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biochem 501 > unit 1 exam > Flashcards

unit 1 exam Flashcards

1
Q

what is the hydrophobic effect

A

the favorable increase in entropy of water when it is released from nonpolar molecules

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2
Q

characteristics of peptide bonds

A

partial double bond character between carbonyl carbon and amide nitrogen

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3
Q

specific activity formula

A

activity/total protein (units/mg)

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4
Q

number of H-bonds in alpha helix

A

(# amino acids)-4

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5
Q

uses for gel electrophoresis

A

separate molecules by size; unfold protein but maintain primary structure

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6
Q

does lower Kd correspond to ligand binding more or less tightly

A

more tightly

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7
Q

myoglobin properties

A

oxygen storage protein
binds to heme (porphyrin ring and iron atom)
iron atom in +2 ox state
monomer
bad transporter
tertiary
hyperbolic O2 binding curve

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8
Q

hemoglobin properties

A

oxygen transporter
tetramer
T state: binds less strongly to O2
R state: binds most strongly to O2

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9
Q

more BPG

A

more T state

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10
Q

less BPG

A

more R state

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11
Q

high affinity state conditions

A

more R state, less BPG, higher pH, less O2 released
(fetal hemoglobin has less BPG)

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12
Q

low affinity state conditions

A

more T state, more BPG, lower pH, more O2 released

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13
Q

Michaelis-Menten assumptions

A

k-2 is negligible
[ES] is constant

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14
Q

oxyanion hole purpose (chymotrypsin)

A

stabilizes transition state (2x in peptide breaking)

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15
Q

hydrophobic pocket purpose (chymotrypsin)

A

substrate binding specificity

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16
Q

histidine purpose (chymotrypsin)

A

gen acid/base
take H+ from ser, protonate amide, take H from H2O, protonate ser

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17
Q

serine purpose (chymotrypsin)

A

covalently bonds to carbonyl carbon

18
Q

asparagine purpose (chymotrypsin)

A

H-bonds to stabilize the positive charge on histidine

19
Q

allosteric enzyme characteristics

A

feedback inhibition
reversible
binding to enzyme makes it more active for substrate
product will shut down production
non michaelis-menten behavior

20
Q

competitive inhibition m-m graph

A

constant vmax
Km increases

21
Q

uncompetitive inhibition m-m graph

A

vmax and Km decrease at same rate

22
Q

mixed inhibition m-m graph

A

vmax decreases
Km increases

23
Q

sphingolipid purpose

A

important immunogenic determinant in blood

24
Q

glycerophospholipid purpose

A

prostaglandins derived from them

25
Q

sterol purpose

A

membrane structural lipid

26
Q

Ramachondran plot purpose

A

gives possible rotations of functional groups
Glycine has most possible rotations because double H group

27
Q

what is a post-translational modification?

A

covalently attaching functional groups after protein translation from ribosome
ex: hydroxyproline for collagen

28
Q

how are peptides (peptide bonds) formed?

A

condensation reaction

29
Q

what kind of amino acids are on the interior of a protein

A

nonpolar hydrophobic

30
Q

Alfinsen RNase folding experiment

A

unfolded proteins, proved they were inactive, refolded, proved they were active
experiment proved that the primary sequence of a polypeptide is sufficient for proper protein folding activity

31
Q

Beta-sheet characteristics

A

contain relatively few amino acid residues
H bonds form between strands
have a tendency to twist and are pleated

32
Q

what are the 3 main catalytic strategies

A

acid/base catalysis, covalent catalysis, metal ion catalysis

33
Q

Do larger Mr values belong to larger or smaller molecules

A

larger

34
Q

how do you count ionizable groups

A

count number of -ate, -ine, -SH, and OH groups and add 2 for the terminal NH3 and COO-

35
Q

do bacteria produce a higher ratio of saturated/unsaturated fatty acids at higher or lower temps

A

higher temps

36
Q

COVID characteristics

A

surrounded by lipid membrane that can be destroyed with soap and simple hand washing

to infect another cell the virus fuses its lipid bilayer with the host cell bilayer and that process depends on viral spike protein binding to receptors on cell surface

37
Q

what is the Bohr effect?

A

binding affinity for O2 decreases at lower pH
- more BPG - more T-state

38
Q

what is the most abundant protein in humans?

A

collagen

39
Q

what is keratin?

A

a fibrous protein found in hair and skin

40
Q

what is a fibrous protein?

A

highly extended protein with repeating helical or beta sheet structure

biochem 501 (4 decks)

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