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POM Exam 1 > L2: Gene Expression Basic Processes > Flashcards

L2: Gene Expression Basic Processes Flashcards

1
Q

biological relevance of gene expression and regulation

A
  • underlies many fundamental processes
  • development
  • cellular function
  • organismal diversity
  • human variation
  • personalized medicine
  • genetic disease
  • cancer
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2
Q

therapeutic relevance of gene expression and regulation

A
  • many therapies and biomedical technologies require understanding and manipulating of gene expression
  • gene therapy
  • recombinant DNA research
  • production of biological therapeutics
  • RNAi therapies
  • CRISPR/Cas9
  • Systems biology
  • IPSCs
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3
Q

genetic differences in drug responsiveness

A
  • lie in non-coding regions

- may affect expression of nearby genes

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4
Q

DNA -> RNA

A
  • mRNA transcribed from template strand with complementary sequence
  • occurs 5’ - 3’ in opposite orientation to template strand
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5
Q

where does RNA polymerase bind

A
  • binds to the promoter

- elongation with RNA pol moving down DNA adding nucleotides to the 3’ end of the transcript

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6
Q

prokaryotic (bacterial) gene expression (and how different from eukaryotic)

A
  • transcription and translation occur in same cellular compartment because there is no nucleus
  • processes occur simultaneously
  • no RNA splicing
  • mRNAs are commonly polycistronic - multiple coding sequences to make different proteins
  • multiple proteins from same transcript
  • all genes transcribed by single RNA polymerase
  • bacterial-induced disease
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7
Q

eukaryotic gene expression (and how different from bacterial)

A
  • multiple compartments
  • genes are monocistronic
  • genes have introns and exons
  • RNA splicing to eliminate introns
  • different classes of genes (tRNA, rRNA, mRNA) transcribed by distinct RNA polymerases
  • DNA packaged into chromatin
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8
Q

where eukaryotic transcription and RNA processing occurs

A
  • nucleus
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9
Q

where eukaryotic translation occurs

A
  • cytoplasm
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10
Q

exons

A
  • coding and untranslated regions
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11
Q

RNA Pol I transcribes

A
  • rRNA genes
  • 28S
  • 18 S
  • 5.8S
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12
Q

RNA Pol II transcribes

A
  • mRNA genes
  • also microRNAs (regulation)
  • snRNAs (RNA splicing)
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13
Q

RNA Pol III transcribes

A
  • tRNA, 5S rRNA, additional small RNAs

- smaller genes

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14
Q

Are all three polymerases found in eukaryotes?

A
  • yes found in all eukaryotes

Each RNA polymerase recognizes a different promoter that differs n sequence

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15
Q

what is the 4th RNA polymerase?

A
  • mitochondria

- have their own

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16
Q

RNA polymerase II promoters

A
  • where RNA polymerase and transcription starts
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17
Q

core promoters

A
  • multiple types and elements
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18
Q

important class of core promoter

A
  • TATA box - TATAA sequence
  • 25 bp upstream of promoter
  • binds TFIID
  • initiator element (Inr) +1
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19
Q

TFIID

A
  • TATA binding protein

- TBP + TAFs

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20
Q

enhancers

A
  • bind TFs

- promote spatial, temporal, and quantitative control of transcription

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21
Q

upstream promoter-proximal elements

A
  • GC rich regions - binds SP1 TF
  • CAAT box - binds C/EBP
  • regulate RNA levels
  • bind transcription factors
  • close to promoter (within 100 bp)
  • elevate the levels of transcription
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22
Q

focused promoters

A
  • focused at one site
  • defined location
  • contain TATA box and Inr elements
  • regulated genes
  • 20% of human promoters
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23
Q

dispersed promoters

A
  • multiple start sites
  • lie within CpG islands instead of TATA boxes
  • housekeeping genes
  • 80% of human promoters
  • GC rich regions
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24
Q

housekeeping genes

A
  • things that are pretty much on all the time.

- regulation of levels doesn’t change very much

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25
Q

regulated genes

A
  • gene that gets turned on at specific times
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26
Q

RNA polymerase II composed of

A
  • core enzyme composed of 12 subunits
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27
Q

General (Basal) transcription factors

A
  • work with RNA polymerase to start eukaryotic transcription

- TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH

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28
Q

TATA binding factor

A
  • TBF

- TBP-Associated Proteins (TAFs) - 13 proteins

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29
Q

TATA binding protein (TBP)

A
  • part of TFIID

- binds TATA box

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30
Q

role of TFIIA and TFIIB

A
  • stabilize TBP binding

- TFIIB positions and recruits RNA polymerase II over promoter

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31
Q

TFIIF role

A
  • assists polymerase II binding

- followed by TFIIE and TFIIH

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32
Q

TFIIH role

A
  • helicase
  • unwinds DNA to open up helix and allow transcription to occur
  • uses energy of ATP hydrolysis
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33
Q

TFIIH kinase role

A
  • phosphorylates the C-terminal domain of polymerase II along with TFIIE
  • RNA polymerase will not transcribe genes until phosphorylation occurs
  • then transcription starts
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34
Q

which transcription factors are not released once transcription begins?

A
  • TBP (remains at promoter to start another round of transcription)
  • TFIIF (remains with Pol II)
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35
Q

First step of transcription initiation

A
  • TFIID binds to TATA box
  • because it contains TBP
  • induces bending of DNA
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36
Q

second step of transcription initiation

A
  • binding of TFIID is followed by binding of TFIIA and TFIIB
  • stabilize TBP binding
  • TFIIB positions and recruits RNA polymerase II over promoter at CRE and recruits TFIID
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37
Q

third step of transcription initiation

A
  • RNA pol II recruited along with TFIIF
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38
Q

fourth step of transcription initiation

A
  • TFIIE and TFIIF are recruited to form transcription initiation complex
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39
Q

what promoter does Pol I use?

A
  • rlnr (ribosomal initiator) plus UPE/UCE sequences

- upstream promoter element

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40
Q

what promoter does Pol II use?

A
  • TATA plus Inr (initiator)
  • Inr plus DPE
  • downstream promoter element
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41
Q

what promoter does Pol III use?

A
  • internal sites (A and C for rRNA)
  • A and B for tRNA
  • has sequence elements that interact with pol III but are downstream of the genes
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42
Q

5S rRNA genes

A
  • TFIIA and TFIIC recognize the promoter
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43
Q

tRNA gene

A
  • TFIIC recognizes the promoter
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44
Q

other gene promoters

A
  • use upstream TATA and PSE

- TATA recognized by TBP

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45
Q

related TBP-like proteins recognized by

A
  • Pol I and Pol III
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46
Q

alpha amanitin toxin

A
  • poisonous mushroom
  • binds to RNA pol II and inhibits transcription
  • causes severe kidney damage and can lead to death
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47
Q

prokaryotic transcription

A
  • only one RNA polymerase for mRNA, tRNA, and rRNA genes
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48
Q

what does rifampin do?

A
  • binds to the beta subunit of RNA pol and prevents initiation
  • does not bind to eukaryotic RNA polymerases which is why we can use it on humans
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49
Q

prokaryotic promoters

A
  • have two short conserved sequences (-35, -10) that are recognized by RNA polymerase
  • looks like TATA box
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50
Q

prokaryotic RNA polymerase structure

A
  • 5 subunits
  • 2 alpha
  • beta
  • beta prime
  • omega
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51
Q

sigma factors

A
  • can vary
  • allow holoenzyme (core + sigma) to recognize promoter
  • allow it to target different promoters
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52
Q

leader

A
  • 5’ untranslated region

- part of mRNA

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53
Q

trailer

A
  • 3’ untranslated region

- has fairly extensive poly(A) tail that gets added on after the gene is transcribed

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54
Q

where do the untranslated regions come from

A
  • exons that get spliced together
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55
Q

where does processing and modification of hnRNA occur?

A
  • in the nucleus
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56
Q

hnRNPs

A
  • interact with hnRNA to facilitate protein interactions, transport, and prevent degradation
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57
Q

hnRNA capped where?

A
  • 5’ end
58
Q

hnRNA poly(A)’d where?

A
  • 3’ end
59
Q

where does the transcript go after it is processed?

A
  • the cytoplasm
60
Q

5’ cap

A
  • 7-methyl-guanosine
  • first nucleotide that gets made
  • odd 5’ to 5’ linkage using guanosine with a methyl group at N terminal (position 7) and position 2 of terminal ribose
61
Q

function of 5’ cap

A
  • makes mRNA resistant to degradation and enhances initiation of translation
62
Q

when does capping occur?

A
  • as mRNA is being transcribed
63
Q

how are methyl groups donated?

A
  • donated by SAM

- SAM regenerated after it donates a methyl group by vitamins B12 and folate (B9)

64
Q

role of RNA pol in capping

A
  • as Pol begins transcription, CTD phosphorylated by TFIIH kinase at Ser 5 binds capping proteins
  • facilitates binding of cap proteins to CTD
  • capping proteins transferred to newly emerged 5’ end of mRNA and cap the mRNA
  • capping proteins put on the 7-methyl G
65
Q

polyadenylation

A
  • mRNA cleaved downstream at 3’ end and poly(A) tail added

- AAUAAA recognition sequence

66
Q

is poly(A) present in the gene?

A
  • no

- added by poly(A) polymerase with the use of ATP

67
Q

what happens once poly(A) is absent?

A
  • shortens over time
  • mRNA degraded after absent
  • way to control how long mRNA lasts
68
Q

function of poly (A)

A
  • mRNA stability
  • transport mRNA from nucleus
  • enhance translation
69
Q

how does polyadenylation occur?

A
  • cleavage specificity factors carried on the CTD of RNA pol II bind to the poly(A) signal sequence
  • cleavage factors (CPSF, CstF) cut 3’ end
  • Poly(A) polymerase recognizes 3’ end
  • aided by CPSF begins synthesizing poly(A) tail
  • Poly(A) binding protein binds to poly A stretch and directs extension of the sequence
  • enhances ability of poly(A) to add more proteins
70
Q

RNA splicing

A
  • removal of introns and joining together of exons to create mature mRNA
71
Q

splicing carried out by

A
  • spliceosome
72
Q

what recruits splicing factors?

A
  • CTD of Pol II
73
Q

snRNPs

A
  • small nuclear RNA + proteins

- consists of the small RNAs: U1, U2, U4, U6 and associated proteins

74
Q

precursor RNA

A
  • specific sequences at 5’ splice acceptor site and 3’ splice donor site + branch site present in the intron
75
Q

conserved sequences at intron-exon junctions

A
  • recognized by spliceosome
  • introns almost always start with GU 3’ site and end with AG at 5’ site
  • A at branch site
76
Q

splicing process

A
  • U1 snRNP binds near first exon-intron junction at 5’ splice site after recognition of it
  • U2 binds to conserved A residue in intron (at branch point sequence)
  • snRNPs U4, U5, and U6 bind to U1-U2 complex and form a loop
  • G at 5’ end of intron is cut and forms a 2’-5’ linkage with A residue at the branch site to form a lariat
  • U1 and U4 released. U5 and U6 shift positions
  • second cleavage occurs at 3’ end of intron after AG
  • exons joined together, intron released along with the remaining parts of the spliceosome, and degraded
  • part of spliceosome ligates the exons together
77
Q

what percent of genetic diseases are due to splice mutations?

A
  • 15%
78
Q

Limb girdle muscular dystrophy symptoms

A
  • weakness and wasting of muscles
79
Q

gene for limb girdle muscular dystrophy

A
  • LMNA

- codes for laming A and C which are intermediate filaments that support the nuclear envelop

80
Q

what happens with limb girdle muscular dystrophy

A
  • exon 8 gets spliced to exon 9
  • change in G to C and exon 9 not spliced to exon 10
  • results in truncated protein and RNA turnover
81
Q

lupus cause

A
  • autoimmune disorder
  • cause is self-antibodies generated against splicing RNPs
  • anti-smith antibodies binds to U1, U2, U4, U5, and U6 snRNPs
  • less than 1% present in healthy individuals
82
Q

anti-nRNP

A
  • anti-U1NRP

- present in 30-40% of lupus patients and interact with U1snRNP

83
Q

mitochondria genome

A
  • distinct genome with rRNA, tRNA, and mRNA genes
  • make own rRNA and tRNA
  • genome is circular and small
84
Q

mRNAs in mitochondria

A
  • encode enzymes involved in electron transport and oxidative phosphorylation
85
Q

what about transcription that takes place in mitochondria?

A
  • they are all nuclear encoded genes
86
Q

how to mitochondria get most of their proteins?

A
  • they import them
  • transcribed in nucleus, translated in cytoplasm, and imported into mitochondrion
  • imported by TOM and TIM
87
Q

70S subunit of prokaryotes composed of

A
  • 50S and 30S
88
Q

50S composed of

A
  • 5S

- 23S +34 proteins

89
Q

30S composed of

A
  • 16S + 21 proteins
90
Q

80S of eukaryotes composed of

A
  • 40S and 60S
91
Q

60S composed of

A
  • 5S

- 5.8S on 28S + 50 proteins

92
Q

40S composed of

A
  • 18S + 33 proteins
93
Q

mitochondria subunit

A
  • 55S
94
Q

55S subunit composed of

A
  • 39S

- 28S

95
Q

mitochondria rRNAs

A
  • 16S

- 12 S

96
Q

transcription and post-transcriptional cleavage of rRNA

A
  • occurs in nucleolus
  • 45S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I and associates with ribosomal proteins
  • 5S RNA is a distinct gene cluster (~100 copies on chromosome 1) and transcribed by RNA polymerase III
  • RNA is methylated and pseudouridylated and 45S RNA trimmed to a 41S precursor
  • 41S with 5S cleaved to 32S with 5S and 20S
  • 32S cleaved to 28S, 5.8S and 5S comes along
  • 20S cleaved to 18S
  • Cleaved into 28S, 18S, and 5.8S by ribonucleases
97
Q

cleavage of 45S rRNA precursor

A
  • ribonucleases cleave 45S into intermediate forms then eventually 28S, 18S, and 5.8S rRNAs
  • 5.8S is hydrogen bonded with 28S
  • snRNAs pair with rRNA precursors and guide location of modification and cleavage enzymes
  • cleave the ends off the spacer sequences
  • occurs in nucleolus
98
Q

function of tRNAs

A
  • adapter molecule that recognizes mRNA triplet code and transfers an amino acid to the growing polypeptide
99
Q

features of tRNAs

A
  • heavily modified bases
  • dihydrouridine
  • ribothymidine
  • pseudouridine
  • loops
  • cloverleaf shape with defined loops
100
Q

tRNAs of mitochondria

A
  • mitochondria have their own tRNAs
101
Q

3’ end of tRNA

A
  • CCA where the amino acid gets attached
102
Q

transcription of tRNA

A
  • tRNA transcribed by RNA polymerase III from internal promoter
103
Q

post transcriptional processing of tRNA

A
  • done by nucleases
  • 5’ and 3’ ends are trimmed
  • small intron is removed and adjacent sequences are spliced (distinct from mRNA splicing)
  • certain bases are modified by snoRNAs and modeling enzymes
104
Q

nucleotidyltransferases

A
  • replaces Us at the 3’ end and adds CCA

- CCA not encoded within the genome

105
Q

highly repetitive DNA

A
  • clustered at centromeres and telomeres - implicated in centromere function and chromosome pairing
106
Q

moderately repetitive DNA

A
  • some are transposable elements are defective transposable elements
  • some are transcribed and produce functional RNAs needed in multiple copies
107
Q

All repeats and LINEs

A
  • transposons or remnants of transposons
108
Q

energy of translation

A
  • GTP and ATP
109
Q

wobble position

A
  • wobble at the third position
  • one way for a tRNA that carries a specific amino acid to recognize a few different codons
  • because of this, we don’t need a tRNA for every codon
110
Q

aminoacyl-tRNA-synthetase

A
  • recognize distinct amino acids and join them to tRNAs

- have proofreading capabilities and can tell when they have the wrong amino acid

111
Q

aminoactyl-tRNA-synthetase reaction

A
  • tRNA is charged covalently with an amino acid on CCA stem
  • requires ATP
  • yields aminoacyl-tRNA
  • syntheses recognize acceptor stem and anticodon site
112
Q

initiation of translation

A
  • starts at AUG codon that codes for methionine
  • eIF2-GTP delivers Met-tRNA to the 40S subunit connected with eIF3
  • tRNA-Met is the only tRNA that can bind to the isolated 40S subunit - connected with GTP
  • Cap at 5’ end of mRNA binds Cap-binding complex which recruits the preinitiation complex to mRNA
  • mRNA binds to 40S subunit
  • eiF4 scans mRNA and finds AUG codon (requires ATP)
  • hydrolysis of GTP and eIF factors released
  • large 60 S subunit binds to form functional ribosome
113
Q

purpose of 40S subunit on mRNA

A
  • connects with eIF3

- blocks premature binding of 60S subunit

114
Q

cap binding complex composed of

A
  • eIF4
115
Q

binding sites

A
  • E - ejection
  • P - peptidyl
  • A - aminoacyl-tRNA
116
Q

met-tRNA binds where

A
  • in the P site in the whole ribosome

- only tRNA that does this.

117
Q

elongation of translation

A
  • mRNA codon in A site determines which aminoacyl-tRNA binds
  • new aminoacyl-tRNA binds elongation factor eEF1A-GTP
  • complex binds to the A site, GTP hydrolyzed, and eEF1A-GDP is released
118
Q

peptide bond formation

A
  • in first round, AA in A site forms a peptide bond with the methionine in the P site
  • amino group of aminoacyl-tRNA attacks carbonyl group of ester linkage of peptidyl-tRNA
  • reaction catalyzed by peptidyltransferase which requires no energy source
119
Q

peptidyltransferase

A
  • not a protein but is the rRNA in the 60S subunit

- part of the 28S subunit

120
Q

translocation of translation

A
  • eEF2 complexes with GTP and binds ribosome
  • makes space in the A site
  • causes a conformational change that moves the mRNA and tRNAs with respect to the ribosome
  • uncharged tRNA moves from the P site to the E site and is released
  • peptidyl-tRNA moves to the P site.
  • next codon occupies A site
  • GTP hydrolyzed
121
Q

termination of translation

A
  • when a stop codon is reached, no aminoacyl-tRNA occupies the A site
  • release factors bind to the ribosome and peptidyltranferase cleaves the peptide chain from the tRNA and protein is released
122
Q

recycling of eEF1A

A
  • important for continuous rounds of translation and translational regulation
  • GTP hydrolyzed to GDP + Pi and eEF1A binds to eEF1Ba
  • eEF1Ba exchanges GDP for GTP on eEF1A
  • eEF1A is ready for the next round of translation
123
Q

polysomes

A
  • mRNAs are often translated by multiple ribosome, each generating a protein
124
Q

protein targeting to sub cellular locations and transport

A
  • proteins have targeting sequences that allow their transport to sub cellular destinations like the Golgi, ER, lysosomes, secretion at membrane
  • proteins have a sequence at the N-terminus
  • Signal recognition particle recognizes signal sequence while the protein is being translated.
  • SRP-protein binds to SRP receptor on RER
  • translation continues to the RER where the signal peptide is cleaved by signal peptidase
125
Q

secretion

A
  • some proteins enter secretory vesicles and are released from the cell or added to the membrane
126
Q

lysosomes targeting

A
  • mannose-6-phosphate -> clathrin coated vesicles -> endoscopes -> lysosomes
127
Q

protein KDEL sequence targets where

A
  • back to RER
128
Q

hydrophobic proteins go where

A
  • membrane
129
Q

chaperones

A
  • proteins that facilitate proper protein folding or prevent aggregation of newly-synthesized proteins
130
Q

heat shock proteins

A
  • induced by heat shock to help cellular protein refold properly and not become denatured
131
Q

chaperonins

A
  • CCT/Tric

- protein to be folded is enveloped by the CCT/Tric barrel and is folded using ATP

132
Q

Diphtheria toxin

A
  • B subunit facilitates entry of A subunit into the cell
  • A subunit catalyzes the addition of ADP-ribose to EF2
  • inhibits EF2 and protein synthesis
  • leads to death
133
Q

role of tetracycline

A
  • binds to bacterial 30S subunit and blocks access of aminoacyl-tRNA to the A site
  • reversible
134
Q

role of puromycin

A
  • resembles aminoacyl-tRNA

- accepts peptide chain and terminates translation

135
Q

role of chloramphenicol

A
  • binds to bacterial 50S subunit and inhibits peptidyltransferase
  • can also inhibit human mitochondrial protein synthesis
136
Q

role of erythromycin

A
  • binds to the bacterial 50S subunit and inhibits translocation
137
Q

role of streptomycin

A
  • binds to the bacterial 30S subunit and prevents initiation
  • also causes misreading of mRNA in which premature termination or incorporation of incorrect amino acids occurs.
138
Q

what is nonsense mediated mRNA due to?

A
  • mutations or mistakes in transcription or splicing where some mRNAs are defective and encode defective or truncated proteins
139
Q

what happens in nonsense mediated mRNA decay?

A
  • detects and degrades the aberrant mRNAs
140
Q

what happens normally in mRNA?

A
  • proteins normally bind the exon-intron junctions
  • stop codon is in the last exon
  • junctions are removed by initial ribosome movement and the mRNA exists the nucleus
  • if all junctions are removed because the ribosome didn’t encounter a stop codon then the mRNA survives
141
Q

what happens abnormally in nonsense mediated mRNA decay?

A
  • premature stop codon encountered
  • distal junctions remain
  • mRNA degraded by Upf proteins

POM Exam 1 (16 decks)

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