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Exam #1 Flashcards

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1
Q

What is the difference between eukaryotic and prokaryotic initiator tRNAs?

A

Prokaryotic tRNAi’s have an N-formylated-methionine attached (from N10-Formyl THF) —> *Only time there is a modified Met*. -*Also, transcription and translation occur concomitantly in prokaryotes because there is no nuclear membrane to separate the processes.* Eukaryotic: Normal Met attached to tRNAi. L7, #20

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2
Q

What is a nucleosome?

A

DNA wrapped 1.75x around a histone octomer (147bp of DNA). -N-terminal tails of histone extend out from nucleosome core. L1, #32

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3
Q

Where does the addition of the CCA sequence to tRNA occur and at which end of the tRNA is it added? What template does it use? Enzyme?

A

-CCA sequence added to the 3’ end in the CYTOPLASM by tRNA nucleotidyl-transferase. *Template-independent; i.e. NO TEMPLATE* L5 #8

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4
Q

What energy is required for eEF-2 during translocation and how many high-energy bonds used?

A

GTP —> GDP + Pi *One high-energy bond* L7 #35

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5
Q

What primer(s) are used for DNA replication?

A

Short (8-10 nt) *RNA* fragments. L2, #7

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6
Q

What interactions do Hsp’s require for their ATPase domain to be functional?

A

Nucleotide-exchange factors —> ADP release/ATP binding. L8 #51

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7
Q

What relieves DNA supercoiling during bacterial replication?

A

Bacterial topoisomerase II; aka *DNA gyrase.* L2, #13

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8
Q

1.) What enzyme extends the telomeres in eukaryotes (it is a ________-dependent ______ polymerase)? 2.) What are its functional components (2)? Describe.

A

1.) Telomerase (an RNA-dependent DNA polymerase). 2.) a.) TERC (*TE*lomere *R*NA *C*omponent): Provides a 3’-AAUCCC-5’ template to guide the insertion of TTAGGG repeats in chromosome ends. b.) TERT (*TE*lomere *R*everse *T*ranscriptase): Acts as reverse transcriptase (DNA —> RNA). L2, #42

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9
Q

What is the initiator tRNA and where does it go on the ribosome?

A

tRNAi (whose anticodon is CAU) contains the AA Met b/c it recognized the start codon; AUG. -It enters the P-site; which is the only time there is a single AA at the P-site. The rest of the following tRNAs enter at the A-site. L7, #16

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10
Q

What are the three co-transcriptional events?

A

1.) 5’-capping. 2.) Removal of introns (splicing). 3.) Addition of PolyA tail. L4, #29

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11
Q

What type of mutation causes Tay Sach’s Disease? Describe (i.e. what type of mutation, at what gene and chromosome, and what is the result).

A

4 bp insertion in exon #11 of the HEXA gene (hexosaminidase A gene) on chromosome 15 = Premature STOP codon. L6, #42

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12
Q

1.) Increased expression of which gene leads to various forms of cancer due to angiogenesis? 2.) Treatment for these cancers?

A

1.) METAP2 gene (codes for MetAP2 enzyme that cleaves N-terminal Met). 2.) Ovalicin and fumagillin L 8 #5

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13
Q

What does Telomerase use as a template to guide the insertion of nucleotide repeats (what are the repeats)?

A

Telomerase contains *sno* (small ribonuclear) RNA to use as a template. -The repeats are *3’-AAUCCC-5’ (RNA) —> DNA = TTAGGG. L2, #42

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14
Q

1.) What are the two types of double-strand break (DSB) repairs? Describe (proteins used, major/minor pathway, mech of repair). 2.) What detects DSB?

A

1.) a.) Non-homologous end-joining – NHEJ (#29); error-prone, major pathway for DSB repair. -Uses a complex containing DNA-dependent protein kinase (DK and Ku proteins bind to the end of the DSB). -Utilizes nucleases and DNA ligases. -*error prone, yet major pathway.* b.) Homologous recombination (#30); error-free. -Use of homologous chromosome as template to repair damaged/missing segment. -Involves the BRCA1 and BRCA2 genes; defects of which can lead to breast and ovarian cancers. -HIGH-FIDELITY repair process. 2.) ATM (ataxia telangiectasia mutated) protein – acts upstream of the 2 repair pathways to detect DSBs. L3, #37

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15
Q

______ Poly A sites are generally stronger than _______ sites.

A

Distal sites generally stronger than proximal sites. L10 #23

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16
Q

Where do you find the transcription start site? What is its nucleotide (generally speaking)?

A

1+ of a gene (downstream). -Usually a purine (A or G). L4, #21

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17
Q

What are the wobble positions for both codon and anticodon?

A

Codon (mRNA): 3’ position (3rd position/nucleotide).

Anti-codon (tRNA): 5’ position (1st position/nucleotide).

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18
Q

How do RNA pol III and II terminate transcription?

A

1.) RNA pol III can terminate transcription by itself when it reaches the termination signal (stretch of 4 T’s), b/c ATs weaker than CGs. 2.) RNA Pol II terminates transcription 50-2000 bp’s downstream of PolyA signal. -RNA transcript is cleaved by an endonuclease 10-30nt downstream of the AAUAAA sequence. L4, #29

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19
Q

What is the function of THIIB?

A

Bridge between TFIID and RNA pol II L9 #20

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20
Q

Which enzyme adds ubiquitin to a protein?

A

E3 L8 #38

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21
Q

What role does the poly A tail play?

A

Poly A tail stabilizes mRNA and allows for exit from the nucleus. L10 #21

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22
Q

What is the definition of reading frame (3 things)?

A

A sequence of triplets that: (1) Code for a protein, (2) Has a start codon, and (3) Has a stop codon. L6, #33

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23
Q

What is alpha-amantin? What are its effects?

A

It is a eukaryotic RNA polymerase inhibitor that, due to its varied effects on the different RNA pol types, is useful in distinguishing between the various types of RNA pol. -Strongly inhibits RNA pol II. -Inhibits mRNA synthesis and, ultimately, protein synthesis.

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24
Q

What compound(s) donate the nucleoside monophosphates required for nucleic acid synthesis?

A

Deoxy-nucleotide triphosphates (dNTPs) —> dATP, dGTP, dCTP, and dTTP. L2, #4

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25
Q

Describe Cockayne syndrome (i.e. defects, mutations, symptoms).

A

Defect in transcription-coupled NER. • Mutation in ERCC8 (CSA) or ERCC6 (CSB) genes. • ERCC6 (CSB) mutations more common (70% of cases). Results in acute photosensitivity, and neurological dysfunction (with neuron demyelination). L3, #23

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26
Q

What is the TF DNA binding domain?

A

Region that recognizes specific bases near the start of transcription. L9 #18

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27
Q

Which enzyme adds activated ubiquitin onto a protein?

A

E3 ligase adds activated ubiquitin onto protein. L8 #41

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28
Q

How is DNA packaged in sperm?

A

Packaged using *protamines* (Arg-rich nucleoproteins). L1, #30

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29
Q

What activity do ALL DNA polymerases share?

A

5’–3’ polymerase. L2, #17

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30
Q

Peptide formation and translocation occur _________.

A

Concomitantly (i.e. at the same time). L7, #16

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31
Q

What is a promoter region?

A

How RNA pol knows where a gene begins. L4, #25

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32
Q

What are the subunits of eukaryotic and prokaryotic rRNA? Which subunit is the ribozyme?

A

Euk: 80s -60s = 28s (ribozyme, large subunit), 5s, 5.8s -40s = 18s (small subunit) Prok: 70s -50s = 23s (ribozyme, large subunit), 5s -30s = 16s (small subunit) Primer 3, #10

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33
Q

What are the functions of THIID (3)?

A

1.) Helps to initially recognize the promoter site. 2.) TBP (TATA-binding protein)!!!! 3.) May be associated with *histone acetyltransferase (HAT)* activity. L9 #20

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34
Q

What and where is the TATA box? (give its other name)

A

aka Hogness: A sequence within the promoter region (≈ -20 to -30 upstream from the start site) that is recognized by RNA pol II. -It is as element of the core promoter.

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35
Q

1.) Which eukaryotic DNA polymerase is responsible for lagging strand synthesis? 2.) Leading strand?

A

1.) DNA pol delta 2.) DNA pol epsilon L2, #31

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36
Q

1.) When DNA twists on itself, what is positive and negative twisting? 2.) What type of twisting does DNA/RNA synthesis lead to?

A

1.) Positive: OVERTWISTING. Negative: UNDERTWISTING. 2.) Positive supercoiling; due to strand separation. L2, #11

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37
Q

Which eukaryotic DNA polymerase is responsible for Mitochondrial DNA replication?

A

DNA polymerase *gamma*. L2, #31

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38
Q

What is XIST?

A

A 17 kb lncRNA that is transcribed *solely from the inactive X chromosome*. It coats the inactive chromosome and silences it. -Results in a BARR BODY. L10, #19

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39
Q

Which heat-shock protein is involved with protein translocation?

A

Hsp70 —> The most abundant Hsp L8 #53

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40
Q

Interspersed repeats, aka _________. Give two examples and describe.

A

Moderately repetitive. 1.) SINE elements: Majority are *Alu repeat sequences*. -Alu elements contain recognition site for restriction enzyme *AluI*. -Transposons; can make additional self-copies. 2.) LINE elements: Flanked by Alu sequences. -Retrotransposons; replicate via an RNA intermediate. L1, #26

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41
Q

1.) What initiates strand opening in prokaryotes? 2.) What unwinds the helix in prokaryotes?

A

1.) DnaA protein 2.) DNA helicase (DnaB complex) *Requires ATP* L2, #9

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42
Q

What are four intercalating agents?

A

Acridine dyes, ethidium bromide, doxorubicin, and thalidomide. L3, #12

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43
Q

What are the general functions of the non-coding 5’ and 3’ UTR regions?

A

3’ UTR confers mRNA stability. 5’ UTR confers translationability (regulates start site). L10 #37

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44
Q

What characteristic of protein binding in Hsp’s is common among most/all types?

A

hydrophobic residues on substrate-binding domain. L8 #50-51

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45
Q

What is PGC-1alpha an example of, and what does it do?

A

PGC-1alpha: A coactivator – coactivates members of the PPAR nuclear receptor transcription factor family to *activate the expression of genes involved in mitochondrial fatty acid oxidation and OXPHOS enzymes*. L9 #23

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46
Q

What is the function of Aminoacyl-tRNA Synthetase? Does it require energy? Describe it’s effect on fidelity of translation. How many different aminoacyl-tRNA synthetases are there?

A

It is the enzyme that charges tRNA with an AA at the 3’-OH on Adenosine. • Requires ATP —> AMP (2 high-energy bonds). • Contributes to high fidelity of translation – recognizes anticodon and charges 3’ end of tRNA. • 20 different aminoacyl-tRNA synthetases; one for each different AA. *-tase = uses energy* L7, #12

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47
Q

Which histone protein is tissue/species-specific?

A

H1 L1, #33

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48
Q

What allows the high fidelity of prokaryotic DNA replication?

A

3’–5’ exonuclease activity of DNA pol III (proofreading/backspace ability). L2, #26

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49
Q

What enzyme relieves supercoiling of DNA (2 types)?

A

1.) Topoisomerase I: Nicks ONE strand and twists DNA to unwind it. 2.) Topoisomerase II: Makes staggered cuts in BOTH strands and unwinds DNA by one turn, then reseals the nick. L2, #13

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50
Q

What makes certain RNA viruses difficult to find a vaccine for?

A

Viral *reverse transcriptase* is prone to errors and high rate of mutations (due to lack of 3’–5’ EXOnuclease activity, i.e. proofreading).

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51
Q

1.) What is nucleotide excision repair used for? 2.) Describe its two distinct pathways?

A

1.) For repair of *thymine dimers*, bulky lesions, and nucleotides with chemical groups attached. 2.) a.) Transcription-coupled: RNA pol stalls, signaling presence of area for repair. -DNA template of genes being actively transcribed are preferentially repaired. b.) Global genomic: Less efficient. L3, #20

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52
Q

Most signal sequences contain a stretch of _________, preceded by ______ residues (e.g. _______)

A

Contain a stretch of *hydrophobic AAs*, preceded by *basic residues (e.g. Arg)*. L7 #63

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53
Q

What two portions of the zinc-finger does the Zn+2 link?

A

Alpha-helical and ß-sheet domains. L10 #6

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54
Q

Which prokaryotic and eukaryotic polymerases have 3’–5’ exonuclease activity?

A

DNA pol I, II, and III (prokaryotes), DNA pol gamma, delta, and epsilon (ALL EXCEPT ALPHA; eukaryotes). *ABLE TO PROOFREAD MISTAKES* L3, #11

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55
Q

What genotoxic chemical creates O6-methylguanine? Repair mechanism?

A

Alkylating agents – can perform *DIRECT REPAIR* via MGMT (O6-methylguanine methyltransferase) —> Transfers methyl group to *cysteine* residue in enzyme active site. L3, #18

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56
Q

What are the ‘stop’ and ‘start codons’? *Give RNA and transcript DNA*

A

Stop: UAA (ATT), UAG (ATC), UGA (ACT). Start: AUG (TAC)

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57
Q

What are the different versions of apo B proteins made as a result of RNA editing and where are they manifested?

A

*From the APOB gene* 1.) Liver: apo B 100 —> LDL recognition of receptor. 2.) Intestine: apo B48 —> Chylomicrons. 48% due to C —> U, causing CAA —> UAA (stop codon). *#’s refer to percentage of gene sequence translated* L10 #39, 40, 41

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58
Q

What drives the polymerization reaction of adding nucleotides to a primer?

A

Hydrolysis of PPi drives polymerization —> When the alpha-phosphate is attacked by the free 3’-OH nucleophile, it displaces Pi, which removes products, thereby driving the reaction forward (to the right). L2, #5

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59
Q

Describe base excision repair (5 steps)

A

1.) Spontaneous deamination replaces C with U (mismatch). 2.) Uracil-N-glycosylase cleaves glycosidic bond, leaving an apyrimidinic site. 3.) Apyrimidinic (AP) endonuclease nicks the DNA. 4.) Deoxyribose phosphate lyase removes the base-free sugar phosphate residue. 5.) DNA pol and DNA ligase fill gap with correct nucleotide and seals the gap (*using dCTP as source of trinucleotide*). L3, #19

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60
Q

What are example of DNA replication inhibitors and why?

A

AZT and 2’-3’-Dideoxyinosine – because they are nucleoside analogs that lack free 3’-OH groups on which further nucleotides can be added. L2, #6

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61
Q

How is the zinc finger structure stabilized?

A

Stabilized by a zinc ion bound to the Cys and His residues of the finger. L10 #6

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62
Q

mRNA is synthesized in the ________.

A

Nucleoplasm; i.e. nucleus L4, #10

63
Q

Give the location and cellular transcripts (what they make) for all three types of RNA polymerases.

A

Pol 1: Nucleolus, makes 18s, 5.8s, and 28s rRNA. Pol 2: Nucleoplasm, makes mRNA precursors, and snRNA. Pol 3: Nucleoplasm, makes tRNA, and 5s rRNA. L4, #24

64
Q

1.) In what direction is mRNA read by the ribosome during translation? 2.) In what direction is DNA read during transcription or replication?

A

1.) 5’ – 3’ 2.) 3’ – 5’

65
Q

Which has a longer half-life, prokaryotic mRNA or eukaryotic mRNA?

A

Eukaryotic ≈ 4hrs Prokaryotic ≈ 5min L4, #16

66
Q

Describe the correlation between N- and C- termini for AAs and the 3’ and 5’ ends of mRNA.

A

N-terminus = 5’ C-terminus = 3’ L6, #32

67
Q

What other sequences are similar to TATA box (2)?

A

CAAT box and GC box. -All part of the core promoter L4, #25

68
Q

What are the functions of THIIF (2)?

A

1.) Helps stabilize TFIIB 2.) Can be phosphorylated L9 #20

69
Q

Where are most mitochondrial proteins made? Why is this strange?

A

Made in the cytosol and translocated to mitochondria. Strange because mitochondria have *their own ribosomes*. L7 #59

70
Q

Ubiquitin is covalently attached to the _______ group of ______ on a targeted protein.

A

epsilon-amino group of Lysine. L8 #38

71
Q

What are CpG islands?

A

*CpG = Cytosine-Guanine linkages via 3’–5’ phosphate*. Stretches of up to 30,000 CG bases repeating over and over, often adjacent to gene-rich areas. -Thought to help regulate gene activity – NEAR PROMOTERS. -Tandem/Highly-repetitive repeats. L1, #23

72
Q

What initiates termination of transcription? What element and factor are involved?

A

Termination site for RNA pol I is an 11 bp T-rich element *(Sal box)*. TRANSCRIPTION TERMINATOR FACTOR-1 (TTF-1) binds to Sal box and helps unwind the hybrid duplex. L4, #29

73
Q

What are the non-traditional “wobble” bases for both tRNA and mRNA?

A

tRNA: Inosine (I). mRNA: Uridine (U).

*TRINA and MURNA*

74
Q

1.) What steps require ATP during protein degradation via proteasome (2)? 2.) What happens to ubiquitin molecule after degradation?

A

1.) Activation of ubiquitin via E1, Unfolding the protein in the proteasome via ATPase. 2.) Regulatory particle releases the ubiquitins for REUSE. L8 #38

75
Q

What does PAH do to nucleotides? Give example.

A

*PAH = Polyaromatic hydrocarbons.* Form reactive epoxides which covalently bind DNA – e.g. Benzo(A)pyrene in cig smoke binds to GUANINE L3, #12.

76
Q

What are three possible outcomes from DNA damage due to ionizing radiation (e.g. gamma-rays, X-rays, cosmic rays, etc.)?

A

1.) Base modifications (e.g. 8-oxoguanine). 2.) Single-strand breaks. 3.) Double-strand breaks. L3, #13

77
Q

What energy is required for eEF-1a during elongation and how many high-energy bonds used?

A

GTP —> GDP + Pi *One high-energy bond* L7 #35

78
Q

What mispairings can result from base deamination (2)?

A

1.) C–G changes to U–A 2.) A–T to Hy–C Hy = Hypoxanthine L3, #8

79
Q

What is unusual about the 5’ end of mRNA?

A

5’ cap contains a 5’P–5’P bond (triphosphate). *7methylG cap* L4, #10

80
Q

Describe the half-life of mRNA.

A

Variable (min to hours). L4, #10

81
Q

What is the TF Activation Domain?

A

Region that interacts with other parts of the transcription machinery (proteins), e.g. RNA pol or other TFs. L9 #18

82
Q

1.) What is at the 5’ end of prokaryotic mRNA? 2.) 3’?

A

1.) NTP (nucleotide triphosphate). 2.) Last base of mRNA. *No modifications* L4, #16

83
Q

What energy is required for amino acid activation during translation and how many high-energy bonds used?

A

ATP —> AMP + PPi *Two high energy bonds* L7 #35

84
Q

What keeps pol III anchored to the template strand? What is the result of this?

A

ß-subunit of Pol III (aka *SLIDING CLAMP*) – Results in *high processivity* (nt/sec). L2, #18

85
Q

What is RNA editing?

A

Modification of mRNA in the cell nucleus *before* translation. L10 #39

86
Q

What enzyme removes the primer in prokaryotic DNA replication? What is this activity called?

A

DNA pol I —> 5’–3’ EXOnuclease. *This is the ONLY prokaryotic DNA polymerase that possesses this activity* L2, #17

87
Q

Describe DNA mismatch repair, i.e. how it is detected, and genes involved (4). What do mutations in the repair genes lead to?

A

Methyl-directed mismatch repair: -*Mut proteins* detect methylated adenine (on parental strand). -4 genes involved: MSH2, MLH1, PMS1, PMS2. -Mutations in these genes results in *hereditary nonpolyposis colon cancer* (HNPCC); aka Lynch syndrome. L3, #24-25

88
Q

1.) What structure(s) protect the ends of chromosomes from degradation and confers stability? Describe 2.) What provides these structures?

A

1.) Telomeres: Many repeats of TTAGGG (*T2AG3*) in human chromosomes. -These repeats (≥1000) form a *T-loop* and confer stability to the ends of chromosomes. 2.) Telomerase – NO TELOMERASE IN SOMATIC CELLS. L2, #39-41

89
Q

Which step of translation requires no energy and why?

A

Transpeptidation; because *28s rRNA* has intrinsic *PEPTIDYL-TRANSFERASE* activity. L7 #42

90
Q

DNA primase is a _____-dependent ______ polymerase.

A

DNA-dependent RNA polymerase. L2, #32

91
Q

1.) Where are zinc-finger motifs found? 2.) Give five examples

A

1.) Steroid receptors 2.) Glucocorticoid receptor (GR), estrogen receptor (ER), thyroid hormone receptor (T3R), vitamin D receptor (VDR). L10 #6

92
Q

Which steps in protein translation are energy-dependent?

A

Initiation, elongation, translocation, and termination. L7 #42

93
Q

In which direction is the template DNA strand read by DNA polymerase?

A

Read in the 3’ –> 5’ direction. L2, #4

94
Q

Compare the transcription *units* of prokaryotes vs eukaryotes.

A

Prokaryotes: Polycistronic (>1 ORF) Eukaryotes: Monocistronic (1 ORF) -Meaning prokaryotes can get multiple proteins by changing reading frame. L4, #10

95
Q

During which phase of the cell cycle is euchromatin present?

A

Present during interphase (not mitosis). *Transcriptionally active* L1, #36

96
Q

In which direction are DNA chains synthesized and why?

A

DNA chains synthesized in the 5’ –> 3’ direction because there is only a free 3’-OH group to act as a nucleophile, and only a 5’-phosphate for the nucleophile to attack. Therefore, only a 5’ –> 3’ orientation is possible *(i.e. you can only add a new nucleotide to the 3’ end)*. L2, #5

97
Q

Upregulation of what would be useful in treatment of diseases associated with protein misfolding?

A

Chaperones L8 #52

98
Q

Where are tandem repeats typically found? Give two examples.

A

Non-coding regions of DNA (e.g. centromeric and telomeric DNA). examples: Satellite DNA or Simple sequence DNA. L1, #24

99
Q

1.) Which translation factor allows for translocation of the ribosome? 2.) Which translation factor brings the Met-tRNAi to the pre-initiation complex and completes the PIC?

A

1.) EF-G (prokaryotes), *eEF-2* for eukaryotes. 2.) eIF-2 —> Brings new tRNA to the P-site. L7 #44

100
Q

What is included in a transcription unit (5)?

A

Coding sequence, 5’ and 3’ UTRs, promoter region(s), and terminator. L4, #21

101
Q

What are the functions of THIIH (3)?

A

1.) KINASE ACTIVITY! – *phosphorylates RNA pol II*. 2.) ATPase. 3) Helicase. L9 #20

102
Q

What genes are among the most frequently affected in human tumors?

A

c-Myc proteins (TFs) L10 #9

103
Q

What is the most common cause for Xeroderma pigmentosum?

A

5-bp deletion in XPA gene (error verification). L3, #22

104
Q

In eukaryotes, while joining the ends of Okazaki fragments, which enzymes… 1.) Remove the RNA primer 2.) Fills in the gap 3.) Seals the gap

A

1.) FEN1 2.) DNA polymerase delta 3.) DNA ligase L2, #33

105
Q

Which mechanisms target cytosolic proteins and extracellular proteins for degradation?

A

1.) Cytosolic proteins: Proteasome degradation via ubiquitin. 2.) Extracellular proteins: In lysosomes via hydrolases. L8 #44

106
Q

What signal directs peroxisomal proteins into peroxisomes?

A

Peroxisomal targeting peptide signal-1 (PTS1): C-terminal tripeptide. L7 #59

107
Q

Roughly how many human protein encoding genes are there? RNA genes?

A

Protein encoding: ≈ 19,000-21,000 RNA genes: ≈ 18,000 L1 #14

108
Q

What is the primary replicative enzyme in prokaryotic DNA replication?

A

DNA pol III. L2, #17

109
Q

What causes 80% of CF cases?

A

3 base deletion; ∆508 = DELETED PHENYLALANINE!!! = Ile 507 (different bases, but AA remains the same…ATC to ATT. *NO FRAMESHIFT* L6b, #48

110
Q

What are the main differences in prokaryotic vs eukaryotic DNA origins of replication? (what is the name for the eukaryotic origins of replication?)

A

Prokaryotes have ONE origin, and eukaryotes have multiple origins – called *Autonomouslt Replicating Sequences (ARS)*. L2, #30

111
Q

What is the eukaryotic *sliding clamp* known as?

A

Proliferating Cell Nuclear Antigen (*PCNA*). L2, #33

112
Q

How is a Poly A tail added?

A

Added post-transcriptionally by *polyadenylate polymerase* without a template – Requires ATP as substrate. L10 #21

113
Q

How do Hsp 70 chaperones aid in translocation of new proteins across organelle membranes?

A

Hsp 70 stabilizes the unfolded state until proteins reach their cellular destination, then they spontaneously fold. L8 #51

114
Q

What is the TF Nuclear Domain?

A

Region that serves as a signal for the TF to go to the nucleus after being synthesized in the cytoplasm. L9 #18

115
Q

Which portions of the zinc-finger motif are over-expressed in some cancers?

A

Ap-1 complex —> c-jun and c-fos (protooncogenes). L10 #7

116
Q

What is the secondary structure of mRNA?

A

Hairpin loops L4, #10

117
Q

rRNAs are made in the _______, except for ______ (2).

A

Nucleolus —> *except for 5S rRNA and tRNAs* L5 #5

118
Q

What is lncRNA?

A

Long non-coding RNA: A regulatory RNA that is > 100 nt. L4, #19

119
Q

What creates the peptide bonds during the elongation phase of translation? Where does it come from?

A

Peptidyl transferase, an intrinsic activity of the 28s eukaryote (23s in prokaryotes) ribosomal subunit (part of the large, 60s subunit). L7, #16

120
Q

What are the protein malfunctions associated with the following diseases? 1.) Huntington 2.) ALS 3.) Parkinson 4.) Alzheimer’s 5.) CF

A

Diseases Associated with Mislfolded Proteins

1.) HuntingTIN —> Forms toxic polyglutamate aggregates 2.) SOD1 —> Superoxide dismutase 3.) alpha-Synuclein 4.) Amyloid-ß (Aß) 5.) CFTR misfolded due to ∆508 L8 #52

121
Q

What is the TF Dimerization Domain?

A

Many TFs work as dimers (two subunits). For these proteins, this domain facilitates interaction with another subunit. L9 #18

122
Q

Where/when would you find… 1.) Shorter 3’UTR 2.) Longer 3’UTR

A

1.) Proliferating cells, cancer cells, and iPSCs (???) 2.) Embryonic development L10 #32

123
Q

1.) Which type of APA are preferred in the nervous system and brain? 2.) Placenta, ovaries, and blood?

A

1.) Distal poly A signals —> isoforms with longer 3’UTRs. 2.) Prefer more proximal sites. L10 #23

124
Q

What are the consensus sequences in both prokaryotes and eukaryotes that mark the starting point for translation?

A

Prokaryotes: Shine-Delgarno Sequence; recognized on 5’ end of mRNA. -Positions ribosome onto mRNA so P-site is on the AUG initiation codon. Eukaryotes: Kozak sequence; ACC*AUG*G. -mRNA scanned from 5’ end to look for FIRST Kozak sequence. L7, #20

125
Q

What signal instructs proteins to be retained in the lumen of ER?

A

ER-Retention Signal (KDEL): On C-terminus. L7 #59

126
Q

Which eukaryotic enzymes are responsible for primer synthesis?

A

DNA primase in conjunction with DNA polymerase alpha; known as the *DNA primase–DNA polymerase alpha complex*. L2, #31

127
Q

What type of nucleotide is inosine? What forms it?

A

Inosine is a pyrimidine created from *hypoxanthine + ribose* = Inosine (I). L6, #14

128
Q

What charge do histones bear and why (i.e. what causes their charge)?

A

Positive charge at physiologic due to high content of Lys and Arg. L1, #31

129
Q

Which phase of transcription is self-sustaining? What is another word for self-sustaining?

A

Elongation; self-sustaining = PROCESSIVE. L4, #23

130
Q

Of what clinical use is HOTAIR? What is it?

A

HOTAIR is a lncRNA that is induced in ≈ 1/4 of human breast cancers. -Elevated HOTAIR level is also predictive of metastasis or progression in colon and liver cancers. L4, #19

131
Q

Describe a proteasome inhibitor, what it’s used for, and how it works.

A

Bortezomib (Velcade): Used for myeloma treatment. -Specifically and reversibly inhibits the Thr residue of the 26S proteasome. -Disrupts cell cycle and induces apoptosis. -Inhitory of IkB complex, and inhibits its translocation into the nucleus = inactivation of multiple downstream pathways important for myeloma cell signaling. L8 #39

132
Q

Concerning *nucleotide excision repair*, which enzymes/complexes are responsible for the following: 1.) Damage sensing (2) 2.) Damage verification (1) 3.) Helicase activity (2) 4.) Endonuclease activity (2)

A

1.) XPC, XPE 2.) XPA 3.) XPB, XPD 4.) XPF, XPG L3, #21

133
Q

What is the result of DNA damage due to UV-radiation?

A

A *thymine dimer* which creates a kink in the DNA (and un-pairs ATs). Can cause melanoma. L3, #14

134
Q

1.) Primase is a ______-dependent ______ polymerase. 2.) Primase is part of the _____ complex, together with _______.

A

1.) DNA-dependent RNA polymerase. 2.) DnaB complex, together with Helicase. L2, #16

135
Q

How is DNA packaged in prokaryotes and what aids the DNA packaging?

A

Circular DNA is *supercoiled*. Positively charged *polyamines* – Spermine or spermidine. NO HISTONES. L1, #29

136
Q

What does nitrous acid do to DNA?

A

Causes base deamination. L3, #12

137
Q

1.) What eukaryotic proteins act as tumor suppressors and how? 2.) How does an oncoprotein counteract the answer to #1? Give an example of one.

A

1.) p53 and BRCA1 repress the transcription of the *TERT* gene, thereby inhibiting telomerase activity. 2.) *c-Myc* (oncoprotein) induces the expression of the TERT gene. L2, #45

138
Q

What do alkylating agents (give 2 examples) do to DNA?

A

Methylates guanine, creating O6-methylguanine, which mismatches with thymine (instead of cytosine). Nitrogen mustard, e.g. chlorambucil, cyclophosphamide. L3, #12

139
Q

Primase provides substrate for _________.

A

DNA polymerase III. L2, #16

140
Q

What activity does DNA polymerase alpha lack?

A

Lacks 3’–5’ exonuclease activity (i.e. no proofreading). L2, #32

141
Q

What is the total number of high-energy bonds needed for formation of every peptide bond during translation?

A

4 TOTAL high-energy bonds. L7 #35

142
Q

Describe the mechanism of action for ATM (ataxia telangiectasia mutated) protein in DSB repair.

A

Serine/threonine kinase: Phosphorylates/activates a number of tumor suppressors (p53, CHK2, H2AX). -Activates DNA damage checkpoint (cell cycle arrest, DNA repair, and/or apoptosis). L3, #27

143
Q

Which DNA polymerases possess an activity that allows for proofreading? What is this activity called?

A

Pol I, pol II, and pol III —> 3’–5’ EXOnuclease activity. L2, #17

144
Q

1.) What enzymes fill in dNTPs of Okazaki fragments? 2.) What enzyme seals the final gap between Okazaki fragments? 3.) What are the dNTP donors that help seal the final gap (prokaryote and eukaryote).

A

1.) DNA pol I (5’–3’ exonuclease activity). 2.) DNA ligase. 3.) AMP from NAD+ (prokaryotes) and from ATP (eukaryotes), via *enzyme-AMP complex*. L2, #23-24

145
Q

What type of mutation is ATG —> ATC (in the template strand), why?

A

Non-sense mutation w/ *premature stop codon (PTC)*, because it went from Tyr to STOP on the mRNA (UAC —> UAG). L6, #24

146
Q

Imported mitochondrial proteins made on free ribosomes have at least one _________.

A

Signal peptide on the N-terminus. L7 #59

147
Q

1.) MetAP2 inhibitors induce what, and how? 2.) Name of drug? 3.) What other syndrome does this treat?

A

1.) Significant and sustained weight reduction —> Suppression of SREBP activity = reduced lipid and cholesterol biosynthesis. 2.) Beloranib 3.) Treatment for Prader-Willi Syndrome L8 #5

148
Q

What is the relationship between Bloom’s syndrome and BLM helicase?

A

BLM gene (HELICASE) normally functions in the repair of DSB by the *homologous recombination pathway*. -In Bloom’s, repair may occur through the error-prone NHEJ pathway, leading to increased genomic instability and predisposition to malignancy. L3, #33.

149
Q

Compare the rate of translation for eukaryotes vs prokaryotes. Why is this?

A

Prokaryotes ≈ 45 nt/sec Eukaryotes ≈ 20 nt/sec Prokaryotes are faster because they have ≈ 2x more ribosomes per mRNA (≈20 rib/mRNA) strand than do eukaryotes (≈10 rib/mRNA). *Rate of transcription correlates to # of ribosomes/mRNA* L4, #16

150
Q

1.) Reverse transcriptase (RT) is a ______-dependent ______ polymerase. 2.) Where is it found in eukaryotes? 3.) What types of viruses possess RT?

A

1.) RNA-dependent DNA polymerase. 2.) Found in *retrotransposons* and in *telomerase*. 3.) Present in *retroviruses (RNA)*, e.g. HIV RT. L2, #36

151
Q

What are the two domains of Hsp’s that help them fold proteins?

A

ATPase domain, and binding domain with hydrophobic residues. L8 #53

152
Q

What is an initiator sequence and where is it found?

A

Initiator sequence, aka Inr: ≈ 6 nt sequence from -2 to +4 that stabilizes the attachment of RNA polymerase to DNA to start RNA synthesis. L4, #25

153
Q

Eukaryotic DNA telomerase is a ______-dependent _______ polymerase. What does it do?

A

RNA-dependent DNA polymerase. DNA telomerase extends the chromosome ends. L2, #31

Medical Genetics (6 decks)

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