EC 1 Oxidoreductases Involved in redox rxns where H, O, or electrons are transferred between molecules

EC 2 Transferases Transfer of atoms (or group of) between two molecules, but excluding those
classified in the other groups
EC 3 Hydrolases Hydrolytic rxns and their reversal
EC 4 Lyases Elimination rxns where group of atoms is removed from the substrate, often
leaving double bonds
EC 5 Isomerases Catalyze molecular isomerizations;
Include epimerases, racemases, intramolecular transferases
EC 6 Ligases Formation of covalent bond joining two molecules, coupled with the hydrolysis
of a nucleoside triphosphate

Units of Enzyme Activity- amount of enzyme needed to Amino Acids and Proteins
produce 1 mol of product under standard conditions *​Enzymes​ are proteins.
*​Proteins ​are composed of amino acids.
KATAL​- per second General Formula:
U- ​per minute
1Kat = 60 000 000 U COO​- ​(carboxyl group)
|
H --C*(α-Carbon or 2-carbon) --- NH​3​+
| (amino group)
R (Side chain)

Amino Acid 3-Letter 1-Letter Abbrev. Amino Acid 3-Letter Abbrev. 1-Letter Abbrev.
Abbrev.
Glycine Gly G Asparagine Asn N
Alanine Ala A Glutamine Gln Q
Valine Val V Lysine Lys K
Leucine Leu L Arginine Arg R
Isoleucine Ile I Histidine His H
Proline Pro P Tyrosine Tyr Y
Serine Ser S Tryptophan (e) Trp W
Threonine Thr T Phenylalanine Phe F
Aspartate Asp D Cysteine Cys C
Glutamate Glu E Methionine Met M

*19 amino acids are ​CHIRAL. ​(see pictures for L- and D- *At physiological pH (pH=7) the amino (α-amino) and
amino acids) carboxylic (α-carboxylic) exist as -NH​3​+​ and -COO -​​ .
*Amino acids used in protein assembly are in Hydropathy​- relative hydrophobicity or
L-configuration hydrophilicity;
* Amino acids in ​L-configuration ​are in the important determinant of protein-chain
S-configuration ​except ​cysteine. folding
L- laevo; D- dextro; S-sinister; R-rectus Peptide bond​ - links amino acids
- groups involved carry no ionic charges
Order of Priority for Most Common Groups (lowest to (-ine or -ate is replaced with -yl but -e is
highest): replaced with -yl for asn, gln, cys only)
-H, -CH​3​, -C​6​H​5​, -CH​2​OH, -CHO, -COOH, -COOR,
-NH​3​, -NHR, -OH, -OR, -SH Chains of…
pKa​- measure of acid strength Dipeptide Two
pH​- measure of acidity Tripeptide Three
Oligopeptide Several (up to 20)
Henderson-Hasselbach equation​: Polypeptide Many (more than 20)
pH = pKa + log (conjugate base/conjugate acid)
Proteins Too many
Amino group​:
(more than 100)
-NH​2​ (conjugate base) <--> -NH​3​+​ (conjugate acid)
Carboxyl group​:
1 amino acid residue = 110 MW
-COO​- ​(conjugate base)<--> -COOH (conjugate acid)
Many proteins have ​400-500 residues.
Residues are numbered from the ​N-terminus to the
C-terminus (1-r).

Levels of Protein Structure:

Primary Structure Linear sequence of amino acid residues
Secondary Structure Regularities in local conformations maintained by H-bonds between H’s and carboxyl O’s of the
peptide backbone
 Beta turns- ​most compact turn
*complete reversal of the polypeptide chain in only four polypeptides often found in antiparallel
B-sheets
Tertiary Structure -Describes the completely folded and compacted polypeptide chain which contain one or more
globular units (domains).
-Stabilized by interactions of side chains of non-neighboring amino acid residues.
-Formation brings distant portions of the primary structure close together
Protein Folding- ​depends on several noncovalent forces (hydrophobic effect, hydrogen bonding,
van der Waals, charge-charge interactions).
Quaternary Structure -Association of two or more polypeptide chains into a multisubunit, or oligometric protein.
-Each subunit is a separate polypeptide chain called a ​monomer ​or simply a chain.
-Multisubunit protein is called ​oligomer.
X-Ray Diffraction​: radiation of any kind is diffracted when passing through a regular, repeating
structure.

Enzymes: Properties and Activities:

Enzymes​- catalyze reactions from 10​3​ to 10​17​ times as Catalase​- catalyzes degradation of H​2​O​2
the non-catalyzed reaction Heme Group​- consists of a porphyrin ring (composed of
- are specific or selective 4 pyrrores) with an Fe II in the center
Chemioselective Acts on a single type of functional NADPH​- Nicotinamide Adenine Dinucleotide Phosphate
group (reduced form)
Example: Benzoic acid or Other coenzymes:
benzaldehyde or benzene alcohol NADH Nicotinamide coenzyme
Regioselective Acts on functional groups ATP Adenosine Triphosphate
chemically situated in different FAD Flavin adenine
regions of the same substrate dinucleotide
molecule Coenzyme A Acetylation enzyme
Examples: o-phthalic acid or Cytochrome C Heme-containing protein
m-phthalic acid coenzyme
Enantioselective Acts on one of the enantiomers of
a chiral compound *Enzymes are sometimes regulated
Ex: (S)-1-phenylethanol or Enzyme Regulation​- is necessary to the maintenance of
(R)-1-phenylethanol a stable intracellular environment
Two Major Strategies:
The importance of chirality: Covalent Modification Reversible
S R interconversion between
Asparagine Bitter Sweet the active and inactive
Carvone Caraway Spearmint forms
Chrysanthe Inactive Active Allosteric Regulation Allosteric sites are
mic acid present in the enzyme
Methadone 50-fold more active where an inhibitor or an
Adrenaline Activity=1 Activity=50 activator can attach
Barbiturates Convulsant Narcotic
Thalidomide Teratogenic Harmless Enzyme Inhibition​- binding of activators or inhibitors
Propranolol Beta-blocke Contraceptive regulate activity in some enzymes
r 1. Uncompetitive inhibition
2. Noncompetitive inhibition
Enzyme “Recognition”: ​“Lock-and-Key” model​ and 3. Mixed inhibition
“Induced-fit” model 4. Competitive inhibition (Classical and
Enzyme - contain a unique, intricately shaped binding Non-classical)
surface called the ​active site.
*Active site​- a small cleft or crevice on an
otherwise large protein.

*Enzymes sometimes require non-protein components

for activity
Cofactors:
1. Essential ions​- inorganic components (e.g
Mg​2+​, Zn​2+​); activator ions (loosely bound);
metal ions of metalloenzymes (tightly bound)
2. Coenzymes​- complex organic molecules;
cosubstrates (loosely bound); prosthetic
groups (tightly bound)
Apoenzyme​- an enzyme lacking an essential cofactor
Holoenzyme​- an intact enzyme with bound cofactor