BIOC 406 Lecture 19

Splicing and Reverse Transcription

Which of the following statements about eukaryotic transcription

is TRUE? If all statements are FALSE, choose (E).

A. mRNA transcript termination can happen anytime and transcript

from the same gene are variable in lengths.

B. Translation of the mRNA begins before transcription is completed.

C. rRNA, mRNA, and tRNA are all transcribed by the same RNA

polymerase.

D. The first step in eukaryotic transcription initiation is binding of the

sigma factor to the promoter.

E. All of the above statements are false.

E. All of the above statements are false.

Which one of the following is NOT a mechanism for gene regulation

in most eukaryotes?

A. Alternative mRNA splicing

B. Histone modification

C. Expression of different transcription factors in different cell types

D. Expression of different RNA Polymerases in different cells.

E. DNA methylation

D. Expression of different RNA Polymerases in different cells.

In the context of cancer epigenetics, what is the significance of the

H3K27M mutation found in diffuse midline gliomas?

A. It converts facultative heterochromatin into constitutive

heterochromatin.

B. It causes the over-expression of Histone Acetyltransferases.

C. It leads to the global loss of the repressive H3K9me3 modification.

D. It leads to the global loss of the repressive H3K27me3 modification.

D. It leads to the global loss of the repressive H3K27me3 modification.

In eukaryotic transcription, what proteins promote chromatin condensation to turn a gene "OFF"?

Repressors

What complex serves as the bridge between activators bound at enhancers and the transcription initiation factors at the promoter?

The Mediator complex

In epigenetic regulation, what do the abbreviations 'Ac' and 'Me' stand for?

Acetylation and Methylation

Which enzymes are responsible for relaxing DNA binding on nucleosomes to open chromatin at promoters?

Histone acetyltransferases (HATs)

How does RNA Pol II contribute to the decompaction of the gene body during transcription?

It recruits Methyltransferases through its phosphorylation.

Epigenetic 'Writers' that add methyl groups to histones are called _____.

Histone methyltransferases (HMTs)

Which class of enzymes acts as 'Erasers' by removing acetyl groups from histones?

Histone deacetylases (HDACs)

Which histone modification is specifically associated with establishing constitutive heterochromatin?

H3K9me3

Genes responsive to signaling molecules and developmental genes are typically rich in _____ heterochromatin.

Facultative

What is the primary histone modification that marks facultative heterochromatin?

H3K27me3

Which enzyme catalyzes the conversion of Cytosine to 5-methylcytosine in a CpG dinucleotide?

DNA methyltransferase (DNMT)

What is the role of TET methylcytosine dioxygenases (TETs) in epigenetic regulation?

They act as 'Erasers' for DNA methylation.

In the context of cancer, what is a 'Dysregulated gene expression program' that leads to vulnerabilities not predicted by genetic changes called?

Transcriptional Addiction

Definition: Exon

A sequence in a gene that is transcribed and remains in mature mRNA to be translated into protein.

Definition: Intron

A sequence in a gene that is transcribed but removed from the mRNA before translation.

Group I introns are described as _____ because they possess the ability to splice themselves.

Autocatalytic

What molecule must provide a free 3' hydroxyl group to initiate the first step of Group I intron splicing?

Guanosine (or a guanine nucleoside/nucleotide)

In the Group II intron splicing mechanism, what specific residue's 2' OH attacks the 5' splice site to form a lariat?

A conserved adenine

The spliceosome is a large ribonucleoprotein complex composed of proteins and _____.

U1

Which snRNA is responsible for the recognition of the 5' splice site?

U1

Which snRNA is involved in branch site recognition and catalysis within the spliceosome?

U2

What is the primary function of the U6 snRNA in the spliceosome?

Catalysis of the splicing reaction.

What does the U4 sRNA do?

repressor and (re)assembly factor

Which statement about mRNA splicing is FALSE?

A. The process is generally carried out by the spliceosome.

B. Splicing can generate different mRNAs from a single gene.

C. The lariat forms when a ribose 2’-OH within the intron attacks

the phosphoester bonds at the 5’ splice site.

D. The lariat RNA becomes part of the mature mRNA.

E. The 2 nucleotides at the 5’ and 3’ ends of the introns are

conserved

D. The lariat RNA becomes part of the mature mRNA.

How does the splicing of Group I introns differ from Group II introns?

A. Group I introns are found only in viruses, while Group II are found

only in humans.

B. Group I introns require the spliceosome, whereas Group II are

autocatalytic.

C. Group I requires a free guanosine cofactor, while Group II uses an

internal conserved adenine.

D. Group I introns remain in the mature mRNA, while Group II are

removed.

C. Group I requires a free guanosine cofactor, while Group II uses an

internal conserved adenine.

mRNA splicing can be used to vastly diversify the repertoire of which immune system proteins?

Antibodies (or Immunoglobulins)

What process describes the flow of genetic information from RNA back to DNA?

Reverse transcription

Why must all viruses, regardless of genome type, produce mRNA?

They lack ribosomes and must use the host's translation machinery to make proteins.

What are the three essential viral enzymes packaged within the HIV virion?

Reverse transcriptase, Integrase, and Protease.

Which HIV gene encodes the structural proteins Matrix (p17), Nucleocapsid (p24), and Capsid?

Gag

Which enzymatic activity of HIV Reverse Transcriptase (RT) is responsible for degrading the RNA strand in an RNA/DNA hybrid?

RNase H activity

Reverse Transcriptase is a multifunctional polymerase that can use both _____ and _____ as templates.

RNA; DNA

What molecules, packaged in the virion, serve as the primers for HIV reverse transcription?

Host tRNAs (specifically tRNA^{Lys})

The final double-stranded viral DNA product of reverse transcription contains identical sequences at both ends called _____.

Long Terminal Repeats (LTRs)

What is the function of HIV Integrase?

It catalyzes the insertion of viral DNA into the host chromosomal DNA.

What is the first step performed by Integrase on the viral DNA ends before integration?

Site-specific endonucleolytic cleavage of the 3' ends.

What complex, containing viral DNA and proteins like Integrase, migrates into the host nucleus?

The pre-integration complex (PIC)

True or False: HIV integration into the host genome is a reversible process.

False (Integration is permanent).

How does the average number of introns per gene generally change as biological complexity increases (e.g., from Yeast to Humans)?

Intron density increases.

In the open chromatin state, which histone modification at H3K4 is typically associated with active transcription?

H3K4me (Methylation)

Which protein complex is responsible for establishing H3K27me3 marks in facultative heterochromatin?

PRC2 (Polycomb Repressive Complex 2)

Within the PRC2 complex, which protein functions as the 'Writer' (methyltransferase)?

EZH2

Which epigenetic modification is generally considered a repressive mark for transcription when found on DNA?

Cytosine methylation (specifically at CpG sites)

The 'Reader' protein that recognizes H3K9me3 to promote constitutive heterochromatin is _____.

Suv39h1/2

In Group II splicing, the intron is released in a characteristic structure called a(n) _____.

Lariat

The HIV 'Pol' gene is translated as a precursor that is cleaved by which enzyme to produce mature viral proteins?

Protease

Which HIV enzyme is responsible for 'strand transfer' during the integration process?

Integrase

What is the primary difference between Group I and Group II introns regarding their requirement for external nucleosides?

Group I requires an external guanosine, while Group II uses an internal adenine residue.

According to the Baltimore Classification, which class (number) represents dsDNA viruses?

Class 1

Which HIV protein is responsible for binding to the host cell and mediating fusion?

gp120 (binding) and gp41 (fusion)

In the context of the human genome, what are SINEs?

Short Interspersed Nuclear Elements (a type of non-LTR retrotransposon).

What term describes the phenomenon where introns and retrotransposons are key players in the development of higher organism complexity?

Drivers of biological complexity

TRUE or FALSE.

Reverse Transcriptase utilizes a host tRNA as a primer for synthesis of DNA.

 

True

 

False

False

TRUE or FALSE.

Retrotransposons are thought to have originated from retroviruses that have lost their ability to infect cells.

 

True

 

False

True

Reverse transcription

 

copies DNA into RNA

 

synthesizes RNA in the 3' to 5' direction

 

uses an RNA template for DNA synthesis

 

synthesizes DNA in the 3' to 5' direction

uses an RNA template for DNA synthesis

Which of the following snRNPs (pronounced "snurps") does not participate in splicing eukaryotic mRNA precursors?

 

U6 snRNP

 

U5 snRNP

 

U3 snRNP

 

U4 snRNP

 

U1snRNP

 

U2 snRNP

U3 snRNP

Which of the following is true about spliceosomes that carry out the splicing of eukaryotic mRNA precursors?

 

The first cleavage step of splicing results in the formation of an intron lariat intermediate

 

The spliceosome consists of five proteins and about 50 RNAs

 

The spliceosome acts in the cytoplasm

 

ATP is required for the cleavage and ligation reactions

The first cleavage step of splicing results in the formation of an intron lariat intermediate