AP Biology Exam Review Notes
Enzyme Function
Reasons for decreased or stopped enzyme function:
Temperature changes: Enzymes have optimal temperatures; deviations can reduce activity.
pH changes: Enzymes function best at specific pH levels; deviations disrupt their structure.
Inhibitors: Competitive or non-competitive inhibitors can block or alter the active site.
Cofactors: Lack of necessary cofactors can prevent enzyme function.
Denaturation: Extreme conditions can unfold the enzyme, rendering it inactive.
Prokaryotic vs. Eukaryotic Cells
Size and Basic Structure:
Prokaryotic: Smaller, simpler structure.
Eukaryotic: Larger, more complex with membrane-bound organelles.
Evolution:
Prokaryotic: Evolved earlier.
Eukaryotic: Evolved later (research for specific timelines).
DNA Structure:
Prokaryotic: Circular DNA, single chromosome, no homologous pairs.
Eukaryotic: Linear DNA, multiple chromosomes, homologous pairs.
DNA Replication:
Prokaryotic: Single origin of replication, chromosome doesn't shorten.
Eukaryotic: Multiple origins of replication, telomeres prevent shortening but chromosomes still shorten.
Genetic Diversity:
Prokaryotic: Increased by mutations and horizontal gene transfer.
Eukaryotic: Increased by mutations, sexual reproduction, and gene transfer.
Gene Expression:
Prokaryotic: Transcription and translation occur in the cytoplasm, no RNA processing.
Eukaryotic: Transcription in the nucleus with RNA processing (splicing, etc.), translation in the cytoplasm.
ATP Generation:
Prokaryotic: Glycolysis, Krebs cycle (if aerobic), and electron transport chain in the cytoplasm and cell membrane.
Eukaryotic: Glycolysis in the cytoplasm, Krebs cycle and electron transport chain in the mitochondria.
Endosymbiotic Theory
Structures supporting the theory in mitochondria and chloroplasts:
Double membrane: Suggests engulfment of a prokaryotic cell.
Own DNA: Circular DNA similar to bacteria.
Ribosomes: Similar to prokaryotic ribosomes.
Explanation of eukaryotic cell complexity: Endosymbiosis explains how eukaryotic cells acquired mitochondria and chloroplasts, adding complexity.
Phosphofructokinase Evolution
Amino acid differences among species (Ananas comosus, E.coli, Homo sapiens, Ophrys apifera, Vulpes zerda) reflect evolutionary relationships.
Phylogenetic tree construction: Species closer together have fewer amino acid differences.
Identifying E. coli: E. coli is likely the most distantly related species, with the most amino acid differences.
Symbiotic Relationships
Ophrys apifera and bee species: Example of mimicry and pseudocopulation.
Type of relationship: Mutualism if both benefit; parasitism if one benefits at the expense of the other; commensalism if one benefits and the other is unaffected.
In this case, since the bee is tricked and doesn't get nectar, and the orchid benefits through pollination, it is a parasitic or deceptive relationship.
Phylogenetic relation:
Represented in a different way (e.g., cladogram).
Prezygotic Barriers
Specific relationship between orchids and pollinators: Illustrates a prezygotic barrier.
Flowering plants lacking the correct shape will not be pollinated, limiting fitness.
Type of barrier: Mechanical isolation (incompatible reproductive structures) or behavioral isolation (lack of attraction).
Impact of Extinction
Extinction of E. longicornis affecting Ophrys apifera: Reduced pollination and decreased fitness for the orchid.
Membrane Transport
Compartmentalization: Membranes maintain different cellular environments.
Thylakoid pH: Low pH inside the thylakoid.
Type of transport: Active transport to pump H+ ions against the concentration gradient.
Necessity: Maintains the proton gradient for ATP synthesis.
H+ ions moving into the stroma:
Type of transport: Facilitated diffusion through ATP synthase.
Transmembrane Protein and Amino Acids
Amino acids (A-F) on the intracellular side: Likely to be polar or charged amino acids due to the aqueous environment.
Hydrogen Ion Concentration and ATP Generation
High hydrogen ion concentration:
Mitochondria: Intermembrane space.
ATP generation: Matrix.
Mnemonic devices: To remember the locations and processes.
Gene Expression Regulation
Gene for protein X expression in somatic cells (skin, liver, muscle), but not fat cells.
Possible reasons for prevented gene expression:
Epigenetic modifications (DNA methylation, histone modification) in fat cells.
Lack of transcription factors in fat cells.
Repressor proteins binding to the promoter in fat cells.
mRNA degradation in fat cells.
Absence of enhancers or activators in fat cells.
Signal Transduction Pathway
Regulation of gene expression of protein X.
Reasons for prevented gene expression:
Receptor not binding the ligand.
Inactive or absent intracellular signaling molecules.
Transcription factor not being activated.
Failure of transcription factor to bind to DNA.
Evolution and Natural Selection
Mutations: Random changes to the genetic code.
Natural selection: Favors mutations that lead to survival traits.
Adaptations: Traits that improve survival in a specific environment.
Disruptions: Can lead to speciation and adaptations.
Natural events: Volcanic eruptions.
Human activity: Invasive species, habitat loss.
Survivors: Outcompete others, leading to new speciation.
Human impact: Changing the environment.
Greenhouse gasses: Increased through fossil fuel burning.
Invasive species: Outcompete native species.
Ecosystem dynamics: Changed by disruptions.
Aerobic Cellular Respiration
Missing reactions: Electron transport chain.
Organisms: Aerobic organisms (because it requires oxygen).
Fructose-1,6-bisphosphate concentration: Likely regulated by ATP.
High ATP: May inhibit phosphofructokinase, reducing fructose-1,6-bisphosphate production.
Positive regulator of α-ketoglutarate:
ADP: Indicates low energy levels and stimulates the Krebs cycle.
Dependent variables to measure respiration rate:
Oxygen consumption: Decrease indicates increased respiration.
Carbon dioxide production: Increase indicates increased respiration.
ATP production: Increase indicates increased respiration.
Heat production: Increase indicates increased respiration.
Role of oxygen: Final electron acceptor in the electron transport chain.
Oxygen deficient conditions: ETC stops, ATP production decreases.
Hemoglobin structure: Quaternary structure (multiple polypeptide chains).
Red Blood Cells
Lack of nucleus: Enables more oxygen transport.
Blood stem cells: Produce new red blood cells through mitosis and differentiation.
ATP production: Glycolysis (anaerobic).
Sickle Cell Disease (SCD)
Genetic disorder: Mutation in the HBB gene.
MscI restriction enzyme: Detects the difference between normal and mutated HBB alleles.
Mutation: Alters the base sequence of the HBB gene, creating or eliminating a restriction site.
Digestion: MscI cuts normal alleles into specific fragments but may not cut the mutated allele, resulting in different fragment sizes.
Gel electrophoresis: Separates DNA fragments by size. Smaller fragments migrate faster towards the positive electrode.
Southern Hybridization
Probes: Identify specific DNA nucleotide sequences.
Denaturation: Breaks hydrogen bonds to form single-stranded fragments.
Radioactive Labeling
Nucleic acids: Radioactive phosphorus.
Proteins: Radioactive sulfur.
Cystic Fibrosis (CF)
Autosomal recessive: Requires two copies of the CF allele.
Student's argument: Incorrect, pedigree doesn't necessarily show autosomal dominant inheritance because carriers in an autosomal recessive disorder can appear in every generation if new individuals keep marrying into the family.
Probability calculation:
Couple 5&6: Calculate the probability of having a child with CF based on their genotypes.
Incorrect models:
Homozygous: Should have two identical alleles.
Heterozygous: Should have two different alleles.
Correct heterozygous model:
Diagram with one red (B) and one yellow (b) allele on homologous chromosomes.
Three-nucleotide deletion (delta F508): Not a frameshift mutation because it’s a deletion of 3 nucleotides (multiples of 3) so it’s not going to cause a shift in the reading frame.
Substitution mutation in the third intron: Would not affect the amino acid sequence because introns are non-coding regions that are spliced out during RNA processing.
Island population: Founder effect and genetic drift.
CF allele frequency: Calculate based on the number of carriers.
Hardy-Weinberg equilibrium: Five conditions:
No mutation
Random mating
No gene flow
No genetic drift
No selection
Island vs. mainland frequency: Comparing CF phenotype frequency.
CFTR Protein
Mucus in lungs: Should be slippery and watery.
CFTR protein function: Transports Cl- ions out of the cell.
Water diffusion: Water diffuses out via osmosis because there is a high solute concentration so lower water potential outside of the cell compared to the environment inside the cell, which is hypotonic to the outside environment. The outside of the cell is hypertonic
Genes and Proteins
Genes code for amino acid sequences.
Proteins: Made of single or multiple polypeptide chains.
Wild-type allele: Dominant or recessive based on protein product.
X-inactivation: Needed to limit protein production from X chromosomes.
Protein comparison: Without X-inactivation, females would produce twice the amount of X-linked proteins compared to males.
Calico Cats
Patches of fur: Due to X-inactivation during development.
Biotechnology and Wildlife Conservation
Restriction enzyme:
Type of bond: Phosphodiester bond.
Type of reaction: Hydrolysis.
Enzyme to join fragment and plasmid: DNA ligase.
Eukaryotic gene insertion: mRNA is copied as cDNA because eukaryotic genes contain introns that prokaryotic cells cannot process.
Enzyme to copy RNA as DNA: Reverse transcriptase.
Cystic Fibrosis Drug
Drugs improve Cl- ion transport through defective CFTR protein by:
Correcting the folding of the protein.
Helping the protein reach the cell membrane.
Increasing the channel