exam 1 Flashcards by Estee C

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

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

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

peptidyl transferanse

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

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

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

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

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

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

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

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

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

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

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which of the ff is not an acidic amino acid?

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

A and C

are both basic

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which of the ff is not an aromatic amino acid?

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

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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! :)

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

true

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which of the ff is not a basic amino acid?

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

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which of the ff is not a polar amino acid?

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

a charged aa

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

steric / spatial effect

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(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

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

true

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

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

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

partial double-bond character

due to resonance

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

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

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

N-terminal

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

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

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

false

N-terminal (amino group) is the beginning

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

polypeptide backbone

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

skin keratin, myosin

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

(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

``` 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 ```

___ 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

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

``` 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 ```

(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

``` _____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

(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

(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

____ 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 ```

(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

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

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

(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

(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

______ 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

_____ 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

(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

(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!