Use LEFT and RIGHT arrow keys to navigate between flashcards;
Use UP and DOWN arrow keys to flip the card;
H to show hint;
A reads text to speech;
57 Cards in this Set
- Front
- Back
|
What type of pH is favourable for RNA degradation? |
Alkaline |
|
|
How does spontaneous RNA break down occur? |
The 2' hydroxyl attics the 5' Phosphate on the adjacent Nucleotide, forming a 2'3'-cyclic monophosphate derivative, and an nucleoside with a hydroxyl group on it's 5' carbon. |
|
|
What are the 4 types of forces/interactions that determine DNAs structure? |
Stacking interactions, occur between th stacked N-bases. The pi electrons in the aromatic rings form temporary dipoles. (van der walls forces)
Electrostatic (repulsion, from the PO4 backbone)
Hydrogen bonds, between bases
Hydrophobic forces, the hydrophobic bases are hidden within the DNA strand, shielded from the water |
|
|
What form of DNA do we deal with? |
B form |
|
|
What are some quantitative traits of B form DNA ? |
-10.5 residues per turn of the helix -right handed -one turn=36 angstroms -contains a major and a minor groove
|
|
|
How big is one angstrom in nanometers? |
0.1 nm |
|
|
Can Pyrimidines be in syn conformation? purines? |
No, pyrimidines have too much steric interference to be sun, must be anti. Purines can be in syn conformation, but it is not as stable as anti. |
|
|
What is the "donor acceptor pattern in the G:C minor groove?
|
Acceptor-donor-Acceptor |
|
|
What is the "donor acceptor pattern in the G:C major groove? |
Acceptor-Acceptor-Donor |
|
|
What is the "donor acceptor pattern in the A:T minor groove? |
Acceptor-Donor |
|
|
What is the "donor acceptor pattern in the A:T major groove? |
Acceptor-Donor-Acceptor-Methyl |
|
|
What is significant about the Major site in B DNA? |
It has more interactions, and it is usually where proteins interact with the DNA? |
|
|
what is the pucker of DNA? |
C-2' Endo |
|
|
how many base pairs are there per turn of DNA? |
10.5 bp |
|
|
What is the melting temperature of DNA defined as? |
The temperature at which 50% of the DNA is denatured. It is at the midpoint of the denaturation curve. |
|
|
How can you tell if you have ds DNA in a solution, or ss DNA? |
DS DNA absorbs less UV light than ssDNA (b/c more bases are exposed in ssDNA.
-Also, dsDNA is more viscous than ssDNA. |
|
|
What four things affect the Melting temperature of DNA? |
pH, [Salt], Temperature, [organic molecules] |
|
|
What happens to ™ when [GC] increases? |
™ increases |
|
|
What happens to ™ when [salt increases]? |
™ increases up to a certain threshold, in which the solution gets "salted out", and the ™ decreases drastically . This is because the negative ions shield the negative charge of the PO4 backbone. |
|
|
If pH increases or decreases, what happens to the ™ of DNA? Why? |
™ decreases. this because other tautomeric forms are favoured. |
|
|
what happens if the concentration of lysine increases in a solution happens (wrt to DNA melting temp) |
Melting temp increases |
|
|
What happens to the ™ of DNA in the prescence of DMSO or urea/ |
™ decreases. |
|
|
What are the 2 steps of DNA renaturation? |
nucletation (where some base pairs form (generally in G:C regions)) and zippering, where the rest of the AAs bind. |
|
|
What are the two types of supercoil, and what do they look like? |
Plectomeme (twisted sheet), and solonoid (ring with a whole in the middle) |
|
|
DNA ahead of the separation is ______ and DNA behind the separation is ______ (ahead is in the direction of synthesis/replication) |
Overwoud (tighter), and under wound ( looser) |
|
|
WHat is Lk? |
Linking number. How many times one ring intersects another ring. If one ring is open, or not closed, the linking number is undefined. --
if there are 2100 Bps and there are 10.5 bp per turn, the Lk is 200. (2100/10.5=200) |
|
|
What is cccDNA? |
Circular covalently closed DNA |
|
|
Does overwound DNA have more Bp per turn than 10.5? |
no, it has less, it is tighter, so less BP per turn? |
|
|
Does under wound DNA have < or > Bp per turn than regular 10.5 bp per turn DNA. |
More DNA per turn. |
|
|
Do proks keep DNA in and under wound or overwound state? Why is this? |
underwound. The underwound state makes it easier for the plasmid to separate for DNA transcription |
|
|
WHat happens when you unwind a prok's chromosome fully? |
It becomes linear. |
|
|
Why does DNA supercoil? |
The reason the supercoil occurs is because the DNA wants to be 10.5bp/turn, so when that number decreases or increases, the DNA wants to supercoil to make the number 10.5 BP/turn
|
|
|
What enzyme is used to change the linking number of a chromosome? |
Topoisomerase |
|
|
What type of DNA does type I topisomerase cut
DO they use ATP?
How much do they change linking number by? |
Single stranded DNA molecules.
No ATP
change linking number by 1
They take DNA to a relaxed state |
|
|
What type of DNA does type II topisomerase cut
DO they require ATP? How many?
How much do they change the linking number by? |
Double stranded DNA molecules
-Thermodynamically they don't require ATP, but their mechanism requires it. It still takes DNA from an overwound/underwound state to relax. Use two ATP in the mechanism
change linking number by +/- 2 |
|
|
WHat form do type I and type II topoisomerases take DNA to? |
the relaxed state (the reaction has a -delta G) |
|
|
What type of residue in the active cite of topisomerase I performs nucleophillic attack on the phopshodiester bond? |
a tyrosine resiude |
|
|
What domain of life are type I and Type II topoisomerases in? |
All domains of life. |
|
|
WHat type of topoisomerase is only in proms? what's it called, what does it do? |
It is a type II isomerase called Bacterial Gyrase. It requires 2 ATP, and it converts relaxed DNA in under wound DNa. |
|
|
how does the bacterial chromosome stay supercoiled. |
By the relative activity of topoisomerases. |
|
|
how does the euk chromosome stay supercoiled? |
By the binding of histones. and the relaxed DNA between nucleosomes |
|
|
What is chromatin? |
DNA + chromatin complex |
|
|
What is the basic unit of chromatin? |
the nucleosome. |
|
|
What is the structure of a histone protein? what form is it in, and what makes it up? |
it is an octomer with 2 copies of 4 different proteins:
H2A, H2B, H3 and H4. |
|
|
What type of amino acids are very prevalent in histones? |
basic AAs. Especially Lysine and Arginine. |
|
|
How does basic lysine groups get removed from the DNA? |
they get turned to neutral by reacting with Acetyl Coa, which adds an acetyl group onto Lysine, forming an Amide. |
|
|
How many times does DNA go around a histone protein? |
1.75 times |
|
|
What is the footprint? |
it is the DNA bound to the histone protein. This won't be digested during digesting with a nuclease. usually 140-150 Bps (# isn't important) |
|
|
What shape does DNA have wrapped around a histone protein? |
a left handed solenoid shape. |
|
|
What is the centre of a chromosome called? |
centromere? |
|
|
what are the ends of chromosomes called? |
telomeres |
|
|
What is the 11 nm fibre? |
DNa wrapped around nucleosome |
|
|
what is the 30nm fibre? |
nucleosomes wound into a helix |
|
|
What sequence formula is repeated at the end of Chromosomes (at the telomeres) What shape does it form? |
TxGy where x,y is between 1-4. Example : TTGGGG A lariat, or a "T-Loop" |
|
|
What type of overhang does a telomere have? |
a 3' overhang |
|
|
What is PNA? |
Peptide nucleic Acid. you can form hybrid structures with DNA/PNA, PNA/ RNA or DNA/RNA |
|
|
Why is PNA/DNA stronger than DNA/DNA |
because there isn't a negative charge on PNA, so there is no repulsion. |
