Macromolecules 3: Proteins

Your Assignment

Your Protein Structure Assignment

1. Define proteins and their function2. What is an amino acid (monomers

joined via dehydration synthesis)3. How is a peptide bond formed?4. What are the main uses of proteins

in cells (plants and animals)??

Your Protein Shape Assignment1. What are the various levels of

protein ‘shape’? (primary, secondary, tertiary, quaternary)

2. How does structure relate to function with regard to proteins?

3. What does it mean to denature a protein?, Give one or more example.

Additional Resources (1)

• The Tree of Life, proteins and DNA module

Additional Resources (2)Protein structure and conformation

links• Molecular Workbench DNA and

protein module• http://www.youtube.com/watch?v=ia

HHgEoa2c8&feature=related• http://www.youtube.com/watch?

v=Q7dxi4ob2O4&feature=related

Protein Functions

Proteins• > 50% of the dry mass of a cell is

proteinProteins are used for:• Structural support• Energy storage• Transport of other substances• Signalling from one part of the

organism to another• Movement• Defence against foreign substance• Enzymes• Humans have tens of thousands of

different proteins• Most structurally sophisticated

molecule, due to unique 3D shape or conformation

Amino Acid (Monomers)Amino acid structure:

NH3 - C - COOH

Amino acids differ due to the R (functional) group

The structure of the R-group determines the chemical properties of the amino acid

Proteins Chemical composition C-H-O-N-(S) Proteins are made up of smaller monomers called AMINO

ACIDS Amino Acids differ ONLY in the type of R (functional)

group they carryAmino acids composed of 3 parts1. Amino Group2. Carboxylic group3. Functional ®-group (Makes 20 different amino acids)

20 Amino Acids

Hydrophilic Amino Acids Polar uncharged amino acids are hydrophilic

& can form H-bondsSerineThreonineGlutamineAsparagineTyrosineCysteine

Hydrophobic Amino Acids Nonpolar amino acids are hydrophobic and are usually

found in the center of the protein. They also found in proteins which are associated with cell membranes.

GlycineAlanineValineLeucineIsoleucineMethioninePhenylalanineTryptophanProline)

Electrically charged Amino Acids

The electrically charged amino acids have electrical properties that can change depending on the pH.

Aspartic AcidGlutamic AcidLysineArginineHistidine

Special Amino Acids

Cysteine can form covalent disulfide bonds Proline had a unique structure and causes

kinks in the protein chain

Amino Acids link together to form polypeptides

• 2 Amino Acids form a covalent bond, called a PEPTIDE BOND,through a condensation reaction to form a dipeptide

• Multiple amino acids can bond to each other one at a time, forming a long chain called a POLYPEPTIDE

Peptide Bonds – link amino acids

Protein shape• Each protein has a

specific, and complex shape

• Proteins are composed of one or more polypeptides

• Different shapes allow proteins to perform different functions

Protein Shape Determines Function• Proteins with only primary and secondary structures are

called fibrous proteins (claws, beaks, keratin, wool, collagen, ligaments, reptile scales)

• Proteins with only 1,2,3 shapes are called globular proteins

• If a protein is incorrectly folded, it can’t function correctly

• Not understood how proteins fold themselves, seem to have molecules called chaperone proteins or chaperonins that assist others

• A protein is denatured when it loses its shape and therefore its ability to function correctly

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Four Levels of Protein Structure/ Conformation

1. Primary - unique linear sequence in which amino acids are joined, can have dire circumstances if changed (insulin)

2. Secondary - refers to three dimensional shapes that are the result of H bonding at regular intervals, due to interactions between the amino acid backbones• alpha helix is a coiled

shape• beta pleated sheet is

an accordion shape

3. Tertiary Complex 3-D globular

shape due to interactions between R groups of amino acids in it• Globular proteins such

as enzymes are held in position by these interactions

4. Quaternary Consist of more than one

polypeptide chain subunits, associated with interactions between these chains 2219

Protein ConformationPrimary Structure – sequence of amino acids

Secondary structure – Folding and coiling due to H bond formation between carboxyl and amino groups of non-adjacent amino acid. R groups are NOT involved.

Tertiary structure – disulfide bridges, ionic bonding, or H-bonding of R-groups

Quaternary structure – 2+ amino acid chains R- group interactions, H bonds, ionic interactions

Primary Structure• A unique sequence of

amino acids in a long polypeptide chain

• Any changes in primary structure can affect a protein’s conformation and its ability to function• Example: Sickle cell anemia

Primary structure• The sequence of amino acids• Involves peptide bonds between the carboxyl and amine groups

LYS VAL PHE GLY ARG CYS

Sickle cell anaemia• Sickling

occurs due to a mutation of the Hb gene, associated with replacement of glutamic acid by valine

Secondary Structure• Segments of the

polypeptide strand repeatedly coil or fold in a pattern which contributes to the overall conformation

• Made by hydrogen bonds between the backbone of the amino acids (amino group and carboxyl groups)

Structures formed include:• α-helices: area with

a helical or spiral shape. Held together by H bonds between every 4th amino acid

• β-pleated sheets: area where 2 or more regions of the polypeptide chain lie in parallel

Secondary Structure

Secondary structure• The amino acids in the primary structure can bond

together to form :

• a) An alpha helix b) a beta pleat

• The bonds involved are hydrogen bonds• Large proteins will have regions containing both

structures

Tertiary StructureMade of irregular contortions from interactions between side chains (R groups)1. Hydrogen Bonds: between polar side groups2. Ionic Bonds: between positively and negatively charged side chains3. Hydrophobic Interactions: non-polar side

chains end up on the inside of a protein, away from water—caused by water excluding these side chains from H bond interactions. Once together, held in place by dipole-dipole interactions

4. Disulfide Bridges: strong covalent bonds between cytosine’s sulfhydryl (-SH) groups

TERTIaRY STRUCTURE• The protein molecule undergoes further

twisting and folding to form a 3 dimensional shape

• The structure is held in place by interactions between R-groups of the different amino acids

Tertiary Structure

Quaternary StructureThe overall protein structure that

results from the aggregation of 2 or more polypeptide subunits

QUATERNARY STRUCTURE• Proteins can contain more than one protein chain• E.g. immunoglobulins (form antibodies)

• The bonds involved are the same as those for tertiary structure

Chain 1

Chain 3 Chain 2

Review: The Four Levels of Protein Folding

Denaturing of ProteinProteins can be denatured by:• Transfer from aqueous solution to an organic

solvent (e.g. chloroform)

• Any chemical that disrupts H-bonds, ionic bonds, & disulfide bridges

• Excessive heat

• Changes in pH

Denaturation• Protein conformation depends on the physical and

chemical conditions of the protein’s environment• pH, salt concentration, temperature, and other aspects of

the environment (aqueous or organic solvent) can unravel or change the conformation of the protein.

• Change in protein shape causes it to lose its function• Some proteins can renature and reform their

conformation, other cannot.

TESTING FOR PROTEINS• Measure out 2cm3 of test solution

into a test tube• Add 2 cm3 of Biuret solution• Shake and record colour change for

each sample

• Positive result = colour change from blue to lilac