The Chemical Basis of Life (Chapter 2 of text)

Outline

Elements, Atoms and Molecules

Types of Chemical bonds
Water
Acids and Bases, pH

How is Chemistry linked to Biology?

All of life is composed of matter, anything that occupies space and has mass.
Matter is made up of chemical elements -substances that cannot be broken down
to other substances by easy chemical means. Ex: oxygen (O), carbon (C),
hydrogen (H), nitrogen (N) copper (Cu), gold (Au), iron (Fe).
Living organisms are made of about 25 chemical elements (see Table 2.1). The
4 main elements are H, C, N and O, making up about 96% of the human body and
of most organisms. Calcium, phosphorus, potassium, sulfur, sodium, chlorine and
magnesium account for about 4 %. Trace elements, like iron and iodine are also
essential, but in very small amounts.
Elements can combine to form compounds a compound is a substance that
contains 2 or more elements combined together. Ex. sodium chloride (salt), vitamins
Most of the compounds in living organisms are made of 3 or more elements.

The Atom: (from Greek word meaning indivisible)

Atom is the smallest unit of an element; unique to each element. Ex. an oxygen atom
is different from a nitrogen atom.
Structure: Physicists managed to split the atom and found 3 parts.
o Proton
- has a single positive electrical charge
- tightly packed in the core of the atom called nucleus
o Neutron
- has no electrical charge (neutral)
- packed along with the protons in the nucleus
- number can vary, does not depend on proton number.
o Electron
- has a single negative electrical charge
- moves around or orbits the nucleus the attraction between the oppositely
charged electrons and protons keep the electrons in orbit.
- electrons mass is very small (1/2000 the mass of a proton)
Atomic number: total number of protons in the nucleus. Each element is
defined by the number of protons it has in its nucleus. Example: Carbon = 6;
Hydrogen = 1; Gold = 79. Fig. 2.4 A, B (Also refer to Periodic table in lab book)
Atomic mass: sum of protons and neutrons in the nucleus. Example: C = 12; H = 1
Isotopes: are different forms of the same element which differ in their atomic mass.
- have the same number of protons but differ in the number of neutrons. (Table. 2.4)
- Ex.12C, 13C and 14C are all isotopes of C with 6 protons but 6, 7 or 8 neutrons.
- 12C and 13C are stable isotopes; 14C is an unstable or radioactive isotope here the
nucleus decays giving off particles and energy.
Connection to Biology: Many uses of Radioactive isotopes, (refer page 21 of text) in
basic research and medical diagnosis.
Dangers: uncontrolled exposure to radio-isotopes damages DNA. Ex. when nuclear

reactors explode leads to increase in cancer rates.

Chemical Bonding

The main players in chemical bonding are electrons

Electrons are arranged at different energy levels around the nucleus - called
electron shells; electrons have more energy the farther they are from nucleus.
The first electron shell closest to the nucleus can hold up to 2 electrons the shell is
full with 2 electrons. When the first shell is filled, electrons occupy the next shell.
The next outer shell can hold up to 8 electrons (full with 8 electrons) and so on.
The no. of electrons in the outermost shell gives an element its chemical property
When the outermost electron shell is not full, the atom is unstable and seeks another
unstable atom to bond or react with. Ex: H = 1, needs 1 to be stable; C = 6 and
needs 4 more electrons to become stable. N = 7; O = 8; (See Fig. 2.6)
Chemical interaction between atoms: 2 kinds
(1) by sharing electrons (2) donating electrons or receiving electrons. Both reacting
atoms finally have complete outer shells and become stable. The reacting atoms are
held together by chemical bonds.
Kinds of chemical bonds:
1. Ionic
2. Covalent
3. Hydrogen
1. Ionic bond: is formed between 2 ions of opposite charge.
Ex: sodium chloride (NaCl) or table salt. (See Fig. 2.7 A, B)
o The Na atom with 11 electrons has only 1 electron in its outermost
shell. The Cl atom has 17 electrons with 7 electrons in its outermost shell.
o Na loses its electron to Cl and and becomes a Na+ ion
o Cl gains an electron and becomes a Cl- ion (chloride ion)
o an ion is an atom or molecule that has gained or lost one or more electrons
and therefore has an electrical charge
o The two ions are attracted to each other by their opposite charge
o NaCl compound is electrically neutral
o Many atoms of Na and Cl go to form NaCl (exists as a crystal)
2. Covalent bond: is a strong bond formed between 2 atoms that share
one or more pairs of outer shell electrons. (Table 2.8)
o 2 or more atoms that are held together by covalent bonds form a
molecule.
o H2 molecule: 2 hydrogen atoms share their electrons. One pair of
electrons is shared, so one covalent bond is formed (single bond)
o O2 molecule: 2 oxygen atoms share 2 pairs of electrons forming a
double bond
o Valence or bonding capacity of atom: equals the number of
electrons needed to fill outer shell. Ex: H=1; O = 2; N = 3; C = 4.
Polar and non polar covalent bonds:
a. In H2 or O2 molecules, the 2 atoms are identical, so they share
their electrons equally (symmetric); in methane(CH4), C and H also
share their electrons equally to form a nonpolar covalent bond.
b. In a water (H2O) molecule, 2 H + 1 O covalently bond to form a H2O
molecule: 2 electrons of O form a bond with 1 electron each from H.

O pulls its shared electrons toward itself much more strongly

compared to H (O is more electronegative) a polar covalent bond
(asymmetric) is formed.
H2O is a polar molecule - V-shaped molecule with unequal charge. O
atom is partially negative and H atom is slightly positive (Fig. 2.9)
3. Hydrogen bond: is a weak bond formed between a H-atom and another atom.
o H-bonds are easily broken and reformed and are very important in biology.
Ex: bonds between water molecules are weak H-bonds (Fig. 2.10)
o Positive charge of a H atom in one water molecule is attracted to a negatively
charged O of a neighboring H2O molecule
o Each H2O molecule can H-bond with 4 other H2O molecules in this way
o H-bonds are important in holding protein and DNA molecules together

Water
Polarity and hydrogen bonding of water molecules give it unusual properties.
Water is the solvent used (used to dissolve chemicals) in all living organisms; in
cells of plants and animals, in blood and plant sap. Water constitutes about 70% of
the earth and makes up 66% of human body weight.
1. Cohesion: water molecules tend to stick together because of the H-bonds between
water molecules called cohesion much stronger for water than for other liquids.
Importance: Plants transport water and nutrients from the roots to the leaves of tallest
trees against the force of gravity!
2. Surface tension: Surface tension is a measure of the stretch of the water surface
how easily the surface of water gives way. H-bonds give water a high surface tension.
This property makes it possible for some insects to walk on the surface of water.
3. Specific Heat: Water has a relatively high specific heat due to its H-bonds. It takes a
large amount of heat energy to raise the temperature of water. When water is heated,
water molecules move faster and the heat energy is used or absorbed to break the Hbonds. When water is cooled, more H-bonds are formed, releasing heat.
This property makes water a very good insulator slowing down both the heating
and cooling process (reason why coastal areas have milder climate).
It provides a better environment for marine life by stabilizing the ocean
temperature. It also helps regulate our internal body temperature
High boiling point (100oC): water has to absorb a huge amount of heat to break all
the hydrogen bonds and become vapor
Evaporative cooling (sweating from the skin of animals and evaporation from
plant leaves) prevent overheating.
4. Ice floats on water because it is less dense than water. In ice, there is more space
between water molecules compared to liquid water - makes the H-bonds in ice more
stable. In liquid water, the water molecules are more tightly packed and the H-bonds
are always breaking and re-forming. (Fig. 2.13)
Importance of ice: In frozen lakes, ice insulates the water below, keeping it warm and
allowing fish and other forms of life to survive.

5. Aqueous solution: water is the solvent of life, inside all cells; what makes water such
a good solvent that can dissolve a large variety of solutes?
Solution: a liquid consisting of a uniform mixture of 2 or more substances.
Solute: substance being dissolved (ex: salt, sugar;)
Solvent: liquid used to dissolve solute (ex: water)
When water is used as the solvent, the solution is called an aqueous solution
The polarity of water molecules attracts the solute molecules or ions.
Ex. in a solution of salt and water the slightly negative O and slightly positive H
surround the ions of Na+ and Cl-. Sugar and many proteins that are polar (but not
ionic) also dissolve in water
Hydrogen bonds between water molecules can easily be broken and re-formed to
form bonds with solute molecules.
Non polar solutes dissolve in non polar solvents (soap and oil/grease)
Polar solutes dissolve in polar solvents (salt or sugar in water)

Acids and Bases concept of pH

All aqueous solutions have small amounts of OH- (hydroxide) and H+ ions.
The relative amounts of these two ions makes a solution basic or acidic
An acid has more H+ ions than OH- ions. The more acidic a solution, the more H+
ions it has; an acid can therefore donate its H+ ions to a solution. Ex: hydrochloric
acid (HCl) dissociates in water into H+ and Cl-. (HCl is the acid in our stomach)
A base has more OH- ions. The more basic a solution, the more OH- ions (lower H+
ions) it has. A base is a compound that accepts H+ ions. Ex: Sodium hydroxide
(NaOH) dissociates in water into Na+ and OH-.
We use pH to measure the amount or concentration of H+ ions in an aqueous
solution. (pH is potential of hydrogen)
Depending on the pH, a solution can be acidic, basic or neutral.
An acid has a pH lower than 7; a base has a pH higher than 7; 7 is neutral pH
The pH scale is not a simple linear scale. It is a logarithmic scale where each unit
changes 10-fold. The scale is from 0 14. (Fig. 2.15)
Ex: lemon juice (pH = 2) has 100 times more H+ ions than tomato juice (pH = 4)
Neutral solution has a pH of 7.0 and is neither acidic nor basic. Ex: pure water has
an equal number of H+ ions and OH- ions.

Importance of pH in biology

pH inside most cells of living organisms is around 7.

pH is critical to a cells survival and function. The molecules in a cell are very
sensitive to even very small changes in pH.
Ex: chemical reactions inside a cell occur at specific pH. Enzymes make these
reactions happen and function only at very specific pHs.
How then do biological systems cope with changes in pH?
Buffers are chemicals that resist changes in pH buffers either accept or donate
H+ ions and maintain the pH inside cells, in blood, etc. Ex. buffers maintain the pH
of blood around 7.4; if it drops to 7 or rises to 8, a person cannot survive.
Significance to environment: uncontaminated rain has a pH of 5.6.

Acid precipitation is rain, fog or snow with a pH less than 5.6; occurs due to air
pollution - sulfur oxides and nitrogen oxides from the exhausts of vehicles are air
pollutants they react with water vapor in the air to form sulfuric and nitric acids
fall to the earth as acid rain.
This harms many ecoystems; Ex. rain with a pH of 2-3 in eastern US has destroyed
forests; when acid rain mixes with water in lakes, fish die due to a low pH.; acid fog
of pH 1.7 recorded near LA.

Chemical reactions

Ex. Hydrogen and oxygen react to form water: 2H2 + O2 H2O

H and O are the reactants and water is the product
Chemical reactions do not create or destroy matter; they only rearrange matter
The no. of molecules on the 2 sides of the arrow are the same; bonds are broken
and remade in a chemical reaction.