Proteins

1. Proteins • Proteins have many structures, resulting in a wide range of functions • Proteins do most of the work in cells and act as enzymes • Proteins are made of monomers called amino acids

2. The Work Proteins Do • Enzymatic Proteins • Selective acceleration of chemical reactions • Digestive enzymes catalyze the hydrolysis of the polymers in food. • Structural Proteins • Support • Insects and spiders use silk fibers to make their cocoons and webs. Collagen and elastin provide a fibrous framework in animal connective tissues. Keratin is the protein of hair, horns, and feathers. • Storage Proteins • Storage of amino acids • Ovalbumin is the protein of egg white, used as an amino acid source for the developing embryo. Casein, the protein of milk, is the major source of amino acids for baby mammals. Plants have storage proteins in their seeds. • Transport Proteins • Transport of other substances • Hemoglobin, the iron-containing protein of vertebrate blood, transports oxygen from the lungs to outer parts of the body. Other proteins transport molecules across cell membranes.

3. The Work Proteins Do • Hormonal proteins • Coordination of an organism’s activities • Insulin, a hormone secreted by the pancreas, helps regulate the concentration of sugar in the blood of vertebrates. • Receptor proteins • Response of cell to chemical stimuli • Receptors built into the membrane of a nerve cell detect chemical signals released by other nerve cells. • Contractile and motor proteins • Movement • Actin and myosin are responsible for the movement of muscles. Other proteins are responsible for the undulations of the organelles called cilia and flagella • Defensive proteins • Protection against disease • Antibodies combat bacteria and viruses

4. Every enzyme has its own substrate, or molecule on which it works. • Enzymes are mostly named according to their substrate and the kind of reaction they catalyse • Hexokinase: changes glucose to glucose-6-phosphate). • The names mostly end in -ase. • such as: Salivary amylase • peptidase Hydrolysis of urea from a cat's urine into CO2 and NH3, which gives its characteristic odor to a litter box in need of cleaning. H2N--C--NH2 + H2O CO2 + 2 NH3 || O Urea water carbon dioxide ammonia This reaction is catalysed by urease, an enzyme produced by bacteria that settle out of the air and reproduce in the litter box. At room temperature and pH 8: 1 molecule of urease catalyses the hydrolysis of 30,000 molecules / second. Without a catalyst this reaction would take about 3 million years. This means that the enzyme increases the speed a trillion times. Some enzymes work even faster than urease, others slower.

5. 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate binds to enzyme. 2 2 Substrate (sucrose) Glucose Enzyme (sucrase) OH H2O Fructose H O 4 Products are released. 3 Substrate is converted to products. • Enzymes • Are a types of proteins that act as catalysts, speeding up chemical reactions Most importantly, while the substrate changes, the enzyme remains unchanged throughout the cycle! Enzymes work very specifically. This specificity occurs because an enzyme actually binds with its substrate(s) to form an Enzyme substrate complex. The substrate binds specifically to a cluster of chemical groupings known as the enzyme's active site. Figure 5.16

6. Polypeptides What element do you see in the amino acid below, that you didn’t find in carbohydrates or lipids? • Polypeptides • Are polymers (chains) of amino acids • A protein • Consists of one or more polypeptides • Amino acids • Are organic molecules possessing both carboxyl and amino groups • Differ in their properties due to differing side chains, called R groups

7. Amino acids • Are linked by peptide bonds A peptide bond is a chemical bond formed between two molecules when the carboxyl group of one molecule reacts with the amine group of the other molecule, thereby releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. In what other biomolecules did we see dehydration synthesis building substances? Amino acids contain the elements: C, H, O, N, and S. Carbohydrates, and lipids!

8. CH3 CH3 CH3 CH CH2 CH3 CH3 H CH3 H3C CH3 CH2 CH O O O O O H3N+ H3N+ H3N+ H3N+ C H3N+ C C C C C C C C C O– O– O– O– O– H H H H H Valine (Val) Leucine (Leu) Isoleucine (Ile) Glycine (Gly) Alanine (Ala) Nonpolar CH3 CH2 S H2C CH2 O NH CH2 H2N C C CH2 CH2 O– CH2 O O O H H3N+ H3N+ C C C C H3N+ C C O– O– O– H H H Phenylalanine (Phe) Proline (Pro) Methionine (Met) Tryptophan (Trp) Figure 5.17 the 20 Amino Acids and their properties...

9. OH NH2 O C NH2 O C OH SH CH2 CH3 OH Polar CH2 CH CH2 CH2 CH2 CH2 O O O O O O H3N+ C H3N+ C H3N+ C C H3N+ C C H3N+ C C C C C H3N+ C O– O– O– O– O– O– H H H H H H Glutamine (Gln) Tyrosine (Tyr) Asparagine (Asn) Cysteine (Cys) Serine (Ser) Threonine (Thr) Basic Acidic NH3+ NH2 NH+ O– O –O O CH2 C NH2+ C C NH Electrically charged CH2 CH2 CH2 CH2 CH2 O O CH2 CH2 C CH2 C H3N+ C H3N+ C O O– O– CH2 C H3N+ CH2 C H O H O– C C H3N+ CH2 H O O– C C H3N+ H O– H Histidine (His) Lysine (Lys) Arginine (Arg) Glutamic acid (Glu) Aspartic acid (Asp) the 20 Amino Acids...continued

10. Amino acid subunits +H3NAmino end Pro Thr Gly Gly Thr Gly Glu Seu Lys Cys Pro Leu Met Val Lys Val Leu Asp Ala Arg Val Gly Ser Pro Ala Glu Lle Asp Thr Lys Ser Tyr Trp Lys Ala Leu Gly lle Ser Pro Phe His Glu His Ala Glu Val Thr Phe Val Ala Asn lle Thr Asp Ala Tyr Arg Ser Ala Arg Pro Gly Leu Leu Ser Pro Tyr Ser Tyr Ser Thr Thr Ala o Val c Val Glu – Lys o Thr Pro Asn Carboxyl end Protein Conformation and Function A protein’s specific conformation (shape) determines how it functions There are four levels of protein structure. • Primary structure • Is the unique sequence of amino acids in a polypeptide

11. H H H H H H O O O O O O O H H H H H H R R R R R R R C C C C C C C C C C C C C N N N N N N N N N N N N N C C C C C C C C C C C C C C R R R R R R H H H H H H H O O O O O O O H H H H H H H  pleated sheet H O H H Amino acidsubunits C C N N N C C C R H O H H H H H H N N N N N N  helix C C O C H H H C C C R R R R R H H C C C C C C O O O O H C R O C C O H C O N N H C C R R • Secondary structure • Is the folding or coiling of the polypeptide into a repeating configuration • Includes the  helix and the  pleated sheet The silken web a spider weaves is composed of the β pleated sheet structure. α-helices are also the most common protein structure element that crosses biological membranes

12. Tertiary structure • Is the overall three-dimensional shape of a polypeptide • Results from interactions between amino acids and R groups

13. Polypeptidechain Collagen  Chains Iron Heme  Chains Hemoglobin • Quaternary structure • Is the overall protein structure that results from the aggregation, or fusion of two or more polypeptide subunits

14. To Recap: The four levels of Protein Structure

15. Sickle-Cell Disease: A Simple Change in Primary Structure • Results from a single amino acid substitution in the protein hemoglobin Sickle-cell hemoglobin Normal hemoglobin Primary structure Primary structure Exposed hydrophobic region . . . . . . Val His Leu Thr Pro Glul Glu Val His Leu Pro Glu Thr Val 5 6 7 3 4 5 6 7 1 2 1 2 3 4 Secondaryand tertiarystructures Secondaryand tertiarystructures  subunit  subunit   Quaternary structure   Hemoglobin A Quaternary structure Hemoglobin S    Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.  Function Molecules donot associatewith oneanother, eachcarries oxygen. Function 10 m 10 m Red bloodcell shape Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen Red bloodcell shape Fibers of abnormalhemoglobin deform cell into sickle shape. Figure 5.21

16. Denaturation Normal protein Denatured protein Renaturation What Determines Protein Conformation? • Protein conformation depends on the physical and chemical conditions of the protein’s environment • Temperature, pH, etc. affect protein structure Denaturation occurs when a protein unravels and loses its native conformation shape. The original structure of some proteins can be “renatured” upon removal of the denaturing agent. Proteins subject to this process include hemoglobin (the oxygen-carrying part of red blood cells)

17. The Protein-Folding Problem • Most proteins • Probably go through several intermediate states on their way to a stable conformation, which is linked to the hydrophobic / hydrophyllic nature of the molecules The black dots in this diagram represent the hydrophobic parts of the polypeptide chain, and as you can see, when it moves to its conformational state, the hydrophobic areas bunch into the middle. In a real protein, this happens on a 3- dimensional scale

18. Chaperonins • Are protein molecules that assist in the proper folding of other proteins Correctlyfoldedprotein Polypeptide Cap Hollowcylinder 2 3 1 The cap attaches, causing the cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide. The cap comesoff, and the properly folded protein is released. Chaperonin(fully assembled) Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end. Figure 5.23 The energy to fold proteins is supplied by adenosine triphosphate (ATP)

19. X-ray crystallography • Is used to determine a protein’s three-dimensional structure X-raydiffraction pattern Photographic film Most Proteins and many biomolecules differ from other molecules because the environment in which they function is aqueous. Therefore most biomolecules can be prompted to form crystals when the solution in which they are dissolved becomes supersaturated. These crystals are loaded into the x ray crystallography machine and the image is made. Diffracted X-rays X-ray beam X-raysource Crystal Nucleic acid Protein (a) X-ray diffraction pattern (b) 3D computer model