Molecular Biology Quiz: DNA Replication and CFTR

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Questions and Answers

What characterizes the role of CFTR protein in epithelial cells?

It acts as a chloride ion transporter. (correct)

It is responsible for protein synthesis.

It exports sodium ions out of the cell.

It helps in glucose absorption.

What is the consequence of CFTR mutations?

Decreased sodium absorption and mucus hydration.

Increased chloride export and mucus hydration.

No effect on electrolyte balance.

Increased sodium reabsorption and mucus dehydration. (correct)

Which enzyme is responsible for synthesizing the RNA primer required by DNA polymerase?

DNA ligase

DNA primase (correct)

DNA helicase

RNA polymerase

What direction does DNA polymerase synthesize new DNA strands?

5' to 3' Signup and view all the answers

How does the replication bubble form in prokaryotes?

By initiator proteins recognizing and binding to the ORI. Signup and view all the answers

What is the role of exonuclease activity in DNA polymerases?

To remove incorrectly paired nucleotides. Signup and view all the answers

In semiconservative replication, how many new strands are created from one original strand?

Two Signup and view all the answers

How many nucleotides can prokaryotic DNA polymerase synthesize per second?

1000 Signup and view all the answers

What is the synthesis direction of DNA polymerase?

5' to 3' Signup and view all the answers

Which enzyme is responsible for sealing the backbone of DNA strands during replication?

Ligase Signup and view all the answers

What is the primary function of the enzyme helicase in DNA replication?

To unwind the DNA double helix Signup and view all the answers

What are Okazaki fragments primarily formed on?

Lagging strand Signup and view all the answers

Why is it important that DNA polymerase builds in the 5' to 3' direction?

To allow the addition of triphosphate for energy Signup and view all the answers

During DNA replication in prokaryotes, the origin of replication (ORI) can be activated under which condition?

When it is fully methylated Signup and view all the answers

Which of the following statements about DnaA is true?

It binds to specific sequences to induce torsional stress Signup and view all the answers

What characteristic of A-T base pairs makes them easier to break open during DNA replication?

They contain fewer hydrogen bonds than C-G pairs Signup and view all the answers

What is the primary function of constitutive heterochromatin?

To contain genes that do not need to be expressed or cannot be expressed Signup and view all the answers

In Sanger sequencing, what is the role of ddNTPs?

To stop DNA synthesis upon incorporation Signup and view all the answers

What characterizes facultative heterochromatin?

It can switch between compact and relaxed states. Signup and view all the answers

Which of the following components is NOT required for Sanger sequencing?

DNA ligase Signup and view all the answers

What is one disadvantage of Sanger sequencing?

It can only sequence up to about 750 bp. Signup and view all the answers

How do eukaryotic ribosomes differ from prokaryotic ribosomes in terms of size?

Eukaryotic ribosomes are about three times larger than prokaryotic ribosomes. Signup and view all the answers

What role do small nucleolar RNAs (snoRNAs) play in eukaryotic rRNA synthesis?

They attach to rRNA for modifications and cleaving. Signup and view all the answers

What is typically included in the reaction mixtures of Sanger sequencing?

dNTPs, ddNTPs, and DNA polymerase Signup and view all the answers

What prevents the incorporation of a second nucleotide in the dNTPs sequencing process?

The absence of a 3' OH group Signup and view all the answers

Which step in the sequencing process ensures that the 3' OH group becomes available again?

Cleave the fluorescent label Signup and view all the answers

What technique is employed to address the problems associated with tandem repeats in genome sequencing?

Employing higher sequencing depth Signup and view all the answers

What is a major challenge when sequencing genomes with low sequencing depth?

Unreliable results in less sequenced regions Signup and view all the answers

How are overlapping sequences managed when assembling new genomes?

Aligning against known genomes Signup and view all the answers

What is the role of CRISPR/Cas9 in gene editing?

To precisely adjust genes in living cells Signup and view all the answers

Why can genome-wide repeats lead to incorrect linking in genome sequencing?

They can confuse the software alignment process Signup and view all the answers

What approach is used in site-directed mutagenesis to introduce mutations?

Designing specific primers for PCR Signup and view all the answers

What is the primary function of the CRISPR/Cas9 system in bacteria?

To serve as a defense mechanism against phages Signup and view all the answers

Which of the following DNA manipulations can be achieved using recombinant DNA techniques?

Gene induction Signup and view all the answers

What type of repair process is Non-Homologous End Joining (NHEJ)?

Fast but often inaccurate Signup and view all the answers

Which option describes a key component of the CRISPR/Cas9 editing tool?

Customizable guide RNA (gRNA) Signup and view all the answers

When does homologous recombination occur during the cell cycle?

After DNA replication in S/G2 phase Signup and view all the answers

What characterizes the DNA sequence targeted by the customized guide RNA in the CRISPR/Cas9 system?

It is specific for a predetermined location Signup and view all the answers

Which of the following is NOT a system used in modern recombinant DNA technology?

Transcription Factor Mutagens Signup and view all the answers

What is the primary function of Hsp70 chaperone during translation?

To bind to hydrophobic parts of polypeptides and prevent premature folding. Signup and view all the answers

What are the components of tRNA crucial for its function?

Anticodon and a binding site for an amino acid. Signup and view all the answers

Which statement best describes wobbling in the context of tRNA?

It refers to an incorrect nucleotide pairing leading to a different amino acid. Signup and view all the answers

What role does rRNA play in the ribosome's function?

It provides structure and catalyzes peptide bond formation. Signup and view all the answers

During prokaryotic initiation of translation, what is the first step?

Binding of the small ribosomal subunit and initiation factors to the ribosome binding site. Signup and view all the answers

What is the function of the large ribosomal subunit during translation?

Forms peptide bonds between amino acids. Signup and view all the answers

How many possible reading frames are there in mRNA?

Three. Signup and view all the answers

What is the initial state of the ribosome before elongation begins?

The initiator tRNA is bound to the start codon with the small subunit. Signup and view all the answers

Study Notes

DNA Replication and Molecular Cloning

The central dogma of molecular biology states that information flows from nucleic acids (DNA and RNA) to proteins, but not the other way around.
DNA is a right-handed double helix with major and minor grooves. Both strands contain complementary information.
Nucleotides consist of a phosphate group, a sugar group, and a base. Pyrimidines (one ring) include cytosine, thymine, and uracil. Purines (two rings) include adenine and guanine.

Organization of the Genome

Prokaryotes have no nucleus and circular genomic DNA that is free within the cell. They also lack organelles and always have a cell wall. One gene typically codes for one protein and there is a higher gene density.
Eukaryotes have a nucleus and linear genomic DNA within the nucleus. They have organelles and plant cells only have cell walls. One gene can code for multiple proteins with lower gene density.

DNA and RNA Structure

DNA is a right-handed double helix with major and minor grooves. Both strands are complementary.
RNA is typically single-stranded and shorter than DNA. RNA can have complex three-dimensional structures when it contains self-complementary sequences. RNA nucleotides contain ribose instead of deoxyribose.

Histone Proteins and Acetylation

Histone proteins and DNA form nucleosomes.
Chemical modifications (e.g., methylation and acetylation) of histone subunits influence their interaction with DNA. Acetylation reduces the interaction strength.
Histone deacetylase complexes (HDAC) inhibitors are used in cancer treatment.

PCR (Polymerase Chain Reaction)

PCR is a method of amplifying a specific piece of DNA using DNA polymerase.
PCR requires primers that target specific sequences and DNA polymerases. Primers are short, single-stranded DNA sequences.
PCR has three main steps: denaturation, annealing, and elongation.

DNA Replication in Prokaryotes and Eukaryotes

Replication is usually bidirectional, starting at the origin of replication.
Enzymes like DNA polymerase, helicase, and ligase are involved.
DNA polymerase builds in the 5' to 3' direction.
Okazaki fragments are segments of newly synthesized DNA on the lagging strand.
DNA polymerase synthesizes DNA in the 5' to 3' direction, while it reads the template in the opposite 3' to 5' direction.
DNA polymerase requires a primer to start DNA synthesis.

Central Dogma

DNA → RNA → Protein (Transcription and Translation).

Cloning Vectors

Cloning vector: a DNA molecule that can carry DNA fragments, which you want to clone
Restriction nucleases cut the plasmid.
DNA ligases join DNA fragment into the vector.
Recombinant DNA results from the combination of vector and fragment.

Origin of Replication (in Prokaryotes)

DNA replication begins at the origin of replication (ORI).
Proteins like DnaA, DnaB, and DnaG are involved in initiating replication.

Origin of Replication (in Eukaryotes)

The origin recognition complex (ORC) recognizes the origin of replication (ORI) in eukaryotes.
Proteins such as Abf1 attract ORC to specific sequences.

DNA Polymerases

DNA polymerases synthesize DNA in the 5' to 3' direction using a DNA template. They require a primer (RNA), made by DNA primase.
Different DNA polymerases exist, and some have exonuclease activity, including 3' to 5' proofreading.

Transcription in Prokaryotes

Prokaryotes have one type of RNA polymerase.
Transcription starts at the promoter region and ends at the terminator region of DNA.
Transcription factors are not needed for the initiation of transcription in prokaryotic cells.
The specific o-factor for a given promoter is important in regulating gene expression.
Transcription initiates when the o-factor associates with RNA polymerase.

Transcription in Eukaryotes

Eukaryotes have three types of RNA polymerases.
Transcription occurs in the nucleus and requires numerous factors for initiation.
mRNA undergoes processing (capping, splicing, polyadenylation) before translation.

tRNA and rRNA synthesis

tRNAs have a cloverleaf shape and are important in translation.
rRNA is a part of the ribosome, the site of protein synthesis, and comes in different sizes in different species.

Protein Folding

Proteins fold into a 3D structure that is determined by interactions between amino acids, including covalent and other non-covalent bonds. This final shape determines protein function.

Mutations

Point mutations: include silent, missense or nonsense.
Deletions and insertions (in-frame or out-of-frame) can alter the amino acid sequence.

Protein Degradation and Aggregation

Misfolded or damaged proteins must be removed.
Protein aggregation occurs when misfolded proteins accumulate in cells leading to cellular damage.
Protein chaperones are involved in folding
Protein degradation systems are important to remove misfolded, damaged or unnecessary proteins

Reporter Genes

Reporter genes assist in tracking protein expression and localization.
Often used to track promoter activity.

DNA Footprinting

Footprinting identifies DNA-protein interactions by protecting DNA regions from degradation. The protected area indicates the location of the protein bound on the DNA strands.

Next-Gen Sequencing

Sequencing methods like Illumina and Oxford Nanopore are used to sequence large portions of the genome.

Site-Directed Mutagenesis

A method to alter specific genes in a targeted way.
Site-directed mutagenesis in eukaryotic cells can be achieved utilising CRISPR/ Cas9.

Gene editing techniques

Precisely adjusting/correcting genes in living cells.
CRISPR/ Cas9, zinc finger nucleases and transcription activator-like effector nucleases are different gene editing methods.

Cloning Steps

Extract the DNA of interest from an organism.
Using Restriction enzymes, cut your DNA fragment.
Inserting the fragment into a plasmid.
Insert the recombinant plasmid into a bacteria.
Grow bacteria and isolate plasmids containing the inserted segment
Validate the clone by confirming that the gene/DNA you want to express is present.

DNA methylation and acetylation

Key regulatory mechanisms for gene expression.
Acetylation and methylation affect gene expression by modifying chromatin structure.
DNA methylation typically represses gene expression, while acetylation usually activates it.

RNA Interference (RNAi)

Method of regulating gene expression at the gene level via introduction of double-stranded RNA's.
This approach interferes with protein synthesis.

CRISPR-Cas9

Widely used gene editing tool based on a bacterial immune system.
It precisely targets specific DNA sequences and can introduce changes.

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Description

Test your knowledge on the essential roles of the CFTR protein and the process of DNA replication. This quiz covers topics such as CFTR mutations, the synthesis of RNA primers, and the functioning of DNA polymerase in both eukaryotic and prokaryotic cells. Perfect for students interested in molecular biology and genetics.