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Dental Biochemistry Exam 1 > Acid/Base and Enzyme Kinetics > Flashcards

Acid/Base and Enzyme Kinetics Flashcards

1
Q

Covalent bonds

A

equal sharing of electrons

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2
Q

What are the types of non-covalent bonds?

A

hydrogen bonds, electrostatic bonds, hydrophobic interactions and van der waals interactions

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3
Q

What are the characteristics of non-covalent bonds?

A

much weaker, require around 5 kcal/mole to break, break quite easily under physiological conditions, determine how molecules interact with each other and the shape of molecules

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4
Q

What are the characteristics of hydrogen bonds?

A

an attractive force between a H atom in a polar covalent bond and the unpaired electrons of another electronegative atom….where H is the donor and the electronegative atom is the acceptor

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5
Q

The strength of hydrogen bonds is dependent on?

A

distance and orientation

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6
Q

What are the characteristics of an electrostatic bond?

A

an attractive force between a negative and positive charged atoms where strength is dependent on distance but not orientation

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7
Q

What are hydrophobic interactions?

A

a solvent effect in water where the water molecules push non-polar molecules together

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8
Q

What determines strength of hydrophobic interactions?

A

the surrounding hydrogen bonds that push the molecules together

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9
Q

what is a van der waal force

A

the attraction between two neutral atoms

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10
Q

Definition of an acid

A

a molecule that can donate or release a H+ ion (proton)

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11
Q

definition of a base

A

a molecule that can accept or react with a hydrogen ion, H+

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12
Q

Conjugate base

A

dissociation of an acid creates a conjugate base that can accept a proton to regenerate the acid

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13
Q

conjugate acid

A

protonation of a base will produce a conjugate acid that can donate the proton to regenerate the base

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14
Q

what acids dissociate completely?

A

strong acids (HCl or H2SO4)

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15
Q

Weak acids and weak bases exist in_______ with their conjugate species

A

equilibrium

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16
Q

definition of pH

A

pH= -log[H+], higher pH means lower H+ and lower pH means higher H+

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17
Q

why are H+ and pH so important?

A

many biological molecules undergo acid-base equilibrium and the amount of acid or base is dependent on H+ concentration……the higher the H+ content the more an acid is favored (AH)

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18
Q

what is Ka?

A

the acid dissociation constant, is a measure of the position of equilibrium

ka is the H+ concentration at exactly half of A is protonated

Ka= [H+][A]/[HA]

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19
Q

what is pKa?

A

pKa=-logKa

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20
Q

Henderson-Hesselbalch equation

A

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

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21
Q

what happens when pH=pKa?

A

exactly half of A is unprotonated and the other have is protonated……equilibrium

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22
Q

What happens when pH is one unit higher than pKa?

A

90% of solution is A (dissociated)

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23
Q

what happens when pH is two units higher than pKa?

A

99+% of solution is A (dissociated)

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24
Q

what happens when pH is one unit lower than pKa?

A

90% of solution will be HA (protonated)

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25
Q

what is buffering?

A

a substance that can react with either H+ or OH- to get rid of excess H+ or OH-. The buffer decreases a pH change

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26
Q

Buffers work well when?

A

pH is near their pKa

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27
Q

what is the most important physiological buffer?

A

bicarbonate

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28
Q

metabolism generates ______ in the body

A

acidity

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29
Q

what is the structure of amino acids?

A

carboxylic acid group, amino group, r group/side chain, and a H all about an alpha caarbon

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30
Q

the carboxyl group of an amino acid is usually _______ while the amino group is usually _______

A

deprotonated, protonated

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31
Q

What are the non-polar amino acids?

A

glycine, alanine, proline, valine, leucine, isoleucine, phenylalanine, methionine, tryptophan

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32
Q

What are the characteristics of non-polar amino acids?

A

have methylene side chains that cannot form hydrogen bonds, usually found in the center of protein structures, are abundant components of protein

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33
Q

What are the polar amino acids?

A

serine, threonine, tyrosine, cysteine, asparagine, glutamine

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34
Q

What are the characteristics of polar amino acids?

A

interact well with water through hydrogen bonding on their side chains, and usually found on the surface of proteins

35
Q

What are the aromatic amino acids?

A

phenylalanine, tryptophan, tyrosine

36
Q

What are the characteristics of the aromatic amino acids?

A

they are usually hydrophobic and buried within protein structures

tryptophan is the least abundant amino acid in proteins

37
Q

what are the sulfer containing amino acids?

A

cysteine and methionine

38
Q

what ate the characteristics of sulfer amino acids?

A

many extracellular proteins are held together in part by disulfide bridges

39
Q

What are the negatively charged amino acids?

A

aspartate and glutamate

40
Q

What are the positively charged amino acids?

A

arginine, lysine and histidine

41
Q

What are the characteristics of the charged amino acids?

A

they mostly protrude at the surface of proteins and are often found making electrostatic interactions with other residues

42
Q

what is a zwitterion?

A

a molecule with a positively charged amino group and negatively charged carboxyl group

43
Q

What is isoelectric point?

A

the pH at which a molecule has no net charge pI= (pk amino group + pk carboxyl group)/2 or pI= (pk1 + pk2)/2 when there re two carboxyl groups

44
Q

What is the overall protein structure?

A

amino acids are joined by peptide bonds/amide bonds, then many amino acids are joined end to end by peptide bonds to form polypeptides, then long polypeptides come together to form a protein

45
Q

what happens in a peptide bond?

A

the carboxyl group of one amino acid is connected to the amino group of another amino acid and they lose their acid-base characteristics…… a water molecule is also lost

46
Q

Peptide bonds have a partial ___________ that makes them planar and rigid because of ______

A

double bond character, electronic resonance

47
Q

What level of protein structure dictates shape and function?

A

primary

48
Q

what is the primary structure of a protein?

A

simple chain of amino acids

49
Q

What are the two secondary protein structures?

A

alpha helix and beta sheets

50
Q

What are the characteristics of alpha helix?

A

the carboxyl oxygen accepts a hydrogen from a residue 4 locations down in the sequence. this repeating interaction stabilizes the helix at which the R groups protrude at regular intervals.

51
Q

What are the characteristics of beta sheets?

A

beta sheets form hydrogen bonds with other beta sheets, adjacent R groups interact and beta turns can be formed by the hydrogen bonding

52
Q

What are triple helixes?

A

cable like structures of great tensile strength, only polypeptides with glycine residues every third position can be used, examples are collagen chains
*****the H on the alpha carbon sticks in the middle so no other R group can fit besides glycine

53
Q

What holds primary structure together?

A

covalent bonds

54
Q

What holds secondary structures together?

A

hydrogen bonds

55
Q

what holds tertiary and quaternary structures together?

A

non-covalent bonds

56
Q

What are globins?

A

protein structures that are primarily alphahelical, have no beta structures, but all helix connected by turns

57
Q

what determines the folding structure of a protein?

A

amino acid sequence

58
Q

what is Keq?

A

a way to describe equilibrium

Keq= products/reactants

59
Q

when Keq>1

A

only a small amount of reactant is present….. it favors the products

60
Q

when Keq<1

A

a small amount of product is present….it favors reactants

61
Q

what does G0 tell us?

A

the same thing as keq

62
Q

G0>1

A

the reaction is non-spontaneous, favors the reactants and absorbs energy

63
Q

G0<1

A

the reaction is spontaneous, favors the products and produces energy

64
Q

Keq and G0 tell us NOTHING about?

A

how fast a reaction goes

65
Q

ATP is thermodynamically____but kinetically _____

A

unstable, stable

66
Q

What is a catalyst?

A

lowers the energy of activation and increases the rate at which a reaction proceeds towards equilibrium

67
Q

Keq and G0 depend on?

A

the initial and final states, which is why they are not altered by the presence of a catalyst

68
Q

Enzymes do not alter the

A

equilibrium of a reaction

69
Q

what is enzyme kinetics?

A

quantitative description of enzyme activity as a function of substrate concentration

70
Q

what is an enzyme catalyzed reaction?

A

at very high substrate concentration the curve approaches a theoretical limit corresponding to the saturation of the catalyst

71
Q

saturation kinetics model

A

E + S <—–> ES ——> E + P

the rate of product formation is proportional to the enzyme substrate complex (ES)

72
Q

Additional Increase in substrate concentration will…….

A

not increase the reaction rate

73
Q

Michaelis Menten Equation is?

A

reaction rate as a function of substrate concentration

74
Q

What is Km?

A

michaelis constant, when the substrate concentration is at half of Vmax meaning half the enzyme is saturated

75
Q

What is Vmax?

A

a measure of the maximum capacity of the enzyme. it depends on how much enzyme is present

76
Q

What is enzyme inhibition?

A

usually refers to reversible inhibition meaning removal of inhibitor results in rapid recovery of enzyme

77
Q

What is enzyme inactivation?

A

refers to irreversible effects

78
Q

what are the two types of reversible inhibitors?

A

competitive and non-competitive

79
Q

What are competitive inhibitors?

A

bind in a mutually exclusive fashion with substrate but inhibition can be overcome by high substrate concentration

80
Q

what are non-competitive inhibitors?

A

do not compete with substrate for same binding site, can bind in the presence or absence of substrate, and inhibition cannot be overcome with high substrate concentration

81
Q

Competitive inhibitors do what to km and vmax?

A

vmax stays the same but km increases

82
Q

non-competitive inhibitors do what to km and vmax?

A

vmax decreases but km stays the same

83
Q

lead and mercury

A

are heavy metals that react with -SH groups and act as irreversible inactivators of many enzymes

Dental Biochemistry Exam 1 (10 decks)

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