Exam #4 Whiteboards

Page 1: Genetic Code & Central Dogma

LO1: The Central Dogma of Molecular Biology

  • Definition: The central dogma describes the flow of genetic information from DNA to RNA to protein.

  • Processes:

    • Transcription: DNA is copied to mRNA.

    • Translation: mRNA is translated into a protein.

LO2: The Genetic Code

  • Rules: Sequence of nucleotides in DNA/RNA determines the sequence of amino acids in proteins.

  • Amino Acids: There are 20 different amino acids. Each amino acid is represented by a specific sequence of three nucleotides called a codon.

  • Codon Characteristics:

    • Total Codons: 64 possible codons.

    • Redundancy: Some amino acids can be coded by more than one codon.

    • Unambiguity: Each codon specifies only one amino acid.

    • Universality: Same codons code for the same amino acids across all organisms.

  • Start and Stop Codons:

    • Start codon: AUG (codes for Methionine).

    • Stop codons: UAA, UAG, UGA (signal the end of protein synthesis).

Transcription and Translation

  • Transcription Process:

    • mRNA is synthesized from DNA using base pairing rules; replace Thymine (T) with Uracil (U).

  • Translation Process:

    • The sequence of codons in mRNA is translated into amino acids to form proteins.

    • The sequence of amino acids determines the protein’s structure and function.

Page 2: Stages of Transcription

LO1: Stages of Transcription

  • Initiation:

    • RNA Polymerase binds to the promoter region of a gene.

    • DNA strands are separated to form a template.

  • Elongation:

    • RNA polymerase synthesizes RNA from the DNA template, growing the RNA from 5’ to 3’.

    • The RNA transcript mirrors the non-template DNA strand.

  • Termination:

    • RNA polymerase reaches the terminator sequence, ending transcription.

LO2: Post-Transcriptional Processing

  • Eukaryotic mRNA Modification:

    • 5' Cap Addition: Stability and recognition for ribosomes.

    • Poly-A Tail Addition: Enhances mRNA stability.

    • Splicing: Removal of introns and joining of exons to form functional mRNA.

Page 3: Protein Translation & Processing

LO1: Stages of Translation

  • Initiation:

    • Binding of small ribosomal subunit to mRNA and start codon.

    • Large ribosomal subunit assembles to form initiation complex.

  • Elongation:

    • tRNA brings amino acids to ribosome according to codons in mRNA.

    • Amino acids are added sequentially to the protein chain.

  • Termination:

    • Ribosome encounters a stop codon; protein synthesizes, and folding occurs.

Post-Translational Processing

  • Chemical Modifications: Attachments of chemical groups that affect protein function.

  • Protein Folding: Proper conformation achieved, assisted by chaperone proteins.

  • Degradation of Misfolded Proteins: Prevents aggregation and potential diseases.

LO3: Anatomy of a Gene

  • Gene Definition: Segment of DNA encoding product (protein/RNA).

  • Key Elements:

    • Core Promoter: Minimal portion necessary for transcription initiation.

    • Transcription Start Site (TSS): Location where RNA synthesis begins.

    • 3' UTR and 5' UTR: Untranslated regions affecting mRNA stability and translation.

    • Exons: Coding regions; remain in mature mRNA.

    • Introns: Non-coding regions removed during splicing.

    • Poly(A) Site: Cleavage and addition site of the poly-A tail.

LO4: Prokaryotic vs. Eukaryotic Translation

  • Prokaryotes: Simultaneous transcription/translation; polyribosomes present.

  • Eukaryotes: Transcription in nucleus, translation in cytoplasm after mRNA processing.

Page 4: Gene Regulation

LO1: Purpose of Gene Regulation

  • Efficiency: Regulates expression to save energy, manage cellular size, and time.

LO2: Prokaryotic vs. Eukaryotic Regulation

  • Prokaryotic Regulation: Primarily at transcriptional level.

  • Eukaryotic Regulation: More complex, allowing intricate control, involving chromatin effects on transcription accessibility.

Chromatin Structure

  • Euchromatin: Open and accessible for transcription.

  • Heterochromatin: Densely packed, usually silences gene expression.

  • Methylation/Acetylation: Affect transcription; methylation can repress while acetylation generally promotes access.

Page 5: Cell Signaling

LO1: Introduction to Cell Signaling

  • Cells communicate through chemical messengers (ligands) and receptors.

Categories of Signaling

  • Types:

    • Autocrine: Signals affecting the same cell.

    • Direct: Through gap junctions between cells.

    • Paracrine: Local signaling to nearby cells.

    • Endocrine: Long-distance signals via hormones.

Signaling Process

    1. Ligand binding causes receptor activation.

    1. Activation triggers a cascade, which leads to cellular responses.

    1. Responses include altered gene expression, metabolism, and cell growth.

Receptor Types

  • Membrane-bound receptors for hydrophilic ligands (e.g., proteins).

  • Intracellular receptors for hydrophobic ligands (e.g., steroids).

Page 6: Mutations

LO1: Definition of Mutations

  • Mutations: Changes in nucleotide sequences, source of genetic variation.

  • Types:

    • Somatic Mutations: Non-heritable, occur in body cells.

    • Germline Mutations: Heritable, passed to offspring.

LO2: Impact of Mutations

  • They can be neutral, deleterious, or beneficial.

    • Neutral: No impact on fitness.

    • Deleterious: Decrease fitness.

    • Beneficial: Increase fitness and provide selective advantage.

LO3: Example of Mutation

  • Mutation in Mc1r gene of rock pocket mouse causes black fur, advantageous in darker habitats.

Page 7: Evolution

LO1: Evolutionary Theories

  • Lamarck: Inheritance of acquired traits.

  • Darwin & Wallace: Natural selection theory.

Key Concepts

  • Acclimation: Changes not inherited.

  • Adaptation: Inherited traits better suited to environments.

  • Fitness: Reproductive success determining allele frequency.

Evidence for Evolution

  • Homologies: Similar structures in different species.

  • Fossil Record: Transitional forms showing evolutionary changes.

  • Biogeography: Distribution patterns supporting common ancestry.

Page 8: Natural Selection

LO1: Definition and Processes

  • Natural Selection: Differential survival and reproduction based on advantageous traits.

  • Non-Random: Affects allele frequency over generations.

Types of Selection

  • Directional Selection: Favoring one extreme phenotype (e.g. peppered moths).

  • Stabilizing Selection: Favoring average phenotypes (e.g. robins' clutch sizes).

  • Diversifying Selection: Favoring extremes in different environments.

LO3: Sexual Selection

  • Preference for traits increasing mating success leading to sexual dimorphism.

Page 9: Hardy-Weinberg Principle

LO1: Hardy-Weinberg Principle

  • Equilibrium: Conditions under which allele frequencies remain constant in a population.

  • Null Hypothesis for Evolution: Testing changes in genotype frequencies against this model.

Conditions for Hardy-Weinberg Equilibrium

  • Large population size, no selection, no migration, no mutation, and random mating.

Evolutionary Mechanisms

  • Natural Selection: Example with brown beetles outcompeting green beetles.

  • Genetic Drift: Random fluctuations affecting small populations.

  • Mutation: Introduces new alleles, altering genotype frequencies.

  • Gene Flow: Movement of alleles between populations affecting genetic diversity.