Gene Transcription and RNA Modification

Final Exam

DNA Replication, DNA, Transcription, Messenger RNA, Translation, and Polypeptide

What is the order?

Translation, DNA Replication, Transcription, DNA, Polypeptide, and Messenger RNA

True

True or False: A prokaryotic gene includes several essential sequences.

DNA

1. Regulatory sequence

2. Promoter

3. Terminator

mRNA

1. Ribosome - binding site

2. Start codon

3. Codons

4. Stop codon

False: Transcription includes 3 core steps.

True or False: Transcription includes 1 core step.

Initiation

RNA polymerase binds to a specific DNA sequence called the promoter and begins synthesizing a complementary RNA molecule

Elongation

RNA polymerase slides along the DNA in an open complex to synthesize RNA

Termination

A terminator is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA

True

True or False: A promoter includes ‘consensus’ sequences for initiation of transcription.

Promoter

A DNA sequence located upstream of a gene (the 5’ or non-coding end) where RNA polymerase binds to initiate transcription

True

True or False: RNA polymerase is the transcription machine.

Sigma factor

Associates with the core transiently to recognize promoter sequences; dissociates prior to elongation

Core Enzyme

5 distinct subunits (a₂BB’w) Beta subunits perform the catalytic synthesis of RNA

False: Sigma factor recognizes promoter sequences.

True or False: Core enzyme recognizes promoter sequences.

True

True or False: RNA transcript is produced by RNA polymerase during elongation.

U

___ is substituted of T in the RNA

RNA polymerase

1. Slides along the DNA, creating an open complex as it moves.

2. The DNA strand, template strand, is used to make a complementary copy of RNA, RNA-DNA hybrid.

3. Moves along the template strand

3’ - 5’

RNA polymerase moves along the template strand in a _______ direction.

5’ - 3’

RNA is synthesized in a _______ direction using nucleoside triphosphate as precursors. Pyrophosphate is released.

False: Transcription can proceed in either direction depending on the promoter.

True or False: Transcription can proceed in one direction depending on the promoter.

1. Rho-dependent

2. Rho-independent

What are the 2 different mechanisms of transcriptional termination in prokaryotes?

Rho-dependent

A mechanism of transcription termination in bacteria where the Rho protein binds to a specific region on the nascent RNA transcript and causing it to release the transcript.

Rho-independent

A process in prokaryotes where transcription stops due to the formation of a stable hairpin structure in the newly transcribed RNA, followed by a region rich in uracil nucleotides.

Intrinsic

Rho-independent is also known as _______ termination.

Compartmentalization

Specialized functions in different organelles requiring additional proteins and the genes that encode them.

Multicellularity

Requires that gene expression be coordinated in the right cells at the correct developmental stages.

True

True or False: Eukaryotic and prokaryotic RNA polymerases share a common structure.

RNA Polymerase I

All ribosomal RNAs except 5s

RNA Polymerase II

All protein-coding non-coding RNAs

RNA Polymerase III

All transfer RNAs and 5s rRNA; some non-coding RNAs

Clamp

Is a mobile domain that controls the opening and closing of the cleft, a deep groove where the DNA template resides.

Rudder

Is a conserved segment of the largest RNAP subunit that interacts with the nascent RNA at the upstream edge of the RNA-DNA hybrid.

Wall

Resides in the cleft, near the active site, and represents the site at which the RNA:DNA hybrid separates.

Bridge

Helix, located in the cleft, interacts with the DNA-RNA hybrid.

Pore

Is the site where the transcribed RNA exits the enzyme.

The core promoter and cis-regulatory sequences make up the __________ region.

Gene control region

TFIID

Composed of TATA-binding protein (TBP) and other TBP-associated factors (TAFs). Recognizes the TATA box of the core promoter of eukaryotic protein-coding genes.

TFIIH

A multisubunit protein that has multiple roles. First, certain subunits act as helicases and promote the formation of the open complex. Other subunits phosphorylate the carboxyl terminal domain (CTD) of RNA polymerase II, which releases it from interacting with TFIIB, thereby allowing RNA polymerase II to proceed to the elongation phase.

True

True or False: Mediator serves as a scaffold for the general transcription factors, RNA polymerase, and other regulators.

1. Allosteric model

2. Torpedo model

What are the two possible models that exist for transcriptional termination in eukaryotes?

Allosteric model

Describes how a protein’s activity is regulated by the binding of molecule at a site other than the active site, leading to conformational changes that affect the protein’s function.

Torpedo model

Proposes that after RNA cleavage at the poly(A) site, a 5’ - 3’ exonuclease degrades the remaining RNA, effectively “chasing” the RNA polymerase and causing its release from the DNA templates, thus terminating transcription.

Prokaryotic

Initiation: Promoter sequences at -10 and -35. Sigma factors direct the core RNA polymerase.

Prokaryotic

Elongation: Single polymerase

Prokaryotic

Termination: Rho-dependent or intrinsic (NusA/G).

Eukaryotic

Initiation: Promoter consists of TATA box and transcriptional start site. General transcription factors bind to the promoter. Many regulatory proteins bind to cis-regulatory sequences to promote or inhibit transcription.

Eukaryotic

Elongation: 3 polymerases (RNA Pol II).

Eukaryotic

Termination: Allosteric or torpedo models.

False: 3

True or False: The pre-mRNA transcript undergoes 1 primary modifications prior to maturation.

1. 5’ Capping

2. Intron Splicing

3. 3’ Polyadenylation

What are the 3 primary modifications prior to maturation in the pre-mRNA transcript?

5’ Capping

1. 7-methylguanosine cap attached via 5’ - 5’ triposphate bridge

2. Important for nuclear export and processing

3. Aids in binding to ribosomes

Intron Splicing

1. Removes large intervening sequences

2. Eukaryotic pre-mRNAs require a spliceosome

3. Alternative splicing can produce different protein products

3’ Polyadenylation

1. The RNA is cleaved at the 3’ end based on consensus sequences

2. Poly-A polymerase adds many adenosine residues at the end

3. Variable lengths

True

True or False: Alternative splicing greatly increases the number of protein products that can be produced by a single gene.