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bio 209 > Lecture 5A - Transcription > Flashcards

Lecture 5A - Transcription Flashcards

1
Q

What does transcription of DNA yield?

A

A single stranded RNA that is complimentary to one strand of DNA (template strand)

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2
Q

What are the general features of transcription? (what, where, similarities/difference b/t RNA and DNA synthesis)

A

Transcription: transfer of genetic information from DNA to RNA

  • Occurs in the nucleus
  • Ribonucleoside triphosphates monomers
  • Only one strand of DNA is template for RNA
  • No primer required => de novo synthesis
  • RNA is unstable, short-lived compared to DNA
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3
Q

Why is relative instability of RNA a good thing?

A

Serves as a means of regulation and gene expression. It can be protected from degradation by RNA binding proteins => regulate RNA stability

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4
Q

Features of RNA produced from transcription? 5 types of RNA?

A
  • Single stranded
  • Complementary to DNA template strand, identical to DNA nontemplate strand (thymidines replaced w/ uracil)

5 types:
- Messenger RNA (mRNA)
- Transfer RNA (tRNA)
- Small nuclear RNA (snRNA)
- Ribosomal RNA (rRNA)
- Micro RNA (miRNA)

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5
Q

What are RNA polymerases? (direction, nuc attack, helicase or no, primer or no)

A
  • Enzymes that catalyze the synthesis of RNA complement to DNA
  • 5’ to 3’ direction
  • Nuc attack by 3’ OH on nucleotidyl phosphorus phosphorus atom w/ elimination of pyrophosphate
  • Localized unwinding and rewinding DNA w/o need for helicase
  • No primer required to initiate polymerization
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6
Q

RNA transcription occurs w/in a ______

A

locally unwound segment of DNA

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7
Q

What is a transcriptional unit?

A

A segment of DNA transcribed to produce one RNA molecule; one or several genes on a single RNA molecule

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8
Q

What is a gene?

A

A unit of genetic information that controls the synthesis of one protein or structural RNA molecule (RNA that is not mRNA)

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9
Q

What is meant by downstream/upstream?

A

Downstream: towards 3’ region of gene

Upstream: towards 5’ region of gene

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10
Q

What is sense/antisense RNA strands? Sense/antisense DNA strands? Relation to template/nontemplate DNA strands?

A

Sense RNA strands encode nucleotides that specify AA of gene products (ex: mRNA)

Antisense RNA strands are complementary to sense strands (ex: miRNA, long noncoding RNA => regulate expression of sense RNA by binding to sense strand as complementary sequence)

Sense DNA strand (nontemplate) is complimentary to antisense DNA strand (template), and identical to sense RNA strands

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11
Q

Overview of eukaryotic transcription: 6 features

A

MORE COMPLEX THAN PROKARYOTIC

  1. mRNA synthesized in nucleus
  2. Proteins synthesized in cytoplasm
  3. Prokaryotic transcription often results in multigenic mRNAs (gene clusters/operons, genes w/ shared function for a process are transcribed in the same piece of RNA)
  4. Eukaryotic transcription often results in monogenic mRNAs
  5. 3 RNA polymerases
  6. 3 modifications of mRNA that help w/ translation and stability
    - 7-methyl guanosine cap on 5’ end
    - Poly-A tail on 3’ end
    - Splicing out introns
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12
Q

What are peri and posttranscriptional processing? Where do they occur?

A

Peritranscriptional processing: modification occurs while transcription is occuring

Posttranscriptional processing: modification occurs on mature mRNA after RNA has been synthesized/transcription complete

All occur in nucleus

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13
Q

3 types of peri-/posttranscriptional processing

A
  1. 5’ end 8 methyl-guanosine cap (peri)
  2. 3’ end polyadenylation (Poly-A tail) (post)
  3. Introns spliced out: non-coding intervening sequences
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14
Q

What is hnRNA? Where does it go? How are transcripts protected from RNases? What is the relative half life of eukaryotic vs prokaryotic RNA?

A

hnRNA: heterogeneous nuclear RNA i.e. primary transcripts in the nucleus that can have diverse function ((snRNA, rRNA, tRNA, mRNA, etc.)

  • Exported to cytoplasm for translation
  • Protected from RNases by RNA binding protein coating, which regulates stability of RNA
  • Eukaryotic RNA has a longer half life than prokaryotic RNA
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15
Q

How many RNA polymerases in eukaryotes? What do they do?

A

Three; RNA polymerase I, II, and III

RNA polymerase I transcribes 5.8S, 18S, and 28S rRNA genes (ribosomes)

RNA polymerase II transcribes all protein-coding genes, snoRNA genes, miRNA genes, siRNA genes, and most snRNA genes

RNA polymerase III transcribes tRNA genes, 5sRNA genes, some snRNA genes, and genes for other small RNAs

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16
Q

How many RNA polymerases in prokaryotes?

A

One

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17
Q

What cofactors RNA polymerases require to initiate transcription? Eukaryote vs prokaryote

A

Eukaryote: many additional proteins called general transcription factors

Prokaryote: single additional protein called sigma factor

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18
Q

What do eukaryotes have to deal w/ in transcription initiation that prokaryotes don’t have to?

A

Packing of DNA into nucleosomes and higher order forms of chromatin structure

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19
Q

What are the three stages of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
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20
Q

Eukaryotic Transcriptional Initiation

A
  • Requires transcription factors
  • Binding of polymerase complex to promoter
  • Unwinding of DNA
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21
Q

What is a promoter sequence? What is the structure of promoter recognized by RNA pol II?

A

DNA sequences where TF bind to

TATA box

22
Q

What are general transcription factors?

A
  • Proteins required for initiation of transcription by RNA Pol II
  • Denoted TFII-X (TFII = TF for Pol II)
  • Bind promoter sequences inn a specific order
23
Q

What initiates transcriptional elongation?

A

The phosphorylation of Pol II “tail” triggers escape from initiation complex

24
Q

What is the direction of transcription determined by? Can transcription occur off of either strand of DNA or just one?

A

Direction: determined by promoter at beginning of each gene

Can occur off of either strand

25
Q

What does DNA bending by transcription factors do?

A

Serves as recruitment site for other proteins that take part in transcription

26
Q

What is the activator protein? How does it get brought to promoter and initiation complex?

A

A protein that activates/enhances transcription; bound to enhancer site typically far from the promoter

DNA can be coiled (chromatin packaging), bringing activator proteins close to initiation complex

27
Q

What does the initiation complex consist of?

A
  • Mediator (binds activator)
  • Chromatin remodeling complex
  • Histone modifying enzyme (HATs and HDACs)
  • RNA processing enzymes
  • RNA polymerase
28
Q

Describe elongation by RNA pol II (euk vs prok, where does it occur, primer or no)

A
  • Same in proks and euks
  • Occurs w/in transcription bubble
  • RNA pol unwinds and rewinds DNA
  • No primer required
  • Short RNA/DNA heteroduplex
29
Q

What recruits RNA processing enzymes? How?

A
  • The tail of RNA pol II
  • Phosphorylation state of tail determines which factors are recruited
30
Q

What happens to 5’ end during elongation? When? Why?

A
  • Peritranscriptional modification => pre-mRNA gets 7-MG cap (unusual 5’-5’ triphosphate bond)
  • Added when chain is ~30 nucleotides in length
  • Function: recognized by posttranslation machinery and protects 5’ end from degradation
31
Q

Describe transcriptional termination (Polyadenylation and cleavage, why polyadenylate?)

A
  • Poly (A) polymerase adds ~200 A’s to 3’ end
  • Coupled w/ cleavage by endonuclease, as polyadenylation occurs right after cleavage
  • Polyadenylation increases stability
32
Q

What are mRNA?

A

Messenger RNAs, code for proteins

33
Q

What are rRNAs?

A

Ribosomal RNAs, form basic structure of ribosome and catalyze protein synthesis

34
Q

What are tRNAs?

A

Transfer RNAs, central to protein synthesis as adaptors b/t mRNA and AA

35
Q

What are snRNAs?

A

Small nuclear RNAs, function in a variety of nuclear processes, including the splicing of pre-mRNA

36
Q

What are snoRNAs?

A

Small nucleolar RNAs, used to process and chemically modify rRNAs

37
Q

What are scaRNAs?

A

Small cajal RNAs, used to modify snoRNAs and snRNAs

38
Q

What are miRNAs?

A

Micro RNAs, regulate gene expression typically by blocking translation of selective mRNAs

39
Q

What are siRNAs?

A

Small interfering RNAs, turn off gene expression by directing degradation of selective mRNAs and the establishment of compact chromatin structures

40
Q

What are noncoding RNAs?

A

Function in diverse cell processes, including telomere synthesis, X-chromosome inactivation, and the transport of proteins into the ER

41
Q

Eukaryotic transcription occurs in _______ and translation occurs in ________

A

Nucleus; cytoplasm

42
Q

Prokaryotic transcription/translation not separated by cellular compartments, often coupled

True

False

A

True

43
Q

Prokaryotic mRNA is _____, allows for coordinated expression for genes w/ same function

A

polycistronic

44
Q

Eukaryotic genes have both expressed and non-expressed sequences - exons and introns|describe

A

Exons: sequences that remain in mature mRNA

Introns:
- Intervening sequences that are spliced out,
- Found in most eukaryotic genes
- Variable in size
- Some sequences w/in introns regulate gene expression
- Mutations occur more rapidly

45
Q

Exons have both coding and noncoding regions, why?

A

Noncoding region is where ribosome binds, esp 5’ and 3’ untranslated regions

46
Q

What is exon shuffling? What is alternative splicing?

A

Exon shuffling: the rearrangement of exons for the evolution of “new” exon combos

Alternative splicing of pre-mRNA: one gene but different transcripts, can modify coding sequence by removing exons

47
Q

Splicing exons together requires highly precise removal of each intron - why?

A

One base addition/deletion will make huge difference => nonfunctional protein, different ORF, etc.

48
Q

What are spliceosomes? Two steps to splicing?

A

Complex RNA/protein structure that carries out RNA splicing

Composition:
- >40 proteins
- numerous snRNA (small nuclear RNA)
- proteins + snRNA complexed as snRNP
- snRNP form spliceosome core

Two steps:
1. Cleavage
2. Ligation

49
Q

Outline of pre-mRNA splicing process

A
  1. Cleave 5’ end
  2. Form lariat
  3. Cleave 3’ end
  4. Release lariat from pre-mRNA
  5. Splicing of adjacent exons (ligation)
  6. Lariat degraded, snRNP recycled

(steps 3-5 are simultaneous)
(refer to slide 51 lec 5A)

50
Q

Splicing abnormalities result in ____

A

Mutations

51
Q

What is the nucleolus the site of?

A

Nucleolus is the site of rRNA and ribosome synthesis

bio 209 (10 decks)

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