Exam 4: Transcription & RNA processing Flashcards Preview

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Flashcards in Exam 4: Transcription & RNA processing Deck (44):
1

Transcription

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

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RNA is different from DNA because

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

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RNA polymerase

unwinds template DNA & creates RNA in 5' to 3' direction
Initiate RNA synthesis without a primer & more prone to error than DNA polymerase

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RNA polymerase I

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

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RNA polymerase III

synthesizes tRNA - then chemically modified to make mature tRNA

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RNA polymerase II

transcribes mRNA

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Promoter

start of transcription

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Terminator

end point of transcription

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General transcription factors

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

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TFIID (transcription factor for Pol II)

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

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TATA box

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

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TBP (TATA binding protein)

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

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High rates of transcriptional initiation require

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)

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Actively transcribed regions of genome are more

Relaxed than inactive regions

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Death cap mushroom (Amanita phalloides)

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

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Rifampicin

antibiotic, inhibitor of RNA polymerase found in bacteria
Eukaryotic Pol II is unaffected - selectively kill bacteria (antibiotic against Mycobacterium tuberculosis)

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Capping

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

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Splicing

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

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spliceosomes

catalyze pre-mRNA splicing
recognize boundaries between exons and introns

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differential (alternate) splicing

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

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Polyadenylation

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

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Ribonucleases

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

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beta-thalassemia

results from reduced synthesis of beta-chain of hemoglobin
reduces amount of hemoglobin that can be formed = profound anemia

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Phenylketonuria (PKU)

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

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Chromatin remodeling complexes

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

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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

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histone deacetylases (HDACs)

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

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DNA methylation

tends to be found in transcriptionally silent regions

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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

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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

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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

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DNA binding proteins

act as nucleation sites - recruit more proteins

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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

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SRE-1 (sterol responsive element-1)

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

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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

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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)

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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

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GRE

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

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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

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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)

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CREB

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

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CBP

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

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Estrogen

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

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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