Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry & Molecular Biology > L39-40: Transcription, RNA processing and Regulation I-II > Flashcards

L39-40: Transcription, RNA processing and Regulation I-II Flashcards

You may prefer our related Brainscape-certified flashcards:
AP® Biology flashcards Biology 101 flashcards
1
Q

Detail three important ways in which RNA differs from DNA

A
  • Contains ribose rather than deoxyribose as sugar - Contains four bases adenine, guanine, cytosine and uracil - Single-stranded structure
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

List two important differences bw DNA polymerases and RNA polymerases

A
  • RNA polymerase can initiate synthesis without a primer - RNA polymerase is more error prone than DNA polymerase, no proofreading activity
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

In what direction does RNA pol synthesize RNA?

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

What class of RNA is ultimately translated into proteins?

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

What names are given to the DNA sequences that i.) specify the transcriptional start point and ii.) specify the transcriptional end point?

A

i.) Promoter ii.) Terminator

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

Describe the typical layout of a gene that is transcribed by RNA polymerase II

A
  • Enhancer (way upstream) - Gene-specific elements: DNA sequences unique to particular genes or groups of genes - CAAT box or GC-rich region: may be present - TATA box: almost invariably found in genes transcribed by Pol II - Gene
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the name of the molecule that synthesizes mRNA?

A
  • RNA pol II
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the name of the molecule that synthesizes rRNA?

A
  • RNA pol I, some Pol III
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the name of the molecule that synthesizes tRNA?

A
  • RNA Pol III
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Can RNA Pol II initiate transcription of DNA? Explain

A
  • No it cannot, it requires help of GTFs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What GTFs are required by RNA Pol II?

A
  • TFIID binds to TATA box, which distorts the DNA helix, acts as signpost and recruits remainder of factors and pol II - Transcriptional initiation complex forms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What sequence are promoter regions rich in? Why?

A
  • Rich in AT sequences and presence of TATA box. - Easier to separate AT base pairs than GC base pairs, by DNA helicase activity of one of the GTFs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the basal transcription complex?

A
  • RNA pol II with GTFs = basal transcription complex - This initiates transcription at a low rate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Discuss rate of DNA transcription in context of basal transcription complex

A
  • Basal transcription complex = RNA pol II with GTFs - This complex initiates transcription at low rates - High rate requires NF1 binding to CAAT box and SP-1 binding to GC-rich sequences
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

By what mechanism does the toxin alpha-amantin function? How are ppl exposed to this? Symptoms? Treatment?

A
  • Death cap mushroom common in cool, damp regions of pacific coast - Genus/species: amanita phalloides - Contains alpha-amantin, which is a Pol II inhibitor - Nausea, vomiting, coma, hepatic encephalopathy from liver failure - Liver failure ~ 48 hour post-ingestion - Tx: gastric lavage, activated charcoal and liver transplant
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How can rifampicin kill certain bacteria yet have low toxicity towards human cells?

A
  • Used to treat mycobacterial infections such as TB and leprosy - It is a specific inhibitor of RNA pol found in many types of bacteria, but euk Pol II is not sensitive to it
17
Q

3 mRNA processing steps

A
  • Capping - Splicing - Polyadenylation
18
Q

What is meant by the capping of pre-mRNA? Is the cap unique to pre-mRNA? Function?

A
  • Methylguanosine is added to the 5’ end of pre-RNA - This distinguishes mRNA from other types of RNA - Required for subsequent processing steps - Protects against degradation - Important for initiation of translation
19
Q

Distinguish exons from introns

A
  • Exons: short regions encoding protein - Introns: long regions of non-coding sequence
20
Q

Discuss pre-mRNA splicing.

A
  • Catalyzed by complex known as spliceosome, which has protein and snRNA compoments involved in catalysis and recognizing exon/intron boundaries - Consensus nt seqs are required for splicing: 5’ splice site, 3’ splice site and branch point within intron - Adenine at branch point attacks 5’ splice site, cutting sugar-phosphate backbone of RNA - 5’ end becomes linked to adenine, forms a loop - Free 3’OH reacts with 5’ end of next exon, joins. Intron released as lariat
21
Q

What is meant by differential or alternative splicing? What are the consequences of this process?

A
  • Splicing allows for more than one protein product to be generated from a single pre-mRNA transcript, which is called differential/alternative splicing - Increases repertoire of proteins produced – ie. catalytic properties, subcellular locations, distinct interactions differ.
22
Q

What is polyadenylation? Describe. What types of RNA molecule are polyadenylated?

A
  • Polyadenylation = addition of 100s of adenine residues to end of mRNA moledule - Stop pt for transcription is specified by a consensus seq in DNA known as polyadenylation signal, which is transcribed into pre-mRNA - This signal is recognized by specific protein factors - This tail is important for RNA stability
23
Q

Where does RNA processing occur? Does pre-mRNA leave the nucleus?

A
  • Nucleus - No, only mature mRNA
24
Q

Describe mRNA stability

A
  • mRNA molecules decay under ribonucleases - There half lifes are variable from hours to minutes
25
Q

Describe beta-thalassemia

A
  • Reduced beta-chain of hemoglobin due to mutation in beta-globin gene at first exon/intron boundary. Mutation at 5’ splice site causes two aberrant mRNA products to be formed
26
Q

Describe molecule basis for PKU

A
  • Inability to convert phenylalanine to tyrosine due to mutation often at 5’ splice donor site in phenylalanine hydroxylase gene - Results in defective splicing, protein produced lacks one exon and is rapidly degraded
27
Q

What roles do chromatin remodelling complexes, histone acetyltransferases (HATs), histone deacetylases (HDACs) and DNA methylation play in controlling the availability of genes for transcription?

A

1.) chromatin remodeling complexes: use ATP to change nucleosome structure temporarily to allow or inhibit transcription 2.) HATs: acetylate lysine residues in histones, reduce net pos charge of protein, weakens histone:DNA interaction, facilitates transcription 3.) HDACs: remove acetyl groups from histone, increasing net pos charge of protein, strengthens histone:DNA interaction, inhibits transcription 4.) DNA methylation: methyl groups added to cytosine, found in silent regions of genome, binds proteins that recruit HDACs to DNA, promoting condensation and inhibiting transcription

28
Q

Describe key structural features of three classes of DNA-binding protein, namely helix-turn-helix proteins, zinc finger proteins and leucine zipper proteins.

A

1.) Helix-turn-helix proteins: two alpha-helices connected by short AA chain. Side chains of AA in one helix recognize DNA 2.) Zinc finger proteins: zinc as structural element, alpha-helix binds DNA 3.) Leucine zipper proteins: dimers where alpha-helix from each monomer forms coil structure, leucine typically found at every seventh position in sequence of polypeptide chain forming alpha-helix

29
Q

In general, how do DNA-binding proteins regulate transcription?

A
  • Binding of these proteins recruit other proteins to DNA, including HATs, chromatin remodeling complexes or HDACs
30
Q

Explain how LDL receptor production changes in response to cholesterol. Discuss mechanism

A
  • Transcription of LDL receptor gene is upregulated in response to low cellular cholesterol - Result: more LDL receptor production and enhanced cholesterol uptake from blood Low-level transcription - SP1 (zinc-finger protein) binds to GC rich regions in LDL receptor promoter - SP1 requires CRSP protein cofactor to be activated - SP1 and CRSP help pol II and GTFS to assemble at promoter - These are all considered basal transcription factors Up-regulated transcription - Requires basal transcription factors - Also SREBP-1a enters into nucleus as triggered by low cellular cholesterol - SREBP-1a binds to SRE and recruits HAT activity plus some other proteins - Result = enhanced transcription of LDL-receptor gene
31
Q

How does the steroid hormone cortisol regulate transcription?

A
  • Cortisol is secreted by adrenal cortex - Binds to and activates receptors in cytoplasm, causing conformational change to that receptor - Accessory proteins dissociate, activated receptors dimerize - Dimerized receptors are imported into nucleus - Bind GRE elements on genome, regulate transcription positively or negatively - Typical result of cortisol is to stimulate gluconeogenesis, glycogen deposition, fat and protein degradation, inhibit inflammatory response
32
Q

Describe regulation of transcription in response to thyroid hormone

A
  • Thyroid hormone becomes bound to receptors that are constitutively in the nucleus and are bound to DNA elements of genes that respond to it - THR (receptor) when not bound to thyroid hormone is dimerized with RXR (retinoid X receptor) - This dimer recruits HDAC, which condenses chromatin and inhibits transcription - Binding of thyroid hormone triggers conformation change in THR, HDAC is released and HAT binds in its place, leads to relaxation of chromatin and enhancement of transcription - Response: stimulated metabolic rate in most tissues
33
Q

What is Rubinstein-Taybi syndrome?

A
  • Inherited condition characterized by hypoplastic maxillar (insufficient growth of midface), prominent nose, intellectual disability, polydactyly, growth retardation - Results from mutation in gene encoding CREB binding protein (CBP) - This gene is implicated in processes related to memory, cognition and developmental processes
34
Q

Discuss roles of the CREB, CBP and PKA in transcriptional control

A
  • PKA phosphorylates and regulates many cytosolic proteins, but is also present in activated form in nucleus under high levels of cAMP - Many genes regulated by PKA contain CRE (cAMP responsive element) in their promoter region - PKA influences transcription by phosphorylation of CREB, which then binds CRE - CREB bound to CRE recruits CBP - CBP then recruits EP300 - CBP/EP300 interacts physically with GTFs. Together CBP/EP300 function as HATs, relaxing chromatin and stimulating transcription
35
Q

What is the mechanism of action of tamoxifen?

A
  • Tamoxifen inhibits estrogen action - It is a competitive inhibitor, blocking estrogen binding to its receptor, however ERE dimer still remains dimerized and bound to DNA - Growth of breast cancer is reduced by disrupting this estrogen signaling

Biochemistry & Molecular Biology (47 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions