Lecture 19 & 20 Flashcards
DNA & RNA structure
Central Dogma
DNA Synthesis (replication) -> RNA Synthesis (transcription) -> Protein Synthesis (translation)
Components of nucleotides
phosphate, pentose sugar and nitrogenous base
Where does the phosphate and base go on the pentose sugar?
Phosphate on the 5’ and base on the 1’
What’s the difference between ribose sugar and deoxyribose sugar?
deoxyribose sugar is missing a oxygen on the 2’
What are the purines and how many carbons?
Adenine and Guanine 9 carbons
What are the pyrimidines and how many carbons?
Cytosin, Thymine and uracil 6 carbons
how man bonds between G and C
3 hydrogen bonds
how many bonds between A and T
2 hydrogen bonds
what makes g-c bonds stronger than a-t?
more hydrogen bonds and when they are stacked, they have stronger dipole bonds
base+sugar=
nucleoside
base+sugar+phosphate group
nucleotide
what’s the difference between thymine and uracil?
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
what is the bond between pentose sugar and the phosphate groups?
phosphodiester bonds
why is DNA and RNA called nucleic acids?
the phosphate groups are acids and DNA is deprotonated at physiological pH so it has a negative charge
What bonds holds DNA together?
dipole and hydrogen bonds?
how many base pairs per turn?
10 base pairs per turn (actually 10.5)
What are major and minor grooves? Why is it important?
Major is with more exposed base pairs and minor is more covered. It allows proteins to recognize the base pairs.
What are characterstics of B form DNA?
- 10.5 base pairs per turns
- right handed
what is Tm?
the temperature at the bonds melt and a double stranded DNA is 50% double and 50% single
what is quenched?
it describes how stacked DNA absorb less UV than unstacked.
How can you melt DNA strand apart?
by using the temp. or chaotropic denaturing agents like urea
The formation and denaturing of DNA is highly_________
cooperative
Why do A-T region unbind fast than G-C regions?
G-C have stronger bonds
What factors can increase Tm?
- high salt concentrations
- longer sequence length
What is super coiling?
is it when circular DNA (plasmids) compact themselves by tightly binding
what are the two ways DNA must be in to be supercoiled
CCC- closed, covalent and circular
topologically closed
Linking number
twist + writhe, how many times one strand would have to go through the other to unwind
Twist and how is it found?
number of full turns of the helix, the number of base pairs divided by the turns per base pair (10)
writhe
the amount of times the double helix crosses itself
left handed writhe
positive value, and harder to separate
right handed writhe
negative value and easier to separate
Why does supercoiled DNA move faster than relaxed?
because is so compacted its counted as a tertiary structure and is probably more dense.
why does DNA need SDS while performing a gel electrophoresis?
DNA is already negatively charged so it doesn’t need the SDS molecules. Agarose gel is used instead.
how does DNA move thorough the agarose gel?
Smaller and more coiled DNA moves the positive end faster.
How does topoisomerase change the linking number?
1) Cleave 1 or both of the DNA strands
2) passage of the segment of DNA through its break
3) Reseals the DNA
What other jobs does topoisomerase do?
it relives the torsional strain of the unwinding DNA
How does topoisomerase affect cancer
Topoisomerase is needed for cell division. the anticancer drugs will target the topoisomerase that is used to help those cells replicate.
Properties of Topoisomerase 1
- nicks only one strand
- changes the linking number by increments of 1
- relaxes the supercoil because it’s thermodynamically favourable
Properties of Topoisomerase 2 (DNA gyrase)
- 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
