Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Genomics SGUL Sem 3 > DNA Hybridization > Flashcards

DNA Hybridization Flashcards

1
Q

What is a pentose sugar?

A

5 carbons that form a cyclical structure with an oxygen bridge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the pyrimidines

A

Cytosine, Thymine, Uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are the purines?

A

Adenine, Guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

On what basis does hydrogen bonding form?

A

Watson and Crick base pairing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Between what two groups does bonding occur?

A

Purines and pyrimidines

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

How many hydrogen bonds are there between T and A?

A

2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

How many hydrogen bonds are there between C and G?

A

3

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Between what base pairs is hydrogen bonding the strongest and why?

A

C and G, 3 H bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are sugar phosphates linked by?

A

Phosphodiester bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What kind of interactions does base stacking involve?

A

Hydrophobic interactions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Why are bases stacked?

A

To exclude water from the inside of the molecule around the bases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Describe what the Van der Waals forces are like in DNA?

A

Individually small but they contribute to the stability

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the backbone of DNA formed by?

A

Phosphodiester linkage

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What do phosphodiester bonds join?

A

3 and 5 prime carbons of deoxyribose of DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does the stability of DNA depend on?

A

Free energy of the molecule
Energy minimisation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What do phosphate groups interact with?

A

Proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What bonds can be broken to denature DNA?

A

Hydrogen bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What disrupts hydrogen bonding?

A

Alkalis
Heat

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is hyperchromicity?

A

Increased absorption of light at 260nm on denaturation

Single stranded DNA absorbs UV light to a greater extent than double stranded DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is Tm?

A

The point at which 50% of all strands separate is called the melting temperature

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What increases as the molecule is denature

A

Absorption

22
Q

What 5 things affect Tm?

A

GC content
Length of molecule

Salt concentration
pH
Mismatches

23
Q

What does a higher Gc content mean?

A

More hydrogen bonds
Higher Tm

24
Q

What is the relationship between the length of DNA and Tm?

A

The longer the contiguous duplex the higher the Tm

More Hydrogen bonds within the molecule greater stability

25
Up until what point does adding more hydrogen bonds increase stability?
Up until 300 bp
26
What does high salt do to DNA duplexes?
Stabilizes them
27
What is the relationship between Na+ and Tm?
High Na+ = High Tm
28
What does increasing the salt concentration do to the stability and Tm?
Stabilizes the structure and increases the Tm Overcomes the effect of mismatched base pairing reducing specificity of base pairing in high salt environments
29
What does increasing salt do to base pairing?
Reduces the specificity of base pairing at a given temperature
30
What are 3 chemicals that disrupt hydrogen bonds?
Urea Formamide Alkali
31
What kind of pH destabilizes DNA duplexes?
High
32
What is a mismatch?
A base pair that is unable to form hydrogen bonds
33
Why do mismatches weaken DNA?
→ It reduces the number of hydrogen bonds → Fewer H bonds means a lower Tm
34
How do mismatches destabilize base pairing?
→ They allow other molecules to penetrate within the structure of the molecule → Shorter contiguous stretches of double stranded sequence = lower Tm →Distorts the structure and destabilises adjacent base pairing
35
What is the reverse of denaturation called?
Renaturation
36
What is renaturation facilitated by?
Slow cooling and neutralization
37
What is hybridization?
Renaturation but with the introduction of a foreign molecule into a solution
38
Why is renaturation favored?
Formation of the structure favors energy minimization which is driven by a change in free energy (∆G)
39
Why do perfect matches have a higher Tm?
→ They are thermodynamically favored over mismatches → Mis-matches destabilise DNA and reduce the Tm
40
How can you manipulate specificity?
Limiting hybridization between imperfectly matched sequences allows to manipulate specificity
41
What is high stringency?
→ Temperature near the Tm → Low salt concentration
42
How does nucleic acid hybridization work?
→ Identifies the presence of nucleic acid containing a specific sequence of bases → A labelled molecule is used to investigate a mixed population of molecules to find out how many of a specific sequence there are
43
How do you find a specific strand within DNA with a probe?
Label a probe and hybridize it with a strand you are looking for that corresponds to a gene
44
What is a probe?
→ A single strand of DA → Labelled with a fluorescent molecule → Used to detect nucleic acids in a diagnostic → Under high stringency conditions will form a perfectly matched duplex with their complement
45
Why is PCR used over gel techniques?
→ Gel techniques are messy → Only detects one gene at a time and small numbers of samples
46
How does a microarray work?
→ Ordered assembly of probes are attached to the surface of a glass matrix → Hybridization is used to attach the complementary molecules to the surface of the matrix → Label visualised and measured → This can measure 50,000 transcripts in a cell
47
What are SNPs?
→ Single nucleotide polymorphisms are the most common type of genetic variation among people → Each SNP represent a difference in a single nucleotide
48
What does the denaturation of a DNA duplex depend on?
Upon the stability of the structure determined by its sequence of bases
49
What do nucleic acid based techniques rely on?
→ The specificity of complementary of base pairing → The avoidance of mis-matches by using stringency and the calculated Tm of the duplex → Manipulating the conditions under which hybridisation is carried out
50
What are the characteristics of a probe?
→ Always single stranded → Can be made from either DNA or RNA depending on the technique → Usually between 20 and 1000 bases in length but relative short synthetic molecules → Made chemically → Labelled with a fluorescent, or luminescent molecule
51
Describe the process of Southern/Northern blotting.
→ DNA or RNA that is separated by gel electrophoresis → Transferred by mass capillary flow of a buffer from a reservoir to a nylon membrane carrying the nucleic acid with it → Captured by and covalently bonded to the membrane → Then hybridised with a labelled probe

Genomics SGUL Sem 3 (21 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions