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Manipulating genomes 2425 Flashcards

1
Q

What is a genome?

A

All of the genetic material of an organism (in animals includes both nuclear and mitochondrial DNA)

The genome encompasses all genetic information, including genes and non-coding regions.

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2
Q

What percentage of total DNA do genes make up?

A

About 1-2% of the total DNA

This small percentage represents the coding regions that directly translate into proteins.

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3
Q

Define exons.

A

DNA that contains sequences that code for proteins (coding DNA)

Exons are the parts of genes that are expressed in the final protein product.

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4
Q

Define introns.

A

DNA that does not code for proteins (non-coding DNA)

Introns are spliced out during mRNA processing before translation.

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5
Q

What are satellite DNA?

A

Short sequences of bases which repeat many times within non-coding DNA

Satellite DNA is often used for DNA profiling due to its variability among individuals.

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6
Q

What is DNA profiling?

A

Producing an image of the patterns in the DNA of an individual

DNA profiling utilizes unique non-coding regions to identify individuals.

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7
Q

What are the five main stages in producing a DNA profile?

A
  • Extracting and amplifying the DNA
  • Digesting the sample using restriction endonucleases
  • Separating the DNA fragments
  • Hybridization
  • Seeing the evidence

Each stage is crucial for obtaining a clear DNA profile for analysis.

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8
Q

What is the purpose of PCR?

A

Used to amplify DNA for: * Genetic testing/screening * Paternity testing * Forensic analysis of evidence * Genetic engineering * Studying evolutionary relationships

PCR enables the analysis of small DNA samples by creating millions of copies.

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9
Q

What temperature is set in the thermocycler to denature DNA in PCR?

A

94-95 °C

This high temperature breaks the hydrogen bonds between DNA strands.

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10
Q

What happens at the annealing stage of PCR?

A

The temperature is decreased to 50-65 °C and the primers anneal to the ends of the DNA strands

This is a critical step for ensuring the primers bind correctly to the target DNA sequences.

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11
Q

What is Taq polymerase?

A

A thermostable DNA polymerase from Thermus aquaticus bacteria

It is used in PCR because it remains active at high temperatures.

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12
Q

What is the role of restriction endonucleases in DNA analysis?

A

They cut DNA into small fragments at specific nucleotide sequences

This allows for the analysis of specific regions of DNA during profiling.

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13
Q

What is gel electrophoresis used for?

A

To separate DNA fragments

This technique allows for the visualization of different lengths of DNA for analysis.

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14
Q

What is the charge of DNA and how does it behave in electrophoresis?

A

DNA is negatively charged and moves towards the positive pole during electrophoresis

This movement is due to the attraction between the negatively charged phosphates of DNA and the positive electrode.

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15
Q

What are variable number tandem repeats (VNTRs)?

A

Repeating short non-coding regions of DNA unique to each individual (except identical twins)

VNTRs are used in DNA profiling for individual identification.

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16
Q

What is Southern blotting?

A

A technique used to transfer DNA fragments from a gel to a membrane for further analysis

Southern blotting allows for the visualization of specific DNA sequences using probes.

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17
Q

What is the Human Genome Project?

A

An international scientific research project to map the entire human genome

The project’s goal was to identify all the genes in human DNA and make the data publicly available.

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18
Q

What is Sanger sequencing?

A

A method of DNA sequencing that uses chain-terminating nucleotides

This technique allows for the determination of the precise order of nucleotides in a DNA molecule.

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19
Q

List the components needed for Sanger sequencing.

A
  • Excess nucleotides (A, T, C, G)
  • Terminator bases (fluorescently labelled)
  • DNA fragment for sequencing
  • DNA primers
  • DNA polymerase

These components work together to synthesize new DNA strands during the sequencing process.

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20
Q

What are terminator bases?

A

Bases that stop DNA synthesis at the point they are added

Also known as dideoxynucleotides (ddNTP)

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21
Q

What is the first step in DNA sequencing using a thermal cycler?

A

Place everything into the thermal cycler and heat to 96°C to separate DNA strands

This occurs due to the breaking of hydrogen bonds.

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22
Q

At what temperature do primers anneal during DNA sequencing?

A

50°C

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23
Q

What occurs at 60°C during DNA sequencing?

A

DNA polymerase synthesizes a new DNA strand using complementary base pairing rules

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24
Q

What is the purpose of adding terminator bases during DNA sequencing?

A

To incorporate terminator bases at random, producing fragments of all possible lengths

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25
How are DNA fragments separated after sequencing?
By capillary electrophoresis
26
What allows the detection of the terminator base at the end of a DNA fragment?
Fluorescent tags
27
How is the sequence of bases read in DNA sequencing?
A laser detects the different colors of fluorescent tags in order of size
28
What can the sequence of bases displayed be used for?
To build the original DNA sequence
29
What is the definition of next-generation sequencing?
Any method of DNA sequencing that has replaced the Sanger method, often referred to as high throughput sequencing
30
What is the human genome approximately composed of in terms of nucleotides?
3.2 billion nucleotides
31
Fill in the blank: The first step in sequencing a whole genome is to extract samples of DNA from _______.
[cells]
32
What is Roche pyrosequencing?
A method that involves building a chain of nucleotides against a template
33
How is light detected in Roche pyrosequencing?
Light released by luciferin is detected when a nucleotide is added to the chain
34
What are the applications of knowing the amino acid sequence of a protein?
To predict how the protein will fold into its tertiary structure
35
What is bioinformatics?
A field of biology that involves the storage, retrieval, and analysis of data from biological studies
36
How can bioinformatics help compare genomes?
It allows scientists to make comparisons with the genomes of other organisms
37
What is the purpose of sequencing the genomes of pathogens in epidemiology?
To identify highly infectious strains and implement appropriate control measures
38
What was the Human Genome Project (HGP)?
An international research program that sequenced the human genome with 99.9% accuracy
39
What is a GMO?
Genetically modified organism, which receives genes from another organism
40
What do restriction endonucleases do?
Cut DNA at specific base sequences
41
What does reverse transcriptase do?
Uses isolated mRNA to produce complementary DNA
42
Fill in the blank: DNA fragments can be amplified using _______ (__________ __________ __________).
[PCR (Polymerase Chain Reaction)]
43
What is the role of primers in DNA sequencing?
Small sections of single-stranded DNA that anneal to the 3' end of the fragment
44
Fill in the blank: The presence of specific DNA fragments can be visualised using _______ blotting.
[Southern blotting]
45
What is the purpose of using fluorescent markers in DNA sequencing?
To identify terminator bases at the end of DNA fragments
46
What is a term for DNA that contains genetic material from more than one organism?
[chimeric DNA] ## Footnote Chimeric DNA is often used in genetic engineering.
47
What is the purpose of a marker gene in genetic engineering?
[to check if a cell has taken up a vector] ## Footnote Marker genes help identify successful recombinant cells.
48
What enzyme is used to join DNA fragments together?
[DNA ligase] ## Footnote DNA ligase forms phosphodiester bonds between adjacent nucleotides.
49
Fill in the blank: The gene can be cut out using __________.
[restriction endonucleases]
50
What method can be used to produce the DNA gene from mRNA?
[reverse transcription] ## Footnote Reverse transcription converts mRNA back to DNA.
51
What are the characteristics of bacterial plasmids used as vectors?
* Small and circular * Replicate separately from the rest of the DNA * Cut with the same restriction endonuclease
52
What is the purpose of using the same restriction endonuclease on a plasmid?
[to create complementary sticky ends] ## Footnote Complementary sticky ends facilitate the joining of DNA fragments.
53
What is the chemical transformation method used for?
[to increase bacterial membrane permeability] ## Footnote This is done by culturing bacteria in a calcium-rich solution.
54
What is electroporation?
[a method that uses an electric current to make cell membranes more porous] ## Footnote This increases the likelihood of plasmid uptake by the cell.
55
True or False: Bacteria that have not taken up the plasmid will be resistant to tetracycline.
[False]
56
What does GM stand for in the context of plants?
[genetically modified] ## Footnote GM plants can be engineered to express desired traits.
57
What is a callus in plant genetic engineering?
[a mass of identical plant cells] ## Footnote Each cell of the callus can be used to grow a new plant.
58
Fill in the blank: GM bacteria can cause __________ of identical plant cells.
[cloning]
59
What is the main challenge in genetically engineering animal cells compared to prokaryotes?
[the difficulty of manipulating the cell membrane] ## Footnote Animal cells have more complex membranes than prokaryotic cells.
60
What are monoclonal antibodies used for?
[pathogen identification and cancer treatment] ## Footnote They are produced from hybridoma cells that secrete a single type of antibody.
61
What is somatic cell gene therapy?
[replacing a mutant allele in a somatic (body) cell] ## Footnote It is a temporary solution as somatic cells have a limited lifespan.
62
What is germline cell gene therapy?
[inserting a healthy allele into germ cells] ## Footnote This allows the healthy allele to be passed to offspring.
63
Fill in the blank: Ethical concerns exist regarding __________ in human embryos.
[germline gene therapy]
64
What are the two types of vectors used to transform human cells?
* viral vectors * liposomes
65
What is the CFTR protein associated with?
[cystic fibrosis] ## Footnote The CFTR gene codes for a channel protein found in cell membranes.
66
What is a key difference between somatic and germ-line gene therapy?
[Somatic therapy does not affect future generations, germ-line therapy does.]
67
Why is gene therapy unlikely to work for Huntington’s disease?
[It is caused by a dominant allele, making it difficult to treat.]
68
What are some ethical issues related to GM microorganisms?
[Potential risks of antibiotic resistance and ecological impacts.]
69
What is the main benefit of using GM plants?
[Increased agricultural efficiency and pest resistance.]
70
What is an artificial chromosome?
[a synthetic structure that can carry multiple genes without integrating into the host genome.]
71
Which statement correctly describes a difference between somatic and germ line gene therapy?
[B. Somatic therapy can target specific tissues in need of treatment, germ line therapy cannot.]
72
How can researchers use PCR to compare E. coli growth rates on cancerous and healthy tissue?
[By amplifying DNA from both tissues and measuring the quantity of E. coli DNA.]
73
What percentage of bacteria is represented in the given context?
60% ## Footnote This percentage is used to quantify the bacterial population in the study.
74
What technique is used to check E. coli growth on mice liver tumors?
Quantitative PCR ## Footnote This technique allows for the comparison of E. coli growth rates on cancerous versus healthy tissue.
75
Why are there very few ethical concerns regarding the genetic engineering of E. coli?
E. coli is a bacterium and does not have sentience or complex social structures ## Footnote Ethical concerns are more prevalent in complex organisms.
76
What is the purpose of pre-implantation genetic diagnosis?
To identify embryos that do not carry defective alleles ## Footnote This is crucial for selecting embryos that can help treat genetic diseases.
77
What disorder is Henry diagnosed with?
Fanconi anaemia ## Footnote Fanconi anaemia is an autosomal recessive disorder characterized by bone marrow failure.
78
What is a 'saviour sibling'?
A sibling conceived to provide stem cells for treating a sibling with a genetic disorder ## Footnote This concept is central to the discussion of ethical issues in genetic engineering.
79
How are stem cells extracted for use in treating genetic diseases?
From the newborn's umbilical cord ## Footnote This method allows for the collection of stem cells that can be used for transplantation.
80
What is the significance of human leucocyte antigen (HLA) in tissue matching?
HLA helps determine compatibility between the donor and recipient ## Footnote The right HLA match is crucial for preventing immune rejection.
81
What does pluripotent mean in the context of embryo cells?
Able to become a variety of tissue types ## Footnote Pluripotent cells can differentiate into almost any cell type.
82
What are the risks involved in pre-implantation genetic diagnosis?
Embryo damage and inaccurate results ## Footnote About 0.6% of embryos may be damaged during the procedure.
83
What type of inheritance pattern does Fanconi anaemia follow?
Autosomal recessive inheritance ## Footnote This means that both parents must carry the allele for the child to be affected.
84
What is the main treatment for Fanconi anaemia?
Bone marrow transplant ## Footnote This treatment aims to replace malfunctioning blood stem cells.
85
What process is used to obtain embryos for implantation?
In vitro fertilisation ## Footnote This process allows for the selection of embryos based on genetic screening.
86
What ethical issues arise from the use of saviour siblings?
Concerns about the commodification of human life and potential psychological impacts ## Footnote The ethics of creating life for the purpose of saving another raises significant moral questions.
87
Fill in the blank: The only treatment with a chance of long-term success for Fanconi anaemia is a _______.
bone marrow transplant
88
True or False: Pre-implantation genetic diagnosis is 100% accurate.
False ## Footnote There is always a risk of incorrect results during screening.

Biology (2 decks)

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