Molecular Biology: RNA and Genome Basics

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Questions and Answers

What role does allolactose play in the lac operon system?

  • It acts as a repressor directly preventing transcription.
  • It binds to the repressor, preventing it from binding to the operator. (correct)
  • It inhibits the activity of beta-galactosidase.
  • It functions as a corepressor, halting lactose metabolism.

In the absence of tryptophan, what happens to the trp operon?

  • The repressor binds to the operator, halting transcription.
  • The operon is permanently inactive regardless of other conditions.
  • RNA polymerase binds to the operator and transcription begins. (correct)
  • Tryptophan is synthesized at a slow rate.

Which statement about catabolite repression is true?

  • Lactose is used preferentially over glucose at all times.
  • Lactose metabolism is fully induced in the presence of glucose.
  • Glucose serves as a less preferred carbon source compared to lactose.
  • Bacteria will grow faster when glucose is present rather than when it is depleted. (correct)

What occurs when tryptophan is in excess within the trp operon?

<p>Tryptophan binds to the repressor, allowing it to bind to the operator. (A)</p> Signup and view all the answers

What is the impact of glucose depletion on bacterial growth when lactose is present?

<p>Bacterial growth slows down but continues after glucose is gone. (B)</p> Signup and view all the answers

What type of mutation is characterized by the addition of one or more bases?

<p>Insertion mutation (D)</p> Signup and view all the answers

What is the primary consequence of a nonsense mutation?

<p>Shorter, non-functional proteins (A)</p> Signup and view all the answers

What type of mutation has no effect on the protein's structure?

<p>Silent mutation (A)</p> Signup and view all the answers

Which event can lead to frameshift mutations due to distortion of DNA?

<p>Intercalating agents (C)</p> Signup and view all the answers

What is a characteristic of chemical mutagens?

<p>Modify normal DNA bases (A)</p> Signup and view all the answers

How does a missense mutation typically affect protein function?

<p>May provide a beneficial change (D)</p> Signup and view all the answers

What is the mutation rate for an average gene during cell division?

<p>One in a million replicated genes (A), One in a billion replicated base pairs (D)</p> Signup and view all the answers

What type of radiation can lead to the formation of thymine dimers?

<p>Non-ionizing radiation (A)</p> Signup and view all the answers

What distinguishes the initiator tRNA in prokaryotes from that in eukaryotes?

<p>Prokaryotes use fMet, while eukaryotes use Met. (C)</p> Signup and view all the answers

Which site on the ribosome is primarily responsible for the formation of peptide bonds?

<p>P site (B)</p> Signup and view all the answers

During translation termination, what event occurs at the A site?

<p>Alignment with nonsense codons. (D)</p> Signup and view all the answers

What is the role of mutagens in mutation?

<p>They are agents that cause mutations. (D)</p> Signup and view all the answers

What is the primary role of histone-like proteins in microbial genetics?

<p>To package and stabilize DNA (B)</p> Signup and view all the answers

What characterizes frameshift mutations?

<p>They involve insertions or deletions of nucleotides. (C)</p> Signup and view all the answers

What is the significance of plasmids in bacterial cells?

<p>They carry genes that can provide advantageous traits through horizontal gene transfer. (A)</p> Signup and view all the answers

Which structural feature is absent in eukaryotic mRNA compared to prokaryotic mRNA?

<p>Shine-Dalgarno sequence (A)</p> Signup and view all the answers

During DNA replication, which enzyme is responsible for synthesizing the new complementary DNA strand?

<p>DNA polymerase III (A)</p> Signup and view all the answers

What role does the E site on the ribosome play during translation?

<p>It releases dissociated tRNAs for recharging. (C)</p> Signup and view all the answers

In the semiconservative model of DNA replication, what does each newly formed double-stranded DNA consist of?

<p>One conserved strand and one newly synthesized strand (C)</p> Signup and view all the answers

How do ribosome sizes differ between bacteria and eukaryotes?

<p>Bacterial ribosomes (70S) are smaller than eukaryotic ribosomes (80S). (D)</p> Signup and view all the answers

What occurs at the origin of replication in prokaryotes?

<p>Topoisomerase II initiates DNA unwinding (A)</p> Signup and view all the answers

Which statement about transcription is accurate?

<p>It produces mRNA by directly copying DNA. (D)</p> Signup and view all the answers

What is the primary function of topoisomerase during DNA replication?

<p>To relax supercoiled DNA strands (C)</p> Signup and view all the answers

What is the primary purpose of the central dogma in molecular biology?

<p>To describe the flow of genetic information within a cell (C)</p> Signup and view all the answers

What is the primary function of mRNA in cellular processes?

<p>To carry the message from DNA to make a protein (D)</p> Signup and view all the answers

What is the characteristic shape of tRNA during protein synthesis?

<p>Clover shape in 2D and L shape in 3D (D)</p> Signup and view all the answers

What is a key characteristic of rRNA?

<p>Makes up 60% of a ribosome and has a stable structure (A)</p> Signup and view all the answers

Which of the following correctly describes the role of genes?

<p>Segments of DNA that encode functional products, usually proteins (C)</p> Signup and view all the answers

How do eukaryotic chromosomes differ from prokaryotic chromosomes?

<p>Eukaryotic chromosomes are linear, diploid, and consist of multiple distinct chromosomes (D)</p> Signup and view all the answers

What is the function of topoisomerases in relation to DNA?

<p>They prevent DNA supercoiling during replication (D)</p> Signup and view all the answers

Which of the following statements about RNA is NOT true?

<p>All types of RNA are stable and long-lived (A)</p> Signup and view all the answers

What best defines the term 'genotype'?

<p>The full collection of genes within an organism's genome (B)</p> Signup and view all the answers

What initiates the transcription process in bacteria?

<p>The binding of sigma factor to the promoter (B)</p> Signup and view all the answers

What is one of the key differences between eukaryotic and prokaryotic mRNAs?

<p>Eukaryotic mRNAs undergo processing before translation (D)</p> Signup and view all the answers

How does RNA polymerase add nucleotides during transcription?

<p>To the 3'-OH group of the growing RNA strand (B)</p> Signup and view all the answers

Which statement describes the process of termination in prokaryotic transcription?

<p>Termination can be Rho-independent or influenced by Rho protein (B)</p> Signup and view all the answers

What role does the 5' cap play in eukaryotic mRNA processing?

<p>It provides a binding site for ribosomes (D)</p> Signup and view all the answers

What is the role of the sigma factor in bacterial transcription?

<p>Directs RNA polymerase binding to the specific promoter (D)</p> Signup and view all the answers

Which of the following accurately describes the transcription speed of RNA polymerase during elongation?

<p>40 nucleotides per second (A)</p> Signup and view all the answers

What happens to the DNA double helix during the transcription process?

<p>It is only partially unwound to form a transcription bubble (B)</p> Signup and view all the answers

Flashcards

Eukaryotic Translation Initiation

In eukaryotes, translation initiation does not use a Shine-Dalgarno sequence but instead utilizes a 5' cap and a 3' poly-A tail.

Ribosome Binding Sites

The ribosome has three sites (A, P, E) to hold tRNAs during protein synthesis.

Peptide Bond Formation

A peptide bond forms between the amino group of the amino acid in the A site and the carboxyl group of the amino acid in the P site.

Ribosomal Translocation

The ribosome moves along the mRNA, shifting tRNAs from the A to P to E sites.

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Termination of Translation

Translation stops when a stop codon enters the A site, and release factors detach the polypeptide.

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Ribosome Size Difference (Prokaryotes vs. Eukaryotes)

Prokaryotic ribosomes are 70S (30S + 50S subunits), while eukaryotic ribosomes are 80S (40S + 60S subunits).

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Initiator tRNA

The first tRNA that binds to the ribosome during translation.

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Point Mutation

A mutation affecting a single base of DNA.

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Haploid Chromosome

A single copy of each chromosome.

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mRNA

Single-stranded molecule that carries genetic instructions from DNA to ribosomes for protein synthesis.

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Extrachromosomal DNA

DNA found outside of the chromosome, but part of the genome.

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rRNA

RNA component of ribosomes; essential for protein synthesis by aligning mRNA, tRNA, and ribosomes, and catalyzing peptide bond formation.

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DNA Replication

Making a copy of DNA. The process of duplicating the DNA molecule.

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tRNA

Small RNA molecule that carries amino acids to ribosomes during protein synthesis; matches mRNA's codon with its anticodon.

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Genome

Complete set of genetic material of an organism, including chromosomes and plasmids.

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Semiconservative Replication

DNA replication where each new DNA molecule has one original and one new strand.

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Origin of Replication

Specific sequence where DNA replication begins.

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Chromosome

Structure that carries genetic information as DNA; organized and packaged DNA within the cells.

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DNA Polymerase III

Enzyme that adds nucleotides to the growing DNA strand during replication.

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Eukaryotic Chromosome

Linear chromosomes found in eukaryotic cells; packaged with histones; several chromosomes exist per cell.

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Prokaryotic Chromosome

Circular chromosomes in prokaryotic cells; single chromosome resides in the nucleoid.

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5' → 3' DNA synthesis

DNA is synthesized in this direction, adding nucleotides to the 3' end.

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Functions of DNA

  1. Inheritance, 2) proteins synthesis regulation.
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Chromatin

Complex of DNA and proteins (histones) that forms chromosomes in eukaryotic cells.

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Lac Operon

A gene system in bacteria that controls the production of enzymes needed for lactose metabolism.

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Repressible Operon

A gene system in bacteria where protein synthesis stops, due to excess amounts of the product that acts as corepressor.

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Catabolite Repression

The regulation of gene expression based on the availability of preferred carbon sources. Glucose is preferred over lactose.

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Allolactose

A molecule that acts as an inducer in the lac operon by binding to the repressor and preventing it from attaching to the operator.

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Corepressor

A molecule that binds to a repressor protein to activate it and allow cessation of production of proteins.

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Point Mutation

A change in a single DNA base.

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Silent Mutation

Changes the DNA sequence but doesn't change the amino acid.

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Missense Mutation

Changes the DNA sequence, leading to a different amino acid.

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Nonsense Mutation

Changes the DNA sequence, producing a premature stop codon.

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Insertion Mutation

Addition of one or more bases into a DNA sequence.

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Deletion Mutation

Removal of one or more bases from a DNA sequence.

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Frameshift Mutation

Mutations that shift the reading frame of the mRNA.

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Mutagen

An agent, like chemicals or radiation, increasing the rate of mutations.

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RNA Polymerase

Enzyme that builds RNA molecules from DNA templates during transcription.

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Transcription Initiation

The start of RNA production where RNA polymerase binds to DNA to begin creating RNA.

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Promoter Sequence

Specific DNA sequence where RNA polymerase binds to start transcription.

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Transcription Elongation

RNA polymerase extends the RNA chain as it moves along the DNA template.

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Transcription Termination

The end of RNA synthesis, marked by the separation of RNA polymerase and the newly made RNA from DNA.

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Monocistronic mRNA

Eukaryotic mRNA that codes for a single protein.

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Polycistronic mRNA

Prokaryotic mRNA that codes for multiple proteins.

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5' cap and 3' poly-A tail

Modifications added to pre-mRNA in eukaryotes to protect it from degradation and aid in translation.

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Study Notes

mRNA

  • Carries message from DNA to make protein
  • Single-stranded, complementary copy of DNA
  • Synthesized through transcription
  • Located in nucleus (eukaryotes) or cytoplasm (prokaryotes)
  • Directs protein synthesis (translation)
  • Interacts with ribosomes
  • Relatively unstable and short-lived

rRNA

  • Structural and catalytic role in ribosomes
  • Stable
  • Synthesized in nucleolus (eukaryotes) or cytoplasm (prokaryotes)
  • Makes up 60% of ribosomes
  • Ensures proper alignment of mRNA, tRNA, and ribosomes during translation
  • Catalyzes peptide bond formation (peptidyl transferase)

tRNA

  • Stable
  • Smallest type of RNA (70-90 nucleotides)
  • Carries correct amino acid to ribosome
  • Contains codon (mRNA) or anticodon (tRNA)
  • Intracellular base pairing creates characteristic 2D (clover) and 3D (L) shapes
  • Does not carry hereditary information (except some viruses)

Genome

  • All of an organism's genetic material
  • Includes chromosomes and plasmids

Chromosomes

  • Structures containing DNA that physically carry genetic information
  • Contain genes

Genes

  • Segments of DNA encoding functional products (usually proteins)

Genotype

  • Genetic makeup of an organism
  • Full collection of genes in the genome

Phenotype

  • Expression of genes
  • Observable characteristics

Eukaryotic chromosome

  • Linear
  • Multiple distinct chromosomes

Diploid

  • Two copies of each chromosome

Histones

  • DNA-binding proteins
  • DNA wraps around histones for attachment

Chromatin

  • Thread of DNA and attached histones
  • Influenced by environmental factors (DNA methylation and epigenetics)

Prokaryotic chromosome

  • Circular
  • Single chromosome in nucleoid
  • Haploid (one copy of each chromosome)

Extrachromosomal DNA

  • DNA external to chromosomes
  • Present in mitochondria and chloroplasts (circular)
  • Also present in DNA latent viruses in host cells
  • Includes plasmids (not essential for growth, but involved in horizontal gene transfer)

Chapter 11 - Mechanisms of Microbial Genetics

Functions of DNA

  • Inheritance
  • Directing/regulating protein synthesis
  • Cell growth & reproduction
  • One gene-one enzyme hypothesis

Central dogma

  • DNA → RNA → Protein

Transcription

  • Info from DNA is transferred to RNA (mRNA)

Translation

  • Info (mRNA) is used to build polypeptide proteins

DNA Replication

  • Proposed models (conservative, semiconservative, dispersive)
  • Semiconservative- each new double-stranded DNA includes one old strand and one new strand
  • Initiation- occurs at the origin of replication
  • Topoisomerase II(DNA gyrase) -relieves DNA supercoiling
  • Helicase- unzips DNA
  • Replication fork-Y shaped region
  • Bidirectional replication-two replication forks
  • Single-stranded binding proteins prevent single-stranded DNA from rejoining
  • Replication begins in 5' → 3' direction
  • DNA polymerase III adds nucleotides
  • RNA primer initiates replication
  • Complementary to template (RNA primase synthesizes)
  • Elongation- addition of nucleotides (1000/sec in prokaryotes)
  • Leading strand is synthesized continuously
  • Lagging strand is synthesized discontinuously, creating Okazaki fragments

RNA Transcription

  • Result is a complementary RNA transcript
  • RNA polymerase transcribes 5’ → 3’
  • Steps
    • Initiation
    • Elongation
    • Termination
  • Termination - RNA polymerase detaches from DNA
  • Rho-dependent or independent.
  • Transcription in bacteria - single RNA polymerase
  • Transcription in eukaryotes - three different RNA polymerases

Prokaryotic vs. Eukaryotic

  • mRNA: Prokaryotic - polycistronic (multiple polypeptides); eukaryotic - monocistronic (one polypeptide)
  • pre-mRNA processing before transport to cytoplasm
  • Addition of 5' cap and 3' poly A tail
  • Intron/exon splicing

Translation

  • Process of translating mRNA into amino acid language by ribosomes
  • Genetic code- relationship between mRNA codons and amino acids
  • Codons- groups of 3 amino acids
  • 64 possible codons (4³), code for 20 amino acids
  • Degeneracy—redundancy—same amino acid can be coded by several codons
  • Start codon AUG (sometimes also Met)
  • 3 nonsense codons (STOP)
  • Protein synthesis machinery includes mRNA template, tRNAs, and enzymatic factors

Ribosomes

  • Site of protein synthesis
  • Prokaryotes - 70S (30S + 50S); Eukaryotes - 80S (40S + 60S)
  • Initiation complex - mRNA, small 30S ribosome subunit, initiator tRNA carrying initiation amino acid, large 50S ribosome subunit
  • Elongation - mRNA read in 5' to 3' direction
  • A,P,E binding sites for tRNAs, amino acids chain elongation
  • Termination - release factors recognize stop codons, polypeptide released, ribosome subunit dissociates

Mutation

  • Heritable change in DNA
  • Types
    • Point mutations
      • Silent: no change in amino acid
      • Missense: change in amino acid.
      • Nonsense: creates a premature stop codon.
    • Frameshift mutations: addition or deletion of nucleotides
  • Mutagens: agents that increase mutation rate
    • Chemical (nitrous acid, nucleoside analogs, intercalating agents)
    • Radiation (ionizing/non-ionizing).

Gene Regulation

  • Operon model in prokaryotes (prokaryotic gene regulation)
    • Promoters, operators, regulatory genes
    • Operon - set of genes transcribed together
  • Repressible/inducible operons (lac operon, trp operon) - mechanisms using repressors/inducers to control gene expression.

Transfer Mechanisms

  • Transformation - uptake of naked DNA
  • Transduction - transfer of DNA via bacteriophages
  • Conjugation - direct transfer of DNA between cells

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