Molecular Biology: DNA Replication Quiz

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Questions and Answers

Which of the following protein complexes is responsible for initially recognizing and binding to the DNA origin of replication?

Cdt1

PCNA

Helicase

Origin Recognition Complex (ORC) (correct)

During DNA replication, which enzyme is primarily responsible for synthesizing the RNA primer on both the leading and lagging strands?

Primase within α-polymerase (correct)

DNA polymerase ε

Ligase

DNA polymerase δ

What is the function of topoisomerase during the initiation of DNA replication?

Separating the two DNA strands at the origin

Stabilizing single-stranded DNA templates

Creating the phosphodiester bonds within the newly synthesized DNA strand

Relaxing the DNA supercoils ahead of the replication fork (correct)

Which of these enzymes is responsible for the synthesis of Okazaki fragments during DNA replication?

DNA polymerase ε (A) Signup and view all the answers

What is the role of RFC (Replication Factor C) during DNA replication?

To deposit PCNA at the primer-template DNA hybrid site. (D) Signup and view all the answers

Which enzyme is primarily responsible for removing the RNA primers and iDNA fragments on the lagging strand?

RNase H/FEN1 (A) Signup and view all the answers

What is the primary function of DNA ligase during DNA replication?

To join Okazaki fragments together. (C) Signup and view all the answers

During transcription, what direction is the template DNA strand read?

3’ → 5’ direction (D) Signup and view all the answers

Which RNA polymerase synthesizes mRNA precursors?

RNA polymerase II (C) Signup and view all the answers

What is the purpose of polyadenylation during post-transcriptional processing of mRNA?

To add a sequence of adenine nucleotides to the 3' end (D) Signup and view all the answers

Which of the following best describes the role of the MCM 2-7 protein complex in DNA replication?

It breaks hydrogen bonds between complementary nitrogenous bases. (B) Signup and view all the answers

What would be the most likely consequence if topoisomerases were not functioning during DNA replication?

The torsional stress in the DNA would prevent further unwinding. (C) Signup and view all the answers

What is the primary function of the Replication Protein A (RPA) during DNA replication?

To prevent the formation of hydrogen bonds in single-stranded DNA. (D) Signup and view all the answers

The Proliferating Cell Nuclear Antigen (PCNA) performs which of the following roles during DNA replication?

It acts as a scaffold for the recruitment of proteins involved in DNA replication. (A) Signup and view all the answers

What is the role of Replication Factor C (RFC) in DNA replication?

It opens the PCNA ring and loads it onto DNA (C) Signup and view all the answers

Which statement accurately describes the activity of DNA polymerases during DNA replication?

They require a DNA template to function. (D) Signup and view all the answers

Which of the DNA polymerases is responsible for the synthesis of the RNA primer?

Polymerase α/primase (B) Signup and view all the answers

What is the primary activity of RNase H during DNA replication?

It removes the iRNA primer except for the last ribonucleotide. (B) Signup and view all the answers

Which of the following is the primary function of aminoacyl-tRNA synthetase?

Attaching the appropriate amino acid to its corresponding tRNA. (B) Signup and view all the answers

What is the function of FEN1 in DNA replication?

It removes the last ribonucleotide of the iRNA primer. (C) Signup and view all the answers

During translation initiation, what is the specific role of fmet-tRNAf?

To bind to the P site of the ribosome in the absence of large ribosomal subunit. (A) Signup and view all the answers

What is the role of DNA ligase in the final stages of DNA replication?

It joins Okazaki fragments on the lagging strand. (C) Signup and view all the answers

What is the role of the ribosome's peptidyl transferase activity?

To catalyze the formation of peptide bonds between amino acids. (B) Signup and view all the answers

What is the specific purpose of the 'scanning' process during translation initiation?

Locating the first AUG start codon for translation within the mRNA sequence. (C) Signup and view all the answers

During translation elongation, what occurs immediately after the formation of a peptide bond?

The tRNA carrying the growing polypeptide chain moves from the A site to the P site. (A) Signup and view all the answers

During translation, which site within the ribosome does the tRNA molecule carrying the growing polypeptide chain occupy prior to translocation?

The A site. (C) Signup and view all the answers

What is the function of release factors during translation?

To bind the stop codon in the A site of the ribosome, and release the synthesized polypeptide. (A) Signup and view all the answers

Which of the following is NOT considered a post-translational modification?

Attachment of tRNA to amino acid (A) Signup and view all the answers

What is the role of chaperone proteins?

To assist in the correct folding of newly synthesized polypeptides. (A) Signup and view all the answers

Which process does result in the addition of a sugar residue to a protein?

Glycosylation. (A) Signup and view all the answers

Study Notes

DNA Replication, Transcription, and Translation

This is a study guide for DNA replication, transcription, and translation.
The key references are Essential Cell Biology by Bruce Alberts, 6th Edition.

DNA Replication

Replication is a semiconservative process. Each strand of the double helix serves as a template for the new, complementary strand.
DNA synthesis proceeds only in the 5' → 3' direction.
Newly added nucleotides are joined by phosphodiester bonds.
DNA replication is enzymatic, requiring numerous protein complexes.
Energy is needed for this process, derived from the hydrolysis of high-energy phosphate bonds.
Key proteins involved:
- Helicase (MCM 2-7 complex): Unwinds DNA by breaking the hydrogen bonds between complementary nitrogenous bases. The MCM 2-7 proteins use ATP during this process.
- Topoisomerases: Relieve torsional stress in DNA caused by unwinding. There are two types, topoisomerase I and topoisomerase II.
- Replication protein A (RPA): Binds to single-stranded DNA segments to prevent the formation of hydrogen bonds and allow DNA polymerase to function.
- PCNA: A ring-shaped homotrimer that acts as a scaffold for proteins involved in DNA replication, repair, chromatin remodeling, and epigenetic regulation. Protects DNA polymerase from falling off the template strand and releases DNA polymerase after each Okazaki fragment is synthesized.
- Replication factor C (RFC): Opens PCNA protein trimer in the presence of ATP, guides DNA into the center of the ring, and then closes the ring to aid in PCNA placement.
- DNA polymerases (α, β, γ, δ, ε): Synthesize DNA; α adds the initial DNA strand; δ and ε are involved in leading and lagging strand synthesis.
- RNase H: Removes RNA primers except for the last one.
- FEN1: Removes the last ribonucleotide of the RNA primer.
- Ligase: Joins deoxyribonucleotides to form phosphodiester bonds by using ATP; specifically, it links Okazaki fragments on the lagging strand.

DNA Replication process limitations/stages

The need to unwind the DNA double helix.
The inability of DNA polymerase to independently initiate the synthesis of a new strand.
The addition of nucleotides occurs only in the 5' → 3' direction.
The specific starting point and sequence within the DNA strand where replication begins.
DNA strand replication involves origin recognition and formation of a pre-replication complex (pre-RC).
The process occurs at origins of replication, which are specific 10,000 base pair sequences in the DNA, thus creating replication factories/foci.
A fragment of DNA replicated from one origin is called a replicon.
Replication forks are formed (bidirectional).
Leading vs. Lagging Strands:
- The leading strand is synthesized continuously.
- The lagging strand is synthesized in sections called Okazaki fragments.

Overview of DNA Replication Stages

Initiation:
- Recognizing origins of replication.
- Forming a pre-RC: ORC attachment, recruitment of Cdt1 and Cdc6, and helicase attachment.
- Separating DNA strands: Helicase breaks hydrogen bonds; Topoisomerases relax supercoils; SSBs stabilize single-stranded DNA to prevent re-annealing.
Elongation:
- Leading strand synthesis: Continuous.
- Lagging strand synthesis: Discontinuous, creating Okazaki fragments.
- Primers: Synthesized by primase. RNase H/ FEN1 removes primers.
- Okazaki fragment synthesis: Completed by DNA polymerase.
- Joining Okazaki fragments: Done by DNA ligase.
Termination:
- Meeting of replication forks.
- Terminal sequences.
- Disintegration of replication complex.
- Telomere synthesis.

Transcription

Transcription is the process of rewriting genetic information from DNA to RNA.
It is based on the complementarity rule (A-U, C-G).
The unit of transcription is the section of DNA between the promoter and the terminator.
DNA is read in the 3' → 5' direction.
RNA (mRNA, rRNA, tRNA) is synthesized in the 5' → 3' direction.
The process is catalyzed by RNA polymerases (I, II, and III). Each type synthesizes different kinds of RNA.

Transcription Stages

Initiation: Formation of a pre-initiation complex involving RNA polymerase and transcription factors. This complex binds to the promoter region to initiate transcription.
Elongation: RNA polymerase moves along the template strand, synthesizing the RNA transcript in the 5' → 3' direction.
Termination: Signals from a terminator sequence cause RNA polymerase to detach from the DNA, releasing the newly made RNA molecule.

Post-transcriptional Processing

Maturation of pre-mRNA to mRNA includes:
- Capping the 5' end.
- Splicing: Removing introns and joining exons (RNA splicing).
- Polyadenylation (adding a poly-A tail) to the 3' end.

Translation

Translation is the synthesis of a polypeptide chain from an mRNA template.
This process is catalyzed by ribosomes, taking place in the cytoplasm and on the rough endoplasmic reticulum.
The core includes polypeptide chain synthesis based on the mRNA sequence and the formation of peptide bonds.

Ribosome Structure

Ribosomes consist of two subunits: small and large.
Both subunits contain proteins and rRNA.
The subunits are only connected during translation.
Subunits contain binding sites for tRNA (aminoacyl-tRNA (A), peptidyl-tRNA (P), and exit site (E)).

Translation Stages

Initiation:
- Pre-initiation complex formation (small ribosomal subunit, initiation factors, and initiator tRNA).
- Small subunit binds to the mRNA 5'UTR, and scans for an AUG start codon.
- Large subunit joins, forming a functional ribosome. Initiator tRNA occupies the P site, and the A site is ready for the next aminoacyl-tRNA.
Elongation:
- Cycles: Consist of binding of tRNA carrying amino acids at the A site, peptide bond formation in the P site, translocation (shifting of ribosome on mRNA), and release of an uncharged tRNA from the E site.
Termination:
- STOP codons (UAA, UAG, UGA) are encountered.
- Release factors bind to the A site.
- Peptidyl transferase adds a water molecule to the chain, releasing the completed polypeptide.
- Ribosome dissociates.

Post-translational Modifications

Many proteins require modifications to function (correct folding, proteolytic processing, cofactor binding etc.)
Specific chemical groups may be added or removed (e.g., phosphorylation, glycosylation).
Chaperone proteins facilitate proper protein folding.
Incorrectly folded proteins can be degraded.

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Description

Test your knowledge on the key processes and enzymes involved in DNA replication and transcription. This quiz covers essential concepts such as the roles of specific protein complexes, enzymes, and mechanisms critical for accurate genetic replication and expression. Perfect for students in molecular biology courses.