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Molecular Cell Biology > (2) Chapter 8: RNA Synthesis and Processing > Flashcards

(2) Chapter 8: RNA Synthesis and Processing Flashcards

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1
Q

Bacterial RNA polymerase

A
  • catalyzes polymerization of NTPs as directed by a DNA template (in 5-3 direction).
  • has 5 subunits: alpha, beta, omega, sigma,
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2
Q

NTPs

A

ribonucleoside 5’ triphosphate

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3
Q

How does transcription initiate in prokaryote cells?

A

de novo, no primer is needed. (promoters are used)

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4
Q

Alpha subunit of bacterial RNA polymerase

A
  • identifies the correct sites for transcription initiation
  • most bacteria have many alpha subunits
  • binds to both -10 and -35 regions
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5
Q

Promoter

A
  • gene sequence to which RNA polymerase binds to initiate transcription
  • 6 nucleotides long
  • located at 10 and 35 bp’s upstream of transcription start site.
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6
Q

consensus sequences

A
  • bases most frequently found in different promoters

- genes that have promoters that differ from consensus sequences are transcribed less efficiently

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7
Q

Bacterial DNA unwinding mechanism

A
  • polymerase unwinds 12-14 bases of DNA then releases sigma group to form an open-promoter complex for transcription
  • polymerase maintains an unwound region of about 15 bps at a time
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8
Q

When is the sigma subunit released from polymerase?

A

after addition of about 10 nucleotides during transcription.

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9
Q

Prokaryote transcription termination

A

-When polymerase encounters a STOP Signal, transcription is terminated

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10
Q

What is the most common stop signal in prokaryote transcription? How does it work?

A
  • GC-rich sequence followed by seven A residues.
  • transcription of this symmetrical inverted repeat sequence results in a RNA segment that forms a stable-loop structure
  • loop distrupts DNA template association
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11
Q

Enzymes involved in metabolism of lactose

A
  • beta galactosidase
  • lactose permease
  • transacetylase
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12
Q

beta-galactosidase

A

-cleaves lactose into glucose and galactose

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13
Q

lactose permease

A

transports lactose into the cell

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14
Q

transacetylase

A

inactivates toxic thiogalactosides that are transported into the cell along with lactose

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15
Q

Operon

A

a single unit that holds genes that encode specific enzymes

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16
Q

operator in prokaryote transcription

A
  • a loci that controls transcription
  • adjacent to transcription initiation site
  • part of operon
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17
Q

repressor in prokaryote transcription

A
  • “i loci”; a loci that controls transcription.
  • encodes a protein that binds to the operator
  • blocks transcription when bound to operator
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18
Q

How does the lactose operon work?

A

when lactose is present in normal cells, it binds to the repressor (i loci) and prevents the repressor from binding to the operator; so, genes are expressed

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19
Q

How is control of transcription mediated?

A

-the interaction of regulatory proteins with specific DNA sequences.

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20
Q

Cis-acting control elements

A

-affect expression of linked genes on the same DNA molecule (the operator)

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21
Q

Negative control of transcription

A

The regulatory protein (the repressor) blocks transcription. Ex) lac operon

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22
Q

Positive control of transcription

A

Regulatory proteins activate transcription

Ex) E.coli

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23
Q

Explain the process of positive control of the lac operon by glucose (prokaryote)

A
  1. If glucose is present: lac operon is repressed, even if lactose is also present
  2. if glucose levels decrease, cAMP levels increase
  3. cAMP binds to CAP
  4. CAP binds to target DNA sequence which is upstream lac operon
  5. CAP facilitated binding of RNA polymerase to the promoter
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24
Q

CAP

A

catabolite activator protein (regulatory protein). active in prokaryote cells

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25
Q

How many polymerases are involved in eukaryotic transcription?Are they complex?

A

-three RNA polymerases transcribe different classes of genes. all are very complex and consist of 12-17 substrates

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26
Q

RNA polymerase II

A

synthesizes mRNA, requires initiation factors that are not associated with polymerase

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27
Q

General transcription factors

A
  • proteins involved in transcription from polymerase II promoters
  • very important
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28
Q

What percentage of genes in the human ganome encode transcription factors?

A

10%

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29
Q

TATA box

A
  • a sequence element found in a promoter

- 10 sequence of bacterial promoters

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30
Q

Inr promoter elements

A

initiator elements, sometimes found as a promoter

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31
Q

TFIIB promoter elements

A

recognition elements, ex. BRE

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32
Q

downstream promoter elements

A

DCE, MTE, DPE

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33
Q

TFIID transcription factor

A

composed of multiple subunits

  • TATA binding protein (TBP)
  • TAFs that bind to the Inr, DCE, MTE, and DPE sequences
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34
Q

formation of polymerase II Preinitiation complex

A
  • has five general transcription factors
    1. TATA binding protein with other subunits
    2. TFIIB
    3. TFIIF
    4. TFIIE
    5. TFIIH
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35
Q

Mediator

A
  • a protein complex of more than 20 subunits
  • binds to nonphosphorylated CTD when transcription initiates
  • released following phosphorylation of CTD when transcription initiates
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36
Q

After transcription is initiated (CTD has been phosphorylated by the mediator) what happens to the phosphorylated CTD?

A

The mediator complex is released.

-the phosphorylated CTD binds elongation and processing factors that facilitate mRNA synthesis & processing

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37
Q

What is the function of RNA polymerase 1 in eukaryotic cells in eukaryotic cells?

A

transcribes rRNA genes

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38
Q

What are the end products of transcription by RNA polymerase 1 in eukaryotic cells?

A

45S pre-rRNA: processed to yield 28S, 18S, 5.8S rRNAs

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39
Q

What two transcription factors recruit RNA polymerase 1 to form an initiation complex in eukaryotic cells?

A
  • UBF (upstream binding factor)

- SL 1 (selectivity factor 1)

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40
Q

Polymerase III (eukaryotic)

A
  • transcribes genes for tRNAs, 5S rRNA, and some small RNAs

- expressed from 3 types of promoters.

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41
Q

Gene transfer assay

A

-identify regulatory sequences of expression in eukaryotic genes

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42
Q

Regulatory sequence

A

Directs expression of the reporter gene in cultured cells, ligated interaction to reporter gene

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43
Q

Reporter gene

A

Encodes an easily detectable enzyme (fluorescent structure)

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44
Q

Cis-acting regulatory sequences

A

Located upstream of transcription start site

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45
Q

What are the cis-acting regulatory sequences that encode thymidine kinase in the herpes simplex virus?

A
  1. TATA

2. GC boxes

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46
Q

Enhancer

A
  • regulatory sequences located farther away from the start site.
  • usually have multiple sequence elements that bind different regulatory proteins that all work together to regulate gene expression
  • activity doesn’t depend on their distance from, or orientation with respect to the transcription initiation site
  • activity is epecific for the promoter of its target gene
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47
Q

How do enhancers function to regulate transcription in eukaryotes?

A

-function by binding transcription factors that then regulate RNA polymerase

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48
Q

DNA looping

A

-allows transcription factors bound to a distant enhancer to interact with proteins associated with the RNA polymerase/mediator complex at the promoter

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49
Q

In B lymphocytes, what controls transcription of immunoglobin genes?

A

An enhancer that is active in lymphocytes, but not other cell types

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50
Q

The regulatory sequence in B lymphocytes is partly responsible for what kind of expression of the immunoglobin?

A

Tissue specific

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51
Q

Immunogobin heavy-chain enhancer

A
  • has at least nine distinct sequence elements that serve as protein binding sites.
  • contains positive & negative regulatory elements
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52
Q

Positive regulatory element

A

Activates transcription in B lymphocytes

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53
Q

Negative regulatory elements

A

Inhibits transcription in other cell types

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54
Q

How is specificity maintained between interaction of enhancers and promoters?

A

-by insulators or barrier elements

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55
Q

Insulators/barrier elements

A

Divide chromosomes into independent domains and prevent enhancers from acting on promoters located in an adjacent domain.

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56
Q

Electrophoretic-mobility shift assay

A

radiolabled DNA fragments are incubated with a protein and then subjected to electrophoresis in a non-denaturing gel. Migration of DNA fragment is slowed by a bound protein

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57
Q

Chromatin immunoprecipitation process

A
  1. cells are treated with formaldehyde to cross-link transcription factors to DNA sequences that they are bound to
  2. chromatin is extracted and fragmented. Fragments of DNA linked to a transcription factor can then be isolated by immunoprecipitation (through PCR)
58
Q

SP1

A

a transcriptional activator

59
Q

Transcriptional activator: function and structure

A

function: bind to regulatory DNA sequences and stimulate transcription.
2 domain structure:
-DNA-binding domain
-Activation domain (stimulates interaction with other proteins like the mediator)

60
Q

Give 4 DNA binding domains

A
  1. Zinc finger domain
  2. steroid hormone
  3. helix-turn-helix
  4. Leucine zipper/ helix-loop-helix
61
Q

ZInc finger domain

A

binds zinc ions and folds into loops (“fingers”) that bind DNA

62
Q

Steroid hormone receptors

A

have zinc fingers; regulates gene transcription in response to hormones like estrogen & testosterone

63
Q

Helix-turn-helix

A

one helix makes most of the contacts with DNA, the other helices lie across the complex to stabilize the interaction

64
Q

homeodomain

A

a helix-turn-helix protein. important in the regulation of gene expression during embryonic development

65
Q

Leucine zipper & helix-loop-helix

A
  • DNA binding domain
  • protein
  • contains DNA binding domains formed by dimerization of two polypeptide chains.
66
Q

Since both leucine zipper and helix-loop-helix proteins can dimerize with one another, what is possible?

A

-combination of distinct protein subunits can form an expanded array of factors that differs both in DNA sequence recognition and in transcription-stimulating activities.

67
Q

How do activation domains stimulate transcription? (2 mechanisms)

A
  1. interact with mediator proteins and general transcription factors (like TFIIB or TFIID) to recruit RNA polymrease and facilitate the assembly of a transcription complex
  2. interact with coactivators to modify chromatin structures
68
Q

How is gene expression regulated?

A

by repressors which inhibit transcription.

69
Q

HOw do repressors work?

A
  • can interfere with binding of other transcription factors

- some compete with activators for binding to specific regulatory sequences

70
Q

active repressors

A
  • have specific regions that inhibit transcription via protein-protein interactions
  • include interactions with specific activator proteins, mediator proteins, or general transcription factors, and corepressors
71
Q

Corepressors

A

modify chromatin structure to inhibit transcription

72
Q

Elongation

A

transcription can be regulated at this stage.

73
Q

NELF

A

negative elongation factor

74
Q

DSIF

A

a negative elongation factor

75
Q

negative elongation

A

causes polymerase to pause within about 50 nucleotides of transcription start site. continuation depends on another factor

76
Q

P-TEb

A

positive transcription-elongation factor-b. continuation after transcription is stopped by negative elongation factors depends on this

77
Q

Where does most transcriptional regulation take place?

A

at the level of initiation

78
Q

Topological associating domains (TADs)

A
  • the domains in which genomes are divided.
  • discrete chromosomal domains
  • hold enhancers and promoters that interact frequently with each other
79
Q

How is eukaryotic DNA packaged?

A

in chromatin

80
Q

Describe the structure of nucleosome

A
  • 147 bp’s of DNA wrapped around 2 molecules each of histones (H2A, H2B, H3, and H4)
  • one molecule of histone H1 bound to the DNA as it enters the nucleosome core particle
81
Q

How can chromatin be altered?

A

-by histone modifications and nucleosome rearrangements

82
Q

Histone acetylation

A
  • Acetylation can modify the amino-terminal tail (which extends outside of the nucleosome)of core histones which are rich in lysine
  • a characteristic of actively transcribed chromatin
83
Q

HIstone Acetyltransferases

A

(HAT)

-associated with transcriptional activators

84
Q

Histone Deacetylases

A

(HDAC) associated with repressors & corepressors

85
Q

What does histone acetylation do?

A
  • neutralizes positive charge of lysine on the amino terminal tails.
  • relaxes chromatin structure
  • increases availability of DNA template for transcription
86
Q

Give four patterns of histone modification that occur in histone tails

A
  • acetylation/deacetylation
  • methylation of lysine and arginine residues
  • phosphorylation of serine residues
  • addition of small peptides to lysine residues (ubiquitin and SUMO)
87
Q

How do Histone modifications affect gene expression?

A
  • by altering chromatin properties
  • providing binding sites for proteins that activate or repress transcription
  • can regulate one another and lead to stable patterns of modified chromatin
88
Q

How is chromatin condensation and formation of heterochromatin induced?

A

-by methylation of H3 lysine-9 and -27 residues. which are binding sites for proteins.

89
Q

What are Distinct chromatin features of promoters and enhancers?

A
  • No nucleosomes, so they are accessbile for binding transcription factors
  • can be digested with DNase via DNase hypersensitive sites
  • promoters are marked by trimethylated lysine
  • enhancers are marked by monomethylated lysine
90
Q

Chromatin remodeling factors

A
  • protein complexes that alter contacts between DNA and histones
  • use energy derived from hydrolysis of ATP
91
Q

What can Chromatin remodeling factors do?

A
  • can reposition nucleosomes
  • can change the conformation of nucelosomes
  • can eject nucleosomes from DNA
92
Q

Elongation factors

A
  • facilitate elongation after initiation of transcription
  • associated with phosphorylated C-terminal domain of RNA polymerase II
  • histone modifying enzymes
  • chromatin remodeling factors
93
Q

epigenetic inheritance

A
  • the transmission of information that is not contained within the sequence of DNA to daughter cells at division
  • provided by histone modification
94
Q

Where are modified histones transferred to?

A
  • from the parental to both progeny chromosomes.

- they direct similar modification of new histones and maintain characteristic patterns of modification

95
Q

DNA methylation

A
  • controls transcription in eukaryotes
  • correlated with transcriptional repression
  • a mechanism for epigentic inheritance
  • plays a role in genomic imprinting
96
Q

When does DNA methylation occur?

A

-follows DNA replication

97
Q

What occurs during DNA methylation?

A

-an enzyme adds methyl groups to the 5-carbon position of cytosines (C) that precede guanines (G)–>
(methylates CpG sequence of daugher strand that is h-bonded to a methylated parental strand)

98
Q

Genomic imprinting

A

expression of some genes depends on whether they come from the mother or father

99
Q

Give an example of genomic imprinting

A
  • gene H19 is transcribed only from the maternal copy.

- it is specifically methylated during the development of male, but not female germ cells

100
Q

What is the function of noncoding RNA molecules? How do they work?

A
  • regulation of transcription
  • form complexes with proteins that modify chromatin and recruit these complexes to their sites of transcription, therefore regulating expression of neighboring genes
101
Q

What are two noncoding RNA molecules?

A
  • microRNAs (miRNAs)

- Long noncoding RNAs (incRNAs)

102
Q

miRNA

A
  • 20-30 nucleotides

- act by RNA interference pathway to inhibit translation or induce degredation of homologous mRNAs, and gene regulation

103
Q

IncRNAs

A
  • commonly repress their target genes by forming complexes with polycomb repressive complex 2 (PRC2)
  • can associate with different chromatin-modifying enzymes and function as repressors or activators
  • some act in trans by recruiting chromatin-modifying complexes (e.g. PRC2) to distant target genes
  • can regulate gene expression in other ways as well.
104
Q

Give an example of how Xist lncRNAs regulate gene expression

A

Xist lncRNAs mediate X chromosome inactivation in mammals and several lncRNAs involved in imprinting.

105
Q

Bacterial mRNAs

A

used immediatly for protein synthesis while still being transcribed

106
Q

How are RNAs other than bacterial mRNAs used for transcription?

A
  • other RNAs must be processed in various ways

- regulation of processing provides another level of control of gene expression

107
Q

pre-rRNA molecule

A

Ribosomal RNAs of both prokaryotes and eukaryotes are derived from a single long pre-rRNA molecule

108
Q

Prokaryotic pre-rRNA molecule

A

cleaved to form 3 rRNAs: 6S, 23S, and 5S

109
Q

Eukaryotic pre-rRNA molecules

A

Have four rRNAs: 16S, 23S, and 5S; 5S rRNA is transcribed from a seperate gene

110
Q

pre-tRNA

A

precursors for tRNAs in prokaryotes and eukaryotes

  • bases are modified at specific positions.
  • about 10% of bases are modified.
111
Q

RNase P

A
  • used to orocess the 5’ end of pre-tRNAs
  • cleaves
  • a ribozyme
112
Q

ribozyme

A

an enzyme in which RNA rather than protein is responsible for catlytic activity

113
Q

CCA terminus

A
  • -the site of amino acid attachement

- processing of the 3’ end of tRNA involves addition of CCA terminus

114
Q

In eukaryotes, When are pre-mRNAs modified?

A

-before export from the nucleus

115
Q

mRNPs

A

messenger ribonucleoprotein particles.

  • RNA binding proteins
  • responsible for mRNA processing, transport, and the regulation of mRNA function
116
Q

Describe processsing of mRNA

A
  • modification of both ends of the initial transcript
  • removal of introns from its middle
  • processing is coupled to transcription
117
Q

CTD of RNA polymerase II function in processing of mRNA

A
  • C-terminal domain coordinates processing
  • (RNA polymerase I & III don’t have a CTD, so this is a specific Rx)
  • a 7-methylguanosine cap is added to the 5’ end of mRNA
118
Q

What is the function of the 5’cap on mRNA

A
  • stabilizes RNA

- aligns RNA on the ribosome during translation

119
Q

How is the 3’ end on mRNA defined?

A

-Polyadenylation: cleavage of the primary transcript and addition of a poly-A-tail
(the addition of about 200 adenines)

120
Q

What are signals for polyadenylation?

A
  • a conserved hexanucleotide (AAUAAA in mammalian cells)

- a G-U rich downstream sequence element

121
Q

What happens to an RNA that has been synthesized downstream of the site of poly-A addition?

A

the RNA is degraded

122
Q

What is the function of splicing in pre-mRNA?

A
  • to remove introns

- a highly specific process so that functional mRNAs can be yielded

123
Q

How does splicing of pre-mRNA proceed?

A
  1. Cleaved at the 5’ splice site (SS) and joining of the 5’ end of the intron to an Adenine within the intron (branch point). Intron forms a loop
  2. Cleaved at the 3’ SS and simultaneous ligation of the exons excises the intron loop
124
Q

Where does splicing take place?

A

-in spliceosomes

125
Q

spliceosome

A

large complexes where splicing takes place.

-have five types of small nuclear RNAs (snRNAs): U1, U2, U4, U5, and U6

126
Q

snRNA

A
  • small nuclear RNAs (U1, U2, U4, U5, and U6.

- complexed with 6-10 protein molecules to form snRNPs

127
Q

snRNP

A

small nuclear ribonucleoprotein particles

-combo of snRNA and protein molecules

128
Q

Spliceosome Assembly initial recognition mechanism

A

recognition of 5’ SS by base pairing between 5’SS consensus sequence and a complementary sequence at the 5’ end of U1 snRNA

129
Q

Spliceosome Assembly process

A
  1. binding of U1 snRNP to the 5’ splice site (SS)
  2. binding of U2 snRNP to the branch point
  3. complex of U4/U6 and U5 snRNPs enters spliceosome
  4. U4 and U1 dissociate from spliceosome and U6 catalyzes both formation of the lariat-like intermediate and ligation of the exons
130
Q

RNA editing

A
  • processing, other than splicing, that can alter the protein-coding sequences of mRNA
  • single base modification reactions
131
Q

What results from the editing of mRNA for apolipoprotein B mRNA

A
  • Apo-B100

- Apo-B48

132
Q

Apo-B100

A

synthesized in the liver by translation of unedited mRNA

133
Q

Apo-B48

A

synthesized in the intestine from edited mRNA in which a C has been changed to a U by deamination

134
Q

function of Apolipoprotein B

A

transports lipids in the blood

135
Q

Processing and Turnover of pre-mRNA

A
  1. over 90% sequences are introns, which are degraded in the nucleus after splicing
  2. processed mRNAs are protected from degredation by enzymes by capping and polyadenylation
136
Q

How are intracellular levels of RNA determined?

A
  • by a balance between synthesis and degredation

- rate of degredation can thus control gene expression

137
Q

Processing and turnover of rRNA and tRNA

A
  • both are very stable in both prokaryotes and eukaryotes

- account for greater then 90% of all RNA

138
Q

Processing and turnover of mRNA in bacterial and eukaryotic cells (separately)

A
  • bacterial mRNAs are rapidly degraded and have half-lives of 2-3 minutes
  • eukaryotic mRNA have half-lives from less than 30 min-20 hours
139
Q

Short lived mRNAs

A
  • code for regulatory proteins

- levels can vary rapidly in response to environmental stimuli

140
Q

Long half-lived mRNAs

A

-encode for structural proteins or central metabolic enzymes

141
Q

Degredation of eukaryotic mRNAs by initiated shortening of poly-A-tails.

A

-often contain specific AU rich sequences near the 3’ ends which act as binding sites for proteins that can either stabalize them or target them for degredation

142
Q

How is degredation of eukaryotic mRNAs regulated?

A
  • extrecellular signals such as growth factors and hormones

- sometimes regulated by both siRNAs and miRNAs

Molecular Cell Biology (16 decks)

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