Structure of a nucleotide
This consists of a nitrogenous base (uracil, adenine, cytosine, guanine and thymine) , a phosphate, and a pentose sugar.
Structure of RNA
- Polymer made up of nucleotides.
- Single, relatively short polynucleotide chain in which the pentose sugar is always ribose
- Organic bases are Uracil, adenine, guanine and cytosine
- One type transfers genetic info from DNA to the ribosomes (mRNA)
- Ribosomes are made up of proteins and another type of RNA (rRNA)
- A third type is involved in protein synthesis (tRNA)
- Pentose sugar is always deoxyribose
- Organic bases are adenine, guanine, cytosine and thymine
- Two strands of polynucleotides joined together by hydrogen bonds between complementary base pairs
- Phosphate and deoxyribose molecules alternate to form the uprights and the organic bases pair together to form the rungs
- Adenine always pairs with Thymine so their quantities are the same
- Cytosine always pairs with Guanine so their quantities are the same
- The molecule is a double helix as the phosphate and deoxyribose wind around one another
- Adenine and guanine are purine
- Cytosine and thymine are pyrimidine
- C-G hydrogen bonds always increase the strength of the molecule
The Stability of DNA
- The phosphodiester backbone protects the more chemically reactive organic bases inside the double helix
- Hydrogen bonds link the organic base pairs forming bridges between the phosphodiester uprights. As there are 3 hydrogen bonds between C-G, the higher the proportion of C-G pairings, the more stable the molecule
Adaptation of DNA for its functions
Functions of DNA
- Long term storage of genetic information
- Encodes for the amino acid sequence of proteins using the genetic code
- Allows cells to replicate for purposes such as making new skin cells
- Very stable structure therefore it rarely mutates when it passes from generation to generation- it does so without change
- Its strands are joined by hydrogen bonds which allow them to separate during DNA replication and protein synthesis
- Extremely large molecule and therefore carries an immense amount of genetic information
- Has base pairs within the helical cylinder of the deoxyribose-phosphate backbone so most of the genetic information is protected from being corrupted by outside chemical and physical forces
- Base pairing leads to DNA being able to replicate and to transfer information as mRNA
The carbon atoms in the pentose molecule are labelled.
The 5' carbon has an attached phosphate group and the 3' carbon has an attached hydroxyl group. When nucleotides are organised into the double strands of a DNA molecule, one strand runs in the 5' to 3' direction, whilst the other runs in the 3' to 5' direction. They are anti-parallel. This is because nucleic acids can only be synthesised in the 5' to 3' direction because the enzyme DNA polymerase can only attach nucleotides to the hydroxyl group on the 3' carbon atom.
Requirements of semi-conservative replication
- The four types of nucleotide with bases A,T,C,G must be present
- Both strands of DNA must act as a template for the attachment of nucleotides
- The enzyme DNA polymerase
- A source of chemical energy to drive the process
The semi-conservative process of DNA replication
1) The enzyme DNA helicase breaks the hydrogen bonds linking the complementary bases together causing the two strands of DNA to separate
2) Each exposed polynucleotide strand acts as a template to which complementary free nucleotides that have been activated bind specifically to their complementary bases
3) Nucleotides are joined together in condensation reactions by the enzyme DNA polymerase to form the 'missing' polynucleotide strand on each of the two original polynucleotide strands.
4) The remaning unpaired bases continue to attract their complementary nucleotides
5) Two identical molecules of DNA are formed, each with one of the original strand and one strand of new DNA molecules, so half the original DNA has been saved.
Evidence of the semi-conservative model
Bacteria were grown in a medium containing isotopes of nitrogen. Those grown in 14N would have lighter DNA than those grown in 15N. The mass of each new DNA molecule would depend on the method by which replication has taken place.
The scientists based their work on 3 facts:
- All bases in DNA contain nitrogen
- Bacteria will incorporate nitrogen from their growing medium into any new DNA that they make
- Nitrogen has two forms: 14N, which is lighter and 15N, which is heavier
Energy- what is it? Why is it important?
Energy is the ability to do work. It is important because all living organisms need it to remain alive. It initially comes from the Sun- plants use solar energy during photosynthesis. Both plant and animal cells need energy for processes such as growth, repair, reproduction, movement etc. This is stored in the form of ATP.
The structure of ATP
It is a phosphorylated macromolecule with 3 parts:
- Adenine- nitrogenous organic base
- Ribose (pentose sugar) which acts as a backbone to which other parts are attached
- Phosphates- a chain of three phosphate groups
How ATP stores energy?
The bonds between phosphate groups are unstable and so have low activation energy, which means they are easily broken. When they do break, they release a considerable amount of energy. It is usually the terminal phosphate that it removed in living cells.
This is a hydrolysis reaction as water is used to break the bonds. ATP hydrolase (ATPase) is the enzyme that catalyses the reaction.
ATP + H2O -----------------> ADP + Pi (inorganic phosphate) + E (energy)
How ATP is synthesised
The conversion of ATP to ADP is reversible and so energy can be used to add an inorganic phosphate to ADP to re-form ATP. The reaction is catalysed by ATP synthase. Water is removed in the process therefore it is a condensation reaction.
This occurs in 3 ways:
1) Photophosphorylation in chlorophyll-containing plant cells during photosynthesis
2) Oxidative phosphorylation in plant and animal cells during respiration
3) Substrate-level phosphorylation in plant and animal cells when phosphate groups are transferred from donor molecules to ADP, e.g in the mitochondrial matrix
Roles of ATP in biological processes
- METABOLIC PROCESSES: ATP provides the energy needed to build up macromolecules from their basic units. For example, making starch from glucose or polypeptides from amino acids.
- MOVEMENT: ATP provides the energy for muscle contraction- it allows filaments of muscle to slide past one another and therefore shorten the overall length of a muscle fibre.
- ACTIVE TRANSPORT: ATP provides the energy to change the shape of carrier proteins in plasma membranes. This allows molecules or ions to be transported against their concentration gradient.
- SECRETION: ATP is needed to form the lysosomes necessary for the secretion of cell products.
- ACTIVATION OF MOLECULES: The inorganic phosphate released during hydrolysis of ATP can be used to phosphorylate other compounds to make them more reactive and so lowers their activation energy in enzyme-catalysed reactions. For example, the addition of phosphate to glucose molecules at the start of glycolysis.
ATP as an immediate energy source
ATP is only an immediate energy source of a cell because the instability of its bonds means it cannot be a long-term energy store. Cells do not store large quantities of ATP but maintain a few seconds' supply. It is a better immediate energy source than glucose because:
- Each ATP molecule releases less energy than each glucose molecule. The energy for reactions is therefore released in small, more manageable quantities rather than the much greater and therefore less manageable release of energy from a glucose molecule
- The hydrolysis of ATP to ADP is a single reaction that releases immediate energy whereas the breakdown of glucose is a long series of reactions therefore energy release takes longer
The structure of a water molecule
- Made up of two hydrogen atoms and one oxygen atom
- The molecule has no overall charge but the difference in electronegativities of oxygen and hydrogen results in both negative and positive dipoles. It is dipolar
- Hydrogen bonds form as opposite dipoles attract, giving water its unusual properties.
Properties of water
- SPECIFIC HEAT CAPACITY: It takes more energy to heat a given mass of water. Water molecules stick together because of the hydrogen bonds (cohesion). This means it takes more (heat) energy to separate them than would be needed if they did not form attractive forces between each other. The boiling point of water is higher than expected. Without hydrogen bonding, water would be a gas. It therefore acts as a buffer against sudden temperature variations, making aquatic environments temperature-stable.
- LATENT HEAT OF VAPORISATION: A lot of heat energy is required to evaporate one gram of water due to its hydrogen bonding. Evaporation of water e.g. sweat is a very effective means of cooling because body heat is used to evaporate the water.
- COHESION AND SURFACE TENSION: Water has large cohesive forces and these allow it to be pulled through a tube, e.g. xylem vessel in plants. Where water molecules meet air they tend to be pulled back into the body of water rather than escaping from it. This force is surface tension and means the water surface acts like a skin and is strong enough to support small organisms such as pond skaters.
The importance of water to living organisms
- Water in metabolism- used to break down many complex molecules by hydrolysis and is also produced in condensation reactions. Chemical reactions can take place in an aqueous medium and water is a major raw material in photosynthesis.
- Water as a universal solvent- it readily dissolves substances. Gases such as oxygen and carbon dioxide; wastes such as ammonia and urea; inorganic ions and small hydrophilic molecules such as amino acids, monosaccharides and ATP; enzymes whose reactions take place in solution.
- Its evaporisation cools organisms and allows them to control their temperature
- It is not easily compressed therefore provides support, for example the hydrostatic skeleton of animals such as earthworm and turgor pressure in herbaceous plants.
- It is transparent and therefore aquatic plants can photosynthesise and also light rays can penetrate the jelly-like fluid that fills the eye and so reach the retina
Inorganic ions and their roles
- Fe2+ : Found in haemoglobin where they play a role in the transport of oxygen
- Hydrogen ions: determine the pH of solutions and therefore functioning of enzymes
- Sodium ions: transport of glucose and amino acids across plasma membranes.
- Phosphate ions: structural role in DNA and a role in storing energy in ATP molecules.