1. Biological Molecules Water, Carbohydrates and Lipids
AS Revision Session 12th March

2. Building Blocks Molecules are made of atoms
Atoms are made of protons, neutrons and electrons
Different types of atoms are called elements
All living things are made primarily by four elements;
Carbon (C), hydrogen (H), oxygen (O) and nitrogen (N)
Other important elements include; phosphorus (P), sulphur (S), sodium (Na), potassium (K), calcium (Ca) and iron (Fe)
Molecules are built from small components called atoms which are built from smaller components known as protons, neutrons and electrons which I hope you are all familiar with.
Different types of atoms are called elements. Elements are distinguished by the number of protons in their atomic nuclei. There are hundreds of elements known in the universe but only a small percentage are present in the living world.
Just like we think of bricks which can be interlocked to build something, all living things are made primarily by four elements; carbon (C), hydrogen (H), oxygen (O) and nitrogen (N). In addition, phosphorus (P) and sulphur (S) also have important roles in the biochemistry of cells. These six are the most abundant elements present in biological molecules.
Other elements; sodium (Na), potassium (K), calcium (Ca) and iron (Fe) also have important roles which will be covered later in this chapter.
This chapter is all about underpinning basic biochemistry and you will need to understand some essential chemistry concepts and rules which we will cover over the course of this week and the next.

3. Bonding
Atoms connect with both atoms of the same element and atoms of different elements by forming bonds to form a molecule
A covalent bond forms when two atoms share unpaired electrons present in the outer orbitals of the atoms
Atoms must follow the ‘bonding rules’
Carbon atoms can form four bonds with other atoms
Nitrogen atoms can form three bonds with other atoms
Oxygen atoms can form two bonds with other atoms
Hydrogen atoms can only form one bond with another atom
Atoms connect with each other by forming bonds. Atoms can bond to other atoms of the same element or atoms of different elements and when two or more atoms bond together, this complex is called a molecule.
A covalent bond forms when two atoms share a pair of electrons. The electrons used to form bonds are unpaired and present in the outer orbitals of the atoms.
When bonding, atoms must follow the bonding rules which are determined by the number of unpaired electrons present in the outer orbitals of different elements.
Carbon atoms can form four bonds with other atoms
Nitrogen atoms can form three bonds with other atoms
Oxygen atoms can form two bonds with other atoms
Hydrogen atoms can only form one bond with another atom
The number of bonds formed by these elements can be no more or less than stated although there are exceptions to this rule which will be covered in later sections. Carbon forms the backbone of most biological molecules.

4. Examples of Covalent Bonding

5. Ions
An atom or molecule in which the total number of electrons is not equal to the total number of protons is called an
If an atom or molecule loses one or more electrons it has a net positive charge and is known as a
If an atom or molecule gains electrons, it has a net negative charge and is known as an
In ionic bonds, one atom in the pair donates an electron and the other receives it. This forms positive and negative ions that are held together by the attraction of the opposite charges.
ion
cation
anion
An atom or molecule in which the total number of electrons is not equal to the total number of protons is called an ion. If an atom or molecule loses one or more electrons it has a net positive charge and is known as a cation. If an atom or molecule gains electrons, it has a net negative charge and is known as an anion.
In ionic bonds, one atom in the pair donates an electron and the other receives it. This forms positive and negative ions that are held together by the attraction of the opposite charges.
Ions in solutions are called electrolytes.

6. Roles of Ions
I wont go through this just for the sake of time but I have included the roles of ions in living organisms as you do not need to be aware of these.

7. Water
Not always an equal share of negative electrons in covalent bonding, sometimes electrons spend more time closer to one atom
This causes the atom with the greater share of negative electrons to be slightly negative (ẟ¯) compared with the other atom in the bond, which will therefore be slightly positive (ẟ⁺)
This creates polar molecules
For example; oxygen has a greater share than hydrogen in an O-H bond
Water is a polar molecule, containing two hydroxyl (OH) groups
As we know, in ionic bonding, atoms give or receive electrons to form ions whereas in covalent bonding, atoms share electrons. However, the negative electrons are not always shared equally by the atoms of different elements. In many covalent bonds, the electrons will spend more time closer to one of the atoms than to the other. The atom with the greater share of negative electrons will be slightly negative (ẟ¯) compared with the other atom in the bond, which will therefore be slightly positive (ẟ⁺). Molecules in which this happens are said to be polar- having regions of negativity and positivity.
Oxygen and hydrogen are examples of elements that do not share electrons equally in a covalent bond. Oxygen always has a greater share of electrons in an O-H bond. Many organic molecules contain oxygen and hydrogen bonded together in hydroxyl (OH) groups and so are slightly polar. Water (H₂O) is an example and in fact contains two hydroxyl groups.

8. Hydrogen Bonding in Water
Positive and negative regions of a water molecule attract each other and form hydrogen bonds
These are weak interactions which break and reform
Polar molecules such as water interact with each other as the positive and negative regions of the molecule attract each other and form bonds known as hydrogen bonds. These are relatively weak interactions which break and reform between the constantly moving water molecules. Though weak, these bonds occur in high numbers.
First diagram shows covalent bond between oxygen and hydrogen, unequal sharing of electrons leads to oxygen being more negative compared with hydrogen.
Second diagram shows that the polar covalent bonds make water a polar molecule.
Third diagram shows hydrogen bonding between different polar water molecules due to attraction between the slightly positive hydrogen and the slightly negative oxygen.

9. Characteristics of Water
Unusually high boiling point
Small molecule, lighter than CO₂ or O₂ yet is liquid at room temp
When water freezes it turns to ice, it becomes less dense as a solid - hydrogen bonds fix the positions of the polar molecules slightly further apart than the average distance in the liquid state which produces a giant, rigid but open structure which is able to float.
Water has cohesive properties - moves as one mass as molecules are attracted to each other
Water also has adhesive properties – water molecules attracted to other materials
Characteristics of water all determined by hydrogen bonding
Water has an unusually high boiling point
Small molecule, lighter than gases carbon dioxide or oxygen, yet is liquid at room temp – this is due to the hydrogen bonding between water molecules, takes a lot of energy to increase the temp of water and cause water to become gaseous (evaporate)
When water freezes it turns to ice, it becomes less dense as opposed to most substances which are more dense in their solid state than liquid. This is because when cooled below 4 degrees, hydrogen bonds form fix the positions of the polar molecules slightly further apart than the average distance in the liquid state which produces a giant, rigid but open structure. What you find is that oxygen is at the centre of this tetrahedral arrangement resulting in a solid that is less dense than liquid water and hence ice floats.
Water therefore has cohesive properties- moves as one mass as molecules are attracted to each other – drinking water through a straw, water uptake through plant roots
Water also has adhesive properties – water molecules attracted to other materials e.g. washing your hands the water doesn’t run straight off

10. Roles of Water
Acts as a solvent in which many of the solutes in an organism can be dissolved
Efficient transport medium due to its cohesive and adhesive properties meaning things stick to it and it can exhibit capillary action
Acts as a coolant, helping to buffer temp changes during chemical reactions – important as enzymes often only active in narrow temperature ranges.
Roles of water in living organisms- wont go through this
Due to it being a polar molecule, water acts as a solvent in which many of the solutes in an organism can be dissolved.
Water makes an efficient transport medium within living things this is due to its cohesive and adhesive properties meaning things stick to it and it can exhibit capillary action.
Water acts as a coolant, helping to buffer temp changes during chemical reactions – important as enzymes often only active in narrow temperature ranges.