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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.