BIOL 150 Lecture Exam IV Study Guide Notes
Chapter 16
Chargaff’s Rule: In DNA, the amount of adenine (A) equals thymine (T), and guanine (G) equals cytosine (C).
Discovery of DNA Structure:
Watson & Crick: Discovered the structure of DNA.
Rosalind Franklin: Contributed significant data using X-ray crystallography.
DNA Molecule Structure: Purine bases (A, G) pair with pyrimidine bases (T, C).
Holding DNA Strands Together: Hydrogen bonds between purine-pyrimidine base pairs.
DNA Replication Model: Semiconservative model.
Definitions Pertaining to DNA Replication:
Origin of replication: Where DNA synthesis starts.
Replication fork: Point where DNA strands separate for copying.
Replication bubble: Unwound DNA segment where strands are templates for new DNA.
Proteins Involved in DNA Replication Initiation:
Topoisomerase: Relaxes DNA structure by making single-strand nicks.
Helicase: Unwinds DNA into single strands.
Single-strand DNA binding protein: Keeps single strands separate during replication.
Primase: Synthesizes a short RNA primer for DNA polymerase to start adding nucleotides.
RNA primer: Short RNA sequence to which DNA polymerase adds DNA nucleotides.
Substrate Molecule Added by DNA Polymerase: DNA nucleotide triphosphate.
Molecule Formed: Pyrophosphate.
Leading and Lagging Strands:
Leading strand: Template strand allowing continuous DNA nucleotide addition towards the replication fork.
Lagging strand: Template strand in the opposite orientation, requiring discontinuous nucleotide addition.
DNA polymerase III: Adds DNA nucleotides to the 3’ end of an existing strand or RNA primer using the original DNA as a template.
DNA polymerase I: Removes RNA primer nucleotides and replaces them with DNA nucleotides.
DNA ligase: Links Okazaki fragments on the lagging strand and joins the leading strand to the rest of the DNA molecule.
DNA Damage: Chemicals, radioactivity, X-rays, UV light, cigarette smoke.
DNA Packaging in Chromosomes: DNA combines with histones into chromatin, forming nucleosomes (beads on a string). Four histone types form the ‘bead’ with DNA wrapped around, and one histone associates with DNA between beads, further organized into 30 nm and 300 nm fibers.
Chapter 17
Gene Expression: The Process by which DNA directs protein synthesis (transcription and translation).
Gene Definition: A DNA region that can be expressed to form a final functional product (polypeptide or RNA).
Location of Transcription & Translation:
Bacterial cells: Both occur in the cytoplasm.
Eukaryotic cells: Transcription in the nucleus, translation in the cytoplasm.
Transcription Definition: Synthesis of RNA from a DNA template, producing mRNA.
Translation Definition: Synthesis of a polypeptide from mRNA, occurring on ribosomes.
RNA Transcript Processing in Eukaryotes: RNA transcripts undergo RNA processing in the nucleus, leading to mature mRNA formation.
Primary Transcript: The initial RNA transcript from a gene.
Genetic Code: Instructions for assembling amino acids into proteins are encoded as a triplet code in DNA, transcribed into codons in mRNA. Each codon specifies one amino acid.
Genetic Code Redundancy and Ambiguity: Redundant means multiple codons can specify one amino acid; unambiguous means no codon specifies more than one amino acid.
Reading Frame: The sequence of three nucleotides that form a single codon which must be translated as a group
Proteins Needed for Transcription:
RNA polymerase II: Unwinds DNA and synthesizes RNA by adding RNA nucleotides to the growing primary transcript.
Transcription factors: Bind to DNA along with RNA polymerase II to form a transcription initiation complex.
DNA Features for Transcription Initiation Complex Formation: RNA polymerase binds to a promoter sequence near the start site, often containing a TATA box.
RNA Processing of Primary Transcript:
A guanosine cap is added to the 5’ end.
A poly(A) tail (250 adenosine nucleotides) is added to the 3’ end.
Introns are removed, and exons are spliced together (RNA splicing) by a spliceosome (small nuclear ribonucleoproteins and proteins).
Functions of mRNA End Modifications: Facilitate transport out of the nucleus, protect against degradation, and help ribosome binding.
Ribozymes: Catalytic RNA molecules that can act as enzymes and splice RNA molecules.
Components Needed for Translation:
mRNA: Made and modified in the nucleus, then exported to the cytoplasm.
Ribosomes: Consist of large and small subunits (RNA and proteins); the small subunit binds mRNA, and the large subunit has A, P, and E sites.
tRNA: Brings specific amino acids to the ribosome and reads mRNA codons via its anticodon.
Wobble: Flexible pairing at the third base of a codon allows some tRNAs to bind to multiple codons.
Aminoacyl tRNA Synthetases: Enzymes that attach amino acids to their respective tRNAs.
Ribosome Binding Sites:
P site: Holds the tRNA with the growing polypeptide chain.
A site: Holds the tRNA with the next amino acid to be added.
E site: Exit site for tRNA molecules.
Translation Stages: Initiation, elongation, termination.
Energy Source for Translation: GTP (not ATP).
Initiation: The small ribosomal subunit binds mRNA and the initiator tRNA (methionine).
Elongation: Sequential addition of amino acids to the polypeptide chain.
Termination: Requires a stop codon in mRNA and release factors.
Polyribosome (Polysome): mRNA molecule with multiple ribosomes translating it simultaneously.
Mutations
Mutations: Changes in the genetic material (DNA).
Point Mutation: Change of a single nucleotide base in DNA.
Base Pair Substitution: A nucleotide and its pair are replaced.
Missense mutation: Codes for a different amino acid.
Nonsense mutation: Replaces an amino acid codon with a stop codon, leading to a truncated, often nonfunctional, protein.
Insertions and Deletions: Gains or losses of genetic material, usually detrimental.
Chapter 18 (First Half)
Operon: Cluster of functionally related genes controlled by a single ‘on/off’ switch, including the operator, promoter, and genes.
Operator: Regulatory switch consisting of a DNA sequence within the promoter.
Repressor: Protein that can switch off the operon by binding to the operator and blocking RNA polymerase.
Repressor Regulation: Encoded by a separate regulatory gene, and can be active or inactive based on other molecules.
Corepressor: Molecule that helps a repressor turn an operon off.
Repressible Operon: Usually on, but a repressor can switch it off (e.g., trp operon).
Inducible Operon: Usually off, but an inducer inactivates the repressor to turn expression on (e.g., lac operon).
Eukaryotic Gene Expression Control: Eukaryotic cells do not use operons, but control gene expression at chromatin modification, gene transcription, RNA modification & processing, mRNA exit to the cytoplasm, mRNA translation & degradation in the cytoplasm, synthesis of the protein in the cytoplasm, degradation of the protein in the cytoplasm, protein modification in the cytoplasm affecting protein activity, transport of protein to final destination in the cell.
Chromatin Structure and Gene Expression: DNA is packaged with histones in chromatin (compacted heterochromatin or relaxed euchromatin). Genes in heterochromatin are usually not expressed. Modifications to DNA and histones determine chromatin state. Addition of acetyl groups to lysine amino acids in histone tails is seen in euchromatin.
DNA Methylation: Methylation of certain DNA bases is related to heterochromatin and decreased transcription.
Genomic Imprinting: DNA methylation regulates expression of maternal or paternal alleles during development.
Epigenetic Inheritance: Passing of chromatin modifications (not DNA sequence) to the next generation.
Eukaryotic Gene Control Elements:
Promoter sequence: Immediately precedes the gene, often with a TATA box.
Proximal control elements: Close to the promoter region.
Distal control elements (enhancers): Far from the gene sequence, interact with the promoter because DNA can bend. Proximal and distal control elements bind transcription factor proteins.
Regulatory Mechanisms: Operate before, during, and after transcription, allowing rapid response to the environment.
Alternate Splicing: Production of different mRNAs from a single primary RNA transcript by splicing out or keeping certain intron sequences.
mRNA Lifespan: Determined by sequences in the 5’ and 3’ untranslated regions.
Noncoding RNA: Transcribed into RNA but do not code for proteins, affecting gene expression by affecting mRNA translation or chromatin configuration. MicroRNA and small interfering RNA affect protein synthesis by blocking translation or causing mRNA degradation.
Chapter 18 (Second Half)
Differential Gene Expression: Regulation of different genes in different cell types.
Cell Differentiation: Process by which cells become specialized in structure and function.
Cytoplasmic Determinants: Special molecules (RNA and/or protein) unevenly distributed in the egg cytoplasm, leading to uneven distribution to daughter cells during cell division.
Induction: Signal molecules from embryonic cells cause transcriptional changes in nearby target cells.
Pattern Formation: Development of the spatial organization of tissues and organs.
Positional Information: Molecular cues tell a cell its location relative to body axes and neighbors.
Bicoid Gene: A maternal effects gene that determines head structures in fruit flies.