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Biology > Manipulating Genomes > Flashcards

Manipulating Genomes Flashcards

1
Q

DNA AND GENE SEQUENCING:

Genome Projects

A

Genome projects are used to determine the sequences of the proteins that derive from the genetic code (the proteome).

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2
Q

DNA AND GENE SEQUENCING:

Medical Advances (Genome Projects)

A

Genome projects identify which genes are responsible for certain inherited diseases.

Potential targets for drug treatment can be identified.
Genetic testing is used to identify if an individual has a specific gene that may cause disease.

Gene therapy is used to replace defective genes with normal, healthy genes.

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3
Q

DNA AND GENE SEQUENCING:

Biotechnology (Genome Projects)

A

Biotechnology is the process of designing useful biological devices and systems to solve specific problems.

Genome projects can help us understand the best designs for biotechnology.
E.g. Investigating the genome can help understand disease. This can be used in developing biomedicine.

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4
Q

DNA AND GENE SEQUENCING:

Evolutionary Relationships (Genome Projects)

A

Genome projects can be used to make comparisons between individuals and between species.

Genetic similarities can be identified.

Genome projects can also be used in forensic testing and parent-child genetic matching (e.g. paternity tests).

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5
Q

DNA AND GENE SEQUENCING:

Genome Sequencing (Genome Projects)

A

Methods used to sequence the genome are constantly changing.

The Human Genome Project sequenced the entire human genome in 2003. This process took 15 years.
Genome sequencing can now be done in a matter of hours.

Genome projects could be used in many more ways in the future as the techniques continue to be improved.

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6
Q

DNA AND GENE SEQUENCING:

DNA Profiling

A

DNA profiling is a technique for analysing samples of DNA and has multiple applications.

DNA ‘profiles’ are specific DNA patterns that can be used to identify people, families and diseases.

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7
Q

DNA AND GENE SEQUENCING:

Applications (DNA Profiling)

A

Once sequenced, and the exact series of nucleotides in the sample has been established, forensic scientists can match the sample up with samples of DNA from known sources.

DNA profiling is used at crime scenes to identify potential criminals, to identify whether somebody is at risk of a genetic disease or simply to find out the degree of relatedness between people.

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8
Q

DNA AND GENE SEQUENCING:

Gel Electrophoresis (DNA Profiling)

A

Gel electrophoresis is a technique for separating the DNA fragments out according to size.

The DNA is loaded into wells at one end of a slab of agarose gel and an electric current is passed through.

The negatively charged DNA moves through the gel towards the positive electrode, with the smaller fragments moving faster and further.

The DNA ends up arranged in bands, with similar length strands grouping together.

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9
Q

DNA AND GENE SEQUENCING:

Polymerase chain reaction (DNA Profiling)

A

DNA is replicated using polymerisation chain reaction (PCR) to increase the sample size:
The DNA is heated to 96oC to denature the strands and provide single-stranded templates for replication.

The reaction is cooled to 60oC to allow primers (short lengths of DNA to which free nucleotides can attach) to anneal to the single strands of DNA.

The reaction is heated to 72oC so that Taq polymerase (the DNA polymerase enzyme used) can work at optimum conditions and rapidly extend the nucleotide chains from the primers.

This process is repeated 25-35 times and the amount of DNA increases exponentially with each repeat.

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10
Q

DNA AND GENE SEQUENCING:

Polymorphisms (DNA Profiling)

A

Humans share 99.9% of DNA with one another.

Certain regions of our genomes do vary greatly, these varying regions are known as polymorphisms.

Polymorphic DNA can be used to distinguish between target individuals and groups.

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11
Q

DNA AND GENE SEQUENCING:

Obtaining DNA (DNA Profiling)

A

DNA samples are obtained from hairs, skin, semen, saliva or any other sample that contains body cells.

DNA is extracted from the nucleus of the cells and isolated from other cellular matter using chemicals such as detergents.

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12
Q

DNA AND GENE SEQUENCING:

Profiling Companies (DNA Profiling)

A

DNA profiling services can analyse a sample of DNA using various genetic markers.

Output from these services can give the person information about who their ancestors were and where they were from, and even the percentage that they are related to Neanderthals.

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13
Q

DNA AND GENE SEQUENCING:

Advantages of Personal Profiling (DNA Profiling)

A

The samples (like saliva) are easy to take at home and then send to the company in the post.

Finding out about previously unknown ancestral ties can be interesting and surprising.

Results can be compared in a large database to discover unknown relatives if they are also in the database.

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14
Q

DNA AND GENE SEQUENCING:

Disadvantages of Personal Profiling (DNA Profiling)

A

Home tests have been criticised for being inaccurate.

Ancestry results can be misleading if only a small part of DNA is profiled.

Basic tests do not give very much information, but comprehensive tests can be very expensive.

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15
Q

GENETIC ENGINEERING:

Recombinant DNA

A

Recombinant DNA is where fragments of foreign DNA are inserted into other sections of DNA.

The fact that the genetic code is universal means that any section of DNA can be taken from one organism and placed inside another.

Once the DNA has been inserted, it is then transcribed and translated to produce proteins.

Transcription and translation are also universal processes.

The process of transferring sections of DNA produces recombinant DNA.

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16
Q

GENETIC ENGINEERING:

Universal Code

A

DNA is made from a sequence of four bases (A, T, C, G).

Every organism uses the four bases as the genetic code to produce proteins.

This means that DNA can be considered a universal code.

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17
Q

GENETIC ENGINEERING:

Fragments

A

The sections of DNA that are transferred are called fragments.

The organism that has received fragments of DNA is said to be transgenic.

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18
Q

GENETIC ENGINEERING:

Genetically Modified Crops (Uses of Recombinant DNA)

A

Recombinant DNA can be used to genetically modify crops to improve their yield.

Traits that can be improved include -
Resistance to disease.
Tolerance to the application of herbicides and pesticides.
Tolerance of adverse environmental conditions (e.g. drought).

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19
Q

GENETIC ENGINEERING:

Genetically Modified Livestock (Uses of Recombinant DNA)

A

Recombinant DNA can be used by farmers to make the production of meat more economically viable.

Traits that can be improved include -
Grow faster and larger.
Resistance to disease.

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20
Q

GENETIC ENGINEERING:

Increase Nutritional Value (Uses of Recombinant DNA)

A

Recombinant DNA can be used to increase the nutritional value of food.

E.g. Rice has been genetically modified to contain Vitamin A. Vitamin A is a common deficiency in Asian countries where rice is widely consumed.

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21
Q

GENETIC ENGINEERING:

Treating Diseases (Uses of Recombinant DNA)

A

Recombinant DNA can be used to produce medicine and hormones to treat diseases.

E.g. Individuals with type I diabetes used to be given pig insulin to control their blood sugar levels. Now human insulin is created using genetically modified bacteria.

22
Q

GENETIC ENGINEERING:

Industry (Uses of Recombinant DNA)

A

Recombinant DNA can be used to manufacture enzymes.

These enzymes can be used in industry.

E.g. Rennet is an enzyme traditionally taken from the stomach of young mammals like calves to produce cheese. It is now possible to make rennet using genetically engineered bacteria.

23
Q

GENETIC ENGINEERING:

Restriction Endonucleases

A

Enzymes called restriction endonucleases bind to recognition sequences.

Each restriction endonuclease binds to a specific recognition sequence (e.g. Eco RI is a restriction endonuclease that binds to GAATTC).

If two restriction endonucleases bind to two recognition sequences surrounding a target gene, the target gene can be cut out of the DNA.

24
Q

GENETIC ENGINEERING:

Recognition Sequences

A

Recognition sequences are sections of DNA where the base sequence has antiparallel base pairs.

Antiparallel base pairs have a sequence of base pairs that are the same but in opposite directions.

Recognition sequences can be used to isolate the target gene if there are two sets of sequences either side of the gene.

25
Q

GENETIC ENGINEERING:

Producing the Fragment (Restriction Endonucleases)

A

DNA fragments can be produced in this way using restriction endonucleases.
The steps involved are -
DNA containing the target gene is mixed with the restriction endonucleases.
Restriction endonucleases bind to the recognition sequences on either side of the target gene.
The target gene is cut out of the DNA.

26
Q

ETHICAL CONCERNS OF GENETIC ENGINEERING:

Spread of Genes

A

Genetically modified (GM) crops and livestock are produced when a beneficial gene is inserted into their genome to improve a certain trait.

The genes could be transferred into other organisms where it is harmful.
E.g. A gene for herbicide resistance could be passed on to a weed, or a gene for antibiotic resistance to pathogenic bacteria.

Genes from genetically engineered (transgenic) crops could also spread to organic crops.

27
Q

ETHICAL CONCERNS OF GENETIC ENGINEERING:

Unforeseen Impacts

A

Genetic modifications to an organism could have unforeseen effects and disrupt normal gene function.

The use of genetically engineered organisms could lead to a reduction in the variety in populations.

If variety in a population decreases, biodiversity also decreases.

Low biodiversity can have negative impacts (e.g. extinction is more likely).

28
Q

ETHICAL CONCERNS OF GENETIC ENGINEERING:

Economic Consequences

A

There could be economic consequences for some countries if genetically engineered crops can be grown in different countries where previously it was not possible.

Companies who are able to invest more money in recombinant DNA technology may out-compete others.

29
Q

ETHICAL CONCERNS OF GENETIC ENGINEERING:

Medical Uses

A

Some activists are concerned that using recombinant DNA in medicine could lead to unethical uses of genetic engineering.

E.g. Selecting specific traits in offspring (designer babies).

30
Q

GEL ELECTROPHORESIS:

Stage 1 - Amplification

A

The DNA sample is extracted from the individual.

This is done by taking a swab inside someone’s mouth or taking a blood sample.

The DNA sample is amplified many times using PCR (polymerase chain reaction).

PCR generates many copies of the same sample.

31
Q

GEL ELECTROPHORESIS:

Stage 2 - Labelling

A

The DNA fragments produced from PCR are labelled using a fluorescent label.

The label allows the DNA fragments to be identified when exposed to UV light.

32
Q

GEL ELECTROPHORESIS:

Stage 3 - Inserting the DNA

A

The many DNA fragments are inserted into a well in a gel.

The gel is covered in a buffer solution that conducts electricity with a positively charged electrode at one end of the gel and a negatively charged electrode at the other end.

DNA is inserted at the negative end of the gel.

33
Q

GEL ELECTROPHORESIS:

Stage 4 - Movement of DNA

A

DNA is negatively charged so when an electric current is passed through the gel, the DNA will move away from the negative electrode towards the positive electrode.

Smaller DNA fragments will move through the gel more quickly and travel further than larger fragments.

34
Q

GEL ELECTROPHORESIS:

Stage 5 - Ladder of DNA

A

The electric current is removed after approximately 10 minutes.

The DNA fragments that are different lengths in a sample will have moved differing distances up the gel.

The presence of DNA fragments in the gel form bands of DNA.

The different bands of DNA in an individual sample produce a ‘ladder’ of DNA.

35
Q

GEL ELECTROPHORESIS:

Stage 6 - Identifying DNA Fragments

A

The different DNA fragments in a sample can be identified by exposing the gel to UV light.

The DNA fragments are fluorescently labelled so UV light shows the bands of DNA present.

36
Q

GEL ELECTROPHORESIS:

Stage 7 - Genetic Fingerprinting

A

The lengths of DNA fragments are determined by the number of repeats in a VNTR (variable number tandem repeat), which is a section of DNA.

The number of repeats varies between individuals.

This means the DNA fragments in an individual will move different distances and the ladder of DNA for every individual will be unique.

The ladder of DNA in an individual is considered their genetic fingerprint.

37
Q

VIVO AMPLIFICATION:

Stage 1 - Forming Sticky Ends

A

A vector is a form of transport for the DNA fragment.

Vector DNA is cut open by enzymes called restriction endonucleases. The enzymes cut the DNA at a specific region called recognition sequences.

Restriction endonucleases cut the vector DNA so that each end has a short single-stranded section.

The ends of the DNA that are single-stranded are called the sticky ends.

38
Q

VIVO AMPLIFICATION:

Stage 2 - Sticky Ends on Fragment DNA

A

The DNA fragments have sticky ends that are complementary to the sticky ends on the vector DNA.

This is because the DNA fragments have either been cut from DNA using the same restriction endonucleases or because several nucleotides have been added onto the ends of the fragment.

39
Q

VIVO AMPLIFICATION:

Stage 3 - Inserting Into Vector DNA

A

The sticky ends on the DNA fragment and vector DNA bind together.

An enzyme called DNA ligase attaches the sticky ends together. This is called ligation.

The DNA fragment has been inserted into the vector DNA. This is recombinant DNA.

40
Q

VIVO AMPLIFICATION:

Stage 4 - Transferring To Host Cell

A

The vector transfers the recombinant DNA to the host cells.

If the vector is a plasmid (small, circular DNA found in bacteria) -
The host cells take up the recombinant DNA via heat-shock. This is where the cells are heated at 42°C for one minute.

If the vector is a bacteriophage (virus) -
The recombinant DNA is injected into host cells.

41
Q

VIVO AMPLIFICATION:

Stage 5 - Inserting Marker Genes

A

The cells that have successfully taken up the recombinant DNA are transformed. Transformed cells are also said to be genetically modified (GM).

Not all the cells will be transformed.

The transformed cells are identified using marker genes.

Marker genes are genes that are inserted along with the recombinant DNA and confer antibiotic resistance.

42
Q

VIVO AMPLIFICATION:

Stage 6 - Identifying Transformed Genes

A

Transformed cells can be identified by placing the cells on an agar plate with antibiotics.

Only cells that have successfully taken up the recombinant DNA will be able to survive on the antibiotic agar plates.

Transformed cells can then be grown in large numbers to amplify the target gene.

43
Q

VITRO AMPLIFICATION (PCR):

Stage 1 - Set Up The Reaction Mixture

A

The DNA fragments are mixed with -
Primers (short sections of DNA).
An enzyme called DNA polymerase (produces new strands of DNA).
Free-floating nucleotides.
Together these components form the reaction mixture.

44
Q

VITRO AMPLIFICATION (PCR):

Stage 2 - Heat To 95°C

A

Heat the reaction mixture to 95°C.

The high heat causes the hydrogen bonds between DNA strands to break and the DNA to separate into two separate strands.

45
Q

VITRO AMPLIFICATION (PCR):

Stage 3 - Cool To 65°C

A

Cool the reaction mixture to 65°C.

This causes the primer to anneal to the two separate strands of DNA.

The primers are complementary to the beginning of the two strands.

46
Q

VITRO AMPLIFICATION (PCR):

Stage 4 - Heat To 72°C

A

Heat the reaction mixture to 72°C.
This is the optimum temperature for DNA polymerase activity.

DNA polymerase produces two new strands of DNA by using the two separated strands of DNA as a template.

DNA polymerase adds free-floating nucleotides that are complementary to the template strands of DNA.
Primers allow the nucleotides to bind to one another and produce a strand of DNA.

47
Q

VITRO AMPLIFICATION (PCR):

Stage 5 - Repeat

A

This process of heating, cooling and heating produces two new strands of DNA from one strand.

The process can be repeated as many times as possible to quickly amplify the number of DNA fragments.

The number of DNA fragments is doubled in each cycle of PCR.

48
Q

GENE THERAPY:

Gene Therapy

A

Gene therapy is a genetic engineering technique used to cure disease.

49
Q

GENE THERAPY:

Procedure

A

Gene therapy involves the introduction of a target gene (the gene that confers a beneficial trait) into the genome.
The genome has been transformed.

The target gene is then transcribed and translated to produce the desired protein.

The protein counteracts the effect of a disease that is caused by a mutation.

50
Q

GENE THERAPY:

Allele Interactions

A

Gene therapy is used to treat diseases that are caused by a mutation in a gene.

The way that gene therapy is used depends on the allele interactions of the gene that causes the disease.

If the mutation is in the recessive allele, a wild-type dominant allele is inserted into the genome. The dominant allele counteracts the mutant alleles.

If the mutation is in the dominant allele, an allele that ‘silences’ the mutant allele is inserted in the genome.

51
Q

GENE THERAPY:

Vectors

A

Gene therapy uses vectors to insert the target gene into the genome.

Vector transport allows the gene to be taken up by the cells of the host. The genome is then transformed.

Types of vector include plasmids and bacteriophages.

52
Q

GENE THERAPY:

Types Of Gene Therapy

A

There are two types of gene therapy -
Somatic therapy - altering of alleles in adult body cells.
Germline therapy - altering of alleles in sex cells. This is illegal in humans.

Biology (2 decks)

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