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

2. 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.

3. Proteins have many structures, resulting in a wide range of functions Proteins account for more than 50% of the dry mass of most cells Protein functions include structural support, storage, transport, cellular communications, movement, and defense against foreign substances [Animations are listed on slides that follow the figure]

5. Enzymes a type of protein Enzymes are a type of protein that acts as a catalyst, speeding up chemical reactions Enzymes can perform their functions repeatedly, functioning as workhorses that carry out the processes of life

6. Enzymes Substrate (sucrose) Enzyme (sucrose) Fructose Glucose

7. Polypeptides --linear chain of Amino Acids Polypeptides are polymers of amino acids A protein consists of one or more polypeptides

8. Amino Acid Monomers Amino acids are organic molecules with carboxyl (--COOH) and amino groups (--NH 2 ) Amino acids differ in their properties due to differing side chains, called R groups Cells use 20 amino acids to make thousands of proteins Amino group Carboxyl group  carbon

9. Amino group Carboxyl group  carbon

10. All living organisms using the same 20 Amino Acids. Below are 9 nonpolar/ hydrophobic amino acids Isoleucine (Ile) Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro) Leucine (Leu) Valine (Val) Alanine (Ala) Nonpolar Glycine (Gly)

11. Asparagine (Asn) Glutamine (Gln)Threonine (Thr) Polar Serine (Ser) Cysteine (Cys) Tyrosine (Tyr) All living organisms using the same 20 Amino Acids. Below are 6 polar/ hydrophilic amino acids

12. LE 5-17c Electrically charged Aspartic acid (Asp) Acidic Basic Glutamic acid (Glu) Lysine (Lys)Arginine (Arg) Histidine (His) All living organisms using the same 20 Amino Acids. Below are 5 VERY polar/ hydrophilic amino acids

13. Ribsomes in the cytoplasm and on the E.R. make proteins There are two types of ribosomes: – Free Ribosomes (located in the cytoplasm) – Bound Ribosomes (located on the Endoplasmic reticulum) Both ribosomes make proteins/ polypeptides by stringing amino acids together.

14. Amino Acid Polymers Amino acids are linked by peptide bonds A polypeptide is a polymer of amino acids Polypeptides range in length from a few monomers to more than a thousand Each polypeptide has a unique linear sequence of amino acids

15. Protein Tutorial Below: Click below for the protein tutorials http://www.wisc- online.com/objects/ViewObject.aspx?ID=AP1 3304http://www.wisc- online.com/objects/ViewObject.aspx?ID=AP1 3304 http://publications.nigms.nih.gov/structlife/c hapter1.html#a1http://publications.nigms.nih.gov/structlife/c hapter1.html#a1

16. Condensation reaction of amino acids to form polypeptide bonds and thus proteins

17. Hydrolysis vs. Condensation Hydrolysis Adds water Breaks down polymers into monomers Example: Breaks down starch into glucose Condensation Removes water Forms new bonds between monomers forming polymers Example: glucose and fructose are bonded together to form sucrose

18. IB Assessment Statment 7.5.1 Explain the four levels of protein structure, indicating the significance of each.

19. PRIMARY STRUCTURE The sequence of amino acids © Anne-Marie Ternes

20. PRIMARY STRUCTURE The numbers of amino acids vary (e.g. insulin 51, lysozyme 129, haemoglobin 574, gamma globulin 1250) The primary structure determines the folding of the polypeptide to give a functional protein Polar amino acids (acidic, basic and neutral) are hydrophilic and tend to be placed on the outside of the protein. Non-polar (hydrophobic) amino acids tend to be placed on the inside of the protein © 2007 Paul Billiet ODWSODWS

21. Infinite variety The number of possible sequences is infinite An average protein has 300 amino acids, At each position there could be one of 20 different amino acids = 10 390 possible combinations Most are useless Natural selection picks out the best © 2007 Paul Billiet ODWSODWS

23. SECONDARY STRUCTURE The folding of the N-C-C backbone of the polypeptide chain using weak hydrogen bonds © Science Student © Text 2007 Paul Billiet ODWSODWS

24. SECONDARY STRUCTURE This produces the alpha helix and beta pleating The length of the helix or pleat is determined by certain amino acids that will not participate in these structures (e.g. proline) © Dr Gary Kaiser © Text2007 Paul Billiet ODWSODWS

26. TERTIARY STRUCTURE The folding of the polypeptide into domains whose chemical properties are determined by the amino acids in the chain MIL1 protein © Anne-Marie Ternes © 2007 Paul Billiet ODWSODWS

27. TERTIARY STRUCTURE This folding is sometimes held together by strong covalent bonds (e.g. cysteine-cysteine disulphide bridge) Bending of the chain takes place at certain amino acids (e.g. proline) Hydrophobic amino acids tend to arrange themselves inside the molecule Hydrophilic amino acids arrange themselves on the outside © 2007 Paul Billiet ODWSODWS

28. Disulfide bonds of tertiary structures of proteins Covalent bonds can form between two adjacent cysteine amino acids. The bond is covalent. The covalent bond stabilises the tertiary shape of a protein.

29. © Max Planck Institute for Molecular Genetics Chain B of Protein Kinase C

31. QUATERNARY STRUCTURE Some proteins are made of several polypeptide subunits (e.g. haemoglobin has four) Protein Kinase C © Max Planck Institute for Molecular Genetics © Text 2007 Paul Billiet ODWSODWS

32. QUATERNARY STRUCTURE These subunits fit together to form the functional protein Therefore, the sequence of the amino acids in the primary structure will influence the protein's structure at two, three or more levels © 2007 Paul Billiet ODWSODWS

34. Result Protein structure depends upon the amino acid sequence This, in turn, depends upon the sequence of bases in the gene © 2007 Paul Billiet ODWSODWS

35. QUATERNARY STRUCTURE In some cases proteins consist of nonpoly- peptide (non-protein) chain called a prosthetic group Example: haemoglobin is linked to a heme group (iron contain molecule) Proteins with a prosthetic group are called conjugated proteins. © 2007 Paul Billiet ODWSODWS

36. PROTEIN FUNCTIONS Protein structure determines protein function Denaturation or inhibition which may change protein structure will change its function Coenzymes and cofactors in general may enhance the protein's structure © 2007 Paul Billiet ODWSODWS

37. IB Assessment Statement 7.5.2 Outline the difference between fibrous and globular proteins with references to two examples of each protein type

38. Fibrous proteins Involved in structure: tendons ligaments blood clots (e.g. collagen and keratin) Contractile proteins in movement: muscle, microtubules (cytoskelton, mitotic spindle, cilia, flagella) © 2007 Paul Billiet ODWSODWS

39. Globular proteins most proteins which move around (e.g. albumen, casein in milk) Proteins with binding sites: enzymes, haemoglobin, immunoglobulins, membrane receptor sites © 2007 Paul Billiet ODWSODWS

41. Examples to know 1.Rubisco 2.Insulin 3.Immunoglobulin 4.Rhodopsin 5.Collagen 6.Spider silk

42. 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.

43. Application: Denaturation of proteins by heat or by deviation of pH from the optimum.