True or false : If oxygen is added to reduced ribonuclease dissolved in 8M urea, and enough O2 is added to form 4 disulfides (the maximum possible), then after the urea is dialyzed out the enzyme will be approximately 100% active.
urea indirectly disrupts ________ interactions
urea indirectly disrupts hydrophobic interactions by disrupting...
The urea indirectly disrupts hydrophobic interactions by disrupting solvent lattices, Thus the protein folds .....
The urea indirectly causes the protein to fold incorrectly, failing to keep SH's in....
consistently native-like pairings
Aspartate transcarbamoylase (ATCase) is an enzyme consisting of ____subunits.
Aspartate transcarbamoylase (ATCase) is an enzyme consisting of 12 subunits arranged as three ______ and two ________.
Regulatory (R) dimers
Catalytic (C) trimers
Aspartate transcarbamoylase (ATCase) is an enzyme consisting of 12 subunits arranged as ____ regulatory (R) dimers and ____ catalytic (C) trimers
Aspartate transcarbamoylase (ATCase) is an enzyme consisting of 12 subunits arranged as three regulatory (R) dimers and two catalytic (C) trimers. This feature of the enzyme's structure is information about its ________ structure.
Beta-mercaptoethanol (BME) denatures some proteins by
reducing protein disulfide bonds to produced unconnected ("free") cystenine SH groups
The BME effect often can be reversed by adding oxygen to the sample because
it will cause cysteines to reform protein disulfides.
How does urea denature proteins?
breaks H-bonds, both in proteins and in organized solvent lattices
The structure of urea H2N-CO-NH2 includes C=O and NH groups, which are H-bond....
acceptors and donors
Urea disrupts protein H-bonds in....
helices and sheets
Urea disrupts protein H-bonds moreover by
disrupting organized solvent lattices around exposed nonpolar group
Urea disrupts protein H-bonds moreover by disrupting organized solvent lattices around exposed nonpolar group so there is little benefit to....
burying nonpolar groups.
What "level" of protein structure is most closely associated with efficient H-bonding between backbone groups?
An example of an alpha helix is secondary because...
all NH and C=O groups are paired except at the two
ends of the cylinder. Repetition of phi-psi angles gives an efficient repetitive pattern of H-bonding.
What "level" of structure is most closely associated with consideration of the 3-dimensional folding of a single chain?
Why is the "level" of structure is most closely associated with consideration of the 3-dimensional folding of a single chain, tertiary?
This level of structure gives XYZ atomic coordinates for all atoms in 3d space : the full folded structure.
In a long alpha helix, the groups which participate in H-bonds of the alpha helix in the first four residues at the beginning (N-terminus) of the helix are ___ .
In the alpha helices trans peptide bond, the C=O points ...
ahead to higher numbered residues
In the alpha helix's trans peptide bond the NH points
behind to a pre-helix region
the NHs in alpha helices arents used so ______ can occur in the region because they lack NH bonds.
The sequence of residues 8 thru 14 in the bovine pancreatic trypsin inhibitor (BPTI) is Pro-Pro-Tyr-Thr-Gly-Pro-Cys. Based on this sequence, one would expect that this segment is likely to ___
be in a region which is not a helix
Why would one expect that this segment (Pro-Pro-Tyr-Thr-Gly-Pro-Cys) is likely to be in a region which is not a helix?
Because there is a high % of pro and gly, which disfavor helix formation.
In an alpha helix, the R group (sidechains) on the amino acid residues are found...
on the outside of the helix spiral
What forms the core of the alpha helix?
The backbone and the H-bond connections between backbone NH and C=O groups.
All sidechains, whether polar or nonpolar,......
extend from the core.
In an amphipathic surface helix, polar sidechains contact ______ and nonpolar sidechains contact______.
the interior of the protein
Two types of amino acids with a low propensity for inclusion in alpha helices are proline (because it lacks a backbone NH donor for H-bonds) and _______
why does proline have a low propensity for inclusion in alpha helices?
because it lacks a backbone NH donor for H-bonds
why does glycine have a low propensity for inclusion in alpha helices?
because it permits too much flexibility, so it can twist in the direction of a left-handed helix instead of being constrained to propagate the normal protein right-handed helix.
When Linus Pauling first proposed the existence of the alpha helix, no data existed for the actual configuration at alpha carbons. He arbitrarily used the D configuration in his model. What was wrong with his published model?
It had a left-handed spiral instead of a right-handed spiral.
What "level" of structure considers the multiple chains (numbers and types) in large protein complexes?
hemoglobin's structure of two alpha chains and two beta chains arranged in a tetrahedron. is an example of the _______ structure.
The peptide bond exhibits
The peptide amide bond has partial double bond character because
there is an extended pi cloud from the N: thru the C=O group.
The peptide amide bond has partial ______ bond character.
Protein denaturation refers to a process involving....
the unfolding of the compact native conformation of each chain.
In many cases, denatured proteins will renature to the native form if they are...
slowly returned to favorable physiological conditions (removal of the denaturing agents).
During folding of a nonmembrane protein into a water-soluble globular conformation, two entropy effects are a(an) ______ protein conformational entropy effect, and a(an) _____ effect for the solvent.
unfav protein effect
fav solvent effect
The word "quaternary" structure refers to which case of "4"?
proteins with any number of multiple subunits, regardless of the total number (2, 3, 4, 5, ...)
Quaternary structure formation is the ____ thing to happen during synthesis, folding, and assembly of a multi-subunit protein structure.
A description of the quaternary
structure of the enzyme aspartate transcarbamoylase is that it has 12 total subunits, comprised of __ regulatory chains (arranged as 3 dimers) and __ catalytic chains (arranged as 2 trimers).
The Ramachandran plot depicts
sterically permitted rotational (dihedral) angles along the backbone chain.
The "level" of protein structure involving repetition of a particular choice of phi and psi angles is
An example of a secondary structure is..
a helix, created by reptition of a particular twisted conformation which is sterically permitted.
TheC-N link is the peptide bond, which has partial double bond character and interacts with the oxygen of the C=O group to form an
extended pi cloud network.
Using CA to represent the alpha carbon and C to represent the carbonyl carbon, which of the backbone bonds exhibits the most restricted rotation in a poly-alanine homopolymer?
C-N because is has partial double bond character.
Which structure is not altered by urea?
urea does not alter primary structures because
Urea does not break peptide bonds, so it does not alter the protein sequence
The beta barrel in triose phosphate isomerase is pure _____
Strands of _______ and coils of _______ alternate along the primary sequence in triose phosphate isomerase
Three subunits arranged in a clockwise planar circular arrangement have a different quaternary structure from a counterclockwise arrangement. (true or false)
The counterclockwise arrangement in a circular quartenary structure is...
the clockwise arrangement viewed from the back side
A protein with four cysteines can form ___ different combinations which each contain two intramolecular SS.
If cys are labeled A,B,C and D, the combinations are ..
(AB,CD) (AC,BD) and (AD,BC) = 3 possibilities
Two types of amino acids with a high probability of occurrence in beta sheets are
Val and ile
Two types of amino acids with a high probability of occurrence in beta sheets are val and ile because
Most portions of beta sheets are buried . so nonpolar residues like val and ile are favored
Two types of amino acids with a low propensity for occurring in beta turns are
ile and val
Two types of amino acids with a low propensity for occurring in beta turns are ile and val because
Turns usually are exposed on the surface at the end of a sheet. Nonpolar residues like ile and val are therefore disfavored in turns.
The type(s) of secondary structure found in myoglobin and hemoglobin are...
each folded chain of myoglobin and hemoglbin has ___ helices plus short segments connecting them.
The number of residues per repeating pattern of backbone structure for the beta sheet is
The number of residues per repeating pattern of backbone structure for the beta sheet is 2.0 because,
Every other residue points above or below the plane of the sheet.
In oligomeric proteins all subunits must be identical (true or false)
false because Adult Hb (an oligomeric proteins) has two types of chains : alpha and beta sequences.
The term "regular" structure refers to a structure which is
constructed by repetition of a particular pattern of H-bonds or dihedral angles.
a repeated pattern, such as a particular combination of phi and psi dihedral angles in helices or sheets.
An example of a family of homologous sequences where there are both monomeric and oligomeric forms in nature is the ____ family.
In the oxygen-binding globin family, myoglobin is a _______ and hemoglobin is a ________.
The important properties of the types of amino acids most prevalent in silk, which permit formation of the structural features of that material, are that they are
small and not ionized
Silk is comprised of layers and layers of_________ efficiently stacked on top of each other.
It would be ____________ to bury ions away from water in a stack of sheets
Large sidechains in silk would probably generate _____________ preventing close packing of layers in the stack of beta sheets
The type(s) of secondary structure found in triose phosphate isomerase (TIM) is (are)
both alpha helix and beta sheet barrel.
The fully woven protein of triose phosphate isomerase has two ___________ layers
In triose phosphate isomerase, The beta barrel of parallel beta strands in the ________ is covered by a layer of parallel alpha helices on the ________
in triose phosphate isomerase, Each helix is opposite in orientation to the beta strand which ...
precedes or follows it.
In hemoglobin the first two oxygens bind ___ than the last two, thereby generating an overall ___ shaped binding curve.
less tightly, sigmoidal
The first two O2's in hemeglobin bind less tightly because
they have to do the extra work of breaking H-bonds and salt bridges in the tense (full deoxy) state.
Weaker binding of the first 2 oxygens in hemeglobin induces..
the T -> R transition
Weaker binding of the first 2 oxygens is followed by stronger binding of the last two oxygens, which gives an _______ curve.
In the full oxy state of Hb, the central pocket between the four subunits is smaller than it is in the deoxy state. (true or flase)
In the full oxy state, there is no room for DPG to bind in the ___________.
When carbon monoxide binds to Hb, it binds at each _____ site _____ tightly than O2
C=O is the same size and shape as O2, so it binds at the
oxygen binding site
Tight binding by C=O prevents binding of O2, leading to
death by C=O poisoning.
The curve shape giving high efficiency of transport of oxygen by hemoglobin is
an S-shaped curve
Efficient transport requires_______ O2 in the lungs and _______ O2 in the muscles
The S-shaped curve shape gives weak binding (promoting O2 _______) in the muscles and strong binding (O2 ________) in the lungs.
Each DPG binding site in Hb is ____ and occurs _____ .
in only one space between the four subunits
There is only 1 binding site for DPG, and it is between the
Diphosphoglycerate is negative (2 phos and 1 COO-), so it binds to a ....
Fetal hemoglobin is comprised of
In muscles, myoglobin binds oxygen _____ tightly than hemeglobin
In muscles, myoglobin binds oxygen more tightly than hemoglobin because
it helps the muscles strip O2 away from Hb in the capillaries.
When oxygen binds to myoglobin or hemoglobin, the iron atom moves further out of the plane of the heme group towards the oxygen. (true or false)
The iron of the heme group is pulled from __________ in the oxy form
two oppositte directions
Histidine and O2 balance each other in the oxy form, pulling on Fe from ____sides of the heme
In deoxy Mb or Hb, the histidine tugs Fe ....
out of the plane towards its side
In deoxy Mb or Hb, the histidine tugs Fe out of the plane towards its side because...
there is no competing tug from the other side.
When O2 is bound to Mb or Hb, the iron is oxidized to Fe+3. (true or false)
Iron remains _____ in both deoxy and oxy forms.
The total number of salt bridges is greater in the deoxy form of hemoglobin (compared with the oxy form). (true or false)
During the T to R transition, the
first two O2 that bind to Hb must break lots of salt bridges, so their binding is ___________.
The seal is able to remain under water for a long time because
the skeletal muscles have a high concentration of Mb.
The [Mb] in seal muscles is_____ times higher than in human muscles.
The sigmoidal shape of the oxygen-binding curve of hemoglobin is critically dependnent on ___ between alpha and beta subunits.
________ and _________ hold together the tense deoxy quaternary structure
weak hydrogen bonds
The Bohr effect relates to the effect of..
Changes in pH affects the histidine ______.
NH+/N: charge state
Changes in pH affect the histidine NH+/N: charge state which affects...
salt bridging to asp COO-.
pH is affected by
C=O binds much more tightly to Hb than O2 binds to Hb. By the time C=O has occupied two of the four O2-binding sites, the remaining sites exhibit consistently ___ O2 binding, which is bad in the ___ .
Strong O2 binding is bad in the muscles, because
it prevents release of O2 to muscle tissue.
In the lungs, CO2 is ___ by exhalation/inhalation. In the muscles, CO2 is ___ by metabolism.
CO2 is exhaled in the
Oxidation of glucose produces CO2 in
The transition from deoxy Hb to oxy Hb affects the binding of DPG. The transition ___ the size of a ___ pocket between the subunits.
Deoxy -> oxy shrinks pocket, squeezing out the...
DPG causes Hb to bind O2 ___ tightly and transport O2 ___ efficiently
much weaker binding in muscles = ______effect
Binding of DPG decreases binding of O2 to Hb. In the lungs this is a ___effect. In the muscles this is a ___ effect. With respect to oxygen transport efficiency, the net effect is ___ .
DPG is ___________ charged.
The adult binding site for DPG includes...
four histidines, two lysines, and two backbone N-terminal groups
In order to bind DPG more weakly in the fetus (so O2 is bound more strongly than in the mother), the adult DPG binding site is mutated to make it ___ positive. The mutation is ___ .
his(adult) -> ser(fetus)
DPG (diphosphoglycerate) = negative, so a more positive binding site would bind it more....
strongly, not more weakly.
The desired effect is to have the fetus bind O2 ___ than the mother. This can be achieved by having the fetus bind DPG ___ than the mother.
weaker DPG binding shifts the rxn to the .....
right (more O2 bound)
In the muscles, CO2 production slightly lowers the pH to 6.8. The pKa's of asp and his are 5.0 and 7.0 respectively. The dominant form at pH 6.8is...
is there a salt bridge?
salt bridge present.
Asp: pH 6.8 > pKa 5, so the deprot _____ dominates
His: pH 6.8 < pK 7.0, so the prot ____ dominates.
In the lungs, the following reaction shifts ___ , H+ ___ , and pH ___ . CO2 + H2O = H2CO3 = (H+) + (HCO3-)
pH increases to > 7
Reactions which promote salt bridges include (his with NH+ (2)hb(DPG) + 4(O2)4 and (DPG) Arrows to show dominance.
The reaction relating DPG binding and O2 binding is ___ . Thus DPG binding ___ O2 binding.
Hb(DPG) + 4O2 -> Hb(O2)4 + DPG
Reactions which promotes salt bridges in Hb tend to enhance formation of the ___ form.
tense (full deoxy)
Salt bridges lock the structure in the____ state
The initial O2 binding needs to break....
The more bridges that are present, the greater the
obstruction to O2 binding,
The more bridges that are present, the greater the impediment to O2 binding, thereby promotoing the _____ form.
The sickle cell anemia mutation generates a(an) ___ in the number of nonpolar residues exposed on the Hb surface. The mutation is....
glu -> val
How does the human body alter the [DPG] in red blood cells to adapt to conditions of (1) high altitude or (2) C=O in cigarette smoke?
high altitude -> higher DPG
smoking -> higher DPG
Enzyme Catalysts are not _________, and don't affect ____
Geometrically, the middle residue of the catalytic triad in trypsin is a
The geometric arrangement of the catalytic triad in trypsin is..
asp(-) his(+) ser(-)
How is chymotrypsinogen converted into chymotrypsin?
The backbone of chymotrypsinogen is enzymatically cleaved at several places, and some short pieces are discarded.
When chymotrypsinogen is cleaved and converted into chymotrypsin, the large pieces are held together by .....
Enzymes are complementary to the ___ .
Complementaritylowers the transition state's free energy since it is.
stably matched to the enzyme
Complementarity lowers the transition state's free energy since it is stably matched tothe enzyme. This decreases the _________ and ________ kinetics.
The enzyme ATCase (aspartate transcarbamoylase) catalyzes the first step in the multi-step synthesis of pyrimidine (single ring) nucleotides. CTP, a pyrimidine, is an inhibitor of ATCase. This is an example of
The enzyme ATCase (aspartate transcarbamoylase) catalyzes the first step in
the multi-step synthesis of pyrimidine (single ring) nucleotides
CTP, a pyrimidine, is an inhibitor of
The inhibitor and substrate bind at ________ sites.
The product of the long assembly line inhibits...
the first step in the biosynthesis pathway.
Dihydroxyacetone contains two
Dihydroxyacetone contains two OH groups. Addition of phosphate uses up....
one of those OH's to make one phosphoester group.
Dihydroxyacetone contains two OH groups. Addition of phosphate uses up one of those OH's to make....
one phosphoester group
The structure of DHAP, dihydroxy-acetone-phosphate, contains ___ C-OH groups.
A noncompetitive inhibitor may decrease substrate binding as representedby a(an) ___ in Ks. Alternatively, it may decrease conversion of S to P as represented by a(an) ___ in k-cat.
Larger Ks (substrate dissociation equilibrium constant) = more _________.
more dissociation = less S bound for conversion into __.
The rate constant k-cat is for...
S -> P
An electrophile is the opposite of a nucleophile. An electrophile is an electron ___ group which attacks an electron ___ group.
Ks is the ___ constant for substrate ___ .
Ks is the substrate (s) dissociation equilibrium constant for...
Triose phosphate isomerase (TIM) converts dihydroxyacetone phosphate into glyceraldehyde-3-phosphate. This requires movement of ___ from
substrate onto the enzyme and from the enzyme back nto the substrate.
COO- and NH+ groups on the TIM enzyme receive and donate ___.
The blood clotting system involves a series of different types of enzymes, each of which activates the next type in the series, leading torapid mobilization of the army of enzymes at the end of the phone tree. This type of system is called a(an) ____.
Some enzymes are regulated by phosphorylation / dephosphorylation. An example of a type of amino acid which may be phosphorylated is
The alcohols ____,____ and ____ may be phosphorylated to generate phosphoesters.
Two of the mechanisms by which enzymes catalyze bimolecular reactions are the proximity mechanism and the orientation mechanism. In these processes the enzymes help to overcome unfavorable ___ effects.
enzyme organizes reactants which hold...
reactive groups next to each other
To compete with substrate for the active site, the competitive inhibitor must resemble.....
the substrate to some extent.
The structure of the substrate ___ resemble a competitive inhibitor. The substrate ___ resemble a noncompetitive inhibitor.
Noncompetitive inhibitors bind at__________, not at the catalytic site.
separate regulatory sites
The role of the asp COO- group in trypsin's catalytic triad is
to stabilize a positive His NH+ neighbor.
The ene-diol intermediate of the DHAP -> ene-diol -> G3P (glyceraldehyde-3-phosphate) isomerization contains
1 C=C bond
2 C-OH groups
Type of inhibition that usually involves inhibitors that are structurally different from the substrate...
A transition state analog may function as a
competitive enzyme inhibitor
When using a competitive inhibitor (I), Michaelis-Menten curves obtained in the presence of I will show ___ and a(an) ___ compared to when I is absent.
the same k-cat
k-cat / km
k1 and k-1 are respectively the association and dissociation rate constants for the series E + S <==> ES. Km for the series E + S <==> ES -> EP is given by
(ways of losing ES) / (ways of gaining ES) =
(k-cat + k-1)/(k1) =
(k-cat + k-dissoc) / k-assoc
Km is approximately equal to ___ , and is large when substrate binding is ___ .
In a Michaelis-Menten plot, Km is read on the
X axis (S-init) at a data point matching a Y-axis value that is 1/2 V-max.
The Michaelis-Menten relationship is plotted as V-init (Y axis) vs ___ (X-axis), and is linear ___ .
(horizontal) at very high [S]
The single-experiment diagram plots ___ (Y axis) vs. ___ (X axis).
The single-experiment diagram plots ___ (Y axis) vs. ___ (X axis). V-init=?
V-init = V-max
The general form of the Michaelis-Menten equation is V-init = [k-cat E-tot S-init] / [S-init + Km] = V-max x [S-init] / [S-init + Km] . In the special case of V-init = V-max/2, S-init=?
S-init = Km
The type(s) of inhibitors not affecting V-max include ___ inhibitors.
The units of k-cat = ___ . The units of Km = ___ .
The units of V-init = ___ . The units of efficiency = ___ .