Understanding Protein Structure

Gabrielle Roberts

Biology Department, Long Island University, Brooklyn, NY

Introduction I. Overview: What is a Protein?

II. Basic Protein Structure

-The Amino acid

-Primary structure: Polypeptide

III. Protein Folding Patterns:

Secondary, Tertiary, Quaternary

PROTEINS

Proteins are biological molecules which play important structural and functional roles within living organisms

FUNCTIONAL PROTEINS

Carry out the vital functions of living systems: chemical reactions, transport,

signaling, etc.

Chemical Reactions: EnzymesEnzymes

Cell Signaling: Hormones

Transport:

Red Blood cellsRed Blood cells

Immunity: Antibodies

STRUCTURAL PROTEINS

-Provide strength and support

Muscle Tissues:

Actin and MyosinActin and Myosin

Hair & Nails: KeratinKeratin

Cytoskeleton:Microtubules, intermediate Microtubules, intermediate filaments, microfilamentsfilaments, microfilaments

Collagen “fibrous protein”:

bones, tendons,bones, tendons,

Basic Protein Structure

• Each protein starts with a basic amino acid chemical structure:

- Amino group

- Carboxylic acid group

- Variable R group

“side chain”

R groups give amino acid their special R groups give amino acid their special chemical and physical propertieschemical and physical properties

Polypeptide formation

• Amino acids combine through a dehydration reaction. The result is the formation of a peptide bond.

Oligo peptide- less than 30-50 amino acids A PolypeptideA Polypeptide is a chain of more than 50 is a chain of more than 50

amino acidsamino acids

It is the Protein’s Primary Structure

Protein Folding Patterns

Determines the specific function of the protein

- Non-functional proteins are proteins that have lost their folding patterns

Conformational Levels

Secondary

Tertiary

Quaternary

Secondary Structure

• Interactions: Hydrogen bonding between backbone (carboxyl group and N-H)

• Type of structures formedType of structures formed:

Alpha helix

Beta pleated sheet

Alpha Helix

• Carboxyl group and N-H are hydrogen bonded inside the helix.

• Hydrophobic

R-groups are on the exterior of the helix

Beta pleated sheet

• Hydrogen bonding between Carboxyl and N-H groups that are far away on the polypeptide chain

Alpha & Beta: Working Together

The green fluorescent proteinThe green fluorescent protein::

Composed of Beta pleated sheets (in yellow) which forms the outside structure of the protein and an alpha helix structure in the interior of the protein (in purple).

Tertiary Structure

Interactions: between distant R side groups in the polypeptide chain and with water.

Disulfide bonds: between cysteine R groups

Hydrogen bonding: (a.) between R-groups containing alcohol and acid, (b.) between an alcohol and an amide or amine,

1. alcohols: serine, Threonine , Tyrosine .2. acids: aspartic acid, glutamic acid 3. amine: lysine4. amide: asparagine

Hydrophobic Interactions: “Van der Waals forces” Between non polar groups:  Valine, Proline

Quaternary Structure

• Not all proteins have a quaternary structure

Interactions: between different polypeptide chains (hydrogen bonding, hydrophobic interactions, Van der Walls)

Quaternary Protein: Antibody

Light chain & Heavy Chain connected by di-sulfide bonds