Untitled Deck

Question 1

What is the purpose of transcription in the context of the central dogma?

Answer 1

Transcription is the process of synthesizing RNA from a DNA template.

Question 2

What are 4 differences between DNA and RNA?

Answer 2

1. DNA is double-stranded, while RNA is single-stranded.
2. DNA contains deoxyribose sugar, whereas RNA contains ribose sugar.
3. DNA uses thymine, while RNA uses uracil. 4. DNA is only pres ent in the nucleus whereas RNA present in cytoplasm and nucleus
   5 . RNA has a 2’ oH group instead of 3’ OH

Question 3

What are the three main types of RNA? What are their functions?

Answer 3

1. mRNA (messenger RNA) - carries genetic information from DNA to the ribosome. 2. tRNA (transfer RNA) - brings amino acids to the ribosome during protein synthesis. 3. rRNA (ribosomal RNA) - forms the core of the ribosome’s structure and catalyzes protein synthesis.

Question 4

Construct the template strand and the mRNA from the non-template strand 5’AATCGAACCCAAAACCT3’. How many hydrogen bonds hold this region of DNA together?

Answer 4

Template strand: 3’ TTAGCTTGGGTTTGGAA5’
mRNA: 5’ AAUCGAAUCCCAAAUCC3’

Hydrogen bonds between A-T and G-C pairs: A-T has 2 bonds, G-C has 3 bonds.

Question 5

What is the purpose of the Pribnow box and the -35 consensus seq? Why are mutations in these regions poorly tolerated by natural selection?

Answer 5

The Pribnow box and -35 consensus sequence are essential for the initiation of transcription. Mutations in these regions are poorly tolerated as they can prevent the initiation of transcription, leading to no protein synthesis.

Question 6

Are the Pribnow box and -35 consensus seq present in eukaryotes? What information is embedded in these seqs?

Answer 6

No, these sequences are specific to prokaryotes. They provide binding sites for RNA polymerase and transcription factors.

Question 7

What are the 3’ and 5’ UTRs?

Answer 7

5’ UTR: where RNA is transcribed upstream to the start codon.
3’ UTR: where RNA is transcribed downstream to the start codon.

Question 8

Describe the role of sigma factor in transcription.

Answer 8

Sigma factor is a subunit of the RNA polymerase holoenzyme. It provides specificity for transcription by binding to the promoter of specific genes to provide RNA polymerase with specificity to bind promoter .

Question 9

Why is there more than one sigma factor in E. coli?

Answer 9

There is more than one sigma factor in E. coli because each sigma factor readily bind and unbind RNA polymerase depending on what genes needs to be transcribed in certain environments.

Question 10

Explain the process of transcription initiation and elongation in bacteria.

Answer 10

1. Sigma factor binds to RNA polymerase, activating it. 2. Sigma factor binds to the promoter, forming a closed complex. 3. RNA polymerase is directed to the +1 nucleotide where transcription begins.

Question 11

Distinguish between intrinsic and rho dependent termination.

Answer 11

Intrinsic termination relies on inverted sequences, and a poly A sequence in the RNA that forms a stem loop that stalls the RNA polymerase. The poly a sequence forms a weak base pairing between the RNA and the DNA causing the RNA polymerase to disassociate. NO ADDITIONAL PROTEINS required

rho-dependent termination requires the rho protein to bind the rut sequence and form a stem-loop. The rho protein can then catch up to the RNA polymerase and lead to its dissociation.

Question 12

What are the roles of the three eukaryotic RNA polymerases?

Answer 12

RNA Pol I: synthesizes rRNA. RNA Pol II: synthesizes mRNA. RNA Pol III: synthesizes tRNA.

Question 13

What are the three most common eukaryotic consensus seqs?

Answer 13

TATA Box: -25 seq, CAAT Box: -80, G-C Rich Box: -90.

Question 14

Are the three common eukaryotic consensus seqs present at every gene?

Answer 14

No, they are not present at every gene; their presence varies among different genes.

Question 15

Define transcription factor.

Answer 15

A transcription factor is a binding protein that facilitates the recruitment of rna polymerase to the consensus sequence and this the initiation of transcription.

Question 16

Explain the order of events for transcription initiation for RNA Pol II.

Answer 16

1. Sigma subunit binds to RNA polymerase, activating it.
2. TBF and TAF bind to the TATA box forming the initial committed complex.
3. TFIIB, TFIIF, and RNA Polymerase II bind to the complex.
4. TFIIE and TFIIH bind, forming the preinitiation complex.
5. RNA polymerase is directed to the +1 nucleotide where transcription begins.

Question 17

Explain the order of events for transcription initiation for RNA Pol III and RNA Pol I.

Answer 17

RNA POL I : the core element initiates transcription and the upstream control element increases transcription..

two proteins (TFs) bind each sequence and rna pol I is recruited to the core element to initiate transcription.

RNA POL III:
consensus seqs BOX A and BOx X are within the transcribable region

TFIIIC bind BOX A TFIIIA binds box c consensus seqs.

rna pol III: will bind these tfs and is recruited to the +1 region.

Question 18

Why do most promoter mutations that change transcription lower transcription rather than raise it?

Answer 18

Most promoter mutations disrupt the binding of RNA polymerase or transcription factors, leading to decreased transcription.

Question 19

Explain how enhancer seqs increase transcription.

Answer 19

Enhancer sequences are typically upstream to increase transcription by binding activator/coactivator proteins which provide additional binding sites for transcription factors that enhance the recruitment of RNA polymerase.

Question 20

Define heterochromatin and euchromatin.

Answer 20

Heterochromatin is tightly packed DNA that is transcriptionally inactive, while euchromatin is loosely packed DNA that is transcriptionally active.

Question 21

Are heterochromatin and euchromatin present in bacteria?

Answer 21

No, these structures are specific to eukaryotes as eukaryotic DNA is associated with histones.

Question 22

Contrast rRNA genes in bacteria and eukaryotes.

Answer 22

In bacteria rRNA genes are dispersed throughout the genome whereas in eukaryotes they exist in tandem and are processed in the nucleolus

Question 23

Explain why Archaeans have an RNA polymerase more similar to Eukaryotes than bacteria.

Answer 23

Archaeans share more similarities in their transcription machinery with eukaryotes due to eukaryotes arose from endosymbiosis of a bacteria into a archaean

Question 24

Explain the process of 5’ capping and its purpose.

Answer 24

addition of a guanine to the 5’ of mrna via a 5’ to 5’ triphosphate linkage

functions:

protect form rapid degradation
facilitate transport across nuclear membrane
facilitates intron splicing
enhance translation efficiency

Question 25

Explain the process of adding the poly-A tail and its purpose.

Answer 25

proteins bind the pre-mRNA and cleaves 15-30 nucleotides downstream of a polyadenylation signal seq

20-200 adenines are added to the 3’ end

Question 26

Are 5’ capping and poly-A tail addition present in bacteria?

Answer 26

No bacteria do not have a post-processing mechanism sich as 5’ capping or poly A-tial.

Question 27

Contrast bacterial transcripts with eukaryotic ones.

Answer 27

Bacterial transcripts are often polycistronic and lack introns, while eukaryotic transcripts are monocistronic and contain introns.

Question 28

Explain the torpedo model of transcription termination in eukaryotes.

Answer 28

The torpedo model suggests that after RNA polymerase transcribes a gene, a 5’ to 3’ exonuclease degrades the RNA downstream, causing RNA polymerase to dissociate.

Question 29

How is the torpedo model similar to rho dependent termination?

Answer 29

Both processes involve a mechanism that leads to the dissociation of RNA polymerase from the DNA template.

Question 30

Define intron and exons.

Answer 30

Introns are non-coding sequences within a gene, while exons are the coding sequences that are expressed.

Question 31

Explain the DNA loops that form when mRNA is hybridized with DNA.

Answer 31

DNA loops form due to the presence of introns in the DNA that are not present in the mature mRNA, resulting in regions of DNA that do not hybridize with the mRNA.

Question 32

Explain intron excision via the spliceosome and self-splicing introns.

Answer 32

several proteins bind the 5’ and 3’ splice site

and RNA forms a stem-loop/lariat structure. One of the proteins dissociates and activates the splicesome then makes a break that exposes 5’ end of the intron and the 3’ end of the exon.

The splicesome then links the 5’ end of the exon to the 2’oh of the branch point.

another breakage happens at the 3’ end and the lariat structure dissociates allow exons to be connected.

Question 33

What is a potential benefit of alternative splicing?

Answer 33

Alternative splicing allows a single gene to produce multiple protein isoforms, increasing the diversity of proteins that can be generated from a single gene.

Question 34

What are the differences between tRNA transcription in bacteria and eukaryotes?

Answer 34

In bacteria, tRNA genes are mostly transcribed along side rRNA.

In eukaryotes, tRNAs are all described individually.