DNA/RNA Structure Flashcards
Whats a Phosphodiester link?
Each DNA/RNA monomer is connected by a phosphate group attached to the 5’ hydroxyl group on one end and the 3’ hydroxyl group on the other.
Whats the pka of a phosphate group?
about 1 (hence nucleic acid)
What is the charge of every monomer unit of DNA/RNA?
Every residue carries a negative charge at a physiological pH.
What are the 4 DNA bases?
Adenine (A), guanine (G), cytosine (C), thymine (T)
What are the 2 types of heterocyclic bases found in DNA/RNA?
Purine and pyrimidine.
What are the 4 RNA bases?
Adenine (A), guanine (G), cytosine (C), uracil (U)
Whats a Glycosidic bond?
The bond between carbon 1’ of a sugar and 9’ or 1’ N of the base
Whats a ribozyme?
RNA molecule capable of catalyzing a chemical reaction.
Whats the difference between a nucleotide and a nucleoside?
Nucleoside contains a nitrogenous base covalently linked to a sugar (ribonuclease), while a nucleotide contains all of this puls its bound to a phosphate group.
Whats special about the 2’ carbon in RNA?
It contains a hydroxyl group that’s crucial for catalytic mechanisms, hence RNA has the capacity for storing information and catalysis. (that’s why biochemist think it came before DNA)
DNA is more stable then RNA. What does that allow DNA to do that RNA cant?
The stability of DNA permits the creation and maintenance of longer genomes.
In the RNA world hypothesis what gave rise to DNA-based organisms?
Initially only RNA, then a mechanism appeared, allowing the conversion of ribose-containing compounds to their deoxyribose counterparts.
WTF’s a tautomer?
Structural isomers that differ only in the location of their hydrogens and the location of their double bonds.
What UV wavelength is used to detect nucleic acids?
260nm
What is a metastable compound?
Theyre thermodynamically favored to break down, but do so very slowly unless there is a catalysis.
Just how stable is DNA?
So stable that even in very dehydrated conditions DNA has been recovered from ancient fossils.
When DNA is in the presence of catalysis intended to break that shit down does it happen fast or slow?
Hydrolysis can happen exceedingly rapid in an aqueous solution.
How to catalyze the hydrolysis of phosphodiester bonds in RNA?
Acid catalysis
Theoretically, polynucleotides should hydrolyze inside the conditions of a living cell. Why is this? And why don’t they?
They should hydrolyze based upon the favorable gibs free energy change involved in the reaction. They dont because its an incredibly slow process without a catalysis.
Why is it important that polynucleotides dont hydrolyze inside a living cell?
Because it ensures that DNA is stable enough to serve as a useful repository of genetic information.
What would an Acid catalyst do In both RNA and DNA?
cleave the glycosidic bond (1’ connecting sugar to base) and the phosphodiester bond, leaving you with a mixture of bases, phosphoric acid, an ribose/deoxyribose.
Whats a Nuclease do?
catalyze the clevage of the phosphodiester bonds in RNA and DNA
The dehydration reaction (water leaves, 2 things connect) which establishes the phosphodiester bonds of a polynucleotide is unfavorable. Instead, hydrolysis of this reaction is favorable. So, How are these polynucleotides actually made then?
Each monomer is presented as a triphosphate, cleavage of the triphosphate provides the necessary free energy to make the reaction thermodynamically favorable.
Whats Primary structure of a nucleic acid?
The nucleotide sequence
How is a polynucleotide sequence usually written?
From 5’ on the left to 3’ on the right.
What’s the most important thing to take note of in terms of primary structure of nucleotides?
Genetic information is stored in the primary structure.
What is secondary structure of a nucleotide?
Its 3 dimensional repetitive structure.
How did Watson and crick know there was 2 strands of DNA in each helical molecule? .
Because of the fiber density
What was “the great leap of intuition” that Watson and crick made?
Their realization that a two-stranded helix could be stabilized by hydrogen bonding between base pairs on opposite strands, but only if they were paird A-T and G-C. ( h-bonds here are 1.1nm apart which could only be possible if paired this way)
How many base pairs is in each turn of the DNA helix, how close are they stacked together?
- Each base pair is rotated by 36 degrees (1/10 of 360). Theyre .34nm apart. Called a helix rise.
Whats chargaffs rule?
Theres always equal amounts of A and T as well as equal amounts of G and C
What is Self-replication?
If DNA strands were separated and new DNA was synthesized along each strand because of complementarity (G-C, A-T) you would get an exact copy of the original.
What is Semiconservative replication?
would produce two copies that each contained one of the original strands and one new strand.
What is conservative replication?
would leave the two original template DNA strands together in a double helix and would produce a copy composed of two new strands containing all of the new DNA base pairs.
What is dispersive replication?
would produce two copies of the DNA, both containing distinct regions of DNA composed of either both original strands or both new strands.
What did Meselson and stahl prove?
That DNA replicates semiconsevatively
What did Meselson and stahl realize about molecules that differed in density by small amounts?
You can separate them by centrifugation in density gradients.
How to create a density gradient?
By centrifuging to equilibrium a concentration of heavy metal salt (like cesium chloride).
How does a density gradient separate nucleic acids?
The nucleic acid molecules suspended in this type of gradient will be of different densities and they’ll migrate towards the point where the solution density equals its own.
What are B form helices?
The standard form you think of with DNA. predominate in the cell
What are A form helices?
DNA fibers prepared under conditions of low humidity. Double stranded RNA as well as hybrid DNA/RNA molecules (one strand DNA one strand RNA) always have this comformation.
Difference between A & B helix hell?
In the B helix the base’s lies close to the axis, which passes through the hydrogen bonds. In the A helix the base lies farther towards the outside, and are strongly tilted with respect to the axis. B has distinguishable major and minor grooves and A’s grooves are nearly identical.
Does a DNA helix follow a straight line?
Naw brah, theyre actually slightly bent.
Can DNA be circular?
Yes,naturally occurring DNA is often circular with no free 5’ or 3’ end.
Why is B-DNA favored inside of anaqueous environment?
B form has definied major and minor grooves so B form can acomidate a “spine” of water molecules in the minor grove so the hydrogen bonding between water molecules and DNA may contribute to its stability (in absence of water A form is favored)
Why does RNA and DNA-RNA hybrids adopt the A from?
Most likely because of their 2’ hydroxyl
Whats a Super coil vs a relaxed circle?
Super boi can’t lie flat on a plane surface and a relaxed circle can. In super coil the helical axis has crosses over its self.
Is a Supercoil rare in DNA?
Nope it’s the usual state of circular DNA.
Super coils usually twist which way?
Left handed
What is a topoisomers?
DNA molecules that differ only in topology
Whats the difference between + and – super coiling?
+ is right handed, - is lefthanded.
How many base pairs is the human genome?
3x10^9 bp
How many errors occure in DNA replication?
Less than 1 error in 10^8 bp’s, but the mistakes that are made contribute to mutations that allow evolution to occur
What is a replisome?
a complex molecular machine that carries out replication of DNA. first it unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthesized.
Whats DNA polymerase?
An enzsyme that guides the pairing of incoming DNA triphosphates. Then catalyzes the formation of the phosphodiester bond.
What is a primer?
a short strand of RNA or DNA (generally about 18-22 bases) that serves as a starting point for DNA synthesis. It is required for DNA replication because DNA polymerases can only add new nucleotides to an existing strand of DNA. The polymerase starts replication at the 3’-end of the primer, and copies the opposite strand.
What is genetic code?
Set of rules that specify which nucleic acid codons correspond to which amino acid
What is mRNa?
Messenger RNA carrys info from DNA to the protein synthesizing machinery of the cell
What do tRNA, mRNA and ribosomes work together to preform translation?
A messenger RNA would be bound to the ribosome, then transfer RNA containing a amminoacid comes to the ribosome one @a time. Each tRNA identifies the appropriate code one and adds the amino acit to the growing polypeptidechain. The ribosome travels don the mRNA so the genetic message can be read and translated.
What’s a twist?
If twist = 10 that means that the linear DNA contained exactly enough base pairs to make 10 helical turns. (positive for right handed and negative for left handed)
Mathmatical equation for linking number?
Link = Twist + writhe
What Is Z-DNA?.
Left handed DNA (both A and B are right handed), most often found in polynucleotides with alternating purines and pyrimidines in each strand. (which means alternating syn and anti conformation) which gives it a zig-zag shape hence Z-DN
What are the two stable orientations of the bases with respect to their deoxyribose rings?
Syn and anti
Are bases usually in the anti or syn position?
Bases for forms A & B are always anti. In Z-DNA pyrimidines are always anti, but purines are always syn.
Whats a Cruciform structure?
Double hairpins, must be palindromic
Whats a A palindromic sequence? .
a nucleic acid sequence on double-stranded DNA or RNA wherein reading 5’ (five-prime) to 3’ (three prime) forward on one strand matches the sequence reading 5’ to 3’ on the complementary strand with which it forms a double helix
What are G-quartets?
4 guanines (G) link together via hydrogen bonds in areas of dna that are guanine-rich
What are G-quadraplexes?
two or more G-quartets can stack on top of each other to form a G-quadruplex.
What is denaturation?
Loss of secondary structure over an extended area.
what factors favor dissociation of double helixes into randomly coiled single chains?
1.) electrostatic repulsion between chains (all parts of DNA have – charge cause of the phosphate group. 2.) if a ridged double helix separated into two flexible random coils then the number of conformations accessible greatly increase and therefore entropy increases.
What is hypochromism?
When nucleotides are polymerized into a polynucleotide and the bases are packed into a helical structure the absorbtion of light (260nm) is reduced (not as intense, same wavelength still)
What is “melting” of a polynucleotide double helix?
The denaturation (loss of secondary structure). Its used this way even though the term isn’t quite correct.
What is a cooperative transitions?
In terms of DNA/RNA it means the helix cant melt bit by bit. Instead the whole structure holds together until its on the verge of instability then it denatures over a very narrow temperature range.
Whats the melting temp of a polynucleotide depend on?
The ratio of (G+C)/(A+T). this is because G+C makes 3 h-bonds and A+T makes 2.
How many hydrogen bonds does G+C make?
3
How many hydrogen bonds does A+T make?
2
What is annealing?
Renaturation. Denaturation is reversible by slow cooling so you allow complementary strands to find each other.
Imposing high levels of superhelical torsion on a DNA molecule can promote what changes?
Local melting, Z-DNA formation, cruciform extension, formation of H-DNA regions, and likely other things yet to be discovered.
