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M2M unit 1 > Proteins > Flashcards

Proteins Flashcards

(72 cards)

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1
Q

Basic AA R groups

A

Can be protonated at physiological pH

Lysine, arginine, histidine

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2
Q

Spongiform Encephalopathy

A

Prp misfolds and caues other proteins to misfold

altered alpha helices to form beta sheets that cause them aggregate forms aggregates with amyloid plauques leading to neuronal loss and gliosis

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3
Q

What is the least hydrophobic of the non-polar AA?

A

Glycine

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4
Q

Cysteine

A

Cys C

Polar uncharged

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5
Q

what AA promote alpha helices?

A

hydrophobic Ala and Leu

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6
Q

Hsp70/Hsp40 in prokaryotes

A

prokaryoties are DnaK or DnaJ

bind to hydrophobic region to prevent aggregation

ATP hydrolysis

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7
Q

Sickle Cell Anemia

A

glutamine undergoes single amino acid change to make hemoglobin stickier and difficult to pass through capilary bed

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8
Q

what does alpha helices make

A

structural: keratin, myosin, fibrinogen
globlar: hemoglobin, myoglobin

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9
Q

Valine

A

Val V

Non polar aliphatic

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10
Q

How do aromatic groups absorb UV light?

A

at 280nm and its used to measure protein concentration. Absorbance is a function of concentration.

As concentration increases so does absorbance.

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11
Q

how does hemoglobin transport Co2?

A

CO2 is converted as Carbamate on amino terminal residues of hemoglobin

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12
Q

what AA promote Beta sheet formation

A

Trp, Ile, Val

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13
Q

DnaJ and DnaK

A

DnaJ binds to unfolded and facilitates DnaK binding.

DnaJ stimulates ATP hydrolysis by DnaK.

DnaK-ADP binds tightly to unfolded protein NT xchange factor stimulates release of ADP

ATP binds to DnaK to dissociate protein

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14
Q

What are the Aromatic AA?

A

hydrophobic as well as relatively non-polar

Phenylalanine, tyrosine, tryptophan

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15
Q

Isoleucine

A

Ile I

non-polar aliphatic

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16
Q

Beta turns

A

180 degree turn accomplished over 4 AA acids hydrogen bond between 1st A and 4th AA made

proline (2nd) or Glycine (3rd)

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17
Q

Relaxed Hemoglobin State

A

High affinity of O2 so when leaving the lungs it remains attached formation triggered by O2 binding.

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18
Q

Phenylalanine

A

Phe F

Aromatic R group

Hydrophobic least polar of the Aromatic group

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19
Q

Alpha helix

A

right hand screw

R groups pointing outward bond

between every 5 residues Carbonyl O and amine

Inner diameter is too small out

diameter fits in major groove of DNA

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20
Q

Aliphatic side chains - meaning

A

carbons in open chain conformation

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21
Q

Amyloidosis

A

generalized protein misfolded in rest of body leading to variety of disease (T2D to cardiac amyloidosis)

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22
Q

Lysine

A

Lys K Polar Basic (positively charged) pKa 10

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23
Q

L Isomer vs D isomer

A

L: with hydrogen backwards is CORN counterclockwise D: with hydrogen backwards is CORN clockwise All amino acids have L isomers

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24
Q

what is the signficance of 1 and 8 lining up in alpha helces

A

allows the formation of a leucine zipper

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25
Serine
Ser S Polar, unchraged
26
Acetyl modificaiton
occurs on lysine, especially on histones
27
y-caroxyglutamate
A blood clotting prothrombin protein Vitamin K added carboxyl group Warfarmin (Coudamin) prevents blood clotting
28
Tyrosine
Tyr T Aromatic R Group hydrophobic and slightly polar (not really) can form H bonds
29
Triple Helix
rich in glycine and proline rich in turns and loops, but proline are hydroxylated via vitamin C allows massive H bonding E very third residue is glycine in collagen
30
Chaperonin
a cap and 2 7 subunit rings in prok GroEL and GroES required for 10-15% coupled to ATP hydorlysis and conformational changes
31
Alanine
Ala A non-polar Aliphatic
32
Collagen
tensile strength, non-stretching tendons, cartilage, bones, cornea long glycine and proline rich Super helical triple helix higher tensile strength than steel wire.
33
Gel Filtration Chromatography
Purify proteins according to size Proteins run through filtration column large flow faster and small slower
34
what happens with pH\>pKa
deprotonated base form denominates
35
What AA are non-polar, aliphatic
Glycine, alanine, valine, leucine, methionine, isoleucine
36
Why does Myoglobin use heme?
\generate free radicals heme not generate free radicals! myoglobin cant bind to O2 itself
37
Edman Degredation
label and remove N terminal AA one at a time and identify
38
Tense Hemoglobin site
Lower binding affinity so in high O2 region of lungs, O2 will bind very easily
39
Protein Prolyl Isomerase
Reforms proline from Trans to the cis formation cis is important in Beta turns
40
Alpha Keratin
tough rigid, hard materials in nails and horns cross linked alpha helices and S-S rich in hydrophobic residues form by alpha helices that coil together to form a coiled coil (left) to combine in a protofilmant and a protofibril and intermediate filament
41
Bortezomib
takes advantage of cancer cells always proliferating and proteasome is in high demand. acts on proteasome inhibitor and this has more pronounced effect on cancer cells. treats multiple myeloma
42
Methylation Modification
Occurs on lysine or arginine can have 1, 2, or 3 methyl groups methylation of histones
43
what aa do not promote beta sheet formation
Pro Gly
44
Polar R Group AA
Serine, Threonine, Cysteine, Asparagine, Glutamine
45
Disulfide Isomerase
correct disulfide bond formation between free cysteines especialy important when there are many free cysteines done on secreted of cell surface proteins
46
Leucine
Leu L non polar aliphatic
47
Tryptophan
Trp, W Aromatic R group Hydrophobic and slightly polar
48
Ion Exchange Chromatography
purify proteins according to charge run through cation exchange resin column with negatively charged beads. Positive charged particles stick and can be eluted with salt
49
Isoelectric Point
point at which the pH at which the protein carries equal number of + and - charge. pI is essentially pKa value pI \> pH = positive charged (lysozyme) pI
50
Arginine
Arg, R Polar Basic (positively charged) pKa 12
51
Histidine
His, H Polar Basic (positively charged) pKa 6.5
52
Hydroxyproline
found in collagen and CT Addition of OH group onto proline is responsible for strength Facilitated by Vitamin C \*Scurvy\*
53
Slk Fibroin
soft, flexible fiber held together by Beta sheet and van der waals intercations
54
Immunoglobulin
one heavy chain composed of 4 beta sheets one ligh chain composed of 2 beta sheets dimers antigen binding domain
55
Asparagine
Asn N Polar, uncharged
56
Proline isomers
most peptide bonds are in trans conformation, but proline has 6% are in cis
57
Methionine
Met, M non-polar aliphatic
58
Histamine
formed from the removal of CO2 from histidine
59
Gleevec
tyrosine kinase inhibitor that treats chronic myelogenous leukemia binds to bcr-abl fused protein to inhibit the kinase
60
Asparate
Asp D Polar Negative (acid) pKa 4.4
61
Acidic AA R groups
Asparate and Glutamate Deprotonated at physiological pH
62
O linked vs N linked glycosylation
O: sugars added to Ser and Thr N linked: sugars added to Asp in sequnes XNX-S/T
63
Bohr effect
pH difference in lung vs tissue to increase O2 transfer
64
what AA do not promote alpha helices?
proline and glycine
65
how is hemoglobin influenced by pH
blood in lungs have higher pH than blood, O2 binds better PH in tissue is lower, thus O2 is released
66
Thryoid hormone
L-thyroxin is formed by modification of tyrosine
67
ALB protein
ALB is a kinase that normally phosphorylates and dephosphorylates as regulatory protein. When fused with BCR, it is always active and leads to continuous phosphorylation - thus leukemia.
68
what is scurvy caused by?
lack of vitamin C Proline does not get hydroxylated so 4-hydroxyproline is not formed
69
Glutamine
Gln, Q polar, uncharged
70
Glutamate
Glu E Polar Negative (acid) pKa 4.4
71
Threonine
Thr, T polar uncharged
72
Kd
[p][L]\[pL] dissociation constant when Kd is higher, binding strength is low when Kd is low, binding strenth is high

M2M unit 1 (6 decks)

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