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M2M unit 1 > Transcription, Translation, and Regulation > Flashcards

Transcription, Translation, and Regulation Flashcards

1
Q

Hemophilia B-Leyden

A

X linked disorder that affect clotting Males have 1% of factor 9 until puberty due to mutation in DNA control element in Factor 9 promoter. At puberty, androgen receptor binds to same promoter and increase transcription so they have 60% of factor 9.

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2
Q

TFIIA

A

stabalizes TBP and TFIIB

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3
Q

Spinal muscular atrophy

A

due to SMN1 mutation can be rescued by alternative splicing of SMN2, which usually splices out exon 7

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4
Q

Basic Leucine Zipper (bZIP)

A

hydrophobic aa every 7 aa with helical domain in between. helical domain is responsible for DNA binding and dimerization C-fos C-jun

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5
Q

MDM2

A

ubiquitin ligase that marks p53 for degradation and inhibits it to make it a tumor promoter while MDM2 is bound.

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6
Q

Elongation of Translation

A

aa-tRNA enters the A-site (delivered by EF1A (euk) and EF-Tu (bac) –> anticodon base pairs with right codon in the mRNA –> peptdie bond is formed when protein chain moves from P site into the A site (requires ATP from tRNA charging) –> Translocation (GTP)

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7
Q

Where is Ferritin IRP located

A

before start codon

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8
Q

Amount of Activator/Repressor Regulation

A

target degradation by amount of protein that is available. APC, MDM2

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9
Q

Intron components

A

5’ GU 3’ AG A residue branch point pyrimidine rich segment near end of intron consensus seqeunce

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10
Q

Translation Initiation in Bacteria

A

Ribosome binds to start codon due to Shine Delgarno sequence upstream of start site. IF1 and IF3 bind to 30S –> mRNA bind tos 30S and SD sequence to place AUG in P site –> IF2 delivers initiation methionine tRNA to P site –> GTP hydrolysis on IF2 to lead to release of initiation factor and binding of 50S

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11
Q

Four RNA polymerases and functions

A

RNA POL I: rRNA in nucloeolus (busiest) RNA POL II: mRNA, snRNA, miRNA, lnc RNA RNA Pol III: tRNA Ecoli RNA: mRNA, tRNA, rRNA

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12
Q

Aspirin function

A

blocks IKB phosphorylation, so NFKB is stuck in the cysotol and transcription is not activated in an immune response

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13
Q

Kozak

A

Euk cells have different start codons that are of different strengths. Kozak sequences has a purine a couple Bs before AUG and a G directly behind it.

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14
Q

Iron Response Element (IRE)

A

RNA stem and loop found in mRNAs that bind to IRPs (Iron response proteins)

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15
Q

Mutations in ssDNA binding protein diseases..

A

1) Carinosynostosis 2) Androgen Insensitivity Syndrome 3) Waardenburg Syndrome Type II

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16
Q

cdc25 vs p53

A

p53 must be phosphorylated to be activates to repress cell cycle. Slow process because p21 needs to be made. cdc25 is normally an activator of cell cycle, so it is repressed with DNA damage. faster because nothing needs to be synthesized.

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17
Q

NFKB

A

associated with inflammation

sequesterd in cytoplasm by IKB that hides Nuclear localization signal. with inflammation, IKB gets phosphorylated and targeted for degradation. Now NFKB can move to nueclues

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18
Q

Id protein

A

a homodimer that is missing the basic domain of the Helix loop helix

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19
Q

IES Driven translation

A

cap independent IRE are structural RNA sound upstream of AUG and recruit 40S and IFs without using cap found in viruses ideal if you want to turn off protein synthesis, but not all

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20
Q

what energy source does Aminacyl tRNA synthetase use?

A

ATP to create an ester bond

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21
Q

CDKN1

A

cip/kip inhibit any CDK complex

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22
Q

High iron conditions

A

IRE-BPs are bound to FE and an’t bind to IRE-RNA since IREBP cant bidn to IRE, mRNA is no longer protected and transferring receptor creation is halted. mRNA proceeds and ferritin is created.

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23
Q

Calcenurin

A

Immune response protein

Removes phosphate group from NDAT, with uncovers NLS to move to nucleus to activate genes in immune system. if blocked, it is an immunosuppresive

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24
Q

CDKs

A

Cyclin Dependent Kinases (ser or thr) use ATP energy to phosphorylate regulator to activate or inhibit replication Present at all times, but is inactive unless bound to cyclin

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25
Q

Tamoxifen

A

anatogonist to estroben binds to Estrogen receptor without providing conformation change for dimerization - thus prevents binding to activation site on DNA and the recruitment of activators. Represses genes normally used in cell growth

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26
Q

Leukemia

A

fusion of HATS with other proteins to misdirect HATS to different region so chromosome and promote creation of proteins that arent supposed to be made

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27
Q

Polycisternic

A

more than one protein encoded on an mRNA

Common in bacteria to have multiple coding regions with multiple SD sequences convenient to make proteins that do similar function at same time ie. heat stress

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28
Q

Translocation

A

Movement of one site From A to P or from P to E Requires GTP

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29
Q

Heterochromatin

A

repressed because DNA is inaccesssible due to 1) hypoacetylation 2) DNA methylation 3) inaccessible to restriction enzymes and DNAse1 digestion 4) contains tandemy repeated segments 5) transcriptionally inactive.

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30
Q

Ferritin

A

sequester Fe outside of cell

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31
Q

Tetracycline

A

affacts aminacyl tRNA binding in A site

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32
Q

Histone DNA interactions

A

are electrostatic phosphodiester bonds in DNA associate with positively charged arginines located on histone folds

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33
Q

CDK7

A

phosphorylates Pol II C-Terminal Domain during promoter clearance

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34
Q

Modularity

A

of SS - DNA BP, modular and contain two major domains that can be switched and mixed to activate a variety of genes

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35
Q

E boxes

A

are bHLH show basic region binds to E box in DNA. when homodimerized by Id protein, but missing basic domain on one side so it can no longer bind to E box. Competative inhibitor to active E box.

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36
Q

What happens to cause transition from G2 to M phase?

A

cycB with CDK2

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37
Q

What happens to cause transition from S into G2 phase?

A

cycA activates and pairs with CDK2

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38
Q

Carinosynostosis

A

premature fusion of skull to lead to mishapen head and no room for brain to grow point mutation in Msx2 homeodomain from proline to histidine. causes tighter binding to DNA to transcribe genes more rapidly and cause premature fusion

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39
Q

mTOR

A

regulates translation initiation

Phosphorylates 4E-BP1 complex to release 4E so it can participate in initiation iwth eIF4F. under stress, 4E-BP is dephosphorylated and sequesters 4E Rapamycin mimics the actions of mTOR and phosphorylates 4E-BP

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40
Q

CDKN

A

CDK inhibitors CDKN2 (ink4) and CDKN1 (cip/kip)

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41
Q

Histone H1

A

binds to linker DNA to condense 10nm fiber into 30 nm fiber

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42
Q

Low iron conditions

A

IRE-BPs are free from Fe and can bind to IRE-RNA Since IREBP is bound to IRE, mRNA is protected and synthesis of transferrin receptor is created. IREBP binds to IRE to block access to the RNA to translate ferritin.

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43
Q

During G1 - CDK levels and pre-initation complex

A

Need to replicate

Low levels of active CDK 4,6 Allows for the building of Pre-RC but it is NOT activated

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44
Q

where is transferrin IRP located

A

after stop codon

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45
Q

What is RB?

A

Retinoblastoma protein 2 homologs p107 and p130 (you might have both or only one) When bound to E2F, it prevents transcription of genes involved in DNA replications. Activation of CDK by cyclin phosphorylates Rb, causing the release of E2F so it can not longer inhibit transcription.

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46
Q

what triggers phosphorylation of eIF2alpha?

A

oxidative stress

double stranded RNA (virus) heat sock UV amino acid depravation Interferon

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47
Q

Energy requirements for Translation

A

charge tRNA 2ATP –> 2AMP deliver aa-tRNA to A site –> GTP –> GDP Translocation GTP –> GDP

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48
Q

ATP dependent Chromatin Remodelers

A

Use ATP to break histone DNA contact and move histone along octamer ex. SWI/SNF

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49
Q

Translation Initiation Euk - Cap Indepenent

A

Internal Ribosomal entry sites drive the process Viruses use IREs to initiate translation after they shut down host cap-dependent synthesis some Euk use too when cells want to shut down protein synthesis, but need emergency response proteins made.

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50
Q

cdc25

A

is an activator of CDKs. Inhibition of it by Chk1 and Chk2 causes it is inhibit CDK action.

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51
Q

During S phase - CDK levels and pre-initation complex

A

Active replication HIhg levels of CDK activates Pre-RC but prevents further building

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52
Q

what blocks phosphorylation of IKB?

A

aspirin

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53
Q

Transferrin Rector

A

transports iron and transferrin into cell

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54
Q

protein binding to mRNA

A

3’ and 5’ UTR can be bound to proteins that affect mRNA stability, localization, degree that ribosomes bind

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55
Q

TATA binding Protein

A

binds to TATA box at minor groove helps direct assembly of initiation complex not highly specific and recognizes variations in TATA boces

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56
Q

Streptomycin

A

affect initiation and elongation in 30S

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57
Q

What happens when p53 is phosphorylated?

A

1) leads to the transcription of P21 (P53 is a TF) 2) p21 binds to whatever CDK is present to prevent from entering into S or M phase.

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58
Q

what CDKs are associated with entry into S phase?

A

CDK 2, 4, 6

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59
Q

Histone Code

A

distinct patterns or combinations of modifications at conserved regions of histone terminal domains that are important in the recruitment of specific chromatin-associated proteins.

60
Q

Iron Response Protein

A

bind to Fe and regulate expression of Ferritin and TFR

61
Q

how is binding specificity determined?

A

non-covalent interactions between atoms in an alpha helix in the DNA Binding domain and atoms at the edge of the base of the major groove of DNA (throguh H bonds and van der walls)

62
Q

Histone Deacetylases

A

HDAC retain positive charge on terminal end (reove acetyl group) to maintain interaction with DNA and prevent access to promoter.

63
Q

what is the goal for somatic cell cycle?

A

duplication of the genome in S phase followed by exact division of genome in M phase t produce two identical daughter cells

64
Q

Reactions of RNA capping

A

1) triphosphatase (cut off triphosphate group) 2) guanylyltransferase (add GTP to form 5’ to 5’ triphsopahte bond. 3) guanin 7 methyl transferase (methylate 7th position)

65
Q

What phase are the sister chromatids separated

A

Anaphase

66
Q

What antibiotics affect peptidyl trasnferase in 50S?

A

Erythromycin, linconmysin, clidamycin, chloramphenicol

67
Q

Rad17

A

senses DNA damage due to radiation (ds and ss breaks) Binds to DNA and recruits ATM and ATR

68
Q

Elongation factor

A

proteins that deliver tRNA and move ribosome down mRNA

69
Q

Marfan’s Syndrome

A

mutations that disrupt splicing of the fibrillin gene transpcript that is involved in the CT of walls of heart and blood vessels

70
Q

CDKN 1 vs CDKN 2

A

CDKN2 is specific to CDK 4,6, while CDKN1 is for any CDK

71
Q

Chk2 and Chk1

A

phosphorylated p53 and represses cdc25.

72
Q

Estrogen Receptor

A

must homodimerzie to bind Estrogen binds to receptor to faciliate the homodimerization and binding of zinc finger to DNA. when bound to DNA requires HAT to recruit Pol and activate Transcription

73
Q

Interferon

A

virus invades cell, cells make interferon in response to viral RNA and cell can either die or survive. Interferon is released form infected cells and activates those cells to synthesize viral proteins and turn off translation (phosphorylated eIF2Alpha) to protect them from virus infection.

74
Q

how are sequence specific DNA binding proteins regulated?

A

1) altering protein conformation by binding to ligand 2) regulating entry into nucleus 3) regulating amount of TF in cell 4) regulating binding to DNA 5) phosphorylation of DNA BP

75
Q

TFIIH

A

creates closed complex composed of 1) XBP 2) XPD 3) p44 4) CDK7

76
Q

Translation Initiation Euk - Cap dependent

A

eIF4E binds to 5’ Cap –> binding brings in other eIF and small ribosomal subunit –> ribosome scans down the message for AUG –> At AGU, large subunit joins and IF release and initiation is achieved.

77
Q

alpha-amanitin

A

non-competative inhibitor in mushrooms for RNA Pol II binds to bridge helix and block RNA elongation

78
Q

U2

A

activates the 2’ OH at the branch point, which attaches a phosphodiester bond just past the GU 5’ splice site. this creates a free 3’ OH on the 5’ exon which attacks the AG 3’ splice site.

79
Q

RNA Capping function

A

1) resistant to exonucleases 2) enhance subsequent maturation steps (splicing) 3) export from nuc 4) association with ribosome via eIF4E 5) removal signals mRNA degradation

80
Q

ATM vs ATR

A

ATM specifically recognizes double stranded breaks ATR recognizes any kind of damage (Ds, stalled rep fork, DNA mismatch, NT damage) Activate Chk2 and Chk1

81
Q

Steps of exit out of G1

A

growth factors accumulate in media to initiate signal cascade of proteins to signal that it is time to divide. (Ras, efos, jun) that lead to the synthesis of cycD1-3 –> cycD binds to CDK4, or 6 CDK4,6 activates cycE –> activates CDK2, which together inhibit RB protein to allow transition to S phase.

82
Q

XBP

A

associated with TFIIH ATP dependent helicase activity near DNA start site.

83
Q

modification that alters activity of SS DNA BP

A

CREB Ligand binds to G protein which phosphorylates CREB. p-CREB recruits CBP (a hat) and recruits RNA Pol II leading to trascription

84
Q

Homeodomain Proteins

A

60 AA 3 alpha helices and a terminal domain Regulate development Hox, Pitl, Msx Affect many genes at once

85
Q

DNA binding activity of Sequence Specific DNA BP inhibition

A

when DNA binding sequence has been altered so cannot activate transcription Id proteins with E boxes

86
Q

Histone Tails

A

exposed site subject to modification that regulate chromatin structure and ability to bind to DNA

87
Q

Rubinstein-Taybi Syndrome

A

gentic disorder, growth and metnal retardation, carniofacial dysmophism, broad thumbs Mutation in one copy of CREB binding protein that acts like a HAT

88
Q

CDKN 2

A

Ink4 CDK inhibitor specific inhibitor to CDK 4,6 competative inhibitor with cyclin D. p16A is frequently mutated in Cancer, so cell cycle is always on.

89
Q

Basic Helix loop Helix

A

Similar to leucine Zipper, with hydrophobic domian, but has loop in between. regulates muscle development myoD, myogenin, myf5

90
Q

How is cycD synthesized?

A

Due to the accumulation of growth factors (Ras, efos, Jun) in the media during G1 t

91
Q

Cell Cycle Checkpoints in G1

A

Size at restriction point (dependent on cyclin accumulation) DNA damage to assess whether you replicate this DNA.

92
Q

Chromatin Remodeler Classes

A

1) ATP dependent 2) Histone Modifying enzymes

93
Q

CD44

A

cell surface glycoprotein contributor to tumor metastasis and migration splice variants are used as diagnostic and prognostic markers

94
Q

HAT

A

Histone acyetyltransferases Acetylate the N-termini Lycine of histone tail To neutralize positive lycine and eleminate electrostatic ineraction with DNA (co-Activator)

95
Q

Fragile X syndrome

A

1:1500 males, mental retardation, dysmophic facial features, in normal: 6-50 CGC repeats at 5”end of FMRI gene to facilitate methylation of cytosine residues and transcription activation. in Fragile X, they have 200+ copies of CGC repeat and silence transcription

96
Q

Promotor Proximal Elements

A

located 200 bp upstream of start site 20bp long regulates tran and binds to factors in cell type specific manners must be near start site

97
Q

Cell Cycle Checkpoint in G2

A

Assess how DNA replication went. Time to fix the mistakes before proceeding to mitosis

98
Q

Ribosome

A

Bacteria small is 30S Euk small is 40S 3 binding sites (A,P,E) small subunit decodes mRNA Large catalytic center of peptidyl transferase

99
Q

E2F

A

binds to RB protein to be a protein inhibitor.

100
Q

Examples of IRE driven tranlsation

A

polio HIV-1 HepA and C

101
Q

APC

A

targets Beta-Catenin, a cell proliferation activator normally B-Catenin is in membrane and if excess exits it is degraded by APC In abnormal situations: WNT signaling leads to phosphorylation and inhibition of APC so B-Catanin cannot be degraded and builds up in cytoplasm. Build up leads to translocation tp nucleus to activate cell growth CANCER!

102
Q

Alternative Splicing

A

1) exon skipping 2) mutation exclusive exons 3) exon truncation/extension at 5’ end by choosing alternative spice site at 3’ 4) exon truncation/extension at 3’ end 5) intron retainment or removal

103
Q

Anisomycin

A

affect peptidyl transferase at 60S (cap dep)

104
Q

Constitutive Heterochromatin vs. Facultative

A

faculative can change to euchromatin based on cell type or development stage

105
Q

Histone Modifying Enzymes

A

Regulate chromatin structure by recruting Histone acytylases and histone deacyetylases

106
Q

TFIIF

A

helps target POL II to promoter by interaction with TFIIB

107
Q

Mutations in DNA contorl elements lead to these disease….

A

1) Thaiassemias 2) Hemophilia B-lyden 3) Fragile X

108
Q

Cycloheximide

A

affect peptidyl transferase at 60S (cap dep)

109
Q

ApoB

A

mRNA is edited by cytosine deamination to change CAA to UAA to make a premature stop codon in the bowel. Thus in the liver you have full length, but in the SI there is a truncated. both are functional, with different functions

110
Q

Formation of Origin of Replication

A

Origin of Replication protein (Orc 1-6) binds to origin cdt1 and cdc6 bind and bring in DNA helicase (Mcm2-7) which forms ring around DNA.

111
Q

BRCA2

A

familial tumor suppressor involved in DNA damage checkpoint. women get both breast and ovarian cancer with this mutation. see fusion of chromosomes in mice. in disease state, DNA damage persists and you get non-homologous recombination

112
Q

Zinc Finger Domains

A

composed of either 4 cysteine or 2 cysteine and 2 Histine 2 anitparalle beta sheets, an alpha helix, all held together by a zinc ion Finger: DNA binding part Nuclear recpetors: estrogen, androgen, retinoic acid

113
Q

Bridge Helix

A

Crab claw in RNA pol that flexes with each addition of rNTP

114
Q

Cell cycle of somatic vs. Germ cells

A

Meiosis: start with diploid and undergo two rounds of meiosis to make 4 haploids. mitosis 2 2n cells Meiosis has 10,000x more recombination between non-sister chromatids than mitosis.

115
Q

Somatic vs. ebryonic cell cycle replication

A

Somatic cells only have one origin of replication and it takes 8-10 hours. Embryo have multiple origins that are used and it only takes 30 minues

116
Q

Overview of DNA checkpoint regulation

A

1) DNA senses DNA damage or replication block 2) they then send signals (kinase) to phosphorylate effectors. 3) effectors stop cell cycle until damage is repaired.

117
Q

Transferrin

A

binds to iron - present when iron is lacking in cells

118
Q

Restriction Point

A

in G1 point at which a cell must make a decision based on the presence of growth factors or hormones are there or whether cell is large enough to undergo DNA replication. and mitosis. most highly regulated step In embryonic cells this is bypassed exit point for cell differentiation

119
Q

CDC7

A

activator of DNA replication activated when Rb is inhibited works with Dbf4

120
Q

Poly A and termination of trascription

A

cleavage and PolyA signal to RNA polymerase to stop if you delete Poly A tail, RNA pol will continue working

121
Q

Nucleosome

A

repeating unit of chromatin, 147 bp of DNA wrapped around octamer of histone proteins approx 1.7 times

122
Q

what is the positive feedback loop during the transition to S phase?

A

Activated CDK 4,6 phosphorylates cycE to activate CDK2 Ireverisble once committed

123
Q

Waardenburg syndrome Type II

A

deafness, pigmentation, anomalies in eyes, mutation in MITF gene, which encodes basic Helix loop helix

124
Q

Kasugamycin

A

affects initiator tRNA binding in 30S subunit

125
Q

Dbf4

A

activator of DNA replication activated when Rb is inhibited works with CDC7

126
Q

Mutation in TFIIH

A

1) Xeroderma Pigmentosum 2) Cockaynes Syndrome 3) Trichothiodystrophy

127
Q

Histone core complex

A

2 molecules each of H2A, H2B, H3 and H4 (octamer)

128
Q

Significant features of RNA POL

A

1) four channels 2) Bridge Helix 3) Sliding clamp (PCNA) 4) C-Terminal Domain

129
Q

TFIIB

A

binds to either side of TBP

130
Q

Alternative Poly A sites

A

1) membrane and secreted cells of immunuglobulin are generated by altnernative Poly A site 2) can lead to cancer because it makes truncated proteins

131
Q

Euchromatin

A

where genes reside, more accessible

132
Q

C-Terminal Domain

A

On RNA pol composed of heptad repeats YSPTSPS reversibly phosphorylated binds to proteins to regulate elongation and processing of pre-mRNA

133
Q

Transcription Factor

A

Activators or Repressors that are encoded on one gene and act on another gene to regulate transcription. Diffuse around nucleus and bind to DNA control elements

134
Q

sequence specific DNA binding proteins - nuclear entry regulation

A

A receptor that is located in the cytosol until it binds to a certain protein or is sequestered by a certain protein, but a event triggers their release and it can freely enter into the nucleus (glucocorticoid and NFKB, Calcenurin)

135
Q

Function of PolyA

A

Protection from degradation Nucleus export bound by PolyA binding protein to enhance translation

136
Q

Androgen Insensitivity Syndrome

A

Feminization or undermasculinization of external genetalia at birth, abnormal 2°, infertility mutation in DNA binding domain or ligand binding domain of androgen receptor (zinc finger) makes them less responsive to androgen.

137
Q

eIF2alpha phosphorylation

A

inhibits ternary complex formation eIF2 brings in t-RNA-Met into P site, so when phosphorylated this does not occur.

138
Q

Termination Factors

A

end the process at the stop codon and dissociate the subunits to be used against

139
Q

What are the classes of activators and repressors?

A

1) sequence specific DNA binding proteins 2) Co-Factors

140
Q

Rapamysin

A

affects phosphorylation of 4EBP at mTOR (cap dependent)

141
Q

Promoter

A

-70 to +30 control direction and frequency of transcription TATA box (-30 bp) promoter proximal elements (-30 to -1000 Bp) Enhancer region (-10,000 to -50,000 bps)

142
Q

Histone Acetylation altered in disease

A

Leukemia Rubinstein-Taybi Syndrome

143
Q

Translation Termination

A

Stop codon detected by release factor (not made out of tRNA) go in same space as tRNA but trigger termination of peptide chain and release of peptide and ribosomal subunits.

144
Q

what happens when RB is inhibited?

A

CDC7 binds to Dbf4 which are both kinases needed for DNA replication

145
Q

During mitosis - CDK levels and pre-initation complex

A

Replication is complete High levels of CDK2 to initiate mitosis prevents the building of pre-replication complex.

M2M unit 1 (6 decks)

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