Properties of WaterWater molecules are highly polarized

• Water is a polar molecule: opposite ends of the molecule have opposite charges– Recall that the oxygen end of the molecule has a partial negative

charge while the hydrogens have a partial positive charge– Recall this leads to formation of hydrogen bonds between water

molecules

• Water is one of the most polar molecules known

- In order to understand the chemical properties of biological molecules, we first need to understand the chemistry of water

Water

- Water has anomalously high melting point, boiling point, surface tension

- Water is the biological solvent for most molecules

This is because water can form hydrogen bonds

A hydrogen bond occurs whenever two electronegative atoms compete for the same hydrogen atom. The hydrogen atom is formally bonded to the donor atom, D, but it also interacts favorably with the acceptor atom, A

–D––H • • • • A–

hydrogen bond

O–––H covalent bond ~460 kJ mol–1

O• • • H hydrogen bond ~20 kJ mol–1

Two interacting water molecules

Hydrogen bonding gives water its unusual properties

• The oxygen nucleus attracts electron more strongly than does the hydrogen nucleus—the electrons are more often in the vicinity of the oxygen atom (2δ-) than the hydrogen (δ+), which generate an electrostatic attraction between the oxygen atom of one water molecule and the hydrogen of another---Hydrogen bond.

• bond angle is 104.5o, slightly less than the 109.5o of a perfect tetrahedron - crowding by the nonbonding orbital of the oxygen atom.

One hydrogen bond is weak , but many hydrogen bonds are strong

The nearly tetrahedral arrangement of H atoms enables each water molecule in the solid state to form up to 4 H-bonds with neighboring water molecules. In the liquid state these H-bonds still form, but they are transient (lifetime < 1 ns), with H-bonds continuously being broken and reformed. The large amount of thermal energy required to break up these H-bonds accounts for the high melting point and boiling point of water.

H-bonds account for high melting/boiling point of water

Van der Waals force

Hydrogen bonds are strong enough to be useful, yet weak enough so that they can be reversibly broken and reformed.

Hydrogen bonds are therefore very important in biochemistry.

The strongest H-bonds are linear

Hydrogen bonds are directional, with the strongest bonds formed when the –D––H•••A– atoms are arranged linearly. The histogram below shows the distribution of hydrogen bond angles in crystal structures of small molecules.

Properties of water

Adhesion

Surface Tension - a measure of the strength of water’s surfaceProduces a surface film on water that allows insects to walk on the surface of water

Cohesion

Attraction between two different substances.Water will make hydrogen bonds with other surfaces such as glass, soil, plant

tissues, and cotton.

Capillary action-water molecules will “tow” each other along when in a thin glass tube. Example: transpiration process which plants and trees remove water from the soil.

Adhesion Also Causes Water to …

There are properties of water that result from its hydrogen bonds:

Water drops

Water is less Dense as a Solid

Solvent Properties

Temperature Effects

High Specific HeatHigh heat of vaporization

Water has high specific heat which means it resists changes in temperature (water must gain or lose more heat for temperature to change)

Properties of water

Excellent solvent for: Ions/charged groupsPoor solvent for hydrophobic groups - fatty acids

Dissolution of polar molecules in water

Water dissolves salts by forming a shell of interacting water molecules around the ions. This weakens electrostatic interactions between the ions and counteracts their tendency to form a crystal lattice. Dissolution of the salt is accompanied by a large increase in entropy as the individual ions become more mobile. The change in free energy of the system is overall very negative (∆G = ∆H – T∆S) and hence dissolution of the salt is thermodynamically highly favored.

Entropy Increases as Crystalline Substances Dissolve

When a nonpolar molecule is inserted into water, the normal network of hydrogen-bonded water molecules is disrupted. The water tries to “bury” the hydrophobic molecule by building a highly structured “cage” of water molecules around it. This is thermo-dynamically unfavorable as it decreases the entropy of the water molecules. Thus, the nonpolar molecules tend to stick together to minimize the amount of “structured” water required to bury them. This is called the hydrophobic effect.

The hydrophobic effect

Neste caso, a entropia �S decresce, pelo que vamos ter �G = �H –T�S, com

�H>0, �S<0e portanto �G>0, ou seja o processo não tem tendência a acontecer

Amphipathic compounds in aqueous solution. By clustering together in micelles, the fatty acid molecules expose the smallest possible hydrophobic surface area to the water, and fewer water molecules are required in the shell of ordered water. The energy gained by freeing immobilized water molecules stabilizes the micelle.

Moléculas anfifílicas

Também chamadas "anfipáticas“

• designa moleculas que contêm simultaneamente grupos polares e não-polares

• O que é o mesmo que dizer - moléculas que são atraídas simultaneamente para ambientes polares e não-polares

• Bons exemplos – ácido gordos

Hydrogen donor

Hydrogen acceptor

Common hydrogen bonds in biological systems. The hydrogen acceptor is usually oxygen or nitrogen; the hydrogen donor is another electronegative atom.

Electronegative atom (H acceptor: O, N with an ion pair of electrons) and Hydrogen atom covalently bonded to another electronegative atom (H donor).

Devido à formação de pontes de H, podemos explicar o facto de biomoléculas como os açúcares ou compostos como os álcoois, aldeidos, cetonas e outros contendo ligações N-H, terem tendência a ser solúveis em água.

• Charged or polar molecules are dissolved easily in water (Hydrophilic). • Nonpolar solvents are poor solvents for polar molecule but easily dissolved

hydrophobic compound (lipid or waxes).• Amphipathic compounds contain regions that are polar or (charged) and nonpolar

Ionization of Water, Weak Acids, and Weak Bases

• Pure Water Is Slightly Ionized

• The Ionization of Water Is Expressed by an Equilibrium Constant

• The pH Scale Designates the H+ and OH-

Concentrations

• Weak Acids and Bases Have Characteristic Dissociation Constants

• Titration Curves Reveal the pKa of Weak Acids

Dissociação da águaDissociação da água

Considere-se o ácido fraco HAA constante de dissociação do ácido é dada por:

HA → H+ + A- Ka = [ H + ] [ A - ] [HA]

Dissociação de electrólitos fracosDissociação de electrólitos fracos

[H3O+]

The pH Scale & some aqueous fluids

Water Chemistry• Water has many characteristics that

make it vital to our bodies.

• Water can act as either an acid or a base, maintaining a stable pH in our bodies.

A equação Henderson-Hasselbalch

Para qualquer ácido HA, a relação entre o pKa, as concentrações existentes no equilibrio, e o pH da solução é dado por:

The Henderson-Hasselbalch Equation

Relates three terms: pH, pKa, and [A-]/[HA]. If you know two of these values, you can determine the third.

pH = pKa + log([A-]/[HA])

When [A-] = [HA]:pH = pKa + log(1)pH = pKa + 0pH = pKa

pka is the pH at which a functional group exists 50% in its protonated form (HA) and 50% in its deprotonated form (A-).

Conjugate acid-base pairs consist of a proton donor and a proton acceptor

Titration curves reveal the pKa of weak acids (acetic acid)

A titration curve is a plot of pH against the amount of NaOH (base) added to a solution which is being titrated. A titration curve can be used to determine the pKa of a weak acid.

• The conc. of the acid in the original solution can be calculated from the volume and concentration of NaOH added-titration curve.

• At the midpoint of the titration, at which exactly 0.5 equivalent of NaOH has been added, [HA]=[A-] and pH=pKa

• The weak acid and its conjugate base can act as a buffer

[ ][ ][ ] aeq KHA

AHK ==

−+Dissociation

constant

Comparison of the titration curves of three weak acids

• The titration curves of these acids have the same shape, they are displaced along the pH axis because the three acids have different strengths.

• Acetic acid, with the highest Ka (lowest pKa) of the three, is the strongest (loses its proton most readily); it is already half dissociated at pH 4.76.

• Dihydrogen phosphate loses a proton less readily, being half dissociated at pH 6.86.

• Ammonium ion is the weakest acid of the three and does not become half dissociated until pH 9.25.

• Stronger acids have higher dissociation constants (Ka), and lower pKa

• Weaker acids have lower dissociation constants (Ka) and higher pKa values

Roles played by proteins:

Insulin

Hemoglobin (O2 transport in blood)

Collagen

Actin, Myosin

Myoglobin – (oxygen storage in muscle)

(bacterial, plant, snake, insect)

Amilase

Antibodies

• The amino acids obtained by hydrolysis of proteins differ in respect to R (the side chain).

• The properties of the amino acid vary as the structure of R varies.

• Twenty common αααα-amino acids have carboxyl and amino groupsbonded to the αααα-carbon atom

• A hydrogen atom and a side chain (R) are also attached to the a-carbon atom

Each amino acid has at least two ionizable groups: COO- and NH3+

Acid-Base Behavior of AAs

Each amino acid has at least TWO groups that display acid-base behavior (gain or accept H+) –the carboxyl group and amino group.

Acid-Base Behavior of AAs

Equilibrium constant: Ka = [A-][H+]/[HA]

pH = -log[H+] …convenient shorthand for writing widelyvariable [H+] concentrations

pKa = -log(Ka) …similar shorthand for writing variable Ka values

subunit organization

overall 3-dimensional shape

local structure (alpha helix, beta strands, loops, turns)

sequence

• Primary structure - determined by covalent bonds

• Secondary, Tertiary, Quaternary structures - all determined by weak forces

Properties of the 20 amino acids that occur in peptides and proteins are crucial to the structure and function of proteins:– Stereochemistry– Relative hydrophobicity or polarity– Hydrogen bonding properties– Ionization properties– Other chemical properties

http://www.rcsb.org/pdb/

Levels of Protein Structure

Primary: amino acid linear sequence. Secondary: α-helices,

�-sheets and loops.Tertiary: the 3D shape of the fully folded polypeptide chain

Quaternary: arrangement of several polypeptide chains

The TwentyAmino Acids

Types of AAs

SMALL: hydrogen or methyl R group

GLYCINEAlanine

NONPOLAR/HYDROPHOBIC: R groups contain largely C, H atoms.

POLAR/HYDROPHILIC: R groups typically contain O, N atoms.

ALIPHATIC: no aromatic rings

VALINELeucineIsoleucineMethonineProline

AROMATIC: contains aromatic rings

PHENYLALANINETyrosineTryptophan

ACIDIC: acid in R group

ASPARTATEGlutamate

BASIC: base in R group

LYSINEArginineHistidine

CHARGEDUNCHARGED: no ionizable group in R group

ASPARAGINEGlutamineSerineThreonineCysteine

Types of AAs

SMALL: hydrogen or methyl R group.GLYCINEAlanine

NONPOLAR/HYDROPHOBIC: R groups contain largely C, H atoms

POLAR/HYDROPHILIC: R groups typically contain O, N atoms

ALIPHATIC: no aromatic rings.

VALINELeucineIsoleucineMethonine*Proline

CHARGEDUNCHARGED: no ionizable group in R group.

ASPARAGINEGlutamineSerineThreonine*Cysteine

an imino acid, with R group bound to amino group thiol group can participate

in disulfide bonding

SpecialAmino Acids

No ionizable groups in their side chains

The 20 different amino acids are commonly abbreviated with 1 or 3-letter codes

a second COOH

Aspartic acid and glutamic acid have a net negative charge at pH 7

Stereochemistry of amino acids

• 19 of the 20 common amino acids have a chiral α-carbon atom (Gly does not)

• Threonine and isoleucine have 2 chiral carbons each (4 possible stereoisomers each)

• Mirror image pairs of amino acids are designated L (levo) and D (dextro)

• Proteins are assembled from L-amino acids (a few D-amino acids occur in nature)

http://www.biology.arizona.edu/biochemistry/problem_sets/aa/aa.html

Estereoquímica de aminoácidos

Estereoquímica de aminoácidos

1. Todos os aminoácidos, excepto a glicina, são quirais2. A nomenclatura D/L baseia-se no D- e L-gliceraldeído3. Os L-aminoácidos predominam na natureza

• Under normal cellular conditions amino acids are zwitterions(dipolar ions):

Amino group = -NH3+

Carboxyl group = -COO-

50

Ionization state as a function of pH

Physiological pH (measure of [H+])

Titration curve for alanine

• Titration curves are used to determine pKa values

• pK1 = 2.4

• pK2 = 9.9

• pIAla = isoelectric point

Net charge is zero

pK1 + pK22

pI =

Isoelectric Point

Isoelectric point: the pH at which an AA or polypeptide has no net charge.

• For a dibasic amino acid:

• For a tribasic amino acid:

pka = 2.4

pka = 9.8

Isoelectric point = average of amino and carboxyl pka values =

pka = 2.2

pka = 9.7

pka = 4.3

Isoelectric point = average of the two numerically closest pka values =

(2.2 + 4.3)/2 = 3.25

(2.4 + 9.8)/2 = 6.1

GLYCINE

GLUTAMATE

Titulação da Glicina

pI = Ponto isoeléctrico

– Note that one starts withall groups in acid form.

– Note how manyequivalents are added

– Note that at 0.5 and 1.5equivalents, pH is equal topK of group beingtitrated.

– Note pH which gives zerocharge is the isoelectricpoint.

– Note where the bufferingcapacity is best

At low pH, both the amino and carboxyl groups are protonated and the molecule has a net positive charge.

Cationic form Zwitterion (neutral) Anionic form

Amino Acids Are Weak Polyprotic Acids

Titration of aminoacidshttp://cti.itc.virginia.edu/~cmg/Demo/markPka/markPkaApplet.html

Solving a problem:

What is the pH of a glycine solution in which the -ααααNH3

+ group is one-third dissociated?

Solution:The appropriate Henderson–Hasselbalch equation is

[Gly-]

[Gly0]

If the α−amino group is one-third dissociated, there is one part Gly- for every two parts Gly0.

The important pKa is the pKa for the amino group. The glycine α-amino group has a pKa of 9.6. The result is

pH = 9.78 + log (1/2)

pH = 9.5

Cross links (disulfide bridges)Prevalent mainly in extracellular proteins

Disulfide bonds can stabilize protein structure by providing crosslink

The Peptide Bond

• has partial (40%) double bond character• is about 0.133 nm long - shorter than a typical single bond but longer than

a double bond• due to the double bond character, the six atoms of the peptide bond group

are always planar.• N partially positive; O partially negative

The Coplanar Nature of the Peptide Bond

Six atoms of the peptide group lie in a plane

Um exemplo de péptido

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