Chemistry for Biologists

Some basic chemistry

Living organisms and chemistry

Biology is about living things - organisms. All living organisms are made of chemicals. To understand biological substances and the changes that take place in living organisms you need a good knowledge of the underlying chemistry. We will build up a picture of the chemicals that make up living organisms by starting small and getting bigger.

The starting point is atoms - the building blocks of all matter. We will then look at how these come together to make elements and compounds.

Atoms

Atoms are the building blocks of all matter. They consist of three sub-atomic particles: protons, neutrons and electrons. Protons and neutrons are found in the nucleus of an atom. Electrons are found in energy levels around the nucleus as shown in the diagram representing a carbon atom with 6 protons, 6 neutrons and 6 electrons.

Sub-atomic particles

Particle Whereabouts in atom Relative mass Charge
Proton Nucleus 1 +1
Neutron Nucleus 1 0
Electron Outside the nucleus 1/1840 -1
Diagram of carbon atom - nucleus with electrons orbiting

Diagram of carbon atom - nucleus with electrons orbiting

In chemistry we are particularly interested in electrons. As you will see later, this is because chemical reactions involve the rearrangement of electrons. Nuclei of atoms (protons and neutrons) usually remain unchanged (except in radioactive decay).

Electrons are arranged in atoms according to their energies. This is called the electronic structure or electronic configuration of the atom. A crude but still useful model says the electrons can be in different energy levels. Electrons in a particular energy level all have the same energy as one another. The lowest energy level can accommodate up to 2 electrons. The second level can accommodate up to 8 electrons. The third level can accommodate up to 18 electrons. The diagram shows the situation for a sulfur atom.

Electronic configuration of sulfur including energy level diagram

Importantly it's only electrons in the outermost energy level of an atom that are involved in chemical bonding.

Elements

An element is a substance made up of atoms with the same number of protons. Elements are the simplest substances known. They can be metals (e.g. iron, copper, sodium magnesium) or non-metals (e.g. carbon, hydrogen, oxygen, nitrogen). There are just over 100 of them.

Each element has its own:

  • name and chemical symbol
  • characteristic physical properties, e.g. density, electrical conductivity, melting point and boiling point
  • characteristic chemical properties, e.g. reactions with water, oxygen, acids and other chemicals

These physical and chemical properties do not change. They can be used to identify an element. Elements are listed in the Periodic table.

Many elements have different isotopes. Although the numbers of protons and electrons are the same in all atoms of a given element, the number of neutrons may differ. For example, in a typical sample of carbon:

  • 98.9% of the carbon atoms have 6 protons, 6 electrons and 6 neutrons
  • 1.1% of the carbon atoms have 6 protons, 6 electrons and 7 neutrons
  • a small trace have 6 protons, 6 electrons and 8 neutrons - carbon-14

This fact is made good use of in radiocarbon dating. The proportion of carbon-14 in living systems is constant because they absorb and re-emit carbon-containing compounds continuously. However, once an animal or plant dies the proportion of carbon-14 in its structure decreases because carbon-14 atoms undergo β-decay to give nitrogen:

Decay of C14 to give N14 and electron

In dead material the carbon-14 atoms are not being replaced and therefore, the older the remains of living things are, the lower the level of radioactivity they show.

This table shows a comparison of the composition of the Earth's crust with that of the human body:

Elements in the Earth's crust (% by mass) Elements in the human body (% by mass)
Oxygen 46.4 Oxygen 65
Silicon 28.0 Carbon 18
Aluminium 8.1 Hydrogen 10
Iron 5.1 Nitrogen 3
Sodium 2.8 Calcium 1.5
Potassium 2.5 Phosphorus 1
Magnesium 2.0 Potassium 0.35
Titanium 0.58 Sulfur 0.25

Note: none of these elements exists freely; all are found chemically combined with other elements in compounds.

Although there are over 100 elements, only 12 or so are used to make biological materials. Living organisms are built predominantly from non-metal elements. However, trace amounts of many metal elements are essential for healthy growth. The most abundant elements in living organisms are:

Element Symbol No. of protons in atom
(atomic number)
No. of electrons in atom Electron arrangement
Carbon C 6 6 2,4
Hydrogen H 1 1 1
Oxygen O 8 8 2,6
Nitrogen N 7 7 2,5
Sulfur S 16 16 2,8,6
Phosphorus P 15 15 2,8,5

Compounds

Elements form compounds. But simply mixing elements together does not make a compound. A chemical reaction is needed.

Atoms of elements combine, but only in certain fixed ratios. The ratios are determined by the combining power of atoms. For example:

  • carbon has a combining power of 4, which means each carbon atom can form 4 bonds
  • hydrogen has a combining power of 1, which means each hydrogen atom can form 1 bond
  • oxygen has a combining power of 2, which means each oxygen atom can form 2 bonds
  • nitrogen has a combining power of 3, which means each nitrogen atom can form 3 bonds

Where does this number come from? The combining power is the number of electrons in an atom that can be used to form chemical bonds. When one atom bonds to another it is these available electrons which are involved, i.e. those in the outermost electron-containing energy level. Their arrangement is always changed by a chemical reaction unlike the electrons in the inner shells. Usually, when atoms react, they achieve a more stable electronic structure.

We use the empirical formula to show the ratio of atoms in a compound. For example:

Compound Molecular formula Empirical formula Ratio of atoms in compound
Carbon dioxide CO2 CO2 1 carbon atom : 2 oxygen atoms
Methane CH4 CH4 1 carbon atom : 4 hydrogen atoms
Sulfuric acid H2SO4 H2SO4 2 hydrogen atoms : 1 sulfur atom: 4 oxygen atoms
Ethane C2H6 CH3 1 carbon atom : 3 hydrogen atoms

The empirical formula is the simplest ratio in which atoms combine to form a compound. The molecular formula tells us how many of each type of atom there are in each molecule of the compound - see below.

Each compound has its own:

  • name and formula (there are different types: empirical formula, molecular formula, structural formula and displayed formula)
  • characteristic physical properties and chemical properties - these can be used to identify a compound.

Atoms are held together in compounds by chemical bonds. However, when atoms bond to one another there is a rearrangement of electrons and the particles present in compounds are no longer atoms. They are ions or molecules.

The compounds that make up living organisms fall into two types:

  • Inorganic compounds, e.g. water (which exists as molecules) and salts (which contain ions such as potassium, calcium and chloride).
  • Organic compounds, e.g. carbohydrates, lipids and proteins, all of which exist as molecules. These may be classified as (a) small biological molecules and (b) large biological molecules and polymers.

Organic compounds can be recognised from their formulae - they all contain the element carbon. The only inorganic compounds that contain carbon are carbon dioxide (CO2), carbon monoxide (CO), salts containing the carbonate ion (CO32-) or the hydrogencarbonate ion (HCO3-) and inorganic carbonyl compounds e.g. Co(CO)6.

Find out more by looking at the sections on:

Mixtures

All the materials we come across in our lives are mixtures. Pure elements or compounds do not exist! Even substances labelled 'pure' contain trace amounts of impurities.

Mixtures contain different compounds (and occasionally elements) mixed together. The substances are not chemically combined and may be separated relatively easily. The characteristics of a mixture are:

  • there is no fixed proportion for the substances present
  • its properties are the same as those of the substances that make it up
  • the substances that make it up can be separated by physical means, e.g. filtration, evaporation and distillation

Living organisms need to be able to separate mixtures. Find out more by looking at the topic:

Chemistry for Biologists logo  In and out of cells

Chemical bonds

Ionic bonding

In the formation of an ionic bond electrons are transferred between atoms, leaving some with fewer electrons and others with more electrons. These are ions. Positively charged ions are called cations and negatively charged ions are called anions.

For example, an electron is transferred from a sodium atom (Na) to a chlorine atom (Cl) to form a sodium ion (Na+) and a chloride ion (Cl-):

Na (2,8,1) and Cl (2,8,7) combine to form Na+ (2,8) and Cl- (2,8,8)

where the numbers in brackets show the electron arrangements in the atoms and ions.

ppt logo  Bonding in sodium chloride

Cations and anions are attracted to one other because of their opposite charges. They are held together in a giant three-dimensional lattice.

NaCl
NaCl - click on image to open

Salts are examples. Like other ionic compounds, many salts are soluble in water. In water, the giant 3-D lattice breaks up into ions which move around relatively freely in solution. Each ion is surrounded by a cluster of water molecules (we say they are hydrated). This can be shown by an equation:

NaCl (s) + aq  -->  Na+ (aq) and Cl- (aq)

where (s) shows a substance is a solid, aq represents water, and (aq) shows an ion is in solution and hydrated.

To understand why this happens you need to know about water. You need to understand the structure of water molecules and bonding, both within a water molecule (polar covalent bonds) and between water molecules (hydrogen bonding).

See the topic on Chemistry for Biologists logo  Water

Hydration is important. It's the diameter of a hydrated ion that determines how quickly the ion passes through a cell membrane.

Covalent bonding

In the formation of a covalent bond electrons are shared between atoms. They are always shared in pairs, so a covalent bond may consist of two, four or six electrons being shared. These are called single, double and triple covalent bonds respectively. It is the mutual attraction of the atoms' nuclei (which are positively charged) for the shared electrons (negatively charged) that hold the bond together.

For example, carbon and hydrogen atoms share electrons to form covalent bonds in methane, CH4.

ppt logo Bonding in methane

Rules about combining power are still obeyed when carbon and hydrogen atoms combine to form ethane, C2H6.

ppt logo Bonding in ethane

Molecules

Clusters of atoms held together by covalent bonds are called molecules. Compounds that exist as molecules are often called molecular compounds. Notice that the formula of ethane is given as C2H6, not CH3 (its empirical formula). C2H6 is the molecular formula of ethane. It shows the actual number of atoms present in the molecule.

But a molecular formula does not show what bonds are present in a molecule. This is done using a structural formula. A simple example to illustrate the idea:

Carbon dioxide is a molecular compound with:

  • Molecular formula CO2
    which shows that one molecule consists of one carbon and two oxygen atoms
  • Structural formula O=C=O
    which shows that four electrons are shared between the carbon atom and each of the oxygen atoms (in other words, two double covalent bonds)

Ethanol is also a molecular compound with:

  • Molecular formula C2H6O
    which shows that one molecule consists of two carbon, six hydrogen and one oxygen atom
  • Structural formula
            Structural formula of ethanol
    which shows that two electrons are shared between the two carbon atoms, two are shared between the carbon and oxygen atoms, two are shared in each carbon-hydrogen bond and in the oxygen-hydrogen bond.

Ethanol
Ethanol - click on image to open

Molecules have three-dimensional shapes. Two atoms held by single covalent bonds are free to rotate relative to one another. This means that molecules can twist, flex and bend. The properties of a molecular compound are determined by:

  • the arrangement of its atoms (which ones are bonded to one another)
  • the strength of the bonding between atoms in a molecule
  • the shape of the molecule (including its ability to adopt different conformations)
  • the bonding between one molecule and another (much weaker than the covalent bonds within a molecule)

Knowledge of structure, bonding and shape is invaluable when it comes to understanding how biological molecules behave.

Molecular models are a really useful tool for 'looking' at molecules. The structure of DNA was derived from a combination of experimental work and model-building. The models used by Crick and Watson were homemade. Nowadays commercial molecular model kits can be bought. But these are being surpassed by software packages that enable 3-D images to be manipulated on screen. You will use molecular modelling throughout much of this guide.

ppt logo The shape of a methane molecule

A reminder about chemical formulae:

  • The simplest ratio in which atoms combine to form a chemical is shown by its empirical formula. For example, ethane's empirical formula is CH3.
  • The number of atoms in a molecule is shown by its molecular formula.
  • The arrangement of its atoms is shown by its structural formula.
  • The arrangement of its atoms in space is shown by its displayed formula.

Some groupings of atoms in a molecule have characteristic reactions no matter what the rest of the molecule looks like. These groupings are called functional groups. Here are some important ones that you will find in biological molecules:

C=C   alkene
-OH   hydroxyl (alcohol)
-COOH   carboxylic acid
-COOR   ester     'R' stands for any alkyl group
-NH2   amine

ppt logo Some important functional groups

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