Brainscape's Knowledge GenomeTM

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


See full index

Genomics > DNA complementarity, hybridisation and its effects > Flashcards

DNA complementarity, hybridisation and its effects Flashcards

1
Q

What 3 structural elements does a nucleotide contain?

A
  • Nitrogenous base
  • Pentose sugar
  • Phosphate group
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What number carbon within the pentose sugar is the nitrogenous base joined to?

A

Carbon 1

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

What number carbon within the pentose sugar is the phosphate group joined to?

A

Carbon 5

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

What other structure is within the pentose sugar and what number carbon is it joined to?

A

Hydroxyl group joined to carbon 3

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

What are the two categories that the nitrogenous bases are classified into? For each category name the 2 bases that belong to it

A
  • Pyrimidines (single ring) - Thymine and cytosine
  • Purines (double ring) - Adenine and guanine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Why can a pyrimidine base only hydrogen bond with a purine base?

A

Because the pairing of a pyrimidine and purine base is energetically favourable as the bases are the right distance apart to allow hydrogen bonding to occur.

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

Why is it the case that Cytosine (Pyrimidine) can only hydrogen bond with Guanine and not Adenine (which like Guanine is also a purine base)?

A

Because Cytosine and Guanine are both able to form 3 hydrogen bonds while Adenine is only able to form 2 hydrogen bonds so it has to pair with Thymine which can only form 2 hydrogen bonds as well.

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

What does the fact that a Cytosine-Guanine pairing can form 3 hydrogen bonds mean for the strength of the pairing when compared to a Adenine-Thymine pairing?

A

It means that the Cytosine-Guanine pairing is stronger than an Adenine-Thymine pairing as it contains one more hydrogen bond per pair.

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

Why is the stability of a DNA molecule with more C-G pairings higher than a DNA molecule with less?

A

More G-C pairings means that for there are more hydrogen bonds within the DNA molecule making it harder to break down (more stable).

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

Name the different forces/bonds within a polypeptide chain of DNA

A
  • Phosphodiester bonds
  • Hydrogen bonds
  • Base stacking
  • Van der waals forces
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Explain the concept of base stacking

A

The arrangement of the bases stacked one above the other within the DNA helix. There are hydrophobic interactions between the stacked bases which excludes water from the internal structure of the double helix.

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

Explain the concept of Van der waals forces

A

Interaction between the nuclei of individual atoms within a molecule. This interaction causes the nuclei to attract each other when they’re too far away and repel each other when they’re too close.

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

Why is DNA a negatively charged molecule?

A

Because the negatively charged phosphate groups are on the outside of the double helix

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

What does it mean to “denature” DNA?

A

Denaturing DNA means to disrupt the hydrogen bonds within a DNA molecule causing it to be converted from one double stranded molecule into 2 single stranded molecules.

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

What are the 2 main ways of denaturing a DNA molecule?

A
  • Heat DNA in solution
  • Induce denaturation using a strong alkali or urea
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

How can the denaturation of DNA be measured?

A

Heat up a solution containing Double stranded DNA molecules and measure the absorbance of UV light at 260nm

17
Q

When measuring DNA denaturation, does the absorbance of UV light at 260nm increase or decrease? Why is this the case?

A

Absorbance of UV light increases as the DNA denatures. The reason for this is because as you denature the DNA you produce single stranded DNA molecules and these absorb more UV light than double stranded DNA molecules.

18
Q

What is the increase in absorbance of UV light as a result of DNA denaturation called?

A

Hyperchromicity

19
Q

What is Tm (melting temperature)?

A

The temperature at which 50% of the DNA strands have been separated during a Denaturation reaction

20
Q

What are the 5 factors that can affect Tm?

A

Guanine-Cytosine content

Length of DNA molecule

Salt concentration of the environment

pH of environment (alkali is a denaturant)

No. Mismatches (unmatched base pairs)

21
Q

How does Guanine-Cytosine content affect Tm?

A

More guanine-cytosine pairs within a DNA molecule means more hydrogen bonds which means a higher Tm as the DNA is more stable.

22
Q

How does molecular length affect Tm?

A

The longer the molecule of DNA the more hydrogen bonds that molecule will have meaning it will be more stable and will therefore have a higher Tm.

However, after 300bp there isn’t any further increase in Tm.

23
Q

How does salt concentration [Na+] affect Tm?

A

The positive charges of the [Na+] ions neutralise the negative charges of the phosphates thus reducing the repulsion force between the phosphates. This increases the stability of the DNA molecule and therefore Tm

24
Q

How does pH affect Tm?

A

Increase in pH causes a decrease in DNA stability and therefore a decrease in Tm. This is because increased pH means increased [OH-]. The OH- ions are able to penetrate into the internal structure of the DNA and disrupt the hydrogen bonds between the bases leading to denaturation.

25
Q

How do mismatches affect Tm?

A

Mismatches reduce the number of hydrogen bonds present within a DNA molecule which reduces the Tm of that molecule.

Mismatches also distort the structure of the DNA and destabilise adjacent base pairs which allows for other molecules such as water and OH- to enter into the internal structure and disrupt hydrogen bonds. This will also reduce Tm

26
Q

What is renaturation?

A

Renaturation is the reformation of a DNA molecule/duplex after it has been denatured

27
Q

How can renaturation be induced?

A

By changing the conditions which have caused denaturation to have occured in the first place e.g.

Cooling the solution or neutralisating of the solution after adding alkali which removes OH- from internal structure allowing hydrogen bonds to reform

28
Q

What is the difference between renaturation and hybridisation?

A

Hybridisation is the formation of a duplex structure of two DNA molecules that have been introduced to one another while renaturation is the re-formation of a duplex that has been previously denaturated.

29
Q

What is stringency?

A

Manipulating the conditions at which hybridisation is performed to limit hybridisation between imperfectly matched sequences.

30
Q

How can high stringency conditions be created?

A

They are created by performing hybridisation at a temperature close to the Tm of the DNA strand or performing it at a low salt concentration

Genomics (18 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions