DNA ATP Adenosine 1

Question 1

How is a nucleoside bonded?

Answer 1

It is bonded in a glycosylic bond

Question 2

What does the 2’ hydroxyl of RNA act as?

Answer 2

It acts as a nucleophile in an intramolecular displacement which breaks the phosphodiester linkage

Question 3

Explain the geometry of the DNA double helix

Answer 3

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

Question 4

How many hydrogen bonds are there between C and G?

Answer 4

3

Question 5

How many hydrogen bonds are there between T and A?

Answer 5

2

Question 6

What does the ratio of GC have to do with the DNA strand?

Answer 6

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

Question 7

What are the minor and major groves?

Answer 7

There is a wider gap in-between the DNA helix on one side and a narrower gap on the other side

Question 8

What does the size of the DNA groves do?

Answer 8

The larger the groove, this makes it more accessible for interactions with proteins that recognize specific DNA sequence

Question 9

What does the secondary structure of DNA have to do with the sequence?

Answer 9

NOTHING! they are both similar so they have very similar shapes and properties

Question 10

What forces stabilize the double helix?

Answer 10

Hydrophobic effect (hydrophobic bases hidden inside the helix)
H-bonding of base pairs
Van der Waals stacking of bases

Question 11

What is ATP composed of?

Answer 11

ATP is a nucleotide 
A base (adenine), sugar (ribose) and 3 phosphate groups

Question 12

How is ATP synthesized from ADP?

Answer 12

When cells break down nutrient molecules (catabolic) and use the available free energy to synthesize ATP from ADP

Question 13

How long is the typical lifetime of an ATP molecule?

Answer 13

Seconds to minutes

time is money or ATP

Question 14

How does ATP generate energy?

Answer 14

By the breakdown of the 3 phosphate bonds

Question 15

How is ATP numbered in terms of alpha, beta and gamma?

Answer 15

Alpha is the first phosphate to connected to the sugar

Question 16

What are the two pathways that ATP goes through to generate energy?

Answer 16

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)

Question 17

What is the chemical equation of the gamma-beta reaction?

Answer 17

ATP—> ADP + Pi

Question 18

What is the chemical equation of the alpha-beta reaction?

Answer 18

ATP—> AMP + PPi

Question 19

Which one releases greater energy?

Answer 19

The alpha-beta linkage reaction releases twice as much energy because it hydrolyses both phosphoanhydride bonds of ATP.

Question 20

What is pyrophosphates?

Answer 20

An enzyme that hydrolyses PPi (pyrophosphate)

Question 21

What is PPi?

Answer 21

Pyrophasphate

2 linked phosphate groups

Question 22

What is Pi?

Answer 22

1 phosphate molecule

Question 23

What is the mechanism of Glutamine synthetase?

Answer 23

1) ATP reacts with glutamate to produce a covalent intermediate
2) NH3 acts as a nucleophile, reacts with the electrophilic carbonyl carbon atom

Question 24

How does ATP provide energy?

Answer 24

Not by simple hydrolysis but through group transfer

Question 25

What are enzyme cofactors?

Answer 25

Things that enzymes need in order for it to work properly

Question 26

What kind of enzyme cofactors are there?

Answer 26

Inorganic ions

Coenzymes

Question 27

What are coenzymes?

Answer 27

complex organic or metalloorganic compounds that act as transient carriers of specific functional groups