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Chapter 12 - Gene Transcription & RNA Modification Flashcards

1
Q

What is a gene?

A

a segment of DNA used to make a functional product either an RNA or a polypeptide

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2
Q

What is the first step in gene expression?

A

Transcription

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3
Q

What is transcription?

A

the act or process of making a copy
- copying of DNA sequences into an RNA sequence
- structure of DNA is not altered and can continue to store information

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4
Q

What are protein-encoding genes?
and what is another name for them?

A
  • Structural Genes
  • encode the amino acid sequence of a polypeptide
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5
Q

What does transcription of a protein coding gene produce?

A

A messenger RNA (mRNA)

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6
Q

What does a messenger RNA or mRNA do?

A
  • makes copies (temporary) of a gene that contains info to make a polypeptide
  • determines the amino acid sequences of a polypeptide during translation
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7
Q

What is the role of the polypeptide in mRNA? (2)

A
  • one or more polypeptides is a protein
  • synthesis of a functional protein determines an organisms traits
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8
Q

List the 3 steps of DOGMA.

A
  1. DNA replication
  2. Transcription
  3. Translation
  4. Polypeptide
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9
Q

Describe the function of Regulatory Sequences

A

Stops things that we already have (don’t waste energy on it)
or
gives us mechanisms to make that really important thing

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10
Q

does mRNA have a promoter?

A

NO!

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11
Q

How many nucleotides make up a codon?

A

3

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12
Q

Why are ribosome binding sites necessary?

A

for translation to make proteins

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13
Q

What are promoters?

A

DNA sequences that “promote” gene expression and direct the exact location for the initiation of transcription

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14
Q

Where are promoters located?

A

just upstream of the site where transcription of a gene begins

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15
Q

Describe Template Strand

A

DNA stand that is transcribed
Non coding

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16
Q

Template vs Coding strand

A

T = makes mRNA
CS = same as RNA

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17
Q

What are other names for the coding strand?

A

Sense strand or non-template strand

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18
Q

List the 3 stages of Transcription

A
  1. Initiation
  2. Elongation
  3. Termination
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19
Q

What does Sigma do?

A

recognizes the promoter since RNA polymerase holoenzyme can’t

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20
Q

What does RNA polymerase holoenzyme do?

A

does the actual transcription

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21
Q

DNA has to be what to allow for what?

A

Open
transcription

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22
Q

When the DNA is open what stage in transcription is that?

A

Initiation

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23
Q

Once the open complex is formed, what happens next?

A

Elongation
- the DNA rewinds back into a double helix (43 nucleotides per second for the rate of RNA synthesis)

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24
Q

How is the open complex formed?

A

RNA polymerase

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25
How does termination occur in RNA synthesis?
when the short RNA-DNA hybrid of the open complex is forced to separate - releases the newly made RNA and the RNA polymerase
26
What are the 2 methods E.Coli has for termination?
1. Rho-dependent 2. Rho-independent
27
What is rho dependent termination?
- in E.coli (bacteria) - requires a protein know as p (rho)
28
What is rho-independent termination?
- in E.coli (bacteria) - does not require p (rho)
29
Describe the process of rho independent termination (2)
faciliated in 2 sequences 1. An uracil rich sequence located at the end of 3' RNA 2. a stem-loop structure upstream of the uracil rich sequence (causes RNA polymerase to pause which will lead to termination)
30
Why is gene transcription more complex than bacteria?
1. larger more complex cells (organelles) 2. added cellular complexity means more genes that encode proteins are required 3. multicellularity adds another level of regulation (expressing genes only in the correct cells at the proper time)
31
What are the 3 RNA polymerase's in Eukaryotes?
1. RNA pol I 2. RNA pol ll 3. RNA pol lll
32
What is RNA pol I ?
transcribes all rRNA genes
33
What is RNA pol II?
its why we look like we do - transcribes all protein encoding (structural) genes.. synthesizes all mRNAS - transcribes some snRNA genes needed for splicing
34
What is the core promoter and where is it found?
- relatively short, consists of a TATA box and transcriptional start site. eukaryotes
35
Why is a core promoter important?
important in determing the precise start for transcription
36
What does the core promoter produce?
Basal transcription meaning a low level of transcription -base level for mRNA
37
What are regulatory elements and where are they found? what do they do?
- found in eukaryotes -influences core promoter - short DNA sequences that affect the binding of RNA polymerase to the core promoter
38
What are the two types of regulatory elements?
1. Enhancers (turn on) 2. Silencers (turn off)
39
What are transcription factors (proteins)?
bind to element sequences and influence rate of transcription
40
What are the 3 categories of proteins required for basal transcription to occur at the promoter?
1. RNA polymerase II 2. General transcription factors (GTFs) - 5 different proteins 3. Mediator (massive mediates signals that could be super far away)
41
What does the CTD do?
carbonixal terminal domain - helps modify RNA after its been transcribed by RNA polymerase II
42
What are the two models for termination of RNA pol II?
1. Allosteric 2. Torpedo
43
What is the torpedo model?
an exonuclease binds to the 5' end of the RNA that is still being transcribed and degrades it in a 5' to 3' direction.
44
What is the allosteric model?
after transcription, the RNA pol II is destabilized and disassociates from the DNA.
45
What are the ways RNA transcripts can be modified?
1. 5' capping 2. 3' poly-A tailing of mRNA transcripts 3. splicing 4. processing of rRNA and tRNA transcripts to smaller functional pieces
46
Analysis of bacterial genes in the 60s & 70s revealed: aka...
1. the sequence of DNA in the coding strand corresponds to the sequence of nucelotides in the mRNA 2. the sequence of codons in the mRNA provides the instructions for the sequence of amino acids in the polypeptide aka Colinearity of gene expression
47
Eukaryotic protein-encoding genes revealed?
they are not always colinear with their functional mRNAS (where RNA modifications come in)
48
What is the role of the 5' Cap?
- allows translation to occur - movement of some RNAs out of the nucleus - early stages of translation - splicing on introns
49
Describe PolyA tail
for stability purposes - added after the gene is completely transcribed
50
What is a poly A tail made up of?
adenine nucleotides
51
What are the 3 types of splicing mechanisms?
1. Group I intron splicing 2. Group II Intron splicing 3. spliceosome
52
What do all 3 splicing mechanisms do?
1. removal of the intron RNA 2. Covalent linkage of the expon (expressed) fragments
53
What is the AG-GU rule?
each intron is cut at each end and these intron ends almost always have GU at the 5' end and AG at the 3' end.
54
What letter is the branch point?
A
55
The splice sites will have what number associated with them?
100
56
Do prokaryotes have introns?
NO because they don't have splicing mechanisms to remove them
57
What is alternative splicing?
A pre-mRNA with multiple introns can be spliced in different ways
58
What does alternative splicing generate?
mature mRNAs with different combinations of exons - two or more polypeptides can be derived from a single gene
59
What does alternative splicing allow for?
an organism to carry fewer genes in its genome yet have a large diversity of polypeptides
60
Alternative splicing is highly ___?
Condensed at 3,4 and 5 on the primary pre-mRNA transcript

Genetics (12 decks)

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