Brainscape's Knowledge GenomeTM

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


See full index

CMMB 411- Doreen > Topic 3 > Flashcards

Topic 3 Flashcards

1
Q

GC is more stable than AT. True or false: this is predominantly due to the extra hydrogen bond in the GC base pair

A

False. This is a misconception.
- GC actually has stronger π stacking compared to AT which is the main contributor to GC’s stability

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

Most DNA is (right-handed/left-handed)

A

Right-handed

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

What does it mean for a DNA helix to be “right-handed”?

A

DNA turns in the direction of your right hand fingers curling inward (with your thumb pointed up)
- If you follow the helix as it twists away from you, the spiral moves in the clockwise direction.

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

Right-handed DNA results when the ribose and base are in (anti/syn) configuration

A

Anti (base is not oriented directly above the ribose)

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

Left-handed DNA results when the ribose and base are in (anti/syn) configuration

A

Syn (base is oriented directly above the ribose)

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

Tautomers/tautomerization

A

Isomeric molecules that can be interconverted by tautomerization, a chemical reaction that often results in the migration of a hydrogen atom

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

Amides tautomerize to…

A

Imides (imidic acid)
- Double bond between carbon and nitrogen, with alcohol group branching off the carbon

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

Keto form tautomerizes to…

A

Enol form
- Double bond between the two carbons with an alcohol group branching off the carbon

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

Guanine is usually found in what tautomeric form? what does it tautomerize to?

A

Usually found in keto form, tautomerizes into enol form

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

Adenine is usually found in what tautomeric form? What does it tautomerize to?

A

Usually found in amino form, tautomerizes into imino form

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

Thymine is usually found in what tautomeric form? What does it tautomerize to?

A

Found in keto form, tautomerizes into enol form

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

Cytosine is usually found in what tautomeric form? What form does it tautomerize to?

A

Found in amino form, tautomerizes into imino form

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

As bases tautomerize, what happens to the hydrogen donors and acceptors?

A

The hydrogen donors and acceptors change around

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

How are tautomeric shifts defined in the context of base pairing?

A

Tautomeric shifts are the spontaneous rearrangements of nitrogenous bases that allow for hydrogen bonding of mismatch base pairs
- Can lead to substitution mutations

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

Describe how DNA’s flexibility helps in DNA repair

A
  • The sugar-phosphate backbone serves as a hinge to rotate the base
  • Leads to homologous recombination and DNA repair
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Describe the Mica experiment

A
  1. DNA is immobilized on a Mica surface (a flat, naturally occurring mineral)
  2. DNase I, a bulky enzyme, cleaves the phosphodiester bonds in the backbone. DNase I is too bulky, so it only cuts the DNA at sites where it’s most exposed (these sites occur at regular intervals)
  3. The fragments are separated on an agarose gel, where the fragment sizes seemed to be multiples of 10.5. This indicated that the enzyme would make a cut in the strand not attached to the mica every 10 nucleotides or so
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What conclusions could be made by the Mica experiment?

A

The DNA makes a 360 degree rotation every ~10.5 nucleotides, or every nucleotide is twisted 36 degrees from the previous one

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

Explain how the major groove is rich in chemical information

A

In the major groove, the different base pairs expose unique patterns of hydrogen bond donors (D), acceptors (A), and other chemical groups like methyl groups (M) and nonpolar hydrogen (H), which provide a “chemical signature” for each base pair that is more distinct than in the minor groove.
- the minor groove presents less distinctive features, making it harder to distinguish between base pairs.
- This method helped with DNA sequencing in the past (but was labouring)

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

Pattern from left to right of hydrogen donors, hydrogen bond acceptors, nonpolar hydrogens and methyl groups in major groove for A-T base pair

A

ADAM
- if A is on the left and T is on the right

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

Pattern from left to right of hydrogen donors, hydrogen bond acceptors, nonpolar hydrogens and methyl groups in minor groove for A-T base pair

A

AHA
- If A is on the left and T is on the right

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

Pattern from left to right of hydrogen donors, hydrogen bond acceptors, nonpolar hydrogens and methyl groups in major groove for G-C base pair

A

AADH
- If Guanine is on the left and Cytosine is on the right

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Pattern from left to right of hydrogen donors, hydrogen bond acceptors, nonpolar hydrogens and methyl groups in minor groove for G-C base pair

A

ADA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Direction of helix orientation in B DNA

A

Right

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Number of base pairs per turn in B DNA

A

10.5

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

Rotation per residue in B DNA

A

36 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Length of A DNA (relative to normal B DNA)

A

Short (squeezed)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Number of base pairs per turn in A DNA

A

11

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Rotation per residue in A DNA

A

33 degrees

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

Length of Z DNA (relative to normal B DNA)

A

Long

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

Number of base pairs per turn in Z DNA

A

12 (6 dimers)
- The helix is arranged in such a way that every two base pairs (a dimer, like CG or GC) form a repeating unit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Rotation per residue in Z DNA

A

30 degrees (60 degrees/dimer)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

__ DNA and __ DNA are both right-handed, while __ DNA is left-handed

A

B, A, Z

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

Diffraction pattern lines are (parallel/perpendicular) to the actual lines in the structure

A

Perpendicular (90 degrees)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

In photograph 51 (Rosalind Franklin’s X-ray diffraction), there was a missing 4th layer line. What was this a result of, and what did this show regarding DNA?

A

The missing 4th layer line was due to destructive interference, and showed that DNA was a DOUBLE helix (because the signals from both strands cancelled each other out)
- Also showed that DNA has major and minor grooves because not all signals had destructive interference (showed that DNA is asymmetrical)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

What’s the pitch of a DNA molecule (the distance between similar structures)?

A

34 Å
- determined by layer lines on photograph 51

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What’s the rise of a DNA molecule (distance between adjacent nucleotides)?

A

3.4 Å
- determined by radius of image of photograph 51

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What does the distance between adjacent dots in the center of photograph 51 tell us?

A

The diameter of the DNA helix, which is 20 Å
- determined by radius between spots on photograph 51

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What is denaturation and what two things usually cause it?

A

Denaturation is the disruption of hydrogen bonds that normally used to maintain the structure and function of a macromolecule
- Caused by heat or extreme pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

What is melting temperature (Tm)?

A

Tm is the transitional mid-temperature at which 50% of double-stranded DNA is denatured into single-stranded DNA.

40
Q

What are the two factors that affect Tm?

A
  1. GC content: higher GC content= higher Tm (because GC has lower entropy, so it’s more stable and because it has an extra hydrogen bond)
  2. Ionic strength of solution: higher salt concentration= higher Tm (because the phosphate backbone of DNA is negatively charged and higher salt= more cations= decreased repelling force between the duplex = increased dsDNA stability = higher Tm)
41
Q

How can we tell if DNA is denatured based on UV absorbance?

A

DNA absorbs UV at a wavelength of ~260 nm. ssDNA absorbs >40% of UV at 260 nm than the dsDNA (because bases are more exposed)
- Known as the hyperchromic effect

42
Q

When dsDNA is heated, it is _____. If it is cooled after, it is _____

A

When dsDNA is heated, it is denatured. If it is cooled after, it is re-associated/re-natured/re-annealed

43
Q

Describe DNA hybridization

A

ssDNA can re-associate with another strand that has “similar” sequence to form a hybrid dsDNA

44
Q

What has DNA hybridization helped with in terms of sequencing in the past?

A

In the past, when sequencing technology was limited, DNA hybridization helped find new genes and diseases. It did this by finding the complement of disease genes.

45
Q

What 3 experimental methods is hybridization especially important for?

A
  • Southern blots (uses DNA:DNA hybrid) and Northern blot (uses DNA:RNA hybrid)
  • DNA and RNA microarray
  • Next-Generation Sequencing
46
Q

What is DNA topology?

A

The mathematical study of the DNA properties in deformation, twisting and stretching

47
Q

Prokaryotic DNA is also known as…

A

Covalently closed, circular DNA (cccDNA)

48
Q

Describe eukaryotic DNA and prokaryotic DNA in terms of flexibility

A

Eukaryotic DNA: Linear, can freely rotate and unwind
Prokaryotic DNA: topologically constraint
- In linear DNA, the ends can unwind to relieve any torsional stress caused by twisting. However, in prokaryotes, where DNA is circular, there are no free ends to allow the molecule to untwist on its own. Any change in twist or supercoiling must be actively managed by enzymes because the closed structure keeps the strands constrained.

49
Q

How does DNA become topologically constrained by replication?

A

When DNA becomes unwound for replication, there is torsional stress applied to the sides of the unwound part. More bulgier twists end up forming as the DNA twists more and more.

50
Q

During transcription, which end of the DNA is overwound? Why?

A

5’ end of the strand that is being transcribed. This is because as the DNA unwinds so RNA pol can transcribe, extra torsional stress is put on the end that it moves towards

51
Q

During transcription, which end of the DNA is underwound? Why?

A

3’ end of the strand that is being transcribed. This is because as the DNA unwinds so RNA pol can transcribe, torsional stress is released from the end it moves away from

52
Q

Describe the linking number (Lk) of DNA

A
  • Describes the topology of a DNA molecule
  • Tells us the amount of torsional stress put on a given DNA molecule
  • Tells us how many turns it would take for the two strands of DNA to completely separate
  • Is an integer
53
Q

What are topoisomers?

A

Different forms of cccDNA molecules that differ only in their linking number

54
Q

True or false: topoisomers migrate the same distance on an agarose gel

A

False
- When a cccDNA undergoes supercoiling and is resolved on an agarose gel, there is no single band but rather two or more bands
- Order of travel from least to most migration is open circular -> linear -> supercoiled (not many loops) -> supercoiled (many loops)

55
Q

What is supercoiled DNA? What is supercoiling determined by?

A

Supercoiled DNA is DNA that twists upon itself because it is underwound or overwound (and thereby strained) relative to B-form DNA
- Supercoiling is determined by writhe, but not by twist -> writhe describes how the overall double-stranded DNA helix is coiled or looped in three-dimensional space (e.g., forming supercoils).
- While twist reflects local helical structure, it’s the writhe that determines whether the DNA becomes supercoiled

56
Q

Positive supercoiling is also known as…

A

Overwound DNA

57
Q

Negative supercoiling is also known as…

A

Underwound DNA

58
Q

Positive supercoiling is when DNA twists…

A

In the same direction as the DNA

59
Q

Negative supercoiling is when DNA twists…

A

In the opposite direction as the DNA

60
Q

Most DNA is found in what type of supercoiling?

A

Negative supercoiling

61
Q

Does negative or positive supercoiling require more energy to unwrap?

A

Positive

62
Q

What type of organisms have positive supercoiling and why?

A

Some bacteria (thermophils) have positive supercoiling (live in a harsh environment, so they require more stable DNA since it’s harder to unwind and takes more energy)

63
Q

What are topoisomerases?

A

Enzymes that create/relief supercoiled DNA by changing the topology of DNA

64
Q

What numbered nitrogen bonds to the sugar in nucleic acids?

A

N1 for pyrimidines, N9 for purines

65
Q

Nucleosomes introduce ______ supercoiling, by introducing _______ nucleosomes

A

Nucleosomes introduce negative supercoiling, by introducing left-handed nucleosomes

66
Q

How would a relaxed, circular DNA molecule go from relaxed to supercoiled with 4 writhes?

A

The DNA is broken by the topoisomerase, one helix is rotated 360 degrees four times, then the ends are rejoined.

67
Q

What are 3 functions of supercoiling?

A
  1. To reduce the space and allow for DNA to be packaged into the small nucleus
  2. To prevent or resolve entanglement of the DNA during cell division (butterfly chromosome structure arises due to DNA condensation. Important to maintain the genome structure to prevent DNA breakage)
  3. Positive supercoiling protects DNA from thermal denaturation and regulates gene expression in extreme conditions (like in thermophil bacteria - but these organisms with positive supercoiling have decreased gene expression compared to negatively supercoiled organisms)
68
Q

What is a disadvantage of positive supercoiling for replication and transcription?

A

Energy is needed to unwrap the DNA for these processes

69
Q

How does negative supercoiling help strand separation?

A

Negative supercoiling stores the free energy required to facilitate strand separation
- If a negatively supercoiled plasmid is “forced” to have the relaxed conformation, it will leave a region unpaired. So, introducing negative supercoils is a way of favouring unwinding of the DNA.

70
Q

Describe how supercoiling can be removed using DNase I?

A
  • By mild digestion with DNase I
  • “nick” the dsDNA by breaking a single phophodiester bond to allow for free rotation of the DNA around the other backbone
  • This free rotation unwinds the supercoils, effectively relaxing the DNA and bringing it back to its normal, relaxed state. Think of it like cutting one string of a tightly twisted rope. When you cut it, the rope can unwind and lose the extra twists.
71
Q

Type I topoisomerase (Topo I) is frequently just referred to as…

A

Topoisomerase

72
Q

Topo I makes a (ssDNA/dsDNA) cut

A

ssDNA

73
Q

Topo I (does/does not) require energy

A

does not
- Relaxes supercoils “passively

74
Q

How many writhes does topo I decrease a supercoiled piece of DNA by? What does this reduce the linking number by?

A

1 writhe
- Reduces the Lk by 1

75
Q

What are the five steps involved in the reaction of topo I?

A
  1. DNA is nicked by the attack of tyrosine
  2. The other side of the cleaved DNA is “held” by the enzyme
  3. The uncleaved DNA strand passes through the opening. This relieves the torsional strain from supercoiling.
  4. Reverse of the nicking reaction (the 5’ phosphate group of the broken strand is re-ligated (rejoined) to the 3’ hydroxyl group on the other side of the break)
  5. Once the DNA strand is re-ligated, the now relaxed or untwisted DNA is released from the enzyme.
76
Q

Why is energy not needed for topo I to act on DNA?

A
  • topo I is covalently linked to the nicked DNA through the OH of its tyrosine (cuts through one of the phosphodiester linkages)
  • At the start of the reaction, one phosphodiester bond is broken, whereas another one is formed while strands rejoin
  • So the number of phosphate bonds is the same throughout the reaction, meaning that topoisomerase I is energetically neutral
77
Q

True or false: type II topoisomerases (Topo II) are also known as gyrases

A

False; Topo II is frequently called “gyrase” but this is not strictly correct because some type II topoisomerases are not gyrases

78
Q

What is gyrase? Where is gyrase found?

A

A type II isomerase that introduces negative supercoils; found in prokaryotes but not eukaryotes

79
Q

Topo II makes a (ssDNA/dsDNA) cut

A

dsDNA

80
Q

Topo II (does/does not) require energy

A

Does

81
Q

How many writhes does the topo II reduce supercoiled DNA by? How much does topo II decrease the linkage number by?

A

2 writhes
- Decreases Lk by 2

82
Q

What are gyrases important for?

A

Important in separating entangled DNA in the cell, e.g. after DNA replication
- DNA gyrase, a type of topoisomerase found in bacteria, introduces negative supercoils into DNA. This process helps alleviate the positive supercoiling that occurs ahead of the replication fork during DNA replication or transcription.

83
Q

Can topoisomerase I catenate/decatenate two double stranded circular plasmids?

A

No, topo II can do this reaction though
- If there’s a strand of ssDNA on both plasmids then yes, topo I can catalyze these reactions

84
Q

The greater the length of reaction between a DNA molecule and a topoisomerase…
(explain what you would see on a gel)

A

The DNA becomes more relaxed (moves from the lower, more supercoiled bands to the higher, more relaxed bands).
- Lk decreases and eventually, each of the adjacent topoisomers in each lane differ by 1 Lk.

85
Q

What is Ethidium Bromide (EtBr) used for in the lab?

A

Staining DNA in agarose gel

86
Q

What can ethidum bromide (EtBr) do to DNA?

A

EtBr decreases the rotation of DNA from 36 degrees to 10 degrees by changing the space between adjacent base pairs

87
Q

If a T tautomerized into its enol form, what would it pair with?

A

G

88
Q

If a C tautomerized into its imino form, what would it pair with?

A

A

89
Q

What direction must the B DNA be twisted in order to get a positive supercoil?

A

Clockwise (in the direction of the DNA twist)

90
Q

What direction must the B DNA be twisted in order to get a negative supercoil?

A

Counterclockwise (opposite to the direction of the DNA twist)

91
Q

Which direction does a negative supercoil loop around a histone core?

A

Clockwise

92
Q

What direction does a positive supercoil loop around a histone core?

A

Counterclockwise

93
Q

What reactions is Topo II useful for?

A

Catenation/decatenation of dsDNA (after replication), and separating entangled DNA after replication

94
Q

Why does π stacking exist?

A

Ensures that the bases are facing the inside of the helix

95
Q

Which of the forms of DNA molecules (B, A or Z) is hollow on the inside?

A

A DNA

CMMB 411- Doreen (9 decks)

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