BIOPHYSICAL AND BIOCHEMICAL PRINCIPLES

Molecular

structure and properties of water Expression of concentration Buffers

WATER
Content:

80% of the mass of living organisms All the chemical reactions of life take place in aqueous solution. Is a reactant or product in many metabolic reactions General formula of water is H2O.

Water Molecule


Composed of: 1 Oxygen Atom 2 Hydrogen Atoms Share electrons forming strong covalent bonds.

Characteristics
made up of two atoms of hydrogen and one atom of oxygen forming a triangular shape (an angle about 105o).  has asymmetrical distribution of charge: one end (the O atom) carries a slightly negative charge ( -) and the other ends of the molecule (the H atoms) carry slightly positive charges ( +).  leads to an unequal / uneven distribution of electrical charge , thus, water is a polar molecule.  atoms results in a water molecule with slight negative and positive sides, called a dipole.


What properties make water such an amazing molecule?

The polarity of water molecules:
allows them to form hydrogen bonds with each other. contributes to the various properties water exhibits.

Water molecules form hydrogen bonds

 The

bonds enable water to dissolve may organic biomolecules that contain functional groups that can participate in hydrogen bonding.  O atoms of aldehydes, ketones and amides provide pairs of electrons (hydrogen acceptors) while alcohols and amines can serve as both hydrogen acceptors and donors.

Formation of hydrogen bonding

In ice, each water molecule is surrounded by four other molecules in a tetrahedral arrangement (left). This new result on liquid water shows that the molecules are connected only with two others. This implies that most molecules are arranged in strongly hydrogen-bonded rings (middle) or chains (right) embedded in a disordered cluster network connected mainly by weak hydrogen bonds. The oxygen atoms are red and the hydrogen atoms are gray in the water (H2O) molecules. (Figure courtesy H. Ogasawara, SSRL).

Molecular Structure of Water



Hydrogen bonds, weak bonds between adjacent molecules, give water its unique properties.

http://www.edinformatics.com/ math_science/dimer.htm

public domain image via Wikipedia Creative Commons

Properties of water
Thermal properties  Heat fusion  Heat vaporization  Specific heat  Density Solvent properties  Dissolve in ionic and polar due to its dipolar and hydrogen bond  Amphipathic

Thermal Properties of Water

1. Density  When water becomes a solid or converts to ice, it expands.  Solid water or ice is less dense than liquid water and therefore it floats on liquid water.  This phenomenon is due to hydrogen bonding.  Water has its maximum density at 4 C where the colder water will freeze forming ice.  This provides insulation by preventing the water below from freezing and allows aquatic ecosystems to survive under sub-zero temperatures. sub-

Molecular Structure of Ice



The lattice structure of ice allows it to float on the waters surface.

Life in Freezing Waters

How do fish survive in super-cooled arctic seas?  They have a variety of antifreezes. The antifreeze molecules allow ice-fish to live in subfreezing water by plugging gaps in existing small ice crystals and preventing the attachment of more ice molecules.  Ice crystal growth is thus effectively stopped.

2. High Latent Heat of Vaporisation



Heat of vaporization is the quantity of heat a liquid must absorb for 1 gram of it to be converted from a liquid to a gas. This means that water must absorb a lot of heat to break hydrogen bonds between its neighbors so that it can convert liquid water into water vapour (gaseous phase). This makes water as an effective coolant where animals sweat and pant to cool themselves) and themselves) plants undergo transpiration.

3. High Specific Heat Capacity

A

great deal of energy is required to raise the temperature of 1 kg by 1 C, which means that sudden temperature changes do not occur easily. remain relatively constant meaning water does not change temperature very easily.

 Temperatures

Because water has a high specific heat, it can minimize temperature fluctuations to within limits that permit life. This moderation occurs because: Heat is absorbed when hydrogen bonds break (heat of fusion whereby acceleration of water molecules occur). Heat is released when hydrogen bonds form. This means that water can absorb a lot of heat before it changes its temperature by 1oC. It also means that water has to lose a lot of heat before it changes its temperature by 1oC.

What gives water its high heat capacity?



As ice is warmed and begins to melt, these hydrogen bonds are increasingly disrupted causing the open spaces in the ice lattice to fill in. As a consequence, density increases; this effect reaches its maximum at 4oC, the temperature at which pure water reaches its greatest density.

4. Cohesion and Surface Tension  Cohesion: intermolecular attraction Adhesion: attraction of water to solid phase (cell wall), molecules "stick together" and has high cohesion.  Water molecules stick to one another = cohesion and surface tension.
 Water

Cohesion  is the bonding of a high percentage of the molecules to neighbouring molecules  involves attractive force between particles of the same kind.  can results in high surface tension.  is due to hydrogen bonding Adhesion  is the clinging of one substance to another of water to the walls of cells.  results in capillary rise.  can results in high tensile strength.

Cohesion and adhesion in plants



long columns of water can be sucked up through the microscopic vessels of plants by tall trees by transpiration stream to the leaves at the top of the plant without breaking.

Surface tension


 

Is a measure of how hard it is to break the surface of a liquid. Is related to cohesion. Is determined by hydrogen bonding.

Solvent Properties of water

 Ability

to dissolve ionic and polar substances.  Determined by: (1) its dipolar structure and (2) its capacity to form hydrogen bonds.

Water is a universal solvent

Dissolution of an ionically bonded compound, sodium chloride, by water molecules. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission. It forms electrostatic interactions with ions and keeps ions in solution.

Water is a universal solvent



Waters bipolar molecule dissolves salts and holds in solution (salts include many compounds that can be dissolved into +/-ions). NaCl Na+ and Cl-

Water molecules separate by breaking strong covalent bond between H and O to form new compounds. CO2 + HOH H2CO3 Because water can disrupt covalent and ionic bonds, it is considered a universal solvent.

Water is a universal solvent

Ions of salts
 Na+

and Cl- dissolves easily in water because dipolar water molecules are attracted to these ions, forming shells of water molecules known as solvation spheres. spheres.

Organic molecules
 With

ionizable groups (carboxyl, amino), polar functional groups (alcohol, aldehyde) also dissolve in water due to ability of the organic molecules to form hydrogen bonds with water molecules.

Hydrophilic and Hydrophobic

Nonpolar molecules are hydrophobic. Polar and ionic molecules have positive and negative charges and are therefore attracted to water molecules because water molecules are also polar Polar and ionic molecules are hydrophilic.

Interaction with water influences the structure of biomolecules

 Covalent

and noncovalent bonds stabilize biological molecules.  These forces can be either attractive or repulsive.  Biomolecules fold to position polar and charges groups on their surface amphipathic.

 Most

biomolecules are amphipathic possess regions rich in charged or polar functional groups as well as regions with hydrophobic character.

This pattern increase the tendency for the formation of energetically favorable charge-dipole, dipole-dipole and hydrogen bonding interactions between polar groups on the biomolecule and water and vice-versa with hydrophobic groups.

Amphipathic molecules


Contain both polar and nonpolar groups (soaps, bile salts and phospholipids). Form micelles in water where the nonpolar tails aggregate in the center away from water and the polar heads form the hydrogen bonds with the surrounding water molecules.

Water is an excellent nucleophile

 Nucleophile

metabolic reactions involve attack by lone pair of electrons on electronelectron-rich molecules  Do not possess formal ve or +ve charge.  Nucleophile attack by water results in the cleavage of amide, glycoside or ester bonds that holds the biopolymers together (process hydrolysis)

Inorganic Compounds
 are

small compounds that do not contain the atoms C and H.  most important ones in humans include carbon dioxide (CO2) water, salts, acids & bases.

Inorganic Compounds
Salts


Ions
electrolytes (charged particles) that must be maintained within a very narrow range in our blood and tissues (i.e. homeostasis);  required for muscle contraction, nerve impulses, etc.;  Examples include Na+, K+, Cl-, Ca+, PO4-; HCO3-,


dissociate (ionize) into ions when dissolved in water. y an anion is formed and y a cation is formed. y Example = NaCl in water. H 2O NaCl ---------> Na+ + Cl--------->

Inorganic Compounds
Acids


Bases


dissociate (ionize) in water into a hydrogen cation, cation, H+ and an anion. y Example = HCl (hydrochloric acid). H 2O HCl -----------> H+ + Cl----------->

dissociate (ionize) in water into a hydroxyl anion, OHanion, and a cation. y Example = NaOH (sodium hydroxide). H 2O NaOH -----------> Na+ + OH----------->

Nonpolar organic molecules

 Cannot

dissolve in water (triglycerides, cholesterol esters).  However, in the presence of amphipathic molecules, they can form an emulsion where the organic molecules are surrounded by the amphipathic molecules that are in contact with water molecules.

Water molecules exhibit a slight but important tendency to dissociate

 Water

can act both as an acid and a base whereby its ionization involves intermolecular proton transfer forming a hydronium ion (H3O+) and a hydroxide ion (OH-) H2O + H2O H3O+ + OH-

pH of some common items. Image from Purves et al., Life: The Science of Biology, Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH (www.sinauer.com) Freeman (www.whfreeman.com), used with permission. (www.whfreeman.com),

Expression of Concentration
 The

concentration of a solution represents the amount of solute dissolved in a unit amount of solvent or of solution.  can be expressed in a variety of ways: -qualitatively; -semi quantitatively; or -quantitative.

Qualitative Expressions of Concentration

A

solution can be qualitatively described as: 1. dilute: a solution that contains a small dilute: proportion of solute relative to solvent, or 2. concentrated: a solution that contains a concentrated: large proportion of solute relative to solvent.

SemiSemi-Quantitative Expressions of Concentration



A solution can be semi-quantitatively described semias 1. unsaturated: a solution in which more solute unsaturated: will dissolve, or 2. saturated: a solution in which no more solute saturated: will dissolve. The solubility of a solute is the amount of solute that will dissolve in a given amount of solvent to produce a saturated solution.

Quantitative Expressions of Concentration



There are a number of ways to express the relative amounts of solute and solvent in a solution which depends on convenience. For example, it is sometimes easier to measure the volume of a solution rather than the mass of the solution. Some expressions for concentration are temperaturetemperature-dependent and others are not.

Expressions of Concentration
 Percent  Molarity  Molality  Mole

Composition (by mass)

Fraction

Percent Composition (by mass)

 

Can consider in 2 ways: The parts of solute per 100 parts of solution. The fraction of a solute in a solution multiplied by 100. To calculate the percent by mass of a solute in a solution must know 1) the mass of the solute in the solution and 2) the mass of the solution. Percent by mass = mass of solute x 100 mass of solution

Molarity
 

The number of moles of solute in exactly one liter of a solution. To calculate the molarity of a solute in a solution must know 1) the moles of solute present in the solution and 2) the volume of solution (in liters) containing the solute. Molarity = moles of solute_________ volume of solution in liters

 Molar

solutions (M) contain one gram mole of the substance per liter.  Molarity of a solution is the number of moles of the substance per one liter of solution. Molarity (mol/L) = concentration (g/L) mol/L) molecular weight (g) (g

Mole
 Mole

(abbrv. mol) composed of 6.022 x mol) 1023 objects known as Avogrados number. number.  A mole of a certain substance is found in one gram mole (g mole) of this substance by weighing the atomic / molecular weight of this substance in grams.

 Normal

solutions (N) contain one gram (N equivalent (g Eq) of the substance per (g Eq) liter.  Equivalent weight = Molecular Weight Valence Normality (eq/L) = Concentration (g/L) Equivalent weight

Molality
 the

number of moles of solute dissolved in exactly one kilogram of solvent.  to calculate the molality of a solute in a solution must know 1) the moles of solute present in the solution and 2) the mass of solvent (in kilograms) in the solution.  Molality = moles of solutes______ mass of solvents in kg

Molal solutions contain one mole of the substance per 1000g of solvent characterized by a fixed ratio between solute and solvent molecules.

1000g of water = 55.5 moles Aqueous solution = 1:55.5 Molality (mol/kg) = (mol/kg) Concentration (g/kg) (g/kg) Molecular weight

Important: Molality determine the osmotic pressure of solutions

Dissociation of water
1 mole (mol) of water weighs 18g 1 liter (L) (1000g) of water contains 1000 18 = 55.56 mol/L Pure water is 55.56 molar A hydrogen in pure water exist as hydrogen ions is 1.8 x 10-9

Dissociation constant, K
 Molar

conc. of H+ ions or OH- ions is 1.8 x OH10-9 multiply with molar conc. of water 55.56.  Result = 1.0 x 10-7 mol/L To calculate K for pure water: K = [H+] [OH-] = [10-7] [10-7] = 1.8 x 10-16 mol/L [OH[H2O] [55.56]

Ion product, Kw
K = [H+] [OH-] = 1.8 x 10-16 mol/L [OH[H2O] Kw = (K) [H2O] = [H+] [OH-] [OH= (1.8 x 10-16 mol/L) (55.56 mol/L) = 1.00 x 10-14 (mol/L)2 Importance of Kw: to calculate the pH of acidic and basic solutions

pH
 defined

as is the negative log of the hydrogen ion concentration pH = - log [H+] To calculate pH: 1) Calculate hydrogen ion conc. 2) Calculate the base 10 logarithm of H+. 3) pH is negative value. pH for pure water, pH= - log 10-7 = - (-7) = 7.0

pH
 pH

Scale ranges from 0 to 14: 0 ------------------7--------------------14 ------------------7--------------------14 acid neutral basic [H+] > [OH-] [H+] = [OH-] [H+] < [OH-]

Physiologic pH = 7.4

Importance of pH
 Knowledge

of the dissociation of weak acids and bases thus is basic to understanding the influence of intracellular pH on structure and biologic activity.  Charge-based separations such as Chargeelectrophoresis and ion exchange chromatography also are best understood in terms of the dissociation behaviour of functional groups

 Low

pH values high conc. of H+ ions  High pH values low conc. of H+ ions

 Many

biochemicals possess functional groups that are weak acids or bases. Carboxyl groups, amino groups, and phosphate esters, whose second dissociation falls within the physiologic range, are present in proteins and nucleic acids, most coenzymes, and most intermediary metabolites.

Importance of dissociation
 Knowing

the dissociation of weak acids and bases understanding the influence of intracellular pH on structure and biological activity.  Methodology / techniques to study dissociation behavior of functional groups : electrophoresis and ion exchange chromatography.

Law of Mass Action

 The

law stating that the rate of any given chemical reaction is proportional to the product of the activities (or concentrations) of the reactants.  In other words, the rate of chemical rate reaction is directly proportional to the product of the molecular concentration of the reacting substances at a given temperature and set of conditions.


Expression from the Law of Mass Action



  

The relative concentrations of reactants and products in terms of a quantity called Keq known as equilibrium constant of the reaction indicating the ratio between the products and the reactants when equilibrium is attained. The value of Keq is only affected by temperature and must be positive. When Keq > 1, at equilibrium the concentration of product(s) is far greater reactants. When Keq < 1, at equilibrium the concentration of reactants is much greater than products.

BUFFERS
 Solutions

that resist changing of pH in spite of the addition of moderate acid or alkali  Composed of either: (1) weak acid and its salt with strong base e.g. acetic acid + sodium acetate (2) weak base and its salt with strong acid e.g. ammonium hydroxide + ammonium chloride

Behavior of weak acids and buffers

 Can

be described quantitatively using the HendersonHenderson-Hasselbalch Equation. Equation. pH = pKa + log [A-]_ [HA]

pH of buffers
 

 

Dissociation of weak acids to buffer system containing acids at equilibrium. HendersonHenderson-Hasselbalch equation shows that the pH of the buffer depends upon the ratio between the concentrations of salt and the acid. At ratio of 1:1, the pH of the buffer = pka The buffering power of the system would be at maximum, the ratio between the salt and acid being least affected by either changes. The stronger the acid, the higher ka, the lower its pka

 It

is important to know that many metabolic reactions are accompanied by the release or uptake of protons, most intracellular reactions are buffered.

Buffering Systems
 Definition:

Buffers are compounds added to solutions to prevent abrupt change in pH. y usually weak acids; y function by donating H+ when needed and by accepting H+ when in excess; y very important in biological systems y Example : carbonic acid (H2CO3) buffering system.

Biological buffers
 Buffering

is an important property in biological systems, for which rapid pH changes can have disastrous consequences.  An effective biological buffer must help maintain blood in the "safe" range of pH 7.357.35-7.45 by resisting pH changes in either direction outside of this range.

Biological buffers


Excursions in the acid direction (i.e., below 7.35) are particularly to be feared, given the variations in production of acids such as lactic acid, pyruvic acid, acetic acid, etc., by metabolism. Production of such acids during peak exercise can lower peripheral blood pH to well below 7.0. The most important single buffer in human blood is the bicarbonate ion.

HCO3-

Physiologic Buffer Systems

 

 

Enzyme is very sensitive to changes to pH. As enzymes are important in controlling metabolic reaction, thus, acid/base formed inside the body should be buffered to allow reactions to proceed. This is the function of the physiological buffer system present in tissues and body fluids. There are 3 systems: (1) Bicarbonate system* (2) Phosphate system (3) Protein system

Bicarbonate buffering system


1. 2.

3.

4.

central to pH regulation in human blood and can respond to pH changes in several ways: The bicarbonate ion is really the conjugate base of carbonic acid . Carbonic acid is very rapidly interconverted with CO2 and water by carbonic anhydrase, making it a transient species. Water is easily absorbed into the system, while CO2 can be expelled by respiration which loss can be controlled via neurological mechanisms. [HCO3-] and [H+] can be manipulated (slowly and incompletely) by physiological mechanisms operating in the kidney.

Blood Buffers
Include all the physiological buffer systems.  All these buffer systems are operative to a certain extent.  It should be noted that: (1) the hemoglobin and oxyhemoglobin systems are responsible for the buffering of most CO2 added to the blood by tissues. (2) the bicarbonate system is the most efficient for the buffering of all acids added to the blood other than carbonic acid. (3) the buffer systems of the blood are so efficient that they keep the blood pH within a very limited range (pH7.35(pH7.357.45) in spite of the continuous addition*.


carbonic acid (H2CO3) buffering system

when pH is rising

H2CO3
Carbonic acid (H+ donor)

HCO3bicarbonate ion (H+ acceptor)

H+
hydrogen ion

when pH is falling

As physiologic pH = 7.4.
pH < 7.4 = acidosis; lethal below 7.0;  pH > 7.4 = alkalosis; lethal above 7.8.


Bicarbonate buffering system



is best suited to deal with acidosis, in part because respiration expels CO2 and thereby diminishes H+. In metabolically active tissues, such as muscle during intense exercise, production of CO2 (and acid, in the form of lactic acid) can lead to a transient fall in local pH. The system in blood can respond quickly to mild acidosis (between pH 7.15 and 7.35) by adjusting the CO2 release rate in the lungs.

Continuous addition of
(1) (2)

(3)

(4) (5)

Large volumes of CO2 due to oxidation of carbohydrates, proteins and fats. Sulfuric and phosphoric acids due to oxidation of proteins, phosphoric acid and uric acids from oxidation of nucleic acids. Ketone bodies from partial oxidation of fats by the liver during starvation and more marked in diabetes mellitus. Lactic acid from the partial oxidation of glucose by the red blood cells and muscles during exercise Amino acids, fatty acids and phosphoric acids due to digestion and absorption of food from the intestines.

BIOLOGICAL IMPORTANCE OF WATER

 As

a universal solvent dissolve substances; used for transport, removal of waste and secretion.  In metabolism hydrolysis reaction  As a lubricant - to aid movement and reduce friction  Giving support.

SUMMARY


Characteristics of water Dipolar and uneven distribution of charge Hydrogen bonding Thermal Properties of water denser than ice high latent heat of vaporisation high specific heat capacity high cohesion

Importance of water As a universal solvent In metabolism As a lubricant Giving support

Summary
 It

has a high specific heat capacity so water can maintain a reasonably constant temperature (homeostasis).  It has a high latent heat of vaporisation so animals use water to cool themselves.  It is less dense as a solid (ice) as ice is a poor conductor.  Water is a good solvent.

Summary of Bicarbonate Buffering System

 CO2
produced

+ H2O
always

[H2CO3]
in equilibrium with species on either side converted to products on left by carbonic anhydrase (RBC)

H+ + HCO3produced by metabolism pre-existing preblood buffer

by available metabolism

directly expelled in lung

adjusted in kidney via physiologic mechanisms unrelated to pH

adjusted in kidney or reacts with bicarbonate to make products on left

adjusted in kidney or reacts with H+ to make products on left