BCH210: Biochemistry

Indole

Aldehyde

Thiol / Sulfhydryl

Proton Donor

A substance that releases hydrogen ions in detectable amounts; an acid. H+ can be easily removed.

Proton Acceptor

A substance that takes up hydrogen ions in detectable amounts; a base. Lone pair can bond with proton.

Amide

Amine

Carboxyl

Carbonyl

Ester

Ether

Hydroxyl

Imidazole

Ketone

Phenyl

Phosphate

Covalent Bonding

Electron sharing between two adjacent atoms. Highest strength and lowest distance.

Ionic interactions

Salt bridges, strength dependent on interaction

Hydrogen Bonds

Strength is proportional to the polarity of the H bond donor & acceptor.

Hydrophobic interactions

Depends on the entropy of water being released, causing hydrophobic regions to come together.

Van der Waals

Relatively weak and depends on the size of the atoms and the distance between them.

Cofactors

Non-protein compound assisting activity

Coenzymes

Organic cofactor

Co-substrate

Temporary coenzyme

Ligand

Reversible binding molecule

Metal Ion

Inorganic cofactor

Prosthetic Group

Permanently bound cofactor

Silent Mutation

mutation with no effect on polypeptide

Non-Conservative mutation

mutation that creates a different polypeptide

Conservative mutation

mutation that creates a similar(ish) polypeptide

Chromotography

Differential partitioning of a molecule between mobile (buffer) and stationary (column) phase.

Size or Shape

Size-Exclusion/Gel Filtration chromatography

Charge

Ion Exchange Chromatography

Binding Interactions

Affinity chromatography

Hydrophobicity

RP-HPLC (Reverse Phase High Pressure Liquid Chromatography)

CM

cation exchange resin, attracts CATs, is AN

DEAE

anion exchange resin, attracts ANs, is CAT

alpha helix

wavelengths 1650-1660

beta sheet

wavelengths 1620 - 1640

beta turns

wavelengths 1675-1695

random coils

wavelengths 1670-1680

alpha helices

CD wavelength 222nm, 208nm (neg) , 195nm (pos)

beta turns

CD wavelength 217nm (neg)

random coil

CD wavelength 198 nm (neg)

Zymogen

inactive precursor of an enzyme

Irreversible Activation Example

Zymogen cleavage

Irreversible Inhibtion Example

Aspirin & COX1

Competitive

the inhibitor binds to the active site, K_m up and V_max the same

Un-Competitive

inhibitor can only bind to the ES complex, K_m and V_max both down

Non-Competitive

inhibitor binds to the enzyme or ES complex, K_m is unchanged and V_max is down

Oxidoreductases

Oxidation-reduction reactions (NADH, NADPH, FADH2 , O2). Examples: Diamine oxidase, lactate dehydrogenase

Hydrolases

Hydrolysis reaction (transfer of fx group to water) Examples: ATPases, Trypsin

Lysases

Addition or cleavage reactions. Usually involves double bonds and/or cyclization. Ex: Carbonic anhydrase, Adenylyl Cyclase

Isomerases

Group transfer within a molecule. Ex: Phosphoglucomutase

Ligases

Joining 2 molecules using nucleotides (ATP/GTP etc.), Ex: Biotin protein ligase

Translocases

Movement of ions or molecules across a membrane, Ex: Flipases, Ca2+-ATPas

Transferases

Functional group transfer between molecules. Examples: PKA