1.

2 - Biological molecules
1.2.1 - monosaccharides and disaccharides
What are organic compounds
- Biological compounds
- All contain carbon atoms, hydrogen, oxygen, and less frequently, nitrogen, phosphorus and sulfur
- Each carbon atom makes four bonds, so can bond with four other atoms
- Four bonds usually form a tetrahedral shape, usually leading to any 3D structure
Carbohydrates
- Used for storing energy, and an important part in the cell wall
- Starch, sucrose and glucose
- Monosaccharides, disaccharides and polysaccharides
Monosaccharides - simple sugars
- One oxygen atom and two hydrogen atoms for each carbon atom
- (CH2O)n - n can be any number
- Triose sugars, n=3, they are important in the mitochondria where glucose is broken down to triose
sugars in respiration
- Pentose sugars, n=5,ribose and deoxyribose,i.e. Deoxyribonucleic acid (DNA), ribonucleic acid (RNA)
- Hexose sugars, n=6, glucose, galactose and
fructose

Disaccharides
- Made of two monosaccharides joined together, in a condensation reaction, a molecule of water is
removed
- This results in a covalent bond between the monosaccharides known as a glycosidic bond
- E.g. sucrose is formed by the joining of alpha glucose and fructose, lactose is alpha glucose and beta
galactose, maltose is two alpha glucose
1.2.2 - carbohydrates - polysaccharides
Polysaccharides
- Many monosaccharides joined by glycosidic bonds
- 3-10 molecules = oligosaccharides
- Very compact so large numbers can be stored
- Glycosidic bonds are easily broken so quick release of monosaccharides for respiration
- Not very soluble in water so have little effect on water potential and cause no osmotic movements
- Glycosidic bonds is split by hydrolysis, it is the opposite of a condensation reaction, water is added to
the bond
Starch
- Energy store in plants, sugars produced in photosynthesis converted to starch
- Long chains of alpha glucose
- Mixture of amylose(unbranched polymer, spirals as it lengthens) and amylopectin(branched polymer)
- Amylose is purely alpha glucose molecules joined by 1-4 glycosidic bonds, which is why the molecules
are long and unbranched
- Amylopectin also has 1-4 glycosidic bonds but there are a few 1-6 g;ycosidic bonds, making it branched
- Amylopectin releases glucose for respiration rapidly
Glycogen
- The only carbohydrate energy store found in animals
- Made of many alpha glucose units, like amylopectin but has more 1-6 glycosidic bonds
- As a result it can be broken down rapidly due to the many branches
Carbohydrates in plants
- Typical starch grain in plants contains 70-80% amylopectin and the rest is amylose
 - Cellulose is an important structural material, made of long chains of alpha glucose joined by 1-4
glycosidic bonds, one of the monomers has to be inverted so the bonding can take place
- OH groups stick out on both sides so hydrogen bonds can form between the partially positive charged
hydrogen atoms of the hydroxyl groups and the partially negative charged oxygen atoms (cross linking)
- They do not coil and remain in very straight
lines
- Most animals do not possess the enzymes
required to digest cellulose (bacteria, fungi and
protozoa)

1.2.3 - Lipids
Fats and oils
- Fats are solids at room temperature and oils are liquid
- Have a lower proportion of oxygen than carbohydrates
- Made of fatty acids(carboxyl group, long hydrocarbon chain and pleated backbone of carbon atoms with
hydrogen atoms attached) and glycerol(C3H8O3) combined with ester bonds
- Fatty acid may be saturated or unsaturated and the length of the carbon chain can differ
- Saturates have no double covalent bonds, unsaturated have one (monounsaturated) or more
(polyunsaturated) double covalent bonds
Forming ester bonds
- Fats and oils form when glycerol combines with one, two or three fatty acids
- Condensation reaction between the carboxyl group of a fatty acid and one of the hydroxyl groups of the
glycerol
- A molecule of water is removed, resulting in an ester bond (esterification)
The nature of lipids
- Many carbon-hydrogen bonds and little oxygen
- When they are oxidised, carbon dioxide and water are the ultimate products, can drive the production of
a lot of ATP
- Hydrophobic nature is a key feature in their role of waterproofing
- They have a very low density
- Dissolve in organic solvents but insoluble in water
Phospholipids
- Inorganic phosphate ions are present in the cytoplasm of every cell, sometimes one of the hydroxyl
groups of glycerol undergoes an esterification reaction with a phosphate group instead of a fatty acid
and a phospholipid is formed
- Fatty acid chains are neutral and insoluble in water, the phosphate head carries a small negative charge
and is soluble in water
- Polar phosphate is hydrophilic and dissolves readily in water, the lipid tails are hydrophobic and do not
dissolve in water
- Molecules either form a monolayer, hydrophilic heads in the water or clusters called micelles, with the
hydrophilic heads pointing outwards
- Monolayer may form between the air and the water but tis is rare, where there are water-based
solutions on either side of the membranes, this may form a bilayer with the hydrophilic heads protecting
the hydrophobic tails
- This is the basis of all membranes
1.2.4 - Proteins
Amino acids
- Amino group (NH2) and a carboxyl group (COOH) attached to a carbon atom
- The R group varies between amino acids, the structure of this affects the way the amino acid bonds with
others in the protein, depending on weather the R group is polar
Forming proteins from amino acids
- Amino acids join by a condensation reaction between
the amino group of one amino acid and the carboxyl
group of another where a water molecule is lost
- Peptide bond is formed and a result is a dipeptide
- More amino acids join and form a polypeptide chain

Bonds in proteins
- Strong peptide bond between amino acids
- Other bonds depending on the R group form to make the 3D structure, hydrogen, disulfide and ionic
bonds
Hydrogen bonds
- Tiny negative charges are present on the oxygen of the carboxyl groups and tiny positive charges are
present on the hydrogen atoms of the amino groups
- Form when the opposite charges attract, they are weak but lots of them together have a firm hold
- Very important in folding and coiling of polypeptide chains
Disulfide bonds
- When two cysteine molecules are close together in the structure of a polypeptide
- Oxidation reaction between two sulfur containing groups, resulting in strong covalent bonds
Ionic bonds
- Between some strongly positive and strongly negative amino acid side chains found deep in protein
molecules, links known as salt bridges
- Strong bonds but not as common ad others
Primary protein structure
- Sequence of amino acids making up a polypeptide chain held together by peptide bonds
Secondary protein structure
- Arrangement of the polypeptide chain into a regular, repeating structure held together by hydrogen
bonds
- Alpha helix coil - peptide bonds form on the backbone and R groups stick out in all directions
- beta pleated sheet - polypeptide chain folds into regular pleats held together by hydrogen bonds
between the amino and carboxyl ends
- Sometimes the polypeptide forms a random coil
Tertiary structure
- 3D organisation imposed on top of the secondary structure of many proteins
- Amino acid chain is folded further into more complicated shapes
- Hydrogen, ionic and disulfide bonds hold the shape in place
- E.g. globular proteins
Quaternary structure
- Only seen when a protein contains many polypeptide chains
- Is is the way that these separate polypeptide chains fit together in 3D
- Bonds holding 3D structures together are affected by temperature and pH
Fibrous proteins
- Little or no tertiary structure
- Long, parallel polypeptide chains with occasional cross linkages that form into fibres
- Insoluble in water and very tough
- Collagen is a fibrous protein giving strength to tendons, ligaments, bones and skin

Primary structure is repeating sequence of glycine with two other amino acids, the three 𝛂-chains are
- It is extremely strong, it is made of 3 polypeptide chains, each up to 1000 amino acids long
-
arranged in triple helix with many hydrogen bonds
Globular proteins
- Complex tertiary and sometimes quaternary structure forming a large spherical shape
- Instead of dissolving in water, they form a colloid
- They are important for your immune system and holding molecules in the cytoplasm
- Haemoglobin is a globular protein made of 574 amino acids arranged in four polypeptide chains held
together by disulfide bonds
- Each chain is held together by an iron containing haem group
Conjugated proteins
- Some proteins are joined to or conjugated to another molecule called a prosthetic group
- Chlorine and haemoglobin are both conjugated proteins
- Glycoproteins have a carbohydrate prosthetic group, helping them hold lots of water and not get broken
down
- Lipoproteins are conjugated with lipids and are important with transporting cholesterol in the blood
- Low density and high density lipoproteins