Exam 4: Transcription & RNA processing

Question 1

Transcription

Answer 1

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

Question 2

RNA is different from DNA because

Answer 2

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

Question 3

RNA polymerase

Answer 3

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

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

Question 4

RNA polymerase I

Answer 4

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

Question 5

RNA polymerase III

Answer 5

synthesizes tRNA - then chemically modified to make mature tRNA

Question 6

RNA polymerase II

Answer 6

transcribes mRNA

Question 7

Promoter

Answer 7

start of transcription

Question 8

Terminator

Answer 8

end point of transcription

Question 9

General transcription factors

Answer 9

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

Question 10

TFIID (transcription factor for Pol II)

Answer 10

general transcription factor

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

Question 11

TATA box

Answer 11

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

Question 12

TBP (TATA binding protein)

Answer 12

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

Question 13

High rates of transcriptional initiation require

Answer 13

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)

Question 14

Actively transcribed regions of genome are more

Answer 14

Relaxed than inactive regions

Question 15

Death cap mushroom (Amanita phalloides)

Answer 15

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

Question 16

Rifampicin

Answer 16

antibiotic, inhibitor of RNA polymerase found in bacteria

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

Question 17

Capping

Answer 17

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

Question 18

Splicing

Answer 18

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

Question 19

spliceosomes

Answer 19

catalyze pre-mRNA splicing

recognize boundaries between exons and introns

Question 20

differential (alternate) splicing

Answer 20

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

Question 21

Polyadenylation

Answer 21

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

Question 22

Ribonucleases

Answer 22

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

Question 23

beta-thalassemia

Answer 23

results from reduced synthesis of beta-chain of hemoglobin

reduces amount of hemoglobin that can be formed = profound anemia

Question 24

Phenylketonuria (PKU)

Answer 24

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

Question 25

Chromatin remodeling complexes

Answer 25

use energy of ATP hydrolysis to change structure of nucleosomes so DNA becomes less tightly bound to histone core

Question 26

Histone acetyltransferases (HATs)

Answer 26

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

Question 27

histone deacetylases (HDACs)

Answer 27

catalyze removal of acetyl groups from histone & promote chromatin condensation inhibit transcription recruited to methylated DNA

Question 28

DNA methylation

Answer 28

tends to be found in transcriptionally silent regions

Question 29

Helix-turn-helix proteins

Answer 29

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

Question 30

Zinc finger proteins

Answer 30

gene regulatory protein zinc is required for protein folding and function alpha-helix makes contact with the major groove of DNA glucocorticoid receptor

Question 31

Leucine zipper proteins

Answer 31

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

Question 32

DNA binding proteins

Answer 32

act as nucleation sites - recruit more proteins

Question 33

LDL receptor gene

Answer 33

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

Question 34

SRE-1 (sterol responsive element-1)

Answer 34

gene specific regulatory sequence, transcription is regulated in response to cholesterol levels

Question 35

SP-1

Answer 35

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

Question 36

SREBP-1a

Answer 36

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)

Question 37

Binding of cortisol to glucocorticoid receptor

Answer 37

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

Question 38

GRE

Answer 38

enhancer element - enhances transcription | can act at a distance and found upstream, downstream, or in middle of gene it regulates

Question 39

thyroid hormone receptors/RXR (retinoid X receptor) complex

Answer 39

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

Question 40

Rubinstein-Taybi syndrome

Answer 40

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)

Question 41

CREB

Answer 41

PKA phosphorylates CREB, which binds to CRE promotor elements and recruits protein CBP (CREB binding protein)

Question 42

CBP

Answer 42

CREB binding protein binds to phosphorylated CREB at CRE region of DNA - recruits EP300 = transcription of PEPCK gene

Question 43

Estrogen

Answer 43

triggers proliferation in many breast cancers - estrogen receptor binds to DNA and recruits additional protein factors that activate transcription of estrogen-sensitive genes

Question 44

Tamoxifen

Answer 44

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