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Flashcards in exam 1 Deck (322):
1

which of the ff amino acids have sulfur in their side chains?
a. methionine
b. alanine
c. threonine
d. aspargine

A

2

___________ is the enzyme that forms peptide bonds between two amino acids during translation

peptidyl transferanse

3

which of the ff amino acid has the smallest side chains?
a. tryptophan
b. alanine
c. glycine
d. methionine

C

4

which of the ff amino acid has a methyl group side chain?
a. tryptophan
b. alanine
c. glycine
d. methionine

B

5

which of the ff amino acid has an indole ring side chain?
a. tryptophan
b. tyrosine
c. histidine
d. methionine

A

6

which of the ff amino acid has a phenol in its side chain?
a. tryptophan
b. tyrosine
c. histidine
d. methionine

B

7

which of the ff amino acid has an imine, aliphatic structure?
a. tryptophan
b. proline
c. glycine
d. methionine

B

8

which of the ff is not an acidic amino acid?
a. arginine
b. glutamate
c. lysine
d. aspartate

A and C

are both basic

9

which of the ff is not an aromatic amino acid?
a. tyrosine
b. phenylalanine
c. tryptophan
d. proline

D

10

which of the ff does not apply to conformational/ protein folding diseases?
a. proteins do not do not function or assemble properly
b. may exhibit defects in cellular trafficking
c. may be from an aa sequence change
d. defects in chaperones

none of the above! :)

11

(T/F) Proteins constitute most of a cell’s dry mass

true

12

which of the ff is not a basic amino acid?
a. arginine
b. histidine
c. lysine
d. aspartate

D

13

which of the ff is not a polar amino acid?
a. threonine
b. tyrosine
c. aspartic acid?
d. tyrosine

C

- a charged aa

14

________ is an effect in which the shape of a molecule influences its
reactions

steric / spatial effect

15

(T/F) the peptide bond allows for free rotation of amino acids in a protein backbone

false!

it is planar an does not permit free rotation

16

(T/F) in the protein backbone, rotation occurs freely around the Cα-C
(psi angle of rotation)
and N-Cα bonds

true

17

which of the ff amino acid has an aromatic benzene-like ring side chain?
a. tryptophan
b. phenylalanine
c. glycine
d. alanine

B

18

the _________ between the carbonyl carbon atom and nitrogen atom of
the peptide bond contributes to its rigidity

partial double-bond character
due to resonance

19

which of the ff amino acids have sulfur in their side chains?
a. glutamine
b. histidine
c. alanine
d. cysteine

D

20

_____ this end of the protein sequence corresponds to the 5' end of the mRNA

N-terminal

21

which of the ff amino acid has a methyl group side chain?
a. tryptophan
b. alanine
c. glycine
d. methionine

C

22

(T/F) the α-carboxyl / t-terminal ? end is considered the beginning of the polypeptide chain

false

N-terminal (amino group) is the beginning

23

_______ is composed of repeating atoms along the core of the polypeptide chain

polypeptide backbone

24

_____ are examples of proteins that have coiled-coil apha helices

skin keratin, myosin

25

which of the ff bonds does not contribute to protein folding?
a. covalent
b. hydrogen
c. ionic
d. van der waals

A

26

(T/F) the alpha-carboxyl
group of one amino acid is joined to the alpha amino
group of another amino acid by an amide bond

true

amide bond = peptide bond

27

_____ is the bond in which an H+ atom is shared between two
electronegative atoms

hydrogen bonds

28

_____ is the complete 3dimensional structure of multisubunit protein complexes/ proteins composed of more than one polypeptide chain

quaternary

29

______ is the bond in which oppositely charged atoms interact with one another

ionic bonds

29

_______ is the bond where short
distance interactions between the fluctuating
electrical charges of the electron clouds around two atoms, very weak interaction

van der Waals attractions

30

______ another weak force aside from the 3 bonds that determine protein folding

Hydrophobic interactions

31

(T/F) minimal disruption of hydrogen
bonding between water molecules is due to the forcing of the Hydrophobic nonpolar sidechains together (of an amino acid) in aqueous environment

true

34

____ forms stronger bonds that causes proteins to unravel / denature

chaotropic agents

35

(T/F) polar side chains of amino acids tend to gather on the outside of the protein where they
can interact with water while Nonpolar aa side chains are buried on the inside to form a tightly packed
hydrophobic core hidden from water

true

36

_____ are the covalent links between the sulfur atoms in the side chains of cysteines

disulfide bonds

36

____ are disulfide bonds that join two parts of the same polypeptide

IntrAchain disulfide bonds

39

(T/F) high concentrations of
reducing agents in the endoplasmic reticulum convert the SS bond back to SH groups therefore disrupting the formation of disulfide bonds

false

high conc in the cytosol

40

(T/F) disulfide bond formation catalyzed in the endoplasmic reticulum

true

41

____ is an example of a reducing agent that disrupts disulfide bonds in the cytosol

glutathione

42

(T/F) hydrogen bonds offer major stabilizing effect on protein structure

false

disulfide bonds stabilizes

43

____ and ____ are examples of secondary protein structure

α-helix and β-pleated
sheets

44

_____ first to sequence the protein sequence of bovine insulin

Frederick Sanger

45

______ are first to describe the α-helix and β-pleated sheet structures in early 1950’s

L. Pauling and R.B. Corey

46

_______ consist of regular, repeating conformations that result from H bonding of amino and carbonyl groups in the polypeptide backbone?

α-helix and β-pleated sheet

47

(T/F) α-helix and β-pleated sheet do not involve bonding between the side chains of the aa’s

true

48

(T/F) the hydrophilic polypeptide backbone of Cell membrane proteins is ydrogen bonded to itself and shielded from the hydrophobic lipids by the nonpolar side chains

true

49

_____ is a very stable structure that results from αhelices
may wrapping around each other

coiled-coil

50

(T/F) coiled-coils Forms when two or three αhelices
have most of their nonpolar side chains
on one side so they can wrap around each other with these side chains facing inward

true

51

which of the ff factors does not contribute to the destabilization of alpha helices?
a. Electrostatic repulsion between similarly charged R groups
b. Steric hindrance due to bulky substitutions on the βcarbons
of R groups
c. presence of reducing agents in the cell
d. presence of proline in the protein structure

C

this disrupts disulfide bonds

52

(T/F) CO block binding of O 2 to myoglobin and more importantly to hemoglobin

true

53

(T/F) Rotation around the bond between the nitrogen of proline and the αcarbon
is severely restricted however, Proline’s α−amino group is still able to participate in H bonding

first statement is true, second one if false!

54

(T/F) β sheet and α helix Both involve Hbonding
between the carbonyl and amino groups
of peptide bonds to form a regular repeating protein conformation

true

55

(T/F) aggregates from protein misfolding are not resistant to proteolysis

false

aggregates are resistant to proteolysis!

56

which of the ff is not a non polar amino acid?
a. phenylalanine
b. aspartic acid
c. tryptophan
d. valine
e. leucine

C

a - hydrophobic, aromatic
b - acidic, charged
c - polar, aromatic
d - phobic, imine
e - phobic

58

(T/F) in beta sheets, H bonds are parallel to the direction of the protein chains like in alpha helix

false

beta sheets = H bonds are perpendicular to protein chain,
alpha chains = H bonds are parallel to protein chain

59

____ a type of beta sheet where H-bonded peptide chains run in opposite directions

antiparallel pleated sheets

(Nterminal and Cterminal ends of the chains are in opposite orientation)

60

which two aa are typically found in "reverse turns" regions?
a. glycine and leucine
b. proline and leucine
c. glycine and proline
d. glycine and alanine

C

glycine = small R group, no crowding

proline = cyclic structure facilitates turn

61

(T/F) the formation of a peptide bond includes gaining an oxygen molecule

false

- loss of a water molecule

61

______ protein structure level where amino acids are covalently linked to form a sequence

primary level

62

(T/F) the heme group is held in place by hydrophobic interactions between the heme and nonpolar R
groups of the protein

true

63

____ a specific region of a protein that can fold
independently of the rest of the protein into a discrete stable structure and which has its own function

Domain (or module)

64

_____ creation of new gene proteinsbelieved
to have originated when the DNA sequences
encoding each domain accidentally became joined

domain shuffling

65

which of the ff is not true regarding a Domain?
a. Larger proteins may contain several dozen domains usually connected by
relatively short unstructured lengths of polypeptide chain
b. Are the modular units from which many larger proteins are constructed
c. Usually between 40-350 aa’s long
d. Small proteins may contain a single domain

none of the above :)

68

____ and ___ are some examples of fibrous tertiary structure

collagen, α-keratin

69

_______ are example of proteins that contain domain shuffling

EFG (epidermal growth factor) chymotrypsin

70

which of the ff is not a charged aa?
a. arginine
b. lysine
c. aspartic acid
d. glutamic acid

none of the above

71

____ are Regions of polypeptide chains that lack discernable repeating pattern such as
the αhelix
or βsheet

Random coil

72

which of the ff is false about random coil?
a. its structure is determined by the aa sequence
b. it represents the most stable conformation of a particular aa sequence
c. Regions of polypeptide chains that lack discernable repeating pattern
d. an example of a denatured or unfolded protein

D

73

which of the ff factors can form
hydrogen bonds with the protein that
are stronger than those within the protein resulting in denaturation?
a. heat
b.high or low pH
c. detergents
d. Urea and guanidine hydrochloride

D

74

___ the most abundant protein in mammals, Secreted by connective tissue cells, a major component of skin and bone

collagen

75

_______ is a steric
relationship of amino acids that are far apart in the
linear sequence

tertiary polypeptide structure

76

(T/F) The hydroxyl groups of hydroxyproline residues form intRAchain H bonds
and H bonds with water molecules that stabilize the triple helix of collagens

false

residues form intERchain H bonds

77

(T/F) tertiary and secondary structures may be indistinguishable from each other

true

79

______ a type of tertiary polypeptide structure that is elongated, and plays a role in the cell that require the molecules to span long distances in the cell

fibrous tertiary structure

80

___ are deposits of protein aggregates occur in and around cells

amyloid

81

____ a water soluble tertiary structure where polypeptides foldsinto a complex compact shape like a ball (spherical) with an irregular surface

globular tertiary structure

82

which of the ff is a hydrophobic aa?
a. isoleucine
b. proline
c. glycine
d. alanine

all of the above!

83

____ and ___ are some examples of globular tertiary structures

most enzymes, hemoglobin

86

_____ is a polypeptide chain in a quaternary structure that may be identical or different, a dimer, trimer, tetramer etc

a subunit

87

______ and _____ are special proteins that assists protein folding in living cells

molecular chaperones and chaperonins (a subset)

88

which of the ff is NOT true about quaternary structures?
a. Subunits are held together by noncovalent forces
b. Multisubunit proteins may exhibit allosteric properties
c. subunits are usually an oligomer
d. Subtle structural changes in one part of the protein cause significant changes
in the structure/function of another part

C

may be dimer, trimer, tetramer, oligomer

89

____ are disulfide bonds that join two different polypeptide

IntErchain disulfide bonds

89

_______ protein structure level where there is a full 3- dimensional organization of a polypeptide chain

tertiary

90

(T/F) Myoglobin structure has no disulfide bonds

true

91

which of the ff does not induce denaturation of proteins?
a. heat
b.high or low pH
c. detergents
d. Urea and guanidine hydrochloride

none of the above

92

which of the ff factors causes disruption of tertiary structures causing protein denaturation?
a. heat
b.high or low pH
c. detergents
d. Urea and guanidine hydrochloride

a

93

which of the ff factors causes alter charges on aa’s and disrupt electrostatic interactions
within the protein resulting in denaturation?
a. heat
b.high or low pH
c. detergents
d. Urea and guanidine hydrochloride

B

94

which of the ff factors can
disrupt electrostatic or hydrophobic
interactions resulting in denaturation?
a. heat
b.high or low pH
c. detergents
d. Urea and guanidine hydrochloride

C

95

(T/F) urea causes formation of weaker H bonds than what exists in the protein causing its denaturation

false

urea causes stronger H bonds

96

(T/F) Denaturation is facilitated by the presence of reducing agents that Reduce disulfide bonds

true

97

which of the ff is not true about molecular chaperones?
a. Prevent the temporarily exposed hydrophobic regions of newly
synthesized proteins from forming aggregates
b. binding of molecular chaperones to partially folded proteins require ATP
c. chaperones make folding process more reliable
d. chaperones lead to exposure of hydrophobic regions in proteins

D

98

_____is an example of a major class of molecular chaperones that responds to heat shock or
other stresses

heatshock
proteins (hsp)

99

which of the ff is not involved in facilitation of protein folding in Cells
a. Organic compounds (vitamins, a cofactor)
b. metal ions (Mg2+)
c. ionic environment
d. guanidine hydrochloride
e. Protein disulfide isomerase

D

this is a denaturant!

100

____ are regions
of secondary structure (of protein) where the chains change direction or fold back

reverse turns

101

___ and ___ are examples of reducing agents that causes denaturation

β-mercaptoethanol, DTT (Dithiothreitol)

101

(T/F) protein denaturants accessibility of reducing agents to
internal disulfide bonds

true

101

____ an example of an ampotheric protein denaturant

SDS - sodium diodyl sulfate

101

(T/F) The iron atom (in the heme group) is in the ferrous (+1) oxidation state

FALSE!

+2 ox state

102

which of the ff is not a potential consequences of protein denaturation?
a. Decreased protein solubility
b. refolding of the protein
c. susceptibility to hydrolysis by proteolytic enzymes
d. loss of biological activity
e. aggregation and precipitation

B

103

(T/F) polar amino acids or polar aa + polypeptide backbone are joined by hydrogen bonding

true

106

____ is an enzyme that catalyzes the correct formation of disulfide
linkages in protein folding in cells

Protein disulfide isomerase

107

______ a type of beta sheet where H bonded peptide chains run in the same direction

parallel pleated sheets

(H bonded peptide chains run in the same direction)

108

which of the ff is NOT true about crystallins in the lens (eye)?
a. thought to function both as structural proteins and
chaperone proteins
b. gene mutation for αcrystallin prevents formation of cataracts
c. Alterations in α−crystallin oligomeric structure : Leads to coaggregation of
αcrystallin
and its substrates
d. mutations in αcrystallin reduces chaperone function

B

mutations can lead to cataract formation

109

________ is a disease that results from vitamin C deficiency leading to an inability to produce
hydroxyproline , a modified aa required for conformational stability of collagen

scurvy

110

which of the ff is NOT true about the alpha helix?
a. Consists of a double polypeptide chain that twists around on itself to form a
rigid cylinder
b. H bonds occur between every fourth peptide bond
c. Link carbonyl group (C=O) of one peptide bond to NH
of another
d. Results in a regular helix with a complete turn every 3.6 amino acids
e. H bonds run parallel to orientation of α−helix

A

Consists of a SINGLE polypeptide chain

110

(T/F) immunoglobulin domain developed more recently in evolution
than the others

True

111

(T/F) Protein aggregates often consist of polypeptides rich in βsheet that typically results from transformation of βsheet structure to αhelicalstructure in misfolded protein

false

αhelical changes to βsheet

112

_____ is the accumulation
of amyloid deposits (various types of fibrillar
proteins) in amounts sufficient to impair normal function

amyloidosis

113

_____ is a small glycoprotein normally found on the outer surface of the plasma membrane are the causative agents of a number of neurodegenerative diseases

Prion proteins (PrP)

114

_____ give an example of a neurodegenerative diseases caused by PrP

- Scrapie in sheep
– CreutzfeldtJakob
disease (CJD) in humans
– Bovine spongiform encephalopathy in cattle (mad cow disease)
– Fatal familial insomnia

115

_____ the misfolded, aggregated form of PrP that causes diseases

PrP Sc (scrapie isoform)

116

____ the person who first determined tertiary structure of myoglobin from a sperm whale Xray crystallography

John Kendrew (late 1950’s), first to be determined

117

which of the ff is true about prions diseases?
a. Normal PrP C is rich in αhelix
b. PrP Sc appears to induce the transformation of PrP C that it contacts into more PrP Sc (propagation)
c. Normal PrP C is rich in βsheet
d. PrP Sc is protease resistant

c

Abnormal PrP Sc is rich in βsheet, forms aggregates, and is protease resistant

118

______ won the 1997 Nobel Prize in Physiology or Medicine for his discovery of "prions

Stanley Prusiner

119

(T/F) the α chain of collagen molecules are similar in structure from an α helix

false

α chain - 3.3 aa/ turn
α helix - 3.6 aa/turn

120

which of the ff is not true for prions?
a. misfolding occurs with accumulation of PrP Sc
b. Can be transmitted by eating the tissues of animals that contain PrP Sc
c. amyloid like deposits can form from Accumulation of PrP Sc
d. PrP sc is rich in βsheet

A

121

(T/F) Proline stabilizes the helical conformation of individual α chains through steric repulsion of its pyrrolidone rings on the outside of the chains (collagen)

true

122

(T/F) cataract formation resulting from mutations in αcrystallin gene maybe due to reduction in chaperone function or Alterations in αcrystallin oligomeric structure

true

123

____ and ___ are the
enzymes that hydroxylate proline and lysine , respectively

Peptidyl proline hydroxylase and peptidyl lysine hydroxylase

(by adding OH groups)

124

which of the ff does not apply to the composition of collagen molecules?
a. a third of aa is glycine
b. rich in valine
c. contains hydroxyproline and hydroxylysine
d. rich in proline

B

125

____ is a requirement for Formation of Hydroxyproline and Hydroxylysine

vitamin c

126

(T/F) In absence of myoglobin protein , Fe of heme group can be oxidized to Fe (III)

true

- so protein + heme is impt in O2 storage

127

(T/F) Glycine allows the three helical α chains to pack tightly together (collagen)

true

128

_____ is a protein misfolding disease caused by mutation in gene that encodes fibrillin protein and is associated with disruption and weakening of connective
tissues throughout the body

Marfan syndrome

129

_____ a PrP Sc disease caused by several different mutations in prion protein gene and affects the cortex

Creutzfeldt-Jakob
disease

129

______ a disease are caused in large part, by the aggregation of
partially unfolded lens proteins; a common cause of blindness

cataracts

129

_____ is made up of 3 3 polypeptide chains hat wrap around one another to form a ropelike superhelix or triple helix that makes up collagen molecules

α chains

129

(T/F) Ascorbic acid is a reducing agent that maintains the enzymes in an active form , presumably by keeping their iron atoms in the reduced ferrous state

true

130

___ and ___ are two evolved two major mechanisms by vertebrates for delivering oxygen to
their cells

1- development of circulatory sytem
2 - Acquisition of oxygencarrying
proteins (myoglobin and hemoglobin)

131

_____ an oxygen carrying protein found in muscle that Serves as a reserve supply of oxygen and facilitates the movement of oxygen
within muscle

myoglobin

132

___ and oxygen carrying protein that transport of CO 2 and hydrogen ions in blood

hemoglobin

133

(T/F) In scurvy, the α chains are hydroxylated, fail to form triple helix and are
degraded immediately

false

α chains are NOT hydroxylated,

134

______ the process which is the major source of ATP in aerobic organisms

oxidative phosphorylation

137

____ the person who first determined the tertiary structure of hemoglobin from horse

Max Perutz (late 1950’s)

138

_____ nonprotein
components that are tightly bound to many
proteins and contribute to their biological activities

Prosthetic groups

139

_____ is a protein without its prosthetic group

apoprotein

140

(T/F) Ability of myoglobin and hemoglobin to bind oxygen depends on presence of heme apoproteins

false!

binding depends on presence of a heme prosthetic group

141

(T/F) Heme consists ofa porphyrin ring and an iron atom

true

142

which of the ff is false regarding the structure of a heme group?
a. The porphyrin isomer is called protoporphyrin lX
b. Iron atom in heme can form 4 bonds
c. Addition of iron to protoporphyrin lX produces the heme group
d. the pyrrole ring are linked by bridging groups by forming a tetrapyrole ring

B

can form 6 bonds

143

*(T/F) Ferric iron (+3 oxidation state) cannot bind oxygen

true

144

which of the ff is false about the structure of myoglobin?
a. 75% of the protein consists of eight α helical segments referred to as
regions A-H
b. its internal portion is made up of nonpolar aa's
c. The polar histidines interact with the heme group and oxygen
d. The exterior of myoglobin contains only polar aa’s

D

The exterior of myoglobin contains both polar AND nonpolar aa’s

145

(T/F) the absence of heme group in myoglobin does not affect the protein conformation

false

In the absence of the heme group (apoprotein) the protein is not as tightly
folded

146

_____ this functions as a gate that regulates entry of O2 into the hydrophobic
pocket to bind heme in myoglobin

His E7

147

____ are repeated combinations of supersecondary structure within a protein with usually short repetitive units

motifs

148

*(T/F) Presence of His E7 forces binding of CO and O 2 at an angle which prevents traces of CO produced through metabolism from occupying
all of the O 2 binding
sites on the hemes

true

149

(T/F) which of the ff is false about CO / O2 binding of heme?
a. 1% of sites in
myoglobin and hemoglobin are blocked by CO produced by body
b. Bent bond weakens interactions of CO with heme and favors O 2 binding
c. Levels of CO bound to heme would be toxic if not for hemeassociated
proteins
that sterically impose a bend in the CO bond
d. all is true

D - all is true!

150

which of the ff is false re oxygen binding in myoglobin?
a. O 2 binding angle is critical for myoglobin function
b. His E7 sterically hinders O2 from binding perpendicularly to the plane of the heme
c. O2 has greater affinity for free heme than CO
d. when free heme is present CO forms a perpendicular bond with
Fe of heme

C

CO = 25k times greater

151

(T/F) the internal structure of myoglobin molecule is completely made up of nonpolar aa's

false

it also contains 2 polar histidine residues

152

(T/F) Fe (III) binds O 2

false

Fe (III) does not bind O 2

153

(T/F ) Oxidative phosphorylation is the major source of ATP in anaerobic organisms

false!

this is impt w/ AEROBIC organisms

154

(T/F) myoglobin consists of four polypeptide chains

false

Mb - one polypeptide chain
Hb - four polypeptide chains

155

(T/F) Hb's α and β chains are similar in length, aa sequence and tertiary
structure to Mb but not all aa between them are the same

true

156

which of the ff is false regarding Hb vs Mb?
a. Mb and Hb are homologs
and myoglobin
b. Hb and Mb have the same heme group
c. their α chain and β chain are derived from a common ancestor
d. both consists of four polypeptide chains

D

Mb - one polypeptide chain
Hb - four polypeptide chains

157

_____ are genes derived from a common ancestor gene,

homologs

158

(T/F) orthologs are same proteins in different species

true

159

(T/F) paralogs are genes that are derived from a single gene that have diverged over time in the same species

paralogs

160

______ the compounds that regulate binding of O 2 by Hb

2, 3 - bisphosphoglycerate
(BPG), H + and CO

161

which of the ff is false regarding functions of Hb vs Mb?
a. both exhibit positive cooperativity (enhances binding if O2)
b. is an allosteric protein whereas Mb is not
c. Hb - binds 4 O2 molevules
d. Mb binds 1 O2 molecule

A

Mb does not exhibit cooperativity

162

____ is a protein that changes from one conformation to another when it binds another molecule or is covalently modified..

Allosteric Protein

163

(T/F) Binding of O 2 to Hb enhances binding/unloading of additional O 2 to all Hb
molecule (positive cooperativity)

false

binding/unloading in the SAME Hb (tetramer) molecule only

164

(T/F) Affinity of Hb for O 2 depends on pH and its binding of CO2 while binding of O 2 to Mb is independent of pH and CO2

true

165

(T/F) O 2 affinity for Hb is further regulated by BPG so because of this property, Hb has higher affinity for O 2 than does Mb

false

BPG regulation results in LOWER Hb affinity to O2

166

(T/F) the S shaped curve of O2 dissiociation for Hb reflects the fact that it exhibits positive cooperativity

true

167

(T/F) the hyperbolic shaped curve of O2 dissociation curve of Mb exhibits a steady increase in O 2 sat.

true

168

(T/F) at 26 torrs, Mb is saturated at 50%

false

Mb is saturated 50% at 1 torr (high affinity at very low pO2)

169

(T/F) Hb is fully saturated with O 2 in the lungs (100 torrs) but releases more than half of its bound O 2 in the capillaries of active muscles and tissues where the pO 2 is20 torrs and the O 2 is really needed

true

170

(T/F) in the quaternary structures of Oxy Hb, two β chains are closer together Fe atom moves into the plane of the porphoryin ring while in deoxy Hb, Fe atom is out of the plane of the heme due to steric repulsion

true

171

which of the ff is not a factor that affects Hb Quaternary Structure and O2 Affinity
a. pH (H + concentration)
b. O2 concentration
c. CO2 concentration
d. Binding of 2,3Bisphosphoglycerate
(BPG) to Hb

B

172

(T/F) Mb exhibits no change in O 2 binding or conformation over a large
range of pH or CO 2 concentration and does not bind BPG

true

173

(T/F) a "shift to the right" in the Hb dissociation curve occurs when pH is low indicating a decrease in O2 affinity

true

174

_______ the interplay between H + , CO 2 , and O2 for meeting the metabolic needs of tissue

Bohr effect

-discovered by Christian Bohr, 1904

175

_____ the form of Hb where the salt bridges in the globin chain creates a tauter (more constrained molecule)

T (tense) form, a deoxy Hb

R form = oxy Hb

176

______ noncovalent
electrostatic interactions between oppositely charged aa side chains in Hb that is affected by pH and are disrupted by oxygenation

salt bridges

177

(T/F) The number of salt links that need to be broken for binding of an O 2 molecule
depends on whether it is the first, second, third, or fourth to be bound

true

178

(T/F) More salt links must be broken to permit binding of last O 2 (requires more
energy) than previous O 2 molecules

false

the binding of FIRST O2 costs more energy

179

(T/F) at low pH (metabolically active sites) the conformation of deoxy Hb is favored, releasing O2

true

180

(T/F) in Hb, the protonation of His 146 of the β chain forms a salt bridge with Asp94 of the
same chain

true

181

(T/F) in Hb, the formation of carbamate stabilizes the T form of the molecule and releases O2

true

182

which of the ff does not promote the release of O2 into metabolically active sites?
a. protonation of His 146
b. formation of carbamate
c. high pH
d. high CO2 concentration

C

low pH dapat! (acidic)

183

(T/F) The O 2 affinity of Hb within RBC’s is lower than that of Hb in free solution

true

184

______ observed the difference in O2 affinity of Hb within RBC and in free soln

Joseph Barcroft

185

________ are the researchers that discovered 2,3bisphosphoglycerate
(BPG) as the substance that affects O2 affinity

Reinhold Benesch and Ruth Benesch

186

(T/F) BPG is an allosteric modulator of Hb and decreases its affinity for O2 and is present in more amounts than Hb in cells

False

BPG and Hb are equimolar/ same molar conc, everything else is true

187

*(T/F) in the absence of BPG, Hb would unload little O2 in passing
through tissue capillaries where the pO 2 is 26 torrs or less

true

188

*(T/F) BPG binds to oxyHb more that deoxyHB which reduces O2 affinity

false!

binds only to deoxyHb

189

which of the ff is false about fetal Hb?
a. has higher affinity for O2 at any given pO2
b. binds BPG less strongly
c. has alpha and βchains
d. forms fewer salt bridges

C

HbF has two γchains
as opposed to two βchains that form fewer salt bridges

190

which of the ff is NOT a basis of protein separation?
a. size
b. charge
c. solubility
d. use of antibodies/ immunological properties

none of these, all are basis for separation

191

(T/F) in protein separation Repeated centrifugation at progressively higher speeds will fractionate cell
homogenates into their components

true

192

(T/F) the size of cellular components can be separated using the same amount of centrifugal force

false

In general, the smaller the subcellular component, the greater is the
centrifugal force required to sediment it

193

which of the ff centrifugation speeds is a mismatch?
a. low - pellets mixed organelles
b. medium - pellets mixed organelles
c. high - microsomes
d. very high - micromolecules

a and d

low - pellets larger particles - nuclei, whole cells, supernatant has organelles

very high - pellets macromolecules

194

which of the ff is false?
a. homogenization is the first step in protein isolation
b. cetrifuhation separates based on size
c. gradient can separate large sediments in homogenates
d. sedimentation is based on size and shape

C

sedimenting thru gradient results in finer separation of components

195

____ involves layering a homogenate as a thin band according to their size and
shape

Velocity Sedimentation

196

_____ a sensitive technique that separates cellular components on the basis of their buoyant density ,
independently of their size and shape

Equilibrium Sedimentation

197

_____ fractioning proteins thru passing a mixture of proteins through a column containing a porous
solid matrix

Column Chromatography of Proteins

198

which of the ff is a mismatch?
a. Charge - ion exchange chromatography
b. Hydrophobicity - hydrophobic chromatography
c. Size - gelfiltration or
exclusion chromatography
d Ability to bind other molecules - affinity chromatography

none of the above

199

_____ protein separation technique that separates by size by passing them thru pores in the beads in the column

Gel Filtration
Chromatography

200

____ protein separation technique an insoluble matrix covalently linked to a specific ligand such as an antibody or enzyme substrate that will bind a specific protein

Affinity Chromatography

201

___ protein separation technique that uses multiple chromatographic techniques are used in series to purify a
protein

Protein Purification by Chromatography

202

____ protein separation technique used to determine size and subunit composition of proteins that uses a highly crosslinked gel of polyacrylamide

SDS Polyacrylamide Gel Electrophoresis

203

______ is a negatively charged (anionic) detergent used in combination of a reducing agent used to electrophorize protein in protein separation

sodium dodecyl sulfate (SDS)

204

(T/F) in an SDS gel, SDS binds to hydrophobic regions causing unfolding of proteins while Reducing agent, βmercaptoethanol,
breaks disulfide bonds

true

205

(T/F) in an SDS gel, larger proteins migrate faster and thus permit approximate
molecular weights to be determined in the presence of known protein standards

false

Smaller proteins migrate faster

206

____ a protein separation technique that uses an antibody to identify a specific protein fractionated on an SDS gel

Immunoblotting (Western Blotting)

207

_____ is a protein separation technique used to determine whether two or more proteins are capable of
forming molecular associations

CoImmunoprecipitation
Studies

208

_____ is the antibody that is tagged with a marker used in immunoblotting to bind to the primary antibody (high affinity to fc regin of IGs)

secondary ab or Protein A

209

_____ is a protein separation method that Separates proteins by their intrinsic charges, uses the idea that each protein has a characteristic isoelectric point

Isoelectric Focusing

210

______ the pH at which the protein has no net charge and therefore does not move in an electric field

isoelectric point

211

______ the protein technique Used to identify proteins by determining their precise masses and the
masses of peptides derived from them

Mass Spectrometry

212

(T/F) trypsin that is used to digest in mass spec targets random proteins

False

the protease trypsin is very specific

213

____ is the most common type of mass spectrometry

matrix-assisted laser
desorption ionization-time-off-light (MALDI-TOF)

214

(T/F) in MALDI-TOF protein technique, peptides that are larger reaches the detector slower than smaller ones

true

215

_____ is one of the fastest enzymes and catalyzes the formation of carbonic acid

Carbonic anhydrase

216

Which of the ff is not true about enzymes?
a. they increase reactivity while maintaining control at normal temp
b. w/o enzymes, reactions occur at much higher or lower temp
c. w/o enzymes, reactions take place slower
d. none of the above

D

all are true

217

____ is the pathway where enzymes catalyze the breaking down foodstuffs into smaller molecules

catabolic pathways

218

___ the pathway that harness the energy from catabolism to synthesize components that cells need/ builds larger molecules from smaller ones

Anabolic or biosynthetic pathways

219

(T/F) Enzymes speed up chemical reactions by increasing the energy barriers that normally block chemical reactions

false

it LOWERS energy barriers

220

(T/F) the Second law of thermodynamics says disorder increases over time, but is reversible (requires energy)

true

221

_____ is the quantity we use to measure disorder

entropy

222

(T/F) To maintain order cells constantly perform chemical reactions that either build up or break down organic molecules

true

223

(T/F) cells violate the 2nd law of therm by converting energy they use to heat

false

conversion of energy to heat generates order

224

(T/F) generated heat in which cells release into the environment where it disorders it so that the total entropy (that of the cell and
its surroundings) increases

true

225

(T/F) the First Law of Thermodynamics states that energy can be converted from one form to another but it cannot be
created or destroyed

true

226

which of the ff applies the first law of therm in cells?
a. the form of energy is the same and will not change; total energy stays same
b. amount of energy in different forms will change; total energy stays same
c. amt of different forms of energy will change; total energy changes
d. both amt of different forms of energy and total energy will not change

B

amount of energy in different forms will change but total amount of energy will stay the same

227

(T/F) In the thermodynamic sense, the loss of (free) energy during a reaction reflects a loss of orderliness

true

228

(T/F) Chemical reactions proceed away from the direction that leads to a loss of free energy and are energetically favorable

False

always towards the loss of energy/ towards disorder = energetically favorable

229

____ is the energy that can be harnessed to do work or drive chemical reactions

free energy

230

_____ is the energy input required to reach a lower state of energy to start a chemical reaction that leaves it in a stable state/ bring the reactants to the transition state

Activation Energy (ΔG o≠)

231

___ is the difference between the energies of the reactants (initial state) and the energies of the products (final state)/

Standard (Gibbs) free energy change (ΔG)

232

_____ Represents the point where the reaction has the necessary amount of energy and the arrangement of the atoms of the reactants are properly positioned
to generate the product

transition state

233

which of the ff is false about enzymes?
a. lowers activation energy to reach transition state
b. creates a new reaction
pathway whose transition state energy is lower
c. concentration of reactants in the transition state does not increase in the presence of enzyme
d. with enzymes ate of the catalyzed reaction is much faster than the uncatalyzed reaction

C

concentration of reactants in the transition state increases in the presence of enzyme

234

*(T/F) Enzymes increase the rate of reactions but do not alter the energy levels of
the reactants or products

true :)

235

which of the ff is false about enzymes?
a. higher temp increases the rate or rxn
b. high temps can denature enzymes = less active
c. some enzymes can function at high temps
d. there is a difference in energy levels of reactants & products of both catalyzed and uncatalyzed rxns

D

there are no differences between the energy levels of the reactants and products of the two reactions - only activation energy changes

236

(T/F) the binding of enzyme-substrate is through covalent interactions

false

through noncovalent interactions

237

(T/F) the active site of enzymes contain amino acids that have specific interactions with substrate

true

238

____ is the model that shows enzyme undergoes a conformational change - active site becomes complementary to the shape of the
substrate only after substrate binds

induced fit model

239

____ the model suggested by Emil Fischer, in which the substrate and active site of the enzyme have complementary 3D
structures

lock-and-key model

240

which of the ff does not affect the rate of enzyme catalytic activity?
a. enzymes
b. substrates
c. inhibitors
d. activators

none of the above!

241

(T/F) in a reaction rate can be expressed in terms of either the rate of appearance of the
product or the rate of the disappearance of either of the reactants

true

242

_____ developed the models of enzyme kinetics

Leonor Michaelis and Maud Menten

(michaelis-menten)

243

which of the ff is not true about the MichaelisMenten
Model of Enzyme Kinetics?
a. enzyme-subs is unchanged during a rxn
b. initial rate depends on breakdown of ES complex to E and P
c. the enzyme is regenerated at the end
d. the products can revert to the initial substrate

D

none of the product reverts to the initial substrate
(since this describes initial stages)

244

_____ the SUBSTRATE CONCENTRATION at which the reaction proceeds at one half its maximal velocity

Km = Michaelis constant (a concentration)

245

(T/F) the initial rate (Vin) of enzyme kinetics depends of the formation of E-s and products

false

depends on the breakdown of ES to E and P

246

(T/F) the first order (K1) of kinetics says that at low [S], Vo is linearly proportional to [S]

true

remember the hyperbolic graph

247

(T/F) the zero order of enzyme kinetics says At high [S], Vo is independent of [S]

true

remember the hyperbolic graph

248

which of the ff is false about Km?
a. a measure of substrate affinity
b. a measure of substrate concentration
c. k-1 is usually greater than k2 for most enzymes
d. at Vmax, Km is not equal to substrate

D

when the velocity of a reaction is half maximal, the substrateconcentration is equal to the Km

249

(T/F) low Km means E-S affinity is low

false

affinity is high, low S conc

250

(T/F) high E-S affinity indicates a lower substrate concentration (Km)

true

251

(T/F) high Km means, high substrate conc, and low E-S affinity

true

252

(T/F) low E-S affinity = low Km

false

low Km = high affinity = low subs conc

253

which of the ff is a match?
a. Km = 10^-6 = low affinity
b. Km = 10^-1 = high affinity
c. Km =10^-6 = high affinity
d. Km = 10^-1 = low affinity

C and D

254

______ states:

V= Vmax[S] / (Km+[S]) = Vmax/2

michaelis-menten equation

255

*(T/F) the michaelis-menten equation says that when the velocity of a reaction is half maximal, the substrate
concentration is equal to the Km

true

256

(T/F) if the substrate concentration is well below the Km, the enzyme may not be very active

true

257

(T/F) if the substrate concentration is close to its K M , it may be functioning
at half its maximal velocity

true

258

___ is the turnover number , where the enzymes are fully saturated with substrate

Kcat

in moles/substrate = (product/mole of enzyme)/second

259

______ states:

1/V = (Km/Vmax) x (1/[S]) + Vmax

Linearizing the Michaelis Menten Equation

aka y=mx + b

260

_____ is an example of a protein with four domains

Src protein kinase

261

____ and ____ are amino acids typically found in reverse turns of a secondary protein structure

glycine (small, can fit) and proline (cyclic structure facilitate turns)

262

______ is an example of a chaotropic reagent for protein denaturation

urea, guanidine hydrochloride

263

_________ are examples of chaperonins

heat shock proteins, GroEL and GroES (bacterial)

264

*(T/F) at low pH, a salt bridge forms between His 146 and Asp 94 of the same beta chain in Hb resulting in the release of O2 to cells

true

265

*(T/F) at low pH, CO2 and alpha amino groups of Hb form carbamate that release O2 to active tissues

true

266

____ is a type of inhibitor that is covalently linked to the enzyme, has a slow dissociation and cannot be separated by physical
methods

Irreversible inhibition

267

________ the type of inhibitor that has a rapid binding equilibrium; enzyme activity is restored when removed

Reversible inhibition

268

(T/F )Enzymes with seryl hydroxyl groups at their active sites cannot be inactivated by irreversible inhibitors

false

can be inactivated!

269

____ and ____ are examples of irreversible inhibition

aspirin and nerve gas poisons

270

_____ irreversibly acetylates
the hydroxyl group
of serine in the active sites of cyclooxygenases

aspirin

271

___ regulate synthesis of prostaglandins involved in gastric protection and inflammation

Cyclooxygenases

272

________ an irreversible inhibitor that bind irreversibly to the active site serine residues of acetylcholinesterase

nerve gas poison

ex. diisoprophylphosphofluoridate (DPF)

273

_____ and enzyme that catalyzes the hydrolysis of acetylcholine, thus terminating the excitation of a muscle after a nerve
impulse

Acetylcholinesterase

274

which of the ff is not a consequence of an irreversible enzyme inhibitor?
a. lower enzyme activity
b. respiratory failure
c. muscle paralysis
d. gastric lining damage

A

275

which of the ff is not true for a competitive inhibitor?
a. binds at the active site
b. resembles a substrate
c. lowers the catalytic rate of an enzyme
d. eliminates the catalytic activity of the enzyme

D

276

which of the ff is not true for non competitive inhibitors?
a. alters the structure of active site
b. binds on site other than the active site
c. increases the rate of enzyme activity
d. diminishes rate of catalysis by enzyme

C

277

(T/F) in a competitive inhibition, the Vmax of an enzyme remains the same while Km decreases

false

Km increases

278

(T/F) in a non competitive inhibition, the Km decreases and the Vmax remains the same

false

Km = same
Vmax = decreases

279

(T/F) in a noncompetitive inhibition, the Km is unchanged while Vmax decreases

True

280

__ is the measure of enzyme inhibitor affinity

Ki

281

(T/F) high Ki indicates higher inhibitor affinity

false

high Ki = less affinity

282

(T/F) low Ki indicates high Ki affinity

true

283

which of the ff is true for a competitive inhibition?
a. cannot cannot be overcome by increasing substrate concentration
b. inhibitor does not interfere with binding of the substrate to the active site
c. Vmax can be reached by increasing [S]
d. Km does not change

C

284

______ examples of treatment using competitve inhibition

methanol and ethylene glycol intoxication

285

(T/F) in using competitive inhibition as a treatment, methanol is prevented from binding to alcohol dehydrogenase using ethelyne glycol

true

286

(T/F) heavy metal ions competitively inhibit enzymes with sulfhydryl groups (SH) that contribute to maintaining the tertiary structure of the protein

true

287

which of the ff is not an example of noncompetitive inhibition?
a. EDTA
b. methanol
c. lead
d. chelating agents

B

288

_____ general term for enzymes that catalyze a hydrolytic cleavage reaction

hydrolases

289

(T/F) the action of hydrolases involve the removal of water to a substrate

false

they add water (hydrolyse)

290

______ are enzymes that degrade proteins by hydrolyzing bonds between amino acids

proteases

291

____ enzymes that synthesize molecules in anabolic reactions by joining two smaller
molecules

synthase

292

____ are enzymes that degrade nucleic acids by hydrolyzing bonds between nucleotides

nucleases

293

____ enzymes that catalyze the rearrangement of bonds within a single molecule

isomerase

294

___ are enzymes that catalyze the polymerization reactions in RNA and DNA synthesis

polymerases

295

__ are enzymes that catalyze oxidation/reduction reactions

oxido-reductase

296

*____ catalyze
addition of phosphate groups to molecules

kinases

297

___ catalyze the hydrolytic removal of phosphate groups from molecules

phosphatases

298

___ catalyze the hydrolysis of ATP

ATPases

299

(T/F) pH can affect E-S binding by protonation of aa in the enzyme

true

300

which of the ff enzymes do not function at neutral pH?
a. pepsin
b. trypsin
c. anhydrases
d. synthases

A and B

pepsin = acidic
trypsin = alkaline

301

____ are Inorganic ions or a (nonprotein) or a metalloorganic molecules that are required by some enzymes to function

cofactors / prosthetic groups

302

_____ a cofactor that typically bind with enzyme through noncovalent interactions

coenzymes

303

addition/removal of a phosphate group does not involve which aa in and enzyme?
a. serine
b. glutamic acid
c. tyrosine
d. threonine

B

304

(T/F) phosphatases add phosphate groups to the sidechain hydroxyl groups of serine, threonine and
tyrosine residues

False

it REMOVES

305

(T/F) metal ion cofactors accept electrons and form coordination bonds w/ substrate/enzyme that help to properly position
reactive groups during catalysis

true

306

(T/F) phosphorylation alters the conformation (due to its neg chages) of enzyme at one site exhibiting an allosteric effect

true

307

(T/F) phosphorylation does not affect the rate of activity of an enzyme

false

activity may either be increased or decreased
by phosphorylation

308

___ are inactive precursors of enzymes that become activated upon proteolytic cleavage of specific covalent bonds within the precursor sequence

zymogens

309

___ are examples of zymogens

chymotrypsinogen
and trypsinogen

(digestive enzymes in stomach and pancrease)

310

(T/F) enterpeptidase cleaves trysinogen which catalyzes the conversion of chymotrypsinogen to chymotrypsin

true

311

which of the ff is a mismatch?
a. Chymotrypsinogen to chymotrypsin
b. enteropeptidase- trypsinogen
c. trypsinogen to trypsin
d. Chymotrypsinogen to trypsinogen

D

312

(T/F) the pancreas produce inactive zymogens that are packed in a lipid membrane to protect itself

true

313

______ a fatal disease caused by premature activation of the proteolytic and lipolytic enzymes of the pancreas that destroys it and its blood supply

acute pancreatitis

314

(T/F) Pancreatic juice also contains a potent trypsin inhibitor which binds very
tightly to the active site of trypsin and blocks activity of any small amount of trypsin that may be present in the pancreas

true

315

____ an enzyme that Catalyzes the cutting of polysaccharide chains in the cell walls of bacteria and hydrolysis of adjacent sugar groups

lysozyme

316

_____ is associated with ATP regeneration in contractile or transport systems found in skeletal and heart muscles and brain

creatinine kinase

317

(T/F) elevated CK-MM levels is an indicator of mycardial damage/ infarction

false

measures CK-MB

318

_______ protein structure level where polypeptide chains are folded into ordered structures maintained by repetitive hydrogen bonding

secondary

318

_____ is the unfolding of a protein

denaturation

318

(T/F) The Anfinsen experiment demonstrated that all information necessary to determine the tertiary structure of a protein is provided by external forces such as signaling factors

false!

tertiary
structure of a protein is provided by its aa sequence (primary structure)

318

________ a PrP Sc disease is caused by a genetic mutation that results in substitution of asparagine for aspartic acid at amino acid 178 and affects the thalamus

Fatal Familial Insomnia (FFI)

319

(T/F) both aspirin and nerve gas poisons irreversibly inhibits enzymes by acetylating the hydroxyl group of serine in their active sites

False

Aspirin acetylates
Dpf phosphorylates

320

_______ discovered the substance 2,3 bisphosphoglycerate

Reinhold and Ruth Benesch

321

(T/F) the affinity of O2 to Hb is higher in cells than in free solution

False

lower in cells, higher in soln

322

(T/F) BPG increases O2 affinity by a factor of 26

false

decreases it!