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 H 2 O (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 structure  The 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" (NH 3 + ) 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 shape is 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 Fe 2+ ion, onto which the oxygen molecules can bind.

 Collagen  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 bones Makes up cartilage and connective tissue Prevents blood that is being pumped at high pressure from bursting the walls of arteries Is 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

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Protein structure  Denaturation  Function of protein Meskerem Ereso

Denaturation  Involves in possible destruction of both the secondary and tertiary structures Denaturation 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 AgentAffected Regions HeatH Bonds 6 M ureaH Bonds DetergentsHydrophobic region Acids, basesSalt bridge and H Bonds SaltsSalt bridge Reducing agentsDisulfide bonds Heavy metalsDisulfide bonds AlcoholsHydration 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 reversible Removal 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 Diwan, Joyce J. (2003). Basic Concepts of Protein Structure. Biochemistry of Metabolism. Retrieved from htm#primary htm#primary Gorga, Frank R. (2007, March 12). Introduction to Protein Structure. Bridgewater State College. Retrieved from Opharctt, Charles E. (2003). Amino Acid Peptide Bonds. Virtual Chembook. Retrieved from

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