A2 cards UNIT 4

1- Transcription

• RNA polymerase attaches to the DNA
• Hydrogen bonds break between base pairs & the DNA molecule unwinds
• RNA nucleotides via complementary base pairing bind to form an mRNA molecule
• When finished the mRNA leaves through a pore in the nuclear envelope

2- Modification before Translation 

• There are genes which don't code for amino acids = INTRONS & those that do code for amino acids = EXONS
• The introns are removed by SPLICING which produces a chain of exons which can change order = more than 1 protein produced from 1 gene

3- Translation

• Starts once the mRNA has attached to a ribosome. The codons face the large subunit.
• On a tRNA, there is an anti-codon which moves along the mRNA change creating a peptide and then polypeptide chain (CONDENSATION REACTION
• This process continues until a stop codon is reached 

Polymerase Chain Reaction

1- A sample of hair/cheek cells is treated with detergent to break open cells and release the DNA

2- A reaction mixture is set up that contains the DNA sample, free nucleotides, primers and DNA polymerase

3- The mixture is heated to 95 degrees to break the hydrogen bonds

4- The mixture is then cooled to 55 degrees so the primers can bind to the strands

5- The mixture is heated to 70 degrees so the DNA polymerase can work --> this lines up the free nucleotides alongside the template strand and then complementary base pairing means new complementary strands are formed

6- 2 new copies of the fragment DNA are formed and 1 cycle is complete

7- The cycle is then repeated and all 4 (2 new and 2 original) strands are used as templates 

1- A fluorescent tag is added (ethidium bromide) so that the DNA fragments can be seen under UV light

2- Fragments of double-stranded DNA are loaded into the wells of an agarose gel in a tank

3- The negatively charged phosphate groups will move the DNA towards the positive electrode 

4- Short fragments move faster and travel further than longer fragments --> DNA fragments, therefore, separate according to length  

5- DNA is transferred to a nylon OR nitrocellulose membrane by solution drawn up through the gel. DNA double strands split and stick to the membrane 

6- The DNA appears as bands under UV light = DNA profile 

These can then be compared --> a match could help identify a person or determine a genetic relationship  

Body Temperature 

Body core temperature is usually 36.2-37.6 degrees. BUT when a person dies their body starts to cool due to the absence of heat-producing chemical reactions --> it falls to the temperature of its surroundings (algor mortis). Core body temperature is usually measured in the rectum or through an abdominal stab. Environmental conditions need to be noted as these will affect how the body has cooled. The cooling of the body will follow a SIGMOID CURVE. Factors that affect post-mortem cooling are body size, body position, clothing, air movement, humidity, temp of surroundings 

Rigor Mortis 

1- Muscle cells become starved of oxygen, and oxygen-dependent reactions stop 2- Respiration in the cells becomes anaerobic and produces lactic acid 3- The pH of cells falls, inhibiting enzymes and thus inhibiting anaerobic respiration  4- The ATP needed for muscle contraction is no longer produced as a result bonds between the muscle proteins become fixed 5- The proteins can no longer move over one another to shorten the muscle, fixing the muscle and joints                        

After death tissues start to break down due to the action of enzymes. Autolysis occurs first --> this is when the body's own enzymes from the digestive tract & from lysosomes break down the cells. Bacteria from the gut and the gaseous exchange system rapidly invade the tissues after death, releasing enzymes that result in decomposition. The loss of oxygen in the tissue favours the growth of anaerobic respiration. 

Signs of Decomposition

1- the first sign is putrefaction - a greenish discolouration of the skin of the lower abdomen --> due to the sulfhemoglobin in the blood. This will spread across the body and will darken to a reddish-green & then turn a purplish-black colour 

2- gas or liquid blisters may appear on the skin --> due to the action of bacteria, gases such as hydrogen sulphide, methane, carbon dioxide, ammonia and hydrogen form in the intestines and tissues --> causes the body to smell and become bloated. As the tissues further, decompose the gas is released and the body deflates. 

3- when the fluid associated with putrefaction drains away, the soft tissue shrinks and the decay rate of the body is reduced 

1- involves pioneer species --> anaerobic bacteria which do not need oxygen to thrive = take over the body

2- blow flies move in (can be within minutes of death) they are attracted to the moisture and smell around orifices & open wounds --> lays eggs & maggots eat tissues

3- beetles feed on the maggots --> lay eggs on carcus. The parasitic wasps lay eggs in fly & beetle larvae

Factors affecting succession - temperature, humidity, where in the world

Blowfly life cycle

23 hours - 1st larvae stage                                                                                                                   27 hours - 2nd larvae stage                                                                                                                 22 hours - 3rd larvae stage                                                                                                             130 hours - pupa                                                                                                                                 143 hours - adult   

• Prokaryotic 
• Cell wall - made of peptidoglycan ---> Gram staining so you can distinguish bacteria into 2 categories

1- Gram positive - thick peptidoglycan layer with teichoic acid embedded in which picks up the stain = purple/blue   

2- Gram negative - thin peptidoglycan layer between 2 membrane layers = pink stain

• Slime capsule - protects from phagocytosis, doesn't dry out, enable to enter host cells without being detected
• Plasmids - code for particular aspects --> production of a particular toxin
• Ribosome (70s)  

• They consist of a strand of nucleic acid enclosed within a protein coat. 
• Some viruses also have an outer envelope taken from the host cell's surface membrane --> this envelope contains lipids and proteins.
• Viral envelopes also contain glycoproteins from the virus itself --> these are antigens 
• The envelope helps the virus attach to the cell and penetrate the surface membrane. 

The Skin - has a hard protein outer layer - keratin - effective in stopping entry of microorganisms gaining access . Entry can occur through wounds but blood clotting can reduce access. Skin flora is harmless and prevents colonisation by other bacteria 

Mucous Membranes - entry of microbes to the lungs is limited by the action of mucus and cilia. The mucus secreted by goblet cells in the trachea and bronchi, traps microbes and other particles --> beating cilia carry the mucus up to the throat where it is swallowed. Secretions in the mouth , eyes and nose contain lysozyme, an enzyme that breaks down bacterial cell walls causing the cell to burst 

Stomach Acid - contains hydrochloric acid, giving a pH of less than 2.0. This kills most bacteria entering with food but is also the optimum pH for pepsin

Gut Flora - Found in the small & large intestines. They may aid in the digestive process & competitively exclude pathogenic bacteria, competing with pathogens for food and space. They also secrete chemicals e.g. lactic acid that are useful in the defence against pathogens 

1- Lysozyme - this is an enzyme that kills bacteria by breaking down their cell walls. It is found in tears, saliva, nasal secretions 

2- Inflammation - 1- immune system cells recognise foreign antigens on the surface of a pathogen and release molecules that trigger inflammation 2- the molecules cause vasodilation around the site of infection, increasing the blood flow to it 3- the molecule also increases the permeability of the blood vessels 4- this increased blood flow brings loads of immune system cells to the site of infection and the increased permeability allows the cells to move out of the blood vessel and into the infected area

3- Phagocytosis - 1- a phagocyte recognises the antigens on a pathogen 2- the cytoplasm of the phagocyte moves round the pathogen engulfing it 3- the pathogen is now contained in a phagocytic vacuole in the cytoplasm 4- a lysosome fuses with the phagocytic vacuole, the enzymes break down the pathogen 5- the phagocyte then presents the pathogens antigens on the surface to activate other immune system cells

4- Interferon -when cells are infected with viruses they produce proteins called interferons these prevent the viruses spreading to uninfected cells by 1- prevent viral replication by inhibiting the production of viral proteins  2- activate the specific response  

1- Humoral Immune Response

1- When a macrophage destroys a pathogen by phagocytosis it will display the pathogens antigen on its cell surface = antigen presenting cell (APC)

2- The APC interacts with a helper T cell and releases a chemical substance called interleukin-1, this is a cytokine (a chemical involved in cell signing)

3- Interleukin-1 stimulates the T helper cells to release another cytokine - interleukin-2 which stimulates the differentiation of effector B cells into plasma cells

4- Plasma cells divide and produce large quantities of antigen-specific antibodies --> these can attach to the pathogen and destroy it by neutralization or agglutination 

5- Exposure to a specific antigen also results in memory B cells being produced. These are ready to initiate a response to the same pathogen if the body becomes infected again in the future  

2- Cellular Immune Response

1- An APC is produced

2- The APC interacts with a specific helper T cell and releases a cytokine a cell involved in cell signalling 

3- The cytokine then releases another cytokine which stimulates the growth and development of antigen-specific cytotoxic T cells

4- Cytotoxic T cells detect the antigen on the surface of the infected body cells and produce perforin. This protein form pores in the target cell's membrane, allowing ions and water in causing lysis of the cell

5- Memory cells are produced 

Helper T Cells - act as coordinators of the immune response. When a pathogen is detected helper T cells produce a chemical signal resulting in the activation of other cells 

Cytotoxic T Cells - these recognise infected cells or tumour cells and destroy them by secreting proteins that cause ruptures to the membrane 

Effector B Cells - these multiply and give rise to plasma cells when activated by helper T cells 

Plasma Cells - these produce large amounts of antibodies which bind to pathogens which will be inactivated

Memory Cells - these circulate in the blood after the pathogen had been destroyed. If stimulated they divide and rapidly produce a secondary immune response 

Transmission of TB

• Carried in the droplets of mucus and saliva released into the air when an infected person talks, coughs or sneezes --> others then inhale the droplets  = droplet infection
• Close contact with an infected person increases the risk of developing TB as do poor health, poor diet and overcrowded living conditions
• It has a thick waxy coat to it is hard for it to be detected and broken down

Transmission of HIV

• Sharing needles
• Unprotected sex
• Direct blood-to-blood transfer can occur through cuts and grazes
• Maternal transmission from mother to unborn child or in breast milk

Done via the lytic pathway = 1- DNA enters cell 2- DNA causes production of copies of viral DNA/RNA 3- and viral production of mRNA --> so that it can produce its own proteins

1- targets CD4 receptors on helper T cells

2- when inside the helper T cell infects & replicates

3- destroys helper t cell & produce more of the taken over/infected cells

4- T killer cells target the infected T helper cells 

= more susceptible to a secondary disease (e.g. TB) --> this is when AIDS is present as this is the terminal stage

Primary Infection

1- inhaled

2- gets into lungs & multiplies and divides

3- attacked by macrophages in a phagocytic way --> forms scar tissue called tubercle's (takes 8 weeks to prevent the spread) --> most go on to live healthy lives 

BUT

1- may be re-activated when there is a weak immune system

2- mycobacterium targets helper T cell reducing the production of antibodies 

• temperature sensitive
• can cause death

3- vulnerable to opportunistic infections e.g. pneumonia 

How do Antibodies work?

• Clumping - directly observe and bind to the surface and then clump together --> enable phagocytosis to happen more easily 
• May stimulate other reaction : 1- destruction of the membrane 2- release of histamine triggering inflammation

Antibiotics:

• Are selectively toxic --> target specific organisms & interfere with metabolism = KILL THEM
• Antimetabolites - block nucleic acid pathways --> interrupt metabolic pathways
• Cell Wall agents - disrupt cell wall = lysis 
• Protein synthesis inhibitors - prevent transcription and translation 

2 ways that antibiotics work:

1- bacteriostatic - inhibits growth of bacteria --> does not immediately kill the bacteria and allows the immune system to do that 

2- bacteriocidal - destroy ALL pathogens 

Bacterial Evolution

1- mutation in the gene

2- when antibiotics are used the sensitive bacteria die BUT the resistant stay around 

3- the resistant bacteria then reproduce and pass on the mutation to their offspring 

4- more bacteria have this changed allele and so are not affected by the antibiotic = increase in allele frequency

• this evolution can be prevented by:
  • use antibiotics sparingly
  • use as few as possible  

1- Natural active immunity - body detects antigens and produces antibodies for specific antigens & produce memory to remember

2- Natural passive immunity - mother passes own antibodies to fetus & post-natal via breast-milk

3- Artificial passive immunity - antibodies are directly transferred to you

4- Artificial active immunity - antigen is actively injected into you to stimulate immune system to produce an immunological memory 

Pro's of Vaccination - protected against disease, protects those who are not vaccinated, reduces costs on NHS 

Con's of Vaccination - allergic reactions, anaphylaxis, allergy's in childhood