Apoptosis

Events of apoptosis

• enzymes breaks down the cell cytoskeleton
• cytoplasm becomes dense with organelles tightly packed
• the cell surface membrane changes and small bits called blebs form.
• chromatin condenses and nuclear envelope breaks. DNA breaks into fragments
• the cells breaks into vesicles that are taken up by phagocytosis. the cellular debris is disposed of and does not damage any other cells or tissues

How it's controlled

• Apoptosis is controlled by cell signalling
• some from the inside the cell and some from outside
• these include cytokines made by cells of the immune system, hormones, growth factors and nitric oxide
• nitric oxide works by making the inner mitochondrial membrane more permeable to hydrogen ions
• it would prevent the formation of the proton gradient needed for ATP synthesis
• proteins are released into the cytosol
• these proteins bind to apoptosis inhibitor proteins and allow the process to take place

Apoptosis and development

• apoptosis is an important part of the tissue development. Extensive division and proliferation is followed by pruning through apoptosis. 
• Excess cells undergo apoptosis and their components are reused. Different tissues use different signals to induce it.
• Examples:the removal of ineffective or harmful T lymphocytes during the development of the immune system

How often does apoptosis take place?

• In children between 8-14 years old, 20-30 billion cells per day undergo apoptosis.
• in a year this is equivalent to the total body ass
• in adults the figure is around 50-70 million cells per day
• the rate of cell death should = the rate of mitosis
• however, not enough apoptosis leads to the formation of tumours. 
• too much leads to cell loss and degradation
• cell signalling helps maintain the right balance

AS Biology F212: Vaccines

A vaccine is a preparation containing antigenic material (e.g. antigens)

Vaccination confers artificial active immunity. (Entry of antigenic material into the body stimulates an immune response, memory cells are produce)

Types of vaccination

1. Live vaccine e.g. Smallpox
   The live vaccine - less harmful pathogen but with similar antigens and can still be induce active immunity
2. Harmless vaccine e.g. measles, TB
   Harmless or attenuated version of the pathogen
3. Dead vaccine e.g. Cholera vaccine
   the pathogen has been killed either by exposure to or chemicals
4. Antigens e.g. hepatitis B
   Preparation of antigens from a pathogen
5. Toxoid vaccine e.g. tetanus
   vaccine consists of harmless form of toxin produced by the pathogen

Herd vaccination

• providing immunity to almost all of the population at risk
• with enough people immune the disease cant spread
• level of immunity needed varies depending on the disease (80-85% for small pox, 95% for measles)

Ring vaccination

• used when a  new case s reported
• vaccinate everyone in the immediate vicinity (house, village, or town)

AS Biology F212: Biological molecules:Proteins

Metabolism is the total of all the biochemical reactions taking place in the cell of an organism.

There  are two types of metabolic reactions:

1. Catabolism: breaking down larger molecules into smaller molecules. e.g. digestion.
2. Anabolism: building up smaller molecules into larger ones. e.g. photosynthesis. 

Nutrients

• Carbohydrates, fats, proteins are macronutrients - they are are needed in large quantities.
• Vitamins and minerals are micronutrients - they are needed in small quantities.
• Water Makes up 70% of a cell
• Fibre*

Use of chemical groups in the body

• Carbohydrates
  Energy storage and supply, structure (e.g. cellulose)
• Proteins
  Structure, transport, enzymes, antibodies, hormones
• Lipids
  Membranes, energy supply, thermal insulation, protective layers, electrical insulation in neurones, some hormones
• Vitamin and minerals
  Form part of some larger molecules, takes part in some metabolic reactions, acts as co-enzymes
• Nucleic Acid
  Information molecules, carries instruction for life
• Water
  Takes part in  many reactions, support in plants, solvent for most metabolic reactions, transport

*Fibre is a carbohydrate, it does not provide nutrients nor energy, it adds bulk to the diet making it easier for gut muscles to push food along - lower risks of constipation and intestinal cancer.

Proteins

Amino acids

• Proteins are made up of individual molecules (monomers) called amino acids.
• They are joined to forma longer chain called polypeptide - which can be combined to form a protein.
• Polypeptides and proteins are therefore polymers.
• There are 20 different amino acids.

• All amino acids contains: Carbon, Hydrogen, Oxygen and Nitrogen.
• In addition, some contains sulphur.

Structure

• They have an amino group (NH2) and a carboxyl group (COOH)
• These roups along with a H atom are attached to a central carbon atom called the alpha-carbon.
• The alpha-carbon atom has an R group attached to it.
• This R group is a variable group - it's different in each of the twenty amino acids.

Where do animals get their amino acids?

• Animals need proteins in their diet.
• These are digested to amino acids and used to produce proteins.
• Excess amino acids can not be stored as the amino group makes them toxic and thus it is removed my deamination in the liver.

Where do plants get their amino acids?

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

Formation of a dipeptide

• Amino cids can link together by forming a peptide bond
• A peptide bond is formed when the carboxyl group of one amino acid combines with the amino group of another with the elimination of H2O
• this is called a condensation reaction
• When two amino acids are joined by a peptide bond they form  dipeptide

Making polypeptides and proteins

• Polypeptides and proteins are synthesised on the ribosomes - protein synthesis.
• This process uses mRNA.
• This puts amino acids together in the right order.
• Different mRNA molecules make different proteins.

Levels of Structures

• Primary structure
  This is the sequence of amino acids in a polypeptide molecule.
  The sequence of amino acids is vital because it determines the ultimate shape of the protein and therefore its function.

• Secondary structure
  This refers to the regular arrangement of the polypeptide chain.
  The alpha-helix is where the polypeptide chain is loosely coiled in a regular spiral.
  The beta-pleated sheet is were the polypeptide chains are more extended than in the alpha helix.
  The C=O and N-H groups from the peptide bond regions are held near to each other so that they for many hydrogen bonds.
  These hold the coils of the alpha-helix and the beta-pleated sheets together and make it a stable structure.

• Tertiary structure
  This is the further folding of the secondary structure which gives it a 3D compact shape.
  It depends on the properties of the variable R-groups in the polypeptide chain.

• R-group bonding
  Disulphide bond - the amino acid, cysteine, contains sulphur. where two cysteines are found close together a covalent bond called disulphide bond forms between chains.
  Ionic bonds - occurs between oppositely charged R groups
  Hydrogen bonds - occur between some R groups - these can be easily broken.
  Hydrophobic/philic interactions - hydrophobic amino acids will be most stable if they are held together with water excluded. Hydrophilic amino acids end to be found on the outside of globular proteins.

• Quaternary structure
  Consists of two or more different polypeptide chains which are held together by bonds between the R groups. 

• Globular proteins
• 3D feature: rolls up to form balls (compact)
• Soluble in water - hydrophilic
• Metabolic
• Examples: Enzymes, plasma proteins, hormones, antibodies
• Fibrous proteins
• Forms fibres (long)
• Insoluble - hydrophobic
• Structural
• Examples: Collagen, keratin

The effect of heat 

• Heat increases kinetic energy in a molecule. - causing molecules to vibrate and breaking some bonds maintaining tertiary structure.
• If enough heat is applied the structure can unravel and the protein can no longer function - denatured.
• Even when cooled it will not take on its original shape/arrangement,

Protein hydrolysis

• Protein breakdown is catalysed by enzymes.
• These enzymes are known as protease enzymes.
• Hormone regulation: hormones need to be broke down so that their effect is not permanent.
• Ageing: skin loses elasticity and becomes wrinkled due to inability to rebuild the protein collagen.

• Collagen
• Fibrous protein
• 3 polypeptide chains
• Twisted triple helix
• polypeptides held together by hydrogen bonds between chains
• this forms a collagen fibril
• many fibrils forms a fibre
• Haemoglobin
• 4 polypeptide chains, 2 alpha and 2 beta
• Each one also has an iron prosthetic group attached
• Globular therefore soluble