Exam 4: Transcription & RNA processing Flashcards

(44 cards)

1
Q

Transcription

A

synthesis of RNA molecules that are complementary in sequence to a DNA template

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

RNA is different from DNA because

A

it contains ribose, it uses uracil to pair with adenine, it is single stranded

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

RNA polymerase

A

unwinds template DNA & creates RNA in 5’ to 3’ direction

Initiate RNA synthesis without a primer & more prone to error than DNA polymerase

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

RNA polymerase I

A

synthesizes ribosomal RNA (rRNA), which is a component of ribosome required for protein synthesis

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

RNA polymerase III

A

synthesizes tRNA - then chemically modified to make mature tRNA

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

RNA polymerase II

A

transcribes mRNA

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

Promoter

A

start of transcription

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

Terminator

A

end point of transcription

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

General transcription factors

A

essential to allow initiation of transcription of genes by Pol II - help Pol II recognize and bind to promotors
Basal transcription complex - initiating transcription only at low rate

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

TFIID (transcription factor for Pol II)

A

general transcription factor

complex of several proteins, contains TBP - binds to TATA box

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

TATA box

A

DNA sequence area in promotor region - always found in genes transcribed by Pol II
Acts as a binding site for general transcription factor, needed for binding of Pol II

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

TBP (TATA binding protein)

A

part of TFIID; binds to TATA box
Distorts DNA and directs other components of general transcription complex & Pol II to promoter - formation of transcriptional initiation complex

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

High rates of transcriptional initiation require

A

additional factors bound to other DNA sequences - GC-rich sequences (bind transcription factor SP-1) & CAAT box (binds transcription factor NF1) & enhancer elements (located further upstream of the promoter)

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

Actively transcribed regions of genome are more

A

Relaxed than inactive regions

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

Death cap mushroom (Amanita phalloides)

A

extremely poisonous fungus
contains toxin alpha-amanitin - inhibitor of Poll II (blocks synthesis of mRNA)
Results in massive liver failure - mRNA degraded during metabolism
No antidote

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

Rifampicin

A

antibiotic, inhibitor of RNA polymerase found in bacteria

Eukaryotic Pol II is unaffected - selectively kill bacteria (antibiotic against Mycobacterium tuberculosis)

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

Capping

A

RNA processing modification at 5’ end of pre-mRNA
“Cap” structure allows cell to distinguish mRNA molecules
Important for further processing & export

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

Splicing

A

in order to form mature mRNA the introns must be removed from the pre-mRNA & exons join together

19
Q

spliceosomes

A

catalyze pre-mRNA splicing

recognize boundaries between exons and introns

20
Q

differential (alternate) splicing

A

a pre-mRNA molecule may contain multiple exons, different subsets of which may be spliced together generating different mRNA molecules
Gives rise to tissue-specific isoforms of enzymes and other proteins

21
Q

Polyadenylation

A

3’ end of RNA specified by DNA signal - polyadenylation signal
transcribed into RNA & recognized by specific protein factors - cleaves RNA molecule and adds “tail” of around 200 adenine nucleotides - poly-A tail

22
Q

Ribonucleases

A

degrade mRNA molecule from both ends - first shortening of poly-A tail, which triggers removal of 5’ cap

23
Q

beta-thalassemia

A

results from reduced synthesis of beta-chain of hemoglobin

reduces amount of hemoglobin that can be formed = profound anemia

24
Q

Phenylketonuria (PKU)

A

inability to convert phenylalanine to tyrosine
due to mutation in phenylalanine hydroxylase gene - single base change in 5’ splice donor site of one particular intron
Incorrectly spliced mRNA and truncated protein that lacks one exon

25
Chromatin remodeling complexes
use energy of ATP hydrolysis to change structure of nucleosomes so DNA becomes less tightly bound to histone core
26
Histone acetyltransferases (HATs)
acetylate lysine residues in histones reduces net positive charge of histones & decreases strength of their interaction w/ DNA (negatively charged) histones located in regions of DNA that are actively transcribed are typically hyperacetylated
27
histone deacetylases (HDACs)
catalyze removal of acetyl groups from histone & promote chromatin condensation inhibit transcription recruited to methylated DNA
28
DNA methylation
tends to be found in transcriptionally silent regions
29
Helix-turn-helix proteins
gene regulatory proteins alpha-helices connected by short chain of amino acids side chains of amino acids in more C-terminal of the two alpha-helices play an important role in DNA binding homeobox proteins
30
Zinc finger proteins
gene regulatory protein zinc is required for protein folding and function alpha-helix makes contact with the major groove of DNA glucocorticoid receptor
31
Leucine zipper proteins
gene regulation protein dimers in which two alpha-helices join together to form a short coiled coil contains hydrophobic residue, typically leucine, at every 7th position = hydrophobic residues down one side positively-charged region interacts with DNA major groove Fos and Jun
32
DNA binding proteins
act as nucleation sites - recruit more proteins
33
LDL receptor gene
responds to low cellular cholesterol increased transcription of LDL receptor gene - results in increased production of LDL receptor protein and enhanced cholesterol uptake from blood
34
SRE-1 (sterol responsive element-1)
gene specific regulatory sequence, transcription is regulated in response to cholesterol levels
35
SP-1
transcription factor binds to GC boxes zinc finger containing protein help with assembly of Pol II requires CRSP (cofactor required for SP-1 activation) necessary but not sufficient for LDL receptor gene activation
36
SREBP-1a
leucine zipper protein that binds to SRE-1 enters nucleus when cholesterol levels fall when bound to SRE-1 recruits HAT - relaxes chromatin & allows for LDL receptor gene transcription (as well as other genes involved in metabolism of fatty acids & cholesterol)
37
Binding of cortisol to glucocorticoid receptor
causes conformational change - frees receptor of associated proteins and exposes DNA-binding domain allows uptake of hormone/receptor complex into nucleus In nucleus binds to DNA at site called GRE (glucocorticoid responsive element) - enhancer element
38
GRE
enhancer element - enhances transcription | can act at a distance and found upstream, downstream, or in middle of gene it regulates
39
thyroid hormone receptors/RXR (retinoid X receptor) complex
found always in nucleus, bound to regulatory DNA sequences absence of bound thryoid hormone, receptors repress transcription by recruiting HDAC activity - chromatin in condensed state thyroid hormone binds, conformation change happens - displacement of HDAC and binding of HAT - relaxation of chromatin and transcription
40
Rubinstein-Taybi syndrome
intellectual disability caused by point mutations, small deletions, and rearrangements within genes encoding CBP & EP300 (which facilitate transcription of PEPCK (phosphoenolypyruvate carboxykinase) as activated by gulcagon - elevated cAMP/PKA)
41
CREB
PKA phosphorylates CREB, which binds to CRE promotor elements and recruits protein CBP (CREB binding protein)
42
CBP
CREB binding protein binds to phosphorylated CREB at CRE region of DNA - recruits EP300 = transcription of PEPCK gene
43
Estrogen
triggers proliferation in many breast cancers - estrogen receptor binds to DNA and recruits additional protein factors that activate transcription of estrogen-sensitive genes
44
Tamoxifen
competitive inhibitor of estrogen receptor can be used to inhibit tumor growth in breast cancer Tamoxifen/receptor complex binds to DNA still, but doesn't recruit additional factors needed to activate transcription