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

Random shit to memorize week 2 Flashcards

(104 cards)

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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
Phosphorlation occurs on _______, _______, and _____ and is important in signal transduction
Ser, Thr, Tyr
26
Gleevec
inhibits kinase activity of bcr-abl and stops continuous production of WBC – treats chronic myelogenous leukemia
27
Ubiquination
ubiquination of protein marks protein for degradation by proteasome
28
Bortezomib
proteasome inhibitor, prevents cancer cells from replicating
29
Sickle Cell Anemia is caused by __________ which makes hemoglobin molecules aggregate
single AA change in hemoglobin
30
Angiotensinagen protein precursor is cleaved by ________ into _________, which is then cleaved _______ to make __________
Renin protease --> Angiotensin I | ACE --> Angiotensin II
31
Collagen has a unique ________ rich in _____ and _______ and is dependent on ___________
triple helix structure, rich in Gly and Pro and is dependent on vitamin C for hydroxyproline production
32
Kd
dissociation constant = [ligand] when 50% of ligands bound
33
Bohr Effect
O2 binds better to hemoglobin at higher pH, and is released well at lower pH
34
Two classes of chaperones
Hsp70/Hsp40 and Chaperonin
35
Hsp70/Hsp40 chaperone helps protein folding by.... | Use ATP?
binding to hydrophobic regions of unfolded protein to prevent aggregation Uses 1 ATP
36
Chaperonin helps protein folding by a several step process: Uses ATP?
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
37
Protein disulfide isomerase
Breaks improperly folded disulfide bonds, allows correct reformation
38
Prolyl Isomerase
Speeds up proline conversion between cis and trans conformations
39
Gel filtration chromatography
protein purification based on size | Beads with small pores, takes small molecules longer to run through column
40
Ion Exchange Chromatography
protein purification based on charge Cation exchange column → - charge beads bind + target protein Use salt to disrupt binding and elute
41
Affinity Chromatography
protein purification based on ligand binding - Protein binds resin with ligand attached - Elute with solution with high concentration of ligand
42
Gel Electrophoresis
protein purity analysis - SDS polyacyrlamide gel used to separate proteins by size - Charge applied to gel, and large proteins move slower
43
Edman Degredation
Determines sequence of AA from N terminus
44
miRNA functions in ____________ and ________
translational repression, mRNA degredation
45
miRNA originates from __________ and uses ______, _______, and ________ proteins
pre-miRNA precursor molecule | Drosha, Dicer, Argonaute
46
siRNA functions in _______ and __________ and requires ________
mRNA degredation, transcriptional silencing | requires a perfect match with target
47
siRNA originates from _______ and uses ______ and ______ proteins
dsRNA | dicer, argonaute
48
when miRNA matches perfectly with the RNA it __________ and when miRNA matches imperfectly with RNA it __________
Imperfect match = RNA degradation OR translational repression Perfect match = RNA degradation
49
piRNA function in _________
transcriptional repression
50
piRNA originate from ________ and are _______ and _______ independent
ssRNA | Dicer and Argonaute independent
51
Long non-coding RNAs are > __________ NTs long
200
52
Argonaut/RISC
RNA induced silencing complex | -Cleaves/degrades RNA
53
Dicer
ribonulcease that cleaves miRNA precursor and dsRNA molecules
54
Drosha
Rnase enzyme, processes newly transcribed primary miRNA in nucleus
55
Restriction Fragment Polymorphism is used to diagnose certain diseases like __________ by __________
- sickle cell anemia (mutation --> longer DNA strand) | - by differentiating DNA sequences of different sizes
56
Southern Blot
looking for specific DNA sequence, use cDNAp probes
57
Northern Blot
looking for specific RNA, use anti-sense cDNA probe
58
Western Blot
looking for specific protein, use antibody probe on SDS-PAGE gel
59
3 stages of PCR
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
PCR vs. Sanger Sequencing (similarities/differences)
- Similarity: both use primers to initation replication | - Difference: PCR uses dsDNA, sequencing uses ssDNA and ddNTPs
61
Plasmids
- vectors, amplify DNA sequences in bacteria - Max insertion of 20kb into E. coli - Transformation is inefficient
62
Bacteriophage
infects E. coli, in order to use its replication machinery to produce recombinant vector (much more efficient transformation)
63
Cosmids
hybrid of bacteriophage and plasmid: use plasmid replication origin; can take up to 45 kb insert into E. coli.
64
BAC vector
bacterial artificial chromosome with insert up to 300kb into E. coli, good for chromosome mapping and sequencing
65
YAC vector
yeast artificial chromosome with insert up to 2mb, chromosome mapping and sequencing
66
Retroviral Vector
can carry very large inserts; introduce DNA into mammalian cells, delivers gene therapy.
67
Microarrays are used to measure _______ but tell you nothing about _________
``` mRNA levels (gene expression) nothing about SIZE of mRNA ```
68
Retinal Blastoma Protein
inhibits cell cycle transition from G1 to S | -Loss of RB = tumors
69
CDK4 + cyclin complex inhibits ________ and allows _________
inhibits RB, and allows cell cycle to advance into S phase
70
Assembly of Pre-RC at the origin of replication occurs only in _______ when _________
G1 | CDK is inactivated
71
Origin recognition complex
binds origin of replication, landing pad
72
MCM Helicase
recruited in G1 to pre-RC complex, activated when cell enters S phase and CDK is activated
73
Activation of Pre-RC occurs only in ________ when _________
S phase | when CDK is activated, and MCM helicase is phosphorylated
74
p53 activates _______ which prevent _________. If mutated then...
CDK inhibitors prevent entry into S phase If mutated = uncontrolled replication, cancer
75
ATM/ATR are protein kinases that phosphorylate ______ , causing _______
p53 | p53 activation, prevents entry into S phase
76
Short read sequencers
- Produce millions of short 100 base-pair reads - Use 1000 bp DNA templates - Low error rate - best for analyzing genotype
77
Long read sequencers
- Produce 10,000 sequencing reads, up to 10,000 bp in length | - High error rate
78
NHEJ
- Ends protected - Occurs anytime in cell cycle - Imperfect - Regulated by 53BPI - Uses: Ku, Artemis complex, Polymerase, Lig-4
79
Ku is used in ________ and acts to __________
NHEJ | acts to recruit DNA PKcs (protein kinase)
80
Artemis complex
processes ends in NHEJ, makes ends suitable for ligation
81
Lig-4
ligase used to restore phosphodiester bonds in NHEJ
82
HR
- 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
Misregulated HR can lead to __________ if __________ are used instead of _____________
loss of heterozygosity homologous chromosomes sister chromatid
84
Normal pathway of Amyloid Precursor protein
APP cleaved by alpha-secretase and then by gamma-secretase
85
Abnormal pathway for Amyloid Precursor protein
APP cleaved by beta-secretase and then by gamma-secretase → AB40 or AB42 (much more toxic)
86
Apolioprotein E
- enzyme that processes/clears out B-amyloid | - 3 allele variations, and one of them (apo 4) is not very good at clearance
87
Cofactor
metal ions bound within the enzyme, used by enzyme to do some chemistry
88
Coenzyme
small molecule bound in enzyme that may provide a functional group to participate in the chemistry
89
Km = ? High Km = Low Km =
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
Kcat = ?
turnover number, # substrate converted to product in a given time when [S] is at saturation
91
Kcat/Km =?
efficiency of an enzyme | -Higher number = better enzyme
92
Competitive Inhibitor
binds only to enzyme, competes with substrate for the active site -Increases Km
93
Uncompetitive Inhibitor
binds ES complex, does not bind active site (binds elsewhere) -Lowers Vmax, changes Km
94
Mixed Inhibitor
binds outside the active site, but can bind either E or ES | -Effects both Km and Vmax
95
Irreversible Inhibitor
act to permanently change the enzyme into a non-functional form -EX) penicillin
96
4 Mechanisms for Enzyme Regulation
1) Allosteric regulation 2) Covalent modification 3) Binding of another protein 4) Proteolytic cleavage
97
BRCA1 regulates ______, and recruits endonucleases and exonucleases when __________
Homologous Recombination | Phosphorylated by ATM
98
Mutation in BRCA1 and 2
cell checkpoint is defective, DNA damage not repaired properly --> chromosome breakage and abnormal recombination -Without BRCA1, 53BPI pushes repair towards NHEJ (more errors)
99
IRES
involved in cap-independent translation initiation
100
Non-polar AA (6)
``` Glycine Alanine Valine Leucine Methionine Isoleucin ```
101
Aromatic AA (3)
Tyrosine Tryptophan Phenylalanine
102
Polar AA (6)
``` Threonine Serine Cysteine Proline Asparagine Glutamine ```
103
Acidic AA (2)
(-) charge Aspartate Glutamate
104
Basic AA (3)
(+) charge Histidine Arginine Lysine

M2M Unit 1 (9 decks)

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