Chemical Basis of Life: Atoms and MoleculesLesson 2

Describe interactions among atoms, including covalent, ionic, hydrogen bonding and non-polar interactions.

Discuss the behaviour of water due to hydrogen bonding and the benefits of water to living organisms.

To understand biology the knowledge of basic chemistry is necessary

Living things are complex structures of atoms and molecules

The chemistry of life is what allows living things to function and interact

1. Living things are living matter comprised of combinations of several elements.

2. Elements are substances that cannot be changed in normal chemical reactions

A. there are 92 naturally occurring elements

ranging from hydrogen to uranium B. Each element has a unique chemical

symbolC. Four elements (C,H,O,N) make up 96% of

most living organisms

Most common elements:

Oxygen (O)Carbon (C)Hydrogen (H)Nitrogen (N)

Minor elements:Calcium (Ca)

Phosphorous (P)

Potassium (K)

Sulfur (S)

Sodium (Na)

Magnesium (Mg)

Chlorine (Cl)

Iron (Fe)

Atoms are the fundamental particles of elements

- Atoms are the smallest components of an element that retains the chemical properties of the element

- Components of atoms include protons, neutrons, and

electrons

Typical Structure of an atom

Atoms

An atom is uniquely identified by itsnumber of protons (its atomic number)

- A proton is a subatomic particle (tiny particles of matter) with one unit of positive charge found in the nucleus of an atom

- The periodic table depicts the elements in order of their atomic number – the number of protons in the nucleus

- The atomic mass or mass number indicates the number of protons and neutrons (protons plus neutrons) in an atom

- Neutrons are uncharged or neutrally charged subatomic particles found also in the nucleus of atoms

- The atomic mass of an atom indicates approximately how much matter that atom contains compared to others

- expressed in Atomic mass units (amu’s) or Daltons

An element has 6 protons and 6 neutrons. What is its atomic mass? What is its mass number?

Some atoms are called isotopes - Isotopes have the same atomic number, but differ

in number of neutrons. (same atomic number, but different mass numbers)

- Radioisotopes are unstable isotopses due to excess neutrons; they tend to break down (decay) emiting radiation (Many are important in scientific research and medicine

Electrons are negatively charged subatomic particles that occupy orbitals

- Orbitals are regions of 3D space that correspond to energy levels.

- An electron’s energy depends on the orbit it occupies (less energy closer to the nucleus, more energy away from nucleus)

- The outermost electron(s) are known as the valence electron(s) and they contain the most energy

- These outer electron(s) occupy what is called the valence shell (most outer orbital)

- Electrons can gain energy and move to farther orbitals or lose energy and move to lower orbitals (closer to nucleus).

Valence electrons determine the chemical behaviour of atoms

Atoms can undergo chemical reactions

- The number and arrangement of valence electrons determines the chemical behaviour of the atom

- Most atoms are unstable and aim to fill their valence shell to become stable

- Stable atoms are very unreactive- max of 2 electrons needed to fill first orbital- max of 8 electrons needed to fill all other orbitals

- Unstable atoms are reactive and may gain, lose or share valence electrons to become stable.

◦What determines the chemical behaviour of a particular element?

◦Oxygen (O) has six valence electrons. It needs how many more electrons to fill its other shell and become stable.

Atoms when they react can chemically combine and form molecules and compounds

- When two or more atoms join and form stable particles they are called Molecules

- Molecules may be composed of different or similar atoms- Eg. H2O, O2, H2, N2 CO2, NH3

- Compounds result when two or more different elements combine- Eg. C6H12O6, H20

- Note: All compounds are molecules but not all molecules are

compounds.

A substance (compound and molecules) can be described by a chemical formula

- Chemical formulas indicate the types of atoms in a substance and their ratio- Examples: H2o, C6H12O6

- Subscripts indicate the number of atoms of a particular element in the chemical. No subscript indicates 1 atom of an element

- Chemical formulas may be shown as emperical (simplest formula), molecular formulas or structural formulas

Types of Chemical Formulas

Emperical CH2ONH2

MolecularH2OC6H12O6

N2H2

Structural

D. Chemical equations describe chemical reactions

1. Reactants- substances that participate in the reaction (generally

written on the left side of the equation)

2. Products – substances that are made ( written on the right side of

the equation

3. Reversible reactions are indicated by double arrows between reactants and products

Samples N2 + 3 H2 → 2 NH3

2 H2O → 2 H2 + O2

2 Na(s) + 2 HCl(aq) → 2 NaCl(aq) + H2(g)

2 H2 + O2 2 H2O

Atoms are joined by chemical bonds

- Chemical bonds are forces of attraction between atoms

- They represent a certain amount of energy; - That amount of energy would be required to break

that bond (activation energy)

- Important Bonds to note- Covalent Bonds- Ionic Bonds- Hydrogen bonds

- In covalent bonds electrons are shared to fill the valence shells of all the atoms involved

- Each atom shares one(1) electron to make a shared pair of electrons

- Covalent bonds are strong chemical bonds

- Single, double or triple covalent bonds can exist

ElectronegativityA large nucleus with many protons attracts electrons more strongly than a small nucleus with few protons

Nonpolar covalent bonds forms when electrons are shared equally◦ Eg. •O2, CO2, CO, CH4, H2

Polar covalent forms when one atom is more electronegative than the other (creates positive and negative ends)

Eg. H2O, water

B. Ionic bonds form between cations and anions

1. An atom becomes an ion when it gains or loses one or more electrons and thus becomes charged

2. Cations are positively charged ions (loses

electron(s))

3. Anions are negatively charged ions (gains electrons(s)), and are named with the

Anions and Cations

Common Cations Common Anions

hydrogen  H+ hydroxide  OH-

sodium  Na+ chloride Cl-

potassium  K+ sulfide  S-2

calcium  Ca+2 bicarbonate  HCO3-

magnesium  Mg+2 carbonate  CO3-2

ferrous  Fe+2 sulfate  SO4-2

ferric  Fe+3 phosphate PO4-3

- Example: a. Sodium (Na+ ) and chloride (Cl-)

ions form sodium chloride (NaCl)

- Hydrogen bonds are weak attractions involving partially charged hydrogen atoms

- Hydrogen bonds individually are weak, but collectively are very strong

In other words a hydrogen atom covalently bonded to an electronegative atom is attracted to another electronegative atom (oxygen or nitrogen)

Example: Water

Ionic bonds form when oppositely charged atoms are attracted to each other

Polar molecules have no charged ends

Covalent bonds occur when valence electrons are shared

Chemical formation- H2O Covalently bonded molecule Essential component of living forms Important medium for living things to exist

Polar Easily dissociates Universal Solvent High Specific Heat High heat of vaporization Important in Metabolism Lubricant Supporting Substance Habitat Etc.

Water molecules are polar covalent

Its Oxygen attracts electrons more strongly than its hydrogens

◦ This creates a dipolar structure

◦ Allows for hydrogen bonding

Water’s ability to hydrogen bond is responsible for several of its properties

Cohesive nature – droplet formation, cling to each other

Capillary Action Adhesive nature – cling to other surfaces

Crystal structure of ice

◦ Water molecules are spaced out by H-bonds

◦ Ice is less dense than liquid water

◦ Water is most dense at 4o C◦ Ice floats on water

Surface ice insulates the liquid water belowThis allows fish, frogs and other aquatic organisms to survive winters in frozen lakes

Water has the tendency to ionize◦ Hydroxyl ion -OH- ◦ Hydronium ion - H+ (or oxonium ion H3O+ )

pH is the measure of the concentration of hydrogen ions (H+) in a substance

At neutral pH, H+ = OH- = 7.0 pH greater than 7.0 is alkaline pH lower than 7.0 is acidic

Acid (pH < 7)◦ Protons donors ◦ Large concentration of hydrogen ions (H+)

◦ Releases H+ in solution

Base (pH > 7)◦ Protons acceptors◦ Low concentration of H+

◦ Releases OH- in solution

Neutral pH is 7.0◦ Concentration of H+ and OH- are equal

Buffers are substances that resists (prevents) changes in pH when an acid or base is added.

Water readily dissolves other polar molecules (and also ionic substances) (hydrophilic molecules)

It does not dissolve non-polar molecules (hydrophobic molecules)

This property is very important in Transport – blood, sap etc. Removal of waste – urine Secretions

Specific heat can be defined as the amount of heat energy required to raise the temperature of 1gm of something by 1 degree Celsius. (It is expressed in calories)

It is how well a substance resists changing its temperature

The amount of heat energy required to raise the temperature of water is quite large;

Its takes a lot of heat to increase the kinetic energy of water molecules and thus break bonds between water molecules

Thus water is fairly stable with changing temperatures; this helps stabilize the Earth’s surface

This is essential for reactions involving enzymes

Much heat energy is required to change liquid water to vapour.

This means that water can absorb or can lose a lot of heat energy without changing its temperature very much.

This buffers the environment against large, rapid temperature changes.

Temperature Control (Cooling) Evaporation Transpiration

Property Benefit to life

a liquid at room temperature, water dissolves more substances than any other common liquid

liquid medium for living things and for the chemistry of life

much heat energy needed to raise the temperature of water aquatic environment slow to change temperature; bulky organisms have stable temperatures

evaporation of water requires a great deal of heat evaporation causes marked cooling; much heat is lost by evaporation of a small quantity of water

much heat has to be removed before water freezes cell contents and water in aquatic environments are slow to freeze in cold weather

ice is at maximum density at 4 °C ice forms on the surface of water, insulating the water below, and allowing much aquatic life to survive freezing

surface water molecules orientate with hydrogen bonds formed inwards

certain animals exploit surface tension to move over water surfaces

water molecules slide past each other easily water flows easily through narrow capillaries (low viscosity)

water molecules adhere to surfaces water adheres to walls of xylem vessels as it is drawn up the stem to the leaves, from the roots

water column does not easily break or pull apart under tension

water can be lifted by forces applied at the top, and so can be drawn up xylem vessels in tree trunks by force generated in transpiration from leaves

water is transparent aquatic plants can photosynthesise at some depth in water

On a scrap piece of paper List two (2) things you understood well from

today’s lesson.

List two (2) things that were confusion.

Submit your paper before leaving