1 Announcements & Agenda (04/25/07) Will Pass Around Sign-In Sheet Indicate 2 times you can meet for review next week Indicate 2 times you can meet for review next week Choices: 4, 5, 7 Choices: 4, 5, 7 4, 5, 7 4, 5, 7 FINAL EXAM TIME: 10:30 am!!! Cumulative with % New Stuff Cumulative with % New Stuff Exam 3 back Fri  Complete HCTA: If >85 % Do Before Exam, You ALL get 2 extra credit points Today Protein Structure (16.5) Protein Structure (16.5) Enzymes ( ) Enzymes ( ) Coenzymes (16.9) Coenzymes (16.9) NO 3pm Review Today 

2 CH 16 Practice Problems (MUST DO 10 OF THESE BY FRI) Will be counted as FINAL QUIZ! (EASY PTS) 16.01, 16.07, 16.11, 16.21, 16.25, 16.27, 16.29, 16.31, 16.33, 16.35, 16.37, 16.39, 16.41, 16.43, 16.49, 16.51, 16.55, 16.61, 16.63, 16.67, 16.69, 16.77, Useful for Exam Prep on CH 16!

3 Last Time: Functions of Proteins Proteins perform many different functions in the body. Proteins perform many different functions in the body. Function of proteins determined by amino acids used and how they are put together in 2-D and 3-D KNOW THE CLASSES!

4 Last Time: Types of Amino Acids 4 main kinds: nonpolar (hydrophobic) with hydrocarbon side chains.nonpolar (hydrophobic) with hydrocarbon side chains. polar (hydrophilic) with polar or ionic side chains.polar (hydrophilic) with polar or ionic side chains. acidic (hydrophilic) with acidic side chains.acidic (hydrophilic) with acidic side chains. basic (hydrophilic) with –NH 2 side chains.basic (hydrophilic) with –NH 2 side chains. Nonpolar Polar Acidic Basic Be able to recognize these 4 kinds, no need to memorize all 20 for the Final Exam!!!!!!!!!!!!!!!!!

5 Last Time: Formation of Proteins The Peptide Bond The peptide bond is an amide bond.The peptide bond is an amide bond. forms between the carboxyl group of one amino acid and the amino group of the next amino acid.forms between the carboxyl group of one amino acid and the amino group of the next amino acid. O CH 3 O O CH 3 O + || + | || + || + | || H 3 N—CH 2 —C—O – + H 3 N—CH—C—O – O H CH 3 O O H CH 3 O + || | | || + || | | || H 3 N—CH 2 —C—N—CH—C—O – peptide bond peptide bond

6 Tour of Protein Structure…

7 Last Time: Primary Structures The nonapeptides oxytocin and vasopressin have similar primary structures.The nonapeptides oxytocin and vasopressin have similar primary structures. Only the amino acids at positions 3 and 8 differ.Only the amino acids at positions 3 and 8 differ.

8 Primary Structure of Insulin Insulin was the first protein to have its primary structure determined.was the first protein to have its primary structure determined. has a primary structure of two polypeptide chains linked by disulfide bonds.has a primary structure of two polypeptide chains linked by disulfide bonds. has a chain A with 21 amino acids and a chain B with 30 amino acids.has a chain A with 21 amino acids and a chain B with 30 amino acids.

9 Modification of insulin

10 Secondary Structure Elements a 3-D arrangement of amino acids in a polypeptide chain.a 3-D arrangement of amino acids in a polypeptide chain. result from intermolecular forces such as hydrogen bondingresult from intermolecular forces such as hydrogen bonding Several types of secondary structureSeveral types of secondary structure Alpha helices Alpha helices Beta sheets Beta sheets Triple helices Triple helices Many more… Many more…

11 Secondary Structure – Alpha Helix a 3-D spatial arrangement of amino acids in a polypeptide chain.a 3-D spatial arrangement of amino acids in a polypeptide chain. held by H bonds between the H of –N-H group and the O of C=O of the fourth amino acid down the chain.held by H bonds between the H of –N-H group and the O of C=O of the fourth amino acid down the chain. a corkscrew shape that looks like a coiled “telephone cord”.a corkscrew shape that looks like a coiled “telephone cord”.

12 Beta Pleated Sheet polypeptide chains side by side.polypeptide chains side by side. hydrogen bonds between chains.hydrogen bonds between chains. has R groups above and below the sheet.has R groups above and below the sheet. is typical of fibrous proteins such as silk, beta- keratin, etc.is typical of fibrous proteins such as silk, beta- keratin, etc.

13 Secondary Structure – Triple Helix three polypeptide chains woven together.three polypeptide chains woven together. typical of collagen, connective tissue, skin, tendons, and cartilage.typical of collagen, connective tissue, skin, tendons, and cartilage.

14 Tertiary Structure overall 3-D shape.overall 3-D shape. determined by attractions & repulsions between side chains of amino acidsdetermined by attractions & repulsions between side chains of amino acids

15 Crosslinks in Tertiary Structures involve attractions and repulsions between the side chains of the amino acids in the polypeptide chain.

16 Example: Globular Proteins have compact, spherical shapes.have compact, spherical shapes. carry out synthesis, transport, and metabolism in the cells.carry out synthesis, transport, and metabolism in the cells. such as myoglobin store and transport oxygen in muscle.such as myoglobin store and transport oxygen in muscle. Myoglobin

17 Quaternary Structure combination of 2 or more protein units.combination of 2 or more protein units. Example: hemoglobin consists of 4 subunits.Example: hemoglobin consists of 4 subunits. stabilized by the same interactions found in tertiary structures.stabilized by the same interactions found in tertiary structures. Hemoglobin

18 Summary of Protein Structure

19 the disruption of bonds in the secondary, tertiary and quaternary protein structures.the disruption of bonds in the secondary, tertiary and quaternary protein structures. heat and organic compounds: break apart H bonds and disrupt hydrophobic interactions.heat and organic compounds: break apart H bonds and disrupt hydrophobic interactions. acids and bases: break H bonds between polar R groups and disrupt ionic bonds.acids and bases: break H bonds between polar R groups and disrupt ionic bonds. heavy metal ions: react with S-S bonds to form solids (among many other things)heavy metal ions: react with S-S bonds to form solids (among many other things) agitation such as whipping that stretches peptide chains until bonds break.agitation such as whipping that stretches peptide chains until bonds break. Denaturation

20 cooking.cooking. the skin is wiped with alcohol.the skin is wiped with alcohol. heat is used to cauterize blood vessels.heat is used to cauterize blood vessels. instruments are sterilized in autoclaves.instruments are sterilized in autoclaves. Applications of Denaturation

21 Enzymes: Biological Catalysts (16.6) Catalyze nearly all chemical reactions taking place in the cells of the body.Catalyze nearly all chemical reactions taking place in the cells of the body. Increase the rate of reaction by lowering the energy of activation.Increase the rate of reaction by lowering the energy of activation.

22 - classified by the reaction they catalyze. - names usually end in –ase & often identify reactant (substrate) and function of enzyme ClassType of Reactions catalyzed OxidoreductasesOxidation-reduction TransferasesTransfer groups of atoms Hydrolases Hydrolysis LyasesAdd atoms/remove atoms to or from a double bond IsomerasesRearrange atoms LigasesUse ATP to combine small molecules Classification of Enzymes

23 How They Work!!! In an enzyme-catalyzed reaction: a substrate attaches to active site.a substrate attaches to active site. an enzyme-substrate (ES) complex forms.an enzyme-substrate (ES) complex forms. Lock & key model (OLD, RIGID MODEL)Lock & key model (OLD, RIGID MODEL) Induced-fit model (CURRENT MODEL)Induced-fit model (CURRENT MODEL) reaction occurs, products releasedreaction occurs, products released an enzyme is used over and over.an enzyme is used over and over. Known functions of enzymes important in medical analysesKnown functions of enzymes important in medical analyses E + S ES E + P

24 Diagnostic Enzymes often determine the amount of damage in tissues.often determine the amount of damage in tissues. that are elevated may indicate damage or disease in a particular organ.that are elevated may indicate damage or disease in a particular organ.

25 Diagnostic Enzymes Example Levels of enzymes CK, LDH, & AST are elevated following a heart attack.are elevated following a heart attack. are used to determine the severity of the attack.are used to determine the severity of the attack.

26 Factors Affecting Enzyme Activity!

27 Enzymes are most active at an optimum temperature (usually 37°C in humans).are most active at an optimum temperature (usually 37°C in humans). show little activity at low temperatures.show little activity at low temperatures. lose activity at high temperatures as denaturation occurs.lose activity at high temperatures as denaturation occurs. Temperature

28 Enzymes are most active at optimum pH.are most active at optimum pH. contain R groups of amino acids with proper charges at optimum pH.contain R groups of amino acids with proper charges at optimum pH. lose activity in low or high pH as tertiary structure is disrupted.lose activity in low or high pH as tertiary structure is disrupted. pH

29 Optimum pH Values Most Enzymes in the body have an optimum pH of about 7.4.the body have an optimum pH of about 7.4. certain organs, enzymes operate at lower and higher optimum pH values.certain organs, enzymes operate at lower and higher optimum pH values.

30 Substrate Concentration As substrate concentration increases, the rate of reaction increases (at constant enzyme concentration).the rate of reaction increases (at constant enzyme concentration). the enzyme eventually becomes saturated giving maximum activity.the enzyme eventually becomes saturated giving maximum activity.

31 are molecules that cause a loss of catalytic activity.are molecules that cause a loss of catalytic activity. prevent substrates from fitting into the active sites.prevent substrates from fitting into the active sites. E + SESE + P E + SESE + P E + I EI no P Enzyme Inhibitors Natural & Synthetic: Lots of drugs work by acting as inhibitors

32 Coenzymes (16.9) Coenzyme: a molecule which is ‘associated’ with the enzyme (but in not part of the amino acid sequence) that helps enzymes prepare the active site for catalytic activity. - many coenzymes derived from vitamins

33 Water-Soluble Vitamins soluble in aqueous solutions.soluble in aqueous solutions. cofactors for many enzymes.cofactors for many enzymes. not stored in the body.not stored in the body. Copyright © 2005 by Pearson Education, Inc. Publishing as Benjamin Cummings

34 Fat-Soluble Vitamins are A, D, E, and K.are A, D, E, and K. are soluble in lipids, but not in aqueous solutions.are soluble in lipids, but not in aqueous solutions. are important in vision, bone formation, antioxidants, and blood clotting.are important in vision, bone formation, antioxidants, and blood clotting. are stored in the body.are stored in the body. More on these on Friday!