Amino acids & Proteins

Amino Acids Amino acids  Are the building blocks of proteins.  Contain a carboxylic acid group and an amino group on the alpha (  ) carbon.  Are ionized in solution.  Each contain a different side group (R). R R │ + │ H 2 N—C —COOH H 3 N—C —COO− │ │ H H Ionized form

Examples of Amino Acids H + │ H 3 N—C—COO− │ Hglycine CH 3 + │ H 3 N—C—COO− │ Halanine

Types of Amino Acids Amino acids are classified as  Nonpolar (hydrophobic) with hydrocarbon side chains.  Polar (hydrophilic) with polar or ionic side chains.  Acidic (hydrophilic) with acidic side chains.  Basic (hydrophilic) with –NH 2 side chains. Nonpolar Polar Acidic Basic Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Nonpolar Amino Acids A non-polar amino acid has  An R group that is H, an alkyl group, or aromatic.

Polar Amino Acids A polar amino acid has  An R group that is an alcohol, thiol, or amide.

Acidic and Basic Amino Acids An amino acid is  Acidic with a carboxyl R group (COO − ).  Basic with an amino R group (NH 3 + ). Basic Amino Acids

(i) Amino acids with Aliphatic Side Chains ( e. g) NameSymbol GlycineGly (G) AlanineAla (A) ValineVal (V) LeucineLeu (L) IsoleucineIle (I) (ii) Amino acids with Side Chains Containing –OH groups NameSymbol SerineSer (S) ThreonineThr (T) TyrosineTyr (Y) (e. g)

(iii) Amino acids with Side Chains Containing Sulfur (e. g) NameSymbol CysteineCys (C) MethionineMet (M) (iv) Amino acids with Side Chains Containing Acidic Groups / Amides NameSymbol Aspartic acidAsp (D) AsparagineAsn (N) Glutamic acidGlu (E) GlutamineGln (Q) (v) Amino acids with side chains containing basic groups NameSymbol ArginineArg (R) LysineLys (K) HistidineHis (H)

(vi) Amino acids with Side Chains containing Aromatic Rings (e. g) NameSymbol HistidineHis (H) PhenylalaninePhe (F) TyrosineTyr (Y) TryptophanTrp (W) (vii) Imino acid (e. g) Proline- Pro (P)

Fischer Projections of Amino Acids Amino acids  Are chiral except for glycine.  Have Fischer projections that are stereoisomers.  That are L are used in proteins. L -alanine D -alanine L -cysteine D -cysteine

A zwitterion (equal No of Ionizable groups of opposite charge with no net charge) Has charged —NH 3 + and COO - groups. Forms when both the —NH 2 and the —COOH groups in an amino acid ionize in water. Has equal + and − charges at the isoelectric point (pI, is the pH midway between pK a values on either side of the isoelectric species). O O ║ + ║ NH 2 —CH 2 —C—OH H 3 N—CH 2 —C—O – Glycine Zwitterion of glycine Zwitterions and Isoelectric Points

In solutions more basic than the pI,  The —NH 3 + in the amino acid donates a proton. + OH – H 3 N—CH 2 —COO – H 2 N—CH 2 —COO – ZwitterionNegative ion at pI pH > pI Charge: 0Charge: 1− Amino Acids as Acids

In solutions more acidic than the pI,  The COO − in the amino acid accepts a proton. + H + + H 3 N—CH 2 —COO – H 3 N—CH 2 —COOH Zwitterion Positive ion at pI pH< pI Charge: 0Charge: 1+ Amino Acids as Bases

pH and Ionization H + OH − + H 3 N–CH 2 –COOH H 3 N–CH 2 –COO – H 2 N–CH 2 –COO – positive ion zwitterion negative ion (at low pH) (at pI) (at high pH)

Essential amino acids  Must be obtained from the diet.  Are the ten amino acids not synthesized by the body.  Are in meat and diary products.  Are missing (one or more) in grains and vegetables. Essential Amino Acids

The Peptide Bond A peptide bond  Is an amide bond.  Forms between the carboxyl group of one amino acid and the amino group of the next amino acid. O CH 3 O + || + | || H 3 N—CH 2 —C—O– + H 3 N—CH—C—O– O H CH 3 O + || | | || H 3 N—CH 2 —C—N—CH—C—O– + H 2 O peptide bond

Naming Dipeptides A dipeptide is named with  A -yl ending for the N-terminal amino acid.  The full amino acid name of the free carboxyl group (COO-) at the C-terminal end.

 Structural  Movement  Transport  Storage  Hormone  Protection  Enzymes Collagen Collagen; bones, tendons, cartilage Keratin Keratin; hair, skin, wool, nails, feathers Myosin & Actin Myosin & Actin; muscle contractions Hemoglobin Hemoglobin; transports O 2 Lipoproteins Lipoproteins; transports lipids CaseinAlbumin Casein; in milk. Albumin; in eggs Insulin Insulin; regulates blood glucose Growth hormone Growth hormone; regulates growth Immunoglobulins Immunoglobulins; stimulate immunity Snake venom; plant toxins Snake venom; plant toxins; Sucrase Sucrase; catalyzes sucrose hydrolysis Pepsin Pepsin; catalyzes protein hydrolysis Functions of Proteins

Primary Structure of Proteins The primary structure of a protein is  The particular sequence of amino acids.  The backbone of a peptide chain or protein. Ala─Leu ─ Cys ─ Met

Secondary Structure – Alpha Helix The secondary structures of proteins indicate the three-dimensional spatial arrangements of the polypeptide chains. An alpha helix has  A coiled shape held in place by hydrogen bonds between the amide groups and the carbonyl groups of the amino acids along the chain.  Hydrogen bonds between the H of a –N-H group and the O of C=O of the fourth amino acid down the chain.

Secondary Structure – Alpha Helix

Secondary Structure – Beta Pleated Sheet A beta-pleated sheet is a secondary structure that  Consists of polypeptide chains arranged side by side.  Has hydrogen bonds between chains.  Has R groups above and below the sheet.  Is typical of fibrous proteins such as silk.

Secondary Structure: β-Pleated Sheet

Secondary Structure: Triple Helix A triple helix  Consists of three alpha helix chains woven together.  Contains large amounts glycine, proline, hydroxy proline, and hydroxylysine that contain –OH groups for hydrogen bonding.  Is found in collagen, connective tissue, skin, tendons, and cartilage.

Protein Structure: Tertiary and Quaternary Levels

The tertiary structure of a protein  Gives a specific three dimensional shape to the polypeptide chain.  Involves interactions and cross links between different parts of the peptide chain.  Is stabilized by Hydrophobic and hydrophilic interactions. Salt bridges. Hydrogen bonds. Disulfide bonds. Tertiary Structure

 The interactions of the R groups give a protein its specific three- dimensional tertiary structure.

Globular Proteins Globular proteins  Have compact, spherical shapes.  Carry out synthesis, transport, and metabolism in the cells.  Such as myoglobin store and transport oxygen in muscle. Myoglobin

Fibrous Proteins Fibrous proteins  Consist of long, fiber-like shapes.  Such as alpha keratins make up hair, wool, skin, and nails.  Such as feathers contain beta keratins with large amounts of beta-pleated sheet structures.

Quaternary Structure The quaternary structure  Is the combination of two or more tertiary units.  Is stabilized by the same interactions found in tertiary structures.  Of hemoglobin consists of two alpha chains and two beta chains. The heme group in each subunit picks up oxygen for transport in the blood to the tissues. hemoglobin

Summary of Protein Structures

Protein hydrolysis  Splits the peptide bonds to give smaller peptides and amino acids.  Occurs in the digestion of proteins.  Occurs in cells when amino acids are needed to synthesize new proteins and repair tissues. Protein Hydrolysis

Hydrolysis of a Dipeptide  In the lab, the hydrolysis of a peptide requires acid or base, water and heat.  In the body, enzymes catalyze the hydrolysis of proteins.

Denaturation involves  The disruption of bonds in the secondary, tertiary and quaternary protein structures.  Heat and organic compounds that break apart H bonds and disrupt hydrophobic interactions.  Acids and bases that break H bonds between polar R groups and disrupt ionic bonds.  Heavy metal ions that react with S-S bonds to form solids.  Agitation such as whipping that stretches peptide chains until bonds break. Denaturation

Denaturation of protein occurs when  An egg is cooked.  The skin is wiped with alcohol.  Heat is used to cauterize blood vessels.  Instruments are sterilized in autoclaves. Applications of Denaturation