Brainscape's Knowledge GenomeTM

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


See full index

Cmmb 411 > Topic 3 > Flashcards

Topic 3 Flashcards

1
Q

What is a nucleoside

What is a nucleotide

A

Sugar and base

Sugar base and phosphate

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

Why is dna called deoxyribose

A

No oh on 2’ carbon

Just H

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

What is a phosphoester bond

A

The bond between the phosphoric acid and the 5’ oxygen of the sugar

Just phosphoester, if whole dna it is phosphodiester

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

What is the glycosidic bond between in dna

A

The 1’ carbons OH and the nh of the base

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

Purines

Pyrimidines

A

Adenine guanine

Cytosine thymine

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

Recongnicze AGCT structures

A

Slide 6

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

Double helix orientation of strands

A

Antiparallel

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

Phosphodiester bond is how many linkages

Phosphoester

A

2

1

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

What method helps us to see the dna size

A

Agarose Gel electrophoresis, smaller further, larger slower

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

How many h bonds are between A-T

G-c

A

2

3

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

What are the two dna chains stabilized by

A

Perpendicular Base pairing and stacking

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

What causes the GC bases to be stronger binded together

A

The benzene ring like structures in the g and c bases causes the hydrophobic force to be greater and pushes the bases close together

Recording slide 10

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

What causes pi stacking

A

The hydrophobic effect dues to vanderwalls forces

More in red slide 10

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

Is dna right handed or left handed

A

Right handed

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

If base faces in toward the sugar its

If our away from sugar

What type of twistings do these cause

A

Syn (left hand twisting)

Anti (right hand twisting)

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

What determines the orientation of bases (anti or syn) in the dna

A

The glycosidic bind that’s connecting them to the sugar

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

What are isomers

A

Same formula different structure

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

Give examples of two isomers

A

Amide to imidic acid (the h on the N goes to o)

Enol to keto ( oh on enols goes to ch)

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

What are tautomers

A

Isomers that are interconverted by migration of a hydrogen atom

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

Give an example of how cytosine becomes a tautomer and how the h bond donors and acceptors in it change

A

The nh2 amino (was a donor) loses H and now becomes acceptor

Slide 12

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

Give an example of how guanine becomes a tautomer and how the h bond donors and acceptors in it change

A

The nh gives it h to c=O

Not the c=o that was acceptor becomes c-oh donor

Slide 12

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

What can cause misplacing between bases

A

Slide 13

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

What are tautomeric shifts

A

Random rearrangements of the nitrogenous bases (due to tautomerization)

lets h binding happen between base pairs that don’t usually pair together (mismatched)

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

What happens after dna replication if a tautomeric shift causes GT and not Gc pairing

A

Recording slide 14

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

What is an example of how DNA is flexible

A

Base flipping

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

What is an example of how DNA is flexible

A

Base flipping

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

What causes base flipping

A

The enzymes involved in homologous recombination and dna repair

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

What is base flipping

A

The enzyme cuts out the h bond in the mispaired base and flips it out

The phosphate backbone acts as a hinge that lets the base flip out of the dna

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

What is the MICA experiment used for

A

It determines helical periodicity

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

What is the steps of the mica experiment

A

Immobllilize dna on the mica surface

do a restriction digest with DNase 1 (cleaves the phosphodiester bond in the back bone)

Run it on a gel electrophoresis and get separated fragments of the dna.

DNase 1 is too bulky to cut down to the bottom strand of the dna that’s right on the mica. So only cuts the outside strand

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

What did the mica experiment tell us and how slide 17

A

There are 10.5 bp per turn of the helix , because Found that the smaller fragments are 10-11 nucleotides

The stronger signals are around 31 to 32, means more abundant dna there,

Multiple of 10.5 nucleotides in school band size meaning in each turn of dna there must be 10.5 nucleotides

Each bp is twisted 36 degrees from the previous one

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

What is the major groove

A

Deeper and wider than the minor groove

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

What do the major and minor grooves tell us

A

Can see what types of base pairing occurs in the bands based on the h bond donor and acceptors

Can see what nucleotide is on which stand of the dna (if gc or cg)

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

What form are most double helical dna in

A

The B from

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

What forms of dna are there

A

B Z A

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

What type of handedness does z form dna have, what does it look like

A

Left handed, longer than normal

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

What type of handedness does A form dna have, what does it look like

A

Right, shorter (squeezed) than normal

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

How do we know that dna is mainly B form

A

Through x ray diffraction where dna is in a crystal and an x ray hits it

The rays are diffracted through the crystal

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

Diffraction parent lines are

A

Perpendicular to the actual lines

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

What does photograph 51 tell us

Slide 27

A

The photo is a diffraction pattern of the dna helix

The space between the layers/mark the rise per base pair (3.4Angstroms)

The centre of the photo to the top show the pitch (the distance that the helix repeats itself, 34A)

Can tell there are 10 bp/turn by dividing 34 by 3.4 (P/R)

The fourth layer line missing tells us that the lines are assymetically place, that there are major and minor grooves in the dna, and helix is double stranded

The radius of the dna is 10A

41
Q

What are the two strand of dna held together by

A

Hydrogen bonds

42
Q

What is denaturation of dna

A

Disrupting the h bonds in the dna

43
Q

What denatured dna

A

Heat or extreme pH

44
Q

What is the melting temp (Tm) of dna

A

The transition temperature where 50% of dna is denatured to ss dna and 50% is still ds

45
Q

What affects the meting temp of dna

A
  • gc content
  • ionic strength of the solution
46
Q

How does GC content contribute to the melting temp

Other than the h binds what causes gc to be hard to break

A

If there are more GC , the melting temp increases

because the 3 h binds are harder to break apart , also GC has lower entropy (so it’s more stable and harder to break)

47
Q

How does ionic strength contribute to the melting temp

A

More salt (ions), higher melting point

Since salt is cations, they stabilize the negative dna backbone

Stabilizing the backbone decreases the repelling force between the duplex (two strands), so increased dsdna stability and higher Tm

48
Q

What wavelength does dna absorb

A

260nm

49
Q

How can we tell if DNA is denatured?

Why

A

Look at the absorbance Because ssDNA absorbs >40% of UV than dsDNA (at 260nm)

This is because the base are exposed in ssdna and are absorbing

50
Q

What do you do to reanneal dna

A

Make them cold

51
Q

What is dna hybridizations

A

Using the denature and reanneal process to make ssDNA reanneal with another strand that has a “similar” sequence

This makes Hybrid dsDNA

52
Q

How can hybridization be useful

A

Southern blots, northern blots

DNA and rna microarray (to assess mutations or indels)

Next generation sequencing

53
Q

When looking at hybrids on a southern blot, what is the probe and what is the sample we want to detect

What about northern

A

The probe is DNA and the sample is also dna

The probe is dna but the sample is rna

54
Q

What is cccDNA

Give an example

A

Covalently closed circular dna

The sugar phosphate backbones of this dna is covalently linked (to make it a circle)

Ex. A bacterial plasmid or very long dsDNA

55
Q

What causes dna to be topologically constrained

A

Unwinding of the dsDNA during replication or transcription causes torsional strain and over winding at the ends

The bubble opens but the ends become twisted

56
Q

What is the linking number

A

A integer number that represents the number of times it takes for one strand of dna to pass through the other strand for the 2 strand to be separated

How many turns are needed to unwrap the double helices so the whole thing is separated

57
Q

Lk =

A

Twist (two stands passing through each other) + writhe (entire thing twisting in itself)

58
Q

What are topoisomers

A

The topology of the DNA is different (but same dna strand)

They only differ in their linking number

59
Q

How can we tell that a dna has topoisomers

A

When the cccdna is pit in a gel , we see two bands or more

These bands are the different topisomers

60
Q

order from larger to smallest the topoisomers of cccdna

Explain why it’s like this

A

Open circular > linear > supercoiled (1) > supercoild (2, more coil)

The supercoild is more packed than the open circular to travels further

61
Q

What is supercooling determined by

A

Writhe not twist

62
Q

What is supercooling determined by

A

Writhe not twist

63
Q

What is supercoiling

A

The circular dna twist upon itself because it’s underwound or overwound relative to its regular B form dna

64
Q

When is something positive supercoiled

Negative

A

When it’s overwound

When it’s under wound

65
Q

Which type of supercoiling requires less energy to unwrap

A

Underwound dna (negative supercoiling)

66
Q

Most organisms have

A

Negative supercoiling

67
Q

Most organisms have

A

Negative supercoiling

68
Q

What kind of some organisms have + supercoiling and why

A

Animals that need to survive in harsh conditions, they would need more energy to unwrap the dna

Slide 45

69
Q

What enzyme can create or relieve supercoiled dna

A

Topoisomerase

They change the topology of the dna

70
Q

What type of super coiling can nucleosomes introfuce

A

Generally negative but also sometimes positive

71
Q

How many times does dna wrap around the nucleosome

A

2 times and can start wrapping from either top or bottom

72
Q

What way does the dna have to start wrapping on the nucleosome to be negative supercoild

What about postive

A

Comes from bottom

Comes from top

73
Q

Why does supercoiling happen

A

To reduce the space the dna takes up and let it be packaged tightly into the small nucleus

Making it compact in chromosomes will prevent the dna strands from tangling during chromosomal segregation (to allow segregation to happen smoothly)

74
Q

What does positive supercoiling help with

A

Protects the dna from thermal denaturation and regulates the expression of genes in extreme conditions

So since the postive supercoiling is harder to unwrap, less likely to be expressed, which save energy for other thing for the organism to survive

Slide 49

75
Q

What does negative supercoiling help with

A

It stores the free energy needed for the circular dna strands to separate during transcription and replication

If the dna was relaxed, a region would be left unpaired , if negative supercoil the dna will unwinds easier

Slide 50

76
Q

How can we remove supercoiling

A

Digest the dna with DNase 1

It nicks the dsDNA strand by breaking only one phosphodiester bond on one strand

This allows free rotation of the dna around the still attached backbone

Then this can relax the dna or twist it and make the supercoil

77
Q

What are the two types of topoisomerase

A

Type 1 and type II

78
Q

What is Type 1 topoisomerase

A

Just called topoisomerase

Makes a ssDNA cut (only one strand)

Passively relaxed supercoils (meaning it doesn’t need atp)

79
Q

How do you count Lk from a supercoil diagram

A

Look at the knee of times the dna crosses itself

That’s the Lk

80
Q

One nick of topoisomerase reduces the linking number by

A

1

81
Q

Explain the reaction of topo 1

A

Topo 1 has tyrosine residues, these residues interact with the dna strands

The tyrosine cleaves one phosphoester linkage in singles strand of dna (via its OH group, it attaches to the cut end of the dna now)

The non cleaved strand is held by one part of topo 1 and the cleaved is held by the other (two hands)

The uncleaved strand gets pulled through the opening and the nicked strand it put back together

A loop is formed and dna is released

82
Q

Why does topo 1 not need to use energy

A

At the start of the reaction, one phosphoester bond is broken and another is formed at the end to being them together

So the number of phosphate bind I. The reaction is the same so net 0 atp used

83
Q

What is type 2 topoisomerase

A

Better way to call it is topo II but some call is gyrase

Makes a dsDNA cut (diff from topo 1)

Require ATP (diff from topo 1)

84
Q

What is a gyrase

What is it in

A

A type II topoisomerase that introduces supercoils

In prokaryotes but not eukaryotes

85
Q

What does topo II do

A

Unwinds the dna better

can fully separate two plasmids (topo 1 can’t because it only reduced Lk by one and plasmids has two)

Cuts linking number by 2 (topo I does only one)

Slide 58

86
Q

When can topo 1 fully separate two plasmids

A

When on of the plasmids have one ssDNA

87
Q

What are topo II important for in terms of dna replication

A

They can fully separate entangled dna in the cell after they’ve replicated

To two separate strands

88
Q

On a gel with supercoild and relaxed dna reacting with topoisomerase, why do the bands blur as more reaction time passes

A

The topoisomerase is forming multiple intermediate forms of the dna which is why many diff sized bands show

89
Q

In the gel with dna topo I and the different topoisomer bands if one band is higher than the other what is the difference in their linking number

A

The difference in linking number is 1

90
Q

What is ethidium bromide used for

A

Dye used To visualize the DNA in PCr

But it’s a carcinogen

91
Q

What is does ethidium bromide do to the dna

A

It inserts itself in between stack bases to make the dna seem longer that is actually is

Changes the degree of rotation from 36 to 10 (lower rotation, longer dna)

This means is decreases the amount of twist and changes the topology of dna

92
Q

Blots:

A

SNOW
DROP

southern : dna

93
Q

Why is gc stronger than at (the main reasons)

A

The hydrophobic force due to the benzene rings in g and c is higher than the force in at

The gc pi stacking allows stronger interaction between them

94
Q

What makes the bases face inside the dna

A

The hydrophobic effect , they aggregates to stay away from water.

95
Q

What nitrogen of ag form the glycosidic bind

What about CT

A

N9

N1

96
Q

What did photo 51 tell you very important

A

DNA has major and minor grooves

97
Q

Negative supercoil on nucleosomes is

Positive is

A

Left handed wrapping (starts from bottom)

Right handed wrapping (starts from top

98
Q

What amino acids are in keto form

In amino form

Are these the dominant froms

A

GT

AC

Cmmb 411 (6 decks)

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