3.8.3 and 3.8.4 gene technologies

Question 1

how many genes and base pairs does a avarage human have

Answer 1

3 billion base pairs

25000 genes

Question 2

what could the information used from sequencing genomes of species be used for

Answer 2

to help cure diseases

To allow us to use genes that provide specific adaptations in some organisms

such as :
withstanding extreme or toxic environments,
cleaning up pollutants or manufacturing biofuels.

Question 3

what is bioinformatics

Answer 3

Bioinformatics is the branch of biology that is concerned with the acquisition, storage, and analysis of the information found in nucleic acid and protein sequence data. Computers and bioinformatics software are the tools of the trade.

Question 4

what can researchers use bioinformatics be used for

Answer 4

identify genes,
establish their functions,
develop gene-based strategies for preventing,
diagnosing, and treating disease,
compare DNA between individuals,
compare DNA between different species.

Question 5

describe the steps of sanger sequencing

Answer 5

1 . sample of DNA is broken into many fragments and inserted in bacteria

2. DNA sample fragments are copied many times by bacteria
3. sample fragments are added to a mixture of primers , DNA polymerase and terminator nucleotides ( labelled with one of four fluorescent dyes)
4. DNA polymerase copies the sample of DNA until a terminator nucleotide is added
5. A mixture of fragments of many diffrent sizes are produced

6/7 . smaller fragments travvel more quickly through the gel, and arrive at the end where they are hit with a laser beam

8. the colour of the emitted light is recorded by the sequencing machine
9. based on the sequence of the light colours emitted , the DNA base sequence can be worked out

Question 6

explain what whole-genome shot gun sequencing is

Answer 6

Shotgun sequencing is a method used for sequencing long DNA strands.

The chain termination method of DNA sequencing (“Sanger sequencing”) can only be used for short DNA strands of 100 to 1000 base pairs.

Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence.

Use computer algorithms to align overlapping segments to assemble the entire genome

basically :

break into random fragments lots of DNA of the same sort , and then watch where they overlap and then from there we can sequence the whole genome

Question 7

what are the medical advancements because of the human genome project

Answer 7

Single nucleotide polymorphisms (SNPs) have been found in the human genome. (Over 1.4 million)

SNPs are single base variations in the genome (caused by a point mutation).

They can be associated be disease and other disorders.

Medical screening allows identification of potential medical problems and allows for early intervention to treat them (hapmap).

Question 8

what are the two diffrent types of DNA probes

Answer 8

radioactively labelled probes – nucleotide with the isotope 32P. The probe can be identified using x-ray film that is exposed to radioactivity

Fluorescently labelled probes – emit light under certain conditions i.e. when the probe has bound to the target DNA sequence.

Question 9

why are prokaryotes easier to sequence than eukaryotes

Answer 9

Relatively easy
Prokaryotes have one, circular piece of DNA not associated with histones
No non-coding portions of DNA

Question 10

what are SNPs

Answer 10

SNPs are singluar base variations in the genome (caused by point mutatiuons ) / (addition / sunstatution)

they can be associated with disorders
medical screening allows identification of potential medical problems which allow for early intervention

Question 11

what are the aplications of knowing the proteome of a prkaryote

Answer 11

identifications of antigens on pathogens to make antibodys /vaccines

classification of bacteria

evolution of bacteria

understanding metabolism of bacteria

Question 12

info card read and recite

Answer 12

Plasmodium falciparumis a species of parasite that causes severe forms ofmalaria
Thousands of these parasites have been used for genome sequencing
Scientists have been searching for differences between their DNA sequences to identify thegenesthat display thehighest level of variationbetween individuals
A high level of variation suggests that those genes are understrong selective pressure.These genes could code for theantigen proteinsfound on the parasites
Once the antigenic genes are identified the antigen they code for can be used in vaccine production
The protein coded for by the specific gene would beinjectedinto people living in areas with malaria to see if they produceantibodiesthat provide immunity against the disease
There is also research being done to identify genes within the parasite’s genome that affect drug resistance and insecticide resistance
Genes that help to protect against severe malaria have also been identified within the human genome

Question 13

what are the disadvantages of sequncing

Answer 13

Decoding the DNA sequence poses daunting moral dilemmas:

re-engineer the human species

prospective parents choose their unborn child’s traits
.
serious side effects to manipulating the genes

employment and health insurance eligibility

Question 14

what is a DNA probe

Answer 14

Short, single stranded length of DNA with a label attached
Use the idea that a ssDNA (probe) can bind to a complimentary base pair with a single strand of DNA (target)
Detect the piece of target DNA by using the label on the probe (label being radioactive labbel or flouresent labbel)

Question 15

what is DNA hybridisation

Answer 15

Base sequences complementary to the allele of the gene we want to find
The double stranded DNA to be tested has its strands separated by heating the DNA.
The separated strands are cooled and mixed with the probe
If the probe is complementary to a section of the DNA strand it will bind. This is DNA hybridisation
The site where the probe binds can be identified by the radioactivity or fluorescent label

Question 16

how would you find a spesific allele

Answer 16

1. probes with the complementory base sequnce are made and replicated thousends of times over and we also add flourent tages to them
2. we then get the DNA strand that we want to test and replicated that many time over , then mix this into the probes with makers on them.

3 heat so that the dDNA can sepirate at around 95oC , then freezw at -60oc to make ssDNA which allow the probes to bind to the DNA

4, wash off any unjoined probes this will make sure that this is note a false test

5. use UV kight innorder to see if any probes have attatched

Question 17

describe how microarrays work

Answer 17

1) take two samples, sample one is health while sample two is cancerous or whatever , extract there mRNA and use reverse transcriptase to make cDNA

2) this cDNA is flourecently labbeled e.g sample 1 is green and sample 2 is red

3) add replicated cDNA with floresent markers into a well wit oligonucleotides ( which are just a sequence of a spesific gene)

4) complementory base pairs will bind to the oilgonucliotides and when shine with UV light they will ilumiate if binded to e.g green

5) therefore sample one has gene x and is expressed while sample 2 does not have gene x and is silanced

Question 18

what are the uses of genetic testing

Answer 18

pre-implantation genetic diagnosis

pre-natal diagnostic testing

newborn baby screening

pre-symptomatic testing for predicting adult-onset disorders such as Huntington’s disease

pre-symptomatic testing for estimating the risk of developing adult-onset cancers eg mutations in tumour suppressor genes

Confirmation that an individual has a suspected disease

forensic/identity testing

Question 19

what is pharmacogenomics and give an example of wwhere it can be used

Answer 19

Looks at how genetic variation affects an individual’s response to a drug.

Pharmacogenomic tests can already identify whether or not a breast cancer patient will respond to the drug Herceptin, whether an AIDS patient should take the drug Abacavir, or what the correct dose of the blood-thinner Warfarin should be.

Question 20

give three reasons for the personanilised medicine approch

Answer 20

Prescribing painkillers – many pain medications need a specific enzyme to activate them.

About ½ the population have genes which alter the function of this enzyme. Screening will allow dosage of the painkiller to be adjusted to compensate for the genes effect on the metabolism of the drug to ensure the safe and effective use.

Vitamin E has been shown to reduce the risk of cardiovascular disease for people with diabetics and a certain genotype but will increase the risk for those with a different genotype.

Screening will ensure the correct advice is given

Question 21

waht are the advantages of gene testing

Answer 21

Gene testing can help to clarify a diagnosis and direct a physician toward appropriate treatments.

Identify people at high risk for conditions that may be
Preventable so they can change their lifestyle (give up smoking, lose weight, eat healthily, avoid mutagens) and have regular checkups

Tests can help families avoid having children with devastating diseases

Question 22

what are the disadvantages of gene testing

Answer 22

There is a possibility for laboratory errors. E.g. sample misidentification, contamination of the chemicals used for testing, or other factors.

The tests give only a probability for developing the disorder and some people will never develop the disease. Scientists believe that other mutations or environmental factors may be needed to cause the disease to develop.

Some believe that if prenatal tests are carried out, finding defective alleles will lead to an increase in the number of abortions

Question 23

what is genetic counselling

Answer 23

Evaluating family history and medical records

Explaining the probability of passing on specific alleles

Explaining the emotional, psychological, medical, social and economics consequences of genetic diseases to help with family planning

Ordering genetic tests

Evaluating the results of this investigation

Patients screened at regular intervals

Advice on lifestyle changes

Helping parents understand and reach decisions
about what to do next

Question 24

waht is the objective of gene theropy

Answer 24

The aim of gene therapy is to treat a genetic disease by replacing defective genes in the patient’s body with copies of a new DNA sequence.

Question 25

what is the cause of genetic disease

Answer 25

A mutation of a gene that causes a recessive allele is often the cause (but not always – Huntington’s is caused by a dominant allele).

Question 26

what are the two ways of replacing defective gene s

Answer 26

Somatic cell therapy – the therapeutic genes are transferred into the somatic (body) cells, of a patient. Any modifications and effects will be restricted to the individual patient only, and will not be inherited by the patient’s e.g. use of liposomes to treat cystic fibrosis.

Germ line therapy – sperm or eggs, are modified by the introduction of functional genes, which are integrated into their genomes. This would allow the therapy to be heritable and passed on to later generations. This is largely prohibited for ethical reasons

Question 27

what are the two vectors that can be used for gene therepy

Answer 27

Viruses:
Insert DNA into host cell
Size limited 8Kb
Integration of vector into host’s DNA can cause side effects

Liposomes –transfer plasmids
Lipid bilayer
Target specific cells and do not elicit an IR
Can carry up to 20Kb but less efficient than viruses

Question 28

how is cystic fibrosis caused

Answer 28

Caused by a mutation in the cystic fibrosis transmembrane regulatory protein

Question 29

what does the CFTR protein do

Answer 29

It helps control the viscosity (or stickiness) of mucus that lines the epithelial cells of the airways, digestive and reproductive systems

Question 30

what happens if the mucus in the air way is too sticky

Answer 30

too sticky: the cilia cannot beat and remove the mucus, which then clogs up airways

Question 31

what happens if the mucus in the air way is too runny

Answer 31

too runny: the mucus can flood the airways

Question 32

what happens when there is excess water in the mucus

Answer 32

Na + channels open and Na + pump starts pumping into the tissue fluid

water moves in to tissue fluid due to osmosis

Cl- move to the tissue fluid

CFTR channel is closed

Question 33

what happens when there is too little water in the mucus

Answer 33

Na + channels close and Na + pump stop pumping into the tissue fluid, Na + moves from tissue fluid to mucus

water moves in to the muscus due to osmosis

Cl- move to the musucs

CFTR channel is open , blocking the sodium channels

Cl - pump starts pumping cells into the cell

Question 34

how is CFTR effect in cystic fibrosis

Answer 34

CFTR is closed and there fore becomes very thick and sticky

therefore the Na+ channels are always open as CFTR does not close them

Question 35

dsecribe the gene therepy technique

Answer 35

The genes are inserted into liposomes (minute spheres of lipid molecules capable of carrying DNA).

This involves wrapping the gene in lipid molecules that can pass through the membranes of lung epithelial cells.

An aerosol inhaler is used to add the non-defective gene to the epithelial cells of the lung.

The liposomes fuse with the phospholipid bilayer of the cell membrane and the DNA enters the cells. These cells start to express the inserted gene by making the protein CFTR.

Question 36

info card

Answer 36

SCID is a rare inherited disease.
People with this disorder are unable to mount a cell-mediated response.
They cannot produce antibodies.
The disorder arises when individuals inherit a defect in the gene that codes for the enzyme adenosine deaminase (ADA).
This enzyme destroys toxins that would otherwise kill white blood cells (specifically T cells). These sufferers need bone marrow transplants and/or injections of ADA

Normal ADA gene isolated from human tissue
ADA gene inserted into a retrovirus
Retrovirus grown in host cells to increase their number
Retrovirus mixed with the patient’s T cells into which they inject a copy of the normal ADA gene
The T cells are reintroduced into the patient’s blood
This lasts for 6-12 months
Long term treatment could be achieved by introducing the normal gene into bone marrow stem cells

Question 37

why is gene therepy not always effective

Answer 37

Delivering the gene to the right place and switching it on

Avoiding the immune response

Make sure the new gene doesn’t disrupt the function of other genes:

The cost - gene therapy therefore often requires an individual, case-by-case approach. This may be effective, but may also be very expensive.