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Biochemistry > Exam One: Learning Objectives > Flashcards

Exam One: Learning Objectives Flashcards

1
Q

What are the four major classes of biomolecules?

A

Amino Acids
Carbohydrates
Nucleotides
Lipids

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2
Q

What is the structure of an amino acid?

A

Central carbon bonded to a carboxyl group, an amino group, a Hydrogen, and an R group

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3
Q

What is the general formula of carbohydrates?

A

(CH(sub2)O)sub n
where n is at least three

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4
Q

What is the simplest form of a carbohydrate?

A

monosaccharides

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5
Q

What is responsible for forming adenosine triphosphate? (ATP)

A

nucleotides

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6
Q

Define nucleotides

A

basic unit of hereditary materials DNA and RNA

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7
Q

What is the structure of a nucleotide

A

five-carbon sugar, a nitrogen-containing ring and one or more phosphate groups

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8
Q

What is the common trait of all lipids?

A

poorly soluble in water

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9
Q

What is the primary structure of a lipid?

A

a long chain of hydrocarbons

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10
Q

Define protien

A

macromolecules formed by the polymerization of amino acids

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11
Q

A __ of energy leads to a __ stable state

A

lowering; more

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12
Q

Define exergonic

A

energy-releasing

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13
Q

Define endergonic

A

energy-absorbing

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14
Q

When delta G < 0 the reaction is

A

spontaneous

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15
Q

When delta G = 0

A

the reaction is at equilibrum

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16
Q

When delta G > 0, the reaction is

A

nonspontaneous

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17
Q

What is the equation that relates gibbs free energy to temperature, enthalpy, and entropy

A

delta G = delta H - TdeltaS

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18
Q

H stands for

A

enthalpy

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19
Q

S stands for

A

entropy

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20
Q

In any spontaneous process, the __ of the Universe increases

A

entropy

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21
Q

When delta S > 0

A

the reaction is spontaneous

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22
Q

If delta H is negative and -T delta S is positive, the reaction will be __ at __ temperatures

A

spontaneous; low

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23
Q

If delta H is positive, and -TdeltaS is negative, the reaction will be __ at __ temperatures

A

spontaneous; high

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24
Q

__ groups release H+ into solution

A

acidic

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25
Q

___ groups remove H+ from solution

A

basic

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26
Q

Nonpolar molecules are __

A

hydrophobic

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27
Q

___ in particular tend to sequester themselves from an aqueous environment

A

hydrocarbons

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28
Q

Polar molecules are ___

A

hydrophillic

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29
Q

What are five examples of hydrophilic substances?

A

polar covalent compounds
sugars
ionic compounds
amino acids
phosphate esters

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30
Q

What are two examples of hydrophobic substances?

A

nonpolar covalent compounds
fatty acids

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31
Q

Are ion-dipole and dipole-dipole interactions soluble with water?

A

yes

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32
Q

Are London dispersion forces soluble in water?

A

no - found in nonpolar attractions

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33
Q

Are ionic bonds soluble in water?

A

yes

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34
Q

Are van der Waals forces soluble in water?

A

no

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35
Q

Define a micelle

A

polar head groups are in contact with the aqueous environment and the nonpolar tails are sequestered from the water

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36
Q

What is the driving force of the formation of micelles and lipid bilayers

A

hydrophobic and hydrophillic interactions

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37
Q

What is a buffer solution?

A

a solution that tends to resist change in pH when small to moderate amounts of a strong acid or strong base are added

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38
Q

What does a buffer solution consist of?

A

mixture of a weak acid and its conjugate base

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39
Q

What are the three main buffer systems in the body?

A

carbonic acid bicarbonate buffer system
phosphate buffer system
protein buffer system

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40
Q

The stronger the acid, the __ the ionization, the __ the pKa, and the __ the pH the compound will produce in a solution

A

greater; lower; lower

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41
Q

What is pKa?

A

inherent property of a compound or functional group

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42
Q

What is the Henderson-Hasselbalch equation?

A

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

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43
Q

What is the difference in a titration curve between a polyprotic acid and a monoprotic acid?

A

polyprotic will have multiple peaks
mono = one

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44
Q

Define equivalence point in terms of pH and pKa

A

equivalence point is when pH and pKa are equal to each other in solution

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45
Q

___ determines ___

A

structure; function

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46
Q

pKa1 represents the __ group

A

a-carboxyl

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47
Q

pKa2 represents the __ group

A

amide

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48
Q

pKa3 represents the __ __ group

A

side chain

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49
Q

Define the isoelectric pH

A

pI - the pH at which a molecule has no net charge

50
Q

Define zwitterions

A

molecules that have both a positive and a negative charge

51
Q

Describes what happens to the amino acid if an acid is added

A

carboxylate group captures a H ion and aa becomes positively charged

52
Q

Describe what happens to the amino acid if a base is added

A

ion removal of the H+ ion from the amino group produces a negatively charged amino acid

53
Q

In addition of a base and an acid to the zwitteron of the amino acid, the amino acid acts to ___ the pH system

A

maintain

54
Q

What is special about Histidine?

A

side chain has a pKa of around 6.5 which is close to physiological pka
exists in both protonated and deprotonated forms
useful at active sites - stabilize or destabilize a substrate

55
Q

pH < pKa amino acid is

A

protonated

56
Q

pH > pKa amino acid is

A

deprotonated

57
Q

How do you calculate the pI of an amino acid?

A

pI = [pKa1 + pKa2] / 2

58
Q

How do amino acids connect to form a polypeptide

A

N terminus (amide group) connects to C terminus (carboxylic acid group)
Loss of H from N and OH from C to form water

59
Q

What is the primary structure of an amino acid?

A

order in which the amino acids are covalently linked together

60
Q

What is the secondary structure of an amino acid?

A

arrangement in space of the atoms in the peptide backbone
contains N and carbonyl groups bonding

61
Q

What are two types of secondary structure?

A

a-helix and b-pleated sheet arrangements

62
Q

What is included in the tertiary structure?

A

3D arrangement of all the atoms in the protein including side chains and prosthetic groups

63
Q

What is the quarternary structure of a protein?

A

interaction of several polypeptide chains in a multi-subunit protein

64
Q

What do phi angles show?

A

angles between C-N bond

65
Q

What do psi angles show?

A

angles between C-C bond

66
Q

Describe structural characteristics of the a-helix

A

stabilized by H bonds parallel to the helix axis within the backbone of a single polypeptide chain

Each amino acid residue is H bonded to the N-H group of the aa four residues away from it in the covalently bonded sequence (counting from N terminus to C)

67
Q

Why is the a-helix so stable?

A

helical conformation allows a linear arrangement of atoms in H bonds
max strength = max stability

68
Q

Describe the structural characteristics of the b-pleated sheet

A

extended peptide chain
forms interchain and intrachain bonds

69
Q

What is an intrachain bond?

A

single chain that is doubled back on itself

70
Q

What is an interchain bond?

A

bond between different chains

71
Q

When is a parallel v. antiparallel sheet formed?

A

parallel - peptide chains run in the same direction
anit-parallel - peptide chains run in opposite directions

72
Q

What are the two types of protein conformations?

A

fibrous
globular

73
Q

What is an example of a fibrous protein?

A

collagen

74
Q

What is an example of a globular protein?

A

myoglobin

75
Q

What is the difference between a fibrous and a globular protein?

A

globular - backbone folds back on itself to produce a more or less spherical shape

76
Q

Describe the structure of the collagen triple helix

A

organized in water-insoluble fibers
three polypeptide chains wrapped around each other in a triple helix
repeating sequence of X-Pro-Gly or X-Hyp-Gly

77
Q

What is the purpose of ionic bonding in protein stability?

A

helps maintain a particular folded area of a protein

78
Q

What is the purpose of H bonding in protein stability?

A

important in intra- and intermolecular interactions of proteins

79
Q

What is the purpose of Disulfide linkages in protein stability?

A

have a strong stabilizing effect on the tertiary structure

80
Q

What is the purpose of dispersion forces in protein stability?

A

makes up for missing bonds

81
Q

What is an advantage to NMR in contrast with X-Ray Crystallography

A

NMR - allows for protein samples in aq solutions - closer environment to proteins in cells rather than crystals

82
Q

Myoglobin

A

single polypeptide chain
globular protein
153 aa residues
prosthetic group - heme group - also in hemoglobin
eight helical a regions, no b
polar exterior, nonpolar interior
2 His groups interact w heme group, bound to O
job of both to bind to O
o curve is hyperbolic

83
Q

Hemoglobin

A

tetramer
four polypeptide chains
two a, two beta
a chain is 141 residues
b chain is 146 residues
both bind oxygen reversibly
exhibits positive cooperativity
o curve is sigmoidal

84
Q

What is the difference between dexoyhemoglobin and oxyhemoglobin?

A

deoxy - unbound form
oxy - bound form

85
Q

What is the purpose of betamercaptoethanol (BME) and urea?

A

BME - used to reduce disulfide bridges to two sulfhydryl groups
urea - facilitate unfolding of the protein and to increase the accessibility of the disulfides to the reducing agent

86
Q

What are two ways denaturation can be completed?

A

heat
extremes of pH

87
Q

How does heat denature a protein?

A

vibrations within the molecule strong enough to disrupt a tertiary structure

88
Q

How do extremes of pH denature a protein?

A

some of the charges are missing
electrostatic interactions are drastically reduced
originally stabilized the native active form of the protein

89
Q

Define allosteric

A

the property of multisubunit proteins such that a conformational change in one subunit induces a change in another subunit

90
Q

How does Bohr’s effect relate to oxygen binding to Hb?

A

an increase in the concentration of H+ (lowering of pH) reduces oxygen affinity

91
Q

Define positive cooperativity

A

binding of the first ligand to an enzyme/ protein increases the affinity for the next ligand

92
Q

The denaturation of ribonuclease can be complete denatured by the actions of ?

A

urea and b-mercaptoethanol

93
Q

What does it mean that hemoglobin is an allosteric enzyme?

A

binding of oxygen to one of the subunits is affected by its interactions with other subunits

94
Q

What reaction is catalyzed by carbonic anhydrase?

A

catalyses the hydration of the carbon dioxide to bicarbonate, which then dissociates to form H ions and bicarbonate

95
Q

What causes hemoglobin to enter the R state?

A

deoxyhemoglobin begins to bind to oxygen, structure relaxes, reaching R state
rotations of the two dimers w respect from another allows transition from T-state to R-State

96
Q

What is the T state?

A

deoxyhemoglobin

97
Q

What is the R state?

A

oxyhemoglobin

98
Q

What factor contributes to conformational changes in Hb, T-state to R-state?

A

oxygen binding
T state - no O affinity
R state - high O affinity

99
Q

What are the two models for the binding of a substrate to an enzyme?

A

lock-and-key model
induced fit model

100
Q

What is the Michaelis-Menten enzyme kinetic simple model?

A

E + S <—> ES —> E + P

101
Q

Describe the lock-and-key model

A

binding of a substrate to an enzyme such that the active site and the substrate exactly match each other in shape

102
Q

Describe the induced-fit model

A

substrate binding to an enzyme such that the conformation of the enzyme changes to accommodate the shape of the substrate

103
Q

The __ Km, the __ efficient the enzyme

A

lower; more

104
Q

The ___ kcat, the __ efficient the enzyme

A

higher; more

105
Q

What are the three assumptions of steady state kinetics?

A

v = k2 [ES]
d[ES] / dt = 0
[S]&raquo_space; [E]

106
Q

Define Km

A

Michaelis-Menten constant
measure of the enzyme’s affinity to its substrate

107
Q

Define kcat

A

turnover number
reflects the number of substrate molecules turned over per unit time

108
Q

Define Vmax

A

maximum rate of reaction when the enzyme is saturated with the substrate

109
Q

Define an ordered mechanism

A

enzyme mechanism where the substrates have to bind to the enzyme in a specific order

110
Q

Define a random mechanism

A

enzyme mechanism where the substrates can bind to the enzymes in any order

111
Q

Define a ping-pong mechanism

A

enzyme mechanism where a substrate binds to the enzyme and releases a product before the second substrate binds to the enzyme

112
Q

Define a ping-pong mechanism

A

enzyme mechanism where a substrate binds to the enzyme and releases a product before the second substrate binds to the enzyme

113
Q

Convert Michealis-Menten into Lineweaver-Burk plot

A

Km/ Vmax = slope

114
Q

Define chymotrypsin

A

proteolytic enzyme that preferentially hydrolyzes amide bonds adjacent to aromatic amino acid residues

115
Q

ATCase and hemoglobin are ___ proteins

A

allosteric

116
Q

Describe the velocity curves of chymotrypsin and aspartate concentration (ATCase)

A

ATCase - sigmoidal
chymotrypsin - hyperbolic

117
Q

Define competitive inhibition

A

decrease in enzymatic activity caused by binding of a substrate analogue to the active site

118
Q

Define noncompetitive inhibition

A

form of enzyme activation in which a substance binds to a place other than the active site but distorts the active site so that the reaction is inhibited

119
Q

Define uncompetitive inhibition

A

type of inhibition where the inhibitor can bind to HS but not fo free E

120
Q

Define an inhibitor

A

a substance that decreases the rate of an enzyme-catalyzed reaction

121
Q

Define an inactivator

A

also known as - irreversible inhibition
covalent binding of an inhibitor to an enzyme, causing permanent inactivation

Biochemistry (8 decks)

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