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Biochem 2 > exam 1 > Flashcards

exam 1 Flashcards

1
Q

which of the ff amino acids have sulfur in their side chains?

a. methionine
b. alanine
c. threonine
d. aspargine

A

A

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2
Q

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

A

peptidyl transferanse

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3
Q

which of the ff amino acid has the smallest side chains?

a. tryptophan
b. alanine
c. glycine
d. methionine

A

C

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4
Q

which of the ff amino acid has a methyl group side chain?

a. tryptophan
b. alanine
c. glycine
d. methionine

A

B

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5
Q

which of the ff amino acid has an indole ring side chain?

a. tryptophan
b. tyrosine
c. histidine
d. methionine

A

A

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6
Q

which of the ff amino acid has a phenol in its side chain?

a. tryptophan
b. tyrosine
c. histidine
d. methionine

A

B

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7
Q

which of the ff amino acid has an imine, aliphatic structure?

a. tryptophan
b. proline
c. glycine
d. methionine

A

B

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8
Q

which of the ff is not an acidic amino acid?

a. arginine
b. glutamate
c. lysine
d. aspartate

A

A and C

are both basic

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9
Q

which of the ff is not an aromatic amino acid?

a. tyrosine
b. phenylalanine
c. tryptophan
d. proline

A

D

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10
Q

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

A

none of the above! :)

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11
Q

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

A

true

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12
Q

which of the ff is not a basic amino acid?

a. arginine
b. histidine
c. lysine
d. aspartate

A

D

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13
Q

which of the ff is not a polar amino acid?

a. threonine
b. tyrosine
c. aspartic acid?
d. tyrosine

A

C

  • a charged aa
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14
Q

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

A

steric / spatial effect

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15
Q

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

A

false!

it is planar an does not permit free rotation

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16
Q

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

A

true

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17
Q

which of the ff amino acid has an aromatic benzene-like ring side chain?

a. tryptophan
b. phenylalanine
c. glycine
d. alanine

A

B

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18
Q

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

A

partial double-bond character

due to resonance

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19
Q

which of the ff amino acids have sulfur in their side chains?

a. glutamine
b. histidine
c. alanine
d. cysteine

A

D

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20
Q

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

A

N-terminal

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21
Q

which of the ff amino acid has a methyl group side chain?

a. tryptophan
b. alanine
c. glycine
d. methionine

A

C

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22
Q

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

A

false

N-terminal (amino group) is the beginning

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23
Q

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

A

polypeptide backbone

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24
Q

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

A

skin keratin, myosin

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25
Q

which of the ff bonds does not contribute to protein folding?

a. covalent
b. hydrogen
c. ionic
d. van der waals

A

A

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26
Q

(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

A

true

amide bond = peptide bond

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27
Q

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

electronegative atoms

A

hydrogen bonds

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28
Q

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

A

quaternary

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29
Q

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

A

ionic bonds

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29
Q

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

A

van der Waals attractions

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30
Q

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

A

Hydrophobic interactions

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31
Q

(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

A

true

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34
Q

____ forms stronger bonds that causes proteins to unravel / denature

A

chaotropic agents

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35
Q

(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

A

true

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36
Q

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

A

disulfide bonds

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36
Q

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

A

IntrAchain disulfide bonds

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39
Q

(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

A

false

high conc in the cytosol

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40
Q

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

A

true

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41
Q

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

A

glutathione

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42
Q

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

A

false

disulfide bonds stabilizes

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43
Q

____ and ____ are examples of secondary protein structure

A

α-helix and β-pleated

sheets

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44
Q

_____ first to sequence the protein sequence of bovine insulin

A

Frederick Sanger

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45
Q

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

A

L. Pauling and R.B. Corey

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46
Q

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

A

α-helix and β-pleated sheet

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47
Q

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

A

true

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48
Q

(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

A

true

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49
Q

_____ is a very stable structure that results from αhelices

may wrapping around each other

A

coiled-coil

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50
Q

(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

A

true

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51
Q

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

A

C

this disrupts disulfide bonds

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52
Q

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

A

true

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53
Q

(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

A

first statement is true, second one if false!

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54
Q

(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

A

true

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55
Q

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

A

false

aggregates are resistant to proteolysis!

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56
Q

which of the ff is not a non polar amino acid?

a. phenylalanine
b. aspartic acid
c. tryptophan
d. valine
e. leucine

A

C

a - hydrophobic, aromatic
b - acidic, charged
c - polar, aromatic
d - phobic, imine
e - phobic
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58
Q

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

A

false

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

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59
Q

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

A

antiparallel pleated sheets

Nterminal and Cterminal ends of the chains are in opposite orientation

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60
Q

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

A

C

glycine = small R group, no crowding

proline = cyclic structure facilitates turn

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61
Q

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

A

false

  • loss of a water molecule
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61
Q

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

A

primary level

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62
Q

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

A

true

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63
Q

____ 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

A

Domain (or module)

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64
Q

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

A

domain shuffling

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65
Q

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

A

none of the above :)

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68
Q

____ and ___ are some examples of fibrous tertiary structure

A

collagen, α-keratin

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69
Q

_______ are example of proteins that contain domain shuffling

A

EFG (epidermal growth factor) chymotrypsin

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70
Q

which of the ff is not a charged aa?

a. arginine
b. lysine
c. aspartic acid
d. glutamic acid

A

none of the above

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71
Q

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

A

Random coil

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72
Q

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

A

D

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73
Q 
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
A

D

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74
Q

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

A

collagen

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75
Q

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

A

tertiary polypeptide structure

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76
Q

(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

A

false

residues form intERchain H bonds

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77
Q

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

A

true

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79
Q

______ 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

A

fibrous tertiary structure

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80
Q

___ are deposits of protein aggregates occur in and around cells

A

amyloid

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81
Q

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

A

globular tertiary structure

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82
Q

which of the ff is a hydrophobic aa?

a. isoleucine
b. proline
c. glycine
d. alanine

A

all of the above!

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83
Q

____ and ___ are some examples of globular tertiary structures

A

most enzymes, hemoglobin

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86
Q

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

A

a subunit

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87
Q

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

A

molecular chaperones and chaperonins (a subset)

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88
Q

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

A

C

may be dimer, trimer, tetramer, oligomer

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89
Q

____ are disulfide bonds that join two different polypeptide

A

IntErchain disulfide bonds

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89
Q

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

A

tertiary

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90
Q

(T/F) Myoglobin structure has no disulfide bonds

A

true

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91
Q

which of the ff does not induce denaturation of proteins?

a. heat
b. high or low pH
c. detergents
d. Urea and guanidine hydrochloride

A

none of the above

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92
Q

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

a

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93
Q

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

A

B

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94
Q 
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
A

C

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95
Q

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

A

false

urea causes stronger H bonds

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96
Q

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

A

true

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97
Q

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

A

D

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98
Q 
\_\_\_\_\_is an example of a  major class of molecular chaperones that responds to heat shock or
other stresses
A

heatshock

proteins (hsp)

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99
Q

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

A

D

this is a denaturant!

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100
Q

____ are regions

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

A

reverse turns

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101
Q

___ and ___ are examples of reducing agents that causes denaturation

A

β-mercaptoethanol, DTT (Dithiothreitol)

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101
Q

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

A

true

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101
Q

____ an example of an ampotheric protein denaturant

A

SDS - sodium diodyl sulfate

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101
Q

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

A

FALSE!

+2 ox state

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102
Q

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

A

B

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103
Q

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

A

true

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106
Q

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

A

Protein disulfide isomerase

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107
Q

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

A

parallel pleated sheets

H bonded peptide chains run in the same direction

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108
Q

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

A

B

mutations can lead to cataract formation

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109
Q

________ 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

A

scurvy

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110
Q

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

A

Consists of a SINGLE polypeptide chain

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110
Q

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

A

True

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111
Q

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

A

false

αhelical changes to βsheet

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112
Q

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

A

amyloidosis

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113
Q

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

A

Prion proteins (PrP)

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114
Q

_____ give an example of a neurodegenerative diseases caused by PrP

A 
- Scrapie in sheep
– CreutzfeldtJakob
disease (CJD) in humans
– Bovine spongiform encephalopathy in cattle (mad cow disease)
– Fatal familial insomnia
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115
Q

_____ the misfolded, aggregated form of PrP that causes diseases

A

PrP Sc (scrapie isoform)

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116
Q

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

A

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

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117
Q

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

A

c

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

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118
Q

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

A

Stanley Prusiner

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119
Q

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

A

false

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

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120
Q

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

A

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121
Q

(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)

A

true

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122
Q

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

A

true

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123
Q

____ and ___ are the

enzymes that hydroxylate proline and lysine , respectively

A

Peptidyl proline hydroxylase and peptidyl lysine hydroxylase

by adding OH groups

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124
Q

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

A

B

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125
Q

____ is a requirement for Formation of Hydroxyproline and Hydroxylysine

A

vitamin c

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126
Q

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

A

true

  • so protein + heme is impt in O2 storage
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127
Q

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

A

true

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128
Q

_____ 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

A

Marfan syndrome

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129
Q

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

A

Creutzfeldt-Jakob

disease

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129
Q

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

A

cataracts

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129
Q

_____ 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

A

α chains

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129
Q

(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

A

true

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130
Q

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

A

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

131
Q

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

A

myoglobin

132
Q

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

A

hemoglobin

133
Q

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

A

false

α chains are NOT hydroxylated,

134
Q

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

A

oxidative phosphorylation

137
Q

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

A

Max Perutz (late 1950’s)

138
Q

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

A

Prosthetic groups

139
Q

_____ is a protein without its prosthetic group

A

apoprotein

140
Q

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

A

false!

binding depends on presence of a heme prosthetic group

141
Q

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

A

true

142
Q

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

A

B

can form 6 bonds

143
Q

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

A

true

144
Q

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

A

D

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

145
Q

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

A

false

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

146
Q

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

A

His E7

147
Q

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

A

motifs

148
Q

*(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

A

true

149
Q

(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

A

D - all is true!

150
Q

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

A

C

CO = 25k times greater

151
Q

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

A

false

it also contains 2 polar histidine residues

152
Q

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

A

false

Fe (III) does not bind O 2

153
Q

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

A

false!

this is impt w/ AEROBIC organisms

154
Q

(T/F) myoglobin consists of four polypeptide chains

A

false

Mb - one polypeptide chain
Hb - four polypeptide chains

155
Q

(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

A

true

156
Q

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

A

D

Mb - one polypeptide chain
Hb - four polypeptide chains

157
Q

_____ are genes derived from a common ancestor gene,

A

homologs

158
Q

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

A

true

159
Q

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

A

paralogs

160
Q

______ the compounds that regulate binding of O 2 by Hb

A

2, 3 - bisphosphoglycerate

(BPG), H + and CO

161
Q

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

A

Mb does not exhibit cooperativity

162
Q

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

A

Allosteric Protein

163
Q

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

A

false

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

164
Q

(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

A

true

165
Q

(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

A

false

BPG regulation results in LOWER Hb affinity to O2

166
Q

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

A

true

167
Q

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

A

true

168
Q

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

A

false

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

169
Q

(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

A

true

170
Q

(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

A

true

171
Q 
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
A

B

172
Q

(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

A

true

173
Q

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

A

true

174
Q

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

A

Bohr effect

-discovered by Christian Bohr, 1904

175
Q

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

A

T (tense) form, a deoxy Hb

R form = oxy Hb

176
Q

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

A

salt bridges

177
Q

(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

A

true

178
Q

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

A

false

the binding of FIRST O2 costs more energy

179
Q

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

A

true

180
Q

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

A

true

181
Q

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

A

true

182
Q

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

A

C

low pH dapat! (acidic)

183
Q

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

A

true

184
Q

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

A

Joseph Barcroft

185
Q

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

A

Reinhold Benesch and Ruth Benesch

186
Q

(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

A

False

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

187
Q

*(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

A

true

188
Q

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

A

false!

binds only to deoxyHb

189
Q

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

A

C

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

190
Q

which of the ff is NOT a basis of protein separation?

a. size
b. charge
c. solubility
d. use of antibodies/ immunological properties

A

none of these, all are basis for separation

191
Q

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

A

true

192
Q

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

A

false

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

193
Q

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

a and d

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

very high - pellets macromolecules

194
Q

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

A

C

sedimenting thru gradient results in finer separation of components

195
Q

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

A

Velocity Sedimentation

196
Q

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

A

Equilibrium Sedimentation

197
Q

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

A

Column Chromatography of Proteins

198
Q

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

A

none of the above

199
Q

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

A

Gel Filtration

Chromatography

200
Q

____ 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

A

Affinity Chromatography

201
Q

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

A

Protein Purification by Chromatography

202
Q

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

A

SDS Polyacrylamide Gel Electrophoresis

203
Q

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

A

sodium dodecyl sulfate (SDS)

204
Q

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

A

true

205
Q

(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

A

false

Smaller proteins migrate faster

206
Q

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

A

Immunoblotting (Western Blotting)

207
Q

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

A

CoImmunoprecipitation

Studies

208
Q

_____ 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)

A

secondary ab or Protein A

209
Q

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

A

Isoelectric Focusing

210
Q

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

A

isoelectric point

211
Q

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

A

Mass Spectrometry

212
Q

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

A

False

the protease trypsin is very specific

213
Q

____ is the most common type of mass spectrometry

A

matrix-assisted laser

desorption ionization-time-off-light (MALDI-TOF)

214
Q

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

A

true

215
Q

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

A

Carbonic anhydrase

216
Q

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

A

D

all are true

217
Q

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

A

catabolic pathways

218
Q

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

A

Anabolic or biosynthetic pathways

219
Q

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

A

false

it LOWERS energy barriers

220
Q

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

A

true

221
Q

_____ is the quantity we use to measure disorder

A

entropy

222
Q

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

A

true

223
Q

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

A

false

conversion of energy to heat generates order

224
Q

(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

A

true

225
Q

(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

A

true

226
Q

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

A

B

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

227
Q

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

A

true

228
Q

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

A

False

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

229
Q

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

A

free energy

230
Q

_____ 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

A

Activation Energy (ΔG o≠)

231
Q

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

A

Standard (Gibbs) free energy change (ΔG)

232
Q

_____ 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

A

transition state

233
Q

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

A

C

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

234
Q

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

A

true :)

235
Q

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

A

D

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

236
Q

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

A

false

through noncovalent interactions

237
Q

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

A

true

238
Q

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

A

induced fit model

239
Q

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

A

lock-and-key model

240
Q

which of the ff does not affect the rate of enzyme catalytic activity?

a. enzymes
b. substrates
c. inhibitors
d. activators

A

none of the above!

241
Q

(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

A

true

242
Q

_____ developed the models of enzyme kinetics

A

Leonor Michaelis and Maud Menten

michaelis-menten

243
Q

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

A

D

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

244
Q

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

A

Km = Michaelis constant (a concentration)

245
Q

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

A

false

depends on the breakdown of ES to E and P

246
Q

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

A

true

remember the hyperbolic graph

247
Q

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

A

true

remember the hyperbolic graph

248
Q

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

A

D

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

249
Q

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

A

false

affinity is high, low S conc

250
Q

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

A

true

251
Q

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

A

true

252
Q

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

A

false

low Km = high affinity = low subs conc

253
Q

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

A

C and D

254
Q

______ states:

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

A

michaelis-menten equation

255
Q

*(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

A

true

256
Q

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

A

true

257
Q

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

A

true

258
Q

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

A

Kcat

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

259
Q

______ states:

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

A

Linearizing the Michaelis Menten Equation

aka y=mx + b

260
Q

_____ is an example of a protein with four domains

A

Src protein kinase

261
Q

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

A

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

262
Q

______ is an example of a chaotropic reagent for protein denaturation

A

urea, guanidine hydrochloride

263
Q

_________ are examples of chaperonins

A

heat shock proteins, GroEL and GroES (bacterial)

264
Q

*(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

A

true

265
Q

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

A

true

266
Q

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

A

Irreversible inhibition

267
Q

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

A

Reversible inhibition

268
Q

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

A

false

can be inactivated!

269
Q

____ and ____ are examples of irreversible inhibition

A

aspirin and nerve gas poisons

270
Q

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

A

aspirin

271
Q

___ regulate synthesis of prostaglandins involved in gastric protection and inflammation

A

Cyclooxygenases

272
Q

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

A

nerve gas poison

ex. diisoprophylphosphofluoridate (DPF)

273
Q

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

A

Acetylcholinesterase

274
Q

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

A

275
Q

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

A

D

276
Q

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

A

C

277
Q

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

A

false

Km increases

278
Q

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

A

false

Km = same
Vmax = decreases
279
Q

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

A

True

280
Q

__ is the measure of enzyme inhibitor affinity

A

Ki

281
Q

(T/F) high Ki indicates higher inhibitor affinity

A

false

high Ki = less affinity

282
Q

(T/F) low Ki indicates high Ki affinity

A

true

283
Q

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

A

C

284
Q

______ examples of treatment using competitve inhibition

A

methanol and ethylene glycol intoxication

285
Q

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

A

true

286
Q

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

A

true

287
Q

which of the ff is not an example of noncompetitive inhibition?

a. EDTA
b. methanol
c. lead
d. chelating agents

A

B

288
Q

_____ general term for enzymes that catalyze a hydrolytic cleavage reaction

A

hydrolases

289
Q

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

A

false

they add water (hydrolyse)

290
Q

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

A

proteases

291
Q

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

A

synthase

292
Q

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

A

nucleases

293
Q

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

A

isomerase

294
Q

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

A

polymerases

295
Q

__ are enzymes that catalyze oxidation/reduction reactions

A

oxido-reductase

296
Q

*____ catalyze

addition of phosphate groups to molecules

A

kinases

297
Q

___ catalyze the hydrolytic removal of phosphate groups from molecules

A

phosphatases

298
Q

___ catalyze the hydrolysis of ATP

A

ATPases

299
Q

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

A

true

300
Q

which of the ff enzymes do not function at neutral pH?

a. pepsin
b. trypsin
c. anhydrases
d. synthases

A

A and B

pepsin = acidic
trypsin = alkaline
301
Q

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

A

cofactors / prosthetic groups

302
Q

_____ a cofactor that typically bind with enzyme through noncovalent interactions

A

coenzymes

303
Q

addition/removal of a phosphate group does not involve which aa in and enzyme?

a. serine
b. glutamic acid
c. tyrosine
d. threonine

A

B

304
Q

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

A

False

it REMOVES

305
Q

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

A

true

306
Q

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

A

true

307
Q

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

A

false

activity may either be increased or decreased
by phosphorylation

308
Q

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

A

zymogens

309
Q

___ are examples of zymogens

A

chymotrypsinogen
and trypsinogen

(digestive enzymes in stomach and pancrease)

310
Q

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

A

true

311
Q

which of the ff is a mismatch?

a. Chymotrypsinogen to chymotrypsin
b. enteropeptidase- trypsinogen
c. trypsinogen to trypsin
d. Chymotrypsinogen to trypsinogen

A

D

312
Q

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

A

true

313
Q

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

A

acute pancreatitis

314
Q

(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

A

true

315
Q

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

A

lysozyme

316
Q

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

A

creatinine kinase

317
Q

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

A

false

measures CK-MB

318
Q

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

A

secondary

318
Q

_____ is the unfolding of a protein

A

denaturation

318
Q

(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

A

false!

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

318
Q

________ 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

A

Fatal Familial Insomnia (FFI)

319
Q

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

A

False

Aspirin acetylates
Dpf phosphorylates

320
Q

_______ discovered the substance 2,3 bisphosphoglycerate

A

Reinhold and Ruth Benesch

321
Q

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

A

False

lower in cells, higher in soln

322
Q

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

A

false

decreases it!

Biochem 2 (13 decks)

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