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AnnouncementsAnnouncements & Agenda& Agenda (04/23/07)(04/23/07)

Pick Up Grade SheetsPick Up Grade Sheets

Exam 3 back later this weekExam 3 back later this week

Class in VWF 102 on Wed!Class in VWF 102 on Wed!

TodayToday Amino acids (16.1-16.3)Amino acids (16.1-16.3) Peptides (16.4)Peptides (16.4) Protein Structure (16.5)Protein Structure (16.5)

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I Thought Exam 3 was…I Thought Exam 3 was…

1.1. Piece of CakePiece of Cake

2.2. Easier than I ExpectedEasier than I Expected

3.3. Mostly What I ExpectedMostly What I Expected

4.4. Much Harder than I ExpectedMuch Harder than I Expected

5.5. Uh Oh…Uh Oh…

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Ch 16: Amino Acids, Ch 16: Amino Acids, Proteins, & Enzymes!Proteins, & Enzymes!

Baaaaaa…….

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Functions of ProteinsFunctions 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

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Proteins are made of Amino AcidsProteins are made of Amino Acids

20 Amino acids 20 Amino acids • are the building blocks of proteins.are the building blocks of proteins.• contain a carboxylic acid group and an amino group on contain a carboxylic acid group and an amino group on

the alpha (the alpha () carbon.) carbon.• are ionized in solution.are ionized in solution.• each contain a different side group (R).each contain a different side group (R).

RR side chain side chain RR ││ ++ │ │HH22NN—C ——C —COOHCOOH HH33NN—C ——C —COOCOO−−

│ │ │ │ HH H H ionized formionized form

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• must be obtained must be obtained from the diet.from the diet.

• not synthesized by not synthesized by the body.the body.

• are in meat and are in meat and diary products.diary products.

• are missing (one are missing (one or more) in grains or more) in grains and vegetables.and vegetables.

““Essential” Amino AcidsEssential” Amino Acids

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Types of Amino AcidsTypes 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 Polar

AcidicBasic

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

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Nonpolar Amino AcidsNonpolar Amino Acids

An amino acid is nonpolar when the R group is An amino acid is nonpolar when the R group is H, H, alkyl, or aromatic. alkyl, or aromatic.

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Polar Amino AcidsPolar Amino Acids

An amino acid is polar when the R group is an An amino acid is polar when the R group is an alcohol, thiol, or amide.alcohol, thiol, or amide.

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Acidic & Basic Amino AcidsAcidic & Basic Amino Acids

An amino acid is An amino acid is • acidic when the R group is a carboxylic acid.acidic when the R group is a carboxylic acid.• basic when the R group is an amine.basic when the R group is an amine.

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Fischer Projections of Amino AcidsFischer Projections of Amino Acids

• are chiral except glycineare chiral except glycine

• have Fischer projections that are stereoisomers.have Fischer projections that are stereoisomers.

• ONLY “L” amino acids used in proteins.ONLY “L” amino acids used in proteins.

L-Alanine D-Alanine L-Cysteine D-CysteineL-Alanine D-Alanine L-Cysteine D-Cysteine

CH2SH

H2N H

COOH

CH2SH

H NH2

COOH

CH3

H NH2

COOH

CH3

H2N H

COOH

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A A zwitterionzwitterion

• has has chargedcharged −NH−NH33++ and COO and COO– – groups. groups.

• forms when both the –NHforms when both the –NH22 and the –COOH groups in and the –COOH groups in

an amino acid ionize in water.an amino acid ionize in water.• has equal + and – charges at the has equal + and – charges at the isoelectric pointisoelectric point (pI). (pI).

O O OO

║║ ++ ║║

NHNH22——CHCH22——CC——OHOH HH33NN——CHCH22——CC——OO––

glycineglycine zwitterion of glycine zwitterion of glycine

ZwitterionsZwitterions

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pH and ionizationpH and ionization

HH++ OHOH––

++ ++

HH33NN–CH–CH22––COOHCOOH HH33NN–CH–CH22––COOCOO–– HH22NN–CH–CH22––COOCOO––

positive ionpositive ion zwitterion zwitterion negative negative ionion

low pHlow pH pI pI high pH high pH

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16.4 16.4 Formation of PeptidesFormation of Peptides

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The Peptide BondThe Peptide Bond

• is an amide bond. is an amide 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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Formation of a DipeptideFormation of a Dipeptide

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Naming Dipeptides (Tri… etc.)Naming Dipeptides (Tri… etc.) (NO NEED TO MEMORIZE NAMING RULES)(NO NEED TO MEMORIZE NAMING RULES)

A dipeptide A dipeptide • is named from the free amine (NHis named from the free amine (NH33

++) using a -) using a -ylyl ending for the name. ending for the name.

• names the last amino acid with the free names the last amino acid with the free carboxyl group (COOcarboxyl group (COO--) by its amino acid name. ) by its amino acid name.

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Tour of Protein Structure…Tour of Protein Structure…

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Primary Structure of ProteinsPrimary Structure of Proteins

• sequence of amino acidssequence of amino acids• different proteins have different sequencesdifferent proteins have different sequences

• the backbone of a peptide chain or the backbone of a peptide chain or protein.protein.

Ala─Leu─Cys─Met

CH3

SH

CH2

CH3

S

CH2

CH2CH O

O-CCH

H

N

O

CCH

H

N

O

CCH

H

N

O

CCHH3N

CH3

CH3CH

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Oxytocin (pitocin) V. du VigneaudOxytocin (pitocin) V. du Vigneaud

Nobel prize in chemistry 1955Nobel prize in chemistry 1955

Uterine contracting and milk letdown hormoneUterine contracting and milk letdown hormone

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Primary StructuresPrimary 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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Newer drugs for diabeticsNewer drugs for diabetics

http://www.rxlist.com/cgi/generic/byetta.hthttp://www.rxlist.com/cgi/generic/byetta.htmm

http://www.diabetesmonitor.com/symlin.hthttp://www.diabetesmonitor.com/symlin.htmm

http://health.dailynewscentral.com/content/http://health.dailynewscentral.com/content/view/0002300/38/view/0002300/38/

Glitazone Glitazone http://www.gpnotebook.co.uk/cache/x2002http://www.gpnotebook.co.uk/cache/x20020419151758067650.htm0419151758067650.htm

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Insulin can be administered by…Insulin can be administered by…

1.1. InhalationInhalation

2.2. InjectionInjection

3.3. oraloral

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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

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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.is typical of fibrous proteins such as silk.

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Secondary Structure – Triple HelixSecondary Structure – Triple Helix

The The secondary secondary structure of a triple structure of a triple helixhelix is is

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

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

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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