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A-level Biologyfor minal chapters! > 8B - Genome projects and making DNA fragments > Flashcards

8B - Genome projects and making DNA fragments Flashcards

1
Q

Genome

A

The entire set of DNA, including all the genes in an organism.

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2
Q

What has allowed us to sequence the genomes of a variety of organisms, from bacteria to humans?

A

Improvements in technology.

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3
Q

What do gene sequencing methods only work on?

A

Fragments of DNA.

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4
Q

What does DNA sequencing involve?

A

Small sequences of DNA that are mapped and then using computer to align and assemble the entire genome.

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5
Q

What has sequencing of the human genome enabled?

A

Identification of single base variations associated with disease and therefore early identification and treatment.

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6
Q

What do you need to do first to carry out sequencing of the entire genome of an organism?

A

You need to chop it up into smaller pieces first. The smaller pieces are sequenced and then put back in order to give the sequence of the whole genome.

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7
Q

When was the Human Genome Project completed?

A

2003

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8
Q

What did the Human Genome Project do?

A

Mapped the entire sequence of the human genome for the first time.

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9
Q

How long did sequencing the human genome take and how did they do it?

A

Took over 13 years using bioinformatics - collecting and analysing biological data using computers and algorithms.

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10
Q

What is bioinformatics?

A

Collecting and analysing biological data using computers and algorithms.

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11
Q

Proteome

A

All the proteins produced by the genome at a given time/under certain conditions.

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12
Q

Cellular proteome

A

Proteins in a given cell type.

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13
Q

Complete proteome

A

Proteins in the whole organism.

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14
Q

Why is it relatively easy to determine the proteome from the DNA sequence of the genome of simple organisms like bacteria?

A
  • They don’t have much non-coding DNA.

- Most prokaryotes have one, circular piece of DNA not associated with histones.

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15
Q

Why is the fact that it is relatively easy to determine the proteome from the DNA sequence of the genome of simple organisms like bacteria useful?

A

Useful in medical research and development - for example, identifying the protein antigens on the surface of disease-causing bacteria and viruses can help in the development of vaccines to prevent the disease.

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16
Q

Give examples of where genome sequencing has helped in determining the proteome of an organism which has helped in the medical field

A

N. meningitis group B bacteria cause meningitis B. Sequencing the genome of these bacteria helped researchers identify antigens for use in developing a vaccine against the disease.

Plasmodium Falciparum genome sequenced, therefore giving us knowledge of proteins produced and hopefully will develop a vaccine for malaria.

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17
Q

What is whole-genome shotgun sequencing?

A
  • Researches cut DNA into many small, overlapping sections.
  • Computer algorithms align overlapping segments.
  • This assembles the entire genome.

Done this way as the genome is too large to sequence all at once.

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18
Q

Why is whole-genome shotgun sequencing used?

A

Done this way as the genome is too large to sequence all at once.

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19
Q

What does SNPs stand for?

A

Single nucleotide polymorphisms.

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20
Q

What is the short way of writing single nucleotide polymorphisms?

A

SNPs

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21
Q

What are SNPs?

A

Single base variations in the genome that are associated with disease and other disorders.

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22
Q

What is screened for in medical screening?

A

Certain SNPs that are associated with a certain disorder.

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23
Q

What has allowed medical screening of SNPs to be possible?

A

Genome sequencing.

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24
Q

Why is it harder to translate the genome of complex organisms?

A
  • More complex organisms contain large sections of non-coding DNA.
  • They also contain complex regulatory genes, which determine when the genes that code for particular proteins should be switched on and off.
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25
Q

Why does the fact that complex organisms contain non-coding DNA make it hard to translate their genome into their proteome?

A

Because it’s hard to find the bits that code for proteins among the non-coding and regulatory DNA.

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26
Q

Has the human genome been mapped?

A

Yes.

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27
Q

How many of our genes are thought to code for proteins?

A

Only 1.5%

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28
Q

What work is being done on the human genome?

A

Human Genome Project.

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29
Q

What is the struggle with the Human Genome Project?

A

Hard to choose whose DNA is used to map as everyone’s is different.

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30
Q

How many codes for human proteins have been identified so far in the human proteome?

A

More than 30000 human proteins.

31
Q

What were many sequencing methods like in the past?

A

Labour-intensive, expensive and could only be done on a small scale.

32
Q

How have sequencing techniques/methods been updated?

A

They are now often automated, more cost-effective and can be done on a large scale.

33
Q

Give an example of a sequencing method that has been recently developed

A

Pyrosequencing - can sequence around 400 million bases in a ten hour period (which is super fast compared to older techniques).

34
Q

Why is pyrosequencing good?

A

It can sequence around 400 million bases in a ten hour period (which is super fast compared to older techniques).

35
Q

What is the benefit of newer, faster techniques such as pyrosequencing being available?

A

Scientists can now sequence whole genomes much more quickly.

36
Q

What does recombinant DNA technology involve?

A

Transferring a fragment of DNA from one organism to another.

37
Q

What can recombinant DNA be used to produce?

A

A protein in the cells of the recipient organism.

38
Q

Why can recombinant DNA be used to produce a protein in the cells of the recipient organism?

A

Because the genetic code is universal and because transcription and translation mechanisms are pretty similar too.

39
Q

Do the recipient and donor organism in recombinant DNA have to be the same species?

A

No

40
Q

What are organisms that contain transferred DNA known as?

A

Transgenic organisms.

41
Q

What are transgenic organisms?

A

Organisms that contain transferred DNA.

42
Q

What is the process of using DNA technology?

A

1) Isolation
2) Insertion
3) Transformation
4) Identification
5) Growth/cloning

43
Q

What is meant by the isolation stage of recombinant DNA technology?

A

Need to identify and isolate gene from the rest of the DNA.

44
Q

What are the 3 methods of isolation in recombinant DNA technology?

A

1) Reverse transcriptase
2) Restriction enzymes
3) ‘Gene machine’

45
Q

What is the combination of 2 organisms DNA called?

A

Recombinant DNA.

46
Q

What is recombinant DNA?

A

The combination of 2 organisms DNA.

47
Q

Explain how reverse transcriptase can be used to isolate a gene

A
  • Most cells only contain 2 copies of each gene, making it difficult to obtain a DNA fragment containing the target gene. But they can contain many mRNA molecules which are complementary to the gene, so mRNA is often easier to obtain.
  • The mRNA molecules can be used as templates to make lots of DNA. Retroviruses contain the reverse transcriptase enzyme which makes DNA from a viral RNA template so it can be transcribed by the host cell into proteins. The DNA produced is called complementary DNA (cDNA).
  • To do this, mRNA is first isolated from cells, Then it’s mixed with free DNA nucleotides and reverse transcriptase. The reverse transcriptase uses the mRNA as a template to synthesise a new strand of cDNA.
48
Q

What is cDNA?

A

Complementary DNA.

49
Q

What does reverse transcriptase do?

A

Makes DNA from a viral RNA template so it can be transcribed by the host cell into proteins.

50
Q

Where is reverse transcriptase found?

A

Retroviruses.

51
Q

What enzyme is found in retroviruses?

A

Reverse transcriptase.

52
Q

Where are restriction endonucleases found?

A

In bacteria.

53
Q

Why do bacteria have restriction endonucleases?

A

To protect themselves from invading viruses.

54
Q

How are restriction endonucleases used by bacteria?

A

To cut up the viral DNA.

55
Q

What do some sections of DNA have in terms of the sequence of nucleotides?

A

Palindromic sequences of nucleotides.

56
Q

What do palindromic sequences of nucleotides consist of?

A

Antiparallel base pairs.

57
Q

What are antiparallel base pairs?

A

Base pairs that read the same in opposite directions.

58
Q

What are restriction endonucleases?

A

Enzymes that recognise specific palindromic sequences (recognition sequences) and cut (digest) the DNA at these places.

59
Q

What are recognition sequences?

A

Specific palindromic sequences where the DNA cuts.

60
Q

What do different restriction endonucleases do?

A

Cut at different specific recognition sequences.

61
Q

Why do different restriction endonucleases cut at different specific recognition sequences?

A

Because the shape of the recognition sequence is complementary to the enzyme’s active site.

62
Q

How can restriction endonucleases be used to isolate the desired gene?

A
  • If the recognition sequences are present at either side of the DNA fragment you want, you can use restriction endonucleases to separate it from the rest of the DNA.
  • The DNA sample is incubated with the specific restriction endonuclease, which cuts the DNA fragment out via a hydrolysis reaction.
  • Sometimes the cut leaves sticky ends and sometimes it leaves blunt ends.
  • Sticky ends can be used to bind (anneal) the DNA fragment to another piece of DNA that has sticky ends with complementary sequences.
63
Q

What are sticky ends?

A

A staggered cut in the two chains forms sticky ends.

Sticky ends have a strand of single stranded DNA which are complementary to each other.

64
Q

What can sticky ends be used for?

A

Sticky ends can be used to bind (anneal) the DNA fragment to another piece of DNA that has sticky ends with complementary sequences.

65
Q

What is a better word for bind?

A

Anneal

66
Q

What does anneal mean?

A

Bind

67
Q

What are blunt ends?

A

A straight cut across both chains forms blunt ends.

68
Q

What will sticky ends join with?

A

Another sticky end but only if it has been cut with the same restriction enzyme - palindromic sequence.

69
Q

Explain how a ‘gene machine’ can be used to isolate a gene

A
  • Required sequence of bases is determined from desired protein. The sequence is first fed into a computer and checked against biosafety/biosecurity standards. The computer then designs a series of small, overlapping strands of nucleotides called oligonucleotides.
  • The first nucleotide in the sequence is fixed to some sort of support, e.g. a bead.
  • Nucleotides are added step by step in the correct order, in a cycle of processes that includes adding protecting groups. Protecting groups make sure that the nucleotides are joined at the right points, to prevent unwanted branching.
  • Short sections of DNA called oligonucleotides, roughly 20 nucleotides long, are produced. Once these are complete, they are broken off from the support and all the protecting groups are removed. The oligonucleotides can then be joined together to make longer DNA fragments.
  • Oligonucleotides are joined together to form an oligosaccharides to make the desired gene.
  • This is replicated into a double strand using PCR and using sticky ends, the gene can then be inserted into a bacterial plasmid which acts as a vector for the gene.
70
Q

What do protecting groups do in a ‘gene machine’?

A

Protecting groups make sure that the nucleotides are joined at the right points, to prevent unwanted branching.

71
Q

Where is the ‘gene machine’?

A

In a lab.

72
Q

What are the benefits of using a ‘gene machine’ for isolation?

A
  • Quick.
  • Accurate.
  • No introns or other pieces of non-coding DNA.
  • Easily transcribed in prokaryotic cells.
  • DNA sequence doesn’t have to exist naturally so any sequence can be made.
  • DNA can be synthesised from scratch, without the need for a pre-existing template DNA.
73
Q

What does a gene machine’ contain?

A

A database with the necessary information to produce the DNA fragment.

A-level Biologyfor minal chapters! (42 decks)

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