1. Proteins Topic 2.4 IBHL Biology

2. Introduction Proteins are a very important biological molecules that are involved in almost every activity that organisms do. They comprise more than 50% of the dry mass in most cells. They are involved in chemical reactions, structures, transport, cell to cell communication, movement, and immunity. They are also the structural component of enzymes. Proteins are constructed from polymers of amino acids and are referred to as polypeptides. They are held together by peptide bonds.

3. 2.4 U1 Amino acids are linked together by condensation to form polypeptides. Amino acids are the sub units of proteins and they bond together to form polypeptides. There are 20 different amino acids and they are distinguished by their R- group but they all have the same generalized structure.

4. Condensation of Amino Acids Condensation reactions can join two amino acids together to form dipeptides or many amino acids together to form large chains called polypeptides (proteins). As each bond (peptide bond) is formed a molecule of water is produced. This process is performed by ribosomes in a process known as translation.

5. 2.4 S1 Drawing molecular diagrams to show the formation of a peptide bond Draw the formation of a peptide bond in your sketch book.

6. 2.4 A2 – There are 20 different amino acids in polypeptides synthesized on ribosomes There are 20 different amino acids used to build thousands of different proteins. The amino acids are distinguished from one another by their R group also known as a side chain. The amino acids can be grouped according to the properties of their side chains. There are polar amino acids, non- polar amino acids and electrically charged amino acids.

8. 20 Different Amino Acids You do not need to know the names of the 20 different amino acids however you should know that organisms can arrange them in polypeptides to produce thousands of different proteins. Also, some amino acids can have variations in their structure which changes their characteristics. For example, a modified version of the amino acid proline known as hydroxyproline is found in the protein collage. It gives collagen, a structural protein found in ligaments, tendons, skin and blood vessels, more stability.

9. 2.4 U3 – Amino acids can be linked together in any sequence giving a huge range of possible polypeptides. # of amino acids Number of possible amino acid sequences 120 1 20 220 2 400 320 3 8 000 420 4 160 000 520 5 3 200 000 620 6 64 000 000 The possibilities of amino acid sequences are huge. Polypeptides contain amino acid numbers ranging from 20 to tens of thousands. This table identifies the infinite possibilities for polypeptide sequences.

10. 2.4 U4 The amino acid sequence is coded for by genes The information needed to produce proteins is stored in DNA. It is coded for by genes that contain three base pairs per amino acid. The sequence of base pairs controls the building of polypeptides during translation. We will cover this in detail in unit 5.

11. 2.4 U5 - A protein may consist of a single polypeptide or more than one polypeptide linked together Some polypeptides are two or more strands linked together. Integrin is an example of a protein that has two separate polypeptides that work together to make connections between structures that are inside and outside of cells. Some polypeptides are a single polypeptide such as lysozyme. It is an enzymes secreted in nasal mucus and tears that kills bacteria by digesting their cell walls.

12. 2.4 U5 - A protein may consist of a single polypeptide or more than one polypeptide linked together Hemoglobin is composed of 4 polypeptides along with a non-polypeptide group known as a heme group. This protein transports o oxygen in the blood. Collagen is composed of three polypeptides. It is a structural protein.

13. 2.4 U6 – The amino acid sequence determines the three dimensional conformation of a protein The conformation of a protein refers to its three dimensional shape. There are 4 levels of protein structure and the level it conforms to is dependent on its amino acid structure. (see handout) Proteins are often described as being globular or fibrous. The sequence of amino acids determines the shape of the protein. Fibrous proteins have a structural role and globular proteins have functional roles in a cells metabolism. http://www.youtube.com/watch?v=yZ2aY5lxEGE

14. Fibrous Proteins Fibrous proteins have a long and narrow shape and are mostly insoluble in water. They are composed of many polypeptide chains organized into a long, narrow shape. Some examples are collagen, a protein that plays a structural role in human connective tissues and actin, a protein found in muscle which plays a role in muscular contractions.

15. Globular Proteins Globular proteins have a rounded shape (three dimensional) and they are mostly soluble in water. Hemoglobin is an example of a globular protein and it is involved in delivering oxygen to body tissues. Insulin is another example of a globular protein and it plays a role in regulating blood glucose levels in humans.

16. 2.4 U7 – Living organisms synthesize many different proteins with a wide range of functions. Organisms synthesize thousands of different proteins in their cells and each protein is different. They have different sequences of amino acids and as mentioned earlier, that sequence determines the shape of the protein and the shape determines the function. Refer to the handout mentioned earlier for a summary of the functions and variety of proteins.

17. Use the following terms to complete the chart on your handout Muscle contraction Membrane transport Hormones Cytoskeletons Tensile strengthening Cell adhesion Immunity Blood clotting Receptors Catalysis Packing of DNA Transport of nutrients & gases

18. 2.4 A1 – Rubisco, insulin, immunoglobulins, rhodopsin, collagen and spider silk as examples of the range of protein functions. Refer to handout and chart completed in class.

19. 2.4 U8 – Every individual has a unique proteome. A proteome is defined as all the proteins produced by a cell, a tissue or an organism. We can use a process known as gel electrophoresis to extract proteins from samples and determine how they are being produced. Antibodies with fluorescent markers are used to identify the proteins. Proteomes are variable from cell to cell due to the fact that cells differ in their functions and activities. While there are many similarities within species, individuals still have many variations within their proteomes which can be due to small differences in the amino acid sequences of proteins.

20. 2.4 A2 – Denaturation of proteins with a wide range of functions. The three dimensional structure of proteins is maintained or stabilized by bonds or interactions between the R-groups of amino acids. These bonds or interactions are weak and can be broken or disrupted fairly easily. When this occurs it cause a change in the conformation of the protein and this is known as denaturation. When a protein is denatured it changes shape and these changes can be temporary or permanent. Two factors than can denature proteins are heat and pH.

21. 2.4 A2 – Denaturation of proteins with a wide range of functions. Extreme changes in pH can cause proteins to denature. It causes changes in the charges on R groups which breaks the bonds or causes new bonds to form. This will alter the structure of the protein. Some proteins are exceptions such as the stomach enzyme pepsin (pH 1.5) Heat can denature proteins because it causes vibrations in the molecule that breaks bonds. Proteins vary in their tolerance of heat and can cause temporary or permanent changes.