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Biology > Manipulating Genomes > Flashcards

Manipulating Genomes Flashcards

1
Q

What is a genome?

A

The entire genetic material that an organism contains

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2
Q

What are genes?

A

Sections of DNA on chromosomes

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3
Q

What are introns?

A

Non-coding sections of DNA

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4
Q

What are tandem repeats?

A

Repetitive sequences of DNA

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5
Q

Where are tandem repeats found?

A

Within introns

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6
Q

What is a variable number tandem repeat (VNTR)?

A

Short nucleotide sequences, organised as a tandem repeat

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7
Q

What are short tandem repeats?

A

Smaller repeated nucleotide sequences

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8
Q

Describe the method for DNA profiling

A
  • Extract DNA
  • Purify with protease to remove histones
  • Cut into fragments with restriction enzymes
  • Gel electrophoresis
  • Nylon membrane placed on gel draws top strand of DNA onto nylon - southern blotting
  • Strands fixed in place by UV/heat
  • DNA probes added match intron base sequence = hybridisation
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9
Q

Why do restriction enzymes cut DNA at specific base sequences?

A
  • Shape of enzyme active site complementary to shape of a particular sequence of bases in DNA
  • ESC can form
  • Relevant bonds can be broken (H bonds between bases and phosphodiester from backbone)
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10
Q

How does gel electrophoresis work?

A
  • DNA fragments put into a well in a block of gel
  • Along with loading dye (DNA visible)
  • Placed in alkaline buffer solution (regulates pH)
  • Electric current passed through gel
  • DNA fragments move towards positive end (phosphate groups = - charge)
  • The smaller the fragments, the further it moves
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11
Q

What is southern blotting?

A

Designed to locate a particular sequence of DNA within a complex mixture

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12
Q

What are DNA probes?

A

Single-stranded DNA used to detect presence of complementary nucleic acid sequences by hybridisation

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13
Q

What is hybridisation?

A

Single-stranded DNA/RNA molecules join to complementary DNA/RNA

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14
Q

Usually, how many different STR’s are looked at when doing a DNA profile?

A

At least 12

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15
Q

Why are at least 12 different STR’s looked at when doing a DNA profile?

A
  • There is a slight chance that 2 people could have the same pattern for one particular STR in their DNA
  • Chances of have the same pattern for 12 different STR’s is much lower
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16
Q

What is a polymerase chain reaction?

A

A method to amplify a DNA sample by making multiple copies of it for analysis

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17
Q

What “ingredients” are needed for PCR?

A
  • Original tiny DNA sample
  • Excess of free nucleotides
  • Primers
  • DNA Taq polymerase enzyme
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18
Q

What are primers?

A

Short pieces of single-stranded DNA which start the copying process

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19
Q

Describe the steps in PCR

A

1- Denaturing phase
- temp inside machine = 90°-95°C for 30 secs
- breaks H bonds between strands
2- Annealing phase
- temp decreased to 55°-60°C
- primers join to both ends of single DNA strands
3- Extension phase
- temp increased to 70°-75°C for 1 min
- optimum temp for DNA Taq polymerase to work
- adds bases to primers, extending complementary strands

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20
Q

What type of DNA polymerase is used in PCR?

A

Taq polymerase that isn’t denatured by high temps

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21
Q

Why might you not get as many copies of the DNA made as expected?

A
  • May not be enough primers
  • Primers may not attach to all DNA strands
  • Insufficient nucleotides available
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22
Q

Give 3 uses of DNA profiling

A

1- Criminal investigations
2- Prove paternity of a child
3- Identify individuals at risk of disease

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23
Q

What is DNA sequencing?

A

The process of determining the nucleic acid sequence

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24
Q

What is the Human Genome Project?

A

An international scientific research project with the goal of determining the sequence of nucleotide base pairs that make up human DNA

25
Q

Describe the principle of DNA sequencing (interrupted PCR)

A
  • DNA is mixed with a primer, DNA polymerase, nucleotides and terminator bases
  • Undergoes PCR where the DNA separates into single strands and primers anneal
  • Nucleotides are added to the new DNA strand, some being terminator bases. Each time a terminator base is added, a strand terminates until all possible chains are produced
  • DNA fragments are separated by electrophoresis
  • Lasers detect colour and sequence
  • Computer analysis of all data gives original DNA sequence
26
Q

What are terminator bases?

A
  • Modified versions of A/T/C/G
  • Labelled with different coloured fluorescent markers
  • Doubly de-oxidised (2 O2 atoms less)
27
Q

What happens if a terminator bases attaches to the fragments of DNA being copied?

A

DNA strand can’t grow any longer

28
Q

What is Next Generation Sequencing?

A

Generates and analyses millions of sequences per run, allowing researchers to sequence, resequence and compare data at a rate previously not possible

29
Q

How has gene sequencing allowed for genome-wide comparisons between individuals and between species?

A
  • Analysing DNA sequence is a more accurate way of classifying organisms
  • The more similar the DNA base sequence, the more closely related
30
Q

How had gene sequencing allowed for the sequence of amino acids in polypeptides to be predicted?

A
  • Proteomics
  • If scientists can work out primary sequence, they can predict (by looking at R groups) how it will arrange itself in secondary and tertiary structures, which then allow predictions about its final 3D shape
31
Q

In what 2 ways is proteomics possible?

A

1- Spliceosomes

2- Protein modification

32
Q

What is a promoter?

A

A region of DNA that initiates transcription of a particular gene

33
Q

Give 3 reasons for genetic engineering

A
  • Make resistant crops
  • GM pathogens
  • Pharming
34
Q

Describe the steps in genetic engineering

A
  • Obtain required gene (mRNA or probes)
  • Restriction enzymes are used to cut open vector
  • Plasmid cut with same restriction enzymes
  • Sticky ends match up
  • Plasmid and DNA mix with DNA ligase to join sugar phosphate backbone together = recombinant DNA
  • rDNA inserted into bacteria via heat shock, electroporation or electrofusion
  • Use marker genes to identify bacteria
35
Q

Describe the 2 ways you can obtain the required gene in genetic engineering

A

Using mRNA

  • Add reverse transcriptase
  • Converts mRNA to a single strand of DNA (cDNA)
  • DNA made double stranded by adding free nucleotides, primers and DNA polymerase

Using a DNA probe

  • Use heat to make DNA single-stranded
  • Add a probe, complementary to gene you are looking for
  • Cut out gene using restriction enzymes
36
Q

Describe the features of a restriction site

A
  • 4-6 b.p long
  • Usually palindromic (reads the same in 5’-3’ and 3’-5’
  • Some of them leave blunt ends whilst others leave staggered ends
37
Q

Describe how transformed bacteria are identified

A

Marker genes
- After GE, 3 types of bacteria are present = no plasmid, with plasmid and with rDNA
- Grow bacteria on ampicillin culture and bacteria with no plasmid die as they have no resistance
- Shine remaining 2 bacteria under UV light and those with rDNA don’t glow as their gene for bioluminescence
has been spliced

38
Q

Describe heat shock

A
  • Temp of culture lowered to 0 degrees

- Rapidly raided to 40 degrees

39
Q

Describe electroporation

A
  • Small current applied to bacteria makes membrane porous
40
Q

Describe electrofusion

A
  • Electric current applied to bacteria increases the rate of uptake
41
Q

Give an example of GM plant

A

GM soy beans

- Contain gene that codes for protein that is toxic to insects

42
Q

Describe the advantages of GM crops

A
  • High yield
  • Less pesticide spray
  • Can be more nutritious
43
Q

Describe the disadvantages of GM crops

A
  • Encourages monoculture
  • Can interbreed with wild plants, creating weed killer resistance
  • Some people don’t eat GM crops
44
Q

What is pharming?

A

Creating pharmaceuticals from animals

45
Q

What are the advantages of pharming?

A
  • Drugs more readily available

- Large-scale drug production

46
Q

What are the disadvantages of pharming?

A
  • Potential animal side effects

- Animals become assets with no feelings

47
Q

What is the purpose of GM pathogens?

A

For disease treatment and research

48
Q

What is the advantage of GM pathogens?

A
  • Previously untreatable diseases are treatable
49
Q

What are the disadvantages of GM pathogens?

A
  • Scientists could become infected
  • Could revert back to original form and cause outbreak
  • Could lead to biological warfare
50
Q

What are the advantages of placing legal copyrights on GM ideas?

A
  • Scientists now hurry to become first to create GM ideas

- Owner generates income

51
Q

What are the disadvantages of placing legal copyrights on GM ideas?

A
  • Poor farmers may not be able to afford GM products
52
Q

What is bioinformatics?

A

The development of software needed for organising and analysing biological data

53
Q

What is computational biology?

A

Using software to create theoretical models of biological models

54
Q

What are the 2 types of gene therapy?

A

Somatic therapy and Germ line therapy

55
Q

What is somatic gene therapy

A
  • Alters alleles of somatic DNA
  • Disease passed to offspring
  • As modification cannot be passed on to offspring
56
Q

What is germ line gene therapy?

A
  • Alters alleles in gametes

- GM is passed to offspring (currently illegal on humans)

57
Q

What are the 3 types of gene therapy vector?

A
  • Viruses
  • Liposomes
  • Artificial chromosomes
58
Q

What are the advantages of gene therapy?

A
  • Increases quality of life for those with genetic disease
  • Prolongs life for those with genetic disease
  • Germ line can prevent offspring getting disease
59
Q

What are the disadvantages of gene therapy?

A
  • Technology may be used for non-medical purposes
  • Expensive
  • Potential to cause more harm than good

Biology (19 decks)

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