AMINO ACIDS Only 20 amino acids are common in proteins. Amino acids are the building blocks of proteins. Only 20 amino acids are common in proteins. They are called -amino acids because amino group is attached to the -carbon, which is next to the carboxylate group. Each amino acid has a name, three-letter abbreviation, and one-letter abbreviation.

AMINO ACID “R” GROUPS Amino acids are categorized into four groups based on the “R” group characteristics. The “R” group can be: 1. neutral and nonpolar (e.g. -CH3), 2. neutral and polar (e.g. -CH2-OH), 3. basic (e.g. -CH2CH2CH2CH2-NH3+), or 4. acidic (e.g.-CH2-COO-).

COMMON AMINO ACIDS

COMMON AMINO ACIDS (continued)

COMMON AMINO ACIDS (continued)

COMMON AMINO ACIDS (continued)

AMINO ACID ZWITTERIONS Amino acids exist as zwitterions, a dipolar ion that results from an internal acid-base reaction. Note that the net charge of the zwitterion is zero.

AMINO ACID ZWITTERIONS (continued) The isoelectric point is the pH at which an amino acid has a net charge of zero. At pH values above the isoelectric point, the amino acid has a net negative value. At pH values below the isoelectric point, the amino acid has a net positive value. Amino acid solutions can act as buffers because they react with both H3O+ and OH-. “R” Group Isoelectric Point Neutral About pH 6 Acidic Less than pH 6 Basic More than pH 6

AMINO ACID PROPERTIES Properties that result from existing as zwitterions: White crystalline solids Relatively high melting points High water solubility

AMINO ACID STEREOCHEMISTRY In 19 of the 20 amino acids, the -carbon is chiral. With few exceptions, the amino acids in living systems are in the L form. Glycine is the achiral amino acid.

STEREOCHEMISTRY Many carbohydrates exist as enantiomers (stereoisomers that are mirror images).

STEREOCHEMISTRY (continued) A chiral object cannot be superimposed on its mirror image. A chiral carbon is one that has four different groups attached to it.

STEREOCHEMISTRY All naturally occurring amino acids exist as L-amino acids The enantiomeric pair are mirror images – also called stereo-isomers. COO- NH3+ R L-Amino Acid D-Amino Acid

AMINO ACID STEREOCHEMISTRY For all amino acids (except glycine), the -carbon is chiral. With few exceptions, the amino acids in living systems are in the L form. COO- NH3+ R

ENANTIOMER PROPERTIES The physical properties of D and L enantiomers are generally the same. D and L enantiomers rotate polarized light in equal, but opposite directions.

ENANTIOMER PROPERTIES (continued) The enantiomer that rotates polarized light to the left is the levorotatory or (-) enantiomer. The enantiomer that rotates it to the right is the dextrorotatory or (+) enantiomer. The D and L designations do not represent dextrorotatory and levorotatory. The property of rotating the plane of polarized light is called optical activity, and the molecules with this property are said to be optically active. Measurements of optical activity are useful for differentiating between enantiomers.

AMINO ACID REACTIONS (continued) Peptide bond formation enables amino acids to make polymers by forming amide (peptide) linkages.

AMINO ACID REACTIONS (continued) Dipeptides are compounds made of 2 amino acids joined by peptide linkage. The order of linkage is important because two different dipeptides can be formed when two unique amino acids react.

AMINO ACID REACTIONS (continued) Peptides are an amino acid polymer of short chain length. A polypeptide is an intermediate chain length polymer with less than 50 amino acids. A protein is a polymer with more than 50 amino acids. An amino acid residue is an amino acid that is part of a polymer. By convention, peptides are written with the N-terminal residue on the left and the C-terminal residue on the right.

IMPORTANT PEPTIDES Vasopressin and oxytocin are hormones released by the pituitary gland and classified as nonapetides. Both have disulfide bridges. They differ only in 3rd and 8th amino acids. Vasopressin (antidiuretic hormone) decreases urine formation. Oxytocin causes uterine contractions.

IMPORTANT PEPTIDES (continued) Adrenocorticotropic (ACTH) hormone is released by the pituitary gland. ACTH contains 39 amino acids. ACTH has no disulfide bridges. ACTH regulates the production of steroids by the adrenal gland.

IMPORTANT PEPTIDES (continued)

PROTEIN SIZE

PROTEIN SIZE (continued) are extremely large natural polymers. have molecular weights of ~6000 – several million u. are too large to pass through cell membranes. are contained inside the normal cells where they were formed. can leak out if cell is damaged by disease or trauma. Protein in urine can indicate damaged kidneys. Heart enzymes in blood can indicate a heart attack. A typical human cell contains 9000 different proteins. The human body contains ~100,000 different proteins.

PROTEIN ACID-BASE PROPERTIES Proteins: take the form of zwitterions. have a characteristic isoelectric point. behave as buffers in solutions. can be in solution or form stable colloidal dispersions. The form depends on the repulsive forces acting between molecules with like charges on their surfaces. Repulsion is weakest at the isoelectric point, when: the net charge is zero; proteins clump and precipitate from solution.

PROTEIN FUNCTIONS

PROTEIN FUNCTIONS (continued)

PROTEIN FUNCTIONS (continued) Catalytic proteins function as enzymes. Structural proteins in animals form the structural materials other than the inorganic components of the skeleton. Storage proteins can store small molecules or ions. Protective proteins are antibodies, a substance that helps protect the body from invasion by viruses, bacteria, and other foreign substances, as well as blood clotting. Regulatory proteins are responsible for hormone regulation of body processes. Nerve impulse transmission proteins are receptors of small molecules that pass between gaps separating nerve cells. Movement proteins are muscle proteins. Transport proteins are proteins that bind and transport numerous small molecules and ions through the body.

PROTEIN SHAPES Fibrous proteins are long rod-shaped or stringlike molecules that intertwine to form fibers (examples: collagen, elastin, & keratin). Globular proteins are spherical-shaped proteins that form stable suspensions in water, or is water soluble (examples: hemoglobin & enzymes).

PROTEIN COMPOSITION Simple proteins contain only amino acid residues. Conjugated proteins contain amino acid residues and other organic or inorganic components (prosthetic groups).

PROTEIN COMPOSITION (continued)

PRIMARY PROTEIN STRUCTURE is the linear sequence of amino acids in a protein chain. determines secondary and tertiary structures. is important for the functioning of proteins; small variations in the primary structure can cause profound differences in the functioning of proteins.

PRIMARY PROTEIN STRUCTURE (continued)

SECONDARY PROTEIN STRUCTURE is determined by hydrogen bonding between amide groups of amino acid residues in the chain. An -helix occurs when a single protein chain twists so it resembles a coiled helical spring; hydrogen bonding occurs between carbonyl and amide every 4 residues. A -pleated sheet occurs when several protein chains lie side by side and are held in position by hydrogen bonds between the amide carbonyl oxygen atoms of one chain and the amide hydrogen atoms of an adjacent chain.

SECONDARY PROTEIN STRUCTURE (continued) An -helix is found in: keratin, myosin, epidermin, and fibrin.

SECONDARY PROTEIN STRUCTURE (continued) -pleated sheets are found extensively only in silk protein.

SECONDARY PROTEIN STRUCTURE (continued) Random coil molecular structure:

TERTIARY PROTEIN STRUCTURE is the specific 3-D shape of a protein resulting from interactions between “R” groups of amino acid residues. has “R” group interactions that include: disulfide bridges, which form between cysteine residues. salt bridges, which are ionic bonds that form between acidic and basic residues. hydrogen bonds, which form between polar residues. hydrophobic interactions, which form between nonpolar residues.

AMINO ACID REACTIONS Oxidation of cysteine, the only –SH containing amino acid, to form a disulfide (-S-S-) bridge:

TERTIARY PROTEIN STRUCTURE (continued)

TERTIARY PROTEIN STRUCTURE (continued) In an aqueous environment, the interaction of hydrophilic and hydrophobic side chains with water also determines shape.

QUATERNARY PROTEIN STRUCTURE All proteins have primary, secondary, and tertiary structure, but not all proteins have quaternary structure. Quaternary structure is the arrangement of subunits that form a larger protein. Subunits are polypeptides that have primary, secondary, and tertiary structure. Conjugated proteins with quaternary structure contain subunits as well as prosthetic groups, which may be organic or inorganic components. Heme is an example of a prosthetic group:

QUATERNARY PROTEIN STRUCTURE (continued) Hemoglobin has: four chains (subunits), which are two identical alpha chains and two identical beta chains. four heme groups. hydrophobic forces that hold the subunits together.

PROTEIN HYDROLYSIS Heat and acid or base can completely hydrolyze proteins. This is an important process in protein digestion (uses enzymes).

PROTEIN DENATURATION Protein denaturation: is the process by which a protein loses its native state (characteristic quaternary, tertiary, and secondary structure). leads to a loss of biological activity (function).

PROTEIN DENATURATION (continued)