Module 6- Manipulating Genomes Flashcards
Define genome
Genome of an organism is all the genetic material it contains
Define introns
Large non coding regions of DNA that are removed from mRNA before it’s translated into a polypeptide chain
Name the 5 steps of producing a DNA profile
1)extracting the DNA
2)digesting the sample
3)separating the DNA fragments
4)hybridisation
5)seeing the evidence
Describe stage 1:extracting the DNA, in the process of producing a DNA sample
-the dna must be extracted from a tissue sample using a polymerase chain reaction where the tiniest amount of tissue can give scientists enough dna to develop a profile
Describe stage 2:digesting the sample, in the process of producing a DNA sample
-strands of DNA are cut into small fragments using enzymes called restriction endonucleases
-different restriction endonucleases cut dna at a specific nucleotide sequence known as restriction or recognition site
-all restriction endonucleases make 2 cuts, once through each strand of the DNA double helix
-restriction endonucleases give scientists the ability to cut dna strands at defined points in introns
Describe stage 3:separating the dna fragments, in the process of DNA profiling
-the cut fragments of dna need to be separated to form a clear and recognisable pattern
-this is done using electrophoresis- a technique that utilises the way charged particles move through a gel medium under the influence of an electric current
-the gel is then immersed in alkali in order to separate the DNA double strands into single strands and separates DNA fragments out according to size
-the single stranded DNA fragments are then transferred onto a membrane by southern blotting where the negatively charged DNA moves through the gel towards the positive electrode with smaller fragments moving faster and further
Describe the process of PCR
-the dna sample to be amplified, an excess of 4 nucleotide bases, small primer DNA sequences and DNA polymerase are mixed in a vial that is placed in a PCR machine aka thermal cycler
-the DNA is heated to 96 deg c to denature the strands and provide single stranded templates for replication by breaking the hydrogen bonds
-the reaction is cooled to 60 deg c to allow primers to anneal to the single strands of dna
-the reaction is heated to 72 deg c so that taq polymerase can work at optimum conditions and can rapidly extend the nucleotide chains from primers
-this process is repeated 25-35 times and the amount of dna increases exponentially with every repeat
What are the applications of DNA profiling
-in the forensic field-DNA profile is compared to a sample taken from a suspect
-prove paternity of a child
-identifying individuals who are at risk of developing a particular disease by identifying specific gene markers
Describe the process of DNA sequencing
1)the dna for sequencing is mixed with a primer (dna polymerase) which is an excess of normal nucleotides and terminator bases
2)the mixture is placed in a thermal cycler
3)at 60 deg c dna polymerase starts to build up new dna strands by adding nucleotides with the complementary base to the single strand dna template
4)each time a terminator base in incorporated instead of a normal nucleotide, the synthesis of dna is terminated as no more bases can be added. After many cycles all of the possible dna chains will be produced with the reaction stopped at every base. The dna fragments are separated according to their length by capillary sequencing. Fluorescent markers on the terminator bases are then used to identify the final base on each fragment. Lasers detect the different colours and therefore the order of the sequence
5)the order of the bases in the capillary tubes shows the sequence of the new complementary strand of dna which has been made. This is used to build up the sequence of the original dna strand. Once a genome is assembled scientists want to identify the genes or part of the genome that code for specific characteristics
Describe the process of next generation sequencing
-instead of using gel or capillaries, the sequencing reaction takes place on a plastic slide known as a flow cell
-millions of fragments of dna are attached to the slide and replicated in situ using PCR to form clusters of identical dna fragments
-the sequencing process still uses the principle of adding a coloured terminator base to stop the reaction so an image can be taken
-as all of the clusters are being sequenced and imaged at the same time the technique is known as next generation sequencing
-this is integrated with computer technology
Define bioinformatics
Development of a software and computing tools needed to organise and analyse raw biological data
Define computational biology
-uses the data from bioinformatics to build theoretical models of different biological systems which can be used to predict what will happen in different circumstances
What does computational biology do?
-works out 3D structures of proteins
-helps to understand gene regulation
How is DNA barcoding used in identifying species?
A section of dna that is small enough to be sequenced quickly and cheaply yet varies enough to give clear differences between species is chosen
-scientists haven’t come up with a suitable region form fungi or bacteria yet
Define proteomics
-study amino acid sequencing of an organisms entire protein complement
What do spliceosomes do ?
-mRNA transcribed from the DNA in the nucleus includes both introns and exons
-before it lines up on the ribosomes to be translated, the introns are removed
-then the exons to be translated are joined together by enzyme complexes known as spliceosomes to give the mature functional mRNA
What is the study of proteomics giving us?
Increased knowledge of the relationship between genotype and phenotype
Define synthetic biology
-the ability to sequence the genome of organisms and understand how each sequence is translated into amino acids along with the increasing ability of computers to manipulate and analyse data
What 3 techniques does synthetic biology include?
-genetic engineering
-use of biological systems
-synthesis of new genes
What does genetic engineering involve?
-a single change in a biological pathway or major genetic modification of an entire organism
What does use of biological systems involve?
-using fixed or immobilised enzymes and the production of drugs from microorganisms
What does synthesis of new genes involve?
-to replace faulty ones e.g for treatment of cystic fibrosis scientists have attempted to synthesise functional genes in the lab and use them to replace the faulty genes of those with CF
What is recombinant DNA?
-where the fragments of foreign DNA are inserted into other sections of DNA
How can DNA be considered to be a universal code?
-as every organism uses the same 4 bases as the genetic code to produce proteins
-because of this, any section of DNA can be taken from one organism and placed inside another where it is r then transcribed and translated to produce proteins
