BIOCHEMISTRY Flashcards
Amphoteric
Amino acids that can donate and accept protons.
pKa
pH at which half of the species are depronated ; [HA]= [A-]
Amino acids exist in different forms at different pH values
- At low pH, AA is fully pronated
- At pH near the pI the AA, the AA is neutral zwitterion
- At high pH, AA is depronated
Isoelectric point (PI)
Averaging 2 pka points.
- AA without charge side chains have PI of around 6
- acidic AA have PI well below 6
- Basic AA have PI well above 6
Dipeptide
2 AA resuides
Tripeptide
2 AA residues
Oligopeptide
have few AA residues
Polypetide
have many (> 20) AA residues
Peptide bond formation
Formed by condensation or dehydration reaction (Loss of H2O). Breaking a peptide bond is a hydrolysis reaction.
Primary Structure
Linear sequence of AA in a peptide and is stabilized by peptides bond
Secondary Structure
Local structure of neighboring AA and stabilized by hydrogen bonds. Alpha helices and Beta pleated sheets. Proline can cause kinks in this structure.
Tertiary Structure
3D shape of polypeptide chain, stabilized by hydrophobic interactions, acid-base interactions, hydrogen bonds and disulfide bonds
Quaternary Structure
Interaction between peptides in proteins that contain multiple subunits
Denaturation
The process through which a protein is unfolded or loses its proper 3D structure. Often losing function.
Enzymes
Biological catalysts. Lower activation energy, increase rate of reaction, do not alter equilibrium constant, are not consumed by reactions, are pH and temperature sensitive, don’t affect overall ∆ G, Very specific
Oxidoreductase
Enzyme that catalyzes oxidation-reduction reactions that involves the transfer of electrons. Ex: Dehydrogenase.
Transferases
Enzymes that move function groups from one molecule to the other
Ex: Kinase
Hydrolases
Enzyme that break bonds with the addition of water.
Ex: Protease
Isomerases
Enzyme that rearrange bonds within a molecule.
Ex: Mutase
Ligases
Enzymes responsible for joining 2 large biomolecules
Exergonic reactions
reactions that release Energy, ∆ is negative
Endergonic reactions
reactions require energy input, ∆ G is positive
Lock and Key theory
hypothesizes that enzymes and substrate are exactly complementary
induced fit model
Hypothesizes that the enzymes and substrate undergo conformational changes to interact fully.
Cofactors or coenzymes
nonprotein molecules that help enzymes, are recruited when needed.
Saturation kinetics
As substrate concentration increases, the reaction rate does well until the maximum values is reached
Cooperative enzymes
Display sigmoidal curve because of change in activity with substrate binding
Feedback inhibition
catalytic activity of an enzyme is inhibited by the presence of high levels of a product later in the same pathway
Reversible inhibition
Ability to replace the inhibitor with a compound of greater affinity or remove it using mild lab treatment
Competitive inhibition
Inhibitor binds to active site, Km increases, Vmax unchanged. We will see change on X axis of line weaver- burk plot
Noncompetitive inhibition
Inhibitor binds at allosteric site, Km unchanged, Vmax decreases. We will see change on Y axis of line weaver- burk plot
Uncompetitive inhibition
Inhibitor binds allosteric site. Km decreases and max decreases. We will see change on X and Y axis of line weaver- burk plot
Irreversible Inhibition
Alters enzymes in that active site is unavailable for prolonged period or permanently changed
Regulatory enzymes
- Allosteric enzymes - can be occupied by activators, increase either affinity of enzymatic turnover
- Phosphorylation or glycosylation can alter activity or selectivity of enzymes
- Zymogens- secreted as inactive form and activated by cleavage
