Module 4 - Gene Structure and Transcription

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Questions and Answers

What is the primary role of RNA polymerase during transcription?

To promote gene amplification

To splice introns from pre-mRNA

To synthesize RNA from a DNA template (correct)

To modify nucleotides post-transcriptionally

How do sense and antisense strands differ in the context of transcription?

The sense strand is non-coding while the antisense strand is coding.

Both strands are used equally in the transcription process.

The sense strand carries the coding information; the antisense strand serves as the template. (correct)

The antisense strand is expressed as protein while the sense strand is not.

What is the role of a promoter in gene expression?

To transcribe the coding region of a gene into a protein

To inhibit the binding of RNA polymerase

To provide a binding site for RNA polymerase to initiate transcription (correct)

To splice exons together during RNA processing

Which nucleotide structure is most directly responsible for the encoding of genes?

Exon Signup and view all the answers

What is the significance of non-coding DNA segments in prokaryotic and eukaryotic genomes?

They potentially regulate gene expression and have roles in genome architecture. Signup and view all the answers

Which strand of DNA serves as the template for RNA synthesis?

Antisense strand Signup and view all the answers

Which of the following accurately describes the RNA produced during transcription?

It is complementary to the template strand and a copy of the coding strand. Signup and view all the answers

What information determines the position and direction of RNA polymerase binding to DNA?

The regulatory elements of the gene including promoter/enhancer regions. Signup and view all the answers

What distinguishes prokaryotic genes from eukaryotic genes?

Prokaryotic genes lack introns and are organized into operons. Signup and view all the answers

What role does RNA polymerase play in the transcription process?

It synthesizes RNA from a DNA template. Signup and view all the answers

Which strand of DNA serves as the template for transcription?

Antisense strand Signup and view all the answers

In the context of eukaryotic genes, which of the following statements is true about introns?

They are removed from the primary transcript during processing. Signup and view all the answers

Which component of RNA differs from DNA in terms of nucleotide structure?

Ribose sugar instead of deoxyribose sugar Signup and view all the answers

What do the 5'-UTR and 3'-UTR refer to in the context of mRNA?

Untranslated regions that flank the coding sequence. Signup and view all the answers

What signifies the start of a protein-coding sequence in mRNA?

The presence of AUG codon Signup and view all the answers

How does the size of eukaryotic genes typically compare to prokaryotic genes?

Eukaryotic genes can be significantly larger, up to 50kB. Signup and view all the answers

Which of the following correctly describes the sense and antisense strands of DNA?

The sense strand has the same sequence as the mRNA produced, while the antisense strand is complementary. Signup and view all the answers

What is the main function of the sigma factor (s) in prokaryotic RNA polymerase?

Promoter recognition Signup and view all the answers

Which RNA polymerase is responsible for synthesizing messenger RNA (mRNA) in eukaryotes?

RNA polymerase II Signup and view all the answers

In eukaryotic transcription, what is the role of transcription factors such as TFIID?

Binding to promoters Signup and view all the answers

What characterizes the template strand in the process of transcription?

It is complementary to the RNA product Signup and view all the answers

During transcription, which part of the RNA polymerase holoenzyme is responsible for catalysis?

Beta subunits (b+b’) Signup and view all the answers

Which type of RNA polymerase is primarily responsible for synthesizing ribosomal RNA (rRNA) in eukaryotes?

RNA polymerase I Signup and view all the answers

What differentiates prokaryotic RNA polymerase from eukaryotic RNA polymerases?

Eukaryotic RNA polymerases consist of several types for different RNA Signup and view all the answers

What role does non-coding DNA play in transcription?

It helps regulate transcription and gene expression Signup and view all the answers

What is the role of TFIIB in the transcription process?

It determines the distance from the TATA element to the start site. Signup and view all the answers

Which statement about eukaryotic RNA polymerases is true?

Eukaryotic RNA polymerases are gene type-specific. Signup and view all the answers

What does the TBP do in the context of RNA polymerase II initiation complex?

It binds to the TATA box and helps in recruiting the polymerase. Signup and view all the answers

Which component is responsible for blocking non-specific binding of RNA polymerase II to DNA?

TFIIB Signup and view all the answers

How does RNA polymerase III initiate transcription of tRNA genes?

It utilizes TFIIIB and is recruited upstream of the start site. Signup and view all the answers

Which of the following statements correctly describes the role of intermediates in transcription?

They serve as templates for RNA synthesis. Signup and view all the answers

What distinguishes RNA polymerase I from RNA polymerase II?

RNA polymerase I is specific to ribosomal RNA synthesis. Signup and view all the answers

Which aspect of transcription is NOT a function attributed to general transcription factors?

Termination of transcription Signup and view all the answers

During the assembly of the RNA polymerase II initiation complex, which factor plays a major role in elongation?

TFIIH Signup and view all the answers

What function do non-coding DNA segments primarily serve in the context of transcription?

They regulate the expression of coding regions. Signup and view all the answers

What is the role of allolactose in the lac operon regulation?

It induces the dissociation of the repressor from the operator. Signup and view all the answers

Which of the following statements accurately describes the characteristics of the lac operon?

It functions under negative feedback control. Signup and view all the answers

What distinguishes polycistronic mRNA from monocistronic mRNA in prokaryotes?

Polycistronic mRNA contains multiple genes under one promoter. Signup and view all the answers

How does lactose affect the lac operon when present in the environment?

It acts as an inducer, leading to de-repression of the operon. Signup and view all the answers

Which of the following components is involved in preventing transcription of the lac operon when lactose is not present?

Repressor protein Signup and view all the answers

What is the primary function of the lac repressor in the lac operon?

To inhibit the initiation of transcription at the operator Signup and view all the answers

How do cis-acting mutations differ from trans-acting mutations in the lac operon?

Cis-acting mutations only regulate adjacent genes. Signup and view all the answers

Which factor is responsible for the activation of the lac operon when glucose is depleted?

Catabolite activation without glucose Signup and view all the answers

What distinguishes trans-acting factors from cis-acting elements?

Trans-acting factors can regulate genes from any location. Signup and view all the answers

What effect do lacOc mutations have on the lac operon?

They lead to constitutive expression regardless of lactose presence. Signup and view all the answers

What type of growth does catabolite repression primarily affect in bacteria?

Diauxic growth, switching from glucose to lactose Signup and view all the answers

Which statement accurately describes the action of trans-acting factors in relation to gene expression?

They promote transcription by binding to distant genes on the chromosome. Signup and view all the answers

What is the consequence of mutations like lacI- in the context of the lac operon?

The repressor is unable to bind to the operator. Signup and view all the answers

What effect does high glucose levels have on the lac operon?

It prevents the lac operon from being expressed even when lactose is present. Signup and view all the answers

What is the primary function of CRP in relation to RNA polymerase?

CRP requires cAMP to enable RNA polymerase to initiate transcription. Signup and view all the answers

Which statement accurately compares the lac operon to the trp operon?

The lac operon is induced by lactose while the trp operon is repressed by tryptophan. Signup and view all the answers

What occurs at the operator when tryptophan is present in relation to the trp operon?

The trp repressor binds to the operator, preventing transcription. Signup and view all the answers

How does cAMP function in the regulation of the lac operon?

It binds to CRP, allowing DNA binding and promoting transcription. Signup and view all the answers

What is a fundamental characteristic of biosynthetic operons like the trp operon?

Their transcription is repressed by the products they synthesize. Signup and view all the answers

What is the role of the cAMP-CRP complex in the presence of low glucose?

It promotes binding of RNA polymerase to the lac promoter. Signup and view all the answers

Which of the following accurately describes positive and negative feedback regulation in operons?

Positive feedback activates operons while negative feedback represses them. Signup and view all the answers

Study Notes

Module 4 - From DNA to RNA, Lecture 1: Genes, Polymerases and Promoters

Aims for the lecture include comparing gene structures in prokaryotes and eukaryotes, describing and explaining transcription principles, RNA polymerase function, sense/antisense coding/non-coding DNA strands, and nucleotide structure/transcription.

Transcriptional Regulation

DNA → Genes → Transcription → RNA → Translation → Protein.

Nature and Structure of Genes

A gene is a genetic unit containing information to produce a functional product (RNA or Protein).
Genes contain structural information (coding DNA), temporal information (developmental), positional information (tissue/cell specific), and inducible information (nutrient, stress, or hormone related).

Prokaryotic Gene Organisation

The promoter defines the transcription start site and direction.
A leader/spacer is a non-translated DNA section.
A cistron is a segment of DNA corresponding to a polypeptide.
Transcription start/stop sites are not the same as translation start/stop sites.
Prokaryotic genes often have multiple genes (cistrons) in one mRNA molecule (polycistronic).

Eukaryotic Class II (mRNA-encoding) Genes

Genes contain a transcribed region, promoter, enhancer, introns, exons, 5'-UTR, and 3'-UTR.
Enhancers are sometimes distal from promoters, containing transcription factor binding sites.
Introns are present in primary transcripts but removed from mature transcripts.
Exons are part of the mature transcript.
UTRs are untranslated regions.

Size of Prokaryotic and Eukaryotic Genes

Eukaryotic genes can be large (~50kB).
Most eukaryotic genes contain non-coding sequences.
Lower eukaryotic and prokaryotic genes are often smaller, related to the size of the polypeptides they produce.

General Mechanism of Transcription

DNA containing a gene is made of a coding (sense) strand (5'-3'), with the same sequence as the RNA product, and a template (antisense) strand (3'-5'), complementary to the RNA product.

Making Sense of Sense and Antisense

mRNA is a copy of the coding strand (same sequence) but complementary to the non-coding strand.

Let's Talk About Promoters

RNA polymerase needs to know where and when to bind to DNA and the direction to start transcription.
Promoters contain regulatory elements like -35 (TTGACA), -10 (TATAAATG "Pribnow Box") and a +1 position.

Transcription "Bubble"

RNA polymerase binds to DNA, melts the double strand, and polymerizes in the 5' to 3' direction of the coding strand.
The RNA produced is a copy of the coding strand, complementary to the template strand.

How Does Nascent RNA Polymerase Know Where and When?

All this information is found within the gene.

Genes Summary

All genes have a regulatory element (promoter/enhancer).
Genes have direction, position, spatial/temporal/inducibility characteristics.
Prokaryotic genes differ from eukaryotic genes in organization and function (cistrons/spacers vs. introns/exons).

Intended Learning Outcomes

Students should have a basic understanding of prokaryotic and eukaryotic gene structure and differences.
Students should have a basic understanding of the transcription process and the role of RNA polymerase.
Students should understand the concepts of sense and antisense in transcription.
Students should understand how nucleotide structure is important for transcription at the molecular level.

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Description

This quiz focuses on the fundamental concepts of gene structure, transcription processes, and the role of RNA polymerases in both prokaryotic and eukaryotic organisms. It covers the nature of genes, how transcription is regulated, and the essential features of promoter regions. Test your understanding of gene organization and structural information vital for RNA and protein production.