BIOL 12 Protein Structure and Function

What is the general structure of an amino acid?

Alpha carbon atom, amino group, carboxyl group, R group side chain, H atom

What is the charge of the amino and carboxyl group at pH 7?

The amino group is protonated and has a +1 charge, the carboxyl group is deprotonated and has a -1 charge

What are the 4 categories of R groups?

• Non polar (hydrophobic)

• Polar charged (hydrophilic)

• Polar uncharged (hydrophilic)

• Unique

What three amino acids can be phosphorylated?

Serine, threonine, tyrosine (all polar uncharged)

What are the amino acids with unique properties?

Glycine

• Single H for R group

• Fits into either hydrophobic or hydrophilic environment

• Often resides where 2 polypeptides come into close contact

Cysteine

• Side chain is polar uncharged

• Can bond w/ another cysteine to form a disulfide bond

Proline

• Hydrophobic character

• Creates kinks in polypeptide chains (helix breaker)

• Rigid structure due to 2 covalent attachment to backbone

How are polypeptides formed?

Condensation reaction → peptide bond

What are the two ends of a polypeptide?

N (amino) terminus and C (carboxyl) terminus

What are the 4 stages of protein structure?

Primary — amino acid residues (sequence)

Secondary — alpha helixes, beta sheets

Tertiary — Polypeptide chain and 3D structure

Quaternary — Assembled subunits

What are alpha helixes important for? Would you expect an alpha helix spanning the lipid bilayer to have mostly hydrophobic or hydrophilic R groups?

Important for integral membrane proteins

Hydrophobic

What bonds connect beta strands?

H-bonds

What do multiple beta strands make?

Beta sheets

Antiparallel vs. parallel beta sheets?

Antiparallel → NC CN NC

Parallel → NC NC NC

What forces maintain a tertiary structure?

Non covalent forces:

Van der Waals forces, H-bonds, ionic bonds

Covalent:

Disulfide bonds between cysteine residues (inter or intramolecular)

What is a homodimer vs. heterdimer vs. homotetradimer?

Homodimer — two of the same subunits

Heterodimer — two different subunits

Homotetradimer — four of the same subunits

Explain the components of phosphorylation