water interacts with other polar substances.
water interacts with ionic substances.
Water weakens the __________ _____ between two ions to make them dissolve.
When dissolved in water, the ions are surrounded by a ________ ______.
Found in ionic and salt bonds.
Attractive and repulsive.
Generates electric field.
This measures polarizability. Represented by "D" in the Coulomb's Law equation.
High D means ____ F.
What is the dielectric constant of water?
What is the range of dielectric constant for proteins?
Low D means ____ F.
The strongest hydrogen bonds are ________.
Van der Waal's interactions
Interactions of 2 uncharged, polarized bonds or a permanent dipole moment and a transient dipole moment induced in a neighboring molecule.
Interactions that are the major factor in protein membrane structure.
This has thermodynamic origin and depends on the fact of high water concentration. Entropy driven.
Type of substance to where one molecule has polar and nonpolar regions. (Hydrophobic and hydrophilic parts.)
pH of human blood.
Out of over 3000 known enzymes all are protein except for 6. What are these 6?
Proteins that determine which reactions do and don't occur.
protein that transports oxygen in the blood.
protein that stores iron.
protein that makes muscles contract.
proteins that bind to foreign substances.
The functions of proteins are dependent on ______ binding. This is the basis of all protein function.
Most amino acids are _ enantiomers.
Which is the only R enantiomer amino acid?
isoleucine and threonine
Which amino acids have two chiral centers? (ABC order)
Which is the only amino acid that is not an alpha amino acid?
Proteins and amino acids change charge depending on the pH. They are __________ species.
A zwitter ion causes the charges to be equal to where there is no net charge. The molecule is said to be ___________.
The relative hydrophobicity or hydrophilicity of each amino acid.
If a molecule has highly positive hydropathy, it is __________.
If a molecule has highly negative hydropathy, it is __________.
Peptide bonds are ______ geometry because of electronegativity difference, so they have no rotation.
This plot helps show the structures in a protein and gives clues to how and where they rotate.
All proteins have this type of structure that is covalent and allows them to link together.
Some proteins have this type of noncovalent hydrogen bonded structure characterized by regularities like alpha helices and beta sheets.
In L amino acids, alpha helices have a _____ handed helix when looking down from the amino terminal.
Alpha helices are formed when the pepto carbonyl from one residue forms a hydrogen bond with a pepto amino group ____ residues away. (TECHNICALLY 3.6 residues/turn)
Alpha helices and beta sheets are connected by _____ and turns.
Regions of a polypeptide, often coded by exxons, that look like they are independently folded. (ex. one of these can be regulatory, while another one is catalytic on the same polypeptide!)
Type of protein structure that gives it 3-D shape.
Type of protein structure that associates two or more proteins into an aligomer.
When quarternary structure links two proteins together, they are called an ________.
Aligomer with two of the same proteins.
Aligomer with two different proteins.
When tertiary structure is lost, the protein has been __________. (done with extreme pH, boiling)
First protein to have its structure determined by X-Ray crystallography.
integral membrane protein
Nonpolar protein that controls what goes in and out of a cell. (8 alpha helices)
Nonpolar protein, mostly beta sheet, that unusually has 4 disulfide bonds. (124 residues/15,000 molecular weight)
____ ______ determines sequencing, ______ determines folding, folding determines ________.
Chemicals that cause denaturation.
Appearance of a protein that has lost secondary and tertiary structure.
Experiment on denaturation:
protein - RNAse A
reagents - MSH and urea
Conclusion - Folding first, disulfide bonds form later.
Usual gel of choice in gel chromatography.
Separation of substances in solution by means of their unequal diffusion through semipermeable membranes
If the protein is an enzyme, _______ _______ may be at the active site and participate in the chemical reaction.
Example of molecular pathology (amino acids): Sickle cell results when _______ changes to ________.
Example of protein evolution: Sequences from enzymes from ______ _______ parasite show similar enzyme sequence of plants that mosquitos eat.
term for protein without a heme.
apoprotein + prosthetic group.
The hemes in myoglobin and hemoglobin both have a ___________ ring.
Hemoglobin and myoglobin cannot bind oxygen alone, the ________ _____ binds the oxygen.
Shorthand for proximal histidine.
Shorthand for distal histidine.
When no oxygen is present in the heme, the distal histidine (H64) is too ___.
When no oxygen binds, the distal histidine (H64) forms a bridge between the _____ and ___.
H64 forces CO to bond at an ______ _______ so that it weakens the bond between the CO and myoglobin/hemoglobin heme.
H64 _________ the bond between O2 and Fe2+ in the heme.
H64 _________ the bond between CO and Fe2+ in the heme.
Adult hemoglobin genotype.
HbF; gamma; strongly
___ is the fetal hemoglobin genotype. Has alpha2_____2 structure. Has one fewer (+) group than HbA, so it captures oxygen more _______.
Sickle cell hemoglobin genotype. Caused by hydrophobic valine.
"The Hill Coefficient." On the binding curve, hemoglobin fits when n=____ for the equation. Hb+ + nO2 <-> Hb(O2)n
Subunit communication occurs because of changes in _____ structure.
The principle of stabilizing deoxyhemoglobin to keep O2 from binding.
When CO bonds to the amino terminus of the hemoglobin, _______ is formed.
Van der Waal's interactions
Interactions that depend on steric complementarity and area of surfaces.
Enzyme organization and location is in the _______.
This is the most important characteristic of an enzyme.
Enzyme class that catalyzes oxidation/reduction reactions.
Enzyme class that catalyze group transfer reactions. (One substrate to another.)
Enzyme class that catalyzes hydrolysis reactions. (H2O added and bonds broken)
Proteases are a part of which enzyme class?
Enzyme class that is NOT hydrolytic. Catalyze the lysis of a substrate which generates a double bond.
Enzyme class that converts L enantiomers to D enantiomers. (Catalyze structural change within a molecule.)
Enzyme class that catalyzes the joining of two substrates.
The transformation of ATP to ADP is catalyzed by which enzyme class?
In the ____, substrate and enzyme concentrations are about equal. In the ______, we keep a much higher substrate than enzyme concentration.
Principle discovered by Michaelis and Menton; where it was discovered that at a certain point, increasing substrate concentration has NO EFFECT on the velocity of a reaction. Vmax can ONLY be increased by increasing enzyme concentration in this case.
enzyme substrate complex
The _____ _______ ______ was a key assumption made by Michaelis and Menton.
Measure of enzyme function.
Measure of catalytic efficiency and preference of an enzyme for certain substrates.
This rate (outside of M and M) limits the rate at which E and S can combine.
Form of reversible inhibition where I ONLY binds to E. (Thus, it takes up active sites and reduces S binding.)
In competitive inhibition, I competitors can be defeated by increasing _ concentration.
Competitive inhibition: Km: _______; Vmax _______.
Succinic dehydrogenase is an examples of a ________ inhibitor.
Form of reversible inhibition where I binds to E or ES complex.
Noncompetitive inhibition: Km: _______; Vmax _________.
Form of inhibition were I binds ONLY to ES. (THUS, adding more substrate does NOT reverse effects.)
Uncompetitive inhibition: Km ______; Vmax ______.
Type of inhibition where an inhibitor forms a covalent bond with an enzyme and deactivates it. "suicide substrate"
Penicillin is used cause ___________ inhibition.
Zymogens are precursors for ________.
Type of covalent modification that turns enzymes on/off.
Type of competitive inhibition where a substrate later INHIBITS the enzyme.
Ligand that speeds the velocity of enzyme on Michaelis Menton.
Enzyme is ______ by the primidine ___.
Enzyme is _______ by the purine ___.
ATP is a _____.
CTP is a _______.
Term for two enzymes that are the same but have different amino acid sequences. (example H4 and M4)
In the heart, H4 oxidizes lactate to _______.
In the muscle, M4 oxidizes pyruvate to ______.
Multienzyme complexes are sometimes called enzyme _________.
The longer the transition state persists in an enzyme substrate reaction, the ____ likely a product will form. This is because it ______ deltaE reaction.
A + B -> (AB) -> A-B
The _____ holds A and B together to speed the reaction rate.
Rigid place on the enzyme where reactions occur that identify polar residues in their clefts.
Type of catalysis that often involves tetrahedral intermediates.
We can isolate intermediates from covalent catalysis and determine what ________ of the enzyme that the substrate bound to.
pH maintained by organisms in order to satisfy enzymes.
Actives sites are formed because of interaction between ________.
In ______-controlled reactions, k1 (the rate of binding) is the rate limiting step. NOT k3.
One of the binding modes of catalysis, that increases effective concentrations of reactants by holding everything close together.
chemical modes of catalysis
e.g. acid/base catalysis; covalent catalysis
binding modes of catalysis
e.g. proximity effect; transition state stabilization
transition state stabilization
Abzymes employ which binding mode of catalysis?
The intermediate of chymotrypsin in esterase activity.
DIFP and TPCK are inhibitors of ___________.
Mechanism of chymotrypsin-catalyzed cleavage of a peptide bond is important because it employs all four modes of ________.
This class of proteases has an active site seryl residue.
tetrahedral; oxyanion hole; hydrophobic
In the chymotrypsin mechanism, part of the substrate forms a _________ (one word) intermediate which is stabilized by interaction with two backbone amides in the _________ ____ (two words). The chemical character of the "specificity pocket" in the case of chymotrypsin is ___________ (one word).
Reagent used in capillary electrophoresis that initiates DNA sequencing.
kcat and specific activity can be classified as ________ numbers.
rate of diffusion
What is the UPPER limit of catalysis?
This number approximates enzyme-substrate dissociation constant for many enzymes.