AS Biology: Proteins

Amino acids

• Proteins are made of monomers called amino acids.
• These monomers join together to forma long chain = polypeptide.
• Polypeptides can be cominted to form a protein. Polypeptides and proteins are polymers.
• There are twenty biologicall important amino acids.
• All amino acids (and so proteins) contain Carbon, Hydrogen, Oxygen and Nitrogen (some contains sulphur)

• Proteins are polymers of amino acids and are made up of a Amino group (NH2) , a carboxyl group (COOH), and the central carbon (α-carbon), hydrogen and a variable group.

Animals needs proteins in their diets. these are digested to amino acids and used to prouce proteins. Excess amino acids cannot be stored and their amino group makes them toxic. This is removed by deamination in the liver.

Plants make the amino acids they need. They use nitrate from the soil to produce amino groups. These are added tot he organic groups made from photosynthesis.

Aminos acids can link together by forming peptide bonds. a peptide bond is formed when the carboxyle group of one amino acids combine with the elimination of water. Therefore it is a condensation reactions. When to amino acids are joining by a peptide bond they form a dipeptide.

• Many amino acids can joing to form a polypeptide chain (series of condensation reactions) = polymerisation. 
• Polypeptides and proteins are synthesised on ribosomes - protein synthesis. It uses mRNA which puts the amino acids together in the right order- different mRNA molecules make different proteins.

Primary structure

This is the sequence of amino acids in a polypeptide molecules.

The sequence of amino acid is important as it determines the shape of the protein and ergo the function.

Secondary structure

This is a regular arrangement of polypeptide chains. The alpha-helix is where the polypeptide chain is loosely coiled in a regular spiral. in the beta-pleated sheet the polypeptide chains are more extended n than alpha helix.

Tertiary structure

This si further folding of the secondary structure which gives a compact 3D shape. It depends on the properties of the different R-groups in the polypeptide chain.

Collagen is a fibrous protein, it has three polypeptide chains and is twisted into a triple helix, polypeptides held together by hydrogen bonds between chains, this forms a collagen fibril, many fibrils form a fibre.

Haemoglobin has 4 polypeptide chains, 2 alpha and 2 beta. Each one has an iron prosthetic group attatched to it. It is a globular protein so it is soluble.

AS Biology: Plant cells and water

Water potential

• Pure water has a water potential of 0 however cells have negative water potential when there are more solute particles than water molecules therefore cells have higher water potential when there are less solute particles and more water molecules
• The plant cells becomes TURGID when water enters by osmosis, vacuole sweels and pushes against the cell wall. Plant cell is FLACCID when the water is lost from the cell and the vacuole shrinks hence the cell loses its shape

Water can travel via three different pathways:

1. Apoplast pathway - water moves through the cell wall

• The cellulose cell wall has many water filled spaces between the cellulose molecule, water can move through these spaces and between cells. The water does not pass through any plasma membranes.

2. Symplast pathway - water moves through the plasma membrane into the cytoplasm

• Water enters the cytoplasm via the plasma membrane. The plasmodesmata allows the movement of water from one cell to the next.

3. Vacuolar pathway - water moves through the vacuole

• This is similar to symplast pathway but the water can now enter and pas through the vacuoles as well.

Water uptake from soil

• The roots have root hair cells, to increase the surface area to absorb minerals by active transport.
• This lowers the water potential in the roots so water moves into the root hair cells by osmosis. 
• Water enter root hair cell by osmosis - minerals are actively transported into xylem. (water moves into xylem my osmosis.) 

Solute can enter the xylem by going through cell membrances - the Casparian strip blocks apoplastic route (outside cells) - water cannot pass between the cell or through cell walls - it must pass into cytoplasm or into symplast pathway

Water moves up the stem due to root pressure, transpirational pull, capillary action

• Transpiration pull - as water molecules are removed from the xylem, more water molecule are pulled to replaced them aka transpirational pull.

Mass flow of water also relies on the properties of water

• Cohesion - the water molecules tend to stick together
• Adhesion - the water molecules also stick the the inside of the xylem vessel
• the drawing of continuous column of water up to xylem vessel is aka cohesion-tension theory

A2 Biology: Respiration - The Krebs Cycle

The Krebs cycle takes place in the mitochondrial matrix. This stage takes place in aerobic respiration.

1. Acetate (carried from the Link reaction by coenzyme A) joins with Oxaloacetate (4C) to form Citrate (6C). CoA is the released to collect more acetate.
2. Citrate is decarboxylated (CO2 is removed) and dehydrogenated (2H is removed) to form a 5C compound. 2H is accepted by a molecule NAD which becomes reduced NAD.
3. 5C compound is also decarboxylated and dehydrogenated to form a 4C compound and a molecule of reduced NAD.
4. 4C compound is changed to another 4C compound and during this change a molecule of ADP is phosphorylated to produce a molecule of ATP. (Substrate-level phosphorylation).
5. The 4C compound then changes into another 4C compound and 2H is removed and accepted by coenzyme FAD which becomes reduced.
6. The other 4C compound go through dehydrogenation  and oxaloacetate is regenerated and another molecule of NAD is reduced. 

There needs to be two turns round the cycle for each molecule of ATP

To conclude: 

• 6 Reduced NAD are produced
• 2 Reduced FAD are produced
• 4 molecules of CO2 are produced
• and 2 ATP are produced