Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

MCB - Molecular Bio > Eukaryotic Transcription and Post-Transcriptional Regulation > Flashcards

Eukaryotic Transcription and Post-Transcriptional Regulation Flashcards

(42 cards)

Start Studying
1
Q

central dogma

A

DNA to RNA to protein

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

gene regulation

A 
chromatin mods (histone mod, acetylation/methylation)
transcriptional control by TFs/Pol
RNA processing control
RNA transport and localisation control
mRNA degradation
translational control
protein activity control
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

transcriptional control

A

chromatin structure
Pol binding
activation factors
additional binding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

chromatin structure modifications

A

highly packed heterochromatin not expressed

acetylation: acetyl to +ve lysines in histone tails loosens chromatin
methylation: condense chromatin
phosphorylation: phosphate next to methylated AA loosen chromatin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

histone code hypothesis

A

chemical mods to histones and DNA determine chromatin configuration so transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

chromatin can move within nucleus to…

A

alter gene expression
active are central
heterochromatin is close to membrane

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

RNA polymerase binding for transcriptional control

A

3 types: RNA Pol I ribosomal RNA gene
RNA Pol II protein coding small RNAs
RNA Pol III tRNA rRNA some snRNA so other small RNAs

initiation complex

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

TATA box (prokaryotes have TATAAT at -10)

A

consensus sequence
in pol II promoters
-25 to transcriptional start

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

RNA Pol II initiation complex

A

pol with TFs fine tune process and stabilise and activate pol

TFIID: TBP (TATA box binding protein) and TAF (regulates DNA binding of pol)

TFIIB: positions RNA pol at start site

TFIIF: stabilises RNA Pol

TFIIE: attracts TFIIH

TFIIH: unwinds DNA and phosphorylates ser5 (in CTD tail of pol II)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

TBP

A

binds TATA box and bends DNA so RNA/TFs can bind and stabilised by TFIIF and E and H help binding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

additional binding and activation factors (activator proteins, TFs, proximal control elements and distal, combinatorial)

A

activator proteins bind to enhancers in promoter region so form mediator complex, sends info from promoter to RNA Pol and tells Pol to transcribe
(some promoters so far from start so needs to bend by DNA-bending proteins)

TFs initiate transcription and help RNA pol

proximal control elements close to TATA while distal enhancers are far away

combinatorial control: comb of control elements active when appropriate activators are present

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

TFs (e.g.)

A

contain DNA binding domains

Leucine zipper TF bind to promoters and cause transcription

recognise specific features of DNA

Zinc finger TF bind promoter

TFs work together

can also inhibit transcription

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

forward genetics

A

identify gene (function) from phenotype e.g. moles, red skin, skin damage is XPD gene functions in DNA repair

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

reverse genetics

A

predict phenotype from gene analysis

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

analysing gene expression

A

single gene: RT-PCR, live cell imaging, promoter studies

all genes: microarrays, RNA sequencing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

RT-PCR

A

cDNA to PCR to electrophoresis

1 gene at a time

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

live cell imaging

Study These Flashcards
A

microscope analyse gene activity and localisation
shows why gene expressed
can fuse to reporter gene (GFP) to see where mRNA expressed in cell

18
Q

promoter analysis

Study These Flashcards
A

to see which enhancer motifs affect transcription

add reporter gene to promoter and transfect to cells and see green colour where expressed

19
Q

ChIP (chromatin immunoprecipitation)

Study These Flashcards
A

Abs for TFs so pull out sequence with TF so find where it binds and see if changes from disease/env
or amplify sequence and gap is where TF binds

20
Q

phylogenetic fingerprinting

Study These Flashcards
A

find sequence where TF binds

21
Q

microarrays

Study These Flashcards
A

study expression of interacting groups of genes
automated
compare patterns
microscrope slide with mRNA hybridised to labelled cDNA so show expression levels
1 spot means 1 gene and darker colour means more gene expressed

22
Q

RNA sequencing

Study These Flashcards
A

show which exons transcribed in a sample
count number of RNAs per exon in sample so calculate expression level of a gene
also identify gene splicing variants

23
Q

what is the point of post-transcriptional regulation of gene expression?

Study These Flashcards
A

for mRNA stability, translation, protein function

24
Q

types of processing

Study These Flashcards
A

capping at 5’ end
poly-A tail to 3’
splicing to remove introns

25
RNA Pol II and regulation
makes mRNA CTD tail - long with loops, 4 serines at position 5 is where phosphorylation happens TFIIH is involved in phosphorylation RNA Pol onto DNA and transcribes it - tail already phosphorylated on serine 5, processing factors can attach to tail and hop to pre-mRNA
26
capping
makes mRNA stable and protects from enzymes and important for export and translation 5' pppNpNp (phosphate and any base) phosphatase removes 1 phosphate so only 2 p's at start G added to this end by guanyl transferase then G methylated another methylation occurs of the downstream base
27
poly-A
3' end polyadenylation 3' sequence: AAUAAA-CA-GU rich region 1. 3' sequence removed by cleavage factor but need to cleave at correct position so don't remove important nucleotides CPSF (cleavage and polya specificity factor) binds AAUAAA G/U rich regions is in part meant to be cleaved and CstF (cleavage stimulation factor F) recognises it CFII (cleavage factor) recognise CA, bend it so PAP (poly A pol) can bind and chop off end tail polyA factor waits will AAUAAA then PAP adds As with ATP and CstF/CFI/CFII removed PABP (poly A binding protein) binds to A tail and helps add As faster
28
introns
remove and ligate 2 exons 5' end splice site and 3' end splice site 'A' branch point in intron where join to form lariat 2 step transesterification 1. hydroxyl group at branch point A that binds to phosphate group causes attached lariat to 3' exon 2. loops removed and 2 exons ligated with esterification
29
snRNPs
small nuclear ribonucleoprotein particles | in spliceosome and 200 other proteins involved
30
specificity (introns exons)
sequence at exon/intron junction at 5' end 3' end and in middle so splicing gives specificity
31
splicing
5' exon/intron junction sequence recognised by U1 snRNP BBP (branch point binding protein) binds to branch point A which is joined by U2AF (U2 auxilliary factor) which helps U2 snRNP find A U4/U6 binds to U1+U2 so conformational change and 1st cut and transesterification forms loop U4+U1 no longer required U6 causes 3' intron/exon cleavage and exons fused afterwards
32
snRNPs give specificity in splicing
U1 has RNA sequence matching 5' exon/intron junction cells don't rely on snRNPs for splicing because exon length same ish but intron size changes so can't cut on basis of distance but conserved in some organism so more accuracy to splicing
33
ESEs
exonic splicing enhancer SR protein binds and shield exon
34
hnRNP
heterogeneous nuclear ribonucleoprotein bind introns and rip up so branch point found so A branchpoint can reach 5' exon/intron junction (because introns quite long sometimes)
35
alternative splicing
evolution, new mRNAs for new function | recognise new parts maybe
36
RNA editing (definition, types, why)
alter sequence of pre-mRNAs (not splicing or methylation) after transcription base insertions cytosine deamination to uracil adenine deamination to inosine (examples lecture 15) to revise mistakes, plasticity for function, defense)
37
base insertions
usually uracil sites missing U specified by guide RNA1 edits by pairing to guide RNA2 e.g. sleeping sickness
38
cytosine deamination to uracil
AA change so new protein e.g. apoliprotein B
39
adenine deamination to inosine
protein change by ADAR (adenosine deaminase acting on RNA) e.g. glutamate receptor
40
ribozymes
catalytic RNAs bind to mRNA to cleave and destroy intron RNA can splice w/o spliceosome RNAse P ribonuclease in processing tRNA and small RNAs, peptidyl transferase ribozyme of ribosome in viruses as well rRNAs of ribosomes can be therapy for cancer
41
regulation of nuclear export of mRNAs
only processed mRNA goes through pore to cytosol because pores restrict movement of molecules needs energy to guide through pore need export or would be degraded
42
miRNA
small RNAs in junk part of DNA, for regulation of transcription, defence, inhibit/destroy transcripts 21-25 nucleotides, non-coding, single strand, matching mRNA so targets specific RISC complex helps (RNA-induced silencing complex) Pol II in miRNA production causes pri to pre to mature single small RNA and cropping dicing so 1 strand digested and 1 to RISC

MCB - Molecular Bio (7 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions