exam 1 Flashcards
which of the ff amino acids have sulfur in their side chains?
a. methionine
b. alanine
c. threonine
d. aspargine
A
___________ is the enzyme that forms peptide bonds between two amino acids during translation
peptidyl transferanse
which of the ff amino acid has the smallest side chains?
a. tryptophan
b. alanine
c. glycine
d. methionine
C
which of the ff amino acid has a methyl group side chain?
a. tryptophan
b. alanine
c. glycine
d. methionine
B
which of the ff amino acid has an indole ring side chain?
a. tryptophan
b. tyrosine
c. histidine
d. methionine
A
which of the ff amino acid has a phenol in its side chain?
a. tryptophan
b. tyrosine
c. histidine
d. methionine
B
which of the ff amino acid has an imine, aliphatic structure?
a. tryptophan
b. proline
c. glycine
d. methionine
B
which of the ff is not an acidic amino acid?
a. arginine
b. glutamate
c. lysine
d. aspartate
A and C
are both basic
which of the ff is not an aromatic amino acid?
a. tyrosine
b. phenylalanine
c. tryptophan
d. proline
D
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! :)
(T/F) Proteins constitute most of a cell’s dry mass
true
which of the ff is not a basic amino acid?
a. arginine
b. histidine
c. lysine
d. aspartate
D
which of the ff is not a polar amino acid?
a. threonine
b. tyrosine
c. aspartic acid?
d. tyrosine
C
- a charged aa
________ is an effect in which the shape of a molecule influences its
reactions
steric / spatial effect
(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
(T/F) in the protein backbone, rotation occurs freely around the Cα-C
(psi angle of rotation)
and N-Cα bonds
true
which of the ff amino acid has an aromatic benzene-like ring side chain?
a. tryptophan
b. phenylalanine
c. glycine
d. alanine
B
the _________ between the carbonyl carbon atom and nitrogen atom of
the peptide bond contributes to its rigidity
partial double-bond character
due to resonance
which of the ff amino acids have sulfur in their side chains?
a. glutamine
b. histidine
c. alanine
d. cysteine
D
_____ this end of the protein sequence corresponds to the 5’ end of the mRNA
N-terminal
which of the ff amino acid has a methyl group side chain?
a. tryptophan
b. alanine
c. glycine
d. methionine
C
(T/F) the α-carboxyl / t-terminal ? end is considered the beginning of the polypeptide chain
false
N-terminal (amino group) is the beginning
_______ is composed of repeating atoms along the core of the polypeptide chain
polypeptide backbone
_____ are examples of proteins that have coiled-coil apha helices
skin keratin, myosin
which of the ff bonds does not contribute to protein folding?
a. covalent
b. hydrogen
c. ionic
d. van der waals
A
(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
_____ is the bond in which an H+ atom is shared between two
electronegative atoms
hydrogen bonds
_____ is the complete 3dimensional structure of multisubunit protein complexes/ proteins composed of more than one polypeptide chain
quaternary
______ is the bond in which oppositely charged atoms interact with one another
ionic bonds
_______ 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
______ another weak force aside from the 3 bonds that determine protein folding
Hydrophobic interactions
(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
____ forms stronger bonds that causes proteins to unravel / denature
chaotropic agents
(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
_____ are the covalent links between the sulfur atoms in the side chains of cysteines
disulfide bonds
____ are disulfide bonds that join two parts of the same polypeptide
IntrAchain disulfide bonds
(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
(T/F) disulfide bond formation catalyzed in the endoplasmic reticulum
true
____ is an example of a reducing agent that disrupts disulfide bonds in the cytosol
glutathione
(T/F) hydrogen bonds offer major stabilizing effect on protein structure
false
disulfide bonds stabilizes
____ and ____ are examples of secondary protein structure
α-helix and β-pleated
sheets
_____ first to sequence the protein sequence of bovine insulin
Frederick Sanger
______ are first to describe the α-helix and β-pleated sheet structures in early 1950’s
L. Pauling and R.B. Corey
_______ 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
(T/F) α-helix and β-pleated sheet do not involve bonding between the side chains of the aa’s
true
(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
_____ is a very stable structure that results from αhelices
may wrapping around each other
coiled-coil
(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
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
(T/F) CO block binding of O 2 to myoglobin and more importantly to hemoglobin
true
(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!
(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
(T/F) aggregates from protein misfolding are not resistant to proteolysis
false
aggregates are resistant to proteolysis!
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
(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
____ 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
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
(T/F) the formation of a peptide bond includes gaining an oxygen molecule
false
- loss of a water molecule
______ protein structure level where amino acids are covalently linked to form a sequence
primary level
(T/F) the heme group is held in place by hydrophobic interactions between the heme and nonpolar R
groups of the protein
true
____ 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)
_____ creation of new gene proteinsbelieved
to have originated when the DNA sequences
encoding each domain accidentally became joined
domain shuffling
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 :)
____ and ___ are some examples of fibrous tertiary structure
collagen, α-keratin
_______ are example of proteins that contain domain shuffling
EFG (epidermal growth factor) chymotrypsin
which of the ff is not a charged aa?
a. arginine
b. lysine
c. aspartic acid
d. glutamic acid
none of the above
____ are Regions of polypeptide chains that lack discernable repeating pattern such as
the αhelix
or βsheet
Random coil
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
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
___ the most abundant protein in mammals, Secreted by connective tissue cells, a major component of skin and bone
collagen
_______ is a steric
relationship of amino acids that are far apart in the
linear sequence
tertiary polypeptide structure
(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
(T/F) tertiary and secondary structures may be indistinguishable from each other
true
______ 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
___ are deposits of protein aggregates occur in and around cells
amyloid
____ a water soluble tertiary structure where polypeptides foldsinto a complex compact shape like a ball (spherical) with an irregular surface
globular tertiary structure
which of the ff is a hydrophobic aa?
a. isoleucine
b. proline
c. glycine
d. alanine
all of the above!
____ and ___ are some examples of globular tertiary structures
most enzymes, hemoglobin
_____ is a polypeptide chain in a quaternary structure that may be identical or different, a dimer, trimer, tetramer etc
a subunit
______ and _____ are special proteins that assists protein folding in living cells
molecular chaperones and chaperonins (a subset)
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
____ are disulfide bonds that join two different polypeptide
IntErchain disulfide bonds
_______ protein structure level where there is a full 3- dimensional organization of a polypeptide chain
tertiary
(T/F) Myoglobin structure has no disulfide bonds
true
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
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
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
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
(T/F) urea causes formation of weaker H bonds than what exists in the protein causing its denaturation
false
urea causes stronger H bonds
(T/F) Denaturation is facilitated by the presence of reducing agents that Reduce disulfide bonds
true
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
\_\_\_\_\_is an example of a major class of molecular chaperones that responds to heat shock or other stresses
heatshock
proteins (hsp)
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!
____ are regions
of secondary structure (of protein) where the chains change direction or fold back
reverse turns
___ and ___ are examples of reducing agents that causes denaturation
β-mercaptoethanol, DTT (Dithiothreitol)
(T/F) protein denaturants accessibility of reducing agents to
internal disulfide bonds
true
____ an example of an ampotheric protein denaturant
SDS - sodium diodyl sulfate
(T/F) The iron atom (in the heme group) is in the ferrous (+1) oxidation state
FALSE!
+2 ox state
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
(T/F) polar amino acids or polar aa + polypeptide backbone are joined by hydrogen bonding
true
____ is an enzyme that catalyzes the correct formation of disulfide
linkages in protein folding in cells
Protein disulfide isomerase
______ 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
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
________ 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
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
(T/F) immunoglobulin domain developed more recently in evolution
than the others
True
(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
_____ is the accumulation
of amyloid deposits (various types of fibrillar
proteins) in amounts sufficient to impair normal function
amyloidosis
_____ 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)
_____ 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
_____ the misfolded, aggregated form of PrP that causes diseases
PrP Sc (scrapie isoform)
____ the person who first determined tertiary structure of myoglobin from a sperm whale Xray crystallography
John Kendrew (late 1950’s), first to be determined
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
______ won the 1997 Nobel Prize in Physiology or Medicine for his discovery of “prions
Stanley Prusiner
(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
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
(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
(T/F) cataract formation resulting from mutations in αcrystallin gene maybe due to reduction in chaperone function or Alterations in αcrystallin oligomeric structure
true
____ and ___ are the
enzymes that hydroxylate proline and lysine , respectively
Peptidyl proline hydroxylase and peptidyl lysine hydroxylase
by adding OH groups
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
____ is a requirement for Formation of Hydroxyproline and Hydroxylysine
vitamin c
(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
(T/F) Glycine allows the three helical α chains to pack tightly together (collagen)
true
_____ 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
_____ a PrP Sc disease caused by several different mutations in prion protein gene and affects the cortex
Creutzfeldt-Jakob
disease
______ a disease are caused in large part, by the aggregation of
partially unfolded lens proteins; a common cause of blindness
cataracts
_____ 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
(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
___ 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)
_____ an oxygen carrying protein found in muscle that Serves as a reserve supply of oxygen and facilitates the movement of oxygen
within muscle
myoglobin
___ and oxygen carrying protein that transport of CO 2 and hydrogen ions in blood
hemoglobin
(T/F) In scurvy, the α chains are hydroxylated, fail to form triple helix and are
degraded immediately
false
α chains are NOT hydroxylated,
______ the process which is the major source of ATP in aerobic organisms
oxidative phosphorylation
____ the person who first determined the tertiary structure of hemoglobin from horse
Max Perutz (late 1950’s)
_____ nonprotein
components that are tightly bound to many
proteins and contribute to their biological activities
Prosthetic groups
_____ is a protein without its prosthetic group
apoprotein
(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
(T/F) Heme consists ofa porphyrin ring and an iron atom
true
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
*(T/F) Ferric iron (+3 oxidation state) cannot bind oxygen
true
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
(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
_____ this functions as a gate that regulates entry of O2 into the hydrophobic
pocket to bind heme in myoglobin
His E7
____ are repeated combinations of supersecondary structure within a protein with usually short repetitive units
motifs
*(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
(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!
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
(T/F) the internal structure of myoglobin molecule is completely made up of nonpolar aa’s
false
it also contains 2 polar histidine residues
(T/F) Fe (III) binds O 2
false
Fe (III) does not bind O 2
(T/F ) Oxidative phosphorylation is the major source of ATP in anaerobic organisms
false!
this is impt w/ AEROBIC organisms
(T/F) myoglobin consists of four polypeptide chains
false
Mb - one polypeptide chain
Hb - four polypeptide chains
(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
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
_____ are genes derived from a common ancestor gene,
homologs
(T/F) orthologs are same proteins in different species
true
(T/F) paralogs are genes that are derived from a single gene that have diverged over time in the same species
paralogs
______ the compounds that regulate binding of O 2 by Hb
2, 3 - bisphosphoglycerate
(BPG), H + and CO
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
____ is a protein that changes from one conformation to another when it binds another molecule or is covalently modified..
Allosteric Protein
(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
(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
(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
(T/F) the S shaped curve of O2 dissiociation for Hb reflects the fact that it exhibits positive cooperativity
true
(T/F) the hyperbolic shaped curve of O2 dissociation curve of Mb exhibits a steady increase in O 2 sat.
true
(T/F) at 26 torrs, Mb is saturated at 50%
false
Mb is saturated 50% at 1 torr (high affinity at very low pO2)
(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
(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
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
(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
(T/F) a “shift to the right” in the Hb dissociation curve occurs when pH is low indicating a decrease in O2 affinity
true
_______ the interplay between H + , CO 2 , and O2 for meeting the metabolic needs of tissue
Bohr effect
-discovered by Christian Bohr, 1904
_____ 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
______ noncovalent
electrostatic interactions between oppositely charged aa side chains in Hb that is affected by pH and are disrupted by oxygenation
salt bridges
(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
(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
(T/F) at low pH (metabolically active sites) the conformation of deoxy Hb is favored, releasing O2
true
(T/F) in Hb, the protonation of His 146 of the β chain forms a salt bridge with Asp94 of the
same chain
true
(T/F) in Hb, the formation of carbamate stabilizes the T form of the molecule and releases O2
true
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)
(T/F) The O 2 affinity of Hb within RBC’s is lower than that of Hb in free solution
true
______ observed the difference in O2 affinity of Hb within RBC and in free soln
Joseph Barcroft
________ are the researchers that discovered 2,3bisphosphoglycerate
(BPG) as the substance that affects O2 affinity
Reinhold Benesch and Ruth Benesch
(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
*(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
*(T/F) BPG binds to oxyHb more that deoxyHB which reduces O2 affinity
false!
binds only to deoxyHb
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
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
(T/F) in protein separation Repeated centrifugation at progressively higher speeds will fractionate cell
homogenates into their components
true
(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
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
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
____ involves layering a homogenate as a thin band according to their size and
shape
Velocity Sedimentation
_____ a sensitive technique that separates cellular components on the basis of their buoyant density ,
independently of their size and shape
Equilibrium Sedimentation
_____ fractioning proteins thru passing a mixture of proteins through a column containing a porous
solid matrix
Column Chromatography of Proteins
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
_____ protein separation technique that separates by size by passing them thru pores in the beads in the column
Gel Filtration
Chromatography
____ 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
___ protein separation technique that uses multiple chromatographic techniques are used in series to purify a
protein
Protein Purification by Chromatography
____ protein separation technique used to determine size and subunit composition of proteins that uses a highly crosslinked gel of polyacrylamide
SDS Polyacrylamide Gel Electrophoresis
______ is a negatively charged (anionic) detergent used in combination of a reducing agent used to electrophorize protein in protein separation
sodium dodecyl sulfate (SDS)
(T/F) in an SDS gel, SDS binds to hydrophobic regions causing unfolding of proteins while Reducing agent, βmercaptoethanol,
breaks disulfide bonds
true
(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
____ a protein separation technique that uses an antibody to identify a specific protein fractionated on an SDS gel
Immunoblotting (Western Blotting)
_____ is a protein separation technique used to determine whether two or more proteins are capable of
forming molecular associations
CoImmunoprecipitation
Studies
_____ 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
_____ 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
______ the pH at which the protein has no net charge and therefore does not move in an electric field
isoelectric point
______ the protein technique Used to identify proteins by determining their precise masses and the
masses of peptides derived from them
Mass Spectrometry
(T/F) trypsin that is used to digest in mass spec targets random proteins
False
the protease trypsin is very specific
____ is the most common type of mass spectrometry
matrix-assisted laser
desorption ionization-time-off-light (MALDI-TOF)
(T/F) in MALDI-TOF protein technique, peptides that are larger reaches the detector slower than smaller ones
true
_____ is one of the fastest enzymes and catalyzes the formation of carbonic acid
Carbonic anhydrase
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
____ is the pathway where enzymes catalyze the breaking down foodstuffs into smaller molecules
catabolic pathways
___ the pathway that harness the energy from catabolism to synthesize components that cells need/ builds larger molecules from smaller ones
Anabolic or biosynthetic pathways
(T/F) Enzymes speed up chemical reactions by increasing the energy barriers that normally block chemical reactions
false
it LOWERS energy barriers
(T/F) the Second law of thermodynamics says disorder increases over time, but is reversible (requires energy)
true
_____ is the quantity we use to measure disorder
entropy
(T/F) To maintain order cells constantly perform chemical reactions that either build up or break down organic molecules
true
(T/F) cells violate the 2nd law of therm by converting energy they use to heat
false
conversion of energy to heat generates order
(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
(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
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
(T/F) In the thermodynamic sense, the loss of (free) energy during a reaction reflects a loss of orderliness
true
(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
____ is the energy that can be harnessed to do work or drive chemical reactions
free energy
_____ 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≠)
___ 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)
_____ 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
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
*(T/F) Enzymes increase the rate of reactions but do not alter the energy levels of
the reactants or products
true :)
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
(T/F) the binding of enzyme-substrate is through covalent interactions
false
through noncovalent interactions
(T/F) the active site of enzymes contain amino acids that have specific interactions with substrate
true
____ 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
____ the model suggested by Emil Fischer, in which the substrate and active site of the enzyme have complementary 3D
structures
lock-and-key model
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!
(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
_____ developed the models of enzyme kinetics
Leonor Michaelis and Maud Menten
michaelis-menten
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
_____ the SUBSTRATE CONCENTRATION at which the reaction proceeds at one half its maximal velocity
Km = Michaelis constant (a concentration)
(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
(T/F) the first order (K1) of kinetics says that at low [S], Vo is linearly proportional to [S]
true
remember the hyperbolic graph
(T/F) the zero order of enzyme kinetics says At high [S], Vo is independent of [S]
true
remember the hyperbolic graph
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
(T/F) low Km means E-S affinity is low
false
affinity is high, low S conc
(T/F) high E-S affinity indicates a lower substrate concentration (Km)
true
(T/F) high Km means, high substrate conc, and low E-S affinity
true
(T/F) low E-S affinity = low Km
false
low Km = high affinity = low subs conc
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
______ states:
V= Vmax[S] / (Km+[S]) = Vmax/2
michaelis-menten equation
*(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
(T/F) if the substrate concentration is well below the Km, the enzyme may not be very active
true
(T/F) if the substrate concentration is close to its K M , it may be functioning
at half its maximal velocity
true
___ is the turnover number , where the enzymes are fully saturated with substrate
Kcat
in moles/substrate = (product/mole of enzyme)/second
______ states:
1/V = (Km/Vmax) x (1/[S]) + Vmax
Linearizing the Michaelis Menten Equation
aka y=mx + b
_____ is an example of a protein with four domains
Src protein kinase
____ and ____ are amino acids typically found in reverse turns of a secondary protein structure
glycine (small, can fit) and proline (cyclic structure facilitate turns)
______ is an example of a chaotropic reagent for protein denaturation
urea, guanidine hydrochloride
_________ are examples of chaperonins
heat shock proteins, GroEL and GroES (bacterial)
*(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
*(T/F) at low pH, CO2 and alpha amino groups of Hb form carbamate that release O2 to active tissues
true
____ 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
________ the type of inhibitor that has a rapid binding equilibrium; enzyme activity is restored when removed
Reversible inhibition
(T/F )Enzymes with seryl hydroxyl groups at their active sites cannot be inactivated by irreversible inhibitors
false
can be inactivated!
____ and ____ are examples of irreversible inhibition
aspirin and nerve gas poisons
_____ irreversibly acetylates
the hydroxyl group
of serine in the active sites of cyclooxygenases
aspirin
___ regulate synthesis of prostaglandins involved in gastric protection and inflammation
Cyclooxygenases
________ an irreversible inhibitor that bind irreversibly to the active site serine residues of acetylcholinesterase
nerve gas poison
ex. diisoprophylphosphofluoridate (DPF)
_____ and enzyme that catalyzes the hydrolysis of acetylcholine, thus terminating the excitation of a muscle after a nerve
impulse
Acetylcholinesterase
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
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
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
(T/F) in a competitive inhibition, the Vmax of an enzyme remains the same while Km decreases
false
Km increases
(T/F) in a non competitive inhibition, the Km decreases and the Vmax remains the same
false
Km = same Vmax = decreases
(T/F) in a noncompetitive inhibition, the Km is unchanged while Vmax decreases
True
__ is the measure of enzyme inhibitor affinity
Ki
(T/F) high Ki indicates higher inhibitor affinity
false
high Ki = less affinity
(T/F) low Ki indicates high Ki affinity
true
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
______ examples of treatment using competitve inhibition
methanol and ethylene glycol intoxication
(T/F) in using competitive inhibition as a treatment, methanol is prevented from binding to alcohol dehydrogenase using ethelyne glycol
true
(T/F) heavy metal ions competitively inhibit enzymes with sulfhydryl groups (SH) that contribute to maintaining the tertiary structure of the protein
true
which of the ff is not an example of noncompetitive inhibition?
a. EDTA
b. methanol
c. lead
d. chelating agents
B
_____ general term for enzymes that catalyze a hydrolytic cleavage reaction
hydrolases
(T/F) the action of hydrolases involve the removal of water to a substrate
false
they add water (hydrolyse)
______ are enzymes that degrade proteins by hydrolyzing bonds between amino acids
proteases
____ enzymes that synthesize molecules in anabolic reactions by joining two smaller
molecules
synthase
____ are enzymes that degrade nucleic acids by hydrolyzing bonds between nucleotides
nucleases
____ enzymes that catalyze the rearrangement of bonds within a single molecule
isomerase
___ are enzymes that catalyze the polymerization reactions in RNA and DNA synthesis
polymerases
__ are enzymes that catalyze oxidation/reduction reactions
oxido-reductase
*____ catalyze
addition of phosphate groups to molecules
kinases
___ catalyze the hydrolytic removal of phosphate groups from molecules
phosphatases
___ catalyze the hydrolysis of ATP
ATPases
(T/F) pH can affect E-S binding by protonation of aa in the enzyme
true
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
____ are Inorganic ions or a (nonprotein) or a metalloorganic molecules that are required by some enzymes to function
cofactors / prosthetic groups
_____ a cofactor that typically bind with enzyme through noncovalent interactions
coenzymes
addition/removal of a phosphate group does not involve which aa in and enzyme?
a. serine
b. glutamic acid
c. tyrosine
d. threonine
B
(T/F) phosphatases add phosphate groups to the sidechain hydroxyl groups of serine, threonine and
tyrosine residues
False
it REMOVES
(T/F) metal ion cofactors accept electrons and form coordination bonds w/ substrate/enzyme that help to properly position
reactive groups during catalysis
true
(T/F) phosphorylation alters the conformation (due to its neg chages) of enzyme at one site exhibiting an allosteric effect
true
(T/F) phosphorylation does not affect the rate of activity of an enzyme
false
activity may either be increased or decreased
by phosphorylation
___ are inactive precursors of enzymes that become activated upon proteolytic cleavage of specific covalent bonds within the precursor sequence
zymogens
___ are examples of zymogens
chymotrypsinogen
and trypsinogen
(digestive enzymes in stomach and pancrease)
(T/F) enterpeptidase cleaves trysinogen which catalyzes the conversion of chymotrypsinogen to chymotrypsin
true
which of the ff is a mismatch?
a. Chymotrypsinogen to chymotrypsin
b. enteropeptidase- trypsinogen
c. trypsinogen to trypsin
d. Chymotrypsinogen to trypsinogen
D
(T/F) the pancreas produce inactive zymogens that are packed in a lipid membrane to protect itself
true
______ 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
(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
____ an enzyme that Catalyzes the cutting of polysaccharide chains in the cell walls of bacteria and hydrolysis of adjacent sugar groups
lysozyme
_____ is associated with ATP regeneration in contractile or transport systems found in skeletal and heart muscles and brain
creatinine kinase
(T/F) elevated CK-MM levels is an indicator of mycardial damage/ infarction
false
measures CK-MB
_______ protein structure level where polypeptide chains are folded into ordered structures maintained by repetitive hydrogen bonding
secondary
_____ is the unfolding of a protein
denaturation
(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)
________ 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)
(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
_______ discovered the substance 2,3 bisphosphoglycerate
Reinhold and Ruth Benesch
(T/F) the affinity of O2 to Hb is higher in cells than in free solution
False
lower in cells, higher in soln
(T/F) BPG increases O2 affinity by a factor of 26
false
decreases it!
