BIOCHEMISTRY

 

Contents

Water
Carbohydrates
Lipids
Proteins
 

 

At least 80% of the mass of living organisms is water, and almost all the chemical reactions of life take place in aqueous solution. The other chemicals that make up living things are mostly organic macromolecules belonging to the 4 groups proteins, nucleic acids, carbohydrates or lipids. These macromolecules are made up from specific monomers as shown in the table below. Between them these four groups make up 93% of the dry mass of living organisms, the remaining 7% comprising small organic molecules (like vitamins) and inorganic ions.

Group name

monomers

polymers

% dry mass

Proteins

amino acids

polypeptides

50

nucleic acids

nucleotides

polynucleotides

18

carbohydrates

monosaccharides

polysaccharides

15

 

Group name

components

largest unit

% dry mass

lipids

fatty acids + glycerol

Triglycerides

10

The first part of this unit is about each of these groups. We'll look at each of these groups in detail, except nucleic acids, which are studied in module 2.

 

WATER

Water molecules are charged, with the oxygen atom being slightly negative and the hydrogen atoms being slightly positive. These opposite charges attract each other, forming hydrogen bonds. These are weak, long distance bonds that are very common and very important in biology.

Water has a number of important properties essential for life. Many of the properties below are due to the hydrogen bonds in water.

 

CARBOHYDRATES

 

Carbohydrates contain only the elements carbon, hydrogen and oxygen. The group includes monomers, dimers and polymers, as shown in this diagram:

Monosaccharides

All have the formula (CH2O)n, where n is between 3 and 7. The most common & important monosaccharide is glucose, which is a six-carbon sugar. It's formula is C6H12O6 and its structure is shown below

or more simply

Glucose forms a six-sided ring. The six carbon atoms are numbered as shown, so we can refer to individual carbon atoms in the structure. In animals glucose is the main transport sugar in the blood, and its concentration in the blood is carefully controlled. 

There are many monosaccharides, with the same chemical formula (C6H12O6), but different structural formulae. These include fructose and galactose.

Common five-carbon sugars (where n = 5, C5H10O5) include ribose and deoxyribose (found in nucleic acids and ATP).

Disaccharides

Disaccharides are formed when two monosaccharides are joined together by a glycosidic bond. The reaction involves the formation of a molecule of water (H2O):

This shows two glucose molecules joining together to form the disaccharide maltose. Because this bond is between carbon 1 of one molecule and carbon 4 of the other molecule it is called a 1-4 glycosidic bond. This kind of reaction, where water is formed, is called a condensation reaction. The reverse process, when bonds are broken by the addition of water (e.g. in digestion), is called a hydrolysis reaction.

There are three common disaccharides:

Polysaccharides

Polysaccharides are long chains of many monosaccharides joined together by glycosidic bonds. There are three important polysaccharides:

Starch is the plant storage polysaccharide. It is insoluble and forms starch granules inside many plant cells. Being insoluble means starch does not change the water potential of cells, so does not cause the cells to take up water by osmosis (more on osmosis later). It is not a pure substance, but is a mixture of amylose and amylopectin.

Amylose is simply poly-(1-4) glucose, so is a straight chain. In fact the chain is floppy, and it tends to coil up into a helix.
Amylopectin is poly(1-4) glucose with about 4% (1-6) branches. This gives it a more open molecular structure than amylose. Because it has more ends, it can be broken more quickly than amylose by amylase enzymes.

Both amylose and amylopectin are broken down by the enzyme amylase into maltose, though at different rates.

Glycogen is similar in structure to amylopectin. It is poly (1-4) glucose with 9% (1-6) branches. It is made by animals as their storage polysaccharide, and is found mainly in muscle and liver. Because it is so highly branched, it can be mobilised (broken down to glucose for energy) very quickly.

Cellulose is only found in plants, where it is the main component of cell walls. It is poly (1-4) glucose, but with a different isomer of glucose. Cellulose contains beta-glucose, in which the hydroxyl group on carbon 1 sticks up. This means that in a chain alternate glucose molecules are inverted.

This apparently tiny difference makes a huge difference in structure and properties. While the a1-4 glucose polymer in starch coils up to form granules, the beta1-4 glucose polymer in cellulose forms straight chains. Hundreds of these chains are linked together by hydrogen bonds to form cellulose microfibrils. These microfibrils are very strong and rigid, and give strength to plant cells, and therefore to young plants.

The beta-glycosidic bond cannot be broken by amylase, but requires a specific cellulase enzyme. The only organisms that possess a cellulase enzyme are bacteria, so herbivorous animals, like cows and termites whose diet is mainly cellulose, have mutualistic bacteria in their guts so that they can digest cellulose. Humans cannot digest cellulose, and it is referred to as fibre.

Other polysaccharides that you may come across include:

 

 

LIPIDS

 

Lipids are a mixed group of hydrophobic compounds composed of the elements carbon, hydrogen and oxygen. They contain fats and oils (fats are solid at room temperature, whereas oils are liquid)

Triglycerides

Triglycerides are commonly called fats or oils. They are made of glycerol and fatty acids.

Glycerol is a small, 3-carbon molecule with three hydroxyl groups.

Fatty acids are long molecules with a polar, hydrophilic end and a non-polar, hydrophobic "tail". The hydrocarbon chain can be from 14 to 22 CH2 units long. The hydrocarbon chain is sometimes called an R group, so the formula of a fatty acid can be written as R-COOH.

 

 

One molecule of glycerol joins togther with three fatty acid molecules to form a triglyceride molecule, in another condensation polymerisation reaction:

Triglycerides are insoluble in water. They are used for storage, insulation and protection in fatty tissue (or adipose tissue) found under the skin (sub-cutaneous) or surrounding organs. They yield more energy per unit mass than other compounds so are good for energy storage. Carbohydrates can be mobilised more quickly, and glycogen is stored in muscles and liver for immediate energy requirements.

Phospholipids

Phospholipids have a similar structure to triglycerides, but with a phosphate group in place of one fatty acid chain. There may also be other groups attached to the phosphate. Phospholipids have a polar hydrophilic "head" (the negatively-charged phosphate group) and two non-polar hydrophobic "tails" (the fatty acid chains). This mixture of properties is fundamental to biology, for phospholipids are the main components of cell membranes.

  • When mixed with water, phospholipids form droplet spheres with the hydrophilic heads facing the water and the hydrophobic tails facing each other. This is called a micelle.

  • Alternatively, they may form a double-layered phospholipid bilayer. This traps a compartment of water in the middle separated from the external water by the hydrophobic sphere. This naturally-occurring structure is called a liposome, and is similar to a membrane surrounding a cell.

Waxes

Waxes are formed from fatty acids and long-chain alcohols. They are commonly found wherever waterproofing is needed, such as in leaf cuticles, insect exoskeletons, birds' feathers and mammals' fur.

Steroids

Steroids are small hydrophobic molecules found mainly in animals. They include:

 

 

PROTEINS

 

Proteins are the most complex and most diverse group of biological compounds. They have an astonishing range of different functions, as this list shows.

 

Proteins are made of amino acids. Amino acids are made of the five elements C H O N S. The general structure of an amino acid molecule is shown on the right. There is a central carbon atom (called the "alpha carbon"), with four different chemical groups attached to it:

Amino acids are so-called because they have both amino groups and acid groups, which have opposite charges. At neutral pH (found in most living organisms), the groups are ionized as shown above, so there is a positive charge at one end of the molecule and a negative charge at the other end. The overall net charge on the molecule is therefore zero. A molecule like this, with both positive and negative charges is called a zwitterion. The charge on the amino acid changes with pH:

 

low pH (acid)  neutral pH high pH (alkali)

charge = +1  charge = 0 charge = -1

It is these changes in charge with pH that explain the effect of pH on enzymes. A solid, crystallised amino acid has the uncharged structure

however this form never exists in solution, and therefore doesn't exist in living things (although it is the form usually given in textbooks).

There are 20 different R groups, and so 20 different amino acids. Since each R group is slightly different, each amino acid has different properties, and this in turn means that proteins can have a wide range of properties. The following table shows the 20 different R groups, grouped by property, which gives an idea of the range of properties. You do not need to learn these, but it is interesting to see the different structures, and you should be familiar with the amino acid names. You may already have heard of some, such as the food additive monosodium glutamate, which is simply the sodium salt of the amino acid glutamate. Be careful not to confuse the names of amino acids with those of bases in DNA, such as cysteine (amino acid) and cytosine (base), threonine (amino acid) and thymine (base). There are 3-letter and 1-letter abbreviations for each amino acid.

 

The Twenty Amino Acid R-Groups (for interest only no knowledge required)

 

Simple R groups

 

Basic R groups

Glycine

Gly G

Lysine

Lys K

Alanine

Ala A

Arginine

Arg R

Valine

Val V

Histidine

His H

Leucine

Leu L

Asparagine

Asn N

Isoleucine

Ile I

Glutamine

Gln Q

 

Hydroxyl R groups

 

Acidic R groups

Serine

Ser S

Aspartate

Asp D

Threonine

Thr T

Glutamate

Glu E

 

Sulphur R groups

 

Ringed R groups

Cysteine

Cys C

Phenylalanine

Phe F

Methionine

Met M

Tyrosine

Tyr Y

 

Cyclic R group

   

Proline

Pro P

Tryptophan

Trp W

 

Polypeptides

Amino acids are joined together by peptide bonds. The reaction involves the formation of a molecule of water in another condensation polymerisation reaction:

When two amino acids join together a dipeptide is formed. Three amino acids form a tripeptide. Many amino acids form a polypeptide. e.g.:

+NH3-Gly — Pro — His — Leu — Tyr — Ser — Trp — Asp — Lys — Cys-COO-

In a polypeptide there is always one end with a free amino (NH2) (NH3 in solution) group, called the N-terminus, and one end with a free carboxyl (COOH) (COO in solution)  group, called the C-terminus.

Protein Structure

Polypeptides are just a string of amino acids, but they fold up to form the complex and well-defined three-dimensional structure of working proteins. To help to understand protein structure, it is broken down into four levels:

1. Primary Structure

  • This is just the sequence of amino acids in the polypeptide chain, so is not really a structure at all. However, the primary structure does determine the rest of the protein structure. Finding the primary structure of a protein is called protein sequencing, and the first protein to be sequenced was the protein hormone insulin, by the Cambridge biochemist Fredrick Sanger, for which work he got the Nobel prize in 1958.
  • 2. Secondary Structure

  • This is the most basic level of protein folding, and consists of a few basic motifs that are found in all proteins. The secondary structure is held together by hydrogen bonds between the carboxyl groups and the amino groups in the polypeptide backbone. The two secondary structures are the a-helix and the b-sheet.
  • The a-helix. The polypeptide chain is wound round to form a helix. It is held together by hydrogen bonds running parallel with the long helical axis. There are so many hydrogen bonds that this is a very stable and strong structure. Helices are common structures throughout biology.

    The b-sheet. The polypeptide chain zig-zags back and forward forming a sheet. Once again it is held together by hydrogen bonds.

    3. Tertiary Structure

  • This is the 3 dimensional structure formed by the folding up of a whole polypeptide chain. Every protein has a unique tertiary structure, which is responsible for its properties and function. For example the shape of the active site in an enzyme is due to its tertiary structure. The tertiary structure is held together by bonds between the R groups of the amino acids in the protein, and so depends on what the sequence of amino acids is. There are three kinds of bonds involved:
  • 4. Quaternary Structure

  • This structure is found only in proteins containing more than one polypeptide chain, and simply means how the different polypeptide chains are arranged together. The individual polypeptide chains are usually globular, but can arrange themselves into a variety of quaternary shapes. e.g.:
  • Haemoglobin, the oxygen-carrying protein in red blood cells, consists of four globular subunits arranged in a tetrahedral (pyramid) structure. Each subunit contains one iron atom and can bind one molecule of oxygen.

    These four structures are not real stages in the formation of a protein, but are simply a convenient classification that scientists invented to help them to understand proteins. In fact proteins fold into all these structures at the same time, as they are synthesised.

    The final three-dimensional shape of a protein can be classified as globular or fibrous.

    globular structure

    fibrous (or filamentous) structure

    The vast majority of proteins are globular, including enzymes, membrane proteins, receptors, storage proteins, etc. Fibrous proteins look like ropes and tend to have structural roles such as collagen (bone), keratin (hair), tubulin (cytoskeleton) and actin (muscle). They are usually composed of many polypeptide chains. A few proteins have both structures: the muscle protein myosin has a long fibrous tail and a globular head, which acts as an enzyme.

    This diagram shows a molecule of the enzyme dihydrofolate reductase, which comprises a single polypeptide chain. It has a globular shape

    This diagram shows part of a molecule of collagen, which is found in bone and cartilage. It has a unique, very strong triple-helix structure. It is a fibrous protein

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