Exam One: Learning Objectives Flashcards
1
Q
What are the four major classes of biomolecules?
A
Amino Acids
Carbohydrates
Nucleotides
Lipids
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
3
Q
What is the general formula of carbohydrates?
A
(CH(sub2)O)sub n
where n is at least three
4
Q
What is the simplest form of a carbohydrate?
A
monosaccharides
5
Q
What is responsible for forming adenosine triphosphate? (ATP)
A
nucleotides
6
Q
Define nucleotides
A
basic unit of hereditary materials DNA and RNA
7
Q
What is the structure of a nucleotide
A
five-carbon sugar, a nitrogen-containing ring and one or more phosphate groups
8
Q
What is the common trait of all lipids?
A
poorly soluble in water
9
Q
What is the primary structure of a lipid?
A
a long chain of hydrocarbons
10
Q
Define protien
A
macromolecules formed by the polymerization of amino acids
11
Q
A __ of energy leads to a __ stable state
A
lowering; more
12
Q
Define exergonic
A
energy-releasing
13
Q
Define endergonic
A
energy-absorbing
14
Q
When delta G < 0 the reaction is
A
spontaneous
15
Q
When delta G = 0
A
the reaction is at equilibrum
16
Q
When delta G > 0, the reaction is
A
nonspontaneous
17
Q
What is the equation that relates gibbs free energy to temperature, enthalpy, and entropy
A
delta G = delta H - TdeltaS
18
Q
H stands for
A
enthalpy
19
Q
S stands for
A
entropy
20
Q
In any spontaneous process, the __ of the Universe increases
A
entropy
21
Q
When delta S > 0
A
the reaction is spontaneous
22
Q
If delta H is negative and -T delta S is positive, the reaction will be __ at __ temperatures
A
spontaneous; low
23
Q
If delta H is positive, and -TdeltaS is negative, the reaction will be __ at __ temperatures
A
spontaneous; high
24
Q
__ groups release H+ into solution
A
acidic
25
___ groups remove H+ from solution
basic
26
Nonpolar molecules are __
hydrophobic
27
___ in particular tend to sequester themselves from an aqueous environment
hydrocarbons
28
Polar molecules are ___
hydrophillic
29
What are five examples of hydrophilic substances?
polar covalent compounds
sugars
ionic compounds
amino acids
phosphate esters
30
What are two examples of hydrophobic substances?
nonpolar covalent compounds
fatty acids
31
Are ion-dipole and dipole-dipole interactions soluble with water?
yes
32
Are London dispersion forces soluble in water?
no - found in nonpolar attractions
33
Are ionic bonds soluble in water?
yes
34
Are van der Waals forces soluble in water?
no
35
Define a micelle
polar head groups are in contact with the aqueous environment and the nonpolar tails are sequestered from the water
36
What is the driving force of the formation of micelles and lipid bilayers
hydrophobic and hydrophillic interactions
37
What is a buffer solution?
a solution that tends to resist change in pH when small to moderate amounts of a strong acid or strong base are added
38
What does a buffer solution consist of?
mixture of a weak acid and its conjugate base
39
What are the three main buffer systems in the body?
carbonic acid bicarbonate buffer system
phosphate buffer system
protein buffer system
40
The stronger the acid, the __ the ionization, the __ the pKa, and the __ the pH the compound will produce in a solution
greater; lower; lower
41
What is pKa?
inherent property of a compound or functional group
42
What is the Henderson-Hasselbalch equation?
pH = pKa + log [A-]/[HA]
43
What is the difference in a titration curve between a polyprotic acid and a monoprotic acid?
polyprotic will have multiple peaks
mono = one
44
Define equivalence point in terms of pH and pKa
equivalence point is when pH and pKa are equal to each other in solution
45
___ determines ___
structure; function
46
pKa1 represents the __ group
a-carboxyl
47
pKa2 represents the __ group
amide
48
pKa3 represents the __ __ group
side chain
49
Define the isoelectric pH
pI - the pH at which a molecule has no net charge
50
Define zwitterions
molecules that have both a positive and a negative charge
51
Describes what happens to the amino acid if an acid is added
carboxylate group captures a H ion and aa becomes positively charged
52
Describe what happens to the amino acid if a base is added
ion removal of the H+ ion from the amino group produces a negatively charged amino acid
53
In addition of a base and an acid to the zwitteron of the amino acid, the amino acid acts to ___ the pH system
maintain
54
What is special about Histidine?
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
pH < pKa amino acid is
protonated
56
pH > pKa amino acid is
deprotonated
57
How do you calculate the pI of an amino acid?
pI = [pKa1 + pKa2] / 2
58
How do amino acids connect to form a polypeptide
N terminus (amide group) connects to C terminus (carboxylic acid group)
Loss of H from N and OH from C to form water
59
What is the primary structure of an amino acid?
order in which the amino acids are covalently linked together
60
What is the secondary structure of an amino acid?
arrangement in space of the atoms in the peptide backbone
contains N and carbonyl groups bonding
61
What are two types of secondary structure?
a-helix and b-pleated sheet arrangements
62
What is included in the tertiary structure?
3D arrangement of all the atoms in the protein including side chains and prosthetic groups
63
What is the quarternary structure of a protein?
interaction of several polypeptide chains in a multi-subunit protein
64
What do phi angles show?
angles between C-N bond
65
What do psi angles show?
angles between C-C bond
66
Describe structural characteristics of the a-helix
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
Why is the a-helix so stable?
helical conformation allows a linear arrangement of atoms in H bonds
max strength = max stability
68
Describe the structural characteristics of the b-pleated sheet
extended peptide chain
forms interchain and intrachain bonds
69
What is an intrachain bond?
single chain that is doubled back on itself
70
What is an interchain bond?
bond between different chains
71
When is a parallel v. antiparallel sheet formed?
parallel - peptide chains run in the same direction
anit-parallel - peptide chains run in opposite directions
72
What are the two types of protein conformations?
fibrous
globular
73
What is an example of a fibrous protein?
collagen
74
What is an example of a globular protein?
myoglobin
75
What is the difference between a fibrous and a globular protein?
globular - backbone folds back on itself to produce a more or less spherical shape
76
Describe the structure of the collagen triple helix
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
What is the purpose of ionic bonding in protein stability?
helps maintain a particular folded area of a protein
78
What is the purpose of H bonding in protein stability?
important in intra- and intermolecular interactions of proteins
79
What is the purpose of Disulfide linkages in protein stability?
have a strong stabilizing effect on the tertiary structure
80
What is the purpose of dispersion forces in protein stability?
makes up for missing bonds
81
What is an advantage to NMR in contrast with X-Ray Crystallography
NMR - allows for protein samples in aq solutions - closer environment to proteins in cells rather than crystals
82
Myoglobin
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
Hemoglobin
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
What is the difference between dexoyhemoglobin and oxyhemoglobin?
deoxy - unbound form
oxy - bound form
85
What is the purpose of betamercaptoethanol (BME) and urea?
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
What are two ways denaturation can be completed?
heat
extremes of pH
87
How does heat denature a protein?
vibrations within the molecule strong enough to disrupt a tertiary structure
88
How do extremes of pH denature a protein?
some of the charges are missing
electrostatic interactions are drastically reduced
originally stabilized the native active form of the protein
89
Define allosteric
the property of multisubunit proteins such that a conformational change in one subunit induces a change in another subunit
90
How does Bohr's effect relate to oxygen binding to Hb?
an increase in the concentration of H+ (lowering of pH) reduces oxygen affinity
91
Define positive cooperativity
binding of the first ligand to an enzyme/ protein increases the affinity for the next ligand
92
The denaturation of ribonuclease can be complete denatured by the actions of ?
urea and b-mercaptoethanol
93
What does it mean that hemoglobin is an allosteric enzyme?
binding of oxygen to one of the subunits is affected by its interactions with other subunits
94
What reaction is catalyzed by carbonic anhydrase?
catalyses the hydration of the carbon dioxide to bicarbonate, which then dissociates to form H ions and bicarbonate
95
What causes hemoglobin to enter the R state?
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
What is the T state?
deoxyhemoglobin
97
What is the R state?
oxyhemoglobin
98
What factor contributes to conformational changes in Hb, T-state to R-state?
oxygen binding
T state - no O affinity
R state - high O affinity
99
What are the two models for the binding of a substrate to an enzyme?
lock-and-key model
induced fit model
100
What is the Michaelis-Menten enzyme kinetic simple model?
E + S <---> ES ---> E + P
101
Describe the lock-and-key model
binding of a substrate to an enzyme such that the active site and the substrate exactly match each other in shape
102
Describe the induced-fit model
substrate binding to an enzyme such that the conformation of the enzyme changes to accommodate the shape of the substrate
103
The __ Km, the __ efficient the enzyme
lower; more
104
The ___ kcat, the __ efficient the enzyme
higher; more
105
What are the three assumptions of steady state kinetics?
v = k2 [ES]
d[ES] / dt = 0
[S] >> [E]
106
Define Km
Michaelis-Menten constant
measure of the enzyme's affinity to its substrate
107
Define kcat
turnover number
reflects the number of substrate molecules turned over per unit time
108
Define Vmax
maximum rate of reaction when the enzyme is saturated with the substrate
109
Define an ordered mechanism
enzyme mechanism where the substrates have to bind to the enzyme in a specific order
110
Define a random mechanism
enzyme mechanism where the substrates can bind to the enzymes in any order
111
Define a ping-pong mechanism
enzyme mechanism where a substrate binds to the enzyme and releases a product before the second substrate binds to the enzyme
112
Define a ping-pong mechanism
enzyme mechanism where a substrate binds to the enzyme and releases a product before the second substrate binds to the enzyme
113
Convert Michealis-Menten into Lineweaver-Burk plot
Km/ Vmax = slope
114
Define chymotrypsin
proteolytic enzyme that preferentially hydrolyzes amide bonds adjacent to aromatic amino acid residues
115
ATCase and hemoglobin are ___ proteins
allosteric
116
Describe the velocity curves of chymotrypsin and aspartate concentration (ATCase)
ATCase - sigmoidal
chymotrypsin - hyperbolic
117
Define competitive inhibition
decrease in enzymatic activity caused by binding of a substrate analogue to the active site
118
Define noncompetitive inhibition
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
Define uncompetitive inhibition
type of inhibition where the inhibitor can bind to HS but not fo free E
120
Define an inhibitor
a substance that decreases the rate of an enzyme-catalyzed reaction
121
Define an inactivator
also known as - irreversible inhibition
covalent binding of an inhibitor to an enzyme, causing permanent inactivation
