Nucleic Acids and Gene Structure

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Questions and Answers

What is a characteristic of prokaryotic genes in terms of transcription termination?

Termination involves structures found on the transcript itself. (correct)

The closest open reading frame is always the only one replicated.

There are no untranslated regions after the termination sequence.

Termination is solely based on the presence of a Stop codon.

Which component is not included in eukaryotic mRNA processing?

Transcription factors (correct)

5' cap structure

Introns

Exons

What is the primary function of RNA polymerase I in eukaryotic cells?

Generate small non-coding RNAs.

Facilitate transcription factor binding.

Synthesize protein-coding mRNA.

Produce ribosomal RNA. (correct)

How many stop codons are present within the genetic code?

3 Signup and view all the answers

What regulates the transcription of eukaryotic genes?

Both upstream and downstream regulatory sequences. Signup and view all the answers

What is true about the redundancy in the amino acid synthesis due to codon usage?

The wobble effect allows for fewer tRNAs than codons. Signup and view all the answers

Which of the following statements is correct regarding eukaryotic promoters?

There can be multiple promoters for a single gene. Signup and view all the answers

What is a defining feature of ribosomal RNA (rRNA) genes in eukaryotes?

They are organized in tandem arrays within the genome. Signup and view all the answers

What role does the CTD (carboxy-terminal domain) of RNA polymerase II play?

Regulates the polymerase's enzymatic activity Signup and view all the answers

Which of the following statements about RNA polymerase II promoters is true?

They show the most variability in gene expression. Signup and view all the answers

What is the primary difference between the major and minor grooves in DNA?

The major groove exposes more groups for protein interaction. Signup and view all the answers

Which element is NOT a core promoter region for RNA polymerase II?

Enhancer region Signup and view all the answers

Why are proteins unable to distinguish between A=T and T=A in the minor groove?

The exposed groups in the minor groove are the same. Signup and view all the answers

What role does TFIIB play in transcription?

It stabilizes and orients TFIID at the promoter. Signup and view all the answers

What is the order of assembly for the general transcription factors during RNA polymerase II recruitment?

D-A-B-F-E-H Signup and view all the answers

How does the Mediator complex influence gene transcription?

It integrates signals from enhancers and activating proteins. Signup and view all the answers

What happens during the phosphorylation of the CTD?

It activates RNA polymerase II. Signup and view all the answers

How do enhancers affect gene expression?

They can activate genes located kilometers away if they are cis. Signup and view all the answers

What is the effect of having all promoter elements present in RNA polymerase II regulation?

It yields the highest degree of transcription. Signup and view all the answers

What is the primary function of silencers in gene regulation?

They bind repressor proteins to block transcription. Signup and view all the answers

What structural feature of RNA polymerase II allows for regulatory control?

The carboxy-terminal domain (CTD) Signup and view all the answers

Why is the recruitment of general transcription factors crucial for RNA polymerase II function?

To form a stable preinitiation complex Signup and view all the answers

What mechanism do insulators use in gene regulation?

They form loops to isolate enhancer effects to specific genes. Signup and view all the answers

What differentiates proteins that bind in the major groove from those that bind in the minor groove?

Proteins in the major groove can differentiate base pairs. Signup and view all the answers

Which transcription factor stabilizes the binding of TFIID and TFIIB?

TFIIA Signup and view all the answers

Which factor is required for the binding of TFIIB at the promoter?

TATA binding protein (TBP) Signup and view all the answers

Which groove of DNA does the TBP (TATA-binding protein) bind to, causing the DNA to bend?

Minor groove Signup and view all the answers

What role does the TATA binding protein (TBP) play in transcription?

It recruits additional proteins to facilitate RNA synthesis. Signup and view all the answers

Which transcription process is characterized by a formation of a transcription bubble?

Initiation Signup and view all the answers

What is one of the primary reasons eukaryotes have more protein coding genes compared to bacteria?

Eukaryotic genes require additional regulatory complexity. Signup and view all the answers

What is a key characteristic of prokaryotic transcription termination?

It involves specific terminator structures in the transcript. Signup and view all the answers

What is significant about eukaryotic genes having multiple open reading frames (ORFs)?

The closest ORF to the promoter is typically the most replicated. Signup and view all the answers

Which RNA polymerase is responsible for producing messenger RNA (mRNA) that encodes proteins?

RNA Pol II Signup and view all the answers

What is the role of the Upstream Control Element (UCE) in RNA Pol I promoters?

It controls the synthesis of ribosomal RNA predominantly. Signup and view all the answers

What does the presence of introns in eukaryotic genes signify?

They are non-coding regions removed during mRNA processing. Signup and view all the answers

Study Notes

Nucleic Acids

Prokaryotic genes have a promoter region, open reading frames (ORFs), and a termination signal.
The termination of transcription in prokaryotes is not solely dependent on a stop codon but also involves termination structures within the transcript itself.
Prokaryotic transcripts contain 3' untranslated regions (3' UTRs) after the termination sequence.
Multiple ORFs can exist, with the one closest to the promoter region often being preferentially replicated.

Eukaryotic genes

Eukaryotic mRNA contains both introns (non-coding) and exons (coding regions) that need to be edited. The introns are removed during processing.
Regulation sequences (800-1000 bp) are present downstream from the promoter.
There can also be upstream regulatory elements and overlapping reading frames.
Multiple promoters in a single gene can generate diverse mRNA transcripts.

Eukaryotic Genes: 3 Specialized Polymerases

Pol I: Produces ribosomal RNA (rRNA). Cells need these consistently in high amounts.
Pol II: Produces messenger RNA (mRNA) and some non-coding RNAs like miRNAs.
Pol III: Produces small, highly abundant non-coding RNAs, like transfer RNA (tRNA), 5S rRNA, and 7SL RNA.

RNA Polymerase I Promoter

Contains an upstream control element (UCE) and a core promoter element (CPE).
Little variation in rRNA promoters within a species, but many copies exist, especially in eukaryotic chromosomes.
rRNA genes are organized in tandem arrays for consistent high-level production.

Initiation of Transcription (Pol I)

UBF (upstream binding factor) binds to the UCE and core sequence.
SL1 (selectivity factor 1) binds to UBF, and the Pol I complex is formed.
TATA-binding proteins (TBPs) can bind to all three polymerases.
The rapid recycling of Pol I allows for the synthesis of large amounts of rRNA from one tandem array to another.

RNA Polymerase III promoter

Promoter structure is more diverse and complex than Pol I promoters.
Production can vary based on regulation, producing different RNA transcripts at different times based on the needs of the cell.
Specialized in producing smaller, highly abundant non-coding RNAs like tRNA, 5S rRNA, 7SL RNA, and U6 snRNP.

RNA Polymerase II promoter

The most diverse and complex control mechanism of the three polymerases.
Expression levels can vary greatly (10,000-fold) in response to stimuli.
Some genes consistently express at high levels while others are expressed only under specific conditions.
Eukaryotic cells have far more protein-coding genes (∼20,000).

RNA Polymerase II structure

RNA polymerase II core enzyme has 12 subunits, some with bacterial homology.
The carboxyl-terminal domain (CTD) of the tail is important for regulating the enzyme's activity and it can be modified by phosphorylation.

RNA pol II core promoters

Elements like BRE (TFII-B Recognition Element), TATA box, INR (Initiator), and DPE (Downstream Promoter Element) affect the specificity and strength of transcription.

Eukaryotic Transcription Cycle

Processes include PIC (pre-initiation complex) formation, bubble formation, initiation, elongation, termination, and recycling, including CTD dephosphorylation.
General transcription factors are required for initiating Pol II transcription.

Core promoter structure and function

Enhancer sequences are important in regulating transcription.
General transcription factors like TFII-D, TFIIA, TFII-B, TFIIF, TFIIE, and TFIIH play essential roles in assembling the pre-initiation complex on the DNA to recruit and bring in the correct polymerase for transcription.

Mediator complex

Integrates signals from enhancers and activating proteins.
Binds to the RNA polymerase II complex to control transcriptional activity.

Insulators

Binding proteins limit the effects of enhancers to specific genes/regions to prevent unwanted transcriptional activation.

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Description

Explore the intricacies of prokaryotic and eukaryotic genes, including their structures, transcription processes, and the role of specialized polymerases. This quiz covers key concepts such as ORFs, untranslated regions, and mRNA processing. Test your understanding of molecular biology fundamentals.