manipulating genomes

Question 1

Describe PCR process in 7 steps

Answer 1

• DNA sample mixed with DNA nucloetides, primers, Mg2+, TAQ DNA polymerase
• mixture heated to 95°C to break H bonds, make 2 single strands of DNA. TAQ doesnt denature.
• cooled to 65°C so primers anneal to 3’ end of strand.
• TAQ binds to where double stranded DNA is.
• Temp raised to 72° for TAQ. Comp base pairing occurs
• when TAQ reaches end, new strand of double created
• process repeated, (heated back to 95°C)

Question 2

whats a palindromic sequence (recognition sequences)

Answer 2

a sequence of DNA bases that consists of antiparallel base pairs

Question 3

whats another way (other than PCR) to get a DNA fragment from an organism’s DNA

Answer 3

restriction enzymes

Question 4

whats a restriction enzyme

Answer 4

enzymes that recognise specific recognition sequences and cut DNA at these places

Question 5

whats gel electrophoresis

Answer 5

a technique that allows DNA fragments, RNA fragments or proteins to be separated on a gel according to size

Question 6

outline the last 4 steps of gel electrophoresis after the gel has been set up

Answer 6

• pour in buffer till gel covered
• electrodes placed in ends of tank
• DNA samples loaded into wells, has overall negative charge
• smaller fragments travel further so can be compared

Question 7

how does gel electrophoresis differ for RNA and proteins

Answer 7

• RNA fragments are same basic method as DNA
• proteins however can be positively charged so they’re mixed with chemicals that denatures them so they all have the same charge.

Question 8

whats a DNA profile

Answer 8

a DNA gel that shows the number of times repetitive, non-coding base sequences are repeated at different loci in an individual. (Banding pattern)

Question 9

Name 3 applications of DNA profiling

Answer 9

• forensic science
• maternity and paternity disputes
• analysis of disease

Question 10

Whats STR sequences of DNA

Answer 10

short tandem repeat sequences, highly variable short repeating lengths of DNA

Question 11

whats a transformed organism

Answer 11

a organism that has had its genes altered by genetic engineering

Question 12

whats recombinant DNA

Answer 12

the name for DNA formed by joining together DNA from different sources

Question 13

whats a transgenic organism

Answer 13

an organism that has been genetically engineered to include a gene from a different species

Question 14

whats a vector (in gene terminology)

Answer 14

something used to transfer DNA into a cell

Question 15

whats electroporation

Answer 15

a technique that uses an electric field to increase the permeability of cell membranes, which allows the cells to take up biological material

Question 16

Name the 3 parts of the process of genetic engineering

Answer 16

1) obtaining DNA containing the desired gene (via restriction enzymes)
2) Making recombinant DNA (vector + DNA fragment, CBP, DNA ligase)
3) transforming cells (transferring gene gene into host cell)

Question 17

Name 2 + and 2 - ethical issue with GMO crops

Answer 17

+reduce amount of pesticides used on crops which are harmful to environment
+designed to be more nutritious/ higher yield
-May encourage monoculture, reduce biodiversity, leave crops vulnerable to disease
-risk of interbreeding of plants creating superweeds

Question 18

whats pharming

Answer 18

producing pharmaceutical using genetically modified organisms, e.g. animals

Question 19

Name 1 + and 1 - ethical issue with pharming

Answer 19

+can be made in large quantities compared to other methods making them more available
-potential harmful side effects of manipulating genes for animals

Question 20

Name 1 + and 3 - ethical issue with genetic modification of pathogens

Answer 20

+previously untreatable diseases can now be treated, reducing suffering they would cause

• scientists researching could be infected, cause mass outbreak
• GM version of pathogen could revert back to original form cause outbreak
• could be used for biowarfare

Question 21

whats somatic gene therapy

Answer 21

a possible treatment option for genetic disorders and some cancers that involves altering defective genes inside body cells

Question 22

whats germ line theory

Answer 22

a possible cure for genetic disorders and some cancers that involves altering defective genes inside sex cells

Question 23

Name 3 + and 3 - ethical issue with gene therapy

Answer 23

+prolong lives of people with life threatening disease
+give people with genetic disease better quality of life
+germ line therapy would allow carrier of disorder to conceive healthy babies
-technology could be misused e.g. cosmetic factors
-potential to harm patient (over expression of genes)
-expensive, money potentially better spent somewhere else

Question 24

name 4 disadvantages of gene therapy

Answer 24

• body may identify vectors as foreign, start immune response
• allele could be inserted to wrong place in DNA
• inserted allele could be over expressed
• effects may be short lived in somatic therapy

Question 25

what is the chain termination method used for

Answer 25

determine the order of bases in a section of DNA

Question 26

describe the 3 steps of chain termination

Answer 26

• mix DNA template strand, DNA Pol, DNA primers, free nucleotides, modified DNA nucleotides
• PCR forms thousand of DNA fragments of varying length
• DNA fragments separated by electrophoresis. Smallest nucleotide goes to bottom of gel. Reading bands from bottom up DNA sequence can be built, one base at a time.

Question 27

why would you use genome sequencing instead of chain termination

Answer 27

chain termination can only be used for DNA fragments up to 750bp long. if you want to sequence the entire genome of an organism you must use genome sequencing.

Question 28

whats a BAC

Answer 28

bacterial artificial chromosome, a man made plasmic used in gene technology

Question 29

Describe the 8 steps of genome sequencing

Answer 29

1) genome cut into fragments(100bp) with restriction enzymes
2) each fragment inserted into a BAC
3) BAC’s inserted into bacteria
4) Bacteria divide, colonies of cloned cells with specific DNA fragments produced. Together colonies make complete genomic DNA library
5) DNA extracted from each colony, cut up with restriction enzymes, produces overlapping pieces of DNA.
6) Each piece of DNA sequenced using chain termination
7) Pieces put back in order to give full sequence from BAC
8) DNA fragments from all of BAC’s are put back in order to complete entire genome

Question 30

describe 6 steps of pyrosequencing

Answer 30

1) DNA cut into frags, split into single strands, strands attached to beads
2) PCR amplifies DNA on each bead
3) beads put into separate wells
4) Free nucleotides added to wells, attach to DNA via CBP
5) enzyme in wells cause light to be emitted when a nucleotide is added to a DNA strand
6) computers analyse occurrence+intensity of light emitted in different wells. Process to interpret DNA sequence.

Question 31

whats synthetic biology

Answer 31

large field of biology that includes building biological systems from artificially made molecules, redesigning biological systems to perform better, and designing new biological systems and molecules that don’t exist in the natural world.

Question 32

whats computational biology

Answer 32

using computer to study biology

Question 33

whats bioinformatics

Answer 33

developing and using computer software that can analyse, organise and store biological data.