PROTEIN SRUCTURES

BY SHRUTHI REDDY 10011G0620

Importance of Proteins
 Muscle structure depends on protein-protein interactions  Transport across membranes involves protein-solute interactions  Nerve activity requires transmitter substance-protein interactions  Immune protection requires antibody-antigen interactions

Functions of Proteins
 Structural  Movement  Transport  Storage  Hormone  Protection  Enzymes
Collagen; Collagen bones, tendons, cartilage Keratin; Keratin hair, skin, wool, nails, feathers Myosin & Actin muscle contractions Actin; Hemoglobin; Hemoglobin transports O2 Lipoproteins; Lipoproteins transports lipids Casein; Casein in milk. Albumin in eggs Albumin; Insulin; Insulin regulates blood glucose Growth hormone regulates growth hormone; Immunoglobulins; Immunoglobulins stimulate immunity Snake venom; plant toxins venom; toxins; Sucrase; Sucrase catalyzes sucrose hydrolysis Pepsin; Pepsin catalyzes protein hydrolysis

Protein Structure
20 Amino Acids

Coded in DNA
Primary

Secondary Tertiary

Self assembly to a single (native) structure. Depends on primary structure and solution conditions

Quaternary

Denatured

Common in foods. Many nonnative forms depending on protein structure, solution conditions (& history) and ingredient interactions

16.2 Amino Acids

Amino acids  Are the building blocks of proteins.  Contain a carboxylic acid group and an amino group on the alpha (E) carbon.  Are ionized in solution.  Each contain a different side group (R). R H2NC COOH H + H3NC COO H ionized form R

Amino Acids
 The monomer unit of proteins

R O C HO
Chiral carbon (Lseries)

C H

NH2

R is the side chain. One of 20 different chemical compounds Some R-groups are acid (other alkali) Some R-groups are water soluble (others are not)

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 NH2 side chains.
Copyright 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Nonpolar

Polar

Acidic

Basic

Nonpolar Amino Acids

A nonpolar amino acid has  An R group that is H, an alkyl group, or aromatic.

Copyright 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Polar Amino Acids

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

Copyright 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Acidic and Basic Amino Acids

An amino acid is  Acidic with a carboxyl R group (COO).  Basic with an amino R group (NH3+).
Basic Amino Acids

Copyright 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

Formation of Peptides

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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 + || H3NCH2CO + CH3 O + | || H3NCHCO

O H CH3 O + || | | || H3NCH2CNCHCO + H2O

peptide bond

Overview
    Primary Structure Secondary Structure Tertiary Structure Quaternary Structure

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.

CH3 CH3 CH CH3 CH3 O H CH O H SH CH2 O H S CH2 CH2 O

H3N CH C N CH C N CH C N CH C O-

Ala Leu Cys Met

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Primary Structures
The nonapeptides oxytocin and vasopressin  Have similar primary structures.  Differ only in the amino acids at positions 3 and 8.

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Primary Structure of Insulin

Insulin  Was the first protein to have its primary structure determined.  Has a primary structure of two polypeptide chains linked by disulfide bonds.  Has a chain A with 21 amino acids and a chain B with 30 amino acids.

Copyright 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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

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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: -Pleated Sheet

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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.
Copyright 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Tertiary Structure
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
non-linear 3 dimensional global but restricted to the amino acid polymer formed and stabilized by hydrogen bonding, covalent (e.g. disulfide) bonding, hydrophobic packing toward core and hydrophilic exposure to solvent A globular amino acid polymer folded and compacted is somewhat functional (catalytic) and energetically favorable interaction!

Tertiary Structure
 The interactions of the R groups give a protein its specific threedimensional tertiary structure.

Copyright 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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

Copyright 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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.

Copyright 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Quaternary Structure
non-linear 3 dimensional global, and across distinct amino acid polymers formed by hydrogen bonding, covalent bonding, hydrophobic packing and hydrophilic exposure favorable, functional structures occur frequently and have been categorized

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

Copyright 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

Protein Structure Determination

 High-resolution structure determination
 X-ray crystallography (~1)  Nuclear magnetic resonance (NMR) (~1-2.5)

 Low-resolution structure determination

 Cryo-EM (electron-microscropy) ~10-15

X-ray crystallography
 most accurate  An extremely pure protein sample is needed.  The protein sample must form crystals that are relatively large without flaws. Generally the biggest problem.  Many proteins arent amenable to crystallization at all (i.e., proteins that do their work inside of a cell membrane).  ~$100K per structure

Nuclear Magnetic Resonance

 Fairly accurate  No need for crystals  limited to small, soluble proteins only.

Protein: The Machinery of Life

NH2-Val-His-Leu-Thr-Pro-Glu-GluLys-Ser-Ala-Val-Thr-Ala-Leu-TrpGly-Lys-Val-Asn-Val-Asp-Glu-ValGly-Gly-Glu-..

Life is the mode of existence of proteins, and this mode of existence essentially consists in the constant self-renewal of the chemical constituents of these substances. Friedrich Engles, 1878

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