Lecture 1 2011 9-10-11 Post

Introduction to BiochemistryBIOS E‐10

Saturday 9‐10‐11

Robin Haynes

BIOS E‐10 Business

1‐ Course details2‐ Our AWESOME team of Teaching Assistants3‐ Review ldquoundergraduate sectionsrdquo4‐ Graduate sections5‐ Office hours6‐ Exams and problem sets7‐ Course policies (detailed in syllabus)8‐ Saturday classes ndash THE GOOD9‐ Saturday classes ndash THE BAD10‐ The obvious

1‐ Course Details

Suggested textbook Essential Biochemistry Pratt and Cornely‐‐Wiley Plus option‐‐

Alternative Lehninger Principles of Biochemistry (5th edition) Nelson and Cox

Head TA Laura Magnotti

Course email address biocheme10gmailcom

Course website httpisitesharvardeduicbicbdokeyword=k81329amppageid=icbpage434280

2‐ Our AWESOME team of Teaching Assistants

Graduate

Undergraduate

Laura MagnottiMary Ellen Wiltrout

Nicole CohenJamie DempseyLyle LopezSarah MahoneyTeresa Morales

3‐ UndergraduateReview sectionsOptional

3 Saturday sections 1215 ndash 115Room 110 ‐ A‐G Sarah Room B‐10 ‐ H‐O TeresaRoom 109 ‐ P‐Z Nicole

2 non‐Saturday sectionsHarvard Campus Mondays 6 ndash 7pm

Sever 308 Jamie

Longwood Campus Tuesdays 530‐ 630Kresge 202 Lyle

4‐ Graduate sectionsMandatory

Starts Today

Room 101b ‐ A‐LRoom 103b ‐ M‐Z

5‐ Office hours

Thursday 735‐935 pm 206 Robinson Hall

6‐ Exams and problem sets

Assignment Graduate Undergraduate

Midterm exam 1 100 100


Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50

Graduate Assignment 50 ‐

Section 100 ‐

Total points 550 400

Problem sets Turn in at start of class or electronic dropbox

Key posted on following Wednesday

Make‐up exams (1 and 2) No makeup exams will be given without prior notification and approval

Regrades Regrades are only allowed if the exam has beencompleted in pen Regrade requests must be submitted inwriting to the instructor or your TF within 1 week of theexam return Regrade requests should clearly indicatewhich question(s) you are requesting us to review and ajustification of your request

7‐ Course Policies

See syllabus for more details

8‐ Saturday class The Good

9‐ Saturday class The Bad

10‐ The obvious

Chemistry of lifeIntroduction to biochemistry

CarbonHydrogenNitrogenOxygenPhosphorus Sulfate

~ 97 of composition of living organisms

6 simple elements combine to form molecules essential to an organismrsquos existence and function

4 Types of Biomolecules

1‐ Amino Acids

Polypeptide or protein

2‐ Carbohydrates (monosaccarides) Disaccharide

Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids


Why is it advantageous for a cell to link monomers into polymers

Very few molecules can combine in many different ways to produce a wide variety of structures

A cell can get by on a limited amount of raw material

Information contained in the monomers can be stored in the stable form of a polymer

Each of the macromolecules are organized around which element

1‐ Hydrogen2‐ Oxygen3‐ Carbon4‐ Nitrogen

Why are cellular organisms carbon based

Bonding versatility

Only single bonds can rotate freely

Rotation around single bonds allows for different conformations

Conformation vs configurationConformation Freedom of rotation around a single bond

Different conformations are freely interconvertable

Configuration (stereochemistry) FIXED spatial arrangement of atoms

(same bonds different configuration)

Configuration is conferred by 1‐ double bonds

2‐ chiral centersGeometric Isomers

EnantiomersDiasteromers

Geometric isomers or cis‐trans isomersDiffer in arrangement of groups with respect to a non‐rotating double bond

Geometric isomers cannot be interconverted without breaking double bonds requires energy

NonsuperimposableChiral

Enantomer

SuperimposableAchiral

Identical Structures

‐An atom attached to 4 different groups is a chiral center (asymmetric C)

‐A molecule is chiral if it cannot be superimposed on its mirror image

‐All chiral molecules contain at least one chiral center

Stereochemistry due to chiral centers4 different substituents bonded to a carbon may

be arranged in 2 different ways in space (2 configurations)

Enantiomers 2 stereoisomers that are mirror images

Diastereomers 2 stereoisomers that are not mirror images

Enantiomers (mirror image) Diastereomers (non‐mirror image)

How many chiral carbons are therein D‐Ribulose

n chiral carbons gives 2n stereoisomers

Common functional groups found in biochemistry

Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl

Energy and ThermodynamicsStudy of heat and power

A living organism is an open systemExchanges both matter and energy with its surroundings

Organisms derive energy from the surroundingsTake up chemical fuels (glucose)

or Absorb energy from sunlight

Organisms convert energy to produce work

Return some energy to the surroundings as heat

Release end product molecules that are less well organized than the starting fuel

Total energyRemains constant

Entropyor disorderincreases

2 Laws of Thermodynamics

Energy cannot be created or destroyed but can change forms

Example A river flowing over a damenergy is harnessed as electricity andand used to produce heat or perform work

First Law Conservation of energy

The energy in the universe remains constant

Energy = the ability to do work mechanical potential electrical chemical

Second law The entropy of the universe increases2 Laws of Thermodynamics

Entropy a measure of a systemrsquos disorder or randomness

Implications for biochemistryNaturally occurring (spontaneous) processes will always proceed towards the state with the least potential energyNaturally occurring (spontaneous) processes must increase the disorder in the universe

Thermodynamics tell us if a reaction is possible and whether it will occur spontaneously

Synthesis of MacromoleculesSpontaneous or not

Building organisms require energy

Thermodynamics and Gibbs free energy

Gibbs free energy (G) usable energy content of a biological system ndash Joules per mol (Jmol‐1)

Gibbs free energy

Enthalpy (H)‐heat content of the system

Reflects the number and kinds of bonds

Entropy (S)‐ measure of disorder

G = H‐T S

Does a process occur spontaneously or not

G gt 0 = not spontaneous Endergonic ‐ require input of energy

G lt 0 = spontaneous Exergonic ‐ release free energy

G = 0 = equilibrium No net change in the energy of the system

∆G does NOT indicate how fast the reaction will proceed (rate) ‐only whether it will occur

G = H‐T S

Effects of H and S on spontaneity

∆H ∆S ∆G = ∆H‐ T∆S

‐ + release of heat increase in entropy ‐spontaneous at all temps

‐ ‐ release of heat decrease in entropy ndashspontaneity depends on temp

+ + increase in heat increase in entropy spontaneity depends on temp

+ ‐ increase in heat decrease in entropy unfavorable at all temps

Letrsquos consider Gibbs Free Energy in terms of chemical reactions

The entropy of a substance increases with itrsquos volumeexample gas molecules

Entropy is therefore a function of concentration

If entropy changes with concentration so must free energy

The free energy change of a chemical reaction depends on the concentrations of reactants and products

Chemical equilibria and free energy

A reactionrsquos free energy change depends on 2 things1) A constant term dependent only on the reaction itself2) A variable term dependent on concentration of

reactants and products

A + B C + D

When a reaction is at equilibrium

Keq = [C]eq[D]eq[A]eq[B]eq

Equilibrium constant

Equilibrium ‐ No net change in [ ] of reactantsEquilibrium DOES NOT mean that the [ ] of reactants and products are =

Concentrations = 10 MTemp = 25degCPressure = 1 atm


ΔGdegrsquo ‐ Standard Free energy change of a reactionunder standard conditions

When not at equilibrium the reactants experience a driving force to reach equilibrium

∆Gdegrsquo = ‐ RT ln Keq

Both ∆Gdegrsquo and Keq are constant for a particular reaction

R = gas constantT = temperature

∆G = ∆Gdegrsquo + RT ln [C][D] [A][B]


But ‐ biochemical rxns donrsquot occur at standard stateWe need to factor in the variable components

∆G is a function of the actual concentrations of reactants and the temperature

A reaction with a + ∆Gdegrsquo (nonspontaneous under standard conditions) may proceed in vivo depending on the concentration of reactants

Many of lifersquos chemical reactions are unfavorableHow do we drive these reactions to occur

1 ‐ You can make an unfavorable reaction favorable by adjusting the [ ] of reactants and products

Dihydroxyacetone (DHAP) Glyceraldehyde 3‐ phosphate (GAP)

When at equilibrium the reaction is endergonic (∆Gdeg lsquo = 75 kJmol)DHAP will not spontaneously convert to GAP

When [GAP] decreases DHAP will spontaneously convert to GAP

Phosphate

[DHAP] [GAP]


2 ‐We couple endergonic reactions with exergonic reactions

Unfavorable Favorable

A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1

= ‐ 5 kJM‐1 Reaction is now favorableA + C rarr B + D

Cells can enable unfavorable reactions by coupling them with favorable reactions (eg ATP hydrolysis)

Real life exampleHow do we make large ordered proteins from individual amino acids

∆G = positive (endergonic)Amino Acids rarr Proteins

ATP rarr AMP + P ‐ P ∆G = negative (exergonic)

By coupling thermodynamically unfavorable processes with sources of high energy cells are able to synthesize large polymers

Living organisms and steady state

Remember living organisms are ldquoopen systemsrdquo and exchange matter and energy with the surroundings

We continuously ingest high enthalpy low entropy nutrients and convert them to low enthalpy high‐entropy waste products

Living organisms only come to equilibrium when this process isdisrupted

Equilibrium = Death

However we do maintain a steady state or homeostasis ‐Properties of the cell are maintained over time

The system reacts to changes in these properties to restore homeostasis

Chemistry of WaterStudy of an aqueous environment

Aqueous solutions and properties of water

1‐ Organisms are mostly water (human 70)

2‐ Influences the shape and function of biomolecules

3‐Medium of most biochemical reactions

4‐ Important for transport of nutrients and waste

5‐Water may itself participate in chemical reactions

O forms covalent bonds with 2 H atoms

H20 has 2 unshared pairs of electrons

O is more electronegative than the Hrsquos (O has a stronger attraction for the electrons)

Unequal electron sharing between the O and the Hrsquos ‐ tetrahedral

This creates a dipole or polarity where the O has a partial ‐ charge and the Hrsquoshave a partial + charge

Structure of H20

H‐bonds result from attraction between the O atom of 1H2O molecule and the H atom of another water molecule

Hydrogen Bonding

H‐ bonds result in cohesiveness and high surface tension ofwater

Structure of Ice ‐ H2O participates in 4 hydrogen bonds

Donates to H bonds

Accepts H bonds

Regular lattice‐like structure

Hydrogen bonding in H2O depends on the phase

No H bonds ~ 34 H bonds 4 H bonds

H20 molecules are in continuous motion ndashH‐ bonds are randomly breaking and forming

At room temperature why does ice melt spontaneouslyWhat would ∆G be What would ∆S be

Hydrogen bonds are not unique to water

N ‐ H O ndash H S ‐ H

C ndash H bonds do not form hydrogen bonds

Common H bonds

Other types of bonds in biochemistry

Covalent Atoms share electrons

Ionic One atom donates anelectron to another atomcreating opposite charges

Van der WaalsWeak attraction between 2 polar non‐chargedparticles (unequaldistribution of charges)

Relative strengths of different bonds

Non covalent interactions are individuallyweak but strong in large numbers

Water as a solvent

Interactions between H2O molecules and the ions gtgt interactions between Na and Cl

Polar water molecules surround ions by aligning their partial charges with oppositely charged ions

Polar ndash hydrophilic ndash soluble in water ndash charged or able to H bond

Nonpolar ndash hydrophobic ndash insoluble in water

Amphiphilic ndash contains both polar and nonpolar components

BP Oil Spill

APolarBNonpolarCAmphiphilic


Ordered H2O formscages around hydrophobic portion

Polar head

Hydrophobic tailscluster less orderedwater

Hydrophobic tailssequester from waterOrdered water is minimal

Entropy increases as H20 becomes less ordered

Hydrophobic effect

Entropy

The hydrophobic effect is very important in protein folding

The hydrophobic effect drives the nonpolar components to cluster away from the water and effectively increases the amount of disordered water

Entropy also plays a role in polar enzyme‐substrate interactions

Binding of substrate to enzymereleases some of the ordered water

Thermodynamic push towardsthe formation of the enzyme‐substrate complex

Also important inhormone‐ligand interactions

Acid Base Chemistry

Why talk about acids and bases

Many biological molecules have functional groups that undergo acid-base reactions therefore the properties of these molecules are affected by acidity of the solutions in which they are surrounded

pH affects the structure and activity of biological molecules

Water in chemical reactions

H20 H⁺ + OH⁻

Proton

Protons exists as hydronium ionsin solution

Hydronium ion gives up a proton

Water acceptsa proton becominga hydronium ion

Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14

Keq and [H20] are constant andare redefined as Kw ndashionization constant of water

Kw = 10‐14 = [H⁺][OH‐] Because Kw is constant the [H⁺] and [OH⁻] must balance each other

Neutral solu on= [H⁺] = [OH‐] = 10 ‐7 (pure water)Acidic solu on= [H⁺] gt 10 ‐7

Basic solution = [H+] lt 10 ‐7

H20 H⁺ + OH⁻

Dissociation constant

Keq[H2O] = [H⁺][OH‐]

pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7

Acids and Bases ‐ Act to alter the pH of a solution

Acid ndash proton donorsBase ndash proton acceptor

Strong acids and bases (HCL and NaOH) ndash ionize completely

HCl donates a proton (H+) increasing the [H+] of the solution = decreases pH

NaOH accepts a proton decreasing the [H+] of the solution = increases pH

HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20

‐ubiquitous in biological systems‐play an important role in metabolism and its regulation

Weak acid and bases

Weak acids and bases do not dissociate completely in H2OTendency of an acid to lose its proton is defined by Keq or Ka

HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base

= Ka Acid dissociation constant

pK = ‐ log KaThe larger the acidrsquos Ka the smaller itrsquos pK and the greater itrsquos strength

‐‐ stronger tendency to lose a proton‐‐

Determining the pH of a solutionHenderson ndash Hasselbach equation

Relates the pH of a solution to the pK of an acidand the [HA] and [A‐]

pH = pK + log [A‐][HA]

When the pH of an acid is equal to the pK of that acid then the acid is half dissociated [A‐] = [HA]

When pH lt pK then [HA] gt [A‐]When pH gt pK then [HA] lt [A‐]

pH Buffers

Various aspects of biological systems work best at well‐defined pHs

Buffers mop up excessive hydrogen ions or hydroxide ions keeping pHs within well‐defined ranges

Enzymes have optimum pHrsquos ‐ enzymes donrsquot function ‐ reactions slow ‐ organism dies

pH buffering ndash titration of a weak acid

1‐ Prior to tritration all the acidis in protonated form (HA)

2‐ Added base causes protonsto dissociate from the acidproducing A‐ until all the acid is in its conjugate base

3‐ At the midpoint

[HA] = [A‐]pH = pK

4‐ Buffering occurs one pH unitabove and below the pK

Biological BufferingBicarbonate system ndash maintains blood pH

H+ + HCO‐3 H2CO3 H2O + CO2

Carbonic acid

Bicarbonate

H+ = buffered by reaction with bicarbonate to form carbonic acid= eliminated by kidneys

CO2 = buffered by the amount of CO2 giving off by the lungs (alteration of breathing ndash controlled by brainstem sensing of pH )

Timing of buffering capacityRegulation by breathing ndash minutes to hoursRegulation by kidney function ndash hours to days


What happens in metabolic acidosis

Blood pH decreases due to an accumulation of H+

How does the body attempt to quickly adjust for the acidosis

Increased ventilation ldquoblowing offrdquo CO2

How does losing CO2 decrease the amount of H+

Shifts the equilibrium of the equation towards making CO2Which decreases the amount of H+


Le Chateliersprinciple

Introduction to Amino Acids

General Structure of Amino Acids

carbonCarboxyl groupAmino group Variable R group

Common to all AAs

R groups differ bySize

Charge20 Standard Amino Acids

Categorization of Amino Acids by R groups

Interior of proteins where they do not interact with water

Side chains seldom participate in chemical reactions


Polar side chains can interact with water because they contain hydrogen‐bonding groups

Glycine cannot form hydrogen bonds but is listed as polar because It is neither hydrophobic nor charged (other sources have it as nonpolar)


Side groups are always charged under physiological conditions

Histidine can accept a protein to form an imidazolium ion (acid)Can act as acid or base

Certain polar‐uncharged amino acids can become charged depending on the environment

Histidine is very versatile in catalyzing chemical reactions ndashvery often in the active sites of enzymes

AA characteristics important for protein structure or function

Cysteine can form disulfide bonds

Cysteine can be oxidized to form a disulfide bond

Very important for protein structure covalent links between polypeptide chains


Amino Acids are ChiralException is Glycine

L‐ Enantiomer D‐ Enantiomer

All AA residues in proteins are in the L‐configuration

Amino acids have characteristic titration curves

‐Every AA has at least 2 ionizablegroups COOH and NH3+

‐AAs with ionizable R groups will have 3

‐Each ionizable group will have a 1) pKa (pKa ndash measure of the

tendency to lose a proton)

2) region of buffering capacity

‐ Ionizable groups act as acids with uarr pH (give up protons)


1‐ Low pH ( ltpK1) = AA is fully protonatedCharge = +1

3‐ pI = Removal of 1st proton is completeRemoval of 2nd proton has begunldquoZwitterionrdquoCharge = 0

2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]

5‐ High pH ( gtpK2) = AA is fully deprotonatedCharge = ‐1

How would you calculate the pI of Glycine

pI = average of pK1 and pk2

of Glutamate

+1 0 ‐1 ‐2

pI = frac12 (pK1 + pKR)

+1 0 ‐1

Find point of 0 charge and calculate theaverage of 2 pKs surrounding 0 charge

Ionization of HistidineCalculate the fraction of histidine that has is imidazole side chain protonated atpH 73

pH 73 = carboxyl is fully deprotonated (COO‐)amino group is fully protonated (NH3+)imidazole group is partially dissociated

pH = pka + log [A‐][HA]

73 = 60 + log [deprot imidazole][prot imidazole]

13 = log [deprot imidazole][prot imidazole]

Antilog 13 = [deprot imidazole][prot imidazole]

= 20 x 101

= 20 x 101

= 20 = deprot1 prot

Fraction of Protonated = 121 = 48

Yes you need to know

1‐ Nomenclature (1 3 letter codes)2‐ Properties of R groups3‐ Recognize structures

No you will not have to draw structures

Amino Acids

Proteins and protein structures

Proteins are comprised of a wide variety of monomers and withvaried charge distribution

Comparison to DNA which has a characteristic structure (double helix) and is comprised of similarly shaped and charged monomers

Proteins have the most diverse properties of all biological polymers and have an incredible number of functions

Proteins Amino Acid polymers

Some important functions of proteins

Protein 3D structure depends on the primary sequence of AAs

Question What happens if you change a single amino acid in the primary sequence

Small changes at the amino acid level can affect structure Sickle Cell Anemia

BIOS E‐10 Business

1‐ Course details2‐ Our AWESOME team of Teaching Assistants3‐ Review ldquoundergraduate sectionsrdquo4‐ Graduate sections5‐ Office hours6‐ Exams and problem sets7‐ Course policies (detailed in syllabus)8‐ Saturday classes ndash THE GOOD9‐ Saturday classes ndash THE BAD10‐ The obvious

1‐ Course Details







Graduate

Undergraduate






Sever 308 Jamie



Starts Today


5‐ Office hours






Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50


Section 100 ‐










10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids










1‐ Course Details







Graduate

Undergraduate






Sever 308 Jamie



Starts Today


5‐ Office hours






Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50


Section 100 ‐










10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids











Graduate

Undergraduate






Sever 308 Jamie



Starts Today


5‐ Office hours






Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50


Section 100 ‐










10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids













Sever 308 Jamie



Starts Today


5‐ Office hours






Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50


Section 100 ‐










10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids











Starts Today


5‐ Office hours






Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50


Section 100 ‐










10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids














Final Exam 100 100

Assignment 1 50 50

Assignment 2 50 50


Section 100 ‐










10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids
















10‐ The obvious






1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids















1‐ Amino Acids



Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids











Polysaccharide


(CH2O)nngt3

3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids










3‐ Nucleotides

Nucleic Acids


4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids










4‐ Lipids









Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids

















Bonding versatility













Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids






















Enantomer














Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids


















Amino

CH3Methyl

Hydroxyl

Sulfhydryl

Acyl group

Carbonyl

Carboxyl

Ester

Phosphoester

Phosphoanhydride

Phosphoryl
























Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids

































Gibbs free energy




G = H‐T S






G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids















G = H‐T S


∆H ∆S ∆G = ∆H‐ T∆S













A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids


















A + B C + D






















Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids



























Phosphate

[DHAP] [GAP]




A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids













A rarr BC rarr D

∆G = + 15 kJM‐1

∆G = ‐ 20 kJM‐1











Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids


















Equilibrium = Death















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids






















Structure of H20


Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids











Hydrogen Bonding



Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids











Donates to H bonds

Accepts H bonds









Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids

















Common H bonds







Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids
















Water as a solvent






BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids













BP Oil Spill




Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids












Polar head




Hydrophobic effect

Entropy







Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids
















Acid Base Chemistry





H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids














H20 H⁺ + OH⁻

Proton




Protonjumping

Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids










Keq = [H⁺][OH⁻][H20]

Ionization of Water

Kw = Keq[H2O] = 10 x 10‐14





H20 H⁺ + OH⁻



pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids










pH = ‐log [H+]

[H⁺] = [OH‐] = 10 ‐7

[H⁺] gt 10 ‐7

[H+] lt 10 ‐7






HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids















HCL + H20 H3O + + Cl‐

NaOH + H30 Na+ + 2H20


Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids











Weak acid and bases


HA H+ + A‐

Keq = [H+][A‐][HA]

Acid Conjugate base









pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids















pH Buffers








[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids














[HA] = [A‐]pH = pK




Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids












Carbonic acid

Bicarbonate
















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids






















Common to all AAs
































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids







































2‐ pK1 = [COOH] = [COO‐]

4‐ pK2 = [NH3+]=[NH2]




of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids












of Glutamate

+1 0 ‐1 ‐2


+1 0 ‐1








= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids
















= 20 x 101

= 20 x 101

= 20 = deprot1 prot





Amino Acids













Amino Acids










Lecture 1 2011 9-10-11 Post

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Transcript of Lecture 1 2011 9-10-11 Post