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AnnouncementsAnnouncements & Agenda& Agenda (04/25/07)(04/25/07)Will Pass Around Sign-In SheetWill Pass Around Sign-In Sheet Indicate 2 times you can meet for review next weekIndicate 2 times you can meet for review next week Choices: T @ 4, T @ 5, T @ 7Choices: T @ 4, T @ 5, T @ 7

W @ 4, W @ 5, W @ 7W @ 4, W @ 5, W @ 7

FINAL EXAM TIME: Thursday @ 10:30 am!!!FINAL EXAM TIME: Thursday @ 10:30 am!!! Cumulative with 10-15 % New StuffCumulative with 10-15 % New Stuff

Exam 3 back Fri Exam 3 back Fri Complete HCTA: If >85 % Do Before Exam, Complete HCTA: If >85 % Do Before Exam, You ALL get 2 extra credit pointsYou ALL get 2 extra credit points

TodayToday Protein Structure (16.5)Protein Structure (16.5) Enzymes (16.6-16.8)Enzymes (16.6-16.8) Coenzymes (16.9)Coenzymes (16.9)

NO 3pm Review NO 3pm Review Today Today

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CH 16 Practice ProblemsCH 16 Practice Problems(MUST DO 10 OF THESE BY FRI)(MUST DO 10 OF THESE BY FRI)Will be counted as FINAL QUIZ! (EASY PTS)Will be counted as FINAL QUIZ! (EASY PTS)

16.01, 16.07, 16.11, 16.21, 16.25, 16.27, 16.01, 16.07, 16.11, 16.21, 16.25, 16.27, 16.29, 16.31, 16.33, 16.35, 16.37, 16.39, 16.29, 16.31, 16.33, 16.35, 16.37, 16.39, 16.41, 16.43, 16.49, 16.51, 16.55, 16.61, 16.41, 16.43, 16.49, 16.51, 16.55, 16.61, 16.63, 16.67, 16.69, 16.77, 16.8116.63, 16.67, 16.69, 16.77, 16.81

UsefulUseful for Exam Prep on CH 16! for Exam Prep on CH 16!

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Last Time: Functions of ProteinsLast 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 Function of proteins determined by amino acidsamino acids used used and how they are put together in 2-D and 3-Dand how they are put together in 2-D and 3-D

KNOW THE CLASSES!KNOW THE CLASSES!

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Last Time: Types of Amino AcidsLast Time: Types of Amino Acids

4 main kinds:4 main kinds:

• nonpolarnonpolar (hydrophobic) (hydrophobic) with hydrocarbon side with hydrocarbon side chains.chains.

• polarpolar (hydrophilic) with (hydrophilic) with polar or ionic side chains.polar or ionic side chains.

• acidicacidic (hydrophilic) with (hydrophilic) with acidic side chains.acidic side chains.

• basicbasic (hydrophilic) with (hydrophilic) with –NH–NH22 side chains. side chains.

Nonpolar PolarNonpolar Polar

AcidicAcidicBasicBasic

Be able to recognize these 4 kinds, no need to memorize all 20 for the Final Exam!!!!!!!!!!!!!!!!!

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Last Time: Formation of ProteinsLast Time: Formation of ProteinsThe Peptide BondThe Peptide Bond

• The peptide bond is an The peptide bond is an amide bondamide bond. . • forms between the carboxyl group of one amino acid forms between the carboxyl group of one amino acid

and the amino group of the next amino acid.and the amino group of the next amino acid.

OO CH CH3 3 OO

++ |||| ++ | ||| ||HH33NN——CHCH22——CC——OO–– + + HH33NN——CHCH——CC——OO––

O HO H CH CH3 3 OO ++ |||| || | ||| ||

HH33NN——CHCH22——CC——NN——CHCH——CC——OO–– peptide bondpeptide bond

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Tour of Protein Structure…Tour of Protein Structure…

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Last Time: Primary StructuresLast Time: Primary Structures• The nonapeptides oxytocin and vasopressin The nonapeptides oxytocin and vasopressin

have similar primary structures.have similar primary structures.• Only the amino acids at positions 3 and 8 differ.Only the amino acids at positions 3 and 8 differ.

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Primary Structure of InsulinPrimary Structure of InsulinInsulinInsulin• was the first protein to have its was the first protein to have its

primary structure determined.primary structure determined.• has a primary structure of two has a primary structure of two

polypeptide chains linked by polypeptide chains linked by disulfide bonds.disulfide bonds.

• has a chain A with 21 amino has a chain A with 21 amino acids and a chain B with 30 acids and a chain B with 30 amino acids.amino acids.

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Modification of insulinModification of insulin

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Secondary Structure ElementsSecondary Structure Elements

• a 3-D arrangement of amino a 3-D arrangement of amino acids in a polypeptide chain.acids in a polypeptide chain.

• result from result from intermolecularintermolecular forces forces such as such as hydrogen bondinghydrogen bonding

• Several types of secondary Several types of secondary structurestructure

• Alpha helicesAlpha helices• Beta sheetsBeta sheets• Triple helicesTriple helices• Many more…Many more…

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Secondary Structure – Alpha HelixSecondary Structure – Alpha Helix

• a 3-D spatial arrangement of a 3-D spatial arrangement of amino acids in a polypeptide amino acids in a polypeptide chain.chain.

• held by H bonds between the held by H bonds between the H of –N-H group and the O of H of –N-H group and the O of CC=O of the fourth amino acid =O of the fourth amino acid down the chain.down the chain.

• a corkscrew shape that loa corkscrew shape that looks oks like a coiled “telephone cord”.like a coiled “telephone cord”.

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Beta Pleated SheetBeta 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-is typical of fibrous proteins such as silk, beta-

keratin, etc.keratin, etc.

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Secondary Structure – Triple HelixSecondary Structure – Triple Helix

• three polypeptide three polypeptide chains woven chains woven together.together.

• typical of collagen, typical of collagen, connective tissue, connective tissue, skin, tendons, and skin, tendons, and cartilage.cartilage.

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Tertiary StructureTertiary Structure

• overall 3-D shape.overall 3-D shape.• determined by determined by

attractions & attractions & repulsions between repulsions between side chains of amino side chains of amino acidsacids

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Crosslinks in Tertiary StructuresCrosslinks in Tertiary Structures

involve attractions involve attractions and repulsions and repulsions between the side between the side chains of the amino chains of the amino acids in the acids in the polypeptide chain.polypeptide chain.

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Example: Globular ProteinsExample: Globular Proteins

• have compact, have compact, spherical shapes.spherical shapes.

• carry out synthesis, carry out synthesis, transport, and transport, and metabolism in the metabolism in the cells.cells.

• such as myoglobin such as myoglobin store and transport store and transport oxygen in muscle.oxygen in muscle.

Myoglobin

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Quaternary StructureQuaternary Structure

• combination of 2 or combination of 2 or more protein units.more protein units.

• Example: hemoglobin Example: hemoglobin consists of 4 subunits.consists of 4 subunits.

• stabilized by the same stabilized by the same interactions found in interactions found in tertiary structures.tertiary structures.

HemoglobinHemoglobin

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Summary of Protein StructureSummary of Protein Structure

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• the disruption of bonds in the secondary, tertiary the disruption of bonds in the secondary, tertiary and quaternary protein structures.and quaternary protein structures.

• heat and organic compounds:heat and organic compounds: break apart H break apart H bonds and disrupt hydrophobic interactions.bonds and disrupt hydrophobic interactions.

• acids and bases:acids and bases: break H bonds between polar break H bonds between polar R groups and disrupt ionic bonds.R groups and disrupt ionic bonds.

• heavy metal ions:heavy metal ions: react with S-S bonds to form react with S-S bonds to form solids (among many other things)solids (among many other things)

• agitationagitation such as whipping that stretches such as whipping that stretches peptide chains until bonds break.peptide chains until bonds break.

DenaturationDenaturation

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• cooking. cooking. • the skin is wiped the skin is wiped

with alcohol.with alcohol.• heat is used to heat is used to

cauterize blood cauterize blood vessels.vessels.

• instruments are instruments are sterilized in sterilized in autoclaves. autoclaves.

Applications of DenaturationApplications of Denaturation

http://www.lifehouseproductions.com/remorgida.htmlhttp://www.lifehouseproductions.com/remorgida.html

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Enzymes: Biological Catalysts (16.6)Enzymes: Biological Catalysts (16.6)

• Catalyze Catalyze nearlynearly all all chemical reactions chemical reactions taking place in the cells taking place in the cells of the body.of the body.

• Increase the rate of Increase the rate of reaction by lowering reaction by lowering the energy of the energy of activation.activation.

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- classified by the reaction they catalyze.- classified by the reaction they catalyze.- names usually end in –ase & often identify reactant - names usually end in –ase & often identify reactant (substrate) and function of enzyme(substrate) and function of enzyme

ClassClass Type of Reactions catalyzedType of Reactions catalyzedOxidoreductasesOxidoreductases Oxidation-reductionOxidation-reductionTransferasesTransferases Transfer groups of atomsTransfer groups of atomsHydrolases HydrolysisHydrolases HydrolysisLyasesLyases Add atoms/remove atoms to orAdd atoms/remove atoms to or

from a double bondfrom a double bondIsomerasesIsomerases Rearrange atomsRearrange atomsLigasesLigases Use ATP to combine small moleculesUse ATP to combine small molecules

Classification of EnzymesClassification of Enzymes

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How They Work!!!How They Work!!!

In an enzyme-catalyzed reaction:In an enzyme-catalyzed reaction:• a substrate attaches to a substrate attaches to active siteactive site..• an enzyme-substrate (ES) complex an enzyme-substrate (ES) complex

forms.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 released reaction occurs, products released • an enzyme is used over and over.an enzyme is used over and over.• Known functions of enzymes Known functions of enzymes

important in medical analysesimportant in medical analyses

EE + S + S EES S EE + P + P

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Diagnostic EnzymesDiagnostic Enzymes

• often determine often determine the amount of the amount of damage in damage in tissues.tissues.

• that are elevated that are elevated may indicate may indicate damage or damage or disease in a disease in a particular organ.particular organ.

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Diagnostic Enzymes Example Diagnostic Enzymes Example

Levels of enzymes Levels of enzymes CK, LDH, & AST CK, LDH, & AST

• are elevated are elevated following a heart following a heart attack.attack.

• are used to are used to determine the determine the severity of the severity of the attack.attack.

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Factors Affecting Enzyme Activity!Factors Affecting Enzyme Activity!

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EnzymesEnzymes• are most active at an are most active at an

optimum temperature optimum temperature (usually 37°C in (usually 37°C in humans).humans).

• show little activity at show little activity at low temperatures.low temperatures.

• lose activity at high lose activity at high temperatures as temperatures as denaturation occurs.denaturation occurs.

TemperatureTemperature

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EnzymesEnzymes• are most active at are most active at

optimum pH.optimum pH.• contain R groups of contain R groups of

amino acids with amino acids with proper charges at proper charges at optimum pH.optimum pH.

• lose activity in low lose activity in low or high pH as or high pH as tertiary structure is tertiary structure is disrupted.disrupted.

pHpH

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Optimum pH ValuesOptimum pH Values

Most Enzymes inMost Enzymes in• the body have an the body have an optimum pHoptimum pH of about 7.4. of about 7.4.• certain organs, enzymes operate at lower and higher certain organs, enzymes operate at lower and higher

optimum pH values.optimum pH values.

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Substrate ConcentrationSubstrate Concentration

As As substrate substrate concentrationconcentration increases,increases, • the the rate of reactionrate of reaction

increases (at constant increases (at constant enzyme concentration).enzyme concentration).

• the enzyme eventually the enzyme eventually becomes saturated becomes saturated giving maximum activity. giving maximum activity.

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• are molecules that cause a loss of catalytic are molecules that cause a loss of catalytic activity.activity.

• prevent substrates from fitting into the active prevent substrates from fitting into the active sites.sites.

E + SE + S ESES E + PE + P

E + I EI no PE + I EI no P

Enzyme InhibitorsEnzyme Inhibitors

Natural & Synthetic: Lots of drugs Natural & Synthetic: Lots of drugs work by acting as inhibitorswork by acting as inhibitors

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

- many coenzymes derived from vitamins- many coenzymes derived from vitamins

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Water-Soluble VitaminsWater-Soluble Vitamins• soluble in aqueous solutions.soluble in aqueous solutions.• cofactors for many enzymes.cofactors for many enzymes.• not stored in the bodynot stored in the body..

Copyright © 2005 by Pearson Education, Inc.Publishing as Benjamin Cummings

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Fat-Soluble VitaminsFat-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, are important in vision, bone formation,

antioxidants, and blood clotting.antioxidants, and blood clotting.• are stored in the body. are stored in the body.

More on these on Friday!