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McG > Quiz 3 > Flashcards

Quiz 3 Flashcards

1
Q

flow of genetic information (basic)

A

protein coding gene transcribed by RNA polymerase into Pre-mRNA
Pre-mRNA processed to mRNA
mRNA is translated by ribosomes into protein

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2
Q

do all genes code for protein

A

no! some code for RNA only

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3
Q

what occurs in the nucleus

A

DNA to RNA transcript (transcriptional control)

RNA transcript to mRNA (RNA processing control)

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4
Q

what occurs in the cytosol

A

mRNA moves out of nucleus (RNA transport and localization control)
mRNA converted to inactive mRNA (mRNA degradation control) OR mRNA converted to protein (translation control)

THEN protein to active or inactive protein (protein activity control)

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5
Q

basic structure of nucleotide

A

base + ribose + phosphate

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6
Q

purines

A

9 membered - A or G

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7
Q

pyrimidines

A

C, T, or U - 6 membered

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8
Q

nucleoside

A

base + ribose

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9
Q

ribose vs deoxyribose

A

ribose has OH/H at 2 position, deoxyribose has H/H at 2 position

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10
Q

attachments in DNA

A

purine or pyrimidine is attached at 1 position on ribose, phosphate group at 5 position

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11
Q

how are nucleotides in nucleic acid chain linked

A

3’ hydroxyl to 5’ phosphate in a phosphodiester bond

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12
Q

how do you read a nucleotide chain

A

5’ to 3’

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13
Q

what stabilizes double stranded DNA

A

hydrogen bonding between G/C base pairs and A/T base pairs, base stacking, hydrophobic interactions.

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14
Q

what would cause DNA to have higher melting point

A

more GC

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15
Q

how do we get DNA to pack into the nucleus

A

using histones and spacer RNA `

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16
Q

nucleosome

A

DNA protein unit wrapped around histone

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17
Q

chromatin

A

DNA in protein bound form

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18
Q

heterochromatin vs euchromatin

A

heterochromatin is tightly wound and not available to transcription machinery. euchromatin is more loosely wound.

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19
Q

what is DNA packaging assisted by

A

polycationic amines (ex: Spermine)

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20
Q

how does DNA become available for transcription

A

acetylations, methylations, phosphorylations

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21
Q

what enzyme replicates DNA prior to cell division

A

DNA polymerase

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22
Q

lagging vs leading strand

A

leading strand is one on which replication fork is moving 3’ to 5’. Replication actually happening 5’ to 3’ because this is the only way DNA polymerase can work.

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23
Q

what transcribes RNA

A

RNA polymerase - only uses one strand of DNA, this is the “template strand”. Again, read in 3’ to 5’ but synthesized 5’ to 3’

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24
Q

coding strand

A

non template strand of DNA, has the same sequence as the coded RNA which was coded from the template strand

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25
Q

promoter

A

DNA sequence recognized by RNA polymerase for binding and transcription

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26
Q

+1 site

A

base pair at which initiation of transcription takes place

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27
Q

RNA polymerases

A

I: transcribes mostly rRNA
II. transcribes protein coding genes (this is what we are dealing with!)
III: transcribes mostly tRNA genes

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28
Q

what is the first nucleotide in pre-mRNA

A

nucleoside 5’ triphosphate

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29
Q

how is RNA pol II activated

A

by phosphorylation. (at end which is highly enriched in serine)

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30
Q

how is RNA pol II deactivated

A

polyadenylation signal and RNA pol II gets released from DNA template and returned to hypophophorylated stated

31
Q

TATA box

A

consensus sequence near the promoter of many genes

32
Q

TFII

A

Transcription Factor for RNA pol II. These bind DNA and each other to direct proper localization of RNA pol II for initiation of transcription at the +1 site.

33
Q

PIC

A

pre-initiation complex. The complete ensemble of protein complexes at the txn initiation site. (TATA binding protein, TBP associated factors, mediator, etc) RNA polymerase eventually binds to these

34
Q

what initiates translation

A

hyperphosphorylation of the carboxy-terminal domain of the largest RNA pol II subunit.

35
Q

cis elements

A

consensus segments on DNA itself that function as binding sites for proteins that will work to increase rate of txn initiation.

36
Q

trans elements

A

proteins that bind to the cis elements

37
Q

different types of cis elements

A

promoter proximal elements: bound by constitutive (unregulated) txn factors are close to promoter

38
Q

type of trans elements

A

bound by regulated txn factors and located far from promoter region

39
Q

how do txn factors work

A

bind to specific DNA target sequences and recruit other proteins (co-activators) that affect formation of PIC of accessibility of DNA for txn initiation

40
Q

HAT

A

histone acetyl transferase - co-activator acetylates histone lysine (+ charge) residues and recruits other proteins that have domains recognizing these tails

41
Q

HDAC

A

histone deacetylase which has an inhibitory effect

42
Q

histone signatures

A

particular modifications of histone proteins are read out by txn machinery to either positively or negatively regulate the rate of txn initiation.

43
Q

co-activators

A

recruited by txn factors

  1. Histone modifying enzyme
  2. Chromatin remodeling complex
44
Q

positioning chromatin remodeling complex

A

reposition nucleosomes on DNA to expose regulatory sequences

45
Q

negative regulation occurs via

A

DNA methylation of C resides in C-phosphate-G dinucleotides - this recruits enzymes that alters local chromatin (ex: MeCP2)

46
Q

MeCP2

A

protein that binds 5 methyl cytosine and recruits a histone deacetylase

1) MeCP2 binds methylated DNA
2) HDAC recruited
3) histone deacetylated – turned OFF

47
Q

epigenetic

A

changes to chromatin that are NOT changing the sequence. these are heritable!

48
Q

5 ways to regulate txn factors

A 
Post TLN modification
Proteolysis 
Localization
Ligand binding
Synthesis
49
Q

KLF1

A

txn factor that turns on B globin gene expression. ALSO turns on BCL11A txn repressor which turns OFF gamma

50
Q

when do you have beta globin and when do you have gamma

A

gamma is fetal - goes down
beta is adult - goes up
alpha is fairly constant

51
Q

where is KLF1 expressed

A

chromosome 19

52
Q

when is KLF1 gene expressed

A

in erythropoiesis program at progenitor cell stage. Modified post translationally by phosphorylation at T41 and is inactive without this phosphorylation.

53
Q

binding site sequence for KLF1

A

CACC box - found -90 of beta globin promoter and multiple KLF1 binding sites are in an enhancer sequence 100 kb upstream

54
Q

LCR

A

Locus control region - KLF1 binding sites in enhancer sequence 100 kb upstream of promoter

55
Q

what role does histone acetylation play in B globin

A

HAT opens up chromatin structure in vicinity of B globin gene promoter, allowing txn to increase 1000 fold

56
Q

HbF composition

A

two alpha and two gamma chains.

57
Q

what is negative regulation of the gamma globin gene accomplished by

A

activity of BCL11A, a txn repressor. This is regulated by KLF1 which means KLF both turns ON beta globin expression and turns OFF gamma globin expression!!!

58
Q

HPFH

A

hereditary persistance of fetal hemoglobin. Gamma chains continue to be expressed at a significant level - this limits tendency of HbS(sickle) to polymerize and pts with >15% HbF show few signs of disease! Also helpful with B-thalassemia who have poor expression of B globin

59
Q

locus for individuals with HPFH

A

contained BCL11A gene on chromosome 2 - single nucleotide polymorphisms that were correlated with HPFH patients included a number on the 2nd intron of this gene which is an enhancer sequence - thus, changes in this enhancer sequence resulted in reduced BCL11A expression and therefore continued txn of gamma globin, even into adulthood.

60
Q

cap at 5’ end of mRNA

A

guanosine nucleotide that has been modified to contain a methyl group at the 7 position on the purine ring. This is linked to the 5’ end of the transcript in an unusual 5’ to 5’ phosphodiester bond

61
Q

what is capped

A

mRNA

62
Q

function of cap

A

serves as a recognition site for binding of proteins that recruit a ribosome and protects pre-mRNA and mRNA from degradation by exonucleases that chew in the 5’ to 3’ direction.

63
Q

poly-A tail

A

at the end of the 3’ UTR sequence, a poly A signal (AAUAAA) signals for endonucleolytic cleavage 10-30 units downstream. poly-A polymerase acts on 3’ hydroxyl that adds 100-200 A residues in a template independent fashion.

64
Q

PABP

A

poly a binding protein. protects 3’ end from degradation by 3’ to 5’ exonucleases

65
Q

what do introns start with

A

GU dinucleotide and end with AG dinucleotide. recognized by loose consensus sequences.

66
Q

branch point

A

near 3’ splice site, A residue in the context of loose consensus sequence

67
Q

SNRP

A

small nuclear ribonucleoprotein particle - part of spliceosome.

68
Q

reactions in splicing

A

2 transesterification reactions (one phosphodiester bond replaced with another)

69
Q

overview of splicing rxn

A
  1. attack of branch point A OH group on the 5’ splice site - get 2’ to 5’ phosphodiester bond
  2. attack of 3’ OH end of the upstream exon on the 3’ splice site which joins upstream and downstream exons in standard 3’ to 5’ phosphodiester bond.
70
Q

ESE sequence

A

in exon - exonic splicing enhancer sequences - RNA boxes bound by SR proteins (rich in serine and arginine). Correct GU and AG of intron (even though there are lots!) can be recognized in the context of these
think “SPLICE REGULATORY!!” for SR protein

71
Q

what does spliceosome recognize

A

actually recognizes EXONS but cleaves introns out. this is why we can have very long introns that definitely contain an AG or GU in their sequence somewhere but won’t get cleaved there!

72
Q

ESS

A

exonic splicing silencer – attach to ESE sites and make it so that the exon isnt spliced out and included in the protein. allows for many many genes to be coded from same transcript.

73
Q

nonsense codon

A

premature stop codon

74
Q

NMD

A

nonsense mediated decay - rapid, target degradation of mRNAs

McG (11 decks)

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