Proteins are an important class of biological

macromolecules which are the polymers of amino

acids.

are biochemical compounds consisting of one ormore polypeptides typically folded intoa globular or fibrous form in a biologically functionalway.

• Biochemists have distinguished several levels of structural

organization of proteins. They are:

– Primary structure

– Secondary structure

– Tertiary structure

– Quaternary structure

• The primary structure of protein refers to the

sequence of amino acids present in the

polypeptide chain.

• Amino acids are covalently linked by peptide

bonds.

• Each component amino acid in a polypeptide is

called a “residue” or “moiety”

• By convention, the 10 structure of a protein

starts from the amino-terminal (N) end and

ends in the carboxyl-terminal (C) end.

Secondary structure refers tohighly regular local sub-structures.

These secondary structures aredefined by patterns of hydrogenbonds between the main-chainpeptide groups.They have a regular geometry,being constrained to specificvalues of the dihedral angles ψand φ on the Ramachandran plot.Both the alpha helix and the beta-sheet represent a way ofsaturating all the hydrogen bonddonors and acceptors in thepeptide backbone.

• Tertiary structure is the three-dimensional conformation ofa polypeptide.

• The common features of protein tertiary structure revealmuch about the biological functions of the proteins andtheir evolutionary origins.

• The function of a protein depends on its tertiary structure.If this is disrupted, it loses its activity.

Quaternary structure is a larger assembly of several protein

molecules or polypeptide chains, usually called subunits in

this context.

The quaternary structure is stabilized by the same non-

covalent interactions and disulfide bonds as the tertiary

structure. Complexes of two or more polypeptides are called

multimers.

Chemical properties of proteins

1. Hydrolysis

Proteins can be hydrolyzed (the peptide bond) by acid or enzymes to

give peptides and free amino acids (e.g. soy sauce, fish sauce.)

Modifies protein functional properties

- E.g. increased solubility.

Increases bio availability of amino acids

- Excessive consumption of free amino acids is not good however.

2. Maillard reaction (carbonyl - amine browning)

Changes functional properties of proteins

Changes color

Changes flavor

Decreases nutritional quality (amino acids less available)

3. Alkaline reactions

Soy processing (textured vegetable protein)

Denatures proteins

Opens up its structure due to electrostatic

repulsion

The peptide bond may also be hydrolyzed

are specialized proteins involved in defending the

body from antigens (foreign invaders). One way

antibodies destroy antigens is by immobilizing them

so that they can be destroyed by white blood cells.

are proteins that facilitate biochemical reactions. They are

often referred to as catalysts because they speed up

chemical reactions. Examples include the enzymes lactase

and pepsin. Lactase breaks down the sugar lactose found in

milk. Pepsin is a digestive enzyme that works in the stomach

to break down proteins in food.

are messenger proteins which help to coordinate certain bodily

activities. Examples include insulin and oxytocin. Insulin

regulates glucose metabolism by controlling the blood-sugar

concentration. Oxytocin stimulates contractions in females

during childbirth.

are responsible for movement. Examples include actin and

myosin. These proteins are involved in muscle contraction and

movement.

are carrier proteins which move molecules from one

place to another around the body. Examples include

hemoglobin and cytochromes. Hemoglobin transports

oxygen through the blood. Cytochromes operate in

the electron transport chain as electron carrier proteins.

Intracellular Trafficking and Protein

Transport

Trafficking : Endoplasmic Reticulum to Golgi to cell membrane

Endoplasmic Reticulum

• Helps move substances within cells

• Network of interconnected membranes

• Two types :

– Rough endoplasmic reticulum

– Smooth endoplasmic reticulum

Rough Endoplasmic Reticulum

• Ribosomes attached to surface

– Manufacture protiens

– Not all ribosomes attached to rough ER

• May modify proteins from ribosomes

Smooth Endoplasmic Reticulum

• No attached ribosomes

• Has enzymes that help build molecules

– Carbohydrates

– Lipids

Golgi Apparatus

• Involved in synthesis of plant cell wall

• Packaging & shipping station of cell

The Golgi apparatus is an organelle found in most eukaryotic

cells. . The primary function of the Golgi apparatus is to process

and package macromolecules, such as proteins and lipids, after

their synthesis. It is important in the processing of proteins for

secretion.

Liquid droplets

• Endocytosis - process by which particles,

solutes, membrane proteins (including receptor-

ligand complexes) and lipids are taken up by

vesicles from the PM. Also used by parasites

and bacteria to get into the host cell.

- Pinocytosis - uptake of extracellular fluid

through endocytosis.

Endocytosis

Trafficking : ER to Golgi to PM

- Phagocytosis - uptake of pathogens as a

defense, clearance of cell debris.

- where proteins from ER are further

processed sorted for transport to final

destinations: outside cell, PM, or lysosomes

Exocytosis - fusion of vesicles derived from TGN with the PM resulting

in insertion of transmembrane proteins into PM or secretion of soluble

proteins into extracellular space.

Trafficking from ER to Golgi complex:

- Transport vesicles (TV): bud from mb of

one organelle & fuse with mb of next

organelle .

Trafficking : ER to Golgi to Lysosome

Receptors take up cargo via receptor-mediated endocytosis

,into clathrin-coated endocytic vesicles which bud into cell

from PM and fuse with early endosomes.

Early endosomes mature into late endosomes, with recycling

of membrane components back to PM.

REFERENCE Voet, Donald; Voet Judith. Biochemistry, 3rd edition, John

Wiley and sons.

Champe, Pamela.C, Harvey, Richard A, Ferrier Denise R(2005). Lippincott’s Illustrated Reviews: Biochemistry, 3rd

edition. Lippincott William and Wilkins.

McKee Trudy, McKee James R (2003), Biochemistry: Themolecular basis of life, 3rd edition, McGraw Hill.

http://esciencenews.com/articles/2011/06/01/new.antibiotics.a.step.closer.with.discovery.bacterial.protein.structure

http://www.eurekalert.org/pub_releases/2010-04/sri-srs042610.php

http://www.physorg.com/news/2011-10-cell-survival-protein-reveals.html

Thank You

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