BIO Chapters 15 & 16 Study Guide

Genes and How They Work

I. How Genes Work

  • Central Dogma of Biology

    • Definition: Describes the flow of genetic information from DNA to RNA to protein.

    • Key components:

    1. Transcription: The process by which the DNA sequence of a gene is transcribed into messenger RNA (mRNA).

    2. Translation: The process in which ribosomes synthesize proteins based on the sequence of mRNA.

    3. Reverse Transcription: The process by which RNA is reverse-transcribed back into DNA, often seen in retroviruses.

A. Transcription

  • Strand of DNA Used: The template strand of DNA is utilized for transcription.

  • Production of Transcription: mRNA is synthesized from the DNA template during transcription.

  • Types of RNA and Their Functions:

    1. Messenger RNA (mRNA): Carries the genetic information from DNA to the ribosome for protein synthesis.

    2. Transfer RNA (tRNA): Transfers specific amino acids to the ribosome during translation, matching the codon on mRNA.

    3. Ribosomal RNA (rRNA): A component of ribosomes, it catalyzes the formation of peptide bonds between amino acids.

  • RNA Polymerase:

    1. Core Polymerase: Comprised of several subunits necessary for the assembly of the enzyme.

    2. Holoenzyme: The active form of RNA polymerase that includes the core enzyme and additional factors for initiation.

    3. Primer Requirement: RNA polymerase does not require a primer to initiate synthesis.

  • Role of the Promoter: A specific DNA sequence where RNA polymerase binds to initiate transcription.

  • Direction of Transcription: Transcription occurs in the 5’ to 3’ direction.

  • Steps of Transcription:

    1. Initiation: RNA polymerase binds to the promoter and begins transcription.

    2. Elongation: RNA polymerase adds nucleotides to the growing mRNA strand.

    3. Termination: The process concludes when RNA polymerase reaches the termination sequence on the DNA, signaling the end of transcription.

  • Prokaryotic Transcription: In prokaryotes, transcription and translation occur simultaneously (coupled).

II. Transcription in Eukaryotes

  • Types of RNA Polymerases and Their Functions:

    1. RNA Polymerase I: Synthesizes rRNA (except 5S rRNA).

    2. RNA Polymerase II: Synthesizes mRNA and some snRNA.

    3. RNA Polymerase III: Synthesizes tRNA, 5S rRNA, and other small RNAs.

  • Components of the Initiation Complex: Various proteins, including general transcription factors bound to a promoter to facilitate transcription initiation.

  • mRNA Modification Post-Transcription:

    1. 5’ Cap: A modified guanine nucleotide added to the 5’ end of mRNA, aiding in stability and ribosome binding.

    2. 3’ Poly-A Tail: A string of adenine nucleotides added to the 3’ end of mRNA, enhancing stability and export from the nucleus.

    3. Intron Removal: Introns (non-coding sequences) are removed from the pre-mRNA during processing.

  • RNA Splicing:

    • Function of Terms:

    1. Introns: Non-coding segments of RNA that are spliced out of the primary transcript.

    2. Exons: Coding segments of RNA that remain after splicing and are translated into protein.

    3. Small Ribonucleoprotein Molecules (snRNPs): Protein-RNA complexes that play a crucial role in splicing.

    4. Spliceosome: A complex of snRNPs and proteins that facilitates the removal of introns and joining of exons.

  • Alternative Splicing: A process that allows for different combinations of exons to be joined, generating multiple mRNA variants from a single gene.

III. Translation

  • Genetic Code:

    • Definition: The set of rules by which information encoded in mRNA is translated into proteins.

  • Codon: A sequence of three nucleotides in mRNA that corresponds to a specific amino acid.

    • Types of Codons:

    1. Stop Codon: A codon that signals the termination of protein synthesis.

    2. Start Codon: The codon (AUG) that initiates translation.

  • Anticodon: A three-nucleotide sequence in tRNA that pairs with a complementary codon in mRNA.

  • Aminoacyl-tRNA Synthetase: An enzyme that attaches the correct amino acid to its corresponding tRNA.

  • Anticodon Loop: The part of tRNA that contains the anticodon, which base pairs with the mRNA codon.

  • Ribosomes:

    • Key Structures:

    1. P Site: The peptidyl site where the tRNA carrying the growing polypeptide chain is located.

    2. A Site: The aminoacyl site where new tRNA molecules enter.

    3. E Site: The exit site for tRNA after it has contributed its amino acid.

    • Peptidyl Transferase: The enzymatic activity of the ribosome that forms peptide bonds between amino acids.

    • Ribosome Binding Sequence (RBS): A sequence in mRNA that helps the ribosome to bind and initiate translation.

  • Elongation Factors: Proteins that assist in the elongation phase of translation, facilitating the addition of amino acids.

  • Transfer RNA Wobble Pairing: The ability of tRNA to bind to multiple codons due to flexibility in the pairing between the third base of the codon and the corresponding base of the anticodon.

  • Release Factors: Proteins that recognize stop codons and facilitate the termination of translation.

  • Importance of Redundant Genetic Code: The redundancy in the genetic code allows for multiple codons to specify the same amino acid, providing a buffer against mutations that can lead to amino acid substitution.

  • Steps of Translation:

    1. Initiation: Formation of the initiation complex, with mRNA, ribosome, and initiator tRNA ready for protein synthesis.

    2. Elongation: Sequential addition of amino acids to the growing polypeptide chain.

    3. Termination: The process concludes when the ribosome encounters a stop codon, leading to release of the completed protein.

  • Protein Targeting: Involves the role of the Signal Recognition Particle (SRP) in directing ribosome-mRNA complexes to the rough endoplasmic reticulum for synthesis of secreted or membrane proteins.

IV. Mutations

  • Types of Mutations:

    1. Point Mutations: Changes in a single nucleotide, significant variations include:
      a. Base Substitution: One nucleotide replaces another.
      b. Silent Mutation: A base substitution that does not change the protein sequence.
      c. Missense Mutation: Changes one amino acid in a protein; includes:
      i. Transition: A purine is exchanged for another purine or a pyrimidine for another pyrimidine.
      ii. Transversion: A purine is exchanged for a pyrimidine or vice versa.
      d. Nonsense Mutation: A base substitution that creates a stop codon, terminating translation prematurely.

    2. Frameshift Mutations: Alterations in the reading frame due to insertion or deletion:
      a. Addition (Insertion): Insertion of one or more nucleotides shifts the reading frame.
      b. Deletion: Removal of nucleotides that shifts the reading frame.

  • Importance of Mutations in Evolution: Mutations can create genetic diversity upon which natural selection acts, contributing to evolution.

V. Control of Gene Expression

A. Introduction

  • Regulatory proteins bind to specific DNA sequences to control gene expression, facilitating or inhibiting transcription based on the cell's requirements.

B. Regulatory Protein Motifs

  • Common motifs include:

    1. Helix-turn-helix: A structure that allows binding to DNA.

    2. Zinc finger: A protein folding motif that stabilizes protein structure in the presence of zinc.

    3. Leucine zipper: A structural motif that facilitates dimerization of proteins, enabling DNA binding.

VI. Prokaryotic Gene Regulation

  • Definitions:

    1. Positive Control: Activation of transcription through the binding of an activator protein.

    2. Negative Control: Inhibition of transcription through the binding of a repressor protein.

    3. Induction: A mechanism that increases gene expression in response to specific stimuli.

    4. Repression: A mechanism that decreases gene expression.

    5. Operon: A cluster of genes transcribed as a single mRNA, typically under the control of a single promoter.

  • Lactose Operon:

    • Components and Roles:

    1. LacI: A repressor protein that inhibits transcription in the absence of lactose.

    2. LacZ: Encodes β-galactosidase, which breaks down lactose.

    3. LacY: Encodes lactose permease, transporting lactose into the cell.

    4. LacA: Encodes thiogalactoside transacetylase, which detoxifies secondary products of lactose metabolism.

    • Default State of the Lactose Operon: The operon is off (not expressed) unless induced by lactose.

    • Activation of the Operon: The presence of lactose leads to the inactivation of the repressor, allowing transcription.

    • Low-Level Expression Explanation: Even without lactose, a low level of expression occurs due to leaky transcription.

    • Role of cAMP and CAP: cAMP levels rise with low glucose availability, activating the Catabolic Activator Protein (CAP), which enhances transcription of the lactose operon.

  • Tryptophan Operon:

    • Default State: The operon is normally on and actively transcribed.

    • Suppression: Excess tryptophan leads to repression of transcription when tryptophan acts as a co-repressor.

  • Inducible vs. Repressible Operons: The lactose operon is an inducible operon while the tryptophan operon is a repressible operon.

VII. Gene Regulation: Transcription Initiation

  • Role of Factors in Transcription Initiation:

    1. General Transcription Factors: Required for the binding of RNA polymerase to the promoter; includes TFIID and its interaction with the TATA box sequence.

    2. Specific Transcription Factors: Factors that enhance or suppress transcription based on specific signals, acting in a tissue-dependent or time-dependent manner.

    3. Promoters: DNA sequences that initiate transcription.

    4. Enhancers: Distal regulatory DNA elements that can increase transcription levels.

    5. Coactivators: Protein complexes that integrate signals from transcription factors to facilitate transcription.

    6. Mediators: Large complexes that bridge the interaction between transcription factors and RNA polymerase II.

VIII. Gene Regulation: Chromosomes

  • Roles of Chromatin Components in Gene Regulation:

    1. Nucleosomes: Basic unit of chromatin, consisting of DNA wrapped around histone proteins, influencing gene accessibility.

    2. Epigenetic Alterations: Changes that affect gene expression without altering DNA sequence, typically through methylation or histone modification.

    3. DNA Methylation: Addition of methyl groups to DNA, often leading to gene repression.

    4. X-chromosome Inactivation: A process in female mammals to equalize gene dosage by randomly inactivating one of the X chromosomes.

    5. Histone Modifications:

    • Acetylation: Typically associated with active transcription, opens up chromatin structure.

    • Methylation: Can either activate or repress transcription, depending on the context.

    • Phosphorylation: Modulates histone interactions with DNA and can impact transcriptional activation or repression.

    1. Chromatin-Remodeling Complexes: Complexes that alter chromatin structure, allowing transcription factors access to DNA.

    2. ATP-dependent Chromatin Remodeling Factors: Use ATP hydrolysis to move nucleosomes along DNA, facilitating gene activation.

IX. Gene Regulation: Post-Transcriptional Regulation

  • Roles of Various Small RNAs:

    1. miRNA (MicroRNA): Small RNA molecules that regulate gene expression by targeting mRNA for degradation or repression when bound to the RNA-induced silencing complex (RISC).

    • RNA-induced Silencing Complex (RISC): A multi-protein complex that mediates gene silencing.

    1. siRNA (Small Interfering RNA): Small RNA fragments that also target mRNA for degradation through RISC; involved in RNA interference.

    • Dicer: An enzyme that processes long double-stranded RNA into siRNA.

    • RISC: Processes the siRNA to bind and degrade complementary mRNA.

  • Alternative Splicing: A regulated process that allows for the generation of diverse protein isoforms from a single gene, often tissue-specific.

  • RNA Editing: A process that alters nucleotide sequences of RNA transcripts after transcription.

  • mRNA Degradation: Mechanisms that control mRNA stability, influencing protein production rates, vital in transgenic plants for gene regulation.