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Biochem > Lecture 1/19 - Central Dogma > Flashcards

Lecture 1/19 - Central Dogma Flashcards

1
Q

Does DNA polymerase require a primer

A

Yes it requires an RNA primer. It can’t get started de novo

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2
Q

Joining of Okazaki fragments

A

ligase

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3
Q

Requirements for DNA transcription

A

RNAP, template DNA, UTP, ATP, GTP, CTP and Mg++ or Mn++ ion

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4
Q

How many different tRNAs

A

61 (3/64 are stop codons)

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5
Q

CAP (catabolic activator protein)

A

CRP (c-AMP Response Protein)

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6
Q

Name the site where RNA Polymerase II (RNAPII) would bind in order to transcribe this gene
into mRNA

A

Promoter region

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7
Q

Name the two possible sites where the transcription factor, SREBP, might bind

A

promotor or enhancer region

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8
Q

What must be loosened or moved out of the way for effective RNAPII binding?

A

Histones

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9
Q

When cholesterol levels drop, the SREBP moves to the Golgi. Describe what happens that
enables SREBP to activate transcription

A

Protease clips SREBP to free it from transmembrane domain and it diffuses to nucleus to find its target DNA element

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10
Q

The 45 S pre-rRNA of eukaryotes

A

a.
Is transcribed by RNA Polymerase I from DNA in the nucleolus region of the nucleus
b. FALSE (not translated) Is processed into 28 S, 18 S, and 5.8 S rRNA pieces that are translated into proteins by
existing ribosomes in the cytoplasm
c.
Provides part of ribosomal structure after it is processed and combined with ribosomal
proteins
d. Is the source of the enzymatic activity for peptidyl transferase present in ribosomes

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11
Q

The synthesis of mRNA in eukaryotes requires…

A

a.
RNA polymerase II
b. General (basal) transcription factors such as TFIID, TFIIB
c.
DOES NOT need An RNA primer
d. A free 3’ hydroxyl group to which the incoming nucleotide will be attached

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12
Q

Histone acetylases

A

a.
Loosen the binding of histones to DNA by adding acetyl groups to histones
b. Are recruited by coactivators that may be bound to transcription factors
c. FALSE
Repress transcription until the acetyl group is removed by Histone deacetylases
d. FALSE Are enzymes that are part of the histone H2a, H2b, H3, and H4 structures

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13
Q

Single strand binding proteins

A

Keep the strands apart

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14
Q

DNA polymerase adds to which end

A

3’

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15
Q

Which ways does replication proceed in the transcription bubble

A

Both ways

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16
Q

Topoisomerase (gyrase)

A

Responsible for straightening out the helixes (unwinds)

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17
Q

Single strand binding proteins

A

Keep the strands apart

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18
Q

DNA polymerase adds to which end?

A

3’

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19
Q

Which ways does replication proceed in the transcription bubble?

A

Both ways

20
Q

Helicase

A

The enzyme responsible for separating DNA strands

21
Q

How many DNA polymerase III’s are in replication bubble

A

2

22
Q

Removal of okazaki RNA primers

A

RNase H and DNA polymerase I

23
Q

Differences between DNA and RNA polymerase

A
  1. RNA polymerase only copies template strand (anti-sense strand)
  2. Doesn’t require primer
  3. Doesn’t have editing function
  4. w/ sigma - holoenzyme; w/o sigma - core enzyme
24
Q

Function of A site in ribosome

A

Where we bring in a new amino acid

25
Q

Function of P site

A

Holding polypedide site

26
Q

Function of E site

A

Let go of polypeptide site

27
Q

peptidyl transferase

A

moves polypetide chain off of middle chain onto amino acid

28
Q

where will methionine be

A

It will always be at the amino end (N-site) of polypeptide chain (will be sticking up from ribosome)

29
Q

How many RNA polymerases do eurkaryotes have? Why?

A

many. Because different polymerases recognize different promoter sequences. Need to be able to regulate mRNA more.

30
Q

Transcription factors

A
  1. Basal transcription factors (need for any transcription)

2. Specific transcription factors

31
Q

Promoter sequences

A

DNA that RNA polymerase recognize; will cause RNAP to stop at the right place. In E. Coli, two promoter sequences are -10 and -35 (from +1 start site)/ They are upstream from the gene.

32
Q

Consensus sequences

A

The sequences at the promoter site

33
Q

Initiation

A
  1. Finding promoter
  2. binding
  3. initiation
34
Q

What does an element refer to?

A

a section of DNA, not RNA

35
Q

RNAP transcription bubble

A

Appears to move because RNAP does the unwinding job itself and RNA closes on its own

36
Q

Methods for RNA transcription termination

A

Rho protein (pull strand off), or hairpin (requires palindromic sequence)

37
Q

How do you tell the difference between a weak and strong promoter

A

By their difference in distance from the transcription start point. Will change the rate of transcription

38
Q

TATA-box-binding-protein (TBP)

A

Binds to DNA first, then attracts other binding factors

39
Q

Purpose of the phosphorylation of mRNA tail

A

Causes RNAP to leave (start transcription)

40
Q

Where are enhancer sequences located along the DNA

A

They are a distance away from gene. Can be upstream/downstream/on another stand (trans). They bind other activators

41
Q

What are silencer elements

A

Like an enhancer element, but it binds other repressors than promoter’s

42
Q

cis-acting elements

A

They are on the same strand. This is the only one prokaryotes have.

43
Q

trans-acting elements

A

Possible with eukaryotes where the enhancer/silencer element is present on a different strand (chromosome)

44
Q

How do coactivators activate transcription?

A

They modify or remove histones with acetyltransferases (HATS)

45
Q

Histone acetylase (HATS)

A

adds acetyl to R group of lysine on histone tails

46
Q

Histone deacetlyase (HDAC)

A

removes acetyl, which represses transcription

47
Q

What is the effect of acetylation?

A

Enhances transcription by removing histones

Biochem (11 decks)

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