 H+ ion concentration in inner thylakoid space & flows out into stroma
 photophosphorylation: light energy + splitting of water to donate electron
 light dependent reactions: Photosystem II (produces ATP) & Photosystem I (produces NADPH)
b. Calvin cycle
 light independent reaction
 carbon fixation through RuBisCo enzyme
 use ATP & NADPH from light reactions to produce of 3C sugars
B. Labs
1. Respiration
Be sure to review the procedures and the conclusions, and understand:
a. Factors that affect rate of respiration
b. How to set up a similar experiment
 What was being measured?
 How was generated CO2 dealt with
c. Controls vs. Experimental
2. Photosynthesis: Floating Disk Lab
Be sure to review the procedures and the conclusions, and understand:
Controls vs. Experimental
C. Sample Free Response Questions
1. The rate of photosynthesis may vary with changes that occur in environmental temperature, wavelength of
light, and light intensity. Using a photosynthetic organism of your choice, choose only ONE of the three
variables (temperature, wavelength of light, or light intensity) and for this variable
 design a scientific experiment to determine the effect of the variable on the rate of
 photosynthesis for the organism;
 explain how you would measure the rate of photosynthesis in your experiment;
 describe the results you would expect. Explain why you would expect these results.
2. Yeast cells are placed in an apparatus with a solution of sugar (a major nutrient for yeast metabolism). The
apparatus detects bubbles of gas released by the yeast cells. The rate of respiration varies with the surrounding
temperatures as indicated by the data
a. Graph the results on the axes provided.
Determine the optimum temperature for
respiration in the yeast.
b. Respiration is a series of enzymecatalyzed reactions. Using your knowledge of enzymes and the data above, analyze and explain the results of
this experiment.
c. Design an experiment to test the effect of varying the pH of the sugar solution on the rate of respiration.
Include a prediction of the expected results.
REVIEW: HEREDITY & MOLECULAR GENETICS
A. Top “10” — If you learned anything from this unit, you should have learned:
1. Meiosis produces haploid gametes
a. Meiosis 1 separates homologous pairs: reduction division
• crossing over in Prophase 1
b. Meiosis 2 separates sister chromatids: produces 4 sex cells
2. Different versions of same gene are called alleles
a. dominant vs. recessive
b. homozygous vs. heterozygous
c. phenotype vs. genotype
3. Mendelian inheritance
a. monohybrid crosses
• Aa x Aa = 3:1 ratio
• Law of Segregation
b. dihybrid crosses
• AaBb x AaBb = 9:3:3:1 ratio
• Law of Independent Assortment
c. test cross
• determine genotype of individual showing dominant phenotype
• unknown (A_) x aa (homozygous recessive)
4. Non-Mendelian inheritance
a. incomplete dominance (pink flower color), co-dominance (blood type), sex linked (mainly X-linked: color
blindness, hemophilia),
5. Chi-square analysis
a. determining if observed results are significantly different from expected results
b. know how to use formula when given & how to interpret results
• degrees freedom (1 less than number of classes of results)
• less than p=.05, then difference can be due to random chance alone & null hypothesis is accepted
6. DNA & RNA
a. DNA: ACTG nitrogen bases, double helix
• A : T, C : G
 DNA Organization: chromatin, histone proteins, euchromatin, heterochromatin
b. RNA: ACUG nitrogen bases, single helix
7. Central Dogma
a. DNA to RNA to protein to trait (one way)
b. transcription (DNA to mRNA)
• in nucleus
• RNA polymerase copies coding strand & produces mRNA
• RNA processing
• introns, exons, 5’ cap, poly-A tail
c. translation (mRNA to protein)
• in cytoplasm
• codons on mRNA read by ribosome
• matched to anticodons of tRNA
• tRNA carries amino acids to mRNA & ribosome assembles polypeptide chain
• initiation, elongation, termination
• start codon (Met) & stop codons, redundancy in code
• universal code (single common ancestor)
8. Viruses
• bacteriophages, capsid, envelope, retroviruses, reverse transcriptase
9. Bacteria
• plasmids, conjugation, transduction, transformation
• regulation of gene expression: operons
• regulatory gene, repressor protein, promoter, operator, structural gene
10. Regulation of genes
a. operons
• prokaryotes
• cluster of genes for enzymes in a pathway
• controlled by repressor protein
• repressible operon (synthesis pathway = tryp operon) vs. inducible operon (digestive pathway = lac
operon)
• inducible enzyme: lac operon, when lactose present binds to repressor & induces
it to release DNA, catabolic pathway
• repressible enzyme: tryp operon, when tryptophan (corepressor) present binds to
repressor & triggers it to bind to DNA, anabolic pathway
b. transcription factors
• proteins which enable bonding of RNA polymerase to gene
11.. Mutations
a. fuel for evolution = variation, genetic change
b. gene duplication, point mutation, insertions, deletion
12. Biotechnology
a. Scientists can modify an organism’s genome by inserting foreign DNA
• bacterial transformation (human insulin gene in E. coli)
• possible because of universal genetic code
b. Techniques
• restriction digest: restriction enzymes, sticky ends
• transformation: restriction enzymes, sticky ends, ligase, amp selection, lacZ screening
• gel electrophoresis: DNA moves in an electrical field (negative to positive), small pieces move further
• RFLP: DNA fingerprinting
B. Labs
1. Genetics of Organisms (Fly Lab)
Be sure to review the procedures and the conclusions, and understand:
a. How to determine genotype of individuals through crosses
b. How to calculate Chi square values
2. Bacterial Transformation & Restriction Analysis
Be sure to review the procedures and the conclusions, and understand:
a. How to set up a similar experiment
b. How to interpret transformation results on LB vs. LB+amp plates
c. How to interpret gel electrophoresis results in restriction analysis
d. Controls vs. Experimental
Practice Questions:
1. In the pedigree, squares represent males and circles
represent females. Individuals who express a particular trait
are represented by shaded figures. Which of the following
patterns of inheritance best explains the transmission of the
trait?
a. Sex-linked dominant
b. Sex-linked recessive
c. Autosomal recessive
d. Autosomal dominant
e. Incompletely dominant
2. These two questions refer to the birth of a child with blood type A to a mother with blood type B.
A. The father must have which of the following blood types?
a. AB only
b. Either AB or B
c. Either AB or O
d. Either AB or A
e. AB or A or O
B. If the father has blood type AB, which of the following statements is correct about the mother?
a. She contributes an IB allele, which is recessive to the father’s IA allele.
b. She contributes an i allele, which is recessive to the father’s IA allele.
c. She contributes an IB allele, which is codominant to the father’s IA allele.
d. She contributes an i allele, which is codominant to the father’s IB allele.
e. She is homozygous for the IB allele.
C. Sample Free Response Questions
1. The unit of genetic organization in all living organisms is the chromosome.
a. Describe the structure and function of the parts of a eukaryotic chromosome. You may wish to include a
diagram as part of your description.
b. Describe the adaptive (evolutionary) significance of organizing genes into chromosomes.
c. How does the function and structure of the chromosome differ in prokaryotes?
2. Meiosis reduces chromosome number and rearranges genetic information.
a. Explain how the reduction and rearrangement are accomplished in meiosis .
b. Several human disorders occur as a result of defects in the meiotic process. Identify ONE such chromosomal
abnormality; what effects does it have on the phenotype of people with that disorder? Describe how this
abnormality could result from a defect in meiosis.
3. A difference between prokaryotes and eukaryotes is seen in the organization of their genetic material
a. Discuss the organization of the genetic material in prokaryotes and eukaryotes.
b. Contrast the following activities in prokaryotes and eukaryotes:
• replication of DNA
• transcription
• gene regulation
• cell division
4. The human genome illustrates both continuity and change.
a. Describe the essential features of two of the procedures/techniques below. For each of the
procedures/techniques you describe, explain how its application contributes to understanding genetics.
• the use of a bacterial plasmid to clone and sequence a human gene
• polymerase chain reaction (PCR)
• restriction fragment length polymorphism (RFLP) analysis
5. In fruit flies, the phenotype for eye color is determined by a certain locus. E indicates the dominant allele and
e indicates the recessive allele. The cross between a male wild-type fruit fly and a female white-eyed fruit fly
produced the following offspring.
a. Determine the genotypes of the original parents (P generation) and explain your reasoning. You may use
Punnett squares to enhance your description, but the results from the Punnett squares must be discussed in
your answer.
b. Use a Chi-squared test on the F2 generation data to analyze your prediction of the parental genotypes. Show
all your work and explain the importance of your final answer.
c. The brown-eyed female in the F1 generation resulted from a mutational change. Explain what a mutation is,
and discuss two types of mutations that might have produced the brown-eyed female in the F1 generation.
REVIEW: EVOLUTION
A. Top “10” — If you learned anything from this unit, you should have learned:
1. Darwin’s Principle of Natural Selection
a. Variation: individuals within a population possess heritable variation within traits
• sexual recombination
• mutation
b. Overproduction: organisms produce more offspring than can survive
c. Competition: those individuals with advantageous adaptations will out-compete others
d. Survival & Reproduction of the Fittest: individuals with favorable characteristics tend to have more
offspring & pass on these traits to their offspring
• alleles for favorable traits increase in the population
• individuals are selected, but populations evolve
2. Selection
a. directional vs. stabilizing vs. disruptive
b. sexual selection
c. genetic drift = effect of chance events
• bottleneck effect (cheetahs)
• founder’s effect (European settlers in Americas)
d. gene flow
3. Evidence
a. fossil record
b. biogeography
• convergent evolution (analogous structures)
c. comparative anatomy
• homologous structures
• vestigial structures
d. comparative embryology
e. comparative genomics (molecular biology)
• universal genetic code
• conserved proteins (hemoglobin, cytochrome C)
f. artificial selection
• agriculture, dog breeding, pesticide resistance, antibiotic resistance
4. Hardy Weinberg equilibrium
a. p + q =1 (allele frequency)
b. p2 + 2pq + q2 =1 (phenotype frequency)
c. H-W conditions:
• infinitely large population
• random mating
• no mutation
• no gene flow (migration in or out)
• no selection
d. 5 fingers of Evolution
5. Speciation
a. biological species concept (Ernst Mayr)
• population able to interbreed & produce viable, fertile offspring
• adaptive radiation (Galapagos finches)
• mechanisms:
 pre-zygotic: habitat factors, temporal factors, behavioral factors, mechanical factors, gamete
factors
 post-zygotic: reduced hybrid viability, reduced hybrid fertility
6. Origin of Life
a. Earth is 4.5 billion years old
b. abiotic origin
• atmosphere of CO2, methane (CH3) & ammonia (NH3) energized by lightning & UV rays
• formation organic compounds in seas (Miller – Urey experiment)
• formation of protobionts & then bacteria (3.5 bya)
B. Labs
1. Hardy-Weinberg Population Genetics Lab
Be sure to review the procedures and the conclusions, and understand:
a. Factors that affect evolution (changes in allele frequency) in populations
b. How & when to use both H-W formulas
c. Compare expected frequencies to actual to test for evolution
C. Sample Free Response Questions
1. Charles Darwin proposed that evolution by natural selection was the basis for the differences
that he saw in similar organisms as he traveled and collected specimens in South America and
on the Galapagos Islands.
a. Explain the theory of evolution by natural selection as presented by Darwin.
b. Each of the following relates to an aspect of evolution by natural selection. Explain three
of the following.
 Natural selection and the formation of insecticide-resistant insects or antibiotic resistant
 bacteria
 Speciation and isolation
 Natural selection and heterozygote advantage
REVIEW: ECOLOGY
A. Top “10” — If you learned anything from this unit, you should have learned:
1. Populations
 group of individuals of same species living in same area (size, density, distribution/dispersion)
 habitat (type of area organism lives) vs. niche (role in ecosystem)
 competition
a. survivorship curves
 Type 1 = most live long life = K-selected = humans, large mammals
 Type 2 = constant death rate = hydra, small mammals
Type 3 = most die young = r-selected opportunists = fish, shellfish
b. age structure (rapid growth vs. declining vs. stable populations)
c. population growth
 limiting factors
– density dependent (competition for resources, parasites & diseases, waste
 products, stress, predation)
– density independent (climate = temperature & rainfall, natural disaster)
 exponential growth (J-shaped, unlimited) vs. logistic growth curve (S-shaped, limited)
 carrying capacity = maximum population supported by habitat
 population cycles
d. human population growth
 exponential = habitat expansion, increase in food supply, advances in medicine, waste treatment
reduces hazard
2. Communities
 interaction of populations
 interspecific competition
 competitive exclusion principle
 no two species can occupy same niche; one outcompetes the other and the second is eliminated
(Paramecium, barnacles)

resource partitioning
– species seemingly coexist in same area, but actually occupying slightly different niches (arboreal
lizards)
 keystone species
– important regulating effect on community, maintains diversity (sea otters & orcas)
b. symbiosis = species interaction
 mutualism +/+ (acacia tree & ants; lichens, N-fixing bacteria & legume plants)
 commensalism +/0 (egrets & cattle)
 parasitism +/– (tapeworm, cowbird) = parasite vs. parasitoid
 predation +/– (carnivores & herbivores)
 competition –/– (interspecific vs. intraspecific)
c. coevolution
 defense mechanisms
– camouflage (cryptic coloration)
– warning coloration (aposematic coloration)
– mimicry
d. ecological succession
 predictable change in composition of species in community over time
 pioneer species (lichens, grasses = opportunistic r-selected) → shrubs (stable Kselected)→ small trees
→ large trees / climax community
 primary (on rock, lava, sand dunes) vs. secondary (old field succession on cropland, stagnant lake
succession)
3. Ecosystems
a. Energy flow/production = energy flows through; 90% lost at each level & 10% transferred to next level
 trophic levels = primary producers, primary consumers, secondary consumers, tertiary consumers,
detritivores & decomposers
 ecological pyramids (pyramids of energy, biomass, numbers)
 food chains & food webs
b. Nutrient cycles = flow of essential elements from environmental pool through food web & recycled back by
decomposers
 cycles: water, carbon, nitrogen, phosphorus
4. Human impact
a. greenhouse effect / global warming
b. ozone deletion
c. acid rain
d. pollution (air, water, land)
e. deforestation
f. loss of species diversity
5. Animal Behavior
• instinct, imprinting (critical period), learning, classical conditioning, operant conditioning (trial-anderror), habituation
• movement: kinesis (undirected change in speed), taxis (directed movement), migration
• foraging: herds, flocks, schools, packs
• social: agonistic, dominance/hierarchy, territoriality, altruistic (kin selection), cooperation,
colonial
B. Labs
1. Dissolved Oxygen Lab
Be sure to review the procedures and the conclusions, and understand:
a. how to measure primary productivity (photosynthesis)
 measure rate of CO2 consumption
 measure oxygen production
 measure biomass production
b. factors that affect dissolved oxygen
 temperature = ↑ temp = ↓ dissolved O2
 photosynthesis = bright light = ↑ dissolved O2
 decomposition = ↑ microbial respiration = consumes O2
 turbulence = ↑ dissolved O2
c. difference between gross productivity & net productivity
 gross productivity = how much CO2 fixed from air into sugars
 net productivity = gross productivity (bottle in light) – respiration (bottle in dark)
C. Sample Free Response Questions
1.According to fossil records and recent published observations, two species of leaf-eating beetles (species A
and B) have existed on an isolated island in the Pacific Ocean for over 100,000 years. In 1964 a third species of
leaf-eating beetle (species C) was accidentally introduced on the island. The population size of each species has
been regularly monitored as shown in the graph..
a. Propose an explanation for the pattern of population density observed in species C.
b. Describe the effect that the introduction of beetle species C has had on the population density of species A
and species B. Propose an explanation for the patterns of population density observed in species A and in
species B.
c. Predict the population density of species C in 2014. Provide a biological explanation for your prediction.
d. Explain why invasive species are often successful in colonizing new habitats.
2. The energy flow in ecosystems is based on the primary productivity of autotrophs.
a. Discuss the energy flow through an ecosystem and the relative efficiency with which it occurs.
b. Discuss the impact of the following on energy flow on a global scale
 Deforestation
 Global climate change
REVIEW: PLANTS
A. Plant Hormones
• auxin: promotes plant growth, cell elongation;
• gibberellins: cell growth, fruit development;
• cytokinins: promote cell growth (cytokinesis)
• ethylene: promote fruit ripening
• abscisic acid (ABA): maintains seed & bud dormancy
B. Plant Transport
 Xylem & Phleom
 Water Potential: solute & pressure
 Transpiration: adhesion & cohesion of water
 Leaf surface: stomata (compromise between photosynthesis and transpiration)
REVIEW: ANIMAL
A. Regulation: Homeostasis is maintained through hormones & nervous system control
• hormone releasing gland, target cells, cell membrane receptors, secondary messengers, cellular
response (produce enzyme or turn gene on)
B. Immune
a. function: protects body from attack by pathogens
b. structure:
• lymph system, leukocytes, lymphocytes, macrophages, B cells, antibodies, T cells
c. adaptations / evolutionary trends:
• innate, non-specific immunity = barrier defense, leukocytes, macrophages
• acquired immunity = lymphocytes, antibodies, memory B & T cells
d. miscellaneous:
• vaccinations trigger immune response
• HIV outwits immune system
e. Non-specific barriers
• skin, anti-microbial proteins, gastric juices, symbiotic bacteria
• Non-specific patrol
• phagocytes, complement proteins, inflammatory response (histamine, vasodilation,
phagocytes)
f. Specific immunity
• lymphocytes, antigens,self vs. nonself
• B cells: antibodies (immunoglobulins), plasma cells, memory cells
• humoral response, attack circulating invaders, bone marrow
• T cells: cytotoxic T cells (killer), helper T cells
• cell-mediated response, attack infected or cancer cells
C. Nervous System
a. function: sensory input, motor function, regulation
b. structure: neuron, axon, dendrites, synapse
c. adaptations / evolutionary trends:
• voltage gated channels & ion-gated channels
• Na & K channels, Na/K pump, neurotransmitters