Ch 16 - Proteins: Structure, Function, and Enzyme Inhibition

Amino acids

Building blocks of proteins - 20 naturally occurring amino acids.

alpha carbon of amino acid

central carbon connecting amine and carboxylic acid is tetrahedral and chiral. Is bonded to the side chain that defines the amino acid

Peptide bonds

The peptide bonds between amino acids are formed through amidation reactions.

Peptide backbone

Peptides have the same amino acid backbone and the AAs are differentiated by their side chains (residues).

Polypeptide

Peptide with many amino acids. A polypeptide is a protein if it has >50 amino acids.

Primary structure

Primary structure is the sequence of amino acids in a protein.

Disulfide bridge

Disulfide bridges are covalent bonds that stabilize the protein structure.

Secondary structure

Secondary structure describes the local folding of the polypeptide chain. Involves H bonding between carboxylic acid and amine in backbone

types of secondary protein structures

alpha helix and beta pleated sheet

Tertiary structure

Tertiary structure describes 3D structure (folding) resulting from interactions within a single polypeptide and with the outside environment.

Prosthetic Group

Prosthetic groups are non-polypeptide units that are tightly and permanently attached to proteins. (example: heme)

Quaternary structure

Interactions between multiple polypeptide chains. Same interactions as tertiary.

Hemoglobin

Hemoglobin is an example of a protein with quaternary structure.

Denaturation

Denaturation is the process in which proteins lose their structure and function.

Ways to denature

Ways to denature include heat, pH changes, mechanical agitation and certain metals

Result of denaturing

The result of denaturing is the loss of biological activity.

Salt bridges

Ionic interactions between charged side chains.

Peptides

Polymers made of amino acid monomers.

C-terminus

End of a peptide with a free carboxyl group.

N-terminus

End of a peptide with a free amino group.

Enzyme-Substrate Complex

Temporary complex formed when substrate binds enzyme.

Induced fit model

Enzyme changes shape to better fit substrate after substrate initially binds via electrostatic forces

Activation energy

Energy required to initiate a chemical reaction.

Enzyme inhibitors

Compounds that prevent enzyme activity.

Competitive inhibitors

Compete with substrate for active site binding.

Non-competitive inhibitors

Bind elsewhere on enzyme altering enzyme activity by changing conformation of enzyme and active site without competing directly for active site

Feedback inhibition

Process where product inhibits its own production, as in cholesterol being its own non-competitive inhibitor

ACE

Enzyme converting angiotensin I to angiotensin II.

Aldosterone

Hormone that promotes salt and water retention. Produced in response to angiotensin II being produced by ACE

Vasoconstriction

Narrowing of blood vessels to increase blood pressure, induced by aldosterone

How does the induced fit model reduce activation energy?

After substrate binding, the enzyme changes shape for better "fit" - reactants/substrate are arranged for optimal reaction efficiency.

Enzyme function

Dependent on pH and temperature conditions. A fever can reduce enzyme function

Amidation reaction

Process forming peptide bonds between amino acids.

amino acid at pH 7.4 (R = neutral)

Amine is + and carboxylate is -. Charges cancel. Amino acid is neutral

lysine at pH 10 (basic)

Amines are neutral. carboxylic acid is conjugate base with -1 charge. total charge is -1.

lysine at pH 1 (acidic)

carboxylic acid is neutral. amines are conjugate acids with +1 charge each. Total charge is +2.

glycine at pH 1 (acidic)

carboxylic acid neutral; amine as conj. acid (+1), total charge is +1.

leucine at pH 11

base in neutral form. carboxylic acid is -. total charge is -1 (leucine is neutral)

aspartic acid acid at pH 1

acids are in neutral form. Base is in conj. acid with +1. Total charge +1

Which amino acids would be on the outside of an enzyme in aqueous solution.

the ionic and polar ones.

Which amino acids would be on the inside of an enzyme in aqueous solution?

non-polar ones.

are amino acids chiral?

Yes (19 out of 20) are chiral.

Which enantiomer of amino acids is naturally produced?

L

How can you tell D or L from a Fischer projection of an amino acid?

amine is on right = D; on left = L

Amino acid fischer projection

C-terminus at top. N-terminus on left for L and right for D. Side chain on the bottom. H opposite amine.