CHAPTER 2

CHAPTER 2

CHEMISTRY AND BIOCHEMISTRY

TOPIC 2: BASIC CHEMISTRY FOR BIOLOGY

1. Matter consists of chemical elements in pure form and in combinations called compounds

2. An element’s properties depend on the structure of its atoms

3. The formation and function of molecules depend on chemical bonding between atoms

4. Chemical reactions make and break chemical bonds

Chemistry is the science dealing with the properties & the transformations (chemical reactions) of all forms of matter

Matter is ….anything that takes up space (volume) or has mass.Matter is made of elements.

Concept 1 Matter consists of chemical elements in pure form and in combinations called compounds

Matter: Anything that takes up space and has mass

States of Matter

ELEMENT = A substance that cannot be broken down into other substances by chemical reactions.

TRACE ELEMENT = Element required by an organism in extremely minute quantities. Example: Fe (Iron)

COMPOUND = A pure substance composed of two or more elements combined in a fixed ratio. Example: NaCI (sodium chloride)

All Matter is composed of :

Atom – Means “unable to be cut” (Greek: atomos)

Smallest possible unit of matter that retains the physical and chemical properties of its element.

Elements

Substances that can’t be broken down into simpler substances

92 naturally occurring elements

25 - 36 chemical elements are essential to life.

96% of human mass is made up of C, H, O, N

Structure of Atoms CHNOPS

Structure of Atoms

Chemistry is the science dealing with the properties & the transformations (chemical reactions) of all forms of matter

Matter is ….anything that takes up space or has mass.

Matter is made of elements.

Structure of Atoms

Atoms contain protons, neutrons, and electrons.

Neutrons – no charge – 1 atomic mass unit

Protons - positive charge – 1 atomic mass unit

Electrons – negative charge – almost no mass

Structure of Atoms

Structure of Atoms

Atomic Number = number of protons In atom

Atomic Mass = mass of protons, neutrons and electrons in atom

Structure of Atoms

CHNOPS

Isotopes

Structure of Atoms

Isotopes – alternative forms of an atom that differ in their number of neutrons (same atomic number, different MASS number)

How are these atoms different from each other?

What can isotopes be used for?

IsotopesISOTOPES Atoms of an element

that have the same atomic number but different mass number. They have the same number of protons, but a different number of neutrons.

RADIOACTIVE ISOTOPE Unstable isotope in which the nucleus spontaneously decays, emitting subatomic particles and/or energy as radioactivity. Loss of nuclear particles may transform one element to another A radioactive isotope has a fixed half-life: HALF LIFE = Time for 50% of radioactive atoms in a sample to decay.

Isotopes DifferingNumbers ofNeutrons

Hydrogen: H1

1

Deuterium: H1

2

Tritium H1

3

Applications of isotopes: Carbon Dating


99% of carbon atoms have 6 neutrons (12C). Most of the remaining 1% of carbon atoms

have 7 neutrons (13C) while the rarest carbon isotope, with 8 neutrons, is 14C.

Both 12C and 13C are stable isotopes while 14C is radioactive

When 14C decays, one of its neutrons is converted to a proton and an electron.

This converts 14C to 14N, transforming the atom to a different element.


By comparing the ratio of radioactive (14C) and stable (12C) isotopes in a fossil with the ratio of isotopes in living organisms, one can estimate the age of a fossil less than 50,000 years old.

Application of isotopes: Nuclear scintigraphy

Diagnostic radiopharmaceuticals – Technetium 99

Iodine 131: diagnosis and treatment of thyroid tumours

PET scanning (positron Emmision Tomography)

CT scanning (computer tomography)Generally short-lived isotopes linked to

chemical compounds to be traced.

Structure of Atoms: Electron Orbitals

There are certain spaces around the nucleus where electrons are likely to be found. The electron is

found a certain distance from the nucleus called a shell. Within a shell is an orbital that holds 2

electrons.

The outermost electron shell is referred to as the valence shell.

Structure of Atoms: electron Orbitals

1. First energy shell can contain a maximum of 2 electrons

2. All other shells can contain a maximum of 8 electrons (there are exceptions)

An atom is most stable when the valence shell contains a full 8 electrons = OCTET RULE

RULESABOUT ELECTRONS!

Structure of Atoms: Electron Orbitals

Structure of Atoms

RULESABOUT ELECTRONS!

Electrons determine chemical reactivity.

Atoms are reactive unless they have a full valence shell of electrons!

Chapter 2 Chemical Principles

Structure of Atoms


Structure of Atoms

Which atoms on the periodic table have a full valence shell?

Which atoms on the periodic table have only one electron in the valence shell?

Which atoms on the periodic table have seven electrons in the valence shell?

A Brief Review: Types of Bonding

INTRAMOLECULAR FORCES

Ionic BondingCovalent Bonding(Polar Covalent bonding)

INTER-MOLECULAR FORCES

Dipole-dipole interactions (Van Der Waals Forces)Hydrogen Bonds

BONDING

IONIC BONDING COVALENT BONDING

non-polar covalent

and

polar covalent

Bonding between elements (in compounds and molecules)

Electronegativity is the tendency of an atom to attract electrons.

If the electronegativity of an atom is high, then it attracts and holds on to electrons.

If the electronegativity of an atom is low, then it tends to give electrons away.

Bonding and electronegativity

Where on the Periodic Table do you find the atoms with high electronegativity?

Where do you find those atoms with low electronegativity?

Which atom has the highest electronegativity?

Bonding and electronegativity

Ionic bonding – Atoms transfer or accept electrons from one another

Look at the following diagram with regards to sodium (Na) and chloride (Cl)

What must each do to fulfill the octet rule?

Ionic Bonding

Ionic

Bonding

Ionic bonding

The sodium ion and the chloride ion will be attracted to each other and form an ionic bond.

Na + Cl -

By looking at the periodic table, can you predict which atoms may form ionic bonds?

The ionic bond is due to the attractive forces between the now positively charged sodium & the negatively charged chloride.

Non-polar covalent bond – equal sharing of electrons

Polar covalent bond – unequal sharing of electrons

What does the word polar mean?

Bonding: Covalent Bonding

Covalent bonding

C H

In the molecule of methane (CH4), the electrons are shared equally between the carbon and hydrogens.

How many electrons are needed to fill the valence shell of carbon?

How many electrons are needed to fill the valence shell of hydrogen?

Bonding: Covalent Bonding

Bonding

Covalent bonding

Covalent Bonding

Polar covalent bond – unequal sharing of electrons

A great example of a molecule with polar covalent bonds is water. Why is water considered polar?

What is a partial positive and partial negative charge?

Polar Covalent Bonding

Polar covalent bond


Bonding

Covalent bonding

Polar covalent bond

Inter-molecular forces: dipole-dipole interactions

and hydrogen bonding

Van Der Waals Forces – Dipole Dipole interactions

Hydrogen Bonding

CHAPTER 2

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