Structure of DNA
- DNA is a polynucleptide made up of many nucleotides that contain deoxyribose (sugar) a phosphate and a base.
- There are 4 possible bases; Adenine, Thymine, Guanine and Cytosine.
- DNA exists as a double helix with hydrogen bonding between the bases encased in a sugar-phosphate backbone.
- Each base can only join with one particular partner (complementry base paring) A ->T G -> C (to remember At The Golf Course)
Nature of the genetic code
- Genes are sections of DNA found on chromosomes that code for proteins
- Protiens are made of amino acids - different protiens have a different number and order of amino acids.
- The order of the bases on a particular gene determins the order of amino acids in a particular protein.
- Each amino acid is coded for by a codon in a gene
- Different sequences of bases code for different amino acids (genetic code)
- In the genetic code, each codon is read in sequence, seperate from the codon before and after it. Base codons don't share bases - the code in non-overlapping.
- The genetic code is also degenerate - there are more possible combinations of codon than there are amino acids. This means that some are coded for by more than one codon.
- Some codons are used to tell the cell when to start and stop the production of proteins. These are called start and stop codons.
mRNA copy made in the nucleus
- RNA polymerase attaches to the DNA at the beginning of the gene
- The H-bonds between the DNA strands break, untwisting the DNA.
- 1 Strand becomes an antisense strand to make a mRNA copy
- RNA polymerase lines up free nucleotides alongside the antisense strand. Complementary base paring = mRNA strand being a reversed copy of DNA (except T --> U in RNA)
- Pared RNA nucleotides join together forming a mRNA strand.
- RNA polymerase moves along the DNA, separating the strands and assembling the mRNA strand.
- RNA polymerase move on, H-bonds in DNA reform and DNA strands re-twist into double helix
- When RNA polymerase reaches a stop codon, it stops making mRNA and detaches from DNA.
- mRNA moves out of the nucleus through a nuclear pore and attaches to a ribosome in the cytoplasm ready for translation.
- mRNA modified before translation.
- Genes contain both introns (non-coding) and exons (coding)
- During transcription both the introns and exons are copied into mRNA
- The introns are removed by a process called splicing
- Splicing is the removal of introns and joining up exons
- Splicing takes place in the nucleus
- Exons can be joined up in different orders to form different mRNA strands
- This allows more than one amino acid sequence (and so more than 1 protein) to come from one gene
- After splicing the mRNA leaves the nucleus for translation.
Occurs on ribosomes in the cytoplasm
Amino acids are joined together forming a protein
1. mRNA attaches to a ribosome and transfer RNA (tRNA) carry amino acids to the ribosome.
2. tRNA, with complimentary anticodon, attaches itself to the first codon by complimentary base paring
3. A second tRNA molecule attaches itself to the next codon on the mRNA in the same way.
4. The amino acids join together via a peptide bond the tRNA molecule moves away leaving its amino acid behind.
5. This process continues, forming a polypeptide chain, until a stop codon on the mRNA strand.
6. The polypeptide chain (protein) moves away from the ribosome
Uses of DNA Profiling
Identification in Forensic Science
- used to link criminals to a scene of crime
- DNA is isolated
- Each sample is amplified using PCR
- PCR products run using electrophoresis. DNA profiles are then compared.
- If samples matched, suspect linked to crime scene
Determining human genetic relationships
- DNA is inherited from our parents
- Therefore the more bands the two DNA profiles match, the more genetically similar the two people are.
DNA profiling of plants and animals
- Used to prevent interbreeding
- DNA profiling can be used to identify how closely related individuals are, the least related individuals will be bread together.
Polymerase Chain Reaction
- A reaction mixture is set up containing; DNA sample, primers, free nucleotides and Tac polymerase.
- The DNA mixture is heated to 95C to break the H-bonds between the DNA strands.
- The mixture is then cooled to between 50C and 65C so primers can anneal to the strands
- The reaction mixture is then heated to 72C so the Tac polymerase will work.
- The Tac Polymerase lines up free DNA nucleotides alongside each template strand. Complimentary base paring means new complementary strands are formed.
- Two new copies of the fragment of DNA are formed and one cycle of PCR is completed.
- The cycle is repeated and 4 strands of DNA are now completed
- Each PCR cycle doubles the amount of DNA. By the end of 32 cycles the DNA sample is almost pure.
- Products of PCR are viewed using gel electrophoresis or shown as peaks on a graph.
Gel electrophoresis is used to separate DNA fragments to be viewed under UV light
Each fragment is separated according to its length
The DNA fragments are dyed using a florescent die before gel electrophoresis
- DNA sample is placed into a well of gel covered in buffer solution
- An electrical current is passed through the gel. DNA fragments are negatively charged so they move towards the positively charged electrode at the other end of the gel.
- Small fragments of DNA travel faster and further down the gel. This separates the fragments according to length.
- The DNA fragments appear as bands under UV light; This is a DNA profile.
- Two DNA profiles can be compared - a match can help identify a genetic relationship.
- Main circular DNA
- Mesosome - infolding of the cell surface membrane. Site of respiration.
- Ribosomes - site of protein synthesis; they occur free in the cytoplasm
- Cell surface membrane
- Pilus (plural pili) - protein tubes that allow bacteria to attach to surfaces
- Plasmids - small circles of DNA
- Cell wall - does not contain cellulose; made of peptidoglcan
- Flagellum - used for cell movement
- Capsule - a mucus layer for protection and allow bacteria to form colonies
Bacteria can be between 0.1 - 1ym
They have no nucleus bound membrane
Can be gram positive or gram negative
They are single celled organelles
Small organic particles that use the hosts metabolic systems to reproduce
Decomposition by Micro-organisms
Micro-organisms, like bacteria and fungi, are an important part of the carbon cycle
When plants and animals die, micro-organisms on them secrete enzymes that decompose the dead organic matter into small molecules as they respire.
When the micro-organisms respire, these small molecules, methane and CO2, are released - this recycles carbon back into the atmosphere
Entry of Pathogens
Pathogens, viruses, bacteria and fungi, can enter the human body via four major routes;
- Through cuts or abrasions in the skin
- Through the digestive system (contaminated food and drink)
- Through inhalation into the respitory system
- Through mucosal surfaces (inside the nose, mouth and genitals)
Prevention of Infection
Stomach acid - has a pH of less than 2 which kills most bacteria (also optimum condition for pepsin). Some pathogens may survive and invade cells in gut wall.
Gut and skin flora - intestines and skin are naturally covered in harmless micro-organisms (called flora) These compete with pathogens for space and nutrients limiting the number of pathogens to cause disease. Flora also secrete lysozomes which cause lysis of bacteria.
Skin - acts as a physical barrier to pathogens and if damaged, blood clots form to prevent entry of pathogens.
Lysozymes - Mucosal surfaces produce secretions that contain the enzyme lysozyme which cause bacteria to lyse.
HIV and AIDS
- The human immunodeficiency virus (HIV) infects and destroys T-helper cells
- HIV infection eventually leads to acquired immune deficiency syndrome (AIDS)
- AIDS is a condition where the immune system deteriorates and eventually fails
- People with HIV are classified as having AIDS when the symptoms of their failing immune system start to appear
- AIDS sufferers generally develop diseases and infections that wouldn't cause serious problems in people with healthy immune systems (opportunistic infections)
- The length of time between infection of HIV and the development of AIDS varies between individuals but is usually 8 - 10 years
- The initial symptoms of AIDS include minor infections of mucus membranes and recurring respitory infections - these are caused by lower than normal number of immune system cells
- As AIDS progresses the immune sells further drop in number. Suffers are now more susceptible to more serious infections.
- During the late stages of AIDS the immune system is very weakened and it is the opportunistic infections, not HIV that kills suffers.
- Mycobacterium Tuberculosis infects phagocytes in the lungs
- It causes the lung disease tuberculosis (TB)
- Most people don't develop TB straight away - their immune system seals off the infected phagocytes in structures in the lungs called tubercles
- The bacteria become dormant inside the tubercles and the infected person shows no obvious symptoms
- Later on, the dormant bacteria become reactivated and overcome the immune system, causing TB
- Reactivation is more likely in the people with weakened immune systems
- The length of time between infection and the development of TB varies between individuals - it can be weeks to years. TB then progresses through a sequence of symptoms.
- The initial symptoms of TB include fever,general weakness and severe coughing, caused by inflammation of the lungs
- As TB progresses, it damages the lungs and, if left untreated, can lead to respiratory failure and death
- TB can also spread from the lungs to other parts of the body and, if left untreated, can lead to organ failure and may lead to death.
- Part of the non-specific immune responce
- Happens at the site of infection of a pathogen (area becomes red, swollen and painful)
- Immune system cells recognise foreign antigens on the surface of a pathogen and release histamine that trigger inflamation
- The molecules cause vasodilation around the site of infection, increasing the blood flow to it.
- The histamine molecules also increase the permeability of the blood vessels
- The increased blood flow brings immune system cells to the site of the infection and the increased permeability allows those cells to move out of the blood vessils and into the infected tissue
- Immune cells can start destroying the pathogen
- Include neutrophils and macropharges (types of white blood cell)
- Engulf pathogens
- Phagocytes recognise the antigen on a pathogen
- Cytoplasm of phagocyte engulfs pathogen
- Pathogen contained in phagocytic vacuole in cytoplasm of phagocyte
- A lysosome fuses with the phagocytic vacuole breaking down the pathogen
- Phagocyte presents pathogen's antigens activating the specific immune response
Produced when cells are infected with viruses
Help prevent viruses spreading to uninfected cells by;
- Inhibiting the production of viral proteins preventing viral replication
- Activating specific immune response to kill infected cells
- Activate other mechanisms in the non-specific immune response
- Tears, saliva and nasal secretions contain an enzyme called Lysozyme
- This enzyme kills bacteria by breaking down the cell walls causing lysis of the bacteria
- Lysozymes protect the body from harmful bacteria in the air and food
Phagocytes Activate T Cells
- A T cell is a type of white blood cell
- Their surface is covered with receptors
- The receptors bind to the antigens presented by the phagocytes
- Each T cell has a different shaped receptor on its surface
- When the receptor on the surface of a T cell meets a complementary antigen, it binds to it (each T cell will bind to a different antigen)
- This activates the T cell - it divides and differentiates into different types of T cells that carry out different functions;
- T-helper cells - release cytokines that activate B cells, T-killer cells and macrophages
- T-killer cells - attach to antigens on a pathogen infected cell and kill the cell
- T-memory cells
Activation of B cells by T-helper cells
- A B cell is a type of white blood cell covered in antibodies (forms of protein)
- Antibodies bind to antigens to form an antigen-antibody complex
- Each B cell has a different shaped antibody on its surface
- When the antibody on the surface meets a complementary antigen, it binds to it (each B cell will bind to a different antigen)
- This then becomes an antigen presenting cell (APC)
- This, together with cytokines produced by the APC, activates the B-cell
- The activated B-cell divides, by mitosis, into B-effector and B-memory cells
- B-effector cells differentiate into plasma cells which secrete antibodies
Antigens and Antibodies
- Plasma cells are clones of the B-cells
- They secrete loads of the antibody, specific to the antigen, into the blood
- These antibodies will bind to the antibodies on the surface of the pathogen to form lots of antigen-antibody complexes
- The variable regions of the antibody form the antigen building sites. The shape of the variable region is complementary to a particular antigen. The variable regions differ between antibodies
- The hinge region allows flexibility when the antibody binds to the antigen.
- The constant regions allow binding to receptors on immune cells. The constant region is the same in all antibodies.
- Disulphide bridges (type of bond) hold the polypeptide chains together.
- Antibodies help to clear an infection by;
- Agglutinating pathogens - each pathogen has 2 binding sites, so an antibody can bind to 2 pathogens at the same time - the pathogens become clumped together which allows phagocytes to engulf multiple pathogens at once.
- Neutralising toxins - antibodies can bind to toxins produced by pathogens. This prevents toxins from affecting human cells.
- Preventing the pathogen binding to human cells
The Production of Memory Cells
- When a pathogen enters the body for the first time the antigens on its surface activate the immune system (primary response)
- The primary response is slow because there aren't many B-cells that can make the antibody needed to bind to the antigen
- Eventually the body will produce enough of the right antibody to overcome the infection. Meanwhile the infected person will show symptoms of the disease.
- After being exposed to an antigen, both T and B cells produce memory cells. These remain in the body for a long time. Memory T-cells remember the specific antigen and will recognise it the second time around. Memory B-cells record the specific antibodies needed to bind to the antigen.
- The person is now immune - their immune system will produce a quicker, stronger immune response (secondary response)
Active and Passive Immunity
- This is the type of immunity achieved when the immune system makes its own antibodies after being stimulated by an antigen.
- Consists of;
- Natural - acquiring immunity through catching a disease
- Artificial - acquiring immunity through vaccination
- This produces long term protection but takes a while to acquire
- This type of immunity is acquired through antibodies made by a different organism
- It consists of;
- Natural - immunity acquired due to antibodies received through the placenta and breast milk
- Artificial - immunity acquired through injection of antibodies
The "Evolutionary Race"
- Over millions of years vertebrates have evolved better and better immune systems - one that fight off a greater variety of pathogens in lots of different ways.
- At the same time, pathogens have evolved better and better ways to evade the immune systems of their hosts.
- This struggle between pathogens and their hosts is known as an evolutionary race.
- Evidence to support the theory of an evolutionary race comes from the evasion mechanisms the pathogens have developed.
The Evasion Mechanisms of HIV
- HIV kills the immune system cells that it infects. This reduces the overall number of immune cells in the body which reduces the chance of HIV being detected.
- HIV has a high rate of mutation in the genes that code for antigen proteins. The mutations change the structure of the antigens and this forms new strains of the virus - this process is called antigenic variation. The memory cells produced for one strain of HIV won't recognise other strains with different antigens, so the immune system has to produce a primary response for each new strain.
- HIV disrupts antigen presentation in infected cells. This prevents immune system cells from recognising and killing the infected cells.
The Evasion Mechanisms of Myctacterium Tuberculosi
- When Myctacterium Tuberculosis bacteria infect the lungs they are engulfed by phagocytes. Here they produce substances that prevent the lysome fusing with the phagocytic vacuole. This means the bacteria aren't broken down and they multiply undetected inside phagocytes.
- This bacterium also disrupts antigen presentation in infected cells, which prevents immune system cells from recognising and killing infected phagocytes.
- Antibiotics are chemicals that kill or inhibit the growth of micro-organisms
- Bactericidal antibiotics kill bacteria
- Bacterostatic antibiotics prevent bacteria growing
- Antibiotics are used in the form of drugs to treat bacterial infections.
- They work because they interfere with metabolic reactions that are crucial for the growth and life of the cell.
- Some inhibit enzymes that are needed to make the chemical bonds in bacterial cell walls. This prevents the bacterial from growing properly. It can lead to death (through lysis).
- Some inhibit protein production by binding to bacterial ribosomes. All enzymes are proteins, so if the cell can't make proteins, it can't make enzymes. This means it can't carry out important metabolic processes that are needed for growth and development.
- Bacterial cells are different from mammalian cells- mammalian cells are eukaryotic, they don't have cell walls, they have different enzymes and have different, larger ribosomes. This means antibiotics can be designed to only target bacterial cells, so they don't damage mammalian cells. Viruses don't have their one enzymes and ribosomes - they use the ones in the host cell, so antibiotics don't affect them.
Investigating Antibiotics on Bacteria
- The bacteria to be tested are spread on an agar plate
- Paper disks socked with antibiotics are placed apart on the plate. Various concentrations of antibiotics should be used. Also a negative control disk socked only in sterile water should be used.
- All procedures should be carried out using the aseptic techniques.
- The plate is incubated at 25-30C for 24-36 hours to allow bacteria to grow (forming a lawn). Anywhere the bacteria can't grow can be seen as a clear patch in the lawn of bacteria called a zone on inhibition.
- The size of the zone of inhibition shows how well an antibiotic works - the larger the zone, the more bacteria were inhibited from growing.
- Bacteria that are unaffected by antibiotics are said to be antibiotic resistant.
Transmission of Hospital Acquired Infections via P
- Hospital acquired infections (HAI) are infections that are caught while a patient is in hospital.
- HAIs can be transmitted through poor hygiene;
- Hospital staff and visitors not washing their hands before and after visiting a patient.
- Coughs and sneezes not being contained
- Equipment and surfaces not being disinfected after they're used.
- People are more likely to catch infections in hospital because many patients are ill, so have weakened immune systems, and they're around other ill people.
- Codes of practice have been developed to prevent and control HAIs;
- Hospital staff and visitors should be encouraged to wash their hands before and after being with a patient
- Equipment and surfaces should be disinfected after they're used.
- People with HIA's should be moved to an isolation ward so they're less likely to transmit the infection to other patients.
Some HAIs are Antibiotic Resistant
- HIAs that are resistant to antibiotics are difficult to treat because antibiotics don't get rid of the infection. This means that HAIs can lead to serious health problems and even death.
- Infections caused by antibiotic resistant bacteria are more common in hospitals because more antibiotics are used there, so bacteria in hospitals are more likely to have evolved resistance against them.
- Codes of practice have been developed to prevent and control HIAs caused by antibiotic resistance.
- Doctors shouldn't prescribe antibiotics for minor bacterial or viral infections.
- Doctors shouldn't prescribe antibiotics to prevent infection.
- Doctors should use narrow spectrum antibiotics if possible.
- Doctors should rotate the use of different antibiotics.
- Patients should take the full course of antibiotics prescribed so the infections are fully cleared.
Determining the Time of Death: Body Temperature
- All mammals produce heat for metabolic reactions like respiration
- From the time of death, the metabolic reactions slow down and eventually stop causing body temperature to fall until it equals the temperature of its surroundings - algor mortis
- The human body cools at a rate of around 1.5C to 2.0C per hour, so from the temperature of the body they can work out an approximate time of death (TOD)
- Conditions such as air temperature, clothing and body weight can affect the cooling rate of a body.
Determining the Time of Death: Stages of Successio
- The type of organism found on a dead body change over time.
- TOD can be estimated from the stage of succession.
- If the body is left to decompose above ground, it will usually follow these stages;
- Immediately after TOD conditions are most favourable to bacteria.
- As bacteria decompose tissues, conditions become favourable to flies and their larvae.
- When fly larvae feed on a dead body they make conditions favourable for beetles.
- As a dead body dries out conditions become less favourable for flies - they leave the body. Beetles remain.
- When no tissue remains, conditions are no longer favourable for most organisms.
- Succession in a dead body is similar to plant succession - the only difference is that most of the early insects remain on the body and other insects colonise it.
- The stage of succession of a body, and the type of organism present is affected by many different factors.
Extent of Decomposition
- Immediately after death bacteria and enzymes begin to decompose the body.
- The extent of decomposition can establish TOD.
- Different conditions affect the rate of decomposition.
- Hours-few days after death - cells and tissues are being broken down by the bodies enzymes and bacteria that were present before death. The skin turns greenish.
- Few days-few weeks - Micro-organisms decompose tissues and organs. This produces gasses which cause the body to become bloated. The skin begins to blister and fall off.
- A few weeks - Tissues begin to liquefy and seep out into the area around the body.
- A few months-years - Only skeleton remains
- Decades-centuries - The skeleton begins to disintegrate until there'e nothing left of the body.
Degree of Muscle Contraction
About 4-6 hours after death, the muscles start to contract and become stiff. This is rigor mortis.
- Rigor mortis begins when muscle cells become deprived of oxygen.
- Respiration still takes place in the muscle cells, but its anaerobic, which causes the build up of lactic acid in the muscle.
- The pH of the cells decreases due to the lactic acid, inhibiting enzymes to produce ATP.
- No ATP means bonds between the myosin and actin become fixed and the body stiffens.
- Smaller muscle in the head contract first, with larger muscles in the lower body body being the last to contract. Rigor mortis is affected by the degree of muscle development and temperature.
It takes about 12-18 hours for full rigor mortis and it wears off after 24-36 hours after TOD.
- When someone dies the body is quickly colonised by a variety of different insects.
- TOD can be estimated by identifying they type of insect present on the body.
- TOD can be identified by identifying the life cycle the insect is in.
- Different conditions will affect the insects life cycle, such as; drugs, humidity, oxygen levels and temperature.