BMSC 200 Module 3: Amino Acids, Peptides and Proteins

amino acids

Building blocks of proteins and proteins are linear polymers of amino acids.
Proteins are made of 20 amino acids.
REMEMBER ALL AMINO ACIDS!!!
They all have a H, C, NH3+, COO- and side chain.
All amino acids create a chiral center and the 4 diff groups have spatial arrangements giving different stereoisomers.

post-translational modification

Some amino acids can be modified after their incorporation into a protein such as phosphorylation which can be reversible.

disulfide bonds

• Form through the oxidation of the sulfhydryl groups of 2 cysteine residues to form a covalent linkage as they stabilize protein structures.
  Ex: when you cook an egg and it becomes white, you are unfolding the protein structures.

non- polar aliphatic amino acids

• Glycine (gly, G) Alanine (ala, A) Valine (val, V) Leucine (leu, L) Isoleucine (ile, I) Proline (pro, P) Methionine (met, M)
• Hydrocarbon side chain
• Residues with non- polar chains often buried in the core of a protein.
• Proline usually combines with glycine as glycine is the smallest and no chiral.
  Methionine is 1 of 2 amino acids with sulfur.

aromatics amino acids

• Histidine can also be an aromatic.
• Tyrosine can be a post- translation modified through phosphorylation.
• Phosphorylation is a mechanism to regulate protein functions.
• Tryptophan can be a popular supplement and a precursor of serotonin.
  -Tyrosin (tyr, Y) Phenylalanine (phe, F) Tryptophan (trp, W)

polar uncharged amino acids

• Serine and threonine can undergo phosphorylation of their hydroxyl group.
• 2 cysteine can form a covalent linkage called disulfide bond.
• Cysteine (cys, C) Asparagine (asn, N) Glutamine (gln, Q) Serine (ser, S) Threonine (thr, T)

positively charged amino acids

• Lys and arg always carry a +1 net charge.
• Lysine (lys, K) Arginine (arg, R) Histidine (his, H)

negatively charged amino acids

• Aspartate and glutamate (known as aspartic acids and glutamic acid, carry a net charge of -1.
• Glutamate is responsible for ⅕ basic tastes; umami.
• Aspartate (asp, D) Glutamate (glu, E)

diprotic and triprotic

• Disprotics will have 2 groups that accept and donate protons.
• Triprotics have ionizable groups (lys, arg, his, asp, glu, cys, tyr)
• Diprotics have 2 buffering regions and tris have 3.
  Ex: If you are given 2 pKa, that means it has 2 buffer regions. If you were trying to find the net charge at some regions then draw out the graph and draw out the structure how would look like.

peptide bonds

• Has a carboxyl group w/ amino acid and an amino group w/ another amino acid.
• Formation is from a condensation rxn of both carboxyl group and amino acid.

main chains

• Constant portion of the polypeptide but not the side chains.
• Consists of NCC NCC NCC which is the amino group, carboxyl group, alpha carbon group.

partial double bond characteristics

• Rotation around the C-N is restricted due to the partial double bond.
• This results in the 6 atoms of the peptide group are rigid and planar.

configuration

• Creates a cis- trans isomer where ) of the carboxyl group and H of the amide nitrogen are usually trans to each other.
• Cis is usually from the steric interference with the side chain groups.

four levels of protein structure

Primary-
Linear sequence of amino acids.
Presented from N (amino) to the C (carboxyl)
Usually seen as letters that represent the amino acids.
Secondary-
Localized interactions within the polypeptide.
Maintained by hydrogen bonds b/w main- chain amide and carbonyl groups.
Ex: -Helices and - sheet
Optimize the hydrogen bonding potential of main- chain where N-H are donor and C=O are acceptors where they can rotate from -180 to 180
Tertiary-
Final folding pattern of a single polypeptide.
Quaternary structure-
Folding pattern when multiple polypeptides are involved.