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MBB 222 > Lecture 19 & 20 > Flashcards

Lecture 19 & 20 Flashcards

DNA & RNA structure

1
Q

Central Dogma

A

DNA Synthesis (replication) -> RNA Synthesis (transcription) -> Protein Synthesis (translation)

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2
Q

Components of nucleotides

A

phosphate, pentose sugar and nitrogenous base

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3
Q

Where does the phosphate and base go on the pentose sugar?

A

Phosphate on the 5’ and base on the 1’

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4
Q

What’s the difference between ribose sugar and deoxyribose sugar?

A

deoxyribose sugar is missing a oxygen on the 2’

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5
Q

What are the purines and how many carbons?

A

Adenine and Guanine 9 carbons

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6
Q

What are the pyrimidines and how many carbons?

A

Cytosin, Thymine and uracil 6 carbons

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7
Q

how man bonds between G and C

A

3 hydrogen bonds

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8
Q

how many bonds between A and T

A

2 hydrogen bonds

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9
Q

what makes g-c bonds stronger than a-t?

A

more hydrogen bonds and when they are stacked, they have stronger dipole bonds

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10
Q

base+sugar=

A

nucleoside

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11
Q

base+sugar+phosphate group

A

nucleotide

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12
Q

what’s the difference between thymine and uracil?

A

thymine has a methyl group on the 2’ carbon but uracil has just an H. it takes energy make a methyl group so it’s not necessary for something temporary

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13
Q

what is the bond between pentose sugar and the phosphate groups?

A

phosphodiester bonds

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13
Q

why is DNA and RNA called nucleic acids?

A

the phosphate groups are acids and DNA is deprotonated at physiological pH so it has a negative charge

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14
Q

What bonds holds DNA together?

A

dipole and hydrogen bonds?

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15
Q

how many base pairs per turn?

A

10 base pairs per turn (actually 10.5)

16
Q

What are major and minor grooves? Why is it important?

A

Major is with more exposed base pairs and minor is more covered. It allows proteins to recognize the base pairs.

17
Q

What are characterstics of B form DNA?

A
  • 10.5 base pairs per turns
  • right handed
18
Q

what is Tm?

A

the temperature at the bonds melt and a double stranded DNA is 50% double and 50% single

19
Q

what is quenched?

A

it describes how stacked DNA absorb less UV than unstacked.

20
Q

How can you melt DNA strand apart?

A

by using the temp. or chaotropic denaturing agents like urea

21
Q

The formation and denaturing of DNA is highly_________

A

cooperative

22
Q

Why do A-T region unbind fast than G-C regions?

A

G-C have stronger bonds

23
Q

What factors can increase Tm?

A
  • high salt concentrations
  • longer sequence length
24
Q

What is super coiling?

A

is it when circular DNA (plasmids) compact themselves by tightly binding

25
Q

what are the two ways DNA must be in to be supercoiled

A

CCC- closed, covalent and circular
topologically closed

26
Q

Linking number

A

twist + writhe, how many times one strand would have to go through the other to unwind

27
Q

Twist and how is it found?

A

number of full turns of the helix, the number of base pairs divided by the turns per base pair (10)

28
Q

writhe

A

the amount of times the double helix crosses itself

29
Q

left handed writhe

A

positive value, and harder to separate

30
Q

right handed writhe

A

negative value and easier to separate

31
Q

Why does supercoiled DNA move faster than relaxed?

A

because is so compacted its counted as a tertiary structure and is probably more dense.

32
Q

why does DNA need SDS while performing a gel electrophoresis?

A

DNA is already negatively charged so it doesn’t need the SDS molecules. Agarose gel is used instead.

33
Q

how does DNA move thorough the agarose gel?

A

Smaller and more coiled DNA moves the positive end faster.

34
Q

How does topoisomerase change the linking number?

A

1) Cleave 1 or both of the DNA strands
2) passage of the segment of DNA through its break
3) Reseals the DNA

35
Q

What other jobs does topoisomerase do?

A

it relives the torsional strain of the unwinding DNA

36
Q

How does topoisomerase affect cancer

A

Topoisomerase is needed for cell division. the anticancer drugs will target the topoisomerase that is used to help those cells replicate.

37
Q

Properties of Topoisomerase 1

A
  • nicks only one strand
  • changes the linking number by increments of 1
  • relaxes the supercoil because it’s thermodynamically favourable
38
Q

Properties of Topoisomerase 2 (DNA gyrase)

A
  • nicks 2 stands and reseals them
  • changes the linking number by 2
  • can relax both negative and positive supercoils
  • can introduce negative supercoiling which is not favourable so it requires energy

MBB 222 (13 decks)

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