Chapter 6
RNA differs from DNA in three aspects __.
1. 2' Ribose instread of 2'deoxyribose. 2. Uracil instead of thymine (uracil lacks 5 methyl group). 3. Usually found as a single polynucleotide chain.
The basic four things Topoisomerases allow...
1. Catenate / Decatenate. 2. Unknotting / disentangling. 3. Allow for DNA Replication to continue. 4. Alow for DNA molecules to be separated.
DNA has periodicity and so in one turn there are how many base pairs?
10 BP.
How many bases per turn does A DNA have?
11 bases per turn.
How long is the minor groove?
12 Angstroms.
Why 2'?
2' because on the 2' carbon there is no OH group, just two hydrogens.
A nucleotide consists of a phosphate joined to a sugar known as __.
2'-deoxyribose.
What is the diameter of the helix?
20 Angstroms (2 nm).
How long is the major groove?
22 Angstroms.
DNA maximally absorbs UV at what wavelength?
260 nm.
Proteins are absorbed at __.
280 nm.
What is the length of one helical turn of DNA?
34 Angstroms.
What is the angle between the BP?
36 degrees.
A nucleotide is ?
A B-S-P.
A nucleoside is ?
A B-S.
A-DNA is seen when?
In DNA-Protein complexes, and in the RNA double helix.
There are two types of writhe what are they?
Interwound (plectonemic writhe) and toroid (spiral).
C0t curves show that DNA renaturation is __.
Inversely proportional to the complexity of the genome.
When ethidium goes between the base pairs it __.
It decreases the twist of DNA (from 36 degrees to 10 degrees).
What does DNA Gyrase do?
It introduces rather than removes negative supercoils.
Why does DNA have a major and minor groove?
It is due to the angle of the glycosidic bond in the narrower regions it is 120 degrees and in the wider regions it is 240 degrees.
What is a twist?
It is the number of times one strand completely wraps around the other strand.
The most important feature of DNA is that __.
It is usually composed of two polynucleotide chains twisted around each other in the form of a double helix.
What is base flipping?
It is when individual bases protrude from the double helix.
What does Type I Topoisomerase do?
It makes single stranded cuts.
How was DNA strand separation monitored?
It was monitored by UV light.
Strand separation is accomplished more easily in __ DNA.
Negatively supercoiled DNA rather than relaxed DNA.
DNA is ___ supercoiled.
Negatively; due to the fact that the Lk is less than the Lk^0.
Is the DNA double helical structure rigid?
No it is not the base pairs can rotate on the BP axis.
RNA exhibits __.
Non-Watson-Crick base pairing.
What is Interwound?
Number of times the long axis is twisted around itself.
What is a toroid or spiral?
Number of times the long axis is wound in a cylindrical manner.
Our DNA is right or left handed?
Our DNA (B DNA) is right handed.
To break these covalent bonds in cccDNA we would have to __.
Pass one strand over the other strand and the number of times we do this is called the linking number.
The linking number is the __.
Passing of one strand over the other strand a certain number of times in order to separate them.
Nucleotides are joined together by what linkage?
Phosphodiester linkage.
Base stacking is the sharing of what?
Pi-Pi electrons.
The ATP required in Type II Topoisomerases is not due to the cutting / rejoining of strands but __.
Promote conformational changes in the topoisomerase-DNA complex rather than to cleave / rejoin DNA.
DNA is wrapped around a ____ core and is called a ___.
Protein; nucleosome (more in Chapter 7).
The repeating unit of Z DNA is?
Purine-pyrimidine dinucleotide repeat.
The bases of DNA fall into two categories and they are __ and __.
Purines and Pyrimidines .
Removal of introns is known as __.
RNA splicing.
How is the base joined to the sugar?
Removal of water and this is done by removing the OH on the 1' carbon of the sugar and the and the H of the base to form a glycosidic bond.
The sugar is joined to the phosphate group by?
Removing the OH on the 5' carbon and removing the H from the phosphate group. This bond is called the phosphoester bond.
What does Type II Topoisomerase require?
Requires ATP.
RNA enzymes are known as __.
Ribozymes .
The pyrimidines are derived from what structure?
Single-ringed structure .
What is writhe?
Supercoiling (torsional stress).
The melting point of DNA is highly determined by what?
The GC content and the ionic strength of the solution.
What is principally responsible for the UV absorption?
The bases.
DNA can denature T/F?
Yes it can denature among certain conditions: 100 degrees, alkali, or denaturants.
Are the two chains anti-parallel?
Yes... 5' phosphate end and 3' OH end is the convention of writing it.
Being "negatively supercoiled" means __.
You have stored energy (so our DNA is wound up with energy stored).
The pYrimidines are __.
cYtosine and thYmine.
cccDNA molecules of the same length but different linking numbers are called __.
DNA topoisomers.
Type II Topoisomerase is usually __.
Dimeric or tetrameric .
The purines are derived from what structure?
Double-ringed structure .
These DNA topoisomers can be separated by __.
Electrophoresis (seen in lab "make a gel") .
What is hybridization?
Forming a double stranded DNA from two different sources.
The bases attach to the deoxyribose by __ linkages at what positions on the pyrimidines and purines?
Glycosidic linkages; N1 pyrimidines and N9 purines.
The oxygen atoms in ___ remain in the keto form.
Guanine, and thymine .
What types of bonds keep DNA stable?
Hydrogen bonds.
What is this increase known as?
Hyperchromicity which is due to base stacking.
Ehthidium increases the __.
Wr .
RNAse P is __.
A riboenzyme responsible for generating tRNA molecules.
Thermophiles have positively supercoiled DNA which can be thought of as __.
A store of free energy that helps keep the DNA from denaturing at elevated temperatures.
When DNA wraps around a protein which type of writhe occurs?
A toroid/spiral writhe .
The linking number is composed of two things called a __.
A twist and a writhe .
RNA double helix represents what type of DNA?
A-DNA due to the 2' OH...
The purines are __.
Adenine and Guanine .
The backbone of DNA is composed of ___.
Alternating sugar and phosphate residues .
In right-handed DNA the glycosidic bond is always syn or anti?
Always anti.
How can you remove supercoils from cccDNA if it is not already relaxed?
By using DNase I.
Topoisomerases can __ and __ DNA.
Catenate and Decatenate .
Z DNA requires a high concentration of what?
Cations .
The phosphoryl groups carry a negative charge so they are stabilized by ___.
Cations which stabilize the double helix further more... When they are not shielded by cations they tend to cause the strands to repel each other.
What does Type II Topoisomerase do?
Change the linking number in steps of two. More specifically, they make transient double stranded breaks, pass a segment of the uncut duplex, and then seal...
Plasmids are?
Circular DNA molecules .
Strands in cccDNA cannot be separated without breaking __.
Covalent bonds.
What is cccDNA?
Covalently, closed, circular DNA.
Prokaryotes have a special Type II Topoisomerase called?
DNA Gyrase.
The higher the salt concentration of the solution _____.
The higher the temperature DNA denatures.
In A DNA the major / minor grooves when compared to the B DNA are?
The major groove in A DNA is narrower than B DNA and the minor groove in A DNA is broader than B DNA.
Is the major or minor groove more abundance in chemical information?
The major groove is this is because the minor groove is less able to accommodate amino acid side chains.
What is the only constraint with twists and writhes?
The only constraint is that the sum of the Twist number (Tw), and writhing number (Wr) must remain equal to the linking number (Lk).
When the temperature of DNA is raised to near the boiling point of water what happens?
The optical density or absorbance at 260 nm increases.
In Z DNA what is syn and what is anti?
The pyrimidines are anti and the purines are syn.
What is responsible in Z DNA for the left-handedness?
The syn conformation of the purines.
The helical crossovers (twist) in a right handed manner are positive or negative?
They are positive; the linking number of the DNA will be positive in value.
Topoisomerases are able to cut and rejoin without the assistance of other proteins or high energy co-factors (ATP...)
This means that ATP is not involved in the cutting / rejoining the strands... It is used for something else...
What can relax supercoiled DNA?
Topoisomerases .
Interwound writhe and spiral writhe along with a writhe and a twist are interconvertible T/F?
True .
RNA can do G:U pairing T/F?
True .
DNA can sometimes form a left-handed helix T/F?
True. This is because the glycosidic bond can actually be in two different conformations syn or anti.
Topoisomerases come in how many types?
Two types.
DNA cleavage occurs when __ residue in the active site of topoisomerase attacks a phosphodiester bond in the backbone of DNA.
Tyrosine .
The hammerhead riboenzyme is found in __.
Viroids (plants).
A DNA is observed when?
When there is low humidity.