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Biology module 6 > Manipulating Genomes > Flashcards

Manipulating Genomes Flashcards

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1
Q

What is the definition of bioinformatics?

A

Using computers to analyse and interpret biological data

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2
Q

What is the definition of computational biology?

A

Using computers to make models of biological systems

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3
Q

What is the definition of genomics?

A

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

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4
Q

What is the definition of proteomics?

A

A branch of biotechnology concerned with applying the techniques of molecular biology, biochemistry, and genetics to analysing the structure, function, and interactions of the proteins produced by the genes of a particular cell, tissue, or organism

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5
Q

What is the definition of synthetic biology?

A

Designing and creating new biological molecules, systems and machines

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6
Q

What is the definition of epidemiology?

A

The branch of medicine which deals with the incidence, distribution, and possible control of diseases and other factors relating to health

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7
Q

What is the definition of polymerase chain reaction?

A

A technique used to amplify (make many more copies) of a small sample of DNA

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8
Q

What is the definition of DNA extraction?

A

Cell surface membranes are broken down with surfactants and proteins digested by proteases. DNA is precipitated out of the remaining solution

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9
Q

What is the definition of electrophoresis?

A

A technique used to separate DNA fragments in order of size; shorter fragments travel further through the gel

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10
Q

What is the definition of satellite regions?

A

Highly repetitive regions of DNA found in all species that vary in length from species to species and person to person

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11
Q

What is the definition of restriction enzymes?

A

Enzymes extracted from bacteria that cut DNA at particular sequences called restriction sites

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12
Q

What is the southern blot?

A

After electrophoresis, the gel is immersed in alkali to separate double strands to single.
Single strands are transferred to a nitrocellulose paper and covered with absorbent paper, drawing the alkaline solution containing DNA through the membrane by capillary action.

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13
Q

What is the definition of probe?

A

Single-stranded pieces of DNA that have complementary base sequences to the satellite region.
Radioactive - identified using photographic film
Fluorescent - identified under UV light.

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14
Q

What is the definition of development and visualisation?

A

Radioactive probes - photographic film placed over nylon membrane. Radioactivity develops certain bands of the film. Photographic copy of the DNA bands is obtained.
Fluorescent probes can be observed under UV light.

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15
Q

What is the definition of anneal?

A

Complementary sequences of single-stranded DNA or RNA to pair by hydrogen bonds to form a double-stranded polynucleotide

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16
Q

What is the definition of blunt end?

A

A fragment of DNA resulting from the breaking of DNA molecule in which there are no unpaired bases or overhangs in the end
_ ____
_ ____

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17
Q

What is the definition of DNA profiling?

A

The process of determining an individual’s DNA characteristics, which are as unique as fingerprints

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18
Q

What is the definition of DNA sequencing?

A

The process of determining the order of bases in a sequence DNA

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19
Q

What is the definition of gene therapy?

A

The introduction of normal genes into cells in place of missing or defective ones in order to correct genetic disorders

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20
Q

What is the definition of genome?

A

The haploid set of chromosomes in a gamete or microorganism, or in each cell of a multicellular organism

21
Q

What is the definition of genotype?

A

The alleles of an individual organism

22
Q

What is the definition of germ line?

A

A series of germ cells each descended or developed from earlier cells in the series, regarded as continuing through successive generations of an organism

23
Q

What is the definition of introns?

A

A segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes

24
Q

What is the definition of ligase?

A

An enzyme that can catalyze the joining of two large molecules by forming a new chemical bond

25
Q

What is the definition of nucleotide?

A

A compound consisting of a nucleotide linked to a phosphate group. Nucleotides form the basic structural unit of nucleic acids such as DNA

26
Q

What is the definition of phenotype?

A

The set of observable characteristics of an individual.

27
Q

What is the definition of plasmid?

A

A genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium. Plasmids are much used in the laboratory manipulation of genes

28
Q

What is the definition of primer?

A

A short single strand of RNA or DNA that serves as a starting point for DNA synthesis. Allows DNA/RNA polymerase to bind.

29
Q

What is the definition of recombinant?

A

A recombinant organism, cell, or piece of genetic material

30
Q

What is the definition of somatic?

A

Refers to the cells of the body in contrast to the germ line cells which usually give rise to the gametes (ovum or sperm)

31
Q

What is the definition of sticky end?

A

A fragment of DNA resulting from the breaking of a DNA molecule in which there are unpaired bases/overhangs in the end.
_ ____
__ ____

32
Q

What is the definition of vector?

A

An organism that does not cause disease itself but which spreads infection by conveying pathogens from one host to another

33
Q

What are the steps of DNA profiling?

A 
Extraction
PCR
Digestion with restriction enzymes
Gel electrophoresis
Southern blotting
DNA hybridisation with probes
Development
34
Q

What can DNA profiling be used for?

A

Forensics (identifying criminal)
Paternity testing (identifying father)
Testing for genetic disease

35
Q

How does gel electrophoresis work?

A

Fragments separated by size.
DNA fragments are injected into a well and an electric current is applied along the gel via electrodes,
Reference samples will be injected into the other wells.
DNA is negatively charged so will be attracted to positive electrode.
Smaller pieces of DNA will move further up the gel as there is less resistance.

36
Q

What is the stationary phase in gel electrophoresis?

A

Gel

37
Q

What is the mobile phase in gel electrophoresis?

A

DNA in solution

38
Q

What do the bands in the gel represent?

A

Fragments of DNA of different lengths

39
Q

How does PCR work?

A

Section of DNA/gene is extracted.
Primers are chosen that are complementary to the start and end of the sequence to be amplified.
Mixture heated to 95 degrees to break hydrogen bonds between the strands of DNA.
Temperature reduced to 55 degrees to allow primers to bind at each end of the sample forming short double stranded sections.
Temperature raised to 72 degrees so Taq polymerase can extend the double stranded section of DNA by adding free nucleotides until it reaches the end of the section. There are now 2 copies.
Heated back to 95 degrees to separate strand and the cycle is repeated.

40
Q

What processes are involved in DNA sequencing?

A

Modified PCR

Electrophoresis

41
Q

What technique is DNA sequencing based on?

A

Sanger sequencing / Chain termination sequencing

42
Q

What is step one in chain termination sequencing?

A

Label 4 test tubes A,T,C,G.

Add to each one a sample of DNA to be sequenced, a radioactive primer, the 4 DNA nucleotides and DNA polymerase.

43
Q

What is added in chain termination sequencing after step one?

A

Small amount of a special modified dideoxynucleotides that can’t form phosphodiester bonds so stop further synthesis of DNA. They are also radioactively labelled.

44
Q

What is the role of the modified dideoxynucleotides in chain termination sequencing?

A

DNA polymerase synthesises many copies of the DNA sample.
Every now and then, at random, a dideoxynucleotide will be added to the growing chain and synthesis of the chain will stop.
A range of DNA molecules will be synthesised ranging from full length to very short.
Test tube A, all the fragments will stop at an A nucleotide.

45
Q

When you have different length fragments in chain termination sequencing what do you do?

A

Gel electrophoresis.
Smallest fragments go furthest. Work out gene sequence by reading from the end (where the shortest fragment is) to the start (where the longest fragment is)

46
Q

What must you remember to do after getting a sequence of bases in gel electrophoresis in chain termination sequencing?

A

That is a complementary sequence to the original sequence so you must replace those bases for the complementary ones.

47
Q

What is different about pyrosequencing compared to chain termination?

A

It involves sequencing by synthesis.

48
Q

Why is it called massively parallel sequencing?

A

Many strands of DNA are sequenced at the same time alongside each other.

49
Q

How does pyrosequencing work?

A

Cut a large piece of DNA into smaller fragments and secure each one in a well on a microarray.
Nucleotides of each base are modified to emit light when they form a phosphodiester bond.
Modified nucleotides are flooded over the wells in a rapidly repeated sequence and when one is incorporated, it emits light.
A camera records the flashes, if more than one nucleotide is incorporated at once more light is emitted.

Biology module 6 (7 decks)

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