+ All Categories
Home > Documents > AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino...

AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino...

Date post: 23-Dec-2015
Category:
Upload: earl-dixon
View: 226 times
Download: 5 times
Share this document with a friend
Popular Tags:
55
AA and Proteins AA and Proteins Robert F. Waters, PhD Robert F. Waters, PhD
Transcript
Page 1: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

AA and ProteinsAA and Proteins

Robert F. Waters, PhDRobert F. Waters, PhD

Page 2: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

OverviewOverview

ProteinsProteins– StructuralStructural– EnzymaticEnzymatic

Amino AcidsAmino Acids Henderson-Hasselbach EquationHenderson-Hasselbach Equation Acidity and AlkalinityAcidity and Alkalinity Gas exchangeGas exchange

Page 3: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

ProteinsProteins

Polypeptides with peptide bondsPolypeptides with peptide bonds– Peptide bondsPeptide bonds

» Endergonic (Consume energy)Endergonic (Consume energy) Need energy and do not occur spontaneouslyNeed energy and do not occur spontaneously

Structural proteinsStructural proteins Soluble proteins (Enzymes)Soluble proteins (Enzymes)

Page 4: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Protein StructureProtein Structure

Primary protein structurePrimary protein structure– Sequence of amino acidsSequence of amino acids

» Nomenclature: ala-glu-gly (N-terminus to C-terminus)Nomenclature: ala-glu-gly (N-terminus to C-terminus) alanylglutamylglycinealanylglutamylglycine

Secondary structure Secondary structure -helix and -helix and -sheet-sheet

Tertiary structureTertiary structure– 3-dimensional folding3-dimensional folding

Quaternary structureQuaternary structure– Multiple subunits of tertiary structuresMultiple subunits of tertiary structures

Page 5: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Protein Structure: PrimaryProtein Structure: Primary

Amino terminusAmino terminus

Carboxyl terminusCarboxyl terminus

Page 6: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Protein Structure:SecondaryProtein Structure:Secondary

Page 7: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Protein Structure: Tertiary and Protein Structure: Tertiary and QuaternaryQuaternary

Page 8: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Forces That Stabilize ProteinsForces That Stabilize Proteins

Ionic bondIonic bond

Hydrogen bondingHydrogen bonding

Hydrophobic interactionsHydrophobic interactions– Hydrocarbons in aqueous solution have force association Hydrocarbons in aqueous solution have force association

with adjacent hydrocarbons by rearrangement of with adjacent hydrocarbons by rearrangement of surrounding water moleculessurrounding water molecules

Van der Waals interactionsVan der Waals interactions– Weak electrostatic attractionsWeak electrostatic attractions

Page 9: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Denaturation of ProteinsDenaturation of ProteinsSoluble Proteins PrecipitateSoluble Proteins Precipitate

DehydrationDehydration HeatHeat RadiationRadiation pHpH ColdCold PressurePressure ChemicalsChemicals Excessive vibrational energy (Microwaves)Excessive vibrational energy (Microwaves) Natural organic substances (e.g., urea)Natural organic substances (e.g., urea) Reducing agentsReducing agents

– e.g., Mercaptoethanol HS-CHe.g., Mercaptoethanol HS-CH22-CH-CH22-OH-OH» Blocks disulfide bond formationBlocks disulfide bond formation

Page 10: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Post-Translational DenaturationPost-Translational Denaturation

Associated with Golgi ApparatusAssociated with Golgi Apparatus– PackagingPackaging– FoldingFolding

HerbicidesHerbicides PesticidesPesticides Neurotoxins (snake venom)Neurotoxins (snake venom)

Page 11: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Example of Precipitation by Example of Precipitation by AcidificationAcidification

Milk proteins (Two Main Types)Milk proteins (Two Main Types)– CaseinCasein

11-casein, -casein, s2s2-casein, -casein, -casein, -casein, -casein, -casein, -lactalbumin, -lactalbumin, --lactoglobulinlactoglobulin

– Whey (serum protein)Whey (serum protein)» Serum albumen, immunoglobulins, lactoferrinSerum albumen, immunoglobulins, lactoferrin

Casein separated from whey by acidification to casein pI of 6.0.Casein separated from whey by acidification to casein pI of 6.0.– Like adding citrus to coffee with creamLike adding citrus to coffee with cream

» Serum (whey)proteins remain in solution while casein Serum (whey)proteins remain in solution while casein precipitatesprecipitates

– Casein with lipids forms micelles (opaqueness of milk)Casein with lipids forms micelles (opaqueness of milk) Whey protein (hydrophilic) is used as protein addition to drinks, Whey protein (hydrophilic) is used as protein addition to drinks,

thickenersthickeners Casein is an excellent emulsifier in the addition of flavoring agentsCasein is an excellent emulsifier in the addition of flavoring agents

Page 12: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Vitamins and Minerals May Give Vitamins and Minerals May Give Color to ProteinColor to Protein

When a vitamin or mineral gives a protein color is called a When a vitamin or mineral gives a protein color is called a chromophore chromophore

FAD or FMN added to apoproteins to form flavoproteins give a FAD or FMN added to apoproteins to form flavoproteins give a yellowish coloryellowish color

Iron with myoglobin in meatIron with myoglobin in meat– Ranges in color from brown to bright redRanges in color from brown to bright red– White poultry meat has low myoglobinWhite poultry meat has low myoglobin– Dark meat has high myoglobin contentDark meat has high myoglobin content– Veal and pork have less myoglobin than beefVeal and pork have less myoglobin than beef

Myoglobin and hemoglobin without iron are colorlessMyoglobin and hemoglobin without iron are colorless Myoglobin and hemoglobin with iron are pink to redMyoglobin and hemoglobin with iron are pink to red Cooking meat dissociates heme to protein, iron and other Cooking meat dissociates heme to protein, iron and other

complexes and produces brown to tan colorcomplexes and produces brown to tan color

Page 13: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Quantifying Protein in SolutionQuantifying Protein in Solution

Based on absorption spectra of aromatic amino acids (~280nm)Based on absorption spectra of aromatic amino acids (~280nm)

– Tryptophan, tyrosine, phenylalanineTryptophan, tyrosine, phenylalanine

– Different proteins may vary in aromatic amino acids but Different proteins may vary in aromatic amino acids but absorption spectra variation is still usefulabsorption spectra variation is still useful

Page 14: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Zymogen SystemZymogen System

Series of enzyme activations for the Series of enzyme activations for the digestion of protein into amino acidsdigestion of protein into amino acids

Protection mechanism against autolysis of Protection mechanism against autolysis of endogenous proteins endogenous proteins

Begins mainly in the stomach and proceeds Begins mainly in the stomach and proceeds to intestineto intestine

Page 15: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

The Stomach:OverviewThe Stomach:Overview

Stomach not a very absorptive organ but—Stomach not a very absorptive organ but—– Water, ETOH, short and medium chain FAs are Water, ETOH, short and medium chain FAs are

absorbedabsorbed Gastric mucosaGastric mucosa

– Chief cells, parietal cells and mucous cellsChief cells, parietal cells and mucous cells» Produce gastric juices called gastrinsProduce gastric juices called gastrins

Page 16: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Summary of Stomach GastrinsSummary of Stomach Gastrins

Parietal Cells of StomachParietal Cells of Stomach– Secrete HCLSecrete HCL

» Denaturation, very little digestionDenaturation, very little digestion

– Secrete Vitamin B12 intrinsic factorSecrete Vitamin B12 intrinsic factor Chief Cells of StomachChief Cells of Stomach

– Secrete gastric lipaseSecrete gastric lipase– Secrete pepsinogensSecrete pepsinogens

» Activated to pepsin by HCLActivated to pepsin by HCL» Activated to pepsin by sutolysisActivated to pepsin by sutolysis

Pepsin cleaves proteins into large oligopeptides (peptones)Pepsin cleaves proteins into large oligopeptides (peptones)

Mucosa cellsMucosa cells– Secrete bicarbonate and mucus Secrete bicarbonate and mucus

Page 17: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Stomach Summary Cont:Stomach Summary Cont:

Stimulation of gastric secretions (Gastrin)Stimulation of gastric secretions (Gastrin)– Protein itselfProtein itself– Vagal stimulationVagal stimulation– Calcium ionsCalcium ions– Alkalination of the stomachAlkalination of the stomach

Gastrin stimulates –Gastrin stimulates –– HCL production (parietal cells)HCL production (parietal cells)

» HCL inhibits gastrin productionHCL inhibits gastrin production» NaCl necessary for HCL productionNaCl necessary for HCL production

– Mucin (mucous cells)Mucin (mucous cells)– Pepsinogen production (chief cells)Pepsinogen production (chief cells)

» Activated by HCL to PepsinActivated by HCL to Pepsin

Page 18: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

ZymogensZymogens

Proenzymes (zymogens) packaged as Proenzymes (zymogens) packaged as zymogen granules in pancreaszymogen granules in pancreas

Pancreatic zymogens are Pancreatic zymogens are serineserine proteases proteases– Trypsin (less than proenzyme form)Trypsin (less than proenzyme form)– ChymotrypsinChymotrypsin– ElastaseElastase

Page 19: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Enteropeptidase ActivationEnteropeptidase Activation

Enteropeptidase produced in intestinal Enteropeptidase produced in intestinal brush borderbrush border– Activates trypsin from trypsinogenActivates trypsin from trypsinogen

» Some activation of trypsin by autolysisSome activation of trypsin by autolysis

» Trypsin activates chymotrypsinogen, elastase and Trypsin activates chymotrypsinogen, elastase and carboxypeptidase A and B (possibly some carboxypeptidase A and B (possibly some aminopeptidases)aminopeptidases)

Carboxypeptidases and Aminopeptidases Carboxypeptidases and Aminopeptidases are called are called ExopeptidasesExopeptidases

Page 20: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Graphic Representation-Graphic Representation-Enteropeptidases and CascadingEnteropeptidases and Cascading

Page 21: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Phosphorous Containing Nerve Phosphorous Containing Nerve GasesGases

Initial studies with acetylcholine esteraseInitial studies with acetylcholine esterase Nerve gas DFPNerve gas DFP

– DiisopropylfluorophosphateDiisopropylfluorophosphate

– Attacks serine hydroxyl groups in enzymes like Attacks serine hydroxyl groups in enzymes like acteylcholine esterase AND serine proteases like acteylcholine esterase AND serine proteases like chymotrypsinchymotrypsin

» Attacks serine 195 in chymotrypsinAttacks serine 195 in chymotrypsin

DFP acts as a pseudo-substrate for the enzymesDFP acts as a pseudo-substrate for the enzymes DFP stops enzymatic reactionDFP stops enzymatic reaction

Page 22: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Graphical Representation of DFPGraphical Representation of DFP

Page 23: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Cysteine ProteasesCysteine Proteases

Attack sulfhydryl group on cysteine in proteinAttack sulfhydryl group on cysteine in protein Examples (mammals have similar proteases)Examples (mammals have similar proteases)

– Papain (papaya)Papain (papaya)

– Bromelain (pineapple)Bromelain (pineapple)

– Ficin (fig)Ficin (fig)

– Actinidin (kiwi fruit)Actinidin (kiwi fruit)

– Caricain, chymopapain, glycyl endopeptidase (from Caricain, chymopapain, glycyl endopeptidase (from latex portion of papaya tree)latex portion of papaya tree)

Page 24: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Lysosomal ProteasesLysosomal Proteases Active at lower lysosomal pHActive at lower lysosomal pH CathepsinsCathepsins

– Cathepsin B (Most abundant)Cathepsin B (Most abundant)» Endopeptidase and ExopeptidaseEndopeptidase and Exopeptidase

– Cathepsin H (Aminopeptidase)Cathepsin H (Aminopeptidase)– Cathepsin K (Abundant in bone resorbing osteoclastsCathepsin K (Abundant in bone resorbing osteoclasts

» Absence causes fragile small bonesAbsence causes fragile small bones

– Cathepsin C (dipeptidyl peptidase)Cathepsin C (dipeptidyl peptidase)» Removes N-terminus dipeptides activating intracellular proteins and maybe other Removes N-terminus dipeptides activating intracellular proteins and maybe other

CathepsinsCathepsins

Bleomycin hydrolaseBleomycin hydrolase– Bleomycin is an anti-cancer drugBleomycin is an anti-cancer drug– Bleomycin hydrolase breaks down bleomycinBleomycin hydrolase breaks down bleomycin

» Unfortunately cancer cells have high amounts of this enzyme causing drug resistanceUnfortunately cancer cells have high amounts of this enzyme causing drug resistance

– Papain-like activity that also binds to DNA?Papain-like activity that also binds to DNA?

Page 25: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Cysteinyl Aspartate-Specific Cysteinyl Aspartate-Specific Proteases (Caspases)Proteases (Caspases)

Involved in programmed cell death Involved in programmed cell death (Apoptosis)(Apoptosis)

Activation of InterleukinsActivation of Interleukins– Caspase-1 (AKA: Interleukin-1Caspase-1 (AKA: Interleukin-1-converting -converting

Enzyme or Enzyme or ICEICE))» Cleaves pro-interleukin-1Cleaves pro-interleukin-1 to form the active to form the active

interleukin-1interleukin-1

Page 26: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Aspartate Proteases (Pepsin-Like)Aspartate Proteases (Pepsin-Like)

Example is gastric proteinase – GastricsinExample is gastric proteinase – Gastricsin– Has similar activity as rennin (chymosin) from Has similar activity as rennin (chymosin) from

the fourth stomach of calfthe fourth stomach of calf» Causes rapid clotting of milkCauses rapid clotting of milk

Used in cheese manufacturingUsed in cheese manufacturing

– Serum protein Renin (NOT rennin) is similar as Serum protein Renin (NOT rennin) is similar as wellwell

Page 27: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Protease Inhibitors-ExogenousProtease Inhibitors-Exogenous

Leupeptin (Inhibits trypsin)Leupeptin (Inhibits trypsin) Boronic Acids (Inhibit serine proteases)Boronic Acids (Inhibit serine proteases) Pepstatin (Inhibit aspartic proteases)Pepstatin (Inhibit aspartic proteases)

– Were “Lead Compounds” for the formation of Were “Lead Compounds” for the formation of HIV protease inhibitorsHIV protease inhibitors

Mercaptans (Inhibit Zn++ metalloproteases)Mercaptans (Inhibit Zn++ metalloproteases)– Bind to Zn++ in some metalloproteasesBind to Zn++ in some metalloproteases

» Captopril Captopril Drug that inhibits Angiotensin-Converting-Enzyme Drug that inhibits Angiotensin-Converting-Enzyme

(ACE)(ACE)

Page 28: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Endogenous Protease InhibitorsEndogenous Protease Inhibitors

Trypsin activation in pancreas would be disastrousTrypsin activation in pancreas would be disastrous– Pancreatic Trypsin InhibitorPancreatic Trypsin Inhibitor

Serpins (Blood)Serpins (Blood)– Inhibit serine proteasesInhibit serine proteases

– 10% of the total protein in blood10% of the total protein in blood 1-protease Inhibitor (1-protease Inhibitor (1-antitrypsin)1-antitrypsin)

Found in Found in -globulin fraction of blood-globulin fraction of blood

» NOTE:One form of emphysema is the hereditary absence of NOTE:One form of emphysema is the hereditary absence of 1-antitrypsin1-antitrypsin

Without this inhibitor, tissue will degrade excessively, e.g. Without this inhibitor, tissue will degrade excessively, e.g. elastin, collagen and proteoglycanselastin, collagen and proteoglycans

Page 29: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Protease Activities-Serine Protease Activities-Serine ProteasesProteases

Page 30: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Amino AcidsAmino Acids Last one described was threonine in 1938Last one described was threonine in 1938 Stereospecific (L-Configuration exclusively)Stereospecific (L-Configuration exclusively)

– D-Amino acids found in bacteriaD-Amino acids found in bacteria Chemical properties associated with stereospecificity and Chemical properties associated with stereospecificity and

side groupsside groups Easily ionized in aqueous solutionEasily ionized in aqueous solution Produces a zwitterion (dipolar chemical structure with + Produces a zwitterion (dipolar chemical structure with +

and – chargesand – charges Zwitterion effect causes crystalline form of amino acids to Zwitterion effect causes crystalline form of amino acids to

have high decomposition temperatures above 200have high decomposition temperatures above 200oo centigradecentigrade– Similar to electrostatic forces holding and NaCl lattice togetherSimilar to electrostatic forces holding and NaCl lattice together

Page 31: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Overall Structure of Amino Overall Structure of Amino AcidsAcids

-Carbon, Carboxyl Group, Amino Group-Carbon, Carboxyl Group, Amino Group– Except imino amino acidsExcept imino amino acids

Enantiomeres (L-Amino acids in proteins)Enantiomeres (L-Amino acids in proteins)– D (Dextro) and L (laevo)D (Dextro) and L (laevo)

Page 32: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Amino Acid Structures-Neutral Amino Acid Structures-Neutral Side GroupsSide Groups

Page 33: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Amino Acid Structures-Aromatic Amino Acid Structures-Aromatic and Acidic Side Chainsand Acidic Side Chains

Page 34: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Amino Acid Structures-Positive Amino Acid Structures-Positive Side GroupsSide Groups

Page 35: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Amino Acid Structures-Polar Amino Acid Structures-Polar Side GroupsSide Groups

Page 36: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Classification by PolarityClassification by Polarity

Page 37: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Essential Amino AcidsEssential Amino Acids

PVT TIM HALLPVT TIM HALL Phenylalanine, valine, trptophan, threonine, Phenylalanine, valine, trptophan, threonine,

isoleucine, methionine, histidine, arginine isoleucine, methionine, histidine, arginine (neonate-child), leucine, lysine(neonate-child), leucine, lysine

Page 38: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Non-Essential Amino AcidsNon-Essential Amino Acids

Synthesized by humansSynthesized by humans– Serine, glycine, cysteine, alanine, aspartate, Serine, glycine, cysteine, alanine, aspartate,

asparagine, glutamate, glutamine, proline, asparagine, glutamate, glutamine, proline, arginine (adult), tyrosine (from phenylalanine)arginine (adult), tyrosine (from phenylalanine)

Page 39: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Non-Protein Amino AcidsNon-Protein Amino Acids

Citrulline is a product of L-arginine Citrulline is a product of L-arginine synthesis (urea cycle) and NO (Nitric synthesis (urea cycle) and NO (Nitric Oxide) metabolismOxide) metabolism

Creatinine is derived from muscleCreatinine is derived from muscle– Plasma amounts Plasma amounts to muscle mass to muscle mass

Ornithine, taurine, homocysteineOrnithine, taurine, homocysteine Biogenic Amine CompoundsBiogenic Amine Compounds

– Dopamine, serotonin, histamineDopamine, serotonin, histamine

Page 40: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Amino Acids and pHAmino Acids and pH

pH = -logpH = -log1010 [H+] ion concentration [H+] ion concentration

– Alkalinity vs. acidityAlkalinity vs. acidity Absorption of AA and pHAbsorption of AA and pH

Page 41: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Henderson-Hasselbach Equation Henderson-Hasselbach Equation (H-H)(H-H)

HA is protonated formHA is protonated form– Conjugate acid or associated formConjugate acid or associated form

AA-- is unprotonated form is unprotonated form – Conjugate base or dissociated formConjugate base or dissociated form

Protonation occurs in acidic solutionsProtonation occurs in acidic solutions Removal of protons in more alkaline Removal of protons in more alkaline

solutionssolutions

Page 42: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

H-H Continued:H-H Continued:

Acidic amino acids Acidic amino acids – Glutamate and aspartate are negatively charged Glutamate and aspartate are negatively charged

acidic amino acids at physiological pHacidic amino acids at physiological pH Basic amino acidsBasic amino acids

– Arginine, lysine, and histidine are positively Arginine, lysine, and histidine are positively charged amino acids at physiological pHcharged amino acids at physiological pH

Page 43: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

pK Values for Amino AcidspK Values for Amino Acids

Page 44: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Titration of Amino Acids with Titration of Amino Acids with (OH(OH--) NaOH-Glycine) NaOH-Glycine

Page 45: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Titration of Amino Acids with Titration of Amino Acids with (OH(OH--) NaOH-Histidine) NaOH-Histidine

Page 46: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Aspects of TitrationAspects of Titration

pI = Isoelectric PointpI = Isoelectric Point– pH where net charges equal zero (0)pH where net charges equal zero (0)

» Histidine pI = 7.7 (6.0 + 9.3)/2 = 7.7Histidine pI = 7.7 (6.0 + 9.3)/2 = 7.7» pHm = (1.8 + 6.0)/2 = 3.9pHm = (1.8 + 6.0)/2 = 3.9

pHm = Maximum ChargepHm = Maximum Charge– pH where number of positive and negative charges are pH where number of positive and negative charges are

maximalmaximal Buffering Range Buffering Range

– Range where change in pH is minimalRange where change in pH is minimal– Approximately +1 pH above pK to –1 pH below pK valueApproximately +1 pH above pK to –1 pH below pK value

» e.g. if a pK value = 6.0, then the buffering range around this pK e.g. if a pK value = 6.0, then the buffering range around this pK would be 5.0 – 7.0would be 5.0 – 7.0

Page 47: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Importance of Regulating pHImportance of Regulating pH Denaturation of ProteinDenaturation of Protein

– EnzymesEnzymes» Charge distributionCharge distribution» Hydrolysis of bondsHydrolysis of bonds

Charge changes on amino acidsCharge changes on amino acids– Substrate specificitySubstrate specificity

Hydroxyl amino acidsHydroxyl amino acids– Serine, threonine, tyrosineSerine, threonine, tyrosine

Quaternary structureQuaternary structure– Proteins, hemoglobin binding of oxygenProteins, hemoglobin binding of oxygen

pK of amino grouppK of amino group– Free amino acid amino group pK = 9.5Free amino acid amino group pK = 9.5– Amino group in a polypeptide pK = 8.0Amino group in a polypeptide pK = 8.0

Page 48: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Extremes of pHExtremes of pH

Acidosis to AlkalosisAcidosis to Alkalosis– Acidotic condition pH=7.0Acidotic condition pH=7.0– Alkalotic condition pH=8.0Alkalotic condition pH=8.0

Normal pH = 7.4Normal pH = 7.4– Venous blood pH = 7.35Venous blood pH = 7.35– Arterial blood pH = 7.45Arterial blood pH = 7.45

» Higher altitude arterial pH = 7.49Higher altitude arterial pH = 7.49

Most extreme limits are pH = 7.0 – 8.0Most extreme limits are pH = 7.0 – 8.0

Page 49: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

AcidosisAcidosis

AcidosisAcidosis– HyperventilationHyperventilation

» Controlled by mid brainControlled by mid brain

– Acidotic comaAcidotic coma» Reduction in myocardial contractionsReduction in myocardial contractions» Reduction in catacholamines (e.g., histamine)Reduction in catacholamines (e.g., histamine)

Reduce vascular tone (shock)Reduce vascular tone (shock) Pumping blood against a non-resistant wallPumping blood against a non-resistant wall

» Hypooxygenated (Cannot bring in enough O2)Hypooxygenated (Cannot bring in enough O2) Excess protons block hemoglobin binding of O2Excess protons block hemoglobin binding of O2

– ““Bohr Effect”Bohr Effect”

Page 50: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Acidosis Continued:Acidosis Continued:

Sources of ProtonsSources of Protons– Volatile acids (Respiratory)Volatile acids (Respiratory)– First conversion is carbonic anhydraseFirst conversion is carbonic anhydrase– Second reaction is spontaneousSecond reaction is spontaneous

– Non-volatile acidsNon-volatile acids» Lactate (Metabolic)Lactate (Metabolic)» Ketones (Liver produces these thinking there is a lack of Ketones (Liver produces these thinking there is a lack of

glucose)glucose)» Sulfuric (From Cysteine Degradation)Sulfuric (From Cysteine Degradation)

HHCOCOHOHCO 33222

Page 51: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

AlkalosisAlkalosis

AlkalosisAlkalosis– HypoventilationHypoventilation– Tetany (Sustained uncontrolled muscle Tetany (Sustained uncontrolled muscle

contraction)contraction)» Muscle contraction controlled mainly by Na in Muscle contraction controlled mainly by Na in

neuron and Ca in muscleneuron and Ca in muscle

» Related to phosphateRelated to phosphate Monobasic and dibasic formsMonobasic and dibasic forms Under alkalosis with the addition of [OH] you form waterUnder alkalosis with the addition of [OH] you form water Also drive reaction to the rightAlso drive reaction to the right

HHPOOPH 2442

OHHHPOOPH 2442

Page 52: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Alkalosis ContinuedAlkalosis Continued

Dibasic form of phosphate can chelate Dibasic form of phosphate can chelate soluble calcium better than monobasic form soluble calcium better than monobasic form to form calcium phosphateto form calcium phosphate

Does not change blood concentration of Does not change blood concentration of calcium only amount that is solublecalcium only amount that is soluble

HHPOOPH 2442

Page 53: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Alkalosis ContinuedAlkalosis Continued

What does calcium do in nerve impulses?What does calcium do in nerve impulses?– Inhibits transport of sodium into nerve during Inhibits transport of sodium into nerve during

the process of depolarization due to a nerve the process of depolarization due to a nerve impulseimpulse

– Under alkalotic conditions more calcium is Under alkalotic conditions more calcium is chelated and removes the controlled blockage chelated and removes the controlled blockage of sodium into nerve (uncontrolled influx of of sodium into nerve (uncontrolled influx of sodium into nerve)sodium into nerve)

» More nerve depolarizationMore nerve depolarization Causes the sustained uncontrolled muscle contraction Causes the sustained uncontrolled muscle contraction

during alkalosis (tetany)during alkalosis (tetany)

Page 54: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Air ExchangeAir Exchange

Partial Pressures of Gases in AirPartial Pressures of Gases in Air– 80% N80% N22

– 20% O20% O22

– .03% CO.03% CO22

1 atm = 760mm Hg (Sea level)1 atm = 760mm Hg (Sea level) Example:Example:

– pNpN22 = .79 * 760 = 608mm Hg = .79 * 760 = 608mm Hg– pOpO22 = .20 * 760 = 152mm Hg = .20 * 760 = 152mm Hg– pCOpCO22 = .0003 * 760 = 0.23mm Hg = .0003 * 760 = 0.23mm Hg

Page 55: AA and Proteins Robert F. Waters, PhD. Overview Proteins Proteins –Structural –Enzymatic Amino Acids Amino Acids Henderson-Hasselbach Equation Henderson-Hasselbach.

Gas ExchangeGas Exchange

pCOpCO22 of blood is around 40mm Hg of blood is around 40mm Hg

pCOpCO22 in lungs is around 35mm Hg in lungs is around 35mm Hg

Partial pressures of respiring cells higher Partial pressures of respiring cells higher yetyet


Recommended