• protein shape is specified by amino acid sequence.
• Amino acids are hooked together by peptide bonds. Peptides lead to a repeating sequence along the polypeptide backbone (protein) from which specific amino acides R or side groups extend.

• Enzymes make reactions occur much faster by concentrating and changing the shape of the substrate
• Single enzyme molecules can be used over and over again to catalyze the same reaction
• enzymes can catalyze both forward and reverse direction
• enzymes are very specific with substrates they bind to. They catalyze only one reaction.

1. surface-string: a rigid protein interacts with a surface loop as the interaction of spindle fibers (tubulin polymers) with a motor protein during mitosis.
2. Helix-helix: coil-coil helixes
3. Surface-surface: complimentary surface interact to hold things together.

• Equilibrium: when the rate of the forward reaction  balances the reverse reaction.
• Chemical Reaction Order: quantity of a reactant consumed; quantity of a product formed in unit time.. example: protein interaction...concentration of protein and what it binds to and to the strength of the bod.

• enzymes having broad substrate specificity are most active against one particular substrate.
• enzymes are generally specific for a particular steric configuration (optical isomer) of a substrate
• Low Km= enzyme is easily saturated; the lower the Km the better the binding (reaction will occur)
• High Km= not easily saturated

Rates of reaction :

 how fast or slow a reaction takes place. 

Four components of single reaction:  

 First enzyme and substrate bind together. Then the enzyme stresses specific bonds in the backbone of the substrate so that they approach the transition state. An acid R group from the amino acid glutamic acid present in the active site of the enzyme speeds up the reaction by providing an acid environment (localized pH change) and then another basic R group from the amino acid apsartane further stabilizes the transition state, water is added to the bond and cleavage occurs. 

• Kinase: Enzyme that tranfers the terminal phosphate group of ATP to a specific amino acid of a specific target protein.
• Polymerase: Enzyme that synthesizes DNA by joining nucleotides together using DNA templates as guides.
• Protease: Enzyme that conducts proteolysis...it begins protein catabolism by hydrolysis of the peptide bonds that link amino acids together in the polypeptide chain forming the protein.
• Synthase: an important enzyme that provides energy for the cell to use through the synthesis of ATP.

• initial interaction between enzyme and substrate is weak, weak interactions rapidly induce conformational changes in enzyme that strengthens binding and brings catalyic sites close to substrate bonds to be altered.
• after binding one or more mechanisms of catalysis generates transition-state complexes and reaction products. 
• possible mechanisms of catalysis are four in number.

Equilibrium constant (K.): Ratio of forward and reverse constants for a reaction and equal to the association constant. 

a A + b B [image] c C + d D

• Ligand: any molecule that binds to a specific site on a protein or another molecule.

• Vmax: Maximum velocity or rate in which the enzyme catalyized a reaction.
• Km.: the approximate measure of the affinity of the substrate for the enzyme.
• Vmax and Km are the two parameters which define the kinetic behavior of an enzyme as a function of (S).

1. Enzyme and substrate bind together. Orients precisely to enourage reaction
2. binding of substrate to enzyme rearranges electrons in substrate creating partial negative and positive charges that favor reaction
3. enzyme strains the bound substrate molecule forces it to transition state to favor reaction shape change on protein stresses the shape change.

• Enzyme cofactor: a non-protein chemical compound that is bound to a protein and is required for the proteins biological activity. "helper molecules" assist in biochemical transformations.

The role of vitamins in metabolism:

• essential organic compounds that the human body cannot synthesize by itself and must therefore, be present in the diet.
• Act as coenzymes for enzymatic reactions.
• Example: Vitamin A needed to make retina in eye.

Vitamin C: (supplement coenzyme)

• causes thicking and hardening of arteries
• Kidney stones
• slows down blood flow/ circulation
• causes cardiovascular diseases because it acts like a pro-oxidant forming white plaques that narrow arteries that lead to heart disease.
• in diabetes it will shut down normal pathway systems for normal radical compounds. (mitochondria commits suicide)

Vitamin E:

• causes thinning of the blood and while exercising blood circulates the body  too quickly which causes it to over work itself. 

Vitamins: essential organic compounds that the human body cannot synthesize by itself and must therefore, be present in the diet. 

1. Vitamin B₂ is better known as riboflavin used to form a coenzyme FAD important in the utilization of oxygen in the cells.
2. Niacin known as nicotinic acid, is also in the B complex of vitamins. Nicotinamide is a part of the important coenzyme,Nicotinamide Adenine Dinucleotide (NAD). This NAD⁺ coenzyme is important during biological oxidations.
3. Thiamin is also known as vitamin B1.The best-characterized form is thiamine pyrophosphate (TPP), a coenzyme in the catabolism of sugars and amino acids. In yeast, TPP is also required in the first step of alcoholic fermentation.

1. Allosteric Control:Regulation of binding affinity for ligands, and/or of catalytic activity, by conformational changes caused by binding of the same or other ligands at other sites on protein ("allosteric effects")

Catalysis by P and O increases the rate of the reaction as enzyme-substrate interactions align reactive chemical groups and hold them close together. This reduces the entropy of the reactants and thus makes reactions such as ligations or addition reactions more favorable, there is a reduction in the overall loss of entropy when two reactants become a single product.

This effect is analogous to an effective increase in concentration of the reagents. The binding of the reagents to the enzyme gives the reaction intramolecular character, which gives a massive rate increase.

1.  At the start of an uncatalyzed reaction there is an electron distribution between water and the carbonyl bonds
2. By pairing the atom with a carbonyl oxygen, an acid causes the atom to move away from the carbonyl carbon, making the atom more attracted to the electronegative oxygen of the water molecule. An acid likes to donate protons (H+) to other atoms.
3. By pairing it with the hydrogen of the water molecule a base causes the atom to move towards the water oxygen making it a better attack group for the carbonyl carbon. A base likes to take up H+.
4. Having appropriately positioned atoms on its surface enzymes can perform both acid and base catalysis at the same time.

• The induced structural rearrangements that take place with the binding of substrate and enzyme produce strated substrate bonds, which facilitates attaining transition state.
• New conformation forces substrate atoms and bulky cataytic groups (aspartate ad glutamate) into conformations that strain existing bonds.
• linking substrate to enzyme, chemical bond forming to cause shape changes.

• Takes place by covalent mechanisms, substrate is orientated to active sites on the enzymes in such a way that covalent intermediate forms between enzyme or co-enzyme and substrate.
• In this reaction the enzyme contains a reactive group, usually a nucleophilic residue which reacts with the substrate through a nucleophilic attack. This is usually carried out by pyridine, which is a better nucleophile than water that has a pKa of 5.5. The charge loss in the reaction during transitional state will then cause hydrolysis to accelerate. The residue becomes covalently attached to the substrate throughout the catalytic reaction adding an additional intermediate which helps stabilize later transition states by lowering the activation energy. The covalent bond is then broken to regenerate enzymes.Example: proteolysis by serine proteases, which include digestive enzymes (trypsin, chymotrypsin, and elastase) and several enzymes of the blood clotting cascade. These proteases contain an active site serine whose R group hydroxyl forms a covalent bond with carbonyl carbon of a peptide bode, causing hydrolysis of the peptide bond.