Exam 2-1 Flashcards
What are tautomers?
Tautomers are two molecules with the same molecular formula but different connectivity - constitutional isomers, in other words - which can interconvert in a rapid equilibrium.
The hydrogen on the base has moved to a different place.
This can effect base-pairing, causing genetic variation.
A DNA molecule is a nucleotide polymer linked what specific type of bond?
A 3’ -> 5’ phosphodiester bond.
What does 5’ -> 3’ mean in terms of the molecule?
Phosphate End -> Hydroxyl End
Describe a single stranded DNA structure.
A single stranded DNA molecule has polarity.
Hydrophilic Side -> Phosphodiester Backbone
Hydrophobic Side -> The Bases
What is one of the forces that drives two DNA molecules together?
Through the polarity of a DNA strand, via hydrophobic and hydrophilic interactions.
What is the difference between a DNA mole and an RNA molecule?
RNA -> 2’ -OH
DNA -> 2’ -H
What is an RNA molecule susceptible to?
It is susceptible to hydrolysis.
Explain the hydrolysis of RNA.
- An -OH can deprotonate that 2’ -OH group on the sugar of RNA.
- The deprotonated O performs a nucleophilic attack on the phosphate of the backbone.
- This yields a cyclic-monophosphate derivative and it shortens the RNA molecule.
- Additional hydrolysis yield other derivatives.
A pair of DNA chains run in what kind of orientation?
They run antiparallel.
5’ -> 3’
3’
Bases pair up using what type of interaction?
Hydrogen bonding.
A T
G C
How are the components of DNA orientated? (i.e. the sugar backbone and the bases)
Sugar backbone -> outside
Bases -> inside
How many hydrogen bondings are there between A T?
What about C G?
A T = 2 H-bonding
C G = 3 H-bonding
Due to the anti-parallel arrangement of DNA, what can be assumed about the two strands?
That they are complementary to each other.
Due to the helical structure of DNA, what does the structure produce between the outsides of the molecule?
They produce what are known as major and minor grooves.
What is the importance of a major groove?
The major groove has enough space that a helical structure can fit inside the area to perform a function, mostly likely will be transcription factor.
What is main structure that DNA takes on, be more specific than just double helix.
It takes on a right-handed helix.
It is the most energetically favorable formation of DNA.
How are the bases oriented within the DNA helix?
The base pairs form a stack on the interior of the helix. Van der Waals interactions between bases stabilize the bases.
This “base stacking” is very energetically favorable. It is important for DNA stability.
The major groove has what advantage over the minor groove?
It major groove has a lot more chemical information as compared to the minor groove.
The major groove is able to accept, donate, and hydrogen bond more easily than the minor groove.
What are three structures that DNA can be described to be?
DNA A form
DNA B form
DNA Z form
Describe all three forms of DNA and why they might be in that form.
DNA A Form
- Right handed, short and broad
- Found when there is a lack of water or dehydration
DNA B Form
- Right handed, longer and thinner
- Most common and most favorable
DNA Z Form
- Left handed, longest, thinnest
- High salt concentrations or highly methylation
What is the central dogma of biology?
Information from a cell that is going to pass onto its offspring via replication, transcription, and translation.
What is a gene?
A segment of information needed for regulating synthesis of an RNA or protein.
What is a genome?
The entire DNA sequence of an organism.
Where is DNA located in eukaryotes? What about prokaryotes? What shape do they take on?
Euk -> Nucleus, linear form
Prok -> Nucleoid, circular or linear form
What is a supercoil?
It is a coil, coiling.
How does supercoiling happen?
To induce supercoiling, a circular molecule is cut and held at one end, while the other is twisted.
This changes the # of bases per turn.
When the strands are ligated back together, DNA twists back to the preferred # of bases per turn. Inducing the supercoil.
What does a clockwise rotation indicate?
Negative supercoiling.
What does a counterclockwise rotation indicate?
Positive supercoiling.
What type of enzyme can induce supercoiling?
Topoisomerases can either introduce or remove supercoiling from DNA in a process that temporarily breaks DNA and twists it.
What’s the general idea of Topoisomerase I?
It removes supercoiling in single stranded DNA.
What is the general idea of Topoisomerase II? (Eukaryotes/Prokaryotes)
In eukaryotes, Topoisomerase II can only REMOVE positive/negative supercoiling.
In prokaryotes, Topoisomerase II (DNA Gyrase) can INTRODUCE negative supercoiling.
That is DNA gyrases main goal.
What is the proposed mechanism of Topoisomerase I?
The phosphodiester bond between the nucleotide is attacked by the OH group of the Tyr723 residue in the active site.
This opens up the strand, allowing for passage, and then gets religated.
What is the proposed mechanism for eukaryotic Topoisomerase II?
It functions as a dimer.
- DNA-1 binds to part of the enzyme.
- DNA-2 binds to the enzyme, but at a different spot.
- DNA-1 is cleaved on both strands, to form a 5’ pohphotyrosol linkage to the enzyme. Meanwhile, DNA-2 is still trapped onto the enzyme.
- DNA-2 then passes through the break from DNA-1.
- DNA-1 is then religated, while DNA-2 is released.
You pretty much cut, moved the strand to the other side, and resealed. All of this is to remove supercoiling.
What is one unique difference between Topo I and Topo II?
Topoisomerase Ii uses the input of two ATP’s to undergo hydrolysis to remove supercoiling.
What is Cipro (Ciprofloxacin)?
A broad range antibiotic INHIBITING topoisomerases.
What is Camptothecin (CPT)?
It i used for cancer treatment in traditional Chinese medicine.
They are CPT analogs and are widely used in chemotherapies.
The drug inhibits DNA polymerase I. Which in turn, stops DNA replication.
How is DNA packed into the nucleus?
DNA is wrapped around protein spools creating what is called a nucleosomes and packaged into helical filaments.
What is a nucleosome?
They are, “beads on a string.”
What is a histone?
Histones are highly alkaline (basic) proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation.
Structurally describe the structure of a histone.
It is a tetramer (an octomer when bound to another gistone) that is composed of four main subunits: H2A, H2B, H3, H4.
What is unique about H3 and H4 histone zones?
They are areas rich in A-T clusters. They seem to prevail at the DNA-histone contact sites and play a role in histone core positioning.
Histones are high in what two AA? Why is this significant?
Lys & Arg.
They are highly charged and it facilitates the interaction with DNA.
Bonding between histones and DNA is via ionic bonding. It is between the positively charged AA and the negatively charged phosphate grouops.
What is the key to regulation of gene activity?
Dynamic changes in chromatin.
What are the four types of modifications in histone-side chains that will act as signals during regulation?
- Acetylation
- Methylation
- Phosphoylation
- Ubiquitnation
Explain the role of the histone tails.
They enable you to have covalent modification.
They can also interact withDNA in a way that can weaken the structure between DNA and histone, allowing access to DNA for other proteins.
Proteins can also use the tails as markers to know where to go.
What is the role of Histone H1?
It is a linker protein/linker histone.
It associates with DNA and links nucleosomes together.
It allows for compaction.
Nuclear scaffolds are typically enriched in what?
Histone H1 and topo II.
What are the two SMC proteins learned in class?
Cohesions and Condensins.
What is the role of a cohesion?
It keeps the two sister chromatids wrapped together as soon as DNA is replicated.
What is the role of a condension?
It condenses chromatin.
As soon as it is ready to function, you get ATP hydrolysis.
