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M2M Unit 1 > Random shit to memorize week 2 > Flashcards

Random shit to memorize week 2 Flashcards

1
Q

Start codon

A

AUG, encodes methionine

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2
Q

Stop Codons

A

UAA, UAG, UGA

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3
Q

IF1 and IF3 bind to _________

A

30S subunit of ribosome

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4
Q

IF2

A

delivers formyl-methionine tRNA to P site to pair with AUG codon

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5
Q

E1

A

binds aminoacyl tRNA and brings it to the A site

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6
Q

Peptidyl transferase center

A

catalyzes peptide bond formation using energy from charged tRNA

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7
Q

E2

A

binds and transfers tRNA from A site to P site

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8
Q

What kind of energy and how much is used to add each AA in translation?

A

GTP and ATP
4 per AA
(2 ATP to charge tRNA, 1 GTP to deliver tRNA to A site, 1 GTP to translocate A–>P site)

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9
Q

Prokaryotic Translation

A

Shine-delgarno

Polycistronic

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10
Q

Eukaryotic translation

A
  • Cap-dependent, IF4E protein

- Kozak sequence

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11
Q

IF4E protein binds _________ and brings in ________

A

binds 5’cap on mRNA, and brings in IFs for translation

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12
Q

Interferon

A

released by cells under viral attack, and signals to nearby cells to prepare for infection by virus

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13
Q

Interferon causes nearby cells to activate ___________ and phosphorylate _________ prevent __________

A

1) activates viral mRNA endonucleases

2) phosphorylate eIF-2, prevent delivery of tRNA-Met to start site

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14
Q

apoB

A

mRNA edited post-transcriptionally to alter function - mRNA in intestine processed by enzymes so it is shorter than mRNA in liver

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15
Q

Rapamycin is a cancer treatment that prevents __________

A

phosphorylation of 4E-BP, preventing formation of translation initiation complex on the 5’cap

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16
Q

Transferrin

When Iron is low, transferrin level ________
When Iron is high, transferrin level ______

A

transports iron into cell
Low iron = increase transferrin
High iron = decrease transferrin

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17
Q

Ferritin

When Iron is low, Ferritin level ________
When Iron is high, Ferritin level ______

A

Sequesters iron

Low iron = decrease Ferritin
High iron = increase Ferritin

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18
Q

Iron response binding protein binds __________ at low iron levels, stopping _______ and stabilizing ________

A

Iron Response Element
stopping ferritin production
stabilizing transferrin

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19
Q

When iron levels are high, iron binds the ________ and allows ________ to be translated and _________ to be degraded

A

Iron response binding protein
allows ferritin to be translated
transferrin degraded

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20
Q

Both insulin and keratin us ________ as an integral part of their structure

A

disulfide bonds

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21
Q

Hydroxyproline

A
  • Stabilizes structure of collagen via H-bonds

- Production is Vitamin C dependent, so no Vitamin C = scurvy

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22
Q

Gamma-Carboxyglutamate

A

Present in blood clotting proteins, Vitamin K dependent, so without vitamin K = bleeding disorders

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23
Q

Coumadin

A

Targets enzyme that modifies AA into gamma-carboxyglutamate

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24
Q

Glycosylation adds a sugar onto the O of ______ and _____ and the N of ________

A

Ser, Thr

Asparagine

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25
Q

Phosphorlation occurs on _______, _______, and _____ and is important in signal transduction

A

Ser, Thr, Tyr

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26
Q

Gleevec

A

inhibits kinase activity of bcr-abl and stops continuous production of WBC – treats chronic myelogenous leukemia

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27
Q

Ubiquination

A

ubiquination of protein marks protein for degradation by proteasome

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28
Q

Bortezomib

A

proteasome inhibitor, prevents cancer cells from replicating

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29
Q

Sickle Cell Anemia is caused by __________ which makes hemoglobin molecules aggregate

A

single AA change in hemoglobin

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30
Q

Angiotensinagen protein precursor is cleaved by ________ into _________, which is then cleaved _______ to make __________

A

Renin protease –> Angiotensin I

ACE –> Angiotensin II

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31
Q

Collagen has a unique ________ rich in _____ and _______ and is dependent on ___________

A

triple helix structure, rich in Gly and Pro and is dependent on vitamin C for hydroxyproline production

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32
Q

Kd

A

dissociation constant = [ligand] when 50% of ligands bound

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33
Q

Bohr Effect

A

O2 binds better to hemoglobin at higher pH, and is released well at lower pH

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34
Q

Two classes of chaperones

A

Hsp70/Hsp40 and Chaperonin

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35
Q

Hsp70/Hsp40 chaperone helps protein folding by….

Use ATP?

A

binding to hydrophobic regions of unfolded protein to prevent aggregation
Uses 1 ATP

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36
Q

Chaperonin helps protein folding by a several step process:

Uses ATP?

A

protein binds to uncapped site → ATP used to move cap over it → protein folds → ATP used to remove cap and release protein
Uses 2 ATP

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37
Q

Protein disulfide isomerase

A

Breaks improperly folded disulfide bonds, allows correct reformation

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38
Q

Prolyl Isomerase

A

Speeds up proline conversion between cis and trans conformations

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39
Q

Gel filtration chromatography

A

protein purification based on size

Beads with small pores, takes small molecules longer to run through column

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40
Q

Ion Exchange Chromatography

A

protein purification based on charge
Cation exchange column → - charge beads bind + target protein
Use salt to disrupt binding and elute

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41
Q

Affinity Chromatography

A

protein purification based on ligand binding

  • Protein binds resin with ligand attached
  • Elute with solution with high concentration of ligand
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42
Q

Gel Electrophoresis

A

protein purity analysis

  • SDS polyacyrlamide gel used to separate proteins by size
  • Charge applied to gel, and large proteins move slower
43
Q

Edman Degredation

A

Determines sequence of AA from N terminus

44
Q

miRNA functions in ____________ and ________

A

translational repression, mRNA degredation

45
Q

miRNA originates from __________ and uses ______, _______, and ________ proteins

A

pre-miRNA precursor molecule

Drosha, Dicer, Argonaute

46
Q

siRNA functions in _______ and __________ and requires ________

A

mRNA degredation, transcriptional silencing

requires a perfect match with target

47
Q

siRNA originates from _______ and uses ______ and ______ proteins

A

dsRNA

dicer, argonaute

48
Q

when miRNA matches perfectly with the RNA it __________ and when miRNA matches imperfectly with RNA it __________

A

Imperfect match = RNA degradation OR translational repression
Perfect match = RNA degradation

49
Q

piRNA function in _________

A

transcriptional repression

50
Q

piRNA originate from ________ and are _______ and _______ independent

A

ssRNA

Dicer and Argonaute independent

51
Q

Long non-coding RNAs are > __________ NTs long

A

200

52
Q

Argonaut/RISC

A

RNA induced silencing complex

-Cleaves/degrades RNA

53
Q

Dicer

A

ribonulcease that cleaves miRNA precursor and dsRNA molecules

54
Q

Drosha

A

Rnase enzyme, processes newly transcribed primary miRNA in nucleus

55
Q

Restriction Fragment Polymorphism is used to diagnose certain diseases like __________ by __________

A
  • sickle cell anemia (mutation –> longer DNA strand)

- by differentiating DNA sequences of different sizes

56
Q

Southern Blot

A

looking for specific DNA sequence, use cDNAp probes

57
Q

Northern Blot

A

looking for specific RNA, use anti-sense cDNA probe

58
Q

Western Blot

A

looking for specific protein, use antibody probe on SDS-PAGE gel

59
Q

3 stages of PCR

A

1) Heat to 95 degrees C (denaturing DNA).
2) Cool to 55 degrees C (allows primers to hybridize).
3) Warm to 72 C at which time the polymerase (Taq polymerase) copies the DNA from dNTPs in solution

60
Q

PCR vs. Sanger Sequencing (similarities/differences)

A
  • Similarity: both use primers to initation replication

- Difference: PCR uses dsDNA, sequencing uses ssDNA and ddNTPs

61
Q

Plasmids

A
  • vectors, amplify DNA sequences in bacteria
  • Max insertion of 20kb into E. coli
  • Transformation is inefficient
62
Q

Bacteriophage

A

infects E. coli, in order to use its replication machinery to produce recombinant vector (much more efficient transformation)

63
Q

Cosmids

A

hybrid of bacteriophage and plasmid: use plasmid replication origin; can take up to 45 kb insert into E. coli.

64
Q

BAC vector

A

bacterial artificial chromosome with insert up to 300kb into E. coli, good for chromosome mapping and sequencing

65
Q

YAC vector

A

yeast artificial chromosome with insert up to 2mb, chromosome mapping and sequencing

66
Q

Retroviral Vector

A

can carry very large inserts; introduce DNA into mammalian cells, delivers gene therapy.

67
Q

Microarrays are used to measure _______ but tell you nothing about _________

A 
mRNA levels (gene expression)
nothing about SIZE of mRNA
68
Q

Retinal Blastoma Protein

A

inhibits cell cycle transition from G1 to S

-Loss of RB = tumors

69
Q

CDK4 + cyclin complex inhibits ________ and allows _________

A

inhibits RB, and allows cell cycle to advance into S phase

70
Q

Assembly of Pre-RC at the origin of replication occurs only in _______ when _________

A

G1

CDK is inactivated

71
Q

Origin recognition complex

A

binds origin of replication, landing pad

72
Q

MCM Helicase

A

recruited in G1 to pre-RC complex, activated when cell enters S phase and CDK is activated

73
Q

Activation of Pre-RC occurs only in ________ when _________

A

S phase

when CDK is activated, and MCM helicase is phosphorylated

74
Q

p53 activates _______ which prevent _________. If mutated then…

A

CDK inhibitors
prevent entry into S phase
If mutated = uncontrolled replication, cancer

75
Q

ATM/ATR are protein kinases that phosphorylate ______ , causing _______

A

p53

p53 activation, prevents entry into S phase

76
Q

Short read sequencers

A
  • Produce millions of short 100 base-pair reads
  • Use 1000 bp DNA templates
  • Low error rate
  • best for analyzing genotype
77
Q

Long read sequencers

A
  • Produce 10,000 sequencing reads, up to 10,000 bp in length

- High error rate

78
Q

NHEJ

A
  • Ends protected
  • Occurs anytime in cell cycle
  • Imperfect
  • Regulated by 53BPI
  • Uses: Ku, Artemis complex, Polymerase, Lig-4
79
Q

Ku is used in ________ and acts to __________

A

NHEJ

acts to recruit DNA PKcs (protein kinase)

80
Q

Artemis complex

A

processes ends in NHEJ, makes ends suitable for ligation

81
Q

Lig-4

A

ligase used to restore phosphodiester bonds in NHEJ

82
Q

HR

A
  • Perfect repair
  • Ends resected
  • Requires presence of sister chromatid
  • Only occurs in S and G2 of cell cycle
  • Leads to genetic diversity in Meiosis
  • Regulated by BRCA1
83
Q

Misregulated HR can lead to __________ if __________ are used instead of _____________

A

loss of heterozygosity
homologous chromosomes
sister chromatid

84
Q

Normal pathway of Amyloid Precursor protein

A

APP cleaved by alpha-secretase and then by gamma-secretase

85
Q

Abnormal pathway for Amyloid Precursor protein

A

APP cleaved by beta-secretase and then by gamma-secretase → AB40 or AB42 (much more toxic)

86
Q

Apolioprotein E

A
  • enzyme that processes/clears out B-amyloid

- 3 allele variations, and one of them (apo 4) is not very good at clearance

87
Q

Cofactor

A

metal ions bound within the enzyme, used by enzyme to do some chemistry

88
Q

Coenzyme

A

small molecule bound in enzyme that may provide a functional group to participate in the chemistry

89
Q

Km = ?
High Km =
Low Km =

A

Km = [S] at ½ Vmax

  • High Km = enzyme has low affinity for substrate
  • Low Km = enzyme has high affinity for substrate (requires less substrate to achieve
90
Q

Kcat = ?

A

turnover number, # substrate converted to product in a given time when [S] is at saturation

91
Q

Kcat/Km =?

A

efficiency of an enzyme

-Higher number = better enzyme

92
Q

Competitive Inhibitor

A

binds only to enzyme, competes with substrate for the active site
-Increases Km

93
Q

Uncompetitive Inhibitor

A

binds ES complex, does not bind active site (binds elsewhere)
-Lowers Vmax, changes Km

94
Q

Mixed Inhibitor

A

binds outside the active site, but can bind either E or ES

-Effects both Km and Vmax

95
Q

Irreversible Inhibitor

A

act to permanently change the enzyme into a non-functional form
-EX) penicillin

96
Q

4 Mechanisms for Enzyme Regulation

A

1) Allosteric regulation
2) Covalent modification
3) Binding of another protein
4) Proteolytic cleavage

97
Q

BRCA1 regulates ______, and recruits endonucleases and exonucleases when __________

A

Homologous Recombination

Phosphorylated by ATM

98
Q

Mutation in BRCA1 and 2

A

cell checkpoint is defective, DNA damage not repaired properly –> chromosome breakage and abnormal recombination
-Without BRCA1, 53BPI pushes repair towards NHEJ (more errors)

99
Q

IRES

A

involved in cap-independent translation initiation

100
Q

Non-polar AA (6)

A 
Glycine
Alanine
Valine
Leucine
Methionine
Isoleucin
101
Q

Aromatic AA (3)

A

Tyrosine
Tryptophan
Phenylalanine

102
Q

Polar AA (6)

A 
Threonine
Serine
Cysteine
Proline
Asparagine
Glutamine
103
Q

Acidic AA (2)

A

(-) charge

Aspartate
Glutamate

104
Q

Basic AA (3)

A

(+) charge

Histidine
Arginine
Lysine

M2M Unit 1 (9 decks)

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