Chapter 20. Proteins & Enzymes. Proteins & Enzymes - page 1

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1 Chapter 20 Proteins & Enzymes Proteins & Enzymes - page 1

2 Proteins & Enzymes Part 1: Amino Acids The building blocks of proteins are -amino acids, small molecules that contain a carboxylic acid and an amino group. The amino group and the carboxylic acid group are bonded to the same carbon. This shared carbon is called the carbon. Amino Acid at Physiological p Amino acids are always ionized at p 7.4. Zwitterion: Essential Amino Acids: amino acids that can NT be produced by the body Proteins & Enzymes page 2

3 There are 20 different amino acids found in proteins which differ only in the side chain (R group). Note the omission of from amino acids. Everyone is supposed to know. Proteins & Enzymes page 3

4 Acidic R Groups and Amino Acid Nomenclature Remember the acid/base chemistry of carboxylic acids and amines. Label the following reactants and products using the names: Aspartic acid; glutamic acid; aspartate; glutamate. - N 3 - N 2 - N 3 - N 2 Proteins & Enzymes page 4

5 Proteins and Enzymes Part 2 has been removed from the course. Proteins & Enzymes page 5

6 Proteins and Enzymes Part 3: An verview of Protein Structure Protein: A polypeptide with a specific biological function Levels of Structure of Proteins Proteins & Enzymes page 6

7 Proteins and Enzymes Part 4: The Primary Structure of Proteins The primary structure of proteins is the amino acid sequence. Peptides: two or more amino acids bonded together The amine group of one amino acid and the acid group of another can undergo an acyl group transfer reaction to form an amide bond (peptide bond). The new molecule is called a dipeptide. More reactions lead to tripeptides, tetrapeptides, etc. and finally polypeptides. Polypeptides are always written with the N-terminus on the left and the C-terminus on the right. The acyl transfer reaction (synthetic dehydration) of threonine (Thr) and valine (Val) to make a dipeptide is shown below. 3 N - 3 N - 3 N N - 2 Draw the neutral forms of each amino acid to help you recognize the synthetic dehydration reaction. Draw an arrow to the peptide bond connecting threonine to valine. Circle the part of the dipeptide that originated from threonine. Circle the part of the dipeptide that originated from valine. What is the relationship between Val-Thr and Thr-Val? Proteins & Enzymes page 7

8 Tripeptides - Use the tripeptide below to answer the following questions. Draw an arrow to each peptide bond. Circle the 3 side chains (R groups) in the following tripeptide. Classify each R group as nonpolar, polar, acidic, or basic. Label the N-terminus and C-terminus Write the peptide sequence. SC 3 3 N N N - - (C 2 ) 2 C 2 Draw the bond-line structure for the tripeptide Glu-Ser-Cys at physiological p. Proteins & Enzymes page 8

9 Proteins and Enzymes Part 5: Secondary Structure Secondary Structure: regular folding patterns in localized regions of the polypeptide backbone. Secondary structure is held in place by -bonds between backbone carbonyls & amino groups. -helix: the polypeptide backbone twists so that -bonds form between C= and an N- group 4 residues (amino acids) further along in the sequence -sheet: the polypeptide backbone is extended and -bonds form between the C= and N- groups on adjacent strands. In parallel sheets, the primary sequence of both stands proceeds in the same directions. In anti-parallel sheets, the primary sequences proceed in opposite directions. Proteins & Enzymes page 9

10 Secondary Structure distinguishes the different types of Fibrous Proteins. Fibrous Proteins primarily found in structural proteins water insoluble small fibrils twist into larger bundles the # of disulfide bonds affects hardness, flexibility & stretchiness -helix: wool, hair & fingernails -sheets: silk & spider webs (small R groups allow close stacking) Collagen is an example of a fibrous protein. Note the 3 -helixes. ther Important Fibrous Proteins Fibrous Protein keratins collagens elastins ccurrence and Function Found in skin, wool, feathers, hooves, silk, finger nails Found in animal hide, tendons, bone, eye cornea, & other connective tissue Found in blood vessels & ligaments where the ability to stretch is important myosins Found in muscle tissue fibrin Found in blood clots Proteins & Enzymes page 10

11 Proteins and Enzymes Part 6: Tertiary Structure Tertiary structure stabilized in 5 ways by R groups (side chains) that can be quite far apart along the amino acid backbone and may include nonpeptide organic molecules or metal ions 1. Covalent bonds disulfide bonds form between cysteine residues R C C N R' C 2 S S 2 C R C C N R' mild [] R C C N R' C 2 S S 2 C R C C N R' 2. -bonding polar groups on side chains (R groups) side chains with peptide back bone 3. Salt Bridges electrostatic interactions between ionized side chains 4. ydrophobic (London/Dispersion) Interactions Globular proteins usually turn their polar groups outward toward the aqueous body fluids while the nonpolar side chains (R groups) move inward away from the water. While the interaction is weak, it usually acts over large surface areas. Collectively, the interactions are strong enough to stabilize some 3 structures. 5. Metal-Ion Coordination Trace minerals (metal cations) form bridges btwn anionic side chains Classify the 3 interactions below. Proteins & Enzymes page 11

12 Identify the 2 & 3 structures in the protein segment shown below. Tertiary Structure and Globular Proteins Tertiary structures make use of -bonding, but the most important force holding globular proteins in place is the hydrophobic effect a process by which the water solvent attracts the polar amino acids to the outside of the protein and squeezes the nonpolar amino acids into the center of the globular protein. ther Important Globular Proteins Globular Protein ccurrence and Function insulin Regulatory hormone for glucose metabolism ribonuclease Enzyme that catalyzes RNA hydrolysis Immunoglobulin Proteins involved in immune response emoglobin Protein involved in 2 transport Albumins Blood transport protein Proteins & Enzymes page 12

13 Proteins and Enzymes Part 7: Quaternary Structure Quaternary Structure the way two or more polypeptide chains are held together by noncovalent interactions to form a single 3-D protein Example: emoglobin consists of four polypeptide subunits, each containing a heme group that binds an 2 molecule emoglobin eme What is the difference between a polypeptide and a protein? Proteins & Enzymes page 13

14 Denaturation An active protein must be in its native conformation. The primary structure is composed of amino acids connected with covalent peptide bonds that are not easily broken. owever, the secondary, tertiary, & quaternary structures are held together with weaker, noncovalent interactions. These structures can be disturbed by heat, agitation, drastic p changes, detergents, salts, organic solvents, etc. in a process called denaturing. Denatured proteins are often said to be unfolded and are no longer able to perform their intended function. Some proteins can spontaneously refold, but most denaturations are essentially irreversible and deactivate the protein. About half of the 223 amino acid residues of the digestive enzyme trypsin are hydrophobic. Describe where in the tertiary structure you would expect to find these residues. Describe where in the tertiary structure you would expect the polar amino acid residues in trypsin to be located. Suppose a polypeptide containing 150 amino acid residues is synthesized in the laboratory. Why is it not correct to call this polypeptide a protein? What part(s) of the protein structure is(are) affected by hydrolysis? Proteins & Enzymes page 14

15 Proteins and Enzymes Part 8: Introduction to Enzymes Enzymes Catalysts increase the rate of a chemical reaction without being changed themselves. Most biological catalysts are protein enzymes that change the way a reaction takes place so that it occurs faster. The reactants in enzyme-catalyzed reactions are called substrates. Enzymes lower the activation energy (Ea) of a reaction by binding one or more substrates into an active site, using hydrophobic or hydrophilic interactions (bonding, dipole-dipole, London, etc.) This binding stretches each substrate into a reactive form and aligns it properly for the chemical reaction to take place. Circle the side chains in each amino acid below. Classify the side chains as hydrophobic, polar, acidic or basic. N 3-3 C - - N 3 N 3 N N N 3 - If the first amino acid above is part of a substrate, hypothesize which of the other three amino acid residues might be present in the active site of an enzyme. Explain your reasoning. Proteins & Enzymes page 15

16 2 Models for the Enzyme Substrate Interaction Lock & Key model: The substrate fits into the active site as a key fits into a lock. Induced Fit model: The enzyme has a flexible active site that changes shape to accommodate the substrate & facilitate the reaction Example: Proteins & Enzymes page 16

17 Energy diagrams comparing uncatalyzed and catalyzed reactions Are these reactions endothermic or exothermic? Identify which reaction is catalyzed. ow could you tell? Draw in a vertical arrow to represent the magnitude of the Ea in the catalyzed reaction. Does the enzyme change the energies of the reactants or products? Does an enzyme change the equilibrium amounts of reactants and products? Explain. Proteins & Enzymes page 17

18 Proteins and Enzymes Part 9: Enzyme Inhibition Enzyme Inhibitors: any compound or environmental condition that prevents an enzyme from performing its function Nonspecific Inhibitors: Nonspecific Inhibition a closer look Effect of Temperature Increase in temperature increases the rate of enzyme catalyzed reactions. The rate reaches a maximum and then begins to decrease. The decrease in rate at higher temperature is due to denaturation of enzymes. Effect of p The catalytic activity of enzymes depends on p and usually has a well defined optimum point for maximum catalytic activity. Proteins & Enzymes page 18

19 Specific Inhibition a closer look Competitive Inhibition vs Non-competitive Inhibition The activity of an enzyme is controlled by the binding at the active site. The activity of an enzyme is controlled by the binding of an activator or inhibitor at a location other than an active site. Feedback inhibition: regulation of an enzyme s activity by the product of a reaction later in a pathway Example: Threonine deaminase is inhibited by the isoleucine. Isoleucine binds to a different site on the enzyme and changes the conformation so that threonine no longer binds properly. 3 N - C threonine deaminase 3 N - C C 3 C 3 threonine C 2 C 3 isoleucine Proteins & Enzymes page 19

20 Allosteric control = Non-competitive Inhibition or Activation Proteins & Enzymes page 20

21 Proteins and Enzymes Part 10: Enzyme Classification & Reaction Catalysis Six main classes: 1. xidoreductase: redox reactions 2. Transferase: transfer functional groups 3. ydrolase: hydrolysis reactions 4. Lyase: addition and elimination reactions 5. Isomerase: isomerization reaction 6. Ligase: bond formation coupled with ATP Proteins & Enzymes page 21

22 xidoreductase: redox reactions; a coenzyme is required C 2 - Lactate NAD dehydrogenase C C 2 - NAD C 3 C 3 1. Label the reaction above to indicate which compound is oxidized and which compound is reduced. 2. Lactate dehydrogenase is the enzyme. What is the name of the term given to NAD in this reaction? Transferase: transfer functional groups (phosphates, acyl groups, amines); often have the name kinase Structure of Functional Group transferred at physiological p 3. Draw the structure of the functional group transferred in the reaction above at physiological p in the box above. Ligase: bond formation coupled with an ATP-ADP reaction 3 C C C ADP P C 2 ATP - C C - C-C 2 4. Describe how you can distinguish between a reaction catalyzed by a ligase enzyme and a reaction catalyzed by a transferase enzyme. Proteins & Enzymes page 22

23 ydrolase: hydrolysis reactions are important for digestion C3 C 3 C 3 2 C C 2 C 3 2 lipase 2 C 2 C C C3 C 3 fat (triglyceride) glycerin fatty acids C 3 5. Draw lines through the bonds in the reactant (fat) that are split apart by the water molecules. 6. Circle the hydroxyl groups in the product(s) that were derived from the water molecules. 7. Box the hydrogen atoms in the product(s) that were derived from the water molecules. Lyase: catalyze the addition of groups such as 2, C 2, or N 3 to a double bond or reverse reaction in which the group is eliminated to create a double bond C carbonic anhydrase 8. Describe how you can distinguish between a reaction catalyzed by a hydrolase enzyme and a reaction catalyzed by a lyase enzyme. Proteins & Enzymes page 23

24 Isomerase: isomerization reaction (rearranges functional groups within a molecule) - C 2 _ phosphoglycerate mutase C 2 P P - 9. The term to describe the relationship between the substrate and product of the reaction above is structural isomer or geometric isomer (circle one). 10. Identify the class of enzyme (oxidoreductase, transferase, hydrolase, lyase, isomerase, or ligase) needed to catalyze each of the following reactions? R a. C C C S CoA 2 R C C C S CoA c. d. e. f. Proteins & Enzymes page 24

25 Proteins and Enzymes Part 11: Enzyme Cofactors Many enzymes are conjugated proteins that require non-protein portions known as cofactors. Cofactors can be metal ions coenzymes - non-protein organic molecules Example of a metal ion cofactor - Zn 2 Carboxypeptidase is an enzyme that requires a Zn 2 ion as a cofactor. This enzyme hydrolyzes the first amide bond at the C- terminal end of peptides. Carboxypeptidase is synthesized in the pancreas and secreted in the small intestine. Proteins & Enzymes page 25

26 Example of a coenzyme cofactor NAD /NAD Lactate dehydrogenase is an enzyme that requires the coenzyme NAD /NAD for enzymatic function. - C 2 C 3 NAD Lactate dehydrogenase - C 2 C 3 NAD Which species has been reduced? Which species has been oxidized? Remember, enzymes catalyze both the forward and the reverse processes. Biochemical reactions are often represented with the coenzymes/ enzymes written in conjunction with the equation reacts to form arrow. Proteins & Enzymes page 26