Lecture 2

Life’s chemical basis

LIF101

3-1-2014Friday Dr. Jonaki Sen

Start with atoms

Atoms form the fundamental building blocks of all matter

Atoms have electrons, protons and neutrons

Elements are made up of identical atoms with the same number of protons

The “Shell model” of electron distribution in an atom

Concentric circles represent successive energy levels

1st shell: up to 2 electrons2nd shell: up to 8 electrons3rd shell: up to 8 electrons

An atom is most stable when it has no vacancies

Atoms fill vacancies by gaining or losing electrons, or by sharing electrons with other atoms

An atom with a different number of electrons and protons carries a charge, and is called an ion

Atoms and Ions

A chlorine atom becomes a negatively charged chloride ion by gaining an electron and filling the vacancy in the third shell.

A sodium atom becomes a positively charged sodium ion by losing an electron in the third shell.

From atoms to moleculesTwo atoms with vacancies can join in a chemical bond which is an attractive force produced when electrons interact and the result is a molecule.

A compound is a molecule that consists of two or more elements

A mixture is an intermingling of substances

The same atoms bonded together in different ways make up different molecules

Types of bondsThe characteristics of a bond arise from the properties of atoms that take part in it .

Ionic BondIs a strong mutual attraction of oppositely charged ions. Example is the ionic bond between the sodium and chloride ion in the salt crystal.

Covalent bondTwo atoms share an electron such that the vacancy of each atom is partially filled. Depending on the number of electrons shared a covalent bond may be a single, double or a triple covalent bond.

Nonpolar covalent bondWhen the participating atoms exert the same pull on the shared electrons.

Polar covalent bondWhen one of the participating atoms can exert a stronger pull on the shared electrons e.g. the oxygen atom in water.

Hydrogen bondA weak attraction between an hydrogen atom and another atom taking part in a separate polar covalent bond.

Why does water play a significant role in living systems?

Polarity of the water molecule

Polar covalent bonds join two hydrogen atoms to one oxygen atom in each water molecule

Properties of Water

Water’s solvent propertiesWater is a solvent that easily dissolves salts, sugars, and other polar substances

Solvent :Liquid that can dissolve other substances

Solute :A dissolved substance

Water molecules dissolve an ionic solid such as NaCl by surrounding the atoms and pulling them apart

Water molecules dissolve a substance by clustering around its ions or molecules and forming hydration shells which separate them.

Hydrophilic substances dissolve easily in water; hydrophobic substances do not

Hydrophilic :Substance that dissolves easily in water, such as salt

Hydrophobic: Substance that resists dissolving in water, such as oil

Life depends on hydrophobic interactions

Polarity of water molecules attracts other polar molecules.

Water is an excellent solvent

Water stabilizes temperature•Temperature: Measure of molecular motion

•Temperature stability is important for homeostasis; most molecules of life function within a certain temperature range

•Because of hydrogen bonding, it takes more heat to raise the temperature of water compared with other liquids

A large input of energy can increase molecular motion and break hydrogen bonds which causes evaporation.

Evaporation :Transition of a liquid to a gas which requires energy (removes heat from liquid).

Evaporative cooling through sweating.

Below 0°C, hydrogen bonds resist breaking and lock water molecules in the bonding pattern of ice.

In ice crystals each molecule of water is tetrahedrally surrounded by four nearest neighbors to which it is hydrogen bonded.

Liquid water has 15% less hydrogen bonding than ice at 0°C.

Structure of liquid water is irregular.

Ice

Liquid water

Ice floats because the molecules pack less densely than in water

Ice insulates the liquid water beneath it and protects aquatic life from freezing.

Water’s cohesionHydrogen bonds cause water molecules to resist separating from each other

Cohesion: Tendency of molecules to stick together .

Pulls water upward in plants.Causes surface tension

Most biological processes occur within a narrow range of pH, typically around pH 7

pH : Measure of concentration of hydrogen ions (H+) in a fluid

concentration : Number of molecules or ions of a solute per unit volume of a solution

ACIDS, BASES and BUFFERS

Acids release hydrogen ions in water; bases accept them

Acid : Substance that releases hydrogen ions in water

Base :Substance that accepts hydrogen ions in water

In liquid water, water molecules spontaneously separate into hydrogen ions (H+) and hydroxyl ions (OH-)

H2O (water) ↔ H+ (hydrogen ions) + OH– (hydroxide ions)

At neutral pH (7), the amounts of H+ and OH– ions are equal

Water

Water dissociates into hydronium (H3O+) and hydroxyl (OH-) ions. For simplicity, let’s refer to the hydronium ion as a hydrogen ion (H+) and write the equilibrium as

The equilibrium constant Keq of this dissociation is given by

in which the terms in brackets denote molar concentrations. Because the concentration of water (55.5 M) is changed little by ionization, expression 1 can be simplified to give

in which Kw is the ion product of water. At 25°C, Kw is 1.0 × 10-14.Note that the concentrations of H+ and OH- are reciprocally related. If the concentration of H+ is high, then the concentration of OH- must be low, and vice versa. For example, if [H+] = 10-2 M, then [OH-] = 10-12 M.

The pH of a solution is a measure of its concentration of H+. The pH is defined as

Ionization of water and pH

pH scale ranges from 0 (most acidic) to 14 (most basic)

One unit on the scale corresponds to a tenfold change in H+ ions

Strong acids give up more H+ ions than weak acids

Hydrochloric acid (HCl) is a strong acid that, when added to water, easily separates into H+ and Cl–

HCl (hydrochloric acid) ↔H+ (hydrogen ions) + Cl– (chloride ions)

A buffer keeps a solution within a consistent range of pH

Most cell and body fluids are buffered because most molecules of life work only within a narrow range of pH

buffer : Set of chemicals that stabilize pH of a solution by alternately donating and accepting ions that contribute to pH

Buffers

An acid-base conjugate pair of a weak acid and its corresponding base (such as acetic acid and acetate ion) has an important property: it resists changes in the pH of a solution. In other words, it acts as a buffer.

The Bicarbonate Buffer System

Carbon dioxide gas becomes a weak acid when it dissolves in the fluid portion of human blood:

H2O + CO2 (carbon dioxide) → H2CO3 (carbonic acid)

Carbonic acid separates into hydrogen ions and bicarbonate ions, which can recombine to form carbonic acid:

H2CO3 (carbonic acid) ↔ H+ + HCO3- (bicarbonate)

Exchange of ions between carbonic acid and bicarbonate keeps blood pH between 7.3 and 7.5 – up to a point

Buffer failure can be catastrophic in a biological system

Example: Too much carbonic acid forms in blood when breathing is impaired suddenly – the resulting decline in blood pH may cause coma

Important points:What are the basic kinds of interactions between atoms?

• Covalent Bond• Non-covalent Bond• Hydrogen Bond• Hydrophobic interactions• Polar covalent bond

What are properties of water that make it suitable for sustaining life? Should know each property and why it is beneficial.

What is pH? How is it calculated?

What is a buffer?

Why is pH important for living systems?

How is buffering done in living systems?

http://home.iitk.ac.in/~jonaki/LIF101/

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The lectures and sample question etc. will all be available at Copy Point, Shopping Complex, IIT Kanpur.