Category Archives: a level biology

Transcription Factors

Intracellular proteins that bind to specific regions of DNA to control transcription are known as transcription factors. Examples include:

  • PIF and DELLA proteins
  • Proteins coded by the regulatory genes of the lac operon
  • cAMP and the second messenger model
  • Products of proto-oncogenes and tumour suppressor genes

Gibberellin and DELLA proteins

DELLA proteins inhibit transcription by binding to a molecule known as PIF. This prevents PIF from transcribing DNA into mRNA. However, DELLA is broken down when the plant hormone gibberellin is present. The PIF is now free to join to the promoter on the DNA and start transcribing it into mRNA, which can then be translated by a ribosome.

In the case of wheat and barley seed germination, amylase is synthesised when the gibberellins destroy the DELLA proteins. This allows the starch in the endosperm of the seed to be broken down to provide a source of carbohydrate for respiration. E.g. the gibberellins turn on the gene for amylase production by destroying the DELLA proteins.

Glossary:

  • DELLA: proteins that inhibit the binding of transcription factors. Regulate amylase production in barley and wheat seeds.
  • Endosperm: tissue that provides a source of energy for the developing embryo of a seed.
  • Gibberellins: plant hormone that is involved in growth, germination and flowering.
  • Intracellular: within a cell, as opposed to extracellular meaning between cells.
  • lac operon: length of DNA found in E. coli that controls the expression of proteins involved in taking up and digesting lactose.
  • PIF: phtochrome-interacting protein, a transcription factor.
  • Proto-oncogenes and tumour suppressor genes: genes involved in the regulation of the cell cycle, growth and programmed cell death (apoptosis).
  • Second messenger model: a process involving intracellular signalling molecules, such as cyclic AMP, that are triggered by extracellular messengers, such as oestrogen.
  • Transcription: the production of mRNA from DNA.
  • Transcription factors: proteins that control the flow of information from DNA to RNA by controlling the formation of mRNA.
  • Translation: the production of a polypeptide by a ribosome from mRNA.

Biological Molecules: Lipids

There are two types of lipid of interest to an A level biologist: triglycerides and phospholipids. Both play important roles in living organisms.

Triglycerides

These are characterised by a glycerol molecule with three fatty acid ‘tails’. The bond between the glycerol and fatty acid is known as an ester bond and is formed by a condensation reaction where water is produced. Hydrolysis is the reverse process and used to digest triglycerides. This is very similar to condensation and hydrolysis of carbohydrates. The actual structural formula of a triglyceride is shown below, with the glycerol molecule on the left. Note that the ester bonds are shown in a dark red colour. The top two fatty acids are said to be saturated as there are no double nods between the carbon atoms. Whereas the third fatty acid is unsaturated, due to the presence of a carbon-carbon double bond.

The formation of one triglyceride leads to three water molecules being produced, as there will be a condensation reaction between each fatty acid and the glycerol molecule. This is modelled in the diagram below:

triglyceride-formation

Triglycerides have several useful functions in organisms:

  • Energy reserve
  • Insulator
  • Buoyancy
  • Source of metabolic water

Phospholipids

Similarly to triglycerides, phospholipids are made of a glycerol molecule. They also have fatty acids, but only two with a phosphate group instead of the third. We describe the phosphate and glycerol as being the ‘head’ of the molecule, with the two fatty acids called ‘tails’. Ester bonds connect the glycerol to the phosphate and fatty acids.

As mentioned in the labels above, the head is polar and so hydrophilic, and the tail is hydrophobic. This causes phopholipids to arrange themselves as a bilayer when in water, allowing the heads to be in contact with water and the tails to be tucked away from the water. See diagram below modelling how a cell might form in water, with the phopholipids arranging themselves into a cell membrane. We will come back to phopholipids in the post about cell membranes.

Glossary

  • Condensation: a chemical reaction involving the joining together of two molecules by removal of a water molecule.
  • Ester bond: the chemical link, -COO-, between the carboxyl group (-COOH) of the fatty acid and hydroxyl group (-OH) of the glycerol.
  • Fatty acid: contain a carboxyl group (-COOH) with a long hydrocarbon tail, often 15-17 carbons long.
  • Glycerol: an alcohol with three hydroxyl groups (-OH)
  • Hydrophilic: water-loving.
  • Hydrolysis: a reaction in which a complex molecule is broken down to simpler ones, involving the addition of water.
  • Hydrophobic: water-hating.
  • Phospholipid: made up of a glycerol molecule, two fatty acids and a phosphate group. Forms the basic structure of all cell membranes.
  • Saturated fatty acid: a fatty acid with no carbon-carbon double bonds (C=C) in its hydrocarbon tail.
  • Triglyceride:
  • Unsaturated fatty acid: a fatty acid with at least one C=C (they are unsaturated because they do not contain the maximum possible amount of hydrogen atoms). Can be monounsaturated with just one C=C, or polyunsaturated with two or more C=C.

 

 

Biological Molecules: Carbohydrates

Carbohydrates are excellent examples of monomers and polymers. Their one unit monomers are known as monosaccharides. Some examples of monosaccharides include:

  • α-glucose
  • β-glucose
  • Galactose
  • Fructose

α-glucose and β-glucose are an example of a structural isomer, both have the same chemical formula, C6H12O6 but the atoms are arranged slightly differently.

alpha-glucose

alpha glucose

The diagram to the left shows the structural arrangement of atoms in α-glucose. Although not shown on the diagram, at each corner of the hexagon between the -H and -OH (or hydroxyl group) there is a carbon atom. These have been labelled clockwise as carbon number 1, carbon number 2 and so on. The only difference between α-glucose and β-glucose is the position of the -OH on carbon number 1. In α-glucose the hydroxyl group is below the plane of the ring, e.g. the H is above it. Whereas in β-glucose, the hydroxyl group is above the plane of the ring, e.g. the H is below it. One way of remembering this is by invoking the Swedish super group ABBA. Alpha (the -OH is) Below (carbon 1), Beta (the -OH is) Above (carbon 1). Hence ABBA, alpha below, beta above. The diagram below summarise this information.

alpha-v-beta-glucose

Disaccharides are made of two monosaccharides joined by a glycosidic bond. Three common disaccharides are shown below, along with the mononsaccharides that make them up.

  • Maltose, made from two α-glucose molecules
  • Sucrose, made from one α-glucose and one fructose molecule
  • Lactose, made from one α-glucose and one galactose molecule

During the reaction between two monosacchrides that results in a disaccharide, water is formed. Therefore we call it a condensation reaction. The process of making maltose is outlined in the diagram below:

condensation

The highlighted -H and -OH groups form the water and leave a -O- that joins the two monosaccharides, which is the glycosidic bond. The glycosidic bond’s precise position is between carbon number 1 on the left hand moecule and carbon number 4 on the right hand molecule, making a 1-4 glycosidic bond. The opposite of this process, e.g. splitting a disaccharide into two monosaccharides with the addition of water, is called hydrolysis.

In terms of a balanced chemical equation for condensation we show the following, note that the disaccharide has two fewer hydrogens and one fewer oxygen, which have formed the water.

C6H12O6 + C6H12O6 → C12H22O11 + H2O

Polysaccharides are carbohydrates with three or more monosaccharides joined together with glycosidic bonds. They are formed by condensation reactions and can be broken down by hydrolysis. Three common polysaccharides are:

Glycogen, a storage molecule found in animals made from α-glucose. Its highly branched and compact shape make it very well suited to this function. The diagram to the right represents this structure, with each circle representing α-glucose.

Starch, a storage molecule found in animals made from α-glucose. It is made up of linear chains of amylose and branched amylopectin chains. Starch is insoluble, meaning that it does not effect the water potential of the cells it is stored in, so does not effect osmosis.

Cellulose, a structural carbohydrate that makes up plant cells’ cell wall made from β-glucose. It forms straight chains that come together as microfibrils to support the cell.

If you would like to know more about how these polysaccharides form and where the glycosidic bonds are located see appendix (i).

We can test for the presence of reducing sugars (e.g. glucose), non-reducing sugars (e.g. sucrose) and starch with the following tests:

  • Test for reducing sugars – add sample to blue Benedict’s solution and heat above 80ºC / boil.  If reducing sugars are present, a red precipitate forms. Small amounts result in a green colour, going through yellow to orange to brick red.
  • Test for non-reducing sugars – first carry out the test for reducing sugars, but you will get a negative result (the Benedict’s solution remains blue). Then add dilute hyrdochloric acid to some of the original sample . Repeat the test for reducing sugars and you should get a positive result, e.g. it turn red.
  • Test for starch – add iodine solution to your sample. It should change colour from orange/brown to black/blue.

Glossary

  • Cellulose: polysaccharide that forms the cell wall in plants, made of β-glucose.
  • Condensation reaction: a chemical reaction involving the joining together of two molecules by removal of a water molecule.
  • Disaccharide: a sugar molecule consisting of two monosaccharides joined together by a glycosidic bond.
  • Glucose: a monosachharide that has two isomers, α-glucose and β-glucose.
  • Glycogen: a polysaccharide made of many glucose molecules linked together, that acts as a glucose store in liver and muscle cells.
  • Glycosidic bond: a C-O-C link between two monosaccharide molecules, formed by a condenstaion reaction.
  • Hyrdolysis: a reaction in which a complex molecule is broken down to simpler ones, involving the addition of water.
  • Hydroxyl group: a pair of atoms (O and H) found in carbohydrates and other molecules.
  • Monosaccharide: a molecule consisting of a single sugar unit with the general formula (CH2O)n.
  • Polysaccharide: a polymer whose subunits are monosaccharides joined together by glycosidic bonds.
  • Starch: polysaccharide found in most green plants as an energy store, formed from chains of amylose and amylopectin.

Appendix (i)

The formation of polysaccharides.

Cellulose forms 1-4 glycosidic bonds to make an unbranched chain, see below:

cellulose

Glycogen forms a mixture of 1-4 and 1-6 glycosidic bonds, hence the branching:

glycogen

The amylose in starch forms 1-4 glycosidic bonds, so is unbranched. However, the amylopectin branches are caused by 1-6 glycosidic bonds:

starch