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Biomed 2 > Genetic information - Transcription > Flashcards

Genetic information - Transcription Flashcards

1
Q

what are the 4 main levels at which transcriptional control is exerted

A

Binding of RNA polymerase: promoters and transcription factors
Long range control: locus control regions
Chromatin remodelling: histones and histone deacetylases
DNA methylation: CpG islands and imprinting

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2
Q

what genes does RNA polymerase I transcribe

A

28s RNA
18s RNA
58s RNA

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3
Q

what genes does RNA polymerase II transcribe

A

all genes that encode snoRNA
most snRNA

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4
Q

what genes does RNA polymerase III transcribe

A

5sRNA
tRNA
some snRNA
and other small RNA

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5
Q

All genes that are transcribed and expressed via mRNA are transcribed by which polymerase

A

RNA polymerase II

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6
Q

what are the differences between bacterial and eukaryotic RNA polymerase II

A

eukaryotic - 12 subunits instead of 5
cannot initiate transcription - no σ factor
has to deal with DNA packed into nucleosomes

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7
Q

function of transcriptional activators

A

Transcriptional activators help attract RNA polymerase II to the promoter, help regulate rate and tissue specificity of gene expression

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8
Q

what does the initiator region highly conserve

A

pyrimidines

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9
Q

where does RNA Pol bind to

A

TATA box

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10
Q

what is elongation

A

Release RNA Pol II from promoter

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11
Q

what is TFII

A

a general transcription factor of RNA polymerase II

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12
Q

how is a pre-initiation complex (PIC) formed

A

The first transcription factor TFIID binds the TATA box
Other transcription factors join it
Once some transcription factors have attached to the TATA box
- More transcription factors bind

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13
Q

how is elongation achieved

A

C-Terminal domain (CTD) phosphorylated
Conformation change – tightens grip
General TFs dissociate
Acquires new proteins – including elongation factors that help process the RNA and increase elongation rate

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14
Q

how do the transcription factors involved in the formation of PIC function to achieve this

A

IID contains TBP which binds to the TATA box
IIA stabilises IID binding to promoter
IIB binds initiation sequence
Pol II binds IIB
IIE stimulates transcription
IIH has kinase and helicase activity

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15
Q

what does a TATA less core promoter contain

A

contain an INR and DPE

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16
Q

what is a DPE

A

downstream promoter element
located at 28+ - 32+
has the sequence AGAC
recognised by TFII I

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17
Q

what causes growth factor deficiency

A

mutation in Pit-1 transcription factor

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18
Q

DNA sequence motifs bound by general transcription factors

A

the general TF, Sp1 binds to GGGCGG
Sp1 is found in all cell types

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19
Q

. DNA sequence motifs that confer tissue specific expression

A

MyoD is a muscle-specific transcription factor
Note all cells have CANNTG but only tissue specific cells have the MyoD TF expressed.

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20
Q

. DNA sequence motifs that confer response to particular stimuli

A

Oestrogen

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21
Q

what are enhancers

A

regulatory sequences that act at a distance

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22
Q

on an immunoglobulin enhancer what is the function of E1-E4

A

B-cell specific Transcription Factor

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23
Q

on an immunoglobulin enhancer what is the function of C1-C3 and Oct

A

C1-C3: General Transcription Factor
Oct: B cell specific Transcription Factor

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24
Q

what determines wether a gene is switched on

A

TF binding

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25
Q

features of a zinc finger DNA binding domain

A

contain a loop of 23 amino acids
usually have multiple zinc fingers
the linker between the zinc fingers is 7-8 amino acids

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26
Q

role of zinc in DNA binding

A

do not directly interact with the DNA but is essential for folding of the DNA
zinc fingers bind to both major and minor grooves

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27
Q

features of a helix-turn-helix (homeodomain)

A

homeodomains are 60 amino acids long
The C terminal alpha-helix 3 is 17 amino acid’s and lies in the major groove
Helices 1 & 2 point away from the DNA

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28
Q

features of basic positively charged binding domains

A

transcription factors with basic binding domain cannot bind to DNA alone
they must dimerise to bind to DNA

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29
Q

features of leucine zipper proteins

A

bind to major groove of DNA with hetero/homodimer via extended α-helices
contain leucine or hydrophobic amino acid in every 7th position in the C-terminal of binding domain
hydrophobic residues form coiled coil domains required for dimerisation

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30
Q

what are the different types of activation domains

A

Acidic amino acids - Gal 4
Glutamine rich - Oct 2
Proline rich - Jun

31
Q

how do transcription factor activation domains work

A

direct interaction with the PIC
recruitment of co-activators

32
Q

what co-activator do transcription factors recruit to modify histones and how does it do it

A

histone acetylase

33
Q

how do inhibitory domains work

A

binds to DNA and prevents TFs with activation domains from binding
bind to PIC and block transcription with its inhibitory domain
recruitment of co-repressors

34
Q

name a co-repressor and how it inhibits transcription

A

histone de-acetylase (HDAT)
- Removes acetyl group of histone units
- restores +ve charge of histone
Close down DNA
Shutting off transcription

35
Q

what is step1 of RNA splicing

A

cleavage at the 5’ splice site
The ribose hydroxyl group (OH) of the A within the branch point acts as a nucleophile and attacks the 5’ splice site

36
Q

what is step 2 of RNA splicing

A

cleavage at the 3’ splice site and joining of the exons
The newly liberated 3’OH group of the 5’ exon becomes a nuclophile and attacks the phosphoryl group at the 3’ splice site

37
Q

what is RNAP II

A

carries many of the proteins involved in splicing

38
Q

features and structure of splicesome

A

Comprised of both RNA (5) and protein (150)
RNA component: small nuclear RNAs (snRNAs)

	U1 U2, U4, U5, U6
      (100-200 nucleotides long)

Each RNA is complexed with 6-10 proteins to form
small nuclear ribonuclear proteins (snRNPs)
Different complexes come in at different stages
Uses ATP

39
Q

structure and function of U1

A

First U1 snRNP binds to 5’ splice site
U1 snRNP consists of U1 snRNA + proteins

40
Q

function of U2 and what does it create

A

binds to branch site - displaces BBP
aided by U2AF
Branch point A residue is excluded creating a single nucleotide bulge

41
Q

which class of RNA splicing has the most eukaryotic genes

A

nuclear pre-mRNA splicing

42
Q

structure of nuclear pre-mRNA splicing

A

Two transesterification reactions (branch site A)

43
Q

what are the features of group II self-splicing

A

Some eukaryotic genes (rare)
Two transesterification reactions (branch site A)
RNA enzyme encoded by intron (ribozyme)

44
Q

what do self splicing introns do

A

folds itself into a specific conformation within the mRNA and catalyses the chemistry of its release

45
Q

features of group I self-splicing

A

Some eukaryotic genes (rare)
Two transesterification reactions (branch site G)
RNA enzyme encoded by intron (ribozyme
same as group II

46
Q

what is important for splice site selection

A

SR proteins

47
Q

features of SR proteins

A

SR proteins are rich in serine & arginine
SR proteins bind to sequences called exonic splicing enhancers (ESEs)
SR proteins recruit the splicing machinery to the nearby splice sites

48
Q

what is alternative splicing

A

A process by which the RNA can be spliced in more than one way
This can result in the formation of 2 or more proteins from the same gene

49
Q

name an example of a gene that is alternatively spliced

A

Calcitonin gene related peptide (CGRP)

50
Q

function of cytosine deaminase

A

amino group on nucleotide ring is removed
converts cytosine into uracil

51
Q

function of adenosine deaminase

A

converts adenosine into inosine

52
Q

how does RNA editing in glutamate receptors effect the cell: adenosine to inosine

A

alters the Ca2+
permeability of the channel

53
Q

what is thalassemia

A

genetic disorder in which there is decreased production of one of the globin chains found in haemoglobin

54
Q

what is the difference between β0 and β+ thalassemia

A

β0 thalassemia major (both genes are affected)
- Develops severe anaemia starting at a few months of age
- Can only survive with the help of frequent blood transfusions
β+ thalassemia minor non-life threatening form of the disease
- Mild anaemia and does not generally require treatment

55
Q

how does β0 thalassemia prevent globin synthesis

A

creation of a cryptic splice site
nonsense protein

56
Q

what is the purpose of the addition of a 5’cap to mRNA transcript

A

protection and marking a mRNA

57
Q

purpose of 3’ processing and polyadenylation to RNA transcript

A

marking as the end of mRNA and protection

58
Q

what is the first step in the addition of a 5’ cap to RNA

A

addition of 7-methyl-guanosine to the 5’ end of RNA

59
Q

when is RNA capped

A

as soon as it emerges from the exit channel of RNA Pol II

60
Q

where are capping enzymes located

A

bound to the RNAP II’s C-terminal domain (CTD)

61
Q

what does the first base at the 5’ end of RNA contain

A

3 phosphates:
alpha
beta
gamma

62
Q

what removes the gamma phosphate

A

RNA triphosphatase

63
Q

what is added to the 5’ end of RNA

A

GMP

64
Q

function of guanylyltransferase

A

removes the beta and gamma phosphates from GTP
converted into GMP

65
Q

how is guanine added to the 5’ end of RNA

A

it is added in reverse to the rest of the transcript
forming a 5’-5’ linkage

66
Q

what does methyltransferase do in terms of 5’ capping

A

adds a methyl group to the guanine

67
Q

why is the C-terminal domain (CTD) of RNAP II central to the process of 5’ capping

A

provides the binding sites for proteins involved in the post-transcriptional modification of the RNA transcript

68
Q

what are the enzymes involved in co-translational capping

A

RNA triphosphatase
Guanylyltransferase
Methyltransferase

69
Q

what is the purpose of a 5’ cap

A

helps distinguish mRNA from other RNA
helps mRNA be properly processed and exported from the nucleus
protects it from degradation in the cell

70
Q

what is a cap-binding complex (CBC) and what is their function

A

they are bound to mRNA
aid in export and protect it from de-capping
serve as marker for pioneer round of translation

71
Q

what is the first step in 3’ processing and polyadenylation

A

the 3’ end is polyadenylated by a string of adenosines ~200

72
Q

function of Poly-A binding proteins (PAB)

A

bind to the poly-A tail and help stabilise the RNA

73
Q

what are the proteins involved in cleaving the RNA

A

cleavage factors I/II (CFI/II)
cleavage stimulation factor (CstF)

74
Q

function of exon junction complex (EJC)

A

binds to close to the splicing junction in association with the spliceosome
EJC is targeted by nuclear export factor I (NXF1) and nuclear export transporter I (NXT1)
RNA is transported through the nuclear pore complex

Biomed 2 (18 decks)

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