Chapter 13 Flashcards
(21 cards)
Energetics within the cell are not standard
- The actual free-energy change of a reaction in the cell depends on:
- The standard change in free energy
- Actual concentrations of products and reactants
Relationship between free energy and the equilibrium constant
ΔG°’ = -RTlnKeq
-when k is greater than 1 or ΔG° is negative the rxn proceeds forward
-when k is 1 or ΔG° is zero the rxn is at equilibrium
when is is less than 1 or ΔG° is positive the rxn proceeds in the revers e
Energetics of Hydrolysis reactions
tend to be strongly favorable (spontaneous)
Energetics of isomerization reactions
have smaller free-energy changes
Isomerization between enantiomers: G = 0
Energetics of of oxidation reactions
- Complete oxidation of reduced compounds is strongly favorable
- In biochemistry the oxidation of reduced fuels with O2 is stepwise and controlled
What are Common biochemical reactions?
1) Cleavage or formation of C-C bonds
2) Cleavage and formation of polar bonds
- Nucleophilic substitution mechanisms
- Addition-elimination mechanisms ( e.g. hydrolysis and condensation reactions)
3) Internal rearrangements
4) Free radical reactions
5) Group transfers
6) Oxidation/reduction reactions
Describe Cleavage of C-H and C-C bonds (homolytic and heterolytic cleavage)
- Covalent bonds can be broken in two ways
- Homolytic cleavage is very rare
- Heterolytic cleavage is common, but the products are highly unstable
General features of Nucleophiles and electrophiles
- Electrophiles are electron acceptors, while nucleophiles are electron donors
- Electrophiles accept electrons because they are either positively charged or have empty valence shells.
- Nucleophiles donate electrons because they either have a negative charge or they have lone pair(s) of electrons in their valence shells.
What is a condensation reaction?
- type of chemical reaction in which two molecules are combined to form a single molecule, usually with the loss of a small molecule such as water.
- formation of carbon-carbon bonds
What is an isomerization reaction?
the process in which a molecule, ion or molecular fragment is transformed into an isomer with a different chemical structure.
What is an addition reaction? What is an elimination reaction?
addition: reaction where two or more molecules combine to form a larger one
elimination: reaction in which two substituents are removed from a molecule in either a one- or two-step mechanism. The one-step mechanism is known as the E2 reaction, and the two-step mechanism is known as the E1 reaction
What are Group transfer reactions
- Proton transfer, very common
- Methyl transfer, various biosyntheses
- Acyl transfer, biosynthesis of fatty acids
- Glycosyl transfer, attachment of sugars
- Phosphoryl transfer, to activate metabolites; also important in signal transduction
Why is Hydrolysis of ATP highly favorable under standard conditions?
The charge separation that results from hydrolysis relieves electrostatic repulsion among the four negative charges on ATP
Better charge separation in products
Better solvation of products
More favorable resonance stabilization of products
Actual G of ATP hydrolysis differs from G’
-The actual free-energy change in a process depends on:
The standard free energy
The actual concentrations of reactants and products
-The free-energy change is more favorable if the reactant’s concentration exceeds its equilibrium concentration
-True reactant and the product are Mg-ATP and Mg-ADP, respectively
G of ATP hydrolysis is Mg++ dependent
Formation of Mg2+ complexes partially shields the negative charges and influences the conformation of the phosphate groups in nucleotides such as ATP and ADP
Several phosphorylated compounds have large G’ for hydrolysis
- Again, electrostatic repulsion within the reactant molecule is relieved
- The products are stabilized via resonance
- The product undergoes further tautomerization
Phosphates: ranking by the Standard free energy of hydrolysis
Phosphate can be transferred from compounds with higher ΔG’ to those with lower ΔG’.
Reactions such as PEP + ADP => Pyruvate + ATP are favorable, and can be used to synthesize ATP.
Hydrolysis of thioesters
Hydrolysis of thioesters is strongly favorable, such as acetyl-CoA
Acetyl-CoA is an important donor of acyl groups:
-Feeding two-carbon units into metabolic pathways
-Synthesis of fatty acids
In acyl transfers, molecules other than water accept the acyl group
Compounds that participate in Oxidation-Reduction reactions (hierarchy from most reduced to most oxidized compounds)
Reduced organic compounds serve as fuels from which electrons can be stripped off during oxidation
Going from most reduced to most oxidized:
Alkane
Alcohol
Aldehyde (ketone)
Carboxylic acid
Carbon dioxide
NAD and NADP are common redox cofactors
They can dissociate from the enzyme after the reaction
In a typical biological oxidation reaction, hydride from an alcohol is transferred to NAD+ giving NADH
Flavin cofactors
allow single electron transfers
Flavin cofactors are tightly bound to proteins
