Lecture 7

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Questions and Answers

What is the primary role of the MCM 2-7 protein complex in DNA replication?

Joining Okazaki fragments

Breaking hydrogen bonds between DNA strands (correct)

Preventing the formation of DNA hairpins

Synthesizing RNA primers

Which enzyme is responsible for relieving torsional stress during DNA unwinding?

Helicase

Primase

DNA ligase

Topoisomerase (correct)

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

Joining Okazaki fragments

Proofreading DNA replication work

Preventing the formation of single-stranded DNA hairpins (correct)

Synthesizing the leading strand

Which protein forms a ring-shaped homotrimer that acts as a scaffold for proteins involved in DNA replication and repair?

PCNA (A) Signup and view all the answers

What is the main role of RFC (Replication Factor C) protein?

Opening and placing PCNA onto DNA (D) Signup and view all the answers

Which of the following is NOT a characteristic of DNA polymerases?

They can initiate DNA synthesis independently (B) Signup and view all the answers

Which enzyme synthesizes the initial RNA primer during DNA replication?

Primase unit of polymerase α (C) Signup and view all the answers

What is the function of the FEN1 enzyme during DNA replication?

Removing the last ribonucleotide of the RNA primer (B) Signup and view all the answers

In what direction does DNA synthesis occur?

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

Which enzyme activity is used by DNA polymerase to proofread its work?

3' → 5' exonuclease (D) Signup and view all the answers

Which enzyme is responsible for joining Okazaki fragments?

DNA ligase (C) Signup and view all the answers

Which DNA polymerase is primarily involved in synthesizing the leading strand?

Polymerase δ (B) Signup and view all the answers

What is a replicon?

A fragment of DNA replicated from one origin (D) Signup and view all the answers

Which molecular complex unwinds the DNA double helix at the origin of replication?

MCM 2-7 complex (A) Signup and view all the answers

Which of these does NOT remove RNA?

Ligase (D) Signup and view all the answers

Which protein complex is responsible for recognizing and binding to the DNA origin of replication?

Origin Recognition Complex (ORC) (C) Signup and view all the answers

In what direction does DNA polymerase synthesize a new DNA strand during replication?

5' to 3' (C) Signup and view all the answers

What is the function of primase during DNA replication?

It synthesizes RNA primers (C) Signup and view all the answers

What are Okazaki fragments?

Short DNA fragments synthesized on the lagging strand (C) Signup and view all the answers

Which enzyme is responsible for joining Okazaki fragments together?

Ligase (D) Signup and view all the answers

What is the role of telomeres in DNA replication?

They prevent the shortening of the lagging strand during replication (A) Signup and view all the answers

Which enzyme is responsible for synthesizing mRNA during transcription?

RNA Polymerase II (D) Signup and view all the answers

What is the function of a promoter in transcription?

It is the DNA region where transcription begins (D) Signup and view all the answers

What is added to the 5’ end of the pre-mRNA during post-transcriptional processing?

Cap (D) Signup and view all the answers

What happens to introns during post-transcriptional processing?

They are spliced out and removed from the pre-mRNA (B) Signup and view all the answers

What is added to the 3' end of a mature mRNA during polyadenylation?

A series of adenine nucleotides (C) Signup and view all the answers

How does helicase participate in DNA replication?

By unwinding the DNA double helix (D) Signup and view all the answers

Which activity is associated with RNA polymerase II

Transcription of genes encoding messenger RNA (mRNA) (C) Signup and view all the answers

Which enzyme is responsible for relaxing supercoiled DNA ahead of the replication fork?

Topoisomerase (D) Signup and view all the answers

Which protein stabilizes ssDNA once the duplex DNA has been unzipped?

RPA (D) Signup and view all the answers

Where does the process of translation typically occur within a cell?

In the cytoplasm and on the rough endoplasmic reticulum (B) Signup and view all the answers

What is the role of the ribosome during translation?

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

Which of the following is NOT a tRNA binding site found on the ribosome?

T site (termination site) (B) Signup and view all the answers

What is the first amino acid in every polypeptide chain synthesized during translation?

Formylmethionine (D) Signup and view all the answers

Which tRNA is involved in the initiation stage of translation?

fmet-tRNAf (A) Signup and view all the answers

Which complex scans for the AUG start codon on the mRNA?

Small ribosomal subunit, initiator tRNA, mRNA (A) Signup and view all the answers

What event occurs immediately after the AUG codon is recognized on the mRNA during translation initiation?

The large ribosomal subunit binds to the complex. (B) Signup and view all the answers

During translation elongation, what is the role of the A site on the ribosome?

It is the site where the tRNA carrying the next amino acid binds. (A) Signup and view all the answers

What enzyme is responsible for catalyzing peptide bond formation?

Peptidyl transferase (A) Signup and view all the answers

During translation elongation, after the peptide bond formation, where does the tRNA without an amino acid move to?

The E site (A) Signup and view all the answers

Which of the following is a stop codon that signals the end of translation?

UAG (B) Signup and view all the answers

What type of protein binds to the stop codon to terminate translation?

Release factor (A) Signup and view all the answers

What does the activity of peptidyl transferase during termination?

Adds a water molecule to peptidyl-tRNA (D) Signup and view all the answers

What is the role of chaperone proteins in post-translational modifications?

They facilitate the correct folding of newly synthesized proteins (A) Signup and view all the answers

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

Transcription (C) Signup and view all the answers

Which of these is the correct order of events in the formation of the pre-replication complex (pre-RC)?

ORC binding to DNA, followed by Cdt1 and Cdc6 recruitment, then helicase recruitment. (B) Signup and view all the answers

What is the role of topoisomerase in DNA replication?

To relax supercoils that form during DNA unwinding. (D) Signup and view all the answers

What is the defining characteristic of the synthesis of the lagging strand during DNA replication?

It is synthesized in segments called Okazaki fragments. (C) Signup and view all the answers

During DNA replication, what is the function of RFC (Replication Factor C)?

To exchange the alpha polymerase for the delta or epsilon polymerase. (A) Signup and view all the answers

What provides the energy necessary for the attachment of a deoxynucleotide to a growing DNA strand?

Hydrolysis of a phosphate bond of the incoming deoxynucleotide triphosphate. (D) Signup and view all the answers

What is the key enzyme responsible for adding DNA nucleotides to Okazaki fragments after the primer has been removed?

ε-polymerase (D) Signup and view all the answers

What is the function of RNase H/FEN1 in DNA replication?

They remove RNA primers from Okazaki fragments. (B) Signup and view all the answers

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

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

What is the main reason why the lagging strand is shorter than the template strand at the end of a linear chromosome?

The RNA primer cannot be replaced at the end of the lagging strand. (C) Signup and view all the answers

In which direction is the template DNA strand read during transcription?

3' → 5' (A) Signup and view all the answers

Which RNA polymerase is responsible for transcribing genes encoding transfer RNA (tRNA)?

RNA polymerase III (A) Signup and view all the answers

What is the first step in freeing RNA polymerase II from transcription factors to initiate RNA synthesis?

The addition of phosphate groups to its tail. (D) Signup and view all the answers

What is the function of a transcription terminator sequence?

It marks the end of the gene and signals the termination of transcription. (A) Signup and view all the answers

What event occurs during the splicing of pre-mRNA?

Removal of introns and joining of exons. (A) Signup and view all the answers

What is the 'polyadenylation' process?

Addition of a series of adenine nucleotides to the 3' end of the mRNA. (B) Signup and view all the answers

What is the primary function of the ribosome during translation?

To catalyze the synthesis of polypeptide chains (C) Signup and view all the answers

During which stage of translation does the ribosome form peptide bonds?

Elongation (C) Signup and view all the answers

Which of these components is part of a ribosome's structure?

rRNA (D) Signup and view all the answers

Which amino acid is always the first to initiate protein synthesis?

Methionine (C) Signup and view all the answers

What role does aminoacyl-tRNA synthetase play in translation?

It attaches amino acids to their corresponding tRNA (C) Signup and view all the answers

Which site on the ribosome is responsible for holding the newly arrived aminoacyl-tRNA during the elongation stage?

A site (B) Signup and view all the answers

What initiates the transition from the initiation to the elongation stage in translation?

Attachment of the large ribosomal subunit (C) Signup and view all the answers

What does the presence of a STOP codon signal during translation?

Termination of translation (C) Signup and view all the answers

What happens to the polypeptide chain at termination of translation?

It is released from the last tRNA (B) Signup and view all the answers

Which of the following modifications is NOT typically part of post-translational modifications?

Transcription (D) Signup and view all the answers

What is the role of release factors during termination of translation?

To recognize the STOP codon (B) Signup and view all the answers

What is the function of chaperone proteins during post-translational modifications?

To assist in correct protein folding (A) Signup and view all the answers

Which of the following is NOT an amino acid modification during post-translational modification?

Decarboxylation (D) Signup and view all the answers

Which of the following best describes the energy source for the formation of phosphodiester bonds during DNA replication?

Hydrolysis of high-energy phosphate bonds (C) Signup and view all the answers

What is the primary function of topoisomerases during DNA replication?

To reduce torsional stress generated by DNA unwinding (A) Signup and view all the answers

How does the RPA protein facilitate DNA replication?

By binding to single-stranded DNA and preventing the formation of double-stranded fragments (A) Signup and view all the answers

How does the PCNA protein contribute to the efficiency of DNA replication?

By acting as a scaffold for recruiting proteins involved in DNA replication and repair and keeping DNA polymerase attached to the template strand (B) Signup and view all the answers

What is the role of the RFC protein in DNA replication?

It hydrolyzes ATP and opens the PCNA protein trimer and loads the DNA inside it. (C) Signup and view all the answers

Which of the following best describes the activity of Polymerase α/primase?

It synthesizes 10 nucleotides of RNA primer, then adds 20-30 deoxynucleotides DNA stretch. (B) Signup and view all the answers

What is the exonuclease activity of DNA polymerases used for during replication?

Proofreading the newly synthesized DNA (C) Signup and view all the answers

What is the function of endoribonucleases in the context of DNA replication?

To cleave RNA strands in the middle of the chain (B) Signup and view all the answers

Which enzyme is responsible for removing the last ribonucleotide of the RNA primer in DNA replication?

FEN1 (C) Signup and view all the answers

What is the role of DNA ligase during DNA replication?

To join DNA fragments by forming phosphodiester bonds (A) Signup and view all the answers

What is a key limitation of DNA polymerase during DNA replication that requires the use of a primer?

It cannot initiate DNA synthesis independently (B) Signup and view all the answers

What is the role of replication factories ('replication foci') during DNA replication?

They contain multiple origins of replication where DNA unwinding occurs. (C) Signup and view all the answers

What is the name of the DNA fragment replicated from one replication origin?

Replicon (C) Signup and view all the answers

Which of the following is the correct order of events leading to DNA strand synthesis?

RNA primer synthesis -> iDNA synthesis -> DNA polymerase 𝛿/𝜀 action (A) Signup and view all the answers

Given a mutation that inactivates the exonuclease activity of DNA polymerase, what would the most likely consequence be?

An increase in mismatches in the DNA (A) Signup and view all the answers

Study Notes

DNA Replication, Transcription, and Translation

This topic covers the fundamental processes of DNA replication, transcription, and translation essential for molecular biology.
Recommended reading material includes Chapter 6 (DNA Replication and Repair) and Chapter 7 (From DNA to Protein) from Essential Cell Biology, 6th Edition.
DNA replication is semiconservative. Each strand serves as a template for a new, complementary strand.
DNA synthesis proceeds only in the 5' to 3' direction.
The reaction is enzymatic requiring numerous protein complexes and energy input from high-energy phosphate bonds.

DNA Replication Proteins

Helicase (MCM 2-7): A protein complex that forms a ring around a single DNA strand, breaking hydrogen bonds between complementary bases.
Topoisomerases (I & II): These enzymes change the DNA's topology reducing torsional stress.
Replication Protein A (RPA): Binds to single-stranded DNA to stabilize it and prevent re-pairing.
Proliferating Cell Nuclear Antigen (PCNA): Forms a ring structure acting as a scaffold, involved in replication and repair processes, protecting DNA polymerase from falling off the template strand and releasing it after each Okazaki fragment is synthesized.
Replication Factor C (RFC): A ring-applying protein that loads PCNA onto the DNA strand. RFC opens the PCNA trimer in the presence of ATP, introduces DNA into the center of the ring, and then closes the ring.
DNA Polymerases (α, β, γ, δ, ε): Enzymes responsible for DNA synthesis. Different DNA polymerases have specific roles in DNA synthesis, such as polymerase delta preferring leading strand replication, while polymerase epsilon prefers lagging strand replication.
RNase H, FEN1 (exonuclease), and Ligase: Enzymes involved in removing RNA primers and joining Okazaki fragments on the lagging strand.

DNA Polymerase

DNA polymerases need a template and a primer to initiate synthesis.
Synthesis occurs in the 5' to 3' direction.
They have a proofreading mechanism (3' to 5' exonuclease activity), operating in polymerization and editing modes.
Primase, part of DNA polymerase alpha, synthesizes a short RNA primer for each Okazaki fragment. These RNA primers are complementary to the template strand and are around 10 nucleotides in length.
DNA polymerase delta and epsilon extend the RNA primer by adding DNA nucleotides.
The initial primer of 20-30 nucleotides for the synthesis of a new DNA strand is added by DNA polymerase alpha

Ribonucleases

RNase H removes RNA primers, except the last ribonucleotide in the DNA chain.
FEN1 removes the final ribonucleotide.
DNA ligase joins Okazaki fragments.

DNA Replication Limitations and Stages

Unwinding the DNA helix is necessary for replication, accomplished by helicase.
DNA polymerase cannot independently initiate a new DNA strand, requiring a primer.
Synthesis occurs in the 5' to 3' direction.
Replication begins with a primer synthesized by primase.
Polymerase α extends the primer for lagging strand synthesis.
After adding 20 to 30 deoxyribonucleotides, polymerase δ or ε begins its action
Replication occurs in stages: initiation, elongation, and termination.
Replication forks are asymmetric, leading to continuous synthesis of one strand and discontinuous synthesis (Okazaki fragments) on the other.
Replication forks have both leading and lagging strands.
Termination occurs when replication forks meet. Termination involves encountering terminal sequence, disintegration of replication complex, and telomere synthesis.

Transcription

Transcription makes RNA from a DNA template.
rRNA, mRNA, and tRNA are produced.
The process involves initiation, elongation, and termination stages.
Initiation requires transcription factors and RNA polymerase II.
Elongation adds ribonucleotides according to the template.
Termination is signaled by a terminator sequence on the DNA.
Post-transcriptional processing includes capping, splicing, and polyadenylation.

Translation

Translation synthesizes a polypeptide chain based on an mRNA molecule.
Ribosomes use mRNA to translate amino acid codes.
It has three stages: initiation, elongation, and termination.
Initiation involves a pre-initiation complex containing a ribosomal subunit, initiation factors, and initiator tRNA (fmet-tRNAf).
Elongation involves adding amino acids to the growing polypeptide chain through successive cycles, including tRNA binding to a site, peptide bond formation, and translocation of the ribosome.
Termination occurs when a stop codon in the mRNA is reached. Release factors bind to the stop codon, triggering polypeptide release. Post-translational modifications are needed to achieve full functionality.

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Description

Test your knowledge on the key proteins and enzymes involved in DNA replication. This quiz covers the roles of various complexes and enzymes such as MCM, DNA polymerases, and RFC, as well as the processes that facilitate DNA synthesis and repair. Challenge yourself with questions about the mechanics of DNA unwinding and synthesis!