6.1.3 Manipulating Genomes Flashcards

1
Q

DEFINITION- Genomics

A

The branch of molecular biology concerned with structure, function, evolution and mapping of genomes

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2
Q

DEFINITION- Gene

A

A section of DNA that contains the complete sequence of bases (codon) to code for a protein

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3
Q

DEFINITION- Thermophilic

A

An extremophile that thrives in relatively high temperatures

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4
Q

DEFINITION- Thermus Aquaticus

A

A species of bacteria that can tolerate high temperatures

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5
Q

DEFINITION- TAQ Polymerase

A

A thermostable DNA polymerase named after the thermophile, Thermus Aquaticus

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6
Q

DEFINITION- Nucleotide

A

The monomer unit used to for nucleic acids, composed of a pentose sugar, phosphate group and nitrogenous base.

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7
Q

DEFINITION- H Bond

A

Weak bonds that can occur whenever theres a slightly negative molecule and slightly positive H

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8
Q

DEFINITION- DNA Primer

A

A short single stranded nucleic acid utilised by all living organisms in the initiation of DNA synthesis

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9
Q

DEFINITION- Amplification

A

A mechanism leading to multiple copies of a chromosomal region of a gene.
Role of PCR

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10
Q

DEFINITION- Restriction enzyme

A

Enzymes that chop strands of DNA into small pieces,

Endonucleases

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11
Q

DEFINITION- DNA ligase

A

An enzyme involved in DNA replication, that catalyses the formation of a phosphodiester bond.

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12
Q

DEFINITION- Plasmid

A

A genetic structure in a cell that can replicate independently of chromosomes

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13
Q

DEFINITION- Transgenic

A

An organism containing genetic material into which DNA from an unrelated organism has been artificially introduced.

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14
Q

Restriction enzyme Details

A
  • Extracted from bacteria
  • Endonucleases
  • Cut DNA at specific points to create palindromic sequences
  • Leave behind sticky ends
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15
Q

Restriction enzyme process

A
  • Each enzyme is specific for a certain base sequence
  • The active site on the enzyme has a specific shape
  • The base sequence has a complimentary shape
  • DNA sugar phosphate backbone is cut at the restriction site
  • Hydrolysis breaks the backbone in different places
  • Leaves a staggered cut (sticky end)
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16
Q

Polymerase Chain Reaction steps and Role

A
  1. Denaturation
  2. Annealing
  3. Extension
    Amplifies DNA
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17
Q

Reaction mixture PCR

A

Extracted DNA
Nucleotides
DNA polymerase
Primers

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18
Q

Denaturation PCR

A

95degrees

H bonds break between DNA strands

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19
Q

Annealing PCR

A

55degrees

Primers bind to strands with H bonds as DNA polymerase cannot bind to single strands

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20
Q

Extension PCR

A

72degrees

DNA polymerase adds free nucleotides in 5 to 3 direction with complimentary base pairs

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21
Q

Differences between PCR and DNA replication

A
  • Only short sequences can be replicated, not whole chromosomes
  • A primer is required
  • Needs to heat and cool to separate the DNA strands, bind on the primers and for DNA replicate
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22
Q

Applications of PCR

A
  • Forensic Science
  • Detecting mutations
  • Monitoring spread of disease
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23
Q

Advantages of PCR

A
  • Quicker
  • Requires less equipment
  • Less space
  • Easier and less costly to run
  • Safer
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24
Q

Advantages to cloning in living organisms (bacterial host)

A
  • Longer sections of DNA can be cloned
  • Less prone to mutation (taq polymerase can insert wrong base)
  • Less expensive set up costs
  • Less technically complex
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25
Q

Gel Electrophoresis Details

A
  • DNA samples are treated with restriction enzymes to create DNA fragments
  • Placed into wells at the negative end of the gel
  • Gel immersed into buffer solution
  • Electrodes are attached so a current can pass through over a set time (2hr)
  • Position of fragments can be shown using dye that stains DNA
  • Separates based on size
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26
Q

Why DNA is drawn towards the positive pole?

Gel Electrophoresis

A

DNA is negative so repelled away from the -ve electrode and attracted to the positive

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27
Q

Why they travel different lengths

Gel Electrophoresis

A

Longer strands move slower because they’re heavier and theres more friction, therefore they move less distance

28
Q

Which stain is used?

Gel Electrophoresis

A

Ethidium Bromide, binds to the DNA and shows up under UV light

29
Q

Gene Probes

A

Short strands of DNA with complimentary base strands to the DNA being investigated, the complimentary binding is called annealing.
50-80 nucleotides long

30
Q

How to label gene probes

A
  1. Radioactively with isotope phosphorus 32, identified with a photographic plate
  2. Fluorescently so they’ll be identified under UV light
31
Q

Uses of Gene probes

A
  • Locate a specific gene for enticing engineering
  • Identify the same gene in a variety of different genomes
  • Identify the presence of particular allele for a genetic disease
32
Q

DNA profiling Steps

A
Extraction 
Digestion 
Separation 
More separation 
Hybridisation 
Development 
More Development 
Every Dinosaur Sings More Highly During Meetings
33
Q

DNA Profiling- Extraction

A

DNA extracted from the sample

34
Q

DNA Profiling- Digestion

A

Restriction endonuclease cut DNA into fragments

35
Q

DNA Profiling- Separation

A

Fragments separated using gel electrophoresis

36
Q

DNA Profiling- More Separation

A

DNA fragments transferred from gel to nylon membrane in a process called southern blotting

37
Q

DNA Profiling- Hybridisation

A

DNA probes are added to label the fragments, the radioactive probes attach to specific fragments.

38
Q

DNA Profiling- Development

A

Membrane with radioactively labelled DNA fragments is placed onto an Xray film

39
Q

DNA Profiling- More Development

A

Development of an Xray film reveals dark bonds where radioactive Fluro DNA Probes have attached.

40
Q

Benefits of using Genomes for medicines

A
  • More powerful medicines
  • Better and safer first time
  • Decrease in overall cost of healthcare
41
Q

Gene Sequencing Reaction Mixture

A

-DNA polymerase
-Many copies of single stranded DNA template
-Free DNA nucleotides
-Modified DNA nucleotides with fluorescent marker
-Primers, approx 20 Base pairs
(All inside a Thermal Cycler)

42
Q

Gene Sequencing Description

A
  1. Primer attaches to 3’ end of template strand allowing DNA polymerase to attach (Annealing) 55degrees
  2. Free nucleotides are added forming C Base pairs (Extension) 72degrees
  3. Polymerase enzyme thrown off when modified nucleotide attaches, acts as a terminator base, each base a different colour. (Extension interrupted)
  4. Varying lengths of DNA strands can be ordered with the end nucleotide tagged with specific colour
  5. Pulled through electrophoresis and the colours are read by lasers
43
Q

Next generation Sequencing

A
  • Easier and quicker
  • Uses plastic slide instead of gel
  • Still uses coloured terminator bases
44
Q

Uses for Comparing Genomes

A
  • Identify genes that are essential for life
  • Verifies useful genes are conserved in evolution
  • Help show evolutionary distance
  • Predicting amino acid sequences
45
Q

Genetic engineering

A

Genetic material can be changed, the gene from one species organism can be inserted into another organism

46
Q

Reasons to genetically Engineer

A
  1. Improve features of an organism
    - Resistance to herbicides
    - Promote muscle growth
  2. Allow organisms to synthesise useful product
    - Insert insulin gene
    - Golden rice
    - Female sheep can produce proteins in milk
47
Q

Overview of Genetic Engineering

A
  1. Obtaining gene
  2. Gene is inserted into a vector
  3. Vector inserts gene into cell
  4. Identifying transformed cells
48
Q

Obtaining a Gene

A

Once identified, it can be cut out a chromosome using restriction enzymes or made via reverse transcription of mRNA. Genes can be sequenced using an automated polynucleotide sequencer.

49
Q

Inserting genes into vectors

A

e. g. Bacterial Plasmids
- Plasmid must be cut with the same restriction enzymes to create complementary sticky ends.
- Plasmid and gene are then mixed with DNA ligase and some combine to form recombinant plasmids.
- Ca Salts and Heat shock can help plasmids enter the bacteria, only 1% do
- Transformed bacteria contain new DNA and are therefore Transgenic.

50
Q

Vector inserts gene into cells

A
  • Viral Transfer, vectors in a virus and the cells are infected inserting DNA in directly.
  • Ti Plasmids, tumour inducing for plants
  • Liposomes, DNA is wrapped in lipid molecules they’re fat soluble so pass through the membrane
  • Direct method DNA shot into cell with mini gun
51
Q

Identifying Transformed Cells

A
  • Fluorescent Marker Genes, found in jellyfish and can be inserted into plasmids with genes so if they glow they have taken up the plasmid
  • Antibiotic Marker Genes, plasmids often contain 2 antibiotic resistant genes, if plasmid is then up they lose one, then use replica plating
52
Q

Replica Plating

A
  • Master plate contains standard nutrient agar and all bacteria colonies grow.
  • Block covered in sterile velvet is placed on it and bacteria sticks
  • Block is then placed on agar containing 1st antibiotic
  • Only bacteria with plasmid grow
  • Then stamped on 2nd antibiotic and only bacteria with resistance to 2nd antibiotic grows
  • Use to identify bacteria to be grown on a large scale
53
Q

Gene Therapy

A

Using genetic technology to treat genetic disorders, replace dysfunctional genes with working copies into cells.

54
Q

Somatic Cell Therapy

A

Adding genes- replace faulty gene

Killing specific cells- programme cancerous cells to express genes that make them weak to the immune system

55
Q

Germ line Therapy

A

Embryo cells have the potential to specialise into any cell type, if a gene is placed in these every body cell will possess it.
However is unethical and illegal

56
Q

Somatic Cell Gene Therapy Issues

A
  • Tricky to get genes into specific cells
  • Short lived so must be repeated
  • Only affects the actual patient
  • Difficult to get gene to function
57
Q

Germline Gene Therapy Issues

A
  • More straightforward to deliver gene into cell
  • All subsequent cells have the functioning gene
  • Unethical to engineer human embryos
  • Genetic manipulation is passed onto children
58
Q

Problems with Vectors

A
  • Immune response, attacks foreign molecules
  • Inefficient, liposome take up rate is low
  • Side Effects, may cause tumours
  • Viral vectors may cause disease
59
Q

Gene Therapy- Cystic Fibrosis

A
  • Gene works incorrectly so sticky mucus builds up

- some trials using liposomes

60
Q

Gene Therapy- SCID

A
  • Severe Combined Immunodeficiency disease
  • T lymphocytes are destroyed due to the build of of toxins after faulty gene prevents immune system working
  • Allele inserted into retrovirus
  • Initially caused leukaemia as inserted in the wrong place.
61
Q

Gene Therapy- Liver disease

A
  • Unable to breakdown ammonia so it builds up in the blood
  • Low protein diet or transplant can help
  • Someone died in trials so they were discontinued
62
Q

Ethics of Genetic Manipulation- Microbes

A
Benefits- Insulin production 
-Produce vaccines 
-Antibiotics 
Risks- Antibiotic resistance 
-Used in warfare 
-Accidentally create worse pathogen
63
Q

Ethics of Genetic Manipulation- Plants

A
Benefits- Pest and herbicide resistant 
-Golden rice 
-Drought resistant 
Risks- Resistant weeds
-Enters food chain
-Reduced biodiversity
64
Q

Ethics of Genetic Manipulation- Animals

A

Benefits- Increased yield
-Spider goats
-Xeno transplants
Risks- Issue of welfare and ethics

65
Q

Ethics of Genetic Manipulation- Humans

A
Benefits- SCID
-Cystic Fibrosis 
Risks- Death from immune system
-Long term effects
-Treatment is continuous which is costly
-Germline is illegal