Protein Structure

Joonwoo Choi

Jennifer Hlaudy

Meskerem Ereso

Protein Structure: Primary, Secondary, Tertiary and Quaternary Levels

Review- Amino acids

amino acid has

the same fundamental structure,

but difference only in the side-

chain (R-group).

a central carbon bonded to:

a hydrogen

an amino group

a carboxyl group

a side chain (R-group)

Peptides/polypeptides Peptide

is composed of amino acids via peptide bonds. A peptide bond is a covalent bond between the amino acids,

with elimination of H2O (dehydration synthesis reaction). If the chain length is short (less than 30 amino acids), it is called a peptide;

longer chains are called polypeptides or proteins.

Protein and Protein backbone

A polypeptide is covalently linked by peptide bonds and

a linear polymer of many amino acids.

The protein backbone is formed by the long peptide

linkages with sequence NCC-NCC-NCC-NCC.

Protein primary structureThe primary Structure of a protein:

is a linear sequence of amino acids

is covalently linked by peptide bonds

has the amino terminal or "N-terminal" (NH3+) at

one end; carboxyl terminal ("C-terminal") (COO-)

at the other.

Protein Secondary Structure

The secondary structure: is that polypeptide chains are coiled and

folded or pleated into different shapes. creates three dimensional shapeis held together by many Hydrogen bonds,

overall giving the shape great stability. Two common examples of secondary structures:

Alpha Helixes Beta Pleated Sheets.

Secondary structure – Alpha helix

An a-helix

is stabilized by hydrogen bonds

between backbone amino(N-H)

and carbonyl groups(C=O).

The hydrogen bonding causes the

polypeptide to twist into a helix.

In an a-helix,

The amino acid R-groups

protrude out from the helically

coiled polypeptide backbone.

Secondary structure – beta-pleated sheet

Beta pleated sheet- Is stabilized by Hydrogen bonds between backbone carbonyl oxygen

and amino H atoms.

- Polypeptide chains can interlock side by side in beta pleated sheet.

- R-groups protrude out from folded polypeptide backbone.

Protein structure

Tertiary

Quaternary

Jennifer Hlaudy

Tertiary Structure

Tertiary Structure - Much of the Hemoglobin molecule is

wound into α helices while much of the Collagen molecule is

made up of left handed helix structures The final 3D structure of a protein is its Tertiary Structure, which

pertains to the shaping of the secondary structure. This may involve coiling or pleating, often with straight chains of amino acids in between.

Proteins with a 3D structure fall into two main types:

Globular - These tend to form ball-like structures where hydrophobic parts are towards the centre and hydrophilic are towards the edges, which makes them water soluble. They usually have metabolic roles, for example: enzymes in all organisms, plasma proteins and antibodies in mammals.

Fibrous - The proteins form long fibers and mostly consist of repeated sequences of amino acids which are insoluble in water. They usually have structural roles, such as: Collagen in bone and cartilage, Keratin in fingernails and hair.

Tertiary structure is held together by four different bonds and interactions: Disulphide Bonds - Where two Cysteine amino acids are

found together, a strong double bond (S=S) is formed between the Sulphur atoms within the Cysteine monomers.

Salt bridges- Interactions as a result of ionic bonds that form between the ionized side chain of an amino acid and the side chain of a basic amino acid.

Hydrogen Bonds - Your typical everyday Hydrogen bonds. Hydrophobic and Hydrophilic Interactions - Some amino

acids may be hydrophobic while others are hydrophilic. In a water based environment, a globular protein will orientate itself such that it's hydrophobic parts are towards its centre and its hydrophilic parts are towards its edges.

Quaternary Structure

Some proteins are made up of multiple polypeptide chains, sometimes with an inorganic component (for example, a haem group in haemoglogin) called a Prosthetic Group. These proteins will only be able to function if all subunits are present.

Quaternary Structure: The structure formed when two or more polypeptide chains join together, sometimes with an inorganic component, to form a protein.

Example of quaternary protein structure

Hemoglobin Collagen Hemoglobin is a water

soluble globular protein which is composed of two α polypeptide chains, two β polypeptide chains and an inorganic prosthetic heme group. Its function is to carry oxygen around in the blood, and it is facilitated in doing so by the presence of the heme group which contains a Fe2+ ion, onto which the oxygen molecules can bind.

Collagen is a fibrous protein consisting of three polypeptide chains wound around each other. Each of the three chains is a coil itself. Hydrogen bonds form between these coils, which are around 1000 amino acids in length, which gives the structure strength. This is important given collagen's role, as structural protein. This strength is increased by the fact that collagen molecules form further chains with other collagen molecules and form Covalent Cross Links with each other, which are staggered along the molecules to further increase stability. Collagen molecules wrapped around each other form Collagen Fibrils which themselves form Collagen Fibres.

Collagen has many functions:Form the structure of bonesMakes up cartilage and connective tissuePrevents blood that is being pumped at high pressure from

bursting the walls of arteriesIs the main component of tendons, which connect skeletal

muscles to bones

Hemoglobin may be compared with Collagen as such:

Basic Shape - Hemoglobin is globular while Collagen is

fibrous

Solubility - Hemoglobin is soluble in water while Collagen

is insoluble

Amino Acid Constituents - Hemoglobin contains a wide

range of amino acids while Collagen has 35% of it primary

structure made up of Glycine

Prosthetic Group - Hemoglobin contains a heme prosthetic

group while Collagen doesn't possess a prosthetic group

http://www.youtube.com/watch?v=lijQ3a8yUYQ

Protein structure

Denaturation

Function of protein

Meskerem Ereso

Denaturation Involves in possible destruction of both the

secondary and tertiary structuresDenaturation is not strong enough to break the

peptide bond, primary structure remain the same.

Denaturation Extent of denaturation or unfolding of the

structures other than primary structure can

be reversible (slightly denatured) or

irreversible (highly denatured).

Proper folding/ structure of proteins in living

cells is facilitated by proteins called

Chaperons.

Modes of protein denaturation

Denaturing Agent Affected Regions

Heat H Bonds

6 M urea H Bonds

Detergents Hydrophobic region

Acids, bases Salt bridge and H Bonds

Salts Salt bridge

Reducing agents Disulfide bonds

Heavy metals Disulfide bonds

Alcohols Hydration layers

HEAT INDUCED DENATURATION OF PROTEIN

High temperature disrupts hydrogen bonds and

non-polar hydrophobic interactions.

increased temperature increases the kinetic energy

and causes the molecules to vibrate so rapidly and

violently that the bonds are disrupted.

The principle is applied for sterilization by denaturing

proteins of bacteria.

Simple example is protein coagulation and re-

association of egg-white on frying an egg.

HEAT INDUCED DENATURATION OF PROTEIN cont.

Urea Induced Denaturation of Protein

Acid-base induced denaturation of protein

Conclusion

Denaturation affects secondary, tertiary and quaternary structures but not the primary structure (peptide bond).

If small extent, denaturation is reversibleRemoval of denaturing agent .

In living cells, denaturation is reversed by proteins called chaperons.

Some denaturations are reversible, for example, a hard boiled egg.

Works Cited

Adam, Sam. (2012). Protein Structure. A Level Note. Retrieved from http://alevelnotes.com/Protein-Structure/61

Diwan, Joyce J. (2003). Basic Concepts of Protein Structure. Biochemistry of Metabolism. Retrieved from http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/part2/protein.htm#primary

Gorga, Frank R. (2007, March 12). Introduction to Protein Structure. Bridgewater State College. Retrieved from http://webhost.bridgew.edu/fgorga/proteins/default.htm

Opharctt, Charles E. (2003). Amino Acid Peptide Bonds. Virtual Chembook. Retrieved from http://www.elmhurst.edu/~chm/vchembook/564peptide.html

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