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BIOMG 3300 > Unit 7 > Flashcards

Unit 7 Flashcards

1
Q

Describe the function of rRNA.

A

Ribsomal RNA. Components of ribosomes help carry out protein synthesis:

  • Bind Shine-Dalgarno
  • Make up active site and most of whole complex
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2
Q

Describe the function of mRNA.

A

Messenger RNA strand made from coding DNA template. Transfers stored genetic information as transcription to be translated into protein.

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3
Q

Describe the function of tRNA.

A

Transfer RNA: Adapter RNAs that translate the codons of mRNA into appropriate amino acids linked on the polypeptide.

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4
Q

Compare the pentose ring of DNA and RNA,.

A

DNA pentose is deoxygenated or has an H at 2’ C where the ribose of RNA has an OH and an H.

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5
Q

Which nitrogen bases (C,A,G,U, and/or T) are found in DNA? In RNA?

A

Typically, DNA has A, T, G, and C.
Typically, RNA has A, U, G, and C. However, the pentose structure - not the bps - is what actually designates molecule as DNA or RNA.

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6
Q

Distinguish between monocistronic and polycistronic mRNA. Is eukaryotic mRNA monocistronic or polycistronic? What about prokaryotic mRNA?

A

Monocistronic - mRNA codes for only one polypeptide product. (most eukaryotic mRNA)
Polycistronic - mRNA codes for two or more different polypeptides. (most prokaryotic mRNA)

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7
Q

Is DNA usually double or single stranded?

A

Double.

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8
Q

Is RNA usually double or single stranded? )? Does single stranded RNA have any double stranded regions?

A

Single stranded. Folds on to itself or finds self complementary regions, where AU and GC pair (+ irregular G-U pair). Exists as right handed single strand helices (base stacking interactions) and forms hairpin duplexes as most common secondary (hydrogen bonding driven) structure.

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9
Q

Give an overview of transcription by RNA polymerase.

A

Essentially identical to mechanism by DNAp:

  • Uses Mg 2+ and Asp to selectively stabilize and destabilize triphosphate group and 3’ OH of terminal
  • Deprotonates and allows nucleophilic attack of phosphate
  • Breaks phosphoanhydride bond and forms stabilized, phosphodiester bond product
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10
Q

Distinguish between RNA polymerases and DNA polymerase I in terms of substrates.

A

DNAp - deoxynucleoside triphosphate (dNTPs) substrates

RNAp - nucleoside-triphosphate substrates (NTPs)

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11
Q

Distinguish between RNA polymerases and DNA polymerase I in terms of whether a primer is needed.

A

DNAp - needs primer (RNA made by primase)

RNAp - does not need primer (binds to and starts synthesis from a promoter)

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12
Q

Distinguish between RNA polymerases and DNA polymerase I in terms of direction of synthesis.

A

DNAp - add 5’ to 3’

RNAp - also adds 5’ to 3’

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13
Q

Distinguish between RNA polymerases and DNA polymerase I in terms of what nucleophilic attack occurs during bond formation.

A

DNAp - deprotonated 3’ OH attacks alpha phosphate of incoming dNTP
RNAp - deprotonated 3’ OH attacks alpha phosphate of incoming NTP

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14
Q

Distinguish between RNA polymerases and DNA polymerase I in terms of the role of pyrophosphate and pyrophosphatase in the overall reaction.

A

DNAp - PPi breakdown by pyrophosphatases drives rxn forward both with Le Chat and thermodynamically.
RNAp - PPi breakdown does not occur as driving mechanism. First added nucleotide retains PPPi group.

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15
Q

Distinguish between RNA polymerases and DNA polymerase I in terms of the requirement of a template.

A

DNAp - uses either and both strands of DNA as identical templates.
RNAp - uses only one strand of DNA - the template strand (rather than non-template)

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16
Q

What is meant by the terms “template” and “non-template” strands with regards to RNA polymerase synthesis?

A

Template = strand which mRNA is synthesized from. Non-template is DNA analog of mRNA.

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17
Q

Does the same strand of the chromosome always serve as the template strand?

A

No.

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18
Q

Discuss the quaternary structure of Taq RNA polymerase.

A

Multiple subunits - beta, beta prime, alpha 2x, and omega. Sigma subunit binds as a specificity factor.

19
Q

Does RNA polymerase have 3’ to 5’ exonuclease activity? Why is it unnecessary?

A

No.

1) Many mRNAs produced
2) Degraded regularly

20
Q

Discuss the general organization of an E. coli promoter.

A

Site recognized by sigma 70. Has consensus sequences around -10 and -35. Some promoters also have a UP (upstream promoter) sequence that is further back (more negative).

21
Q

What is meant by the term “consensus sequence”?

A

The sequence that is made up of the most commonly found base at each site in the sequence - theoretical, however, and not necessarily a real sequence possessed by any organism.

22
Q

Define the numbering system which is used to identify regions such as the -10 and -35 regions.

A

0 refers to the start site of transcription. Positions before this site are -# and after are +#.

23
Q

What are promoters?

A

Sequence where RNAp binds to the DNA, but not necessarily where it begins transcription. Promoter sequences can exist before or after site of transcription initiation.

24
Q

What is the significance of the -35 and -10 regions around an E.

A

These are consensus sequence sites that direct binding of RNAp with the sigma factor.

25
Q

What is the relationship between the “strength” of a promoter (i.e. the frequency at which transcription is initiated at a particular promoter) and the degree of match to a consensus sequence?

A

Closer to consensus sequence = stronger promoter

26
Q

What is the function of the sigma (σ) subunit?

A

Specificity factor for RNAp. Localizes RNAp to promoter sites.

27
Q

Discuss the events in transcription initiation.

A

1) Sigma factor and RNAp associate
2) Binding of holoenzyme to promoter = closed complex binding
3) RNAp opens strands and begins transcription = open complex and initiation
4) promoter clearance and dissociation of sigma factor

28
Q

Is transcription usually regulated at the level of initiation, elongation, or termination? Is it ever regulated at the other levels?

A

Regulated at initiation mostly. Can be regulated at any of these levels.

29
Q

Discuss two distinguishing features of the termination signal in the mRNA in rho independent termination of transcription in prokaryotes.

A

1) Palindromic sequence shortly before termination site - forms mRNA hairpin.
2) AAA sequence in template - gives UUU sequence in mRNA that binds and causes kinetic pause to allow for hairpin formation and detachment of mRNA.

30
Q

Describe the sequences typically found at a eukaryotic promoter. How do these sequences compare to those found at a prokaryotic promoter?

A

1) TATA box before initiation site
2) Initiator sequence (Inr) right after initiation site
3) Can have many different up stream regulatory sequences

31
Q

What is a transcription factor?

A

A protein that binds to regulatory sequence and regulates transcription initiation.

32
Q

Discuss the formation of a primary transcript and its processing to an mRNA.

A

Primary transcript hot off the DNA.
mRNA is post processed by:
1) 5’ G cap assembly
2) Cleavage of non coding end sequence and addition of Poly A tail at 3’ end (polyadenylation)
3) RNA splicing (to remove introns) by snRNAs (small nuclear RNAs) for spliceosomal introns and by themselves (lariat formation) for self splicing

33
Q

Describe and list two functions of the cap.

A

1) Protect end from degradation

2) Help mRNA localize to ribosome.

34
Q

Do all eukaryotic genes contain introns? Do most?

A

No (not histone coding genes) and yes.

35
Q

Does splicing take place at the level of DNA or RNA?

A

RNA.

36
Q

Point out features at exon-intron junctions that provide signals for correct splicing. What are the consequences of imprecise splicing?

A

Key signal sequence (5’ GU —- AG 3’) attracts U1 (snRNA) binding and induces spliceosomal splicing.

37
Q

How do individual snRNAs locate the consensus sequences that flank introns?

A

It is complementary to an snRNA sequence.

38
Q

Point out the location and identity of the nucleotide that will make the initial attack on the 3’ end of the exon in self splicing introns.

A

Nucleophilic adenine inside the intron makes the initial attack on the 3’ end of the last intron nucleotide.

39
Q

What is the “lariat structure”?

A

A looped structure formed by the attack of the internal adenine on the end of the intron and resulting self splicing.

40
Q

What is the function of the poly (A) tail?

A

1) Protect mRNA from degradation

2) Serve as binding site for various proteins.

41
Q

Discuss the key steps in the addition of a poly (A) tail.

1) Is the tail encoded in the gene?
2) Name the enzymes involved in making the poly (A) tail.
3) Does this enzyme add residues in a template directed manner like DNA polymerase?

A

1) No, there is a cleavage site sequence located in a non coding region at the 3’ end, however. AAUAAA sequence right before cleavage site and G and U rich sequence after.
2) Polyadenylate polymerase
3) No, no template required.

42
Q

Distinguish between mRNA post transcriptional processing and “RNA editing.”

A

Modification by alteration of sequence vs RNA editing by directly altering the bases.

43
Q

Distinguish between poly A site choice and alternative splicing.

A

1) Alternative splicing - different exons may be removed in addition to introns so the ligated products give splice variants.
2) Alternative cleavage - multiple possible cleavage sites means longer or shorter mRNA products depending on where the polyadenylation takes place

BIOMG 3300 (8 decks)

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