AQA(B) AS Module 1: Core Principles

Contents

 

Biological Molecules Water
  Carbohydrates
  Lipids
  Proteins
  Enzymes
Cells Eukaryotic Cells
  Prokaryotic Cells
  Cell membrane
  Movement across Cell Membranes
  From Cells to Organisms
Physiology Gas Exchange in Humans
  Gas Exchange in Fish
  Gas Exchange in Plants
  Digestion in Humans
  Digestion in Fungi
Techniques Biochemical Tests
  Chromatography
  Cell Fractionation
  Enzyme Kinetics
  Microscopy

 

These notes may be used freely by A level biology students and teachers, and they may be copied and edited. I would be interested to hear of any comments and corrections.

Neil C Millar (nmillar@cwcom.net) 14/6/00

Biological Molecules

Life on Earth evolved in the water, and all life still depends on water. 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 four 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 (d-) and the hydrogen atoms being slightly positive (d+). 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 = 3-7. The most common & important monosaccharide is glucose, which is a six-carbon or hexose sugar, so it's formula is C6H12O6. Its structure is:

or more simply

Glucose forms a six-sided ring, although in three-dimensions it forms a structure that looks a bit like a chair. 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 isomers of glucose, with the same chemical formula (C6H12O6), but different structural formulae. These isomers include fructose and galactose.

Common five-carbon, or pentose sugars (where n = 5, C5H10O5) include ribose and deoxyribose (found in nucleic acids and ATP) and ribulose (which occurs in photosynthesis).

Disaccharides

Disaccharides are formed when two monosaccharides are joined togther 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. Bonds between other carbon atoms are possible, leading to different shapes, and branched chains.

This kind of reaction, where H2O 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.

In general:
  •  
  • polymerisation reactions are condensations
  •  
  • breakdown reactions are hydrolyses

There are three common disaccharides:

Polysaccharides

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

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.

  • 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 b1-4 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 and also to materials such as paper, cotton and sellotape.

    The b-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.

    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 alcohol 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, but it is always an even number because of the way fatty acids are made. The hydrocarbon chain is sometimes called an R group, so the formula of a fatty acid can be written as R-COO-.

    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 facting the water and the hydrophobic tails facing eachother. 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:

    Terpenes

    Terpenes are small hydrophobic molecules found mainly in plants. They include vitamin A, carotene and plant oils such as geraniol, camphor and menthol.

     

    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.

    structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle)

    enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others)

    transport e.g. haemoglobin (oxygen), transferrin (iron)

    pumps e.g. Na+K+ pump in cell membranes

    motors e.g. myosin (muscle), kinesin (cilia)

    hormones e.g. insulin, glucagon

    receptors e.g. rhodopsin (light receptor in retina)

    antibodies e.g. immunoglobulins

    storage e.g. albumins in eggs and blood, caesin in milk

    blood clotting e.g. thrombin, fibrin

    lubrication e.g. glycoproteins in synovial fluid

    toxins e.g. diphtheria toxin

    antifreeze e.g. glycoproteins in arctic flea

    and many more!

    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 ionised 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, but 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

     

    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