DNA ATP Adenosine 1 Flashcards
How is a nucleoside bonded?
It is bonded in a glycosylic bond
What does the 2’ hydroxyl of RNA act as?
It acts as a nucleophile in an intramolecular displacement which breaks the phosphodiester linkage
Explain the geometry of the DNA double helix
Forms a right handed double helix
Hydrophilic sugar phosphate backbone is outside of the helix
The hydrophobic bases are inside the helix
A with T
C with G
How many hydrogen bonds are there between C and G?
3
How many hydrogen bonds are there between T and A?
2
What does the ratio of GC have to do with the DNA strand?
The higher the ratio of GC, the more difficult it is to separate because the two DNA strands because they have 3 hydrogen bonds in between rather than 2
What are the minor and major groves?
There is a wider gap in-between the DNA helix on one side and a narrower gap on the other side
What does the size of the DNA groves do?
The larger the groove, this makes it more accessible for interactions with proteins that recognize specific DNA sequence
What does the secondary structure of DNA have to do with the sequence?
NOTHING! they are both similar so they have very similar shapes and properties
What forces stabilize the double helix?
Hydrophobic effect (hydrophobic bases hidden inside the helix)
H-bonding of base pairs
Van der Waals stacking of bases
What is ATP composed of?
ATP is a nucleotide A base (adenine), sugar (ribose) and 3 phosphate groups
How is ATP synthesized from ADP?
When cells break down nutrient molecules (catabolic) and use the available free energy to synthesize ATP from ADP
How long is the typical lifetime of an ATP molecule?
Seconds to minutes
time is money or ATP
How does ATP generate energy?
By the breakdown of the 3 phosphate bonds
How is ATP numbered in terms of alpha, beta and gamma?
Alpha is the first phosphate to connected to the sugar
What are the two pathways that ATP goes through to generate energy?
1) Hydrolysis of the link between gamma and beta phosphate (nucleophilic attack of the gamma phosphate)
2) Hydrolysis of the alpha-beta linkage
(nucleophilic attack of the alpha phosphate)
What is the chemical equation of the gamma-beta reaction?
ATP—> ADP + Pi
What is the chemical equation of the alpha-beta reaction?
ATP—> AMP + PPi
Which one releases greater energy?
The alpha-beta linkage reaction releases twice as much energy because it hydrolyses both phosphoanhydride bonds of ATP.
What is pyrophosphates?
An enzyme that hydrolyses PPi (pyrophosphate)
What is PPi?
Pyrophasphate
2 linked phosphate groups
What is Pi?
1 phosphate molecule
What is the mechanism of Glutamine synthetase?
1) ATP reacts with glutamate to produce a covalent intermediate
2) NH3 acts as a nucleophile, reacts with the electrophilic carbonyl carbon atom
How does ATP provide energy?
Not by simple hydrolysis but through group transfer
