Lecture 19 & 20

Question 1

Central Dogma

Answer 1

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

Question 2

Components of nucleotides

Answer 2

phosphate, pentose sugar and nitrogenous base

Question 3

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

Answer 3

Phosphate on the 5’ and base on the 1’

Question 4

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

Answer 4

deoxyribose sugar is missing a oxygen on the 2’

Question 5

What are the purines and how many carbons?

Answer 5

Adenine and Guanine 9 carbons

Question 6

What are the pyrimidines and how many carbons?

Answer 6

Cytosin, Thymine and uracil 6 carbons

Question 7

how man bonds between G and C

Answer 7

3 hydrogen bonds

Question 8

how many bonds between A and T

Answer 8

2 hydrogen bonds

Question 9

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

Answer 9

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

Question 10

base+sugar=

Answer 10

nucleoside

Question 11

base+sugar+phosphate group

Answer 11

nucleotide

Question 12

what’s the difference between thymine and uracil?

Answer 12

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

Question 13

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

Answer 13

phosphodiester bonds

Question 13

why is DNA and RNA called nucleic acids?

Answer 13

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

Question 14

What bonds holds DNA together?

Answer 14

dipole and hydrogen bonds?

Question 15

how many base pairs per turn?

Answer 15

10 base pairs per turn (actually 10.5)

Question 16

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

Answer 16

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

Question 17

What are characterstics of B form DNA?

Answer 17

• 10.5 base pairs per turns
• right handed

Question 18

what is Tm?

Answer 18

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

Question 19

what is quenched?

Answer 19

it describes how stacked DNA absorb less UV than unstacked.

Question 20

How can you melt DNA strand apart?

Answer 20

by using the temp. or chaotropic denaturing agents like urea

Question 21

The formation and denaturing of DNA is highly_________

Answer 21

cooperative

Question 22

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

Answer 22

G-C have stronger bonds

Question 23

What factors can increase Tm?

Answer 23

• high salt concentrations
• longer sequence length

Question 24

What is super coiling?

Answer 24

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

Question 25

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

Answer 25

CCC- closed, covalent and circular topologically closed

Question 26

Linking number

Answer 26

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

Question 27

Twist and how is it found?

Answer 27

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

Question 28

writhe

Answer 28

the amount of times the double helix crosses itself

Question 29

left handed writhe

Answer 29

positive value, and harder to separate

Question 30

right handed writhe

Answer 30

negative value and easier to separate

Question 31

Why does supercoiled DNA move faster than relaxed?

Answer 31

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

Question 32

why does DNA need SDS while performing a gel electrophoresis?

Answer 32

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

Question 33

how does DNA move thorough the agarose gel?

Answer 33

Smaller and more coiled DNA moves the positive end faster.

Question 34

How does topoisomerase change the linking number?

Answer 34

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

Question 35

What other jobs does topoisomerase do?

Answer 35

it relives the torsional strain of the unwinding DNA

Question 36

How does topoisomerase affect cancer

Answer 36

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

Question 37

Properties of Topoisomerase 1

Answer 37

- nicks only one strand - changes the linking number by increments of 1 - relaxes the supercoil because it's thermodynamically favourable

Question 38

Properties of Topoisomerase 2 (DNA gyrase)

Answer 38

- 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