BIOCHEM: Protein folding

Describe some or all protein function and structures (6)

• Cell signaling - Hormone Proteins

• Digestion

• Metabolism

• Membrane Proteins

• Immune Protection

• Cell replication and Maintenance

Describe the properties of amino acids and how they relate to protein structure and function

Amino Acids consist of an amino group, a carboxyl group and a side chain that varies in functional group. Amino acids are all chiral except for glycine. The amino and carboxyl groups’ differing pKa values allow it to be a zwitterion in solution.

What are the different chemical properties of the different groups of amino acid side chains? (4)

• Nonpolar side chain

• Polar uncharged side chain

• Polar side chains, positive charge

• Polar side chain, negative charge

how do amino acids join to form peptides and proteins?

Amino acids join together by forming a peptide bond. The carboxyl group of one amino acid joins with the amino group of another to form a dipeptide.

Explain the importance of the peptide bond and describe its structure and key properties

The peptide bond is between an amine group and a carboxyl group of neighbouring amino acids. The resulting C=O bond on one of the carbon resonates so causes planarity for max pi-bond overlap. This bond has a dipole. The bond is primarily trans.

Define primary, secondary, tertiary and quaternary levels of protein structure

Primary – amino acid sequence of a protein

Secondary – local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residues

Tertiary – three-dimensional (3D) structure of a complete protein chain Quaternary – interchain packing and structure for a protein that contains multiple protein chains

Define the properties of the 𝛼-helix, β-sheet, and turns

The 𝛼-helix is a right-handed spiral that has an important H-bond between the carbonyl of amino acid n and the N-H bond on the amino residue n+4. The side chains point out from the helix, which increases stability. Has a dipole which is positive at the N-terminus.

β-sheets are comprised of ~2-10 β-strands, which are composed of ~6 amino acids. Strands are connected by H-bonds. β-sheets can have a parallel or antiparallel orientation between their strands (antiparallel strands have H-bonds orthogonal to their strand orientations.

What are the three main atoms in an Amino acid residue, and what are the symbols for the angle between them?

The main chain atoms in a protein are N, C𝛼 , C’

The bond angles between N and C𝛼 , are called by the Greek letters Φ (phi) and between C𝛼 and C’ are called by the Greek letters Ψ (psi)

These angles take on values ranging from 0 to +/- 180°

The chain angle between C’ and N is called by the Greek letter ⍵ (omega) and is usually very close to either 180°or 0°

Describe the interactions that stabilize the tertiary structure of a protein.

• Helix – turn – helix

• beta - hairpin: common, antiparallel, varying length

• Greek key: 4 antiparallel strands

• Strand – helix – strand:

Outline the steps involved in folding a newly synthesized protein, including the role of chaperones.