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Biochem Quiz 2 > Transcription > Flashcards

Transcription Flashcards

1
Q

prokaryotic transcription initiation mechanism

A
  1. RNA polymerase holoenzyme binds the promoter region to recognized sequences like the TATA box or Pribnow box (-10 from transcription start site) 2. RNA polymerase unwinds DNA, looses the 5th subunit, and begins to synthesize RNA chain
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2
Q

prokaryotic transcription elongation mechanism

A

mononucleotides are added to mRNA by RNA polymerase

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3
Q

RNA polymerase

A

catalyzes RNA synthesis, doesn’t need a primer, no exonuclease activity (higher error rate)

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4
Q

prokaryotic transcription termination mechanism

A

RNA polymerase gets to a stop sequence and dissociates

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5
Q

Operon

A

a single transciption unit that contains multiple genes with only one promoter (usually genes have common metabolic purposes)

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6
Q

Lac Operon

A

3 genes in one operon in bacteria that help metabolize lactose

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7
Q

Lac Operon Regulation No Lactose (presence or absence of glucose)

A

no lactose = repressor protein (trans acting) upstream is constitutively expressed so it binds the operator and promoter to stop transcription

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8
Q

Lac Operon Regulation Lactose Present (no glucose)

A

Lactose (inducer) binds th repressor and it dissociates from the operator/promoter and transcription is induced (cAMP high = LOTS MADE)

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9
Q

Lac Operon Regulation Glucose and Lactose

A

lactose inducing transcription, but low levels of cAMP from glucose present (so not helping) = a little mRNA will be made

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10
Q

Lac Operon Regulation No Glucose

A

If glucose is absent, cAMP binds CAP and together they bind upstream (-60) of RNA polymerase and allow for more efficient transcription

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11
Q

Lac Operon Regulation Glucose (no lactose)

A

If glucose is available, no transcription of lac operon (cAMP levels low)

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12
Q

trans-acting factor

A

factor that can bind other factors (cis-acting) anywhere in the genome - doesn’t have to stay on the same operon or chomosome

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13
Q

cis-acting factor

A

like the operator and promoter these factors must be physically connected to the genes they regulate (will regulate whatever is downstream of them)

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14
Q

polycistronic organization

A

one mRNA containing multiple genes or coding sequences (cistrons) that will be translated seperately but come from one operon

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15
Q

Organization of Eukaryotic gene

A

gene consists of Introns (noncoding) and Exons (coding)

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16
Q

eukaryotic enhancer

A
  1. Enhancers determine when and where a gene will be expressed through binding sites for regulatory factors (enhancers are usually silenced by regulatory/transcription factors until needed) 2. cis-acting (must act on the chromosome where its located) 3. regulated by insulator elements to keep its activity from spreading the length of the chromosome
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17
Q

eukaryotic promoter

A

cis-acting sequences up or downt stream of the transcription start site that bind RNA pol 2

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18
Q

Introns and Exons

A

introns - noncoding, exons - coding

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19
Q

3 post-transcriptional modifications to mRNA

A
  1. capping (5’ cap) 2. splicing (get introns out) 3. Poly A tail
20
Q

Cis-acting sequences in eukaryotic transcription

A
  1. core promoter elements (direct assembly of RNA polymerase & transcription factors - close to start site, ex. TATA box) 2. promoter proximal sequences (located w/in 200 bp upstream, help assemple general transcription factors 3. enhancers (50 kbp up or downstream, binding sites for activators or repressors)
21
Q

Recent significant discoveries in the human genome

A
  1. 1.2% of genome is coding and can be organized as solitary genes or gene families (ex. Beta-globin) 2. 75% junk DNA (45% of that is repetitive DNA) 3. can detect single nucleotide polymorphisms (SNPs) between species 4. LOTS MORE GOING ON!
22
Q

Eukaryotic RNA polymerases

A

1.RNA pol 1 - transcibes ribosomeal subunits 2. RNA pol 2 - TRANSCRIBES PRE-mRNA 3. RNA pol 3 - transcribes tRNA, rRNA, snRNA 4. mitochondiral RNA pol (mtRNA pol)

23
Q

eukaryotic transcription initiation mechanism

A
  1. RNA pol 2 recognizes TATA box - 25-35 bp upstream (or another downstream promoter) with help of general transcrition factors (TFII..) that recognize and help to unwind the DNA and phosphorylate RNA pol 2 so it can elongate the transcript
24
Q

eukaryotic transcription elongation mechanism

A

RNA pol 2 adds ribonucleotides to the growing chain, but for the new chain to be stable 3 steps must be coupled with trancription (5’ capping, 3’tail, splicing)

25
Q

5’ cap

A

5’-5’ linkage to the ribonucleotide that is attached to mRNA as it is being synthesized to protect the 5’ end from degradation, assists with initiation

26
Q

Splicing

A

spliceosome (lots of proteins in the complex) removes intron from pre-mRNA by recognizing the 5’ splice donor (GU) and 3’ splice acceptor (AG) points to cut out each intron

27
Q

Branchpoint on an Intron

A

single A in an mRNA intron that serves as an attachment point for the 5’ end of the intron once it is spliced out

28
Q

mRNA processing as a regulatory mechanism

A

pre-mRNA can be spliced in different ways to produce distinct mRNA molecules

29
Q

Polyadenylation

A

poly(A) tailis 30-150 adenylate residues added to the 3’ end of the mRNA by poly(A) polymerase (noncoding), assists with termination

30
Q

DNA bound transcriptional factors

A

activators and repressors

31
Q

How do enhancers and DNA bound transcriptional factors determine gene expression and cell fate?

A
  1. Enhancers determine when and where a gene will be expressed through binding sites for regulatory factors (enhancers are usually silenced by regulatory/transcription factors until needed), 2. enhancers have multiple binding sites for different transcription factors so that a few transcription factors can regulate many genes
32
Q

How do DNA bound transcription factors in eukaryotic cells regulate transcription initiation?

A

The transcription factors can stay at the promoter site and RNA pol 2 can reinitiate another round of transription

33
Q

organization of the prokaryotic gene

A

promoter + transcription unit (part that is copied to RNA)

34
Q

Promoter

A

binding site for RNA polymerase

35
Q

mRNA

A

single stranded polynucleotide identical to one strand of DNA except U for T

36
Q

coding strand

A

DNA strand identical to mRNA (this is the strand that will be referenced)

37
Q

non-coding strand

A

DNA strand complimentary to mRNA

38
Q

coding region

A

region of RNA that codes the protein, has untranslated sequences to each side

39
Q

Start Codon

A

AUG, marks beginning of coding sequence

40
Q

Stop Codons

A

UAA, UAG, UGA, signals end of sequence

41
Q

Codon

A

3 nucleotides in a particualr order specific to an amino acid (degenerate)

42
Q

Bacterial RNA polymerase

A

4 subunits form the core enzyme, 5th subunit associates to form the holoenzyme (apoenzyme + coenzyme)

43
Q

transcription start site

A

first nucleotide of the transcriptional unit (+1), anything upstream is negative, anything downstream is positve (example: TATA box -10 or -35 region)

44
Q

Drosophilia example of regulation

A

the enhancer has both binding sites for repressors and activators - relative concentration and affinities of each determines the expression of the gene

45
Q

3 Examples of co-activators and co-repressors that are recruited to the promoter in eukaryotes

A
  1. mediator complex (controls assembly and activity of preinitiation complex) 2. histone modifying factors (factors that target N-terminal tails of histones to loosen or tighten the structure) 3. ATP-dependent chromatin remodeling complexes (clear nucleosomes from the promoter - unwraps DNA to promote RNA pol 2 access)
46
Q

Nuclear Hormone Receptors

A

example of regulatory factors that have both an activation and repression domain. NHR has a DNA binding domain and a hormone binding domain. (steroid (lipid) hormones bind the hormone binding domain to change the receptor conformation so that activators can bind)

47
Q

Explain role of HATs and HDACs in regulating transcription

A

HATs acetylate and promote transcription, HDACs deacetylate and suppress transcription

Biochem Quiz 2 (4 decks)

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