AP Bio Unit 6

DNA and RNA Structure

• DNA is a double-stranded helical molecule composed of nucleotide monomers.
• Nucleotides consist of:
  • A five-carbon sugar called deoxyribose.
  • A phosphate group.
  • One of four nitrogenous bases (A, T, G, C).
• Each strand has a sugar-phosphate backbone (covalently bonded deoxyribose sugars and phosphate groups).
• Bases with complementary shapes bind through hydrogen bonds:
  • Adenine (A) binds with Thymine (T).
  • Guanine (G) binds with Cytosine (C).
• Base pairing rules:
  • A - T
  • G - C
• Strands are antiparallel (oriented upside down relative to one another).

DNA Structure and Heredity

• Information Storage: The sequence of bases (A, C, T, G) codes for RNA and protein sequences.
• Replicability: Base pairing (A-T, G-C) allows each strand to serve as a template for synthesizing a complementary strand.
• Ensures high-fidelity transmission of genetic information.
• Stability: Double helix protects the base sequence.
• Mutability: Low level of mutation allows for change and evolution.

DNA vs. RNA

• DNA
  • Molecule of heredity in all cell-based organisms.
• RNA
  • Hereditary molecule in some viruses (e.g., HIV, SARS).
  • Involved in information transfer for protein synthesis (mRNA, tRNA, rRNA).
  • Involved in gene expression regulation (e.g., splicing out introns).

Genetic Information Storage: Prokaryotes vs. Eukaryotes

• Prokaryotes
  • DNA is stored in looped circular chromosomes.
  • Genomes range from 100,000 to 10,000,000 base pairs.
  • DNA is naked (not wrapped around proteins).
• Eukaryotes
  • DNA is organized into multiple linear chromosomes.
  • DNA is wrapped around histones.
  • Eukaryotic genomes are much larger.
    • Human genome: 3,200,000,000 base pairs.
    • Some plant genomes: 150,000,000,000 base pairs.

Plasmids

• Small, extra-chromosomal loops of DNA.
• Commonly found in bacteria, less common in archaea, rarely in eukaryotes.
• Involved in horizontal gene transfer (conjugation).
• Often carry genes for antibiotic resistance.
• Used in genetic engineering for replicating DNA and expressing engineered genes in bacterial cells.

DNA Replication

• Semi-Conservative Replication: Each daughter DNA double helix consists of one conserved strand from the parent molecule and one newly synthesized strand.
• Process: Enzymes use each strand of the double helix as a template to synthesize new daughter strands.

DNA Replication Start

• Helicase finds the origin of replication and separates the double-stranded DNA by breaking hydrogen bonds.
• Creates a replication fork.

Enzymes in Replication

• DNA Polymerase: Key enzyme that binds new nucleotides to the three-prime end of a growing strand.
• Requires an RNA primer to start the process.
• Primase: Enzyme that lays down the RNA primer.
• Single Strand Binding Proteins: Keep the double helix from rewinding.

Leading vs. Lagging Strand

• Leading Strand: DNA replication is continuous; DNA polymerase follows the opening replication fork.
• Lagging Strand: DNA polymerase synthesizes in the opposite direction; replication is discontinuous.
• Results in Okazaki fragments (short sequences).
• Each fragment requires a primer.

Further Enzymes in Replication

• DNA Polymerase I: Removes RNA primers and replaces them with DNA.
• DNA Ligase: Seals the gaps between fragments with sugar-phosphate bonds to create complete daughter strands.

Central Dogma

• DNA → RNA → Protein
• Information flows from DNA triplets to mRNA codons to amino acids.
• A gene is a sequence of DNA nucleotides that codes for RNA, which codes for protein.

Forms Of RNA

• mRNA (messenger RNA): Linear molecule carries instructions from DNA to ribosomes.
• rRNA (ribosomal RNA): Composes ribosomes and binds amino acids during protein synthesis.
• tRNA (transfer RNA): Brings specific amino acids to ribosomes.
• Small RNAs: Involved in eukaryotic gene regulation.

Transcription

• Creation of RNA from DNA.
• RNA polymerase binds with the promoter on DNA.
• Transcribes the template strand into RNA.
• RNA polymerase reads DNA in the 3' to 5' direction and synthesizes RNA in the 5' to 3' direction.
• Transcription ends when RNA polymerase reaches a terminator region and dissociates from DNA.

Template Strand

• Also called the non-coding strand, antisense strand, or minus strand.
• The strand that gets transcribed into RNA.
• The complementary strand is called the coding strand (sense strand or positive strand) because it has the same sequence of nucleotides as the mRNA (with U substituting for T).

Prokaryotic Transcription

• No nucleus; transcribed RNA can immediately be translated by ribosomes into protein.
• Multiple ribosomes often read the same RNA strand (polysomes).

Genetic Code

• Code used by living things to translate nucleotide sequences into amino acid sequences.
• Groups of three RNA nucleotides (codons) code for one amino acid.
• The code is nearly universal, specific, and redundant (synonymous codons).

How to Read A Genetic Code Chart

• To translate a codon like AUG, find A in the first nucleotide section, U in the second, and G in the third.
• AUG codes for methionine.
• Multiple codons can code for the same amino acid, often with the first two nucleotides being more important.

Translation

• mRNA contains codons specifying the order of amino acids.
• Ribosome connects amino acids to create a polypeptide.
• tRNAs bring amino acids to the ribosome-mRNA complex.
• tRNAs have an anticodon and an amino acid binding site.

Ribosomes

• General-purpose protein factories.
• String together amino acids to form polypeptides based on mRNA instructions.
• Have a large and small subunit.
• Three tRNA binding sites: E (exit), P (polypeptide), and A (amino acid).

Translation Beginning

• Processed mRNA leaves the nucleus through a nuclear pore.
• The small ribosomal subunit binds with the mRNA and moves to the start codon (AUG).
• A tRNA with matching anticodon (UAC) binds to AUG, carrying methionine.
• The large subunit binds, placing the tRNA with methionine in the P site.

Translation Elongation

• The next tRNA comes to the A site, bearing a new amino acid.
• The ribosome catalyzes a peptide bond between the P and A site amino acids.
• The ribosome translocates (moves over one codon).
• A dipeptide is now hanging off the P site amino acid, and the A site is empty.
• The tRNA in the E site exits, and a new tRNA enters at the A site.
• The cycle continues, adding amino acids to the growing polypeptide chain.

Translation Termination

• The ribosome reaches a stop codon.
• Stop codons code for a release factor (a protein).
• The release factor binds with the stop codon, causing the ribosome to dissociate and the polypeptide to be released.
• The polypeptide folds into a functional protein.

Operons

• System of gene regulation in prokaryotes with control elements.

Operon Structure

• Structural genes (code for protein).
• Operator (where a repressor protein binds).
• Promoter (where RNA polymerase binds).
• Regulatory gene (produces the regulatory protein, usually a repressor).

Trip Operon

• Codes for enzymes that make tryptophan.
• If no tryptophan is in the environment: the regulatory protein cannot bind with the operator, and RNA polymerase can transcribe the structural genes.
• When tryptophan is present: tryptophan binds with the repressor protein, causing it to change shape and bind with the operator, blocking RNA polymerase.
• Tryptophan is a co-repressor.
• The system only produce tryptophan synthesizing enzymes when necessary. Saves energy

Lac Operon

• Codes for enzymes that digest lactose.
• If lactose is present: lactose binds with the repressor protein, causing it to change shape so it can't bind with the operator, and RNA polymerase can transcribe the structural genes.
• If lactose is absent: the repressor binds with the operator, blocking RNA polymerase.
• Lactose is the inducer.
• Don't produce lactose digesting enzymes when not necessary, Saves energy.

Lac Operon: Negative Feedback

• Lactose turns the system on, leading to lactose digestion.
• Digestion removes lactose, causing the repressor to bind with the operator, turning the system off.
• The system quiets or repress itself.
• Trip Operon is also negative feedback.
• Absence of Tryptophan starts transcription.
• Production of tryptophan puts tryptophan at high enough concentration to bind with the repressor protein allowing the repressor protein to bind to operator shutting down transcription.
• Both TRIP and LAC negative feedback systems.

E. Coli Metabolism of Glucose and Lactose

• E. Coli prefers to metabolize glucose because it's a monosaccharide.
• When glucose is present, E. Coli eats it and grows rapidly.
• When glucose runs out, there's a lag in growth during the activation of the lac operon and lactose digesting enzymes.
• When lactose runs out, there's another lag until another food source is introduced.
• You have to understand operons in order to succeed in AP biology.

Eukaryotic Gene Regulation

• Multicellular eukaryotes are composed of trillions of cells organized into specialized tissues.
• Every cell has the same DNA, but cells need to know which genes to express.
• Gene regulation is influenced by environmental factors.
• Every cell has different DNA but need to know gene expression.
• Most eukaryotic DNA is non-coding.