Amino acids, peptides,

and
proteins
 Properties of Amino Acids

• capacity to polymerize
• novel acid-base properties
• varied structure and
chemical functionality
• chirality
• D –amino acids are not found proteins but found in
nature.
• Crystalline amino acids are colorless, odorless, and
melt with decomposition at temperature more than 200
°C.
• The physical properties of amino acids are resemble
those of inorganic salt such as sodium chloride
• The name protein is giving to compounds containing
more than 100 amino acids. An amino acid unite in a
polypeptide or protein is called residue.
 Functions of proteins

1. Enzymes : biological catalysis that are vital to all living systems.

They are simple or conjugated proteins.
2. Structural proteins: proteins that hold living systems together
such as collagen.
3. Hormones: proteins that act as messengers such as insulin.
4. Transport proteins: proteins that carry molecules and ions from
one place to another in the living system such as hemoglobin
carry oxygen from lung to cells.
5. Protective proteins: proteins that destroy any foreign substance
released into the living system by an infections agent.
6. Toxin: proteins that are poisons such as snake venom.
 Basic Amino Acid Structure
carboxyl group

 a-carbon is chiral
(except for glycine) amino group

 at pH 7.0 uncharged
amino acids are
zwitterions
 amino acids have a a-carbon
tetrahedral structure side chain
• Proteins are make about two third of dry weight of
cell.
• Major compounds of muscle, skin, and bones
• The molecular weight varied from several
thousand to several million.
• Treated with a boiled acids or bases solution
hydrolyzed the smaller compounds.
• Twenty amino acids are obtain from hydrolysis of
all living systems.
Amino Acid Enantiomers

•Steroisomers / enantiomers
•Biological system only
synthesize and use L-amino-
acids
 Amino Acid Classification
• Aliphatic
• Aromatic Hydrophobic
• Sulfur containing
• Polar/uncharged
Hydrophillic
• basic/acidic
 Aliphatic (alkane) Amino Acids

•Proline (pro, P)- cyclic “imino acid”

Hydrophobicity

•Glycine(gly, G)-only non-chiral amino acid, not hydrophobic

•Alanine (ala, A) – R-group = methyl-group

•Valine (Val, V) –Think V!

•Leucine (Leu, L) –

•Isoleucine (Ile, I) -2 chiral carbons

 Aromatic Amino Acids
• All very hydrophobic
• All contain aromatic group
• Absorb UV at 280 nm
• Phenylalanine (Phe, F)
• Tyrosine (Tyr, Y) – -OH ionizable (pKa = 10.5), H-Bonding
• Tryptophan (Trp, W) – bicyclic indole ring, H-Bonding
 Sulfur Containing Amino
Acids
• Methionine (Met, M) – “start” amino
acid, very hydrophobic

• Cysteine (Cys, C) – sulfur in form of

sulfhydroyl, important in disulfide
linkages, weak acid, can form
hydrogen bonds.
 Acidic Amino Acids
• Contain carboxyl groups (weaker acids than a-carboxyl-
group)
• Negatively charged at physiological pH, present as conjugate
bases (therefore –ate not –ic acids)
• Carboxyl groups function as nucleophiles in some enzymatic
reactions
• Aspartate –

• Glutamate –
 Basic Amino Acids
• Hydrophillic nitrogenous bases
• Positively charged at physiological pH
• Histidine – imidazole ring protonated/ionized, only amino
acid that functions as buffer in physiol range.
• Lysine - diamino acid, protonated at pH 7.0
• Arginine - guianidinium ion always protonated, most basic
amino acid
Polar Uncharged Amino Acids
• Polar side groups, hydrophillic in nature, can form hydrogen
bonds

• Hydroxyls of Ser and Thr weakly ionizable

• Serine (Ser, S) – looks like Ala w/ -OH

• Threonine (Thr, T) – 2 chiral carbons

• Asparagine (Asn, N) – amide of aspartic acid

• Glutamine (Gln, Q) – amide of glutamic acid

Essential/Non-Essential Amino Acids

• Essential –histidine, isoleucine,

leucine, lysine, methionine,
phenylalanine, threonine, tryptophan,
valine
• Non-essential – alanine, arginine*,
aspartate, asparagine, cysteine*,
glutamate, glutamine, glycine*,
proline*, serine, tyrosine*
 Titration Curve for Alanine
pK1 carboxylic acid = 2
pK2 amino group = 10
pI = (pK1+ pK2)/2

pI (isoelectric point) = the pH at which the number of positive and

negative charges on a population of molecules is equal (i.e. no net charge).
Peptide bond formation
 Reaction of amino acids
• The thiol side chain is oxidized by the
oxygen in air or oxidizing agent to form two
cysteine molecules.
 Note
• The zwitterions ions and peptide bond
formation is added to reaction of amino
acids.
Bond types in proteins
the following bonds responsible for
formation of protein structures:
1. Covalent bonds
2. Hydrogen bonds
3. Metal ligands
4. Ionic interactions
5. Disulfide bonds
6. Non-bond interactions
Deamination
 Protein Structure

Primary Assembly
STRUCTURE

PROCESS
Secondary Folding

Tertiary Packing

Quaternary Interaction
• Hydrogen bond is the responsible for secondary
structure.
• The attractive force in addition to hydrogen bond
between parts of proteins that important in
determining their shape.
• The α-amino acid coil as right handed screw
• The β-plated sheet structure are arranged side by
side and are hold together by hydrogen bond
between chains.
• The silk fibers is proteins that exist as a β-pleated
sheets