Module 6- Manipulating Genomes

Question 1

Define genome

Answer 1

Genome of an organism is all the genetic material it contains

Question 2

Define introns

Answer 2

Large non coding regions of DNA that are removed from mRNA before it’s translated into a polypeptide chain

Question 3

Name the 5 steps of producing a DNA profile

Answer 3

1)extracting the DNA
2)digesting the sample
3)separating the DNA fragments
4)hybridisation
5)seeing the evidence

Question 4

Describe the process of extracting the DNA during the process of producing a DNA sample

Answer 4

-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

Question 5

Describe the process of digesting the sample during the process of producing a DNA sample

Answer 5

-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

Question 6

Describe the process of separating the dna fragments during the process of producing a DNA sample

Answer 6

-the cute 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

Question 7

Describe the process of PCR

Answer 7

-the dna sample to be a,Plainfield, 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 an 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

Question 8

What are the applications of DNA profiling

Answer 8

-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

Question 9

Describe the process of DNA sequencing

Answer 9

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

Question 10

Describe the process of next generation sequencing

Answer 10

-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

Question 11

Define bioinformatics

Answer 11

Development of a software and computing tools needed to organise and analyse raw biological data

Question 12

Define computational biology

Answer 12

-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

Question 13

What does computational biology do?

Answer 13

-works out 3D structures of proteins
-helps to understand gene regulation

Question 14

How is DNA barcoding used in identifying species?

Answer 14

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

Question 15

Define proteomics

Answer 15

-study amino acid sequencing of an organisms entire protein complement

Question 16

What do spliceosomes do ?

Answer 16

-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

Question 17

What is the study of proteomics giving us?

Answer 17

Increased knowledge of the relationship between genotype and phenotype

Question 18

Define synthetic biology

Answer 18

-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

Question 19

What 3 techniques does synthetic biology include?

Answer 19

-genetic engineering
-use of biological systems
-synthesis of new genes

Question 20

What does genetic engineering involve?

Answer 20

-a single change in a biological pathway or major genetic modification of an entire organism

Question 21

What does use of biological systems involve?

Answer 21

-using fixed or immobilised enzymes and the production of drugs from microorganisms

Question 22

What does synthesis of new genes involve?

Answer 22

-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

Question 23

What is recombinant DNA?

Answer 23

-where the fragments of foreign DNA are inserted into other sections of DNA

Question 24

How can DNA be considered to be a universal code?

Answer 24

-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

Question 25

What produces recombinant DNA?

Answer 25

The process of transferring sections of DNA (fragments)

Question 26

What is the organism called who receives fragments of DNA?

Answer 26

Transgenic

Question 27

What are the 3 stages of genetic engineering?

Answer 27

Isolating the desired gene, formation of recombinant DNA, transferring the vector

Question 28

Describe the first stage of genetic engineering- isolating the desired gene

Answer 28

-most common technique uses restriction endonucleases to cut the required gene from the DNA of an organism
-these regions with unpaired exposed bases are called sticky ends
-the sticky ends makes it a lot easier to insert the desired gene into DNA of a different organism
-you can also use the enzyme reverse transcriptase to produce a single strand of complementary DNA
-this makes it easier to identify the desired gene as a particular cell will make specific types of mRNA

Question 29

Describe the second stage of genetic engineering- formation of recombinant DNA

Answer 29

-the DNA isolated by restriction endonucleases must be inserted into a vector that can carry it into a host cell
-the most commonly used vectors in genetic engineering are bacterial plasmids
-once a plasmid gets into a new host cell it can combine with the host DNA to from recombinant DNA
-the plasmid is cut open using restriction endonuclease and has complementary sticky ends to the sticky ends of the DNA fragment and they line up
-DNA ligaments forms phosphodiester bonds between the sugar and the phosphate groups open the 2 strands of DNA joining them together.

Question 30

Describe the third stage of genetic engineering- transferring the vector

Answer 30

-the plasmid with the recombinant DNA must be transferred into he host cell in a process called transformation
-one method of transformation is electroporation where a small electrical current is applied to the bacteria which makes the membranes very porous and so the plasmids move into the cells
-the power of the electric current has to be carefully managed or the membrane will be permanently damaged or destroyed which in turn destroys the whole cell

Question 31

How have prokaryotes been engineered?

Answer 31

-bacteria and other microorganisms have been genetically modified to produce many different substances that are useful to people e.g insulin

Question 32

How have plants been engineered?

Answer 32

-transgenic plant cels form a callus, which is a mass of GM plant cells each of which can be grown into a new transgenic plant
-transgenic plant cells can also be produced by electrofusion

Question 33

Can animals been engineered?

Answer 33

-its harder to engineer the DNA of eukaryotic animals as animal cell membranes are harder to manipulate

Question 34

What are ethical concerns of genetic engineering?

Answer 34

-inserting genes distrusts normal gene functioning
-leads to a reduction in the variety of a population so extinction is more likely
-companies who are able to invest more money into recombinant DNA may outcompete others
-using recombinant DNA in medicine could lead to unethical uses of genetic engineering e.g designer babies
-biodiversity is reduced if herbicides are overused to destroy weeds

Question 35

Pros of GM crops

Answer 35

-extended shelf life so reduced food waste
-crops can survive in adverse conditions
-nutritional value of crops could be increased
-increased yield through increased pest, herbicide and disease resistance

Question 36

What is a patent and how would it affect the use of GM crops?

Answer 36

-one concern about GM crops is that people in less economically developed countries will be prevented from using them by patents and issues of technology transfer
-a patent is where no one else can use GM seeds without payment which creates issues for poorer farmers in developing countries

Question 37

What is somatic cell gene therapy?

Answer 37

-replacing the mutant allele with a healthy allele in the affected somatic (body) cells
-only a temporary solution for the treated individual as somatic cells have a limited life so are replaced by stem cells which will still are the faulty allele
-they will still pass on the faulty allele to any children they have
-treats haemophilia and immune diseases

Question 38

What is germ line therapy?

Answer 38

-insert a healthy allele into the germ cells or an embryo immediately after fertilisation (as part of IVF)
-is illegal to do for human embryos in Mostar countries due to ethical and medical concerns due to maybe choosing desirable or cosmetic characteristics of offspring