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Biochemistry > First Pass Miss Exam 3 > Flashcards

First Pass Miss Exam 3 Flashcards

1
Q

What are the three most common bases to methylate?

A
  1. 5-methylcytidine
  2. N6-methyladenosine
  3. 5-hydroxymethylcytidine
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2
Q

What are the tautomeric forms of DNA?

A

A/C - amino -> imino (doublebond to N)

T/G - lactam -> lactim (doublebond from O to adjacent N, making an alcohol)

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3
Q

What is the most common wrong base pairing?

A

A = C, in cytosine’s imino form.

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4
Q

What is the only form of left-handed DNA?

A

Z form. B form is regular with 10.5 bp per turn, and 3.4 A rise per nucleotide = 36 A per turn

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5
Q

Name two antibiotics that target topoisomerases?

A
  1. Nalidixic acid

2. Ciprofloxacin

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6
Q

What is doxorubicin?

A

anti-cancer drug targeting type 1 topoisomerase.

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7
Q

What histone mediates nucleosome packing?

A

Histone H1. Their genes are organized into clusters.

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8
Q

What is needed to break down DNA fibers and loops on a nuclear scaffold?

A

Type 2 topoisomerase - normally used to break up catenanes, which are a production of bacterial DNA replication

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9
Q

What is the telomere sequence?

A

TTAGGG

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10
Q

What enzymes are involved in homologous recombination?

A
  1. Endonuclease to introduce single-strand nicks and allow for strand invasion
  2. RecA - requires strand invasion + branch migration = large homologous swap
  3. Resolvase - an endonuclease to break the 3D Holliday structure
  4. DNA ligase
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11
Q

What is the function of the enzymes involved in site-specific recombination?

A

excisionases + integrases, which can add or remove DNA at specific att sites (attachment sites)

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12
Q

Why is site-specific combination important immunologically?

A

It is the way in which antibiotic diversity is made

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13
Q

What is the difference between transposons with long terminal repeats vs short inverted repeats?

A

Short - encodes only transposase (an integrase), simple transposon
Long - encodes both transpose + a reverse transcriptase to make a new DNA copy. Also has a very long promoter included

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14
Q

What is exon shuffling?

A

The process by which two transposons flank an exon, and the transposase accidentally cuts out the exon and puts it in another gene, giving that gene a new protein domain

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15
Q

What is the Alu sequence?

A

A short inverted repeat transposon which requires an external reverse transcriptase. Makes up about 5% of our genome, originated from the 7SL RNA gene, a signal recognition peptide

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16
Q

What is the L1 transposon?

A

transposon making up 4% of our genome

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17
Q

What are the two types of spontaneous mutagenesis? Relative frequency?

A
  1. Deamination - about 100 C-U events per day

2. Depurination - 10000 per day, mostly guanine

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18
Q

What are the deamination reactions?

A

C->U
5-meC -> T
A -> HX
G -> X

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19
Q

Where is oxidation of nucleotides most common?

A

In mitochondria

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20
Q

What is the mechanism of action of mustard gas?

A

Hydroxylates the lactim form of guanine

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21
Q

What enzymes are involved in the methylation mismatch repair system in E.Coli?

A

MutH - nicks the hemimethylated DNA as it recognizes the 6-methylA on GATC sequence
MutS/MutL - complexes which bind the mismatch site and pull together until a MutH reaches, after which exonuclease will rip out this pace and reform

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22
Q

What enzyme is primarily involved in base-exicision repair?

A

DNA glycosylase, to remove defective base.

Then endonuclease opens, DNA poly I replaces, DNA ligase seals

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23
Q

What are the main subunits of E. coli RNA polymerase?

A

beta - catalytic
beta prime - DNA binding
alpha - binds upstream promoter which is not always present
sigma - directs polymerase to a specific promoter around -10 that is rich in T’s and A’s, leaves when the complex is “open” that is DNA is opened

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24
Q

What is rho-independent termination?

A

Termination via hairpin loop, as polymerase is slowed from C-G rich region

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25
Q

What is rho dependent termination?

A

Rho is a hexameric helicase which binds the mRNA transcript at a speicifc site and pulls itself via ATP up into the RNA polymerase active site

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26
Q

What is the primary RNA polymerase in eukaryotes?

A

RNA polymerase II

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27
Q

What are the important proteins required for Pol II function?

A

Pol II - the RNA polymerase catalytic subunit
TBP - binds the TATA box (binding protein) at around -30, induces a sharp bend in the DNA as a molecular saddle
TFIIH - Transcription factor 2 helicase - unwinds the DNA in the active site. Also a kinase which phosphorylates the carboxy terminal of Pol II for activation

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28
Q

How is the 5’ cap made?

A

Addition of 7-methylguanosine to 5’ nucleotide in RNA transcript, via adding GMP to a NDP, then methylating via SAM. Methyl groups can also be added to the next couple 2’ hydroxyls via SAM.

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29
Q

What is a group 1 intron?

A

Self splicing -> external GTP attacks the 5’ splice site

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30
Q

What is a group 2 intron?

A

Self-splicing w/ ribozyme - 2’ OH of an adenine at a “branch site” starts the reaction at 5’ splice site

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31
Q

What is a spliceosome?

A

Complex which uses small nuclear RNA’s + proteins in higher eukaroytes to carry out the group II mechanism.

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32
Q

What 3 complexes are involved in polyadenylation?

A
  1. Upstream - sees polyadenylation signal
  2. Downstream - sees G/U downstream element, bends between this site and upstream
  3. Cleavage / polyadenylation site - between 1/2, adds the tail at the bent site
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33
Q

What is the functional difference between alternative cleavage / polyadenylation patterns and alternative splicing patterns?

A

Alternative cleavage / polyA - multiple polyA cleavage sites downstream the gene

Alternative splicing - multiple 3’ splice sites

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34
Q

What is the function of the CRP protein in the lac operon?

A

Binds the CRP site upstream the lac operon when glucose is low and cAMP is high (cAMP-Reactive Protein). This functions to recruit the RNA polymerase. Makes sure the lac operon is not on if there is enough glucose but the lac repressor is not binding the lac operators (O1-O3) because there is enough allolactose in the cell.

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35
Q

Where does homeodomain bind?

A

DNA in its major groove, via helix-turn-helix.

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36
Q

What amino acid are leucine zippers rich in to bind DNA?

A

Lysine + arginine in the DNA binding region for their + charge.

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37
Q

What are the three domains of the zinc fingers? Which is highly conserved?

A
  1. Hormone binding
  2. DNA binding - highly conserved with two zincs complexed to histidines or cysteines.
  3. RNA polymerase II transcription activating
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38
Q

How do you “name” a DNA sequence with regards to its transcription action?

A

According to its action: Enhancer or silencer. Enhancers will bind activators, silencers will bind repressors

39
Q

What is the function of mediator?

A

Recruited by activators when they bind to enhancer sites on the DNA, will recruit TBP + TFIIH to phosphorylate carboxy terminus of RNA Poly II.

-> activates histone modification enzymes (methylation, acetylation, phosphorylation) to expose chromatin for downstream effects

40
Q

What are three ways in which repressors could work?

A
  1. Displace mediator complex
  2. Bind a silencer DNA sequence
  3. Interfere with transcription machinery
41
Q

What is the function of dicer?

A

An endonuclease which cleaves duplex RNA’s so they can become small temporal (stRNA) or small interfering (siRNA) and bind to mRNA transcripts to shut them off.

42
Q

What are the three major differences between mitochondrial and normal codons?

A

Normal STOP encodes tryptophan
Normal Arginine encodes STOP
Normal Isoleucine encodes Methionine

43
Q

What is the only working horizontal wobble?

A

I to A,

it also bonds with both U and C

44
Q

What is the overhanging sequence of the acceptor arm of tRNA?

A

3’ overhang of CCA

45
Q

What are the two non-obvious arms of tRNA?

A
  1. TphiC -> contains pseudouridine, a base with attachment at C5 rather than C1
  2. D arm - contains 2-3 dihydrouridine residues
46
Q

What is the difference between class1 and class2 aminoacyl-TRNA synthetases?

A

Class 1: Has a Rossman fold motif of parallel beta-sheets to interaction with minor group
Class 2: Has antiparallel beta sheets to interact with major groove of tRNA acceptor arm

47
Q

How do the aminoacyl-tRNA synthetases work?

A

Form aminoacyl-adenylate via cleavage of ATP at alpha phosphate, only interact with carbonyl.

3’-OH of A on CCA sequence of acceptor arm attacks the carbonyl and transfers again. The amino group is never used as a nucleophile and always left open.

48
Q

What part of the ribosome recognizes the Shine-Dalgarno sequence? What is this sequence?

A

16S rRNA of 30s subunit. It is a purine rich sequence

49
Q

What are the three main initiation factors and their functions?

A

IF-1 and IF-3 hold the 30S subunit onto the Shin-Dalgarno Sequence.
IF-2 recruits formyl-Met to the peptidyl site while holding GTP.

GTP hydrolysis occurs to pull the 50S subunit onto the entire complex.

50
Q

What are the functions of EF-Tu and EF-Ts?

A

EF-Tu has basically the same function as IF-2 for initiation, in that it brings amino acids to ribosome. This time in the A site, then cleaves the GTP to leave it there. EF-Ts is the factor which allows the GDP and EF-Tu to dissociate, before being displaced again by GTP

51
Q

What part of the 50S subunit has peptidyl transferase activity?

A

23 S rRNA - is a ribozyme. Allows A site amino to attack carbonyl of P site, leans each tRNA into the next site.

52
Q

What factor is required for translocation of tRNA’s?

A

EF-G -> mimics the structure of EF-Tu with GDP bound, hydrolyzes GTP to push the tRNA partially in the A site fully forward into the P site

53
Q

What are the factors involved in termination?

A

RF-1 or RF-2 bind when there is a stop codon -> water is used as nucleophile to cleave the AA chain. Still must be entirely dissociated via EF-G-GTP entering the A site to push the whole thing along

54
Q

What is the structure of a normal mitochondrial leader sequence and what cleaves it off?

A

Amphipathic alpha-helix.

Cleaved by a matrix metalloprotease to allow folding

55
Q

What are the three enzymes responsible for ubiquination?

A

E1: Activates ubiquitin by attaching to E1, via ATP hydrolysis
E2: Conjugating enzyme, determines what lysine E3 should attach it to
E3: Catalytic subunit which dimerizes with E2, moves the ubiquitin onto the protein of interest

56
Q

What is the structure of the proteosome?

A

Two 19S subunits and a 20S subunit. 19S subunit binds the poly-Ub substrate, cleaves the Ub and sends it through the 20S subunit with proteolytic activity

57
Q

What are the differences between myristoyl and palmitate anchors? What type of proteins are they meant to anchor?

A

Myristoyl - linked via N-terminal amino acid, co-translationally
Palmitate or Farnesyl Anchors - post-translational, need to be conjugated to protein via an internal cysteine by an enzyme which can recognize the folded protein

They anchor peripheral membrane proteins

58
Q

What are the differences between O and N-linked glycoproteins?

A

N-linked: Attach entire core polysaccharide sequence to Asparagine amide from Dolichol-P in the ER, and have this modified in the Golgi.

O-linked: Add to Serine or threonine in the Golgi- one at a time.

59
Q

How are acid hydralases targeted for lysosomes and how could this lead to a lysosome storage disease?

A

A mannose residue in N-linked is phosphorylated in the Golgi to have it targeted to lysosomes. A mannose deficiency or defect in this path could lead to this

60
Q

What is cleaved via Mono-ADP-Ribosylases?

A

B3: NAD+

61
Q

How does Hsp70 / Hsp40 work?

A

DNAK / DNAJ
Hsp70: Binds hydrophobic sequences in elongating DNA
Hsp40: Cycles ATP/ADP
Prevents folding of proteins during import to mitochondria via MTS

62
Q

How does Hsp60 / Hsp10 work?

A

Hsp60s form the donuts and Hsp10s form the cap which cycles ATP. Heptamer, donuts, etc (GroEL/ES)

63
Q

What’s the major misfolded protein in Parkinson’s?

A

Alpha-synuclein

64
Q

What’s the major misfolded protein in ALS?

A

Superoxide dismutase

65
Q

What’s the Alzheimer’s enzyme which breaks down the amyloid precursor protein in the wrong way?

A

Beta-secretase

66
Q

What is the major motif of the prion protein?

A

Beta-sheet, in the hPrP protein, becomes sc instead of c

67
Q

What causes Osteogenesis imperfecta?

A

Gly in Gly-X-Y sequence of amino acids in Type 1 collagen is converted to a bulky amino acid, preventing triple helix folding + assembly into fibrils.

68
Q

What are Goodpasture’s and Alport’s syndromes?

A

Goodpastures = autoimmune to Type 4 collagen, attacks GBM

Alport’s = Hereditary nephritis - mutations in Type 4 collagen causing defective assembly of glomerular BM

69
Q

For glycosylation of procollagen in the ER, what amino acid receives galactose then glucose?

A

O-linked: Hydroxylysine (fibrillar)

N-linked: Asparagine (non-fibrillar only)

70
Q

What is the function of disulfide isomerase?

A

Forms inter-intrachain disulfide bonds of procollagen in the ER

71
Q

What is the function of lysyl oxidase and where is it?

A

Outside the fibroblasts, deaminates the side chains of some lysine residues to form allysine and hydroxyallysine

72
Q

What is osteolathyrism?

A

inhibition of lysyl oxidase which causes bone problems + aortic aneurysms + spine deformities. Can be from the Lathyrus sweet pea which contains beta-aminopropionitrile or from chelating agents which chelate copper cofactor for the enzyme

73
Q

What is scleroderma and what is the major warning sign?

A

Multiorgan disease due to collagen overproduction. Causes Raynaud’s phenomenon - blue fingertips or toes due to cold or stress, as well as “claw hands” which cannot be closed due to heavy connective tissue.

74
Q

What is one enzyme deficiency which could be responsible for Ehlers-Danlos syndrome?

A

Procollagen peptidase - the enzyme outside of fibroblasts that cleaves procollagen to tropocollagen.

Classic symptoms: hypermotility of joints and stretchy skin

75
Q

What are the two main domain types in elastin?

A
  1. Hydrophobic - lysine-rich to form crosslinks

2. Hydrophobic - valine rich for hydrophobic interaction, causing elasticity

76
Q

How is elastin synthesized?

A

Via tropoelastin in RER, extracellular space which contains lysyl oxidase will form desmosine / isodesmosine via specific allysine sequence generations

77
Q

Why does smoking increase the risk of emphysema?

A

Causes oxidation of key methionine residue of alpha1-antitrypsin, which inhibits elastase

78
Q

What is the structure of fibronectin?

A

Homodimer glycoprotein, many different binding domains in a “string of beads”. Important for cell adhesion + migration. Loss of this favors tumor cell metastases

79
Q

What types of chains make up laminins?

A

Alpha, beta, and gamma chains. Alpha chain binds integrins, and is mutated in muscular dystrophies

80
Q

What is entactin / nidogen?

A

Linker protein attaching to proteoglycans, integrins, and Type 4 collagen.

81
Q

What is the core structure of GAGs / mucopolysaccharides?

A

Disaccharides of uronic acids + amino sugar with is also acetylated

82
Q

What is the sequence by which core proteins attach GAGs?

A

Core protein -> Xyl-Gal-Gal, except for hyaluronic acid + keratan sulfate proteoglycans

83
Q

Where are heparan sulfates found?

A

Cell surfaces

84
Q

Where is heparin found?

A

Mast cells, liver

85
Q

Where is dermatan sulfate found?

A

Skin, blood vessels

86
Q

Where are chondroitin + keratan sulfates found?

A

Cartilage, tendons, bone

87
Q

What is the function of link proteins vs core proteins in aggrecan?

A

Core proteins - hold the Xyl-Gal-Gal then chondroitin / keratan sulfate directly
Link proteins: Hold the core proteins attached to the hyaluronic acid

88
Q

What causes mucopolysaccharidoses?

A

Specific GAG chains cannot be broken down in lysosomes, requires sulfatases, proteases, and exoglycosidases

89
Q

What happens one one is deficiency in tissue inhibitors of MMPs?

A

Matrix metalloproteases (with zinc cofactor) are hyperactive and cause skeletal dysplasia, arthritis, and coronary artery disease if uncontrolled. Similar to alpha1-antitrypsins in terms of antagonistic actions to proteases.

90
Q

How can excess caspase expression help cancer cells metastasize faster?

A

Initiates detachment of cells from its surroundn tissue structures

91
Q

What are procaspases vs effector caspases?

A

Procaspases are secreted in response to cell death receptors which bind TNF or Fas

Effector caspases are cysteine proteases activated via death domains bound by procaspases, or via cytochrome C

92
Q

What is the function of Bcl-2?

A

Antagonize apoptosis by being induced when survival factors bind, and PI-3-K / Atk pathway is activated

Function by preventing leakage of cytochrome C from mitochondria, limiting the number of effector caspases

93
Q

What is the function of p21 CDKI?

A

Prevents phosphorylation of Rb, induced by p53 if there is DNA damage

Biochemistry (14 decks)

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