Chapter 6 - Gene Expression at the Molecular Level
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Questions and Answers

What is the main functional product of protein-coding genes?

  • Ribosomal RNA (rRNA)
  • Messenger RNA (mRNA)
  • Transfer RNA (tRNA)
  • Polypeptide (correct)
  • Which type of RNA is synthesized from non-coding RNA genes?

  • Functional RNA (correct)
  • mRNA
  • DNA
  • Polypeptide
  • During elongation, RNA is synthesized in which direction?

  • Random direction
  • 3’ to 5’ direction
  • 5’ to 3’ direction (correct)
  • 3’ to 2’ direction
  • What is the strand called that is used as a template for RNA synthesis during transcription?

    <p>Template strand</p> Signup and view all the answers

    Which feature is a difference between RNA polymerases and DNA polymerases?

    <p>RNA polymerases do not have exonuclease activity</p> Signup and view all the answers

    What does alternative splicing of mRNA allow for?

    <p>Creation of multiple proteins from a single gene</p> Signup and view all the answers

    How does the sequence of the coding strand compare to the sequence of the mRNA produced?

    <p>Identical, with U instead of T</p> Signup and view all the answers

    What primarily differentiates basic transcription processes in prokaryotes and eukaryotes?

    <p>The complexity of associated protein components</p> Signup and view all the answers

    What is the initial role of aminoacyl tRNA during translation?

    <p>It binds to the A site through codon/anticodon recognition.</p> Signup and view all the answers

    What is the result of the peptidyl transfer reaction?

    <p>A peptide bond is formed between the amino acid in the A site and the polypeptide chain.</p> Signup and view all the answers

    What occurs during the translocation process of the ribosome?

    <p>tRNA moves from the A site to the P site.</p> Signup and view all the answers

    What triggers the termination of translation?

    <p>Recognition of a stop codon by release factors.</p> Signup and view all the answers

    What happens to the tRNA in the P site once the polypeptide is released?

    <p>It exits the ribosome via the E site.</p> Signup and view all the answers

    What is the function of the 5' cap in mRNA processing?

    <p>It promotes the binding of ribosomes during translation.</p> Signup and view all the answers

    What type of sequences do exons represent in mRNA?

    <p>They are coding sequences that appear in the mature mRNA.</p> Signup and view all the answers

    Which polymerase is NOT involved in eukaryotic transcription?

    <p>RNA polymerase IV</p> Signup and view all the answers

    What is the role of polyadenylation in mRNA processing?

    <p>It adds adenines to the 3' end, aiding in stability and export.</p> Signup and view all the answers

    What component is primarily responsible for catalyzing the splicing of pre-mRNA?

    <p>snRNPs</p> Signup and view all the answers

    What is the primary purpose of alternative splicing?

    <p>To generate different protein products from the same gene</p> Signup and view all the answers

    How do eukaryotes differ from prokaryotes in terms of transcription initiation?

    <p>Eukaryotes require general transcription factors, while prokaryotes use sigma factors.</p> Signup and view all the answers

    Which statement about introns is true?

    <p>Introns are removed from pre-mRNA during the splicing process.</p> Signup and view all the answers

    What is gene expression?

    <p>The conversion of encoded information in a gene into a functional product.</p> Signup and view all the answers

    What was Archibald Garrod's contribution to genetics?

    <p>He linked mutant genes to metabolic diseases.</p> Signup and view all the answers

    What does the one gene – one enzyme hypothesis suggest?

    <p>Each gene controls the production of one specific enzyme.</p> Signup and view all the answers

    What type of protein is primarily associated with Beadle and Tatum's research?

    <p>Enzymes.</p> Signup and view all the answers

    How did Beadle and Tatum categorize the mutant strains of Neurospora crassa?

    <p>By enzyme defects involved in arginine synthesis.</p> Signup and view all the answers

    What does a mutation in a gene potentially affect?

    <p>Gene function due to alterations in the gene sequence.</p> Signup and view all the answers

    What is an inborn error of metabolism?

    <p>An inherited disease caused by a defective gene affecting metabolic processes.</p> Signup and view all the answers

    What was the main organism studied by Beadle and Tatum?

    <p>Neurospora crassa.</p> Signup and view all the answers

    Why do some proteins consist of two or more polypeptides?

    <p>To perform complex biological functions.</p> Signup and view all the answers

    What is one of the roles of enzymes in biochemical pathways?

    <p>To catalyze each step in the pathway.</p> Signup and view all the answers

    What does the term 'degenerate' refer to in the context of the genetic code?

    <p>The ability of multiple codons to specify the same amino acid.</p> Signup and view all the answers

    Which component of tRNA is specifically responsible for binding to the amino acid?

    <p>3' single-stranded region (Acceptor stem)</p> Signup and view all the answers

    What is the primary function of aminoacyl-tRNA synthetases?

    <p>To catalyze the attachment of amino acids to tRNA.</p> Signup and view all the answers

    In what direction is the mRNA read during translation?

    <p>5' to 3'</p> Signup and view all the answers

    What is the role of the start codon in mRNA?

    <p>To determine the reading frame of the mRNA.</p> Signup and view all the answers

    How is accurate tRNA charging ensured?

    <p>By having one aminoacyl-tRNA synthetase per amino acid.</p> Signup and view all the answers

    What distinguishes eukaryotic mRNA initiation from bacterial mRNA initiation?

    <p>Eukaryotic mRNA requires cap-binding proteins for binding.</p> Signup and view all the answers

    Which site on the ribosome is the location where a new aminoacyl-tRNA enters during translation?

    <p>A site</p> Signup and view all the answers

    What is the consequence of inserting or deleting bases in groups other than three from an mRNA sequence?

    <p>It changes the reading frame and alters the entire amino acid sequence.</p> Signup and view all the answers

    What is the shape of eukaryotic ribosomes composed of?

    <p>Ribosomal RNAs and multiple proteins.</p> Signup and view all the answers

    Study Notes

    Gene Expression at the Molecular Level I

    • Gene expression is the process of converting genetic information into a functional product
    • It is studied at both the molecular and trait levels
    • Mutations are heritable changes in genetic material affecting gene function by altering the gene sequence
    • Research on mutations has shown the relationship between normal genes and functional proteins, and abnormal genes and non-functional proteins.
    • Inborn Errors of Metabolism are inherited diseases where abnormal levels of homogentisic acid accumulate, demonstrating a link between mutant genes, defective enzymes, and metabolic diseases.

    Archibald Garrod

    • Studied patients with metabolic defects, such as alkaptonuria
    • In 1908, proposed a link between a mutant gene, missing/defective enzyme and metabolic disease, calling it an "inborn error of metabolism"

    Phenylalanine Metabolism

    • Mutations can cause phenylketonuria or tyrosinosis or alkaptonuria
    • Mutations in genes related to these pathways cause metabolic disorders

    Beadle and Tatum

    • Discovered Garrod's work in the early 1940s
    • Studied Neurospora crassa (common bread mold)
    • Determined minimum growth requirements
    • Focused on amino acid synthesis
    • Hypothesized that genes encode enzymes, and mutations can cause defects in enzymes needed for amino acid synthesis.
    • Proposed that each step in a biochemical pathway is catalyzed by a different enzyme, controlled by a different gene.
    • Collected mutant strains needing arginine supplementation for growth
    • Explored precursor molecules' effects on mutant strain growth
    • Identified three genes and enzymes for arginine synthesis
    • Found mutant strains grouped according to defective enzymes. Demonstrated single gene controlling synthesis of single enzyme

    The Central Dogma of Gene Expression

    • The fundamental principle of gene expression
    • Shows the flow of genetic information from DNA to RNA to protein
    • Includes processes like replication, transcription, and translation

    Prokaryotes vs. Eukaryotes

    • Prokaryotes have simpler gene expression processes. Transcription in the cytoplasm, no modifications occur. Translation takes place immediately.
    • Eukaryotes are more complex, with transcription in the nucleus and subsequent RNA modifications (splicing etc), and separate translation in the cytoplasm.

    Genes

    • Organized units of DNA sequences transcribed into RNA
    • Protein-coding genes produce mRNA specifying amino acid sequences, to eventually make proteins
    • Non-coding RNA genes (e.g., tRNA, rRNA) produce functional RNA molecules

    Gene Organization

    • DNA segments organized into promoter, transcribed region, and terminator (signals for transcription start and end)
    • Regulatory sequences influence transcription rate
    • The transcribed region carries the amino acid sequence coding information

    Three Stages of Transcription

    • Initiation - RNA polymerase binds to promoter using sigma factor, forming an open complex
    • Elongation - RNA polymerase moves along template strand, creating RNA in 5' to 3' direction, complementary to template
    • Termination - RNA polymerase reaches the terminator sequence, and the RNA transcript and RNA polymerase dissociate from DNA template

    A Closer Look at Elongation

    • RNA synthesis is 5' to 3'
    • Uracil (U) in RNA replaces Thymine (T) of DNA.
    • Template strand of DNA is used as a template and read in the 3' to 5' direction
    • Coding strand has same sequence as mRNA, except T instead of U

    Transcription along the Chromosome

    • DNA strand used as template can differ for adjacent genes.
    • Determined by promoter sequence location

    Eukaryotic Transcription

    • Eukaryotes contain three RNA polymerases instead of one, and need several initiation factors
    • Basic features are identical, but each step involves greater complexity compared to prokaryotes.

    Eukaryotic RNA Processing

    • Pre-mRNA undergoes capping, splicing, and polyadenylation
    • Capping involves adding a 5' cap (7-methylguanosine)
    • Splicing removes non-coding introns, joining exons
    • Polyadenylation involves adding a poly-A tail at the 3' end

    RNA Processing: Capping

    • Covalent attachment of 7-methylguanosine to the 5' end of the mRNA transcript (5' cap)
    • Occurs while RNA polymerase synthesizes the pre-mRNA
    • Recognized by cap-binding proteins
    • Needed for mRNA nucleus exit
    • Protects mRNA and binds to ribosome for translation

    RNA Processing: Tailing

    • Adds poly-A tail (100-200 adenines) to the 3' end of the mRNA
    • Helps with export from the nucleus and enhances mRNA stability
    • Allows mRNA to persist longer in the cytoplasm

    RNA Processing: Splicing

    • Removes non-coding introns and joins exons
    • Catalyzed by the spliceosome (snRNPs)
    • snRNPs are made of snRNA & protein
    • Alternative splicing allows different gene products through variation on how exons are joined

    The Genetic Code

    • Specifies the relationship between mRNA nucleotide sequence and corresponding polypeptide amino acid sequence
    • Codons are three-nucleotide sequences specifying amino acids or signaling start/stop
    • Examples: CCC = proline, GGC = glycine
    • tRNAs bind to mRNA codons using anticodons

    The Genetic Code: Degeneracy

    • Multiple codons may specify the same amino acid
    • Using 3 bases, 64 different codons are possible (4^3). But there are only 20 different amino acids

    Bacterial mRNA Organization

    • Contains ribosomal-binding site, start codon, coding sequence, and stop codon
    • Specified to code for specific amino acid sequence

    Reading Frame

    • Start codon defines the reading frame
    • Adjacent codons are read as triplets in a 5' -> 3' direction
    • Insertions/deletions (not multiple of 3) lead to altered amino acid sequences

    The Translation Machinery

    • mRNA carries the genetic code for amino acid sequence
    • Ribosomes are the sites of protein synthesis, composed of proteins and rRNA molecules, and have A, P, and E sites
    • tRNAs carry amino acids, with anticodons that match mRNA codons

    tRNAs

    • Diverse tRNAs encoded by different genes, sharing common features, and a cloverleaf structure
    • Have an anticodon to recognize their mRNA codon
    • Acceptor stem binds amino acid

    Aminoacyl-tRNA Synthetases

    • Enzymes attach amino acids to tRNA molecules.
    • There is one amino acid-specific synthetase for each of the 20 amino acids
    • Two-step reaction to create charged (aminoacyl-tRNA)

    Ribosomes

    • Macromolecular structures where translation takes place.
    • Composed of proteins and rRNAs forming large/small subunits
    • Eukaryotic ribosomes combine 40S and 60S to form 80s ribosomes, prokaryotic are 30S and 50S forming 70S

    Ribosome Structure

    • rRNA determines overall ribosome shape
    • tRNAs bind to A, P, and E sites for polypeptide elongation

    Three Stages of Translation

    • Initiation - mRNA, tRNA, and ribosomal subunits combine
    • Elongation - Ribosome moves along mRNA, forming polypeptide chain
    • Termination - Stop codon signals the end of translation and release of the polypeptide chain

    Translation Initiation in Bacteria

    • mRNA binds to the small ribosomal subunit
    • Initiator tRNA binds to the start codon (AUG)
    • Large ribosomal subunit binds to form the complete initiation complex

    Eukaryotic Initiation

    • mRNAs lack ribosomal binding sites
    • Cap-binding proteins and initiation factors required
    • Start codon is more variable and often the first AUG codon

    Elongation -1

    • Aminoacyl-tRNA binds to A site on ribosome
    • Recognized by codon/anticodon matching
    • Peptidyl tRNA is in P site

    Elongation -2

    • Peptide bond forms between amino acids at A and P sites
    • Catalyzed by rRNA (ribozyme activity)
    • Polypeptide chain moves from P site to A site

    Elongation -3

    • Ribosome shifts along the mRNA by one codon
    • Uncharged tRNA moves from P to E site exiting
    • New aminoacyl-tRNA enters A site

    Termination

    • Translation stops when a stop codon is reached in the A site
    • Release factors bind and complete polypeptide release, leading to ribosome sub-unit dissociation

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