BIOC 192 - Module 1 (Protein structure and function)

Central dogma

This explains how genetic information flows across a cell. From DNA, to RNA and finally to proteins.

ATP

energy currency of the cell

What are the 4 groups attached to the central alpha carbon of an amino acid?

Amino group, acid group, hydrogen and R group

Which amino acid is the only exception to having a chiral center?

Glycine (its R-group is just a Hydrogen atom, meaning the central carbon is not chiral).

How is a peptide bond formed, and what are its key structural characteristics?

Formed via a condensation/dehydration reaction between the alpha-carboxyl group of one amino acid and the alpha-amino group of the next. Characteristics: It has partial double-bond character due to resonance, making it planar and rigid (restricting rotation around the C-N bond).

How many different amino acids are there?

20

Enzymes which break down proteins

Proteases

Protein which breaks starch down into sugars

Amylase

Enzyme which helps metabolise alcohol

Alcohol dehydrogenase

Hormone in cell signalling to take up glucose

Insulin

Protein which binds oxygen in the lungs and carries it in the blood to tissues for use in metabolism

Hemoglobin

Membrane protein which generates ATP for use in cellular functions

ATP synthase

Protein for DNA replication that binds to one strand of DNA and adds the complementary strand to it

DNA polymerase

Protein that creates a single strand of RNA that is complementary to one of the strands of duplex DNA

RNA polymerase

What is the main experimental technique used to determine protein structure?

Protein crystallography

Imino acid which does not have a protonated side chain

Proline (P), Pro

4 classifications of amino acids

Non-polar side chains, Polar side chains uncharged, Polar side chains charged acidic and basic

Two types of amino acid abbreviations

3 letter and 1 letter

pKa value

The pH at which the amino acid or protein group is 50% ionised

Isoelectric point (pI)

The pH at which the net chrage of an amino acid or protein is zero

When an amino acid is modified after it has been added to a protein

Post translational modification

Bond that forms when two cysteines for a covalent bond

Disulfide bond

What does a hydrophobic core help with in a protein

Stability of the protein structure

What is the alpha domain family?

Amphipathic helices with side-chains packed closely together with a hydrophobic core

What is the alpha/beta family?

A mixture of alpha and beta structure, creates barrel shape which is hydrophobic in the core.

What is the antiparallel family?

Mostly antiparallel structure

What are the key steps involved in folding a protein?

Primary, secondary and tertiary

What is a chaperone and what role do they play in protein folding?

Molecular chaperones are helper proteins that bind to unstable polypeptide chains to ensure they achieve the correct three-dimensional shape without becoming stuck or clumped together.

What is the role of enzymes

Catalyse thermodynamically favourable reactions by lowering activation energy

Three properties of coenzymes

Small organic molecules, carriers of electrons, atoms or functional groups and are often derived from vitamins.

What do isomerases do?

Transfer of atoms/groups within a molecule to yield and isomeric form

What do ligases do?

Join two molecules together and form a new bond

Two classes of cofactors

Inorganic and organic

How do enzymes lower Gibbs free energy?

Ground state destabilization and/or stabilize transition state, making it happier.

4 types of enzyme-substrate bonds

Ionic bonds, hydrogen bonds, Van der Waals interactions and covalent bonds

What do enzymes bind most effectively with?

The transition state of the reaction

Three properties of metal ion catalysis

Act as Lewis acids to polarize water or other functional groups, good sites for electron transfer (redox) and substrate orientation due to specific coordination geometry

What does an acid-base catalysis involve?

H+ transfer

What does covalent catalysis involve?

Formation of a reactive, short-lived intermediate which is covalently attached to the enzyme

What does Kcat mean?

The number of substrate molecules converted to product, per unit of time, when E is saturated with substrate.