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CSF final > Final Review Block 1 > Flashcards

Final Review Block 1 Flashcards

1
Q

blood buffering equation

A

CO2 + H20 –> H2CO3 –> HCO3- + H+

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2
Q

influence of water on protein folding

A

proteins will fold to minimize unfavorable interactions- will have charged/hydrophilic groups externally and hydrophobic groups internally

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3
Q

hydrophobic amino acids (8)

A 
valine- Val, V
alanine- Ala, A
leucine- Leu, L
isoleucine- Ile, I
tryptophan- Trp, W
tyrosine- Tyr, Y 
phenylalanine- Phe, F
methionine- Met, M
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4
Q

Basic amino acids (3)

A

Histidine- His, H
Lysine- Lys, K
Arginine- Arg, R

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5
Q

Acidic Amino Acids (2)

A

glutamate- Glu, E

Aspartate- Asp, D

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6
Q

Polar amino acids (4)

A

serine- Ser, S
threonine- The, T
asparagine- Asn, N
glutamine- Gln, Q

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7
Q

Special amino acids (3)

A

cysteine- Csy, S
proline- Pro, P
glycine- Gly, G

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8
Q

special feature of Histidine

A

pKa is very close to physiologic pH

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9
Q

special feature of cysteine

A

can make disulfide bonds

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10
Q

special feature of proline

A

rigid structure d/t presence of ring

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11
Q

special feature of glycine

A

smallest R group (H)

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12
Q

special feature of Trp, Phe, Tyr

A

contain aromatic rings

Phe is the largest

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13
Q

special feature of serine and threonine

A

can be phosphorylated

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14
Q

what is the HH equation?

A

pH = pKa + log [A-]/log[HA]

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15
Q

what are the normal values for pka, pH, [CO2], [HCO3]

A 
pka = 6.1
pH = 7.35-7.45
[CO2] = 1.2 mM
[HCO3] = 24 mM
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16
Q

what is the ultimate determinant of final protein structure?

A

primary structure (linear polypeptide sequence)

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17
Q

describe peptide bonds

A

bonds between individual aa, rigid and do not allow for rotation

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18
Q

describe a-helix

A

each COO- is H-bonded to H that is 3.6 aa residues away

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19
Q

what disrupts a-helix?

A

proline rigid ring structure

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20
Q

b-sandwich? b- turns?

A

b-sandwich: interaction between the internal hydrophobic surfaces of 2 b-sheets
b-turns: 4 aa that form a sharp bend to reverse the direction, proline is good bc of built-in bend, glycine good bc of its small size

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21
Q

describe coiled-coil, example?

A

interaction of hydrophobic residues on 2 adjacent a-helices, ex is leucine zipper, commonly seen in transcription factors

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22
Q

describe zinc finger, example?

A

cys and his residues bind Zn, also seen in transcription factors with Zn binding DNA

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23
Q

what are peptidyl propyl cis-trans isomerases?

A

enzymes that facilitate the conversion of proline residues from trans to cis configuration

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24
Q

what are protein disulfide isomerases?

A

enzymes that catalyze formation of disulfide bonds

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25
Q

what are the chaperone proteins?

A 
molecular chaperones (Hsp70)
chaperonins (GroEL-GroES)
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26
Q

describe the function of Hsp70

A

molecular chaperone, prevents denaturation during fever by binding to exposed hydrophobic residues and preventing aggregation, use ATP

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27
Q

describe the function of GroEL-GroES

A

chaperonin, forms hydrophilic folding chamber that sequesters unfolded proteins and allows them to fold properly, uses ATP

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28
Q

describe collagen structure

A

Gly-Pro-X motif, proline can be hydroxylated allowing for the formation of cross-bridges and increased stability. normal collagen = two a-1 and one a-2

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29
Q

describe OI (severe and mild mutation)

A

autosomal dominant
severe- missense mut for glycine, results in normal amount of abnormal collagen (not able to fold properly)
mild- loss of 1 a-1 allele, leads to small quantities of normal collagen

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30
Q

describe survy

A

results from ascorbic acid def – ascorbic acid is a cofactor for proline hydroxylation, in the absence of ascorbic acid, cross linkages cannot form and collagen in weaker

31
Q

describe protein-ligand specificity

A

shape of the binding site is compatible to the ligand to allow for multiple covalent interactions (hand in glove vs. induced fit)

32
Q

what is the typical purpose of farnesylation/myristylation?

A

addition of fatty acid to anchor protein to a membrane

33
Q

3 types of chromatography

A

size- smaller molecules go through pores in beads, larger molecules move through faster
ion exchange- (+) proteins bind (-) beads and uncharged or (-) proteins move through after, (+) removed with salt
affinity

34
Q

what is a “cation exchange column”?

A

lined with (-) charges

35
Q

describe western blot

A

used to eval proteins (1-2) uses antibody probe

36
Q

describe SDS-PAGE

A

proteins denatured/linearized by SDS
SDS gives surface negative charge
will separate based on molecular wt
smaller particles will move faster/farther

37
Q

describe 2D gel electrophoresis

A

separation based on size and charge

can be useful for assessing level of phosphorylation, can be used for larger protein volume (100s)

38
Q

describe mass spectrometry

A

can be used for 1000s, provides info for identification

39
Q

why is the active site of an enzyme usually located in a cavity?

A

to restrict access of water to area– water can disrupt ligand binding

40
Q

what are the ways in which enzymes decrease activation energy? (3)

A
  • orient molecules favorably
  • separate charge to favor a reaction
  • strain a substance toward transition state
41
Q

what is the role of His in hemoglobin?

A

binds to iron and prevents it from oxidizing

42
Q

what happens if iron in heme oxidizes?

A

methmegolbinemia

43
Q

what is the hill coefficient?

A

measure of cooperativity

44
Q

what are the 2 states of hemoglobin?

A

R state- high O2 affinity

T- state- low O2 affinity

45
Q

how is hemoglobin transitioned from T to R?

A

when 1st O2 binds, iron will move into plane and pull His with it, when His moves it causes a conformation change that leads to the subunit in the ab pair moving, this enhances hemoglobin’s ability to bind O2

46
Q

what is BPG?

A

intermediate of glycolysis

binds to T state and stabilizes it

47
Q

what is the Bohr effect?

A

increased H+ = increased CO2, when CO2 is increased, hemoglobin will have decreased affinity for O2 and it will be released into tissues (T state His 146 is Hbonded to Asp94)

48
Q

oxygen dissociation curve

A

right shit- decreased affinity for O2 = more released into tissues = T state

left shift- increased affinity for )2 = less released into tissues = R state

49
Q

what conditions favor R-state?

A

hold onto O2:
High O2
decreased CO2
decreased BPG

50
Q

what conditions favor T-state?

A

release O2:
low O2
high CO2
high BPG

51
Q

what would hemoglobin want to give up O2 if BPG is high?

A

BPG is an intermediate of glycolysis, thus if increased glycolysis is occurring, this is an indication that tissues need O2, so BPG stabilizes hemoglobin T state so that it can release O2 into tissues for OXPHOS

52
Q

what is the effect of fetal hgb on the curve?

A

fetal hemoglobin has a higher affinity for O2, causes a left shift

53
Q

what is the basis for base pairing?

A

chargaff’s rules AT, CG

54
Q

SLE

A

autoantibodies to DNA, leads to inflammation, tissue injury, organ dysfunction

55
Q

what is RNA more easily degraded that DNA

A

presence of 2’OH leaves RNA more susceptible to hydrolysis

56
Q

most abundant type of RNA

A

rRNA (80%)

57
Q

what is the usual “form” for monosaccharides? what can alter it?

A

usually D form, with OH on the right

can be altered with epimerases

58
Q

what type of polysaccharide cannot be digested by humans?

A

cellulose b(1,4)

59
Q

what are GAGs?

A

sugars with repeating units of disaccharides

60
Q

what aa form O-linked sugars?

A

serine, threonine

61
Q

what aa forms N-linked sugars?

A

asparagine

62
Q

what is the double bond configuration for almost all biologic systems?

A

cis

63
Q

what FA are prominent on the outer leaflet? inner?

A

outer- phos-choline, sphingomyelin, glycolipids

inner- phos-serine, phos- linositol

64
Q

what are flippases? floppases?

A

flippases- enzymes that move phos-serine from outer to inner against gradient
floppases- move phos-choline and sphingolipids from inner to outer against gradient

65
Q

where are the membrane components synthesized?

A

phospholipids- ER
glycolipids- ER, golgi
cholesterol- in membranes of ER

66
Q

what will decrease membrane fluidity?

A

increased cholesterol, increased length of FA tails, lipid rafts

67
Q

what will increase membrane fluidity?

A

increased polyunsaturated fats

68
Q

what causes sickle cell anemia?

A

AR, glu-val at 6th position of b subunit of hgb

69
Q

when does sickling occur?

A

any situation that decreased O2, will lead to polymerization of hgb via hydrophobic interactions

70
Q

what tests are done for sickle cell?

A

NBS- cation exchange column chromatography, isoelectric focusing

71
Q

what is the main source of pain in SCA?

A

vaso-occlusion in post-capillary venules

72
Q

1 cause of death in pts with SCA

A

acute chest syndrome

73
Q

what reduces the risk of CVA?

A

transfusion

74
Q

how does hydroxyurea treat SCA?

A

increases fetal hgb levels

CSF final (3 decks)

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