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Biochem midterm 2 > Midterm 1 > Flashcards

Midterm 1 Flashcards

1
Q

What is a covalent bond?

A

2 atoms sharing a pair of electrons, a really tight bond

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2
Q

What is a hydrogen bond?

A

Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a covalently bound hydrogen and a lone pair of electrons

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3
Q

Water is a good solvent for what type of molecules?

A

charged and polar
- amino acids and peptides
small alcohols
carbohydrates

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4
Q

Water is a poor solvent for what type of molecules?

A

nonpolar substances.
nonpolar gases
aromatic moieties
aliphatic chains

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5
Q

What is an ionic interaction?

A

electrostatic attraction between oppositely charged ions.

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6
Q

What is a hydrophobic interaction?

A

interaction between hydrophobic compounds and water.

hydrophobic compounds tend to cluster together to increase entropy

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7
Q

What are Van der waals interactions?

A

weak interaction between two atoms depending on their distance from each other.

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8
Q

What are the colligative properties of water?

A

boiling point, melting point and osmolarity

do not depend on the nature of the solute, just the concentration

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9
Q

What are the non-colligative properties of water?

A

viscosity, surface tension, taste and color

depend on the chemical nature of the solute.

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10
Q

Describe water adhesion

A

binding between water and something else (plastic or glass). menisque.

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11
Q

Describe water cohesion:

A

binding between water and water by hydrogen bonds, surface tension.

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12
Q

Describe proton hopping

A

proton moving along a chain of covalent and hydrogen bonds interchangeable in water.

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13
Q

What is the formula for pH?

A

pH= -log[H+]

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14
Q

What is the formula for the equilibrium constant?

A

concentration of product/concentration of reactants.

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15
Q

What is a conjugate acid?

A

a substance that gained a proton

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16
Q

What is a conjugate base?

A

a substance that lost a proton.

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17
Q

What is the difference between a strong acid and a weak acid?

A

A strong acid will more easily lose its proton than a weak acid.

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18
Q

Give the formula for pka

A

pka=-logKa

ka=keq

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19
Q

What is the relationship between a strong acid and its pka?

A

stronger the acid, lower its pka

high pka= weak acid

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20
Q

What is a buffer system?

A

weak acid and conjugate base that resists change in pH when acid or base are added.

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21
Q

When is the greatest buffering capacity of a system?

A

when ph=pka

there is a 50:50 mixture of acid and anion forms of the compounds

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22
Q

When is the buffering capacity of a system lost?

A

when the pH differs from pka by more than 1 pH unit

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23
Q

Give the handerson-hasselbach equation

A

ph=pka+ log [conjugates base]/[weak acid]

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24
Q

What are the biological functions of proteins?

A

catalysis
transport
structure
motion

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25
Q

Describe the formation of a peptide bond

A

condensation reactions of 2 amino acids put together.

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26
Q

Name the 4 groups in amino acids

A

H group
Carboxyl group
Amino group
R group

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27
Q

What are the particularities of aromatic amino acids?

A

possess a cyclic group

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28
Q

What is the only amino acid that is not chiral?

A

glycine

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29
Q

What is the particularity of cysteine?

A

can form disulfide bonds

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30
Q

Why is proline unique?

A

the R group is cyclical (non polar)

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31
Q

What are the two amino acids containing sulphur atoms?

A

methionine and cysteine

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32
Q

What is the function of reversible modifications of amino acids?

A

increase or decrease a protein activity.

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33
Q

What is the charge of an amino acid with a neutral R group at low pH?

A

positive

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34
Q

what is the charge of an amino acid with a neutral R group at high pH?

A

negative.

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35
Q

What is a zwitterion?

A

single-molecule has both a positive and negative charge

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36
Q

How do you calculate the isoelectric point?

A

average between the two pka concerned for the formation of that molecule.

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37
Q

What forces are stabilizing protein structure?

A

non-covalent forces

(ionic, hydrophobic, van der Waals, disulphide, hydrogen bond

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38
Q

Why are disordered regions important in proteins?

A

for interactions with other proteins.

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39
Q

What is a resonance hybrid?

A

the double bond can move from the C=O to C=N

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40
Q

what is the phi angle?

A

the angle between the Carbon-N bond

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41
Q

what is the psi angle?

A

the angle between the Carbon-Carbonyl bond

42
Q

What are the two regular arrangements in the secondary structure of proteins?

A

alpha helix

et beta-sheets

43
Q

What amino acids are considered helix breakers?

A

proline and glycine

stretches of bulky or charged amino acids

44
Q

Where would we find the negatively charged residues in a helix?

A

near the positive end (amino terminus)

45
Q

Where would we find the positively charged residues in a helix?

A

near the negative end (carboxyl terminus)

46
Q

What residues are preferred in beta sheets?

A

large aromatic or branched residues

47
Q

What amino acids are more likely to be found in b turns?

A

proline (position 2) and glycine. (position 3)

48
Q

What interactions stabilize the tertiary structure?

A

numerous weak interactions

49
Q

What characterizes a fibrous protein?

A

insoluble

consist of a single type of secondary structure

50
Q

What characterizes a globular protein?

A

often contains several types of secondary structures

51
Q

What is a protein domain?

A

part of a polypeptide chain that is independently stable or could undergo movements as a single entity.

52
Q

Name 4 fibrous proteins?

A

alpha-keratin
myosin
collagen
silk fibroin

53
Q

What makes silk fibroin so flexible?

A

sheets are held together by numerous weak interactions.

54
Q

What are the advantages of the quaternary structure of proteins?

A

accumulates a greater number of weakly stabilizing interactions. gain in stability
relative reduction in exposed surface
improves catalysis or tight regulation
slower though.

55
Q

What type of protein are the enzymes mostly?

A

globular

56
Q

What is a prosthetic group?

A

cofactor tightly bound to protein

57
Q

What is an apoenzyme?

A

enzyme without cofactor

58
Q

What is a holoenzyme?

A

enzyme with coenzyme

59
Q

What is an organic cofactor?

A

coenzyme

60
Q

What is the function of oxidoreductases?

A

enzyme that catalyzes the transfer of electrons

61
Q

What is the function of a transferase?

A

enzyme that catalyzes a group transfer reaction

62
Q

What is the function of a hydrolase?

A

enzyme that catalyzes hydrolysis (transfer of functional groups to water)

63
Q

What is the function of a lyase?

A

cleavage of C-C, C-O, C-N or other bonds by elimination, leaving double bonds or rings or adding groups to double bonds.

64
Q

What is the function of an isomerase?

A

transfer of groups within molecules to yield isomeric forms.

65
Q

What is the function of ligase?

A

formation of C-C, C-S, C-O and C-B bonds by condensation reactions coupled to cleavage of ATP or similar cofactor

66
Q

How do the enzymes accelerate reactions?

A

decrease the activation energy

67
Q

What allows the enzyme to decrease considerably the activation energy?

A

enzyme specificity,

transition state, conformational change.

68
Q

What are the three catalytic mechanisms of enzymes?

A

acid-base catalysis
covalent catalysis
metal ion catalysis

69
Q

What is the principle of acid-base catalysis?

A

give and take protons

70
Q

What is the principle of covalent catalysis?

A

a transient covalent bond between the enzyme and the substrate.

71
Q

What is the principle of metal ion catalysis?

A

involves a metal ion bound to the enzyme. stabilizes negative charges.

72
Q

What two-step reaction is catalyzed by chymotrypsin?

A

acylation (fast)

deacylation (slow)

73
Q

At what pH does chymotrypsin work better?

A

basic pH.

74
Q

What are the two catalysis mechanisms involved in the peptide cut by chymotrypsin?

A

base catalysis

covalent catalysis

75
Q

What is the principle behind column chromatography?

A

proteins with a lower affinity for the solid phase will wash off first. protein with higher affinity will retain on the column longer

76
Q

What is the principle of ion exchange chromatography?

A

protein migrates through the column according to its physical-chemical (charge) properties

77
Q

what is the principle of size exclusion chromatography?

A

larger proteins migrate first, small proteins enter numerous pores and take a longer path.

78
Q

What is the principle of affinity chromatography?

A

protein can bind to a ligand, antibody, or other proteins. purification depends on the affinity of interaction (or affinity of binding)

79
Q

What is the principle of electrophoresis?

A

the electric field pulls protein according to their charge

80
Q

What does SDS do in SDS PAGE?

A

gives all proteins a uniformly negative charge

denaturing.

81
Q

What is the function of SDS page?

A

analyze proteins based on their molecular weight

82
Q

What is the difference between SDS page, non-reducing SDS page and native page?

A

SDS page: denature and gives a negative charge. + break of disulfide bond
non-reducing: only negative charge, not breaking the disulfide bond
native: no detergent. no denaturation. slight charge only

83
Q

What is the function of isoelectric focusing?

A

can be used to determine the pI of a protein

84
Q

What is 2D electrophoresis?

A

separate proteins by pI and by molecular weight.

SDS-PAGE+ isoelectric focusing

85
Q

What is the maximum velocity?

A

when the reaction reaches a plateau

86
Q

What is the Michaelis Menten constant?

A

the concentration of substrate providing half of the enzyme maximal velocity.
km

87
Q

Describe the saturation kinetics?

A

at high substrate concentration, velocity is not proportional to [S]

88
Q

What is the Michaelis-Menten equation?

A

V0=Vmax[S]/Km+[S]

89
Q

Give the definition and the equation for the turnover number?

A

Kcat=Vmax/[ET]

Kcat= number of S molecules converted to P per time.

90
Q

What is the equation for enzyme efficiency?

A

Kcat/Km

91
Q

What gives you the slope value in the Lineweaver-Burk plot?

A

Km/Vmax

92
Q

What gives you the y-intercept in the Lineweaver-Burk plot?

A

1/Vmax

93
Q

What gives you the x-intercept in the Lineweaver-Burk plot?

A

-1/Km

94
Q

What is the function of inhibitors?

A

compounds that decrease an enzyme’s activity

95
Q

What is competitive inhibition?

A

competes with the substrate for binding. binds active site. does not affect catalysis.
- no change in Vmax, increase in Km
lines intersect at the y axis

96
Q

What is uncompetitive inhibition?

A

only bind to Enzyme-substrate complex. does not affect substrate binding. inhibits catalytic function.
decrease in V max, an apparent decrease in Km. parallel lines

97
Q

What is mixed inhibition or non-competitive inhibition?

A

binds enzyme with or without substrate
to inhibit both substrate binding and catalysis.
decrease v max, the apparent change in km.
lines intersect left from the y-axis. or start from the same point and diverge.

98
Q

Define irreversible inhibitors

A

react with the enzyme. one inhibitor molecule can permanently shut off one enzyme molecule. powerful toxins.

99
Q

Name the 4 processes by which an enzyme can be regulated?

A
  • noncovalent modification
  • covalent modification
  • irreversible
  • reversible
100
Q

What are allosteric effectors?

A

noncovalent modification.

can improved or reduce enzymatic catalysis

101
Q

What covalent modifications can regulate protein activity?

A

phosphorylation
adenylation
acetylation
myristoylation.

102
Q

What are zymogens?

A

proenzyme
inactive precursor of an enzyme.
irreversible covalent modification can activate zymogens

Biochem midterm 2 (3 decks)

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