Molecular Biology: DNA Replication & Transcription

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Questions and Answers

What is the role of the Rho factor in Rho-dependent termination of transcription?

It binds to a pause site on the RNA transcript.

It converts mRNA into amino acids.

It binds to the rut site on mRNA and helps disassociate RNA polymerase. (correct)

It synthesizes mRNA from the DNA template.

What structural feature is characteristic of Rho-independent termination?

The formation of a hairpin loop in the RNA transcript. (correct)

Binding of Rho factor to the mRNA.

A specific sequence on the DNA template strand.

The presence of a poly-A tail in the mRNA.

Which protein is involved in the Rho-independent termination process?

NusA protein (correct)

RNA polymerase

Rho factor

Ribosomal RNA

What is the main outcome of Rho factor's helicase activity during transcription termination?

It causes the mRNA and RNA polymerase to disassociate. Signup and view all the answers

What are the three major structures required for the process of translation?

mRNA, ribosomes, and amino acids. Signup and view all the answers

How is the lagging strand synthesized during DNA replication?

Intermittently as DNA is unwound Signup and view all the answers

What role does DNA ligase play in DNA replication?

It joins Okazaki fragments together Signup and view all the answers

What is produced as DNA polymerase moves away from the replication fork on the lagging strand?

Okazaki fragments Signup and view all the answers

What does DNA polymerase I do during DNA replication?

It removes RNA primers and replaces them with DNA Signup and view all the answers

What connects the 3’-OH of a growing strand to the 5’-phosphate of an Okazaki fragment?

Phosphodiester bonds formed by DNA ligase Signup and view all the answers

What occurs at the termination site during bidirectional replication?

Replication forks meet and conclude synthesis Signup and view all the answers

Which of the following is true about Okazaki fragments?

They are shorter than the leading strand Signup and view all the answers

How many terminator sequences are reported to exist on the E. coli chromosome?

Ten Signup and view all the answers

What role do sigma factors play in transcription initiation?

They help RNA polymerase recognize promoter sequences. Signup and view all the answers

Which sigma factor in E. coli is primarily responsible for transcribing most genes during normal cell growth?

RpoD (σ70) Signup and view all the answers

What process occurs when RNA polymerase denatures a short stretch of DNA?

Transcription bubble formation Signup and view all the answers

What replaces thymine in RNA during transcription?

Uracil Signup and view all the answers

How does the cell control the expression of specific genes?

By regulating sigma factor availability. Signup and view all the answers

Which type of organisms possess unique sigma factors for transcription initiation?

Prokaryotes only Signup and view all the answers

In which part of the transcription process does RNA polymerase synthesize RNA at a rate of approximately 45 bases per second?

Elongation Signup and view all the answers

What drives the addition of nucleotides during the RNA synthesis process?

Hydrolysis of high-energy phosphate bonds from incoming nucleotides Signup and view all the answers

What is the primary role of transfer RNA (tRNA) in translation?

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

How many unique codons are there in the genetic code?

64 Signup and view all the answers

What does the term 'wobble' refer to in the context of codons?

The flexibility of base pairing for the third codon position. Signup and view all the answers

What is the correct description of a codon?

A sequence of three nucleotides that specifies an amino acid. Signup and view all the answers

Why is the genetic code considered to be redundant?

Some amino acids can be coded by multiple codons. Signup and view all the answers

Which statement correctly describes the universality of the genetic code?

It is universal with some minor variations in certain organisms. Signup and view all the answers

What is the final step in the expression of protein-encoding genes?

Decoding mRNA into amino acids at the ribosome. Signup and view all the answers

What is the significance of the 'wobble position' in relation to mutations?

It minimizes the effects of some mutations on amino acid sequences. Signup and view all the answers

What is the function of the start codon in translation?

It serves as the start site for translation. Signup and view all the answers

Which of the following describes the role of stop codons in translation?

They function to terminate the translation process. Signup and view all the answers

What are the three sites found in a ribosome during translation?

Acceptor, peptidyl, and exit sites. Signup and view all the answers

What is the role of ribosomal RNA (rRNA) in ribosome function?

It contributes to ribosome structure and catalyzes peptide bond formation. Signup and view all the answers

During which stage of protein synthesis is the first amino acid placed in position?

Initiation. Signup and view all the answers

What does the elongation stage of translation involve?

The sequential addition of amino acids as specified by mRNA. Signup and view all the answers

Which molecule catalyzes the formation of peptide bonds during translation?

Peptidyl transferase within rRNA. Signup and view all the answers

How is the ribosome correctly aligned on the mRNA during translation initiation?

By binding to the Shine-Dalgarno sequence via 16S rRNA. Signup and view all the answers

Study Notes

Replication Fork Dynamics

The lagging strand is synthesized intermittently as DNA is unwound.
DNA polymerase only synthesizes in the 5' to 3' direction.
The lagging strand produces Okazaki fragments as DNA polymerase moves away from the replication fork.
DNA polymerase 1 removes RNA primers and replaces them with DNA.
DNA ligase joins the fragments together.

Terminating Replication and Segregating Sister Chromosomes

Bidirectional replication results in the two replication forks meeting each other at a termination site halfway around the chromosome.
There are as many as ten terminator sequences (ter) on the E. coli chromosome.
DNA strands start to separate at 10 base pairs upstream (TAT AAT).

Transcription: Initiation

RNA polymerase needs help to recognize the promoter.
Sigma factors recognize different promoter sequences in the genome.
The number and type of sigma factors vary between bacterial species.
The cell controls gene expression by controlling the availability of sigma factors.
In E.coli, there exist seven sigma factors, with RpoD (σ70) being the “housekeeping” sigma factor, transcribing most genes in growing cells.
RpoH (σ32) is a “heat shock” sigma factor, turned on when bacteria are exposed to heat, expressing heat shock proteins like DNA repair enzymes.
RNA polymerase denatures a short stretch of DNA to expose nucleotides for transcription.
Sigma factors are unique to prokaryotes.
Sigma factors are homologous to transcription factor B in archaea and Transcription factor II B in eukaryotes.

Transcription: Elongation

RNA polymerase moves along the template, synthesizing RNA at 45 bases per second.
RNA is synthesized using the (-) / antisense strand as a template.
Uracil replaces thymine in RNA.
Energy for elongation is provided by hydrolyzing the high-energy phosphate bond from incoming nucleotides.

Transcription: Termination

RNA polymerase continues until it reaches a terminator.
There are two main transcription termination signals in bacteria: Rho factor dependent and Rho independent.
Rho-dependent termination uses a protein called Rho and a strong pause site at the end of the gene.
Rho-independent termination relies on a GC-rich terminator sequence that forms a hairpin loop in the RNA transcript.
This loop structure causes the newly synthesized mRNA to be released and the polymerase to disassociate.

Rho-Dependent Termination

Rho factor binds to a rut site on mRNA and scans until it reaches RNA polymerase, which is stalled at a pause site.
Rho's helicase activity causes everything to disassociate.

Rho-Independent Termination

A GC-rich terminator sequence forms a hairpin loop in the RNA transcript.
Along with the NusA protein, the hairpin loop causes the newly synthesized mRNA to be released and the RNA polymerase to disassociate.

Translation Overview

It converts information from mRNA (nucleic acids) to synthesize proteins (chains of amino acids).
Requires three major structures: mRNA, ribosomes, and tRNA.
mRNA carries the information.
Ribosomal RNA (rRNA) serves as a scaffold for the ribosome.
tRNA converts the information from mRNA to protein by carrying amino acids to the ribosome.

Translation - Messenger RNA (mRNA)

Carries information.
Must be decoded into amino acids by ribosomes.
A codon, a three base pair long genetic code word, specifies an amino acid.

The Genetic Code

The genetic code is three nucleotides long, called a codon.
There are 64 different codons.
The code is universal and used by all living things.
The code is redundant, meaning up to six different codons can code for a single amino acid.
The third position of the codon is the wobble position, which is less important than the 1^st or 2^nd.

Wobble

Wobble allows for less strict base pairing in the third position of the codon.
It eliminates the need for a unique tRNA for each codon.
It decreases the effect of some mutations.

Translation - Start Codon

AUG encodes for the amino acid methionine and is the start site for translation.
Aligns the ribosome on the correct reading frame.

Translation- Sense Codons

61 codons that specify the ~20 amino acids.

Translation - Stop Codons

Three codons, UAA, UAG, and UGA, do not encode amino acids and terminate translation.
Recognized by release factor.

Translation - Ribosomes

Ribosomes are the translation "machines".
Composed of proteins and rRNA.
Link amino acids together to make polypeptides.
Recognize and bind to the ribosome-binding site.
Begin translation at the start codon and move along the mRNA in a 5' to 3' direction.
Catalyze the formation of a peptide bond between amino acids.

The Ribosome

Consists of the A (acceptor) site, where tRNA carrying amino acids binds.
P (peptidyl) site, where tRNA attached to the growing polypeptide chain binds.
E (exit) site, where empty tRNA leaves the ribosome.

Role of Ribosomal RNA (rRNA) in Translation

16S rRNA is needed for initiation of translation.
It binds to the Shine-Dalgarno sequence (ribosome binding site).
Binds to the 3' CCA end of aminoacyl-tRNA.
23S rRNA is a ribozyme that catalyzes peptide bond formation.

The Three Stages of Protein Synthesis

Polypeptide synthesis happens in three stages: initiation, elongation, and termination.
Initiation brings the two ribosomal subunits together with mRNA, placing the first amino acid at the start codon.
Elongation sequentially adds amino acids as directed by the mRNA transcript via tRNA.
Termination is when the stop codon and release factor release the completed protein and recycle the ribosomal subunits.

The Three Stages of Protein Synthesis in More Detail

Initiation: The ribosome assembles around the mRNA and the first tRNA carrying methionine attaches to the start codon, AUG, of the mR NA.
Elongation: The ribosome moves along the mRNA, reading codons and adding the corresponding amino acids to the growing polypeptide chain.
Termination: The ribosome encounters a stop codon, UAA, UAG, or UGA. A release factor protein binds to the stop codon causing the ribosome to detach from the mRNA and the polypeptide is released.

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Description

This quiz covers key concepts in DNA replication and transcription processes, including the roles of various enzymes like DNA polymerase and RNA polymerase. Understand the dynamics of replication forks, lagging strand synthesis, and the initiation of transcription. Test your knowledge on terminator sequences and gene expression control.