DNA Replication Overview

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Questions and Answers

What is the primary function of helicase during DNA replication?

To unwind the DNA double helix (correct)

To remove RNA primers

To synthesize the lagging strand

To add nucleotides to the growing DNA strand

Which enzyme is responsible for synthesizing the leading strand during DNA replication?

DNA Pol delta

DNA Pol epsilon (correct)

DNA Pol 1

Primase

What role do SSBP proteins play during DNA replication?

They introduce negative supercoils to prevent DNA breakage

They remove RNA primers

They protect single strand DNA from recombining (correct)

They bind to the origin of replication

In theta replication, what occurs after the DNA strands are split apart?

Two new DNA circles separate, completing replication Signup and view all the answers

What is the primary function of the MCM complex during DNA replication?

To unwind DNA for replication Signup and view all the answers

What is the key characteristic of rolling circle replication?

It creates a long continuous strand from a nicked DNA Signup and view all the answers

What is the function of ligase in DNA replication?

To bind and seal together DNA strands Signup and view all the answers

Which component of the RNA Polymerase holoenzyme is responsible for the catalysis of RNA synthesis?

Beta subunit Signup and view all the answers

What protective role do telomeres play in chromosomes?

They protect chromosomes from degradation Signup and view all the answers

What mechanism does Rho-independent termination utilize to stop transcription?

A hairpin followed by a string of uracils Signup and view all the answers

Which sequence is recognized to initiate translation in eukaryotic mRNA?

Kozak sequence Signup and view all the answers

Which enzyme removes RNA primers and replaces them with DNA nucleotides?

DNA Pol 1 Signup and view all the answers

Which RNA Polymerase is responsible for synthesizing rRNA genes for ribosome assembly?

RNA Pol I Signup and view all the answers

What role does the Sigma factor play in the RNA Polymerase holoenzyme?

It guides the holoenzyme to specific promoter regions Signup and view all the answers

Which protein recognizes the UAG and UAA stop codons during translation termination?

RF-1 Signup and view all the answers

What is the primary function of TFIID in the transcription initiation process?

To stabilize RNA Polymerase II binding Signup and view all the answers

What is a characteristic of somatic mutations?

They affect only body cells and not offspring. Signup and view all the answers

Which mutation turns an amino acid codon into a stop codon?

Nonsense Mutation Signup and view all the answers

What defines a frameshift mutation?

It shifts the reading frame of the gene. Signup and view all the answers

What happens during a tautomeric shift?

Bases pair incorrectly during replication. Signup and view all the answers

What is a gain of function mutation?

A mutation that enhances or creates a new protein function. Signup and view all the answers

Which type of mutation does not affect the protein's function?

Silent Mutation Signup and view all the answers

What is a dynamic mutation?

A mutation that changes in severity over generations. Signup and view all the answers

Which type of mutation compensates for the effects of another mutation?

Suppressor Mutation Signup and view all the answers

What is the function of aminoacyl tRNA synthetase?

To attach the correct amino acid to its matching tRNA Signup and view all the answers

Which component of the ribosome is primarily responsible for ensuring that the correct tRNA matches with the mRNA codons?

30S small ribosomal subunit Signup and view all the answers

What role does the Shine-Dalgarno sequence play in protein synthesis?

It serves as a recognition site for the ribosome to commence translation. Signup and view all the answers

Which IF protein is responsible for preventing premature tRNA binding at the ribosome's A site?

IF-1 Signup and view all the answers

What is the purpose of the EPA sites in the ribosome during translation?

To organize the binding and release of tRNAs during protein synthesis Signup and view all the answers

What is unique about Fmet tRNA in comparison to regular methionine tRNA?

It carries formylmethionine, initiating protein synthesis in bacteria. Signup and view all the answers

During protein synthesis, which of the following best describes the function of the 16S rRNA?

It binds to mRNA, ensuring correct codon recognition. Signup and view all the answers

Which factor plays a crucial role in bringing the initiator tRNA to the ribosome using GTP for energy?

IF-2 Signup and view all the answers

What role do guide RNAs play in cellular processes?

They direct enzymes to specific DNA or RNA targets. Signup and view all the answers

What is the significance of alternative splicing in RNA processing?

It allows for multiple proteins to be produced from a single gene. Signup and view all the answers

What is the primary function of tRNA during protein synthesis?

To bring amino acids to the ribosome. Signup and view all the answers

Which type of RNA is primarily involved in gene silencing?

miRNA Signup and view all the answers

What are the four levels of organization of proteins?

Primary, secondary, tertiary, quaternary Signup and view all the answers

What does lncRNA primarily do in cellular processes?

Regulate gene expression and chromatin structure. Signup and view all the answers

Which type of RNA is directly involved in the modification of rRNA?

snoRNA Signup and view all the answers

What does the one gene-one colinear polypeptide concept refer to?

The sequence of nucleotides in a gene determines the sequence of the resulting protein. Signup and view all the answers

What is the term for the loss of a purine base from DNA?

Depurination Signup and view all the answers

Which repair mechanism directly reverses DNA damage without cutting the strand?

Direct repair Signup and view all the answers

What type of mutation occurs when the wrong base is added to DNA during replication?

Incorporated error Signup and view all the answers

Which of the following describes the effect of hydroxylamine on cytosine?

It causes cytosine to pair incorrectly with adenine. Signup and view all the answers

What is an intercalating agent's primary function?

Causing insertions or deletions during replication Signup and view all the answers

Which of the following repair methods uses a matching DNA sequence as a guide for accurate repair?

Homology Directed Repair Signup and view all the answers

What mutation type happens when a piece of DNA is missing?

Deletion Signup and view all the answers

Which enzyme uses light energy to repair DNA damage caused by UV rays?

Photolyase Signup and view all the answers

Study Notes

DNA Replication

Theta replication: Circular DNA (like in bacteria) copies itself. It opens at an origin, forms a bubble, and two enzymes replicate DNA in opposite directions. Two new DNA circles result.
Rolling circle replication: A nick is created in one DNA strand. The intact strand acts as a template, while the nicked strand is unwound and copied. This creates a long continuous strand that can be cut into pieces later. This method is common in viruses and plasmids.
dNTPs: Building blocks of DNA, consisting of a deoxyribose sugar, a nitrogenous base, and three phosphate groups.
RNA primer: Short RNA strand that initiates DNA replication.
Initiator protein: Recognizes and binds to the origin of replication, starting the process.
Helicase: Unwinds the DNA double helix.
Gyrase: Introduces negative supercoils to prevent DNA from tangling or breaking during unwinding.
SSBP: Protein that binds to single-stranded DNA to stabilize it and prevent it from forming unwanted structures. This is important during replication or repair when DNA is single-stranded.
Primase: Creates short RNA primers.
DNA polymerase I: Removes RNA primers and replaces them with DNA nucleotides.
DNA polymerase II: Involved in DNA repair, helping fix errors during replication.
DNA polymerase III: Main enzyme for DNA replication; adds nucleotides to the growing DNA strand.
Ligase: Glues together DNA strands.
DNA Pol alpha: Starts DNA replication by adding initial RNA-DNA primer to DNA strand.
DNA Pol epsilon: Synthesizing leading strand during replication.
DNA Pol delta: Synthesizes lagging strand during DNA replication and helps with repair.
Nucleosome: Basic unit of DNA packaging in cells. Consists of DNA wrapped around histone proteins.
Histone: Proteins that help organize DNA into nucleosomes.
Chromatin: Material that makes up chromosomes. Consists of DNA wrapped around histone proteins, forming nucleosomes.
Telomere: Protective cap at the end of each chromosome. Prevents degradation and attachment to other chromosomes.
Telomerase: Enzyme that maintains telomere length by adding repetitive DNA sequences to their ends.
MCM Complex: Unwinds DNA for copying. A motor that helps open up DNA for other enzymes to work.
ORC: Protein group that binds to the origin of replication on DNA, marking the starting point for replication. Helps recruit other proteins that begin unwinding the DNA.

RNA Processing

rNTPs: Building blocks of RNA, consisting of a nitrogenous base, a ribose sugar, and three phosphate groups.
RNA polymerase holoenzyme: multi-part enzyme complex consisting of alpha (2 copies) beta, beta prime, and omega subunits. Sigma factor guides the RNA polymerase to promoter regions on DNA for initiation of transcription.
Rho dependent vs Rho independent transcription termination: Rho protein recognizes a specific RNA sequence, moves along the RNA, and disrupts the DNA-RNA hybrid to terminate transcription. Rho-independent termination relies on a hairpin loop followed by uracils to destabilize the DNA-RNA hybrid.
Kozak Sequence: Sequence that initiates translation (5'GCCa or gCCAUGG3').
EF-G, EF-Tu, Ef-Ts: Facilitate translocation, delivery of aminoacyl-tRNA, and guanine nucleotide exchange.
RF-1, RF-2, RF-3: Recognize stop codons and facilitate polypeptide release from the ribosome.
RNA polymerase I, II, III: Pol I transcribes rRNA genes, while Pol II transcribes mRNA, snRNA, and miRNA. Pol III transcribes tRNA, 5S rRNA etc.
TFIIA: Stabilizes binding of TFIID to promoter.
TFIIB: Helps RNA polymerase II recognize start site & bind to TFIID.
TFIID: Contains TBP (TATA-binding protein) that helps RNA polymerase to bind to the promoter.
TFIIE: Recruits/ Regulates TFIIH
TFIIF: Escorts RNA Pol II to promoter & stabilizes complex
TFIIH: Unwinds DNA, phosphorylates RNA Pol II to start transcription.
RAT1: 5' to 3' exonuclease in eukaryotes. Helps in transcription termination by degrading RNA from the 5' end.
PIC: Set of transcription factors assemble at promoter. They prepare DNA and RNA Pol for beginning transcription.
Mediator: Protein complex that links transcription factors to RNA polymerase II. It helps control gene expression by communicating between enhancers, promoters, and the transcription machinery.

Co-linearity, Codons, UTRs; mRNA processing

Co-linearity: Direct correspondence between DNA and amino acid sequence.
5' UTR and 3' UTR: Regions at the ends of mRNA that are not translated into protein but play roles in translation regulation and mRNA stability.
snRNAs: Type of RNA that assists in splicing.
Spliceosome: Complex of snRNAs and proteins that removes introns from pre-mRNA and joins exons.
3' Poly A Tail: String of adenines added to the 3' end of mRNA, protecting it from degradation.
5' cap: Modified guanine added to the 5' end of mRNA, aiding in translation.
Branch point: Special adenine in the middle of introns, crucial for splicing process.
Alternative splicing: Different combinations of exons are joined together, resulting in multiple RNA/mRNA versions from a single gene, creating more protein isoforms.

Gene Mutations and DNA Repair

Somatic mutations: Occur in body cells and affect only the individual.
Germinal mutations: Occur in gametes and can be inherited.
Base substitutions (transition/transversion): Changes in a single nucleotide base.
Insertions: Addition of nucleotides.
Deletions: Removal of nucleotides.
Frameshift mutations: Shifts the reading frame of the gene.
In-frame mutations/ deletions: Do not shift the reading frame but still change the protein.
Tautomeric shifts: Changes in chemical structure of bases leading to mispairing.
Dynamic mutations: Changes in severity over generations, often involves repeated expansions.
Forward mutation: Changes function in a typical direction.
Reverse mutation: Restores original function.
Missense mutation: Changes one amino acid.
Nonsense mutation: Changes a codon to a stop codon, shortening the protein.
Silent mutation: Changes codon, but not the amino acid.
Neutral mutation: Does not affect protein function.
Loss-of-function mutation: Reduces or eliminates protein function.
Gain-of-function mutation: Creates a new or enhanced function.
Conditional mutation: Phenotype change only under certain conditions.
Lethal mutation: Causes death, often during development.
Suppressor mutation: Compensates for another mutation.
Spontaneous replication errors: Mistakes in DNA copying that occur naturally.

Other Key Concepts

EPA sites: Ribosome binding sites during protein synthesis.
MET tRNA: Carries methionine in eukaryotes, initiating protein synthesis.
Endonuclease: Enzyme that cuts DNA within a strand.
Jumping Genes (Transposable Genetic Elements): DNA segments that can move within the genome, including: Class I and Class II retrotransposons
snoRNAs: modify rRNA by adding methyl groups, impacting ribosome function.
siRNAs and miRNAs: Involved in gene silencing (regulating gene expression) through mRNA degradation or blocking translation.
Crispr RNA: used for gene editing.
LncRNA: Non-coding RNA type, involved in gene expression, chromatin structure, and cellular processes.

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Description

Explore the intricate processes of DNA replication, focusing on theta and rolling circle replication methods. Learn about key components like dNTPs, RNA primers, and essential proteins involved in unwinding and stabilizing DNA. This quiz is essential for understanding molecular biology concepts related to DNA.