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BCH 4053

Final Exam Concepts

TermDefinition
primary structure the amino acid sequence of a protein
secondary structure local arrangement of the protein in regards to alpha helices and beta sheets
tertiary structure the 3D folding a protein into its final form
quaternary structure when multiple tertiary structures come together to form a multi-subunit protein
consensus sequence the calculated order of most frequent residues found at each position in a sequence alignment
protein domains sections of a protein that can function independently if they were to be cleaved off
chaotropic agents a molecule in water solution that can disrupt the hydrogen bonding network between water molecules
hydrophobic collapse the early stage of protein folding that takes only 5 ms
molten globule much of the secondary structure of the native protein but little of its tertiary structure
folding funnel assumes that a protein's native state corresponds to its free energy minimum under the solution conditions usually encountered in cells
Bohr effect hemoglobin's oxygen binding affinity is inversely related both to acidity and to the concentration of carbon dioxide.
allosteric regulation the regulation of a protein by binding an effector molecule at a site other than the protein's active site.
symmetry model of allosterism postulates that enzyme subunits are connected in such a way that a conformational change in one subunit is necessarily conferred to all other subunits
sequential model of allosterism holds that subunits are not connected in such a way that a conformational change in one induces a similar change in the others. Thus, all enzyme subunits do not necessitate the same conformation; substrates bind via an induced fit protocol.
lock and key model both the enzyme and the substrate possess specific complementary geometric shapes that fit exactly into one another
induced fit model only the proper substrate is capable of inducing the proper alignment of the active site that will enable the enzyme to perform its catalytic function
prosthetic group A permanently associated coenzyme
epitope the part of an antigen that is recognized by the immune system
paratope the part of an antibody which recognizes an antigen
antigen any structural substance which serves as a target for the receptors of the immune system
transition state analogs chemical compounds with a chemical structure that resembles the transition state of a substrate molecule in an enzyme-catalyzed chemical reaction
cofactor metal ions
coenzyme small organic molecules
reaction molecularity the number of colliding molecular entities that are involved in a single reaction step
reaction order the index, or exponent, to which its concentration term in the rate equation is raised.
therapeutic index a comparison of the amount of a therapeutic agent that causes the therapeutic effect to the amount that causes toxicity.
lead compound used as a starting point to design even more efficient drug candidates.
clinical trial phases Phase I assesses the safety and tolerability of a drug. Phase II tests the efficacy of a drug candidate against the target disease and to assess dosing requirements. Phase III confirms the efficacy of a drug candidate and monitor its long-term effects.
double blind test neither subjects nor doctors know which group of patients receive the drug candidate or control compounds
integral proteins hydrophobic and are immersed into the lipid bilayer
peripheral proteins connected to the surface of the lipid bilayer
lipid-linked proteins membrane-associated proteins that contain covalently linked anchoring lipid molecules.
membrane skeleton maintains the shape of the cell and is important for cellular motion, intracellular transport and cellular division.
lipid rafts considered to be organizing centers for the intracellular signaling system.
intrasteric regulation the binding of Ca2–CaM to this peptide segment extracts the autoinhibitor from MLCK’s active site, thereby activating the enzyme
membrane potential the difference in electric potential between the interior and the exterior of a biological cell.
action potential a short-lasting event in which the electrical membrane potential of a cell rapidly rises and falls, following a consistent trajectory.
receptor desnitization decreasing the response to a signalling molecule when that agonist is in high concentration
fluid mosiac model the components of the plasma membrane are able to move laterally or sideways throughout the membrane
signaling peptide a short peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway
high energy compounds molecules with bonds that are hydrolyzed with large negative values of  deltaG
oxidoreductases catalyze redox reactions (transfer of e- or H atoms); ex: NAD+, NADP+, FAD, FMN
transferases catalyze the reactions of functional group transfer; ex: acetyltrasferases
hydrolases catalyze hydrolysis reactions; ex: peptidases, ATPases
isomerases catalyze the interconversion between isomers; ex: racemaes, toposiomerases
ligases catalyze the joining of two large molecules, which is usually accompanied by hydrolysis of ATP; ex: DNA ligase
lyases catalyze the non-hydrolytic cleavage of chemical bonds or the addition of groups (often water) to double bonds; ex: decarboxylase
chymotrypsin FYW, unless followed by P; pH=8
trypsin RK, unless followed by P; pH=8
endopeptidase V8 E; pH=8
elastase VAGS, unless followed by P; pH=8.5
competitive inhibition Km(app) increases; crosses the non-inhibitor line at the y-axis
uncompetitive inhibition Km(app decreases; V(max) decreases; parallel to non-inhibitor line
mixed (non-competitive) inhibition V(max) decreases; crosses the non-inhibitor line to the left of the y-axes
A DNA pitch of 2.5 nm; 11 bp/turn
B DNA pitch of 3.4 nm; 10.5 bp/turn
uniporter moves only one molecule in one direction; ex: GLUT1
symporter moves two molecules in one direction; ex: SGLT1
antiporter moves two molecules in opposite directions; ex: Na/K pumps
Created by: JacobGant