2.4 - Proteins

Essential Idea: Proteins have a very wide range of functions in living organisms.

2.4 Proteins Understandings: Amino acids are linked together by condensation to form polypeptides   There are 20 different amino acids in polypeptides synthesized on ribosomes Amino acids can be linked together in any sequence giving a huge range of possible polypeptides The amino acid sequence of polypeptides is coded for by genes A protein may consist of a single polypeptide or more than one polypeptide linked together The amino acid sequence determines the three-dimensional conformation of a protein Living organisms synthesize many different proteins with a wide range of functions Every individual has a unique proteome Applications: Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk are examples of the range of protein functions Denaturation of proteins by heat or by deviation of pH from the optimum Skill: Draw molecular diagrams to show the formation of a peptide bond

I. Amino Acids A. 20 different amino acids 1. R groups give amino acids variability 2. Same 20 used in virtually all organisms 3. In humans, 11 can be made by the body, but 9 must be ingested in food (“essential amino acids”) 4. Strung together in different combinations to form polypeptides Central Carbon Amine group (NH2) Carboxylic group (COOH) Hydrogen atoms (H) Variable side chain (R)

II. Polypeptides Formed by condensation reactions between amino acids to form peptide bonds (and broken down by hydrolysis) 1. 2 amino acids together is a dipeptide, 3 or more a polypeptide

II. Proteins A. Protein or polypeptide? What’s the difference? Both are amino acids covalently bonded together, but a protein has done all its processing and folding and is ready to do its function Protein Polypeptide

Primary Structure - the order in which amino acids are strung together 1. This order is coded for by genes

C. Secondary Structure - carboxyl groups and amine groups of the non-adjacent amino acids interact and form hydrogen bonds with each other, resulting in either alpha helix or beta pleated sheet ***Both types of secondary structure are generally found in all proteins

D. Tertiary Structure - 3-D folding created by bonds forming between the R groups of the various amino acids (hydrogen bonds, ionic bonds, disulfide bridges, and non-polar interactions are the most common) 1. Can result in globular or fibrous structures

E. Quaternary Structure - Some (not all E. Quaternary Structure - Some (not all!) proteins are composed of multiple polypeptides or are associated with prosthetic groups (non-polypeptide molecules like iron, lipids, sugars, vitamins)

III. Protein Function The function of a protein is entirely dependent on its shape! 1. Quaternary structure is dependent on tertiary structure which is dependent on secondary structure which is dependent on primary structure – if you change the primary structure, you change the protein’s secondary, tertiary, and quaternary structure, making it unable to perform its function

Proteins have a wide variety of functions Regulate reactions (enzymes) Transport molecules (hemoglobin) Chemical messengers (hormones, neurotransmitters) Channels and pumps in the cell membrane Cell-to-cell communication (transmit/receive signals) Fight disease (antibodies) Provide structure and support Contract to cause movement

C. Environmental factors can affect protein folding 1 C. Environmental factors can affect protein folding 1. Temperature – puts stress on bonds 2. pH – change in concentration of H+ or OH- ions interferes with hydrogen bond formation 3. Denaturation is a structural change in a protein that results in the loss (usually permanent) of its biological properties

IV. Proteome A. The entire unique set of proteins that an individual is capable of producing