DNA Structure and Replication

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Questions and Answers

Which chemical linkage is responsible for creating the backbone of a single strand of DNA?

  • Hydrophobic interaction
  • Peptide bond
  • Hydrogen bond
  • Phosphodiester bond (correct)

What does the term 'directionality' refer to in the context of a DNA strand?

  • The complementary base pairing rules (A with T, G with C).
  • The specific sequence of nucleotides.
  • The orientation of the strand, defined by the 5' and 3' ends. (correct)
  • The ability of DNA to form a double helix.

Which of these enzymes is NOT directly involved in bacterial DNA replication?

  • Primase
  • DNA Polymerase I
  • RNA Polymerase (correct)
  • DNA Polymerase III

During DNA replication in bacteria, what is the PRIMARY function of DNA ligase?

<p>To seal the gaps between Okazaki fragments on the lagging strand. (A)</p> Signup and view all the answers

Why is the high fidelity of replicative DNA polymerases essential for cell survival?

<p>To ensure accurate transmission of genetic information to daughter cells. (B)</p> Signup and view all the answers

What is the primary reason telomeres are composed of repetitive sequences?

<p>To provide a binding site for proteins that protect the ends of chromosomes from degradation. (C)</p> Signup and view all the answers

How does negative supercoiling contribute to bacterial DNA compaction and function?

<p>It compacts the DNA and facilitates strand separation for replication and transcription. (D)</p> Signup and view all the answers

What is the role of topoisomerases in managing DNA topology?

<p>They introduce or remove supercoils in DNA to relieve torsional stress. (D)</p> Signup and view all the answers

Which of the following BEST describes the arrangement of DNA within a nucleosome?

<p>DNA is tightly wound around a core of eight histone proteins. (B)</p> Signup and view all the answers

What information does capillary electrophoresis data provide in STR profiling?

<p>The length of the DNA fragments containing the STR loci. (D)</p> Signup and view all the answers

In the context of STR profiling and population genetics, what does the Hardy-Weinberg Equilibrium (HWE) principle allow us to predict?

<p>The genotype frequencies in a population based on allele frequencies. (D)</p> Signup and view all the answers

During PCR for STR analysis, what is the function of the primers used?

<p>To initiate DNA synthesis at the target STR region. (A)</p> Signup and view all the answers

Which strand of DNA is used by RNA polymerase as a template during bacterial transcription?

<p>The non-coding (antisense) strand. (C)</p> Signup and view all the answers

During bacterial transcription, what is the role of the sigma factor?

<p>To recognize and bind to specific promoter sequences on the DNA. (D)</p> Signup and view all the answers

How does the 'open complex' contribute to the initiation of bacterial transcription?

<p>It allows single-stranded DNA regions for RNA polymerase to access the template strand. (C)</p> Signup and view all the answers

Which of the following BEST describes the primary difference between RNA polymerase and DNA polymerase in their ability to initiate strand synthesis?

<p>DNA polymerase requires a primer to initiate synthesis, while RNA polymerase does not. (C)</p> Signup and view all the answers

What is the function of general transcription factors (GTFs) in eukaryotic transcription initiation?

<p>They assist in the recruitment of RNA polymerase II to the promoter. (C)</p> Signup and view all the answers

In eukaryotic transcription, what is the role of enhancers and silencers?

<p>They regulate transcription by interacting with transcription factors. (C)</p> Signup and view all the answers

How does termination of transcription in eukaryotes differ from that in bacteria?

<p>Eukaryotic termination is often coupled with RNA processing events, while bacterial termination is more direct. (A)</p> Signup and view all the answers

What is the primary function of the 5' cap and 3' poly-A tail added to eukaryotic mRNA molecules?

<p>To protect mRNA from degradation and enhance translation efficiency. (C)</p> Signup and view all the answers

Flashcards

Nucleotide structure

A nucleotide consists of a nitrogenous base, a pentose sugar (ribose or deoxyribose), and one to three phosphate groups.

DNA structure: Bonds & Carbons

Phosphodiester bonds link nucleotides, 1'-5' carbons in ribose give directionality, forming the DNA backbone.

DNA Complementarity/Directionality

DNA strands are complementary (A with T, G with C) and run in opposite directions (5' to 3' and 3' to 5').

RNA vs DNA structure

RNA contains ribose sugar, uses uracil (U) instead of thymine (T), and is typically single-stranded.

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Holoenzyme definition

A holoenzyme is a complete, active enzyme consisting of an apoenzyme (protein portion) and a cofactor (non-protein portion).

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Key Bacterial DNA Replication Enzymes

Primase synthesizes RNA primers, Polymerases I/III replicate DNA, Topo-II relieves supercoiling, Helicase unwinds DNA, Ligase joins fragments.

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DNA Pol I vs. DNA Pol III

DNA pol I has 5'-3' exo activity (removes RNA primers); DNA pol III is the main replication enzyme.

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Telomeres and Telomerase

Telomeres are repetitive sequences at chromosome ends, protected by telomerase to prevent degradation.

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Bacteria vs Eukaryote DNA

Bacteria have circular DNA, no nucleus; Eukaryotes have linear DNA, nucleus, and more complex DNA organization.

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High Polymerase Fidelity

Replicative DNA polymerases have high fidelity that is achieved through proofreading.

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Supercoiling

Supercoiling is the overwinding (positive) or underwinding (negative) of DNA, affecting DNA compaction.

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Topoisomerases I/II

Topoisomerases relieve torsional stress during DNA replication by cutting and rejoining DNA strands.

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Eukaryotic Compaction

Eukaryotic DNA is compacted into chromatin, involving nucleosomes and histone proteins.

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Nucleosome Structure

Nucleosomes are basic units of chromatin, consisting of DNA wrapped around histone proteins.

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Open Complex

Open complex is the region of DNA unwound for transcription initiation. Sequence helps its formation for polymerase binding.

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Consensus Sequence

Consensus sequences are highly conserved DNA sequences that are used by the polymerase to bind to the DNA.

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Eukaryotic Initiation

Transcription initiation in eukaryotes involves general transcription factors (GTFs) binding to the promoter region.

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Basal Transcription

Basal transcription is the minimal level of transcription needed, supported by GTFs at the core promoter.

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Enhancers and Silencers

Enhancers increase transcription; silencers decrease transcription. Some elements act in cis, some in trans.

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mRNA Modifications

Modifications include 5' capping, splicing, and 3' polyA tailing, affecting stability and translation.

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Study Notes

DNA Structure

  • Nucleic acids are composed of nucleotides consisting of a sugar, a phosphate group, and a nitrogenous base
  • DNA features phosphodiester bonds and 1'-5' carbons in its ribose structure
  • Double-stranded DNA exhibits complementarity and directionality
  • RNA structure differs from DNA

DNA Replication

  • Replication complex: Includes various proteins and enzymes necessary for DNA replication
  • Holoenzyme: the complete, functional form of an enzyme complex, including all necessary subunits and cofactors
  • Bacterial DNA replication: involves initiation, elongation, and termination
  • Key enzymes: primase, DNA polymerases I and III, Topoisomerase II, helicase, and DNA ligase, along with 5'-3' and 3'-5' exonuclease activities
  • DNA Polymerases I and III differ in exonuclease activities
  • Telomeres and telomerase ensure the protection of free DNA ends
  • Significant differences exist in DNA replication in bacteria versus eukaryotes
  • Replicative DNA polymerases exhibit high fidelity
  • Processivity is a characteristic of replicative DNA polymerases
  • Conditional mutants are vital for studying essential genes, including those involved in DNA replication

DNA Organization in Chromosomes

  • Bacterial DNA: compaction occurs at different levels and can involve supercoiling (positive and negative) with topoisomers and topoisomerases I/II
  • Eukaryotic DNA: levels of compaction involve specific proteins
  • Nucleosomes are composed of specific components
  • DNAse I in the Knoll's experiment was used to discover the nucleosomal "DNA footprint"

STR Profiling

  • Capillary electrophoresis data interpretation is used in STR profiling
  • Hardy-Weinberg Equilibrium (HWE) is applied in calculations of random chance expectations for STR profiles
  • PCR test kits require a specific number of primers for one STR locus within a population, located with respect to the locus

Bacterial Transcription

  • Transcription: initiation, elongation, and termination must be explained in detail
  • Cis-acting and trans-acting elements are involved
  • Anti-sense strand and sense strand must be defined
  • Open complex: required for transcription
  • DNA sequence facilitates its formation
  • RNA and DNA polymerases differ uniquely in their ability to initiate strand synthesis, howevery, they share some similarities
  • Consensus sequence: important in bioinformatics
  • Protein binding sites tend to be well-conserved DNA sequences
  • Sigma factor functions in a specific manner
  • Termination in bacteria: occurs through two different mechanisms

Eukaryotic Transcription

  • Transcription initiation in eukaryotes involves general transcription factors (GTFs)
  • GTFs have a specific order of operations
  • Basal transcription must be defined
  • Enhancers, silencers, and transcription factors function as cis- or trans-acting elements
  • Three RNA polymerases in eukaryotes transcribe different genes
  • Termination: similarities and differences exist between eukaryotes and bacteria

RNA Modification

  • There are six types of RNA modification, each modifying RNA specifically
  • Splicing and processing are two major forms of RNA modification. Splicing does not typically occur out of order, and it involves cis- and trans-acting elements
  • Introns have a specific advantage
  • 5' capping and 3' polyA-tailing modifications are important

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