3.8.3 and 3.8.4 gene technologies Flashcards
3.8.3 and 3.8.4 gene technologies
how many genes and base pairs does a avarage human have
3 billion base pairs
25000 genes
what could the information used from sequencing genomes of species be used for
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.
what is bioinformatics
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.
what can researchers use bioinformatics be used for
identify genes,
establish their functions,
develop gene-based strategies for preventing,
diagnosing, and treating disease,
compare DNA between individuals,
compare DNA between different species.
describe the steps of sanger sequencing
1 . sample of DNA is broken into many fragments and inserted in bacteria
- DNA sample fragments are copied many times by bacteria
- sample fragments are added to a mixture of primers , DNA polymerase and terminator nucleotides ( labelled with one of four fluorescent dyes)
- DNA polymerase copies the sample of DNA until a terminator nucleotide is added
- 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
- the colour of the emitted light is recorded by the sequencing machine
- based on the sequence of the light colours emitted , the DNA base sequence can be worked out
explain what whole-genome shot gun sequencing is
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
what are the medical advancements because of the human genome project
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).
what are the two diffrent types of DNA probes
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.
why are prokaryotes easier to sequence than eukaryotes
Relatively easy
Prokaryotes have one, circular piece of DNA not associated with histones
No non-coding portions of DNA
what are SNPs
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
what are the aplications of knowing the proteome of a prkaryote
identifications of antigens on pathogens to make antibodys /vaccines
classification of bacteria
evolution of bacteria
understanding metabolism of bacteria
info card read and recite
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
what are the disadvantages of sequncing
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
what is a DNA probe
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)
what is DNA hybridisation
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
how would you find a spesific allele
- probes with the complementory base sequnce are made and replicated thousends of times over and we also add flourent tages to them
- 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
- use UV kight innorder to see if any probes have attatched
describe how microarrays work
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
what are the uses of genetic testing
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
what is pharmacogenomics and give an example of wwhere it can be used
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.
give three reasons for the personanilised medicine approch
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
waht are the advantages of gene testing
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
what are the disadvantages of gene testing
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
what is genetic counselling
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
waht is the objective of gene theropy
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.
what is the cause of genetic disease
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).
what are the two ways of replacing defective gene s
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
what are the two vectors that can be used for gene therepy
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
how is cystic fibrosis caused
Caused by a mutation in the cystic fibrosis transmembrane regulatory protein
what does the CFTR protein do
It helps control the viscosity (or stickiness) of mucus that lines the epithelial cells of the airways, digestive and reproductive systems
what happens if the mucus in the air way is too sticky
too sticky: the cilia cannot beat and remove the mucus, which then clogs up airways
what happens if the mucus in the air way is too runny
too runny: the mucus can flood the airways
what happens when there is excess water in the mucus
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
what happens when there is too little water in the mucus
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
how is CFTR effect in cystic fibrosis
CFTR is closed and there fore becomes very thick and sticky
therefore the Na+ channels are always open as CFTR does not close them
dsecribe the gene therepy technique
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.
info card
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
why is gene therepy not always effective
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.
