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Molecular Biology & Genetics > 2. Studying DNA > Flashcards

2. Studying DNA Flashcards

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1
Q

What at first was thought to be the carrier of genetic material and why?

A

Protein

Had greater diversity

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2
Q

Griffiths Experiment

A

Smooth (bad) and rough (not bad) bacteria

Found that harmless R bacteria would be transformed by taking up genetic material from S and became harmful

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3
Q

What are the bases in DNA?

A

Guanine
Adenine
Thymine
Cytosine

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4
Q

What are the bases in RNA

A

Guanine
Adenine
Uracil
Cytosine

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5
Q

What are the 3 main constituents of necleotides that make up DNA?

A

Base
Sugar (deoxyribose)
Phosphate

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6
Q

What is Chargaff’s rule?

A 
%A = %T
%G = %C
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7
Q

What are the advantages of DNA over RNA?

A

DNA is more stable

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8
Q

What are the key characteristics of DNA?

A

Capacity for replication
Capacity to store information
Capacity to express information
Capacity for variation by mutation

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9
Q

What is the structural difference between RNA and DNA’s sugar?

A

Ribose has an O molecule on the bottom of the 2’C

Deoxyribose doesn’t

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10
Q

What bond holds the DNA backbone together?

A

3’-5’ phosphodiester bonds

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11
Q

Which of the bases are purines?

A

Adenine

Guanine

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12
Q

Which of the bases are pyrimidines?

A

Uracil
Thymine
Cytosine

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13
Q

Why are H bonds good for joining strands of DNA?

A

Week enough to be seperated in localised areas without using too much energy
Strong enough overall to hold it together

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14
Q

What’s at the 5’ end of DNA?

A

A phosphate group

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15
Q

What’s at the 3’ end of DNA

A

A hydroxyl group

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16
Q

Which part of DNA is hydrophlic?

A

The sugar-phosphate backbone

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17
Q

Which part of DNA is hydrophobic?

A

The bases

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18
Q

What is the general method for extracting DNA?

A

Sample disruption
Release of cell contents
Extraction
Purify and concentrate DNA

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19
Q

What methods of disrupting samples to get DNA are there?

A

Mechanical
Chemical lysis
Osmotic - put them in pure water and they burst due to osmotic shock
Enzymatic

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20
Q

Lysate

A

The contents of a lysed cell

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21
Q

Traditional method of extracting DNA

A

Mix cells with phenol-chloroform solution and centrifuge
Forms solvent and aqueous phase
DNA in aqueous phase

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22
Q

Why does DNA appear in the aqueous phase in phenol-chloroform extraction?

A

Because DNA is hydrophilic

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23
Q

Ethanol precipitation method of purify and concentrate DNA

A

DNA is insoluble in ethanol

High speed centrifugation makes a pellet of DNA that can be re-suspended in a small volume of clean H2O

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24
Q

What are the advantages of nucleic acid purification kits?

A

Allow preparations of high purity

Quick and easy

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25
Q

What are the disadvantages of nucleic acid purification kits?

A

Expensive

Solutions may be of unknown compisition

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26
Q

What setting on the spectophotometer reads how much DNA is in a sample?

A

A260

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27
Q

What setting on the spectophotometer reads the purity of DNA in a sample?

A

A280

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28
Q

What is the optical density to dsDNA (ng/ul) equivalent?

A

1.0 OD = 50ng/ul

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29
Q

Equation for the concentration of DNA using a spectrophotometer?

A

DNA conc (ng/ul) = A260 OD x dilution factor x 50

30
Q

Equation for the purity of DNA using a spectrophotometer?

A

= A260 / A280

31
Q

What does a ratio of A260 and A280 at ~1.8 tell us the sample is?

A

Pure DNA

32
Q

What does a ratio of A260 and A280 at ~2.0 tell us the sample is?

A

Pure RNA

33
Q

What does a ratio of A260 and A280 at <1.6 tell us the sample is?

A

Other contaminants

34
Q

Why do A-T base pairs separate at a lower temperature than C-G pairs?

A

A-T has 1 less H bond

35
Q

What does the Tm value indicate when heating DNA?

A

The temperature at which half the base pairs are denatured and half remain intact

36
Q

If two different samples have different Tm values what does this tell us?

A

The DNA with the higher Tm value has a greater amount of C-G base pairs

37
Q

What is reannealing of DNA?

A

When single strands of DNA find their complimentary strands to reform a double helix

38
Q

What happens to DNA if you cool it quickly after melting it?

A

The single strands don’t reanneal

39
Q

Non-repetitive DNA

A

Sequences that are unique and occur in only one place in the genome

40
Q

Repetitive DNA

A

DNA sequences that are present in more than one copy per genome

41
Q

Multigene families

A

Collection of similar genes

Often clustered together

42
Q

What is a pseugogene?

A

Genes that have lost protein coding ability

43
Q

What can cause pseudogenes?

A 
A premature stop codon
Insertion
Deletion
Frameshift mutation
Loss of a promotor
44
Q

Highly repetitive DNA (satellite DNA)

A

Short sequences repeated many times

45
Q

Types of middle repettitive DNA

A

Minisatellites
LINES
SINES

46
Q

Minisatellites

A

Variable number of tandem repeats
Sequences about 5-100 bp long
Repeated many times end to end
Varies between individuals

47
Q

Which type of repetitive DNA is used in DNA fingerprinting?

A

Minisatellites

48
Q

LINES

A

Long interspersed sequences

Up to 6000 bp

49
Q

SINES

A

Short interspersed sequences
100-500 bp
Don’t code for anything

50
Q

Transposons

A

Jumping genes

Piece of DNA that can move around then genome

51
Q

What is the cause of repetitive DNA?

A

Transposons

52
Q

What enzymes cut DNA?

A

Restriction enzymes

53
Q

Why are blunt ends harder to allow annealing than sticky ends?

A

No H bonds form from overlapping tails of DNA

Makes it harder for DNA ligase to make the phosphodiester bonds

54
Q

Is DNA positively or negatively charged?

A

Negatively

55
Q

How does gel electrophoresis work?

A

Negative charged DNA moves towards + electrode

Smaller DNA can fit through gaps in gel better than large so travel closer to the + electrode

56
Q

How does DNA move in gel electrophoresis?

A

By reptation

57
Q

What do you use to visualise the DNA in gel elctrophoresis?

A

Ethidium bromide

58
Q

What tool is used to compare the movement of the DNA samples in gel electrophoresis?

A

A DNA ladder

59
Q

Polyacrylamide gels

A

Better for smaller fragments of DNA than agarose

Much better resolution - can distinguish difference of 1 bp

60
Q

How do plasmids behave in agarose?

A

They can supercoil under the tortional stress

Supercoiled plasmids move move than non-supercoiled as they are more streamlined

61
Q

Restriction fragment length polymorphisms (RFLP)

A

Can be used to detect some diseases caused by a single base pair change

62
Q

How can RFLP be used be used to detect diseases caused by a single base pair change?

A

Single change causes a loss of a a particular recognition site for an restriction enzyme
When applied the restriction enzyme doesn’t make the cut it usually would in that place
Using gel electrophoresis you can identify the longer than normal length of DNA that wasn’t cut

63
Q

Name 3 uses of restriction enzymes

A

Cutting and pasting genes for cloning
Checking whether cloning was successful
Diagnostics

64
Q

What is the hyperchromic effect?

A

DNA when heated becomes single stranded
ssDNA is less compact than dsDNA
ssDNA will have a higher A260 reading

65
Q

Which base pairs separate at a lower temperature?

Why?

A

A-T

They have 2 H bonds between them while C-G has 3

66
Q

How is aragose gel made?

A

Boiled with water then cooled

67
Q

What are tandem repeats?

A

Repeated sequences of DNA or RNA that lie next to each other

68
Q

Satellite DNA

A

Highly repetitive DNA
Found as clusters of tandem repeats
Permanently coiled tightly into heterchromatin

69
Q

What does VNTR stand for?

A

Variable number tandem repeats

70
Q

Variable number tandem repeats

A

Short tandem repeats

Fewer copies than satellite DNA

Molecular Biology & Genetics (8 decks)

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