Manipulating Genomes Flashcards

1
Q

What is the polymerase chain reaction used for

A

Generate many copies of DNA fragments - amplification

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2
Q

In PCR what is often used to cut DNA fragments

A

Restriction enzymes

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3
Q

What does the reaction mixture for the PCR contain

A

Original DNA
Primers - small sections of nucleotides
Taq DNA polymerase
And free DNA nucleotides

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4
Q

Describe the steps in the PCR (4)

A
  • Double stranded DNA sample
  • Heat to 95 degrees - separate strands
  • add primers and reduce temp to 55 degreees (allow hydrogen bonds to form) primers anneal (bind)
  • raise temperature to 72 degrees DNA polymerase binds and extends primers using free nucleotides
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5
Q

How do restriction enzymes work

A

Used to obtain DNA fragments from a genome

Some sections of DNA have palindromic sequences (read the same both ways - forward and backward)

Restriction enzymes recognise specific sequences and cut/ digest at these sites - cuts can leave sticky ends

Different restriction enzymes cut at different sequences as shape of sequence is complimentary to shape of active site

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6
Q

Describe gel electrophoresis

A
  • use of electrical currents to separate DNA/RNA fragments by size
  • agarose gel used as it has large pores
  • nucleotides are negatively charged so are attracted towards anode
  • larger fragments can’t move through agarose as quickly as smaller fragments
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7
Q

How are proteins put through gel electrophoresis
- when are they often used

A

They have different charges so we mix with a chemical first to denature them - they all now have the same charge
- often used in disease diagnosis

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8
Q

What is the method for DNA sequencing

A

Chain termination method
Enables us to determine nucleotide sequences on DNA fragments

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9
Q

Why are nucleotides marked with fluorescent dyes

A

To show what nucleotides are present in a sequence
Mark the end of a fragment - chain terminator

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10
Q

Define Pyrosequencing

A

a nongel-based DNA sequencing technique that detects inorganic pyrophosphate released during DNA synthesis

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11
Q

What are the chain termination method and pyrosequencing used for

A

DNA fragments smaller than 1000 base pairs

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12
Q

Why do we have to cut genomes into smaller fragments to be able to sequence

A

Because the chain termination reaction and pyrosequencing can only be carried out with small fragments - less than 1000 base pairs

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13
Q

What is BAC

A

Bacterial artificial chromosome (agent)

an engineered DNA molecule used to clone DNA sequences in bacterial cells

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14
Q

What are the uses of sequencing

A
  • allowed for the sequence of amino acids in polypeptide chains to be predicted
  • development of synthetic biology - creating biological molecules from scratch
  • computational biology ( using a computer to study biology) and bioinformatics ( data store) has also developed
  • evolutionary relationships - cytochrome C
  • epidemiology ( study of diseases)
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15
Q

What does genetic engineering involve

A

Modifying the genome of an organism by introducing a gene from another organism

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16
Q

What do we call organisms that have been genetically engineered

A

Transgenic or transformed

17
Q

What are the three stages of the genetic engineering process - describe them

A
  1. Use restriction enzymes to isolate the desired gene
  2. Recombinant DNA is made - vector DNA is isolated, and cut open using restriction enzyme in step 1. Using same R.E. Means sticky ends are complimentary. DNA fragment inserted into vector DNA using DNA lignase
  3. Transforming cells - vector is used to transfer recombinant DNA into bacterial cells (host cells)
    Bacteriophage injects DNA into host cell which integrates with bacterial DNA
    Plasmid vectors are placed in a mixture with host cells and electric field created. This increases permeability of host plasma membranes and allows plasma to enter - electroporation
18
Q

Describe how recombinant DNA is made in genetic engineering

A

Vector DNA is isolated

Vector DNA is cut open using restriction enzyme that was used to obtain original desired gene

As same R.E. Used, means the sticky ends of vector DNA are complimentary to DNA fragment

DNA fragment inserted into vector DNA using DNA lignase (joins sugar phosphate)

19
Q

Part 3 of genetic engineering process
How are cells transformed

A

Vector is used to transfer recombinant DNA into bacterial cells (host cells)

Bacteriophage injects DNA into host cell which integrates with bacterial DNA

Plasmid vectors are placed in a mixture with host cells and electric field is created, this increases permeability of host plasma membranes and allows plasmids to enter - electroporation

20
Q

Why have we genetically modified soybeans

A

They are an important food source but are susceptible to insect pests

GM soybeans contain a gene that codes for a protein that is toxic to some insects

Gene taken from bacteria BACILLUS THURIUNGIENSIS (B+) and put int plasmid from a second bacteria AGROBACTERIUM TUMEFACIENS

21
Q

What are the two bacterium used to genetically modify soy beans
1 - from where gene is taken
2 - vector DNA

A
  1. Bacillus thuringiensis
  2. Agrobacterium tumefaciens
22
Q

What are the ethical issues of genetically modifying crops
Pros and cons

A

Pros: Less use of chemical pesticides
Increased yield and food

Cons: Monoculture - less biodiversity, vulnerable to disease.

23
Q

What are the pros and cons of genetically modifying pathogens

A

Pros: Potential treatments of disease
E.g. tumour cells have receptors for poliovirus - GM the virus to inactivate the disease causing genes

Cons: ethical issues -
Lab troubles and mass outbreak of pathogen

If someone with ill intentions gets hold of this knowledge and biowarfare kicks off

Could the GM version um-GM itself and mss outbreak?

24
Q

What is pharming

A

Genetically modifying animals for drugs

25
Q

What is antithrombin deficiency

A

Produces too many blood clots

26
Q

How are goats genetically modified to combat antithrombin deficiency

A

GM a goat embryo and insert it into a female - all offspring produce milk with antithrombin
Selective breed desired offspring

27
Q

What are the issues with ownership of GM organisms

A

Companies will want money for the products
Large companies will have a lot of power

Poorer countries might not be able to afford the medicines and crops

28
Q

What is gene therapy

A

Altering alleles inside cells to cure genetic disorders

29
Q

What are the two ways of carrying out gene therapy

A
  1. If the disorder is caused by two mutated recessive alleles, then a working dominant allele can be added
  2. If it is caused by a mutated dominant allele then it is ‘silenced’ - fragment of DNA is inserted into the middle of the allele so it no longer works
30
Q

Describe somatic gene therapy
What is the problem with this type

A

Altering somatic cells (diploid)

Cystic fibrosis - recessive disease
Therefore a functioning dominant allele is inserted into cells lining the lungs

Con: offspring would not inherit new gene as sex cells have not been altered

31
Q

What is germline gene therapy

A

Altering sex cells (haploid), zygotes and early embryonic stem cells (<8days)

As a result all cells in organism contain altered DNA so MAY pass this onto offspring

Germline therapy in humans is currently illegal

32
Q

What are the ethical debates of gene therapy
Pros and cons

A

Pros:
- prolong life of those suffering with life-threatening genetic disorders
- improve quality of life as it eases symptoms
- germline therapy would allow carriers of genetic disorders to conceive offspring without the disorder
- germline therapy could decrease overall number of individuals suffering from genetic disorders and cancers
Cons:
Technology could be used for other reasons
Expensive - could money be going elsewhere
Potential the therapy could cause more harm than good

33
Q

What are the disadvantages of gene therapy

A
  • inserted alleles may get overexpressed and result in other problems
  • vectors could be recognised as foreign and start an immune response
  • an allele could be inserted into the wrong place within the DNA and lead to unknown impacts
  • effects may be short-lived in somatic therapy