Processes SL 2.4, 2.6, 2.7

2.4: Proteins

Polypeptides Chains of amino acids joined together by peptide bonds Result of condensation reactions (also know as translation). How many amino acids are in a dipeptide? 30 seconds – what do you know about polypeptides? Polypeptide = many amino acids Oligopeptide = less than 20 amino acids

Contains two polypeptide chains Human insulin Contains two polypeptide chains - Insulin is a small protein, one chain has 21 amino acids, the other has 30.

Titin One of the largest polypeptides found so far Found in muscles Contains 34, 350 amino acids in humans. In mice there are 35, 213 amino acids!

R-groups You do not need to memorise the different R-groups. BUT, you do need to know that amino acids vary due to the R-group. There are 20 different amino acids, and they can be categorised based on the R-group. Pg. 89, table 1. Although there are only 20 amino acids, they can be modified. E.g collagen can be modified to be more stable by exchanging proline for hydroxyproline.

Patterns, trends & discrepancies… Most organisms on Earth use the same 20 amino acids to form proteins. Theories as to why include: These 20 amino acids were the ones produced when life first developed. Natural selection: these are the most favourable amino acids for making proteins. Common ancestry Not all species use the same 20 amino acids, there are of course some exceptions to this rule. Why do you think this happened?

Diversity A dipeptide contains two amino acids. These can be any combination of the 20. A ribosome can link any of the amino acids. Therefore the possibilities can be calculated by: 20n (n = number of amino acids in a polypeptide Number of amino acids Number of possible amino acids sequences 1 201 20 2 202 400 3 203 8,000 4 204 160,000

The ‘open reading frame’ This is the section of a DNA strand containing genes which code for a polypeptide. Each amino acid is coded for by 3 bases Therefore, in theory, a polypeptide with 400 amino acids would require a gene with a base sequence of 1,200 bases. The open reading frame is only a small part of the total DNA code.

Lysozyme 1 polypeptide Nasal mucus, tears. Kills bacteria by digesting the substance in the cell wall.

Integrin Two polypeptides Membrane protein

Collagen Three polypeptides Structural protein (tendons, ligaments, skin & blood vessels) High strength, limited stretch.

Haemoglobin Four polypeptides Oxygen binding protein in RBC.

The Conformation of proteins Polypeptides do not remain in long chains. Attractions/bonding between the R-groups can lead to four basic structures. Conformation is another term for 3D structure

Functions Catalysis (enzymes to catalyse reactions) Immunity (antibodies) Muscle contraction DNA packing Cytosketeton (structure within membrane) Recepetors (binding sites on membrane) Tensile strengthening (fibrous proteins in skin) Hormones (insulin, FSH etc.) Blood clotting Membrane transport Transport (including nutrients & gas) Cell adhesion How many functions of proteins can you think of? 12! HWK: Write a short report (no more than 1000 words) explaining the biotechnological applications of proteins e.g. stain removers.

Examples to know Rubisco Insulin Immunoglobulin Rhodopsin Collagen Spider silk Research, prepare notes and present to the class.

Proteomes The total of all the proteins produced by a cell, a tissue or an organism. Gel electrophoresis is used to identify the proteins in a sample – florescent markers are attached to antibodies for specific proteins. Proteomes vary, because different cells produce different proteins. The proteome for each individual is unique.

Assessment Design an experiment to investigate the effect of either temperature or pH on egg albumin. You will conduct this experiment next lesson. You will be assessed on your data collection & processing skills ONLY.