L2: Structure of DNA & RNA Flashcards
Primary Structure of DNA
- phosphoester bond: attaches sugar to phosphate (creates backbone)
- glycosidic bond: attaches base to sugar
- conventionally read from 5’ to 3’
Secondary structure of DNA
- Watson-Crick base pairing: conventional interaction (A:T and G:C)
- antiparallel
- major and minor groove
- can be right- or left-handed
secondary structure of DNA - handness of helix
- Depends on upward direction of overlying DNA strand:
1. points to the left, then left-handed helix
2. points to the right, then right-handed helix
secondary structure of DNA - why do the grooves differ in size
- due to the geometry of the base pairs
- angle between the glycosidic link
connecting the base to the sugar
-
secondary structure of DNA - explain the angle between the glycosidic link for the 2 grooves
- link pointing down – minor groove
- link pointing up – major groove
major and minor grooves - why is this important
- DNA-protein interactions happen on the major groove bc:
1) major groove is more physically accessible
2) major groove is more chemically informative
major and minor grooves - chemically informative
- major groove presents chemical information that is:
1) greater in quantity than the minor groove
2) unambiguous, unlike minor groove
major and minor grooves - how is it chemically informative
- proteins fit into the DNA by reading different categories on the DNA
- major grooves will show a different ‘set up’ depending on the order of bases while a minor groove may continue to be the same
major and minor grooves: chemically informative - what are the different categories
- Hydrogen bond donor (+)
- Non-polar hydrogen
- Hydrogen bond acceptor (-)
- Methyl group
major and minor grooves: chemically informative - different categories for A-T within the major groove
- from left to right:
1. Hydrogen bond acceptor
2. Hydrogen bond donor
3. Hydrogen bond acceptor
4. Methyl group
major and minor grooves: chemically informative - different categories for A-T within the minor groove
- from left to right
1. Hydrogen bond acceptor
2. Non-polar hydrogen
3. Hydrogen bond acceptor
major and minor grooves: chemically informative - different categories for T-A within the major groove
- from left to right:
1. Methyl group
2. Hydrogen bond acceptor
3. Hydrogen bond donor
4. Hydrogen bond acceptor - different from A-T
major and minor grooves: chemically informative - different categories for T-A within the minor groove
- from left to right
1. Hydrogen bond acceptor
2. Non-polar hydrogen
3. Hydrogen bond acceptor - same as A-T
major and minor grooves: chemically informative - different categories for G-C within the major groove
- from left to right:
1. Hydrogen bond acceptor
2. Hydrogen bond acceptor
3. Hydrogen bond donor
4. Non-polar hydrogen
major and minor grooves: chemically informative - different categories for G-C within the minor groove
- from left to right:
1. Hydrogen bond acceptor
2. Hydrogen bond donor
3. Hydrogen bond acceptor
major and minor grooves: chemically informative - different categories for C-G within the major groove
- from left to right:
1. Non-polar hydrogen
2. Hydrogen bond donor
3. Hydrogen bond acceptor
4. Hydrogen bond acceptor - different from G-C
major and minor grooves: chemically informative - different categories for C-G within the minor groove
- from left to right:
1. Hydrogen bond acceptor
2. Hydrogen bond donor
3. Hydrogen bond acceptor - same as G-C
explain DNA strand denaturation
- DNA can undergo reversible strand separation which is needed for replication
- heating up denatures it
- cooling allows it to go back together (renaturation)
DNA strand denaturation - what is melting temperature (Tm)
temperature at which half the base pairs in a double stranded DNA molecule have denatured
DNA strand denaturation - what can affect melting temperature
- length of DNA molecule
- Percentage of G:C content
- ionic strength of solution
DNA strand denaturation: what affects Tm? - length of DNA molecule
- longer duplexes have a higher Tm
- bc those are held together more tightly by more base interactions
DNA strand denaturation: what affects Tm - Percentage of G:C content
- increases Tm
- due to 3 hydrogen bonds per base pair (as opposed to 2 in A:T)
- G:C has stronger stacking interactions with neighboring base pairs
DNA strand denaturation: what affects Tm - ionic strength of solution
- increases Tm
- negatively charged phosphates of backbone repel each other across two DNA strands (promotes lower Tm)
- cations shield and neutralize these charges and stabilize the helix (stops it from pulling against each other)
what form is DNA found in?
- linear in eukaryotes
- circular in prokaryotes and in plasmids
