Topic 6 - Immunity, Infection and Forensics

Question 1

Define “DNA profile” and draw a flow chart outlining the steps in making a DNA profile

Answer 1

A DNA profile is a visual record of some sections of our DNA (introns). As our DNA base sequences are not identical to other people, they can be used to identify an individual.

Step 1 – extract the DNA from cells with a nucleus
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Step 2 – protease enzymes are used to remove histone proteins
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Step 3 – specific restriction enzymes are added to cut the DNA into fragments
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Step 4 – separate the fragments by mass using gel electrophoresis, to create a banding pattern

Question 2

Explain the role of DNA primers, DNA nucleotides and DNA polymerase in PCR

Answer 2

DNA primers – short, single strands of DNA are complementary to part of the template strand and so bind with it (by base pairing). This prevents the other DNA template strands from simply joining back to each other. Also, DNA primers are needed to help make the missing strand as DNA polymerase needs a double-stranded sequence to start from

Free DNA nucleotides – these will bind to the template strand by base pairing

DNA polymerase – this enzyme will build the missing DNA strand by base pairing (using the single strand as a template for the new strand)

Question 3

Describe the two properties of DNA fragments that determine how far they travel in gel electrophoresis

Answer 3

1. DNA carries a negative electrical charge, so the fragments move towards the positive electrode
2. Smaller / less dense fragments move through the gel quicker, so they travel further than the larger fragments

Question 4

Explain the role of DNA probes in gel electrophoresis and describe how they can be labelled

Answer 4

A DNA probe is a single strand of DNA used to identify the target DNA sequence. It will bind by base pairing as it is complementary to the target sequence.

The DNA probe is tagged with either radioactive phosphorus or a fluorescent marker – this makes the target fragment visible to the scientist (seen as a banding pattern)

Question 5

Suggest how DNA profiling can be used to answer questions about identity in different situations

Answer 5

1. study the patterns of bands produced (their number, position, widths)
2. bands will be in certain positions due to their mass
3. if two profiles have very similar banding patterns it suggests that they are more closely related to each other than two profiles which have less similar banding patterns
4. in evolutionary terms, if two species have similar banding patterns they have a more recent common ancestor than two species whose banding patterns are less similar.

Question 6

Explain why DNA profiling isn’t infallible

Answer 6

a complete DNA profile would definitely be unique, but the DNA is only sampled

as only a few repeated sequences are analysed, it is less likely to be completely unique, particularly if the people are closely related

Question 7

Describe the sequence of events that result in muscles going into rigor mortis

Answer 7

Following death, the sarcoplasmic reticulum decomposes

This releases the Ca2+ ions into the sarcoplasm

Ca2+ ions bind to troponin, and the troponin changes shape

This moves the tropomyosin, allowing myosin to bind to the actin binding site

Myosin cannot let go once the ATP has run out

Question 8

Define autolysis and describe what causes it

Answer 8

Autolysis refers to the destruction of a cell through the action of its own enzymes

Autolysisis a response to injury or infection and generally does not occur in healthy cells.

Question 9

Describe the similarities and differences between succession on a corpse and plant succession

Answer 9

Plants – end result is a climax community / which takes a long time to form / occurs over a large area / pioneer species replaced by later colonists

Body – no climax community / succession is fast / takes place over a small area / pioneer species often persist throughout the succession

Question 10

Describe how viruses can vary in structure

Answer 10

All viruses have a capsid (protein coat) / nucleic acid inside the capsid / are particles not cells / cannot reproduce without a host cell / either cause humans harm or have no effect on us (but never beneficial)

Variability – may have dsDNA, ssDNA, or RNA / some have an outer envelope taken from the cell surface membrane of the host cell (enveloped viruses)

Question 11

Define the term pathogen

Answer 11

Disease-causing organisms

Question 12

Describe the inflammation response and explain its usefulness

Answer 12

1. Area goes red and swollen – due to arrival of extra blood flow
2. Due to vasodilation of arterioles leading to the damaged area (due to release of histamine)
3. Capillaries leakier than normal due to histamine
4. Feels hot as lots of respiration is occurring here (e.g. mitosis of WBCs, antibody production)
5. Painful to touch as nerve endings are very sensitive

Question 13

Explain the roles antibodies have in the immune response

Answer 13

Made by plasma cells they:

(i) cause agglutination – an antibody can attach to two pathogens at the same time, which clumps the pathogens together. This stops the pathogens from reproducing or infecting cells, and eventually a phagocyte will engulf the antibodies and the pathogens

(ii) neutralise toxins – antibodies can bind to toxins and prevent them from affecting our cells

(iii) prevent pathogens binding to our cells – by binding to the pathogen the antibody may block the cell surface receptor that the pathogen needs to bind to the host cell.

Question 14

Define “antigen presenting cells” and explain how they come about

Answer 14

Any cell which has either been attacked by a pathogen, or has engulfed a pathogen (e.g. a macrophage)

Molecules from the pathogen (called antigens, e.g. glycoproteins) are placed in the cell surface membrane of the cell

This is now called an antigen-presenting cell (APC)

This allows T lymphocytes to bind to the antigen and respond, or a phagocyte to engulf the cell and destroy it

Question 15

Describe the role of T-killer cells in the specific immune response

Answer 15

T killer cells destroy any cells which have non-self antigens in their cell surface membrane.

They attach to the antigen (and therefore to the cell) and then dividing to make an active clone.

T killer cells next release enzymes which make holes in cell surface membrane of the infected cell. This allows ions and hence water to enter the cell; the cell then swells and bursts and is destroyed.

Question 16

Explain the importance of B and T memory cells

Answer 16

B memory cells and T memory cells are made during a primary infection

They are clones of the original cell

They remain in our bodies, so that when there is a second infection the immune response is much faster

Question 17

Describe the adaptations that the TB bacterium has to evade the immune system

Answer 17

Their thick waxy cell wall makes them difficult to digest so they remain inactive but alive in macrophages

The waxy cell wall acts as a barrier to antibiotics, and prevents them from drying out

They can remain dormant for many years, only becoming active again if the immune system is weakened

They can suppress lymphocyte activity (so reducing antibody production and T killer cell attack)

Question 18

Explain 3 symptoms of TB

Answer 18

1. Persistent cough (more than 2 weeks) – lungs are irritated by the tubercle – body’s attempt to remove the dead tissue
2. Coughing up blood – blood vessels in the lungs are damaged
3. Severe breathing problems (cough up greenish sputum) – tubercle has destroyed lung tissue, reducing the surface area of the lung, reducing the lung’s ability to do gas exchange (lack of oxygen going into the blood)
4. Loss of weight (hence the old name “consumption”) – due to appetite loss and vomiting
5. Extreme fatigue – lack of oxygen getting into blood in the lungs, so not enough respiration can occur to release energy
6. Night sweats – possibly due to fever-causing molecules released by immune cells or the TB bacteria

Question 19

Define the term “retrovirus”

Answer 19

A virus that contain RNA instead of DNA in its capsid

HIV is a retrovirus

Question 20

Explain why substitution mutations have a different impact on the final protein to insertion / addition or deletion mutations

Answer 20

For a substitution mutation, at worst there will be one wrong amino acid in the primary structure (which may or may not affect the shape of the protein)

Insertion or deletion of one or two bases is more serious as it results in a frame shift, meaning potentially every amino acid from that point onwards is wrong

If three bases are inserted or deleted, and these make up a single triplet, then this is less serious as only one amino acid in the primary structure is wrong
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Question 21

Explain how a substitution mutation may have no effect on the final protein at all

Answer 21

A substitution mutation may have no effect on the final protein as the same amino acid may be coded for (degenerate code) so the primary structure is unchanged

Question 22

Explain why bacteria and viruses evolve very quickly and explain why this is a problem for the immune system and for the development of treatments

Answer 22

Both reproduce very quickly (for most bacteria it is once every 30 minutes, whilst viruses burst out of cells in large numbers every couple of hours), so mutations occur frequently

Both also have large populations, so mutations are likely to occur in some of them, so they evolve quickly

Specific immune cells and antibodies will not recognise the mutated pathogen, so the body has to have a new primary response each time

Similarly drug treatments (e.g. the flu vaccine) have to be continually updated as the next version of the pathogen may be unaffected by the treatment

Question 23

Describe the selection pressure that antibiotics provide for bacteria and explain the importance of a patient completing a treatment of antibiotics

Answer 23

Antibiotics kill (bactericidal) or stop bacteria reproducing (bacteriostatic) in a number of ways (see notes pack)

Failure to complete the course of antibiotics may mean that resistant bacteria survive and reproduce to cause a second bout of the infection, which now needs treatment with a different antibiotic

Question 24

Explain how horizontal evolution can occur in bacteria, and the benefit of this to bacteria

Answer 24

Bacteria may copy a plasmid that provides antibiotic resistance and pass it to an adjoining bacterium (via a pilus)

This means that DNA is shared without reproduction occurring

The receiving bacterium is now also resistant

Question 25

Describe how a pathogen may evolve resistance to a drug

Answer 25

Pathogens live in large populations and reproduce quickly so the chances of some developing resistance alleles through a random mutation to DNA is high

The antibiotic / drug is the selection pressure

These pathogens survive the drug and reproduce

Their offspring also have the resistance alleles

The allele frequency for the resistance alleles increases

Question 26

Describe how STRs vary and why they can be used to identify individuals

Answer 26

STRs can be 2-50 base pairs long.

STRs can be repeated between 5 and several hundred times at a specific locus.

The number of repeats can be highly variably amongst different people.

If a range of STRs is analysed, it is highly unlikely that two people will have the same number of repeats at each locus, i.e. there is a lot of variation in the number of repeats at each locus.

Differences in the number of repeats at STR loci can be used to identify individuals.

Question 27

Know how DNA can be amplified using the polymerase chain reaction (PCR)

Answer 27

In each cycle of PCR the number of DNA strands is doubled by semi-conservation replication.

A reaction tube containing DNA, DNA primers, DNA polymerase, free nucleotides and buffer is heated to 95oC.
Hydrogen bonds holding the two DNA strands together break and the strands separate.

The reaction tube is cooled to 55oC.
DNA strands could re-anneal at this temperature. However, it is more likely that the DNA primers, which are added in excess, will attach to the complementary sequence on the long DNA molecule.

The reaction tube is heated to 70oC.
The is the optimum temperature for the DNA polymerase used. Nucleotides attach to complementary bases on the long DNA molecule and the polymerase extends the primer by catalysing the formation of phosphodiester bonds between the end of the primer and the free nucleotides.

The cycle is repeated between 28-32 times to get a lrge enough DNA sample.