BIOLOGY TOPIC 6

Infection, immunity and forensics

Forensic science key questions

1. What is the identity of the individual?

2. When did they die?

3. How did they die?

IDENTIFICATION OF BODY

• Personal belongings (passport, driving license e.t.c)

• Unique features (tattoos/surgery scars)

• Fingerprinting

• Dental records

• DNA profiling

EXON

The sequence of DNA bases that codes for a sequence of amino acids

INTRON

The sequence of DNA bases that DOESN’T code for a sequence of amino acids.

Which contain short-tandem repeats

Process of pre-mRNA to mRNA

The introns are spliced out to leave the exons that code for amino acids to make proteins     

Theory of DNA profiling

Relies on individuals with unique DNA base sequences

There is a large amount of DNA that doesn’t code for proteins

Inside introns are STR’s (short tandem repeats) that are repeating base sequences.

PROCESS OF DNA PROFILING

1. Obtain DNA sample

2. Create DNA fragments: using resttriction enzymes to cut DNA by targeting base sequences, breaking phosphodiester and Hydrogen bonds= sticky ends

3. Amplify DNA fragments (PCR)

4. Separate DNA fragments (gel elctrophoresis)

5. Visualise the fragments

PCR (similar to DNA replication)

Polymerase chain reaction to amplify the dna fragments.

1. DNA fragments, primers, DNA (Taq) polymerase and free nucleotides are added to a thermocycler- 95 degrees temp casues DNA strands to separate

2. Primers join to their complementary bases at 55 degrees

3. synthesis of DNA- temp increases to 70 degrees (optimum temp for DNA polymerase), DNA polymerase attaches nucleotides to along each of their separated DNA strands.

4. The more cycles= exponential increase of quantity of DNA

(repeated 20-50 times)

GEL ELECTROPHORESIS

Separates the DNA fragments from PCR.

1. DNA placed onto agarose gel in an electrophoresis tank submerged into a buffer solution and connected to positive+negative electrodes

2. DNA is negatively charged so  they move through the gel towards the anode.

3. Smaller fragments move fastes and furthest

4. A DNA marker is added to a gel which contains fragments of known length

5. These are then incubated with a DNA probe

6. Sample is shone under UV light and positions of DNA bands are seen and compared 

TIME OF DEATH (Forensic entomology)

Body Temperature- When a person dies, the body starts to cool as heating processes (respiration) stops (algor mortis)

Muscle stiffness - After death, respiration stops, oxygen is not diffused in. This causes anaerobic respiration and produces lactic acid which reduces the pH, denaturing the active site of enzymes. This means the substrate cannot bind and ATP is not generated. Muscle fibres do not have any enerfy for contraction and so become fixed in place (rigor mortis)

DECOMPOSITION

Microorganisms in and out of the body release extracellular enzymes that breaks down the body’s polymers into monomers.

1. Few hours-days: skin turns green as cells+ tissues are broken down

2. Few days-few weeks: methane released and body becomes bloated skin starts to fall off

3. After several weeks- tissues liquifey and leak outside of body

4. Few months-few years- body tissues completely broken down and only bones remain

5. After several decades- bones disintegrate and nothing remains of body.

STAGES OF SUCCESSION

• Few hours- Flies appear on body and lay eggs (larvae)- takes 24 hours to hatch

• Beetles- eat decomposed body fat

• Other insects e.g moths feed on liquified parts of the corpse + any clothes on the body

• Other insects appear once the bodys proteins have been digested- they feed on food in the digestive system that were not fully digested

• Burying beetle- eats dead flesh

• When the body is fully decomposed, all the remaining insects leave.

How the body PREVENTS INFECTIONS:

1. Mucus membrane- contains lysozyme which kills bacteria damaging their cell wall and bursting them open (chemical barrier)

2. Skin- physical barrier, blood clots minimises entry of pathogens

3. Trachea- contains goblet cells which secrete mucus and trap pathogens (chemical barrier)

4. Stomach- highly acid which can denature proteins and kill pathogens (chemical barrier)

INFLAMMATION

Histamines trigger dilation of blood vessels and permeability of capillary walls

Phagocytes and killer cells attracted to site of infection- chemotaxis

NON-SPECIFIC IMMUNE RESPONSE:

Fast- acting and has the same response for all pathogens

1. Interferons (proteins) released by cells in presence of pathogens

2. Antigens on pathogen bind to receptor on phagocyte (macrophage)

3. Phagocyte engulfs pathogen via endocytosis

4. pathogen becomes enclosed in a vesicle

5. lysosome fuses with vesicle and lysozymes released to break down pathogen and released from phagocyte via exocytosis.

6. Phagocyte takes the pathogens antigens and presents it on its surface (antigen presenting cell)

LYMPHOCYTES

T- cells: produced in bone marrow and mature in thymus gland

types: T helper, T memory, T killer

B- cells: produced and matured in bone marrow

have antibody receptors and divide by mitosis to produce plasma cells+ B memory cells

SPECIFIC IMMUNE RESPONSE

1. T helper cells bind to APC via complementary CD4 receptors

2. T helper cells release cytokines to activate next steps e.g activating B cells and producing T killer cells

3. T killer cells kill the pathogens—- T memory cells produced

4. B cells differentiate into plasma cells which secrete antibodies—— B memory cells

ANTIBODIES

After infection, the body makes memory cells which help the body launch a quicker immune response for a future infection of the same pathogen

ACTIONS OF ANTIBODIES

• Agglutination- 2 binding sites mean antibodies can clump several pathogens together= more efficient phagocytosis

• Antibodies can bind to toxins released by pathogens which is engulfed by ohagocytes

• Neutralisation- They can block the antigens of pathogens preventing them from entering body cells 

SHAPE OF AN ANTIBODY

The specifity of the antibody depends on its variable regions

The constant regions are the same for all antibodies

Each antibody has a different shaped variable region~ due to different amino acid sequences

The variable region is complementary to a specific antigen forming an antibody- antigen complex.- from the B cell

SPLICING~ one gene many proteins

After transcription, prior to leaving the nuclear pore:

The mRNA is spliced (pre-mRNA)- introns are cut out using restriction enzymes

The remaining exons piece together to form mature mRNA which leaves the nucleus via the nuclear pore for translation

example question: (how can one gene can give rise to more than one protein)

ALTERNATIVE SPLICING

Certain exons can be recombined into different orders to make different codons, which will code for a different sequence of amino acids which determing how the protein folds= new protein 

BACTERIA STRUCTURE

• small single celled prokaryotes

• lacks membrane-bound organelles

• 70S ribosomes

• No nucleus- only have dna loop/ plasmid

• cell wall with peptidoglycan

• cell memrbane with mesosome cell membrane folding

• capsule- prevents cell dehydration

• flagella- movement

• pili- allows bacteria to attach to other cells/ surfaces and transfer substances

VIRUS STRUCTURE

• non-cellular

• nucleic acid core- either DNA or RNA

• can be single or double stranded

• No membrane/cytoplasm/ribosomes

• some have an outer envelope layer from the membrane phospholipids

• contains proteins in caspid

• attachment proteins- sticks out of capsid/ envelope to allow the virus to attach itself to a host cell

ACTIVE IMMUNITY

When an antigen enters the body triggering a specific immune response (long term immunity)

Natural active: from exposure to pathogens

Artificial active: from vaccination

PASSIVE IMMUNITY

Acquired without an immune response- antibodies gained from another source

Natural passive: e.g babies receiving antibodies from placenta of mother

Artificial passive: Given by an injection

This doesn’t activate the immune system so no memory cells are enabled= short term immunity

But antibodies appear in blood immediately than in active.

VACCINATION

Contains antigens that are put into the body to induce artificial active immunity

either dead/weakened pathogens/ antigens

produces long term immunity as they cause memory cells to produced and a stronger secondary response

ANTIGENIC VARIATION

Vaccinations need to be constantly modified to keep up with changes of a pathogen’s antigens

The change is due mutations that change the shape/ structure of the antigens

THE EVOLUTIONARY RACE

both hosts and pathogens evolving at the same time

HIV evasion mechanism: kills T helper cells, reducing no. cells to detect the virus due to high mutation rate= new strains of the virus which are not detected by memory cells and prevents cells from presenting antigens to surface

TB evasion mechanism: produces substances that prevents a lysosome from fusing with the phagocytic vacuole= they multiply + disrupt antigen presentation

TB (Mycobacterium tuberculosis)

1. Transmission- when infected people with the active form of TB cough/ sneeze and transmit liquid lipid droplets of TB bacteria in the air

2. uninfected people inhale these droplets (more likely in overcrowded areas)

3. Inside the lungs: the bacteria is engulfed by phagocytes. The bacteria may survive and reporiduce in phagocytes

4. Over time, the infected phagocytes become encased in tubercles in the lungs- bacteria remain dormant

5. The bacteria CAN become activated and attack the immune system at a later stage e.g if HIV arises

6. the length of time between infection and developing TB can vary from a few weeks to a few years

SYMPTOMS OF TB

First symptoms- fever, fatigue, coughing

secondary: lung inflammation and respiratory failure and spread to other parts of the body- organ failure

HIV- Human immunodeficiency virus

• Transmitted through: bodily fluids (mucus/saliva) in blood transfusions, sexual intercourse or sharing needles.

• It contains RNA (enveloped virus) with reverse transcriptase and integrase enzymes

REPLICATION OF HIV

The virus infects T helper cells in the blood.

1. attachment proteins on virus binds to CD4 receptors of t helper cells

2. Capsid is released into T cell and releases RNA via endocytosis

3. Reverse transcriptase uses viral RNA as a template to make complementary viral DNA

4. this DNA is inserted into host DNA (human) via integrase enzyme

5. It uses the host enzymes to produce viral proteins

6. These assemble to form copies of viral particles that bud from the host cell and infect other T helper cells

SYMPTOMS OF HIV

Flu-like symptoms

over a long period of time, the virus reducces the number of T helper cells meaning they cannot activate B cells, so less/no antibodies are produced

This leads to AIDS (acquired immune deficiency syndrome):

immune system is so weak it can no longer fight off normal infections (oppurtinistic)

can lead to TB infections and spread to other organs= death

FACTORS AFFECTING SPREAD OF HIV

Age, existing infections, strain of HIV and access to healthcare

TYPES OF ANTIBIOTICS

Antibiotics damage bacteria cells only

1. BACTERICIDAL- kill bacterial cells

2. BACTERIOSTATIC- inhibit bacterial growth

How do bacteriostatic work

• Interfering with the growth of bacteria:

• breaks down peptidoglycan cell wall

• binding to ribosomes to prevent protein synthesis

• viruses+ eukaryotic cells are not damaged by antibiotics because they dont have cell walls and have different ribosomes+ enzymes

CPAC 15: Investigating effects of different antibiotics

1. transfer bacterial culture (e.coli) onto agar plate using sterile pipette and spread using innoculating loop (lawning technique)

2. stelirise by passing equipment through bunsen burner before and after use

3. soak paper discs into different antibiotics: Tetracycline, Chloramphenicol and amoxycillin and in control (water)

4. Place each disc in a quarter of the agar plate

5. Lightly tape the lid onto petri dish and invert and incubate at 25 degrees for 24 hours

6. Measure zone of inhibitions for all anitbiotics, larger zones means they are the most effective- use stats test

HOSPITAL ACQUIRED INFECTIONS

Measures to reduce risk of infections:

• staff and visitors must wash hands regularly

• when infected with a HAI they must be isolated to prevent spread

• surfaces and equipment disinfected before and after use

ANTIBIOTIC RESISTANCE:

HAI’s are caused by antibiotic resistant bacteria e.g MRSA resistnace to methicillin

Hospitals provides a selection pressure for natural selection:

1. random mutations

2. the bacterial infection is treated with antibiotics which only kill most of the bacteria

3. the resistant with advantageous alleles survuve and pass these genes (binary fission and transfer of genes through pili)

4. the resistance increases in population= antibiotic can no longer work.