Molecular Catalysis and Energetics Flashcards
Chemical systems tend to _ free energy
minimize
What is free energy?
the amount of energy available to do work
What direction does the reaction proceed if G<0?
toward the products
What direction does the reaction proceed if G=0?
at equilibrium
What direction does the reaction proceed if G>0?
toward the reaction
What are most biosynthetic reactions?
thermodynamically unfavorable, but are driven forward by coupling to a more strongly favorable reaction
The second reaction _ the products of the first reaction, _
consumes; preventing reversal of the first reaction which would otherwise be favored
How does a peptide bond form?
results from a condensation reaction between the carboxyl group of one amino acid and the amino group of another
What are the N-terminus and C-terminus?
exposed amino grup and carboxyl group
What forms the peptide backbone?
a repeating series of C and N atoms
How are residues in a polypeptide numbered?
from the N-terminus
Peptide bond formation requires _
activated amino acid precursors; formation of high energy bond with AMP, using ATP as the donor
What cannot be used directly for synthesis of DNA or RNA?
nucleoside monophosphates nor nucleoside diphosphates because G>0
What must nucleoside monophosphates and diphosphates first convert to?
nucleoside triphosphates using ATP as a phosphate donor
What can be used directly for synthesis of DNA or RNA?
nucleoside triphosphates can be joined in a reaction that releases pyrophosphate, which is rapidly converted to two phosphates because G<0.
DNA/RNA polymerization requires _
energy
What happens in DNA/RNA polymerization
- hydrolysis of a nucleoside triphosphate generates a nucleoside monophosphate and energy, both needed for the reaction
- pyrophosphate hydrolysis to monophosphate (by pyrophosphatase) releases additional energy and is coupled to bond formation
What does a favorable free energy change tell us?
whether a reaction will occur spontaneously
What is an activation energy?
the threshold that must be overcome for a reaction to proceed
What is the function of enzymes?
work by lowering the activation energy barrier
Can a favorable reaction still occur if activation energy is high?
very few molecules will be able to proceed, making the reaction slow
What is the transition state?
the highest point on the energy scale between substrate and product; short lived
Where are metal ions and cofactors bound?
in the active site and are required for function
Active sites are usually _ among different organisms, even if the rest of the protein is more _
conserved; diverged
How can enzymes catalyze reactions?
- by bringing two reactive substrates together (proximity catalysis)
- by destabilizing the substrate, increasing its free energy (ground-state destabilization)
- by stabilizing the transition state, lowering the barrier to the reaction
- by leading the reaction through an alternative set of stages that have a smaller energy barrier than the uncatalyzed reaction; transient reaction intermediates
What is nucleophilic displacement?
involves the movement of an electron from an electron-rich atom (nucleophile) to an electron-poor atom (electrophile)
What is a nucleophilic attack?
encouraged when a proton is removed by a general base on an enzyme - here the H+ on the ‘ OH is removed
What do enzymes provide?
groups that act as acids or bases and encourage proton movements
What are intermediates?
transition state structures that have additional bonds and can interact favorably with other molecules in the reaction
What are the steps of RNAse A degradation of RNA?
- histidine 12 removes a proton from the 2’ OH of one ribose and histidine 119 donates a proton to the 1’ O of a second sugar
- breaks the bond holding the nucleotides together, and a cyclic phosphate intermediate is formed
- histidine 12 donates a proton to the 2’ O, re-forming the 2’ OH. histidine 119 accepts a proton from a water molecule and the remaining OH binds to P
