AP Biology Exam Notes

Helicase Unzipping

• Helicase: Unzips DNA strands.
• Single-Stranded Binding Protein: Prevents strands from re-annealing.
• Topoisomerase: Relieves tension in the strands.
• RNA Primase: Lays down RNA primers to start replication.
• DNA Polymerase: Adds nucleotides.
• DNA Polymerase I: Removes RNA primers and replaces them with DNA.
• Ligase: Seals the gaps between Okazaki fragments.
• Semi-Conservative Replication: Each new DNA molecule contains one original strand and one new strand.

Protein Synthesis

• Central Dogma: DNA → RNA → Protein.
• Transcription:
  • Initiation: RNA polymerase binds to a promoter region on a gene.
  • Elongation: RNA polymerase adds RNA nucleotides.
  • Termination: A polyadenylation signal halts transcription.
  • RNA polymerase is used to make mRNA.
  • After mRNA is built, it exits the nucleus and goes to the cytoplasm.
• RNA Processing (Eukaryotes only): Takes place in the nucleus and before translation in eukaryotes.
  • Spliceosomes: Remove introns and join exons together.
• Ribosomes: Large and small subunits that translate mRNA into proteins.
  • Proteins made by free ribosomes go to the cytoplasm.
• Key Players:
  • mRNA: Copies DNA instructions.
  • tRNA: Brings amino acids to the ribosome.
  • rRNA: Ribosomes are made of rRNA and proteins.
• Translation:
  • Initiation: mRNA binds to the ribosome.
  • Elongation: tRNA brings amino acids to the ribosome, forming a polypeptide chain.
  • Termination: A stop codon signals the end of translation.
• Eukaryotic vs. Prokaryotic Cells
  • Eukaryotes have a nucleus, so RNA processing must occur before translation can begin in the cytoplasm

Gene Expression

• Promoter: A piece of DNA where RNA polymerase binds.
• Operons (Prokaryotes): Control region of DNA for multiple genes, found in bacteria.
  • Promoter: Where RNA polymerase binds.
  • Operator: Part of the promoter where a repressor binds.
  • Repressor: Turns the operon off.
  • Corepressor: Changes the repressor to activate it.
  • Inducer: Causes the repressor to fall off the operator, turning the operon on.
• Outcomes: Gene expression can be turned on or off.
  *Natural Causes of mutations: errors during DNA replication.

Eukaryotic Transcription Regulation

• RNA Polymerase: Binds to mRNA.
• Promoter: Where RNA polymerase binds to start of the gene.
• TATA Box: Where specific transcription factors bind.
• Transcription Factors: Regulate transcription.
• Enhancer: Where activators bind. Activator binds to the enhancer of DNA, upstream to the gene.
• Activators: Start transcription.
• Mediator Proteins: Help RNA polymerase bind to the promoter region.
• Bending Proteins: Fold DNA to allow activators to interact with the promoter region.
• Activators, mediator proteins, transcription factors & RNA polymerase are all involved in initiation and beginning transcription.
• In eukaryotes, repressors block activators from binding to the promoter.

Chromatin Structure

• Heterochromatin: DNA tightly wound around histone proteins (condensed).
• Euchromatin: DNA loosely wound around histone proteins (less condensed, more accessible for transcription).

Mutations

• Silent Mutation: Codes for the same amino acid.
• Missense Mutation: Codes for a different amino acid.
• Nonsense Mutation: Codes for a stop codon.

Viruses

• Can insert DNA into genes, leading to disorders.
• Chemical mutagens or carcinogens can disrupt DNA replication or damage it.
• Tumor suppressor genes and proto-oncogenes are genes that when mutated, can lead to cancer.
• Transformation: Bacterium picks up plasmids left behind
• Conjugation: Bacterium exchange plasmids with another
• Transduction: Viruses inject DNA instructions in the host Cell, then the DNA gets mixed in the cell & gets seperated into a new Virus. Different combinations of materials making a new Virus.

Further Mutation Causes and Outcomes

• Environmental Factors:
  • Radiation, chemicals, and viruses can cause mutations.
• Outcomes:
  • Mutations cause genetic variation.
  • Natural selection favors beneficial mutations, but harmful mutations can be eliminated over time through natural selection.

Biotechnology

• Genetic Engineering: The process of directly altering DNA.
• Recombinant DNA Molecule: DNA molecule used to carry foreign genetic material; plasmids are commonly used.
• Transformation organism takes up recombinant plasmid DNA from the environment.
• Products used to produce proteins or be cloned to study genes.
• PCR (Polymerase Chain Reaction): Copy specific DNA sequences in large quantities from a sample.

Cell Cycle

• Chromosomes: Store genetic information, ensure DNA is copied, and organize DNA for cell division.
• Purpose: To allow cells to grow, replicate DNA, and divide into two new cells.
• Purpose of Mitosis: To separate the homologous pairs.
  • Prophase: Spindles form.
  • Metaphase: Homologous pairs line up in the middle.
  • Anaphase: Homologous pairs separate.
  • Telophase: The cells separate.
• Makes identical diploid cells
  *Chromosomes Store genetic info, ensure DNA is copied & Seperated during cell division, Regulate gene expression & inher-tence.
  *Haploid Gamete = Egg & Sperm
  *Diploid = Body cell. Sometic cell
  *Law of Segeration Each gamete recives I Allele of each gene
  *Law of independent Assortment: Homologous Chromosomes align independently at the metaphase plate.

Meiosis

• Crossing Over: Creates new combinations of genes on each chromosome.
• Independent Assortment: Occurs during meiosis I. Homologous chromosomes align independently at the metaphase plate.

Cell Communication

• Cells need to communicate for growth and response to changes.
• Process:
  1. A ligand binds to a receptor on a target cell.
  2. A signal transduction pathway relays the signal into the cell.
  3. The cell responds by changing gene expression.
• Amplification: One signal molecule activates many molecules, amplifying the response.
• Hydrophilic Ligands: Bind to surface receptors.
• Hydrophobic Ligands: Cross the membrane and bind to internal receptors.
• Protein Hormones: Hydrophilic and cannot pass through the membrane by themselves.
• Steroid Hormones: Hydrophobic and can pass through the membrane (slower response).
• Kinase: An enzyme that adds a phosphate group.
• Phosphorylation Cascade: A series of kinases activate each other by phosphorylation, leading to a cellular response.
• Purpose: Amplifies the signal and allows for regulation of the response.

Energy and Enzymes

• Exergonic Reaction: A chemical reaction where energy is released.
• Endergonic Reaction: A chemical reaction where energy is absorbed.
• Enzymes
  • Active Site: Where the substrate binds to create a chemical reaction.
  • Allosteric Site: Allows molecules to activate/inhibit the enzyme.
• Activation Energy: The minimum amount of energy required to start a reaction or process.
• Inhibitors:
  • Competitive Inhibitor: Blocks the substrate from binding to the active site.
  • Non-Competitive Inhibitor: Molecule binds to allosteric site to change the shape of the active site.
• Feedback Inhibition: A mechanism where the end product of a metabolic pathway inhibits an enzyme early in that pathway.

Ecology

• Photoautotrophs: Use sunlight for energy.
• Chemoautotrophs: Use chemical energy.
• Energy Flow: Flows one way (sun → heat).
• Nitrogen Cycle:
  • Nitrogen-Fixing Bacteria: Converts atmospheric nitrogen ($N<em>2$) to ammonia ($NH</em>3$).
  • Nitrifying Bacteria: Convert ammonia ($NH<em>3$) into nitrite ($NO</em>2$) and then into nitrate ($NO_3$).
  • Denitrifying Bacteria: Convert nitrate ($NO<em>3$) back into atmospheric nitrogen gas ($N</em>2$).
• Nitrogen is used to make proteins and nucleic acids.
• Population Dynamics:
  • Growth: Births, immigration.
  • Decline: Deaths, emigration.
• Density-Dependent Factors: Affect a population's size/growth based on the population density; examples include disease and predation.
• Density-Independent Factors: Affect populations regardless of their density; examples include natural disasters.
• Population Growth Curves:
  • J-curve = exponential growth.
  • S-curve = logistic growth.
  • Carrying Capacity: The maximum population size an environment can sustain.
• Symbiotic Relationships:
  • Mutualism: Both benefit.
  • Parasitism: One benefits, one is harmed.
  • Commensalism: One benefits, the other is neither harmed nor benefitted.

Photosynthesis

• Equation: $6CO<em>2 + 6H</em>2O + Light \rightarrow C<em>6H</em>{12}O<em>6 + 6O</em>2$
• Light-Dependent Reactions: Convert solar energy into ATP and NADPH.
  • Location: Thylakoid membrane.
• Calvin Cycle: Uses ATP and NADPH to build glucose.
  • Location: Stroma.
  • Stages:
    1. Carbon fixation.
    2. Reduction.
    3. Regeneration.
• Carbon fixation = mixture of $CO_2$ into organic melecules
• $63p$ is made at the end and used to make Glucose

Evolution

• Gene Pool: Total collection of all alleles for all genes in a population.
• Natural Selection Components: Variation, inheritance, selection, time.
• Pathways of Natural Selection: Adaptation & Speciation.