What are proteins and peptides made of, and what is unique about the bond that connects these components?

Proteins/peptides are chains of amino acids joined by amide linkages (i.e. peptide bonds).

The peptide bond joins the carboxyl of one amino acid to the amino group of the next.  It is a rigid bond due to tautomerism.

§  Enzymes: catalyze biochemical reactions

§  Contractile structures

§  Transport molecules: O₂/CO₂ carriers (i.e. hemoglobin)

§  Structural

Describe the general solubility properties of proteins.

Three major categories:

§  Fibrous and insoluble: i.e. collagen, elastin, and a-keratin

§  Globular and soluble: i.e. albumin and hemoglobin

§  Fibrous and soluble: i.e. fibrinogen

Describe what primary, secondary, tertiary and quaternary structures of proteins are.

§  Primary structure: the amino acid sequence

§  Secondary structure: result from rotation of the bonds in the amino acid chain (except the rigid peptide bond); can form the following structures:

o   a helix

o   b pleated sheet

o   b reverse turns

o   Random coiling

§  Tertiary structure: the helix and pleated sheet domains are folded to form a more compact structure; generally, the hydrophobic regions fold to the core and they hydrophilic regions extend out into solution

§  Quaternary structure: multiple polypeptide chains are held together by non-covalent forces to form one structure

What are the commonly occurring modifications of amino acids found in some proteins?

§  Acetylation: N-terminal residue of the protein is acetylated, making the proteins more resistant to degradation

§  Carboxylation: addition of ¾COOH

§  Hydroxylation: addition of ¾OH

§  Glycosylation: addition of glucose

§  Phosphorylation: addition of phosphate

§  Disulfide linkages: links different parts of the polypeptide chain together

What amino acids are sometimes found to be phosphorylated in proteins?

Amino Acids with OH group

Serine, Threonine, Tyrosine

§  a helix: tightly coiled helical formation; stabilized by hydrogen bonding between imido N-H on one part of the chain with an oxygen on a carbonyl 4 residues further down the chain; found in keratin

§  b pleated sheet: result from hydrogen bonding between neighboring chains; the hydrogen bonds are oriented perpendicular to the long axis of the chain; antiparallel is the most stable; found in g crystalline in eyes

§  b reverse turns: due to hydrogen bonding of amino acid sequences in the same chain; result in reversals in directions of the peptide chains (forms a U turn)

What stabilizes higher order structures in proteins?

§  Electrostatic attraction of charged residues (salt bridges)

§  Internal hydrogen bonding

§  Short-range Van der Waals and London dispersion forces between neutral residues (dipole-dipole and polarizability)

§  Entropy driven hydrophobic effect

What amino acids are likely to carry charges on side chains at neutral pH?

Seven total):

Aspartic acid, Glutamic acid, Tyrosine, and Cysteine: may carry negative charges

Lysine, Arginine, and Histidine: may carry positive charges

 What are zinc fingers, kringle domains, and leucine zippers?

Zinc fingers: a protruding loop of 12 amino acids formed when a zinc ion is complexed to four amino acids; found in some DNA binding proteins

Kringle domains: large loops held in place by 3 disulfide bonds

Leucine zippers: arrangements of leucines along one side of an a helix between two proteins

1. Detergents
2. Chaotropic agents
3. High temperatures (50-60°C or ­)
4. Drastic pH changes
5. Organic solvents

What is the hydrophobic effect?

Occurs in the tertiary structure of the protein; it is folded in such a way as to put the hydrophobic regions into the core with the hydrophilic regions extending out into solution.

Ex. when water is place in a hydrophobic solution, the water molecules will tend to bunch up and create a cage around the hydrophobic molecules.