Lecture 12: Introduction to Metabolism Flashcards
First Law of thermodynamics
- for any physical or chemical change, the total amount of energy (in the universe) remains constant
–> when energy is converted from one form to another, the total energy before and after the conversion is the same
–> energy is neither created or destroyed
Second law of thermodynamics
- when energy is converted from one form to another, some of that energy becomes unavailable to do work, resulting in increased entropy (in the universe)
Entropy
- measure of the disorder in as system and is based on the fact that energy transformation processes are never 100% efficient
–> it takes energy to impose order on a system
–> unless energy is applied to a system, it will be randomly arranged or disordered
Enthalpy
- total energy = the usable energy (free energy G) plus the unusable energy (entropy)
H = G + TS
T = temperative in kelvin
Change in energy
delta G = delta H - T (delta S)
positive = energy consumed
negative = energy released and reaction can occur spontaneously
Exergonic
release free energy (delta G negative) and are spontaneous
–> catabolism
Endergonic
- consume free energy
- delta G is positive and are nonspontaneous
–> anabolism
Free energy for reaction in a biological system
Values for k Eq in biological reactions
K eq > 1 : - delta G, proceeds forward
K = 1 : delta G = 0, is at equilibrium
K < 1 : + delta G, proceeds in reverse
Types of metabolic pathways
metabolism: sum of chemical reactions in an organism
catabolism: sum of energy releasing (exergonic) processes. the degenerative phase of metabolism
anabolism: sum of energy using (endergonic) processes. biosynthetic phase of metabolism
* catabolism provides the building blocks and energy for anabolism
overall sequence = metabolic pathways
anabolism: precursor and cell macromolecules
precursors: amino acids, sugars, fatty acids, nitrogenous bases
macromolecules: proteins, polysaccharides, lipids, nucleic acids
catabolism: energy containing nutrients and energy depleted end products
nutrients: carbohydrates, fats, proteins
energy depleted end products: C02, H20, NH3
Five priniciple characteristics of metabolic pathways
* stem from their function of generating products for cellular
- metabolic pathways are IRREVERSIBLE due to at least one highly exergonic reaction conferring directionality
- they have INDEPENDENT CATABOLIC and ANAMOLIC interconversion routes for intermediates
- they each have a FIRST COMMITTED STEP
- they are REGULATED, most often on the level of enzymes catalyzing specific metabolic steps
- they occur in SPECIFIC CELLULAR LOCATIONS
Irreversibility of metabolic pathways
- at least one highly exergonic reaction conferring directionality
metabolic pathways: catabolic and anabolic interconversion routes
independent routes for the two processes
Metabolic pathways: first step
committed
metabolic pathways: regulation
most often on the level of enzymes catalyzing specific metabolic steps
metabolic pathways: locations
- specific cellular locations
Metabolic pathways: connection and arrangement
highly interconnected and nonlinearly arranged
Types of metabolic reactions:
- reactions that make and break bonds of carbons with other carbons
- internal rearrangements, isomerizations, eliminations
- free radical reactions
- group trasnfer reactions
- oxidation-reduction reactions
reactions that make and break bonds of carbons with other carbons
- aldol condensation
- claisen ester condensation
- decarboxylation of a b-keto acid
internal rearrangements, isomerizations, eliminations
glucose 6 phosphate –> fructose 6 phosphate
other?
free radical reactions
coproporphyrinogen III
coproporphyrinogenyl III radical
protoporophyrinogen IX
group trasnfer reactions
glucose –> glucose 6 phosphate
oxidation reduction reactions
lactate –> puryvate
transfer potentials
- protons, electrons or functional groups can be transferred during biochemical reactions
–> tendency of such reactions to occur can be quantified
Cellular work
- types
- process
- chemical
- transport
- mechanical
- to do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an andergonic one
–> most energy coupling in cells is mediated by ATP
phosphorylated adenosine derivatives
1 = AMP
2=ADP
3 = ATP
ATP hydrolysis and Mg 2+
- formation of Mg2+ complexes partially shields the negative charges and influences the conformation of phosphate groups in necleotides such as ATP and ADP
- between 2 end ones for ATP: MgATP2-
- between only 2 for ADP: MgADP-
Daily human requirement for ATP
- the average adult human consumes approximately 11,700 Kj of food energy per day
- assuming thermodynamic efficiency of 50%, about 5860 KJ of this energy ends up in form of ATP
- Assuming 50Kj of energy required to synthesize one mole of ATP, the body must cycle through 5860/50 or 117 moles of ATP per day (=65kg of ATP per day)
- the typical adult human body contains 50 g ATP/ADP
- each ATP must be recycled nearly 1300 times per day
How many times is each ATP molecule recycled per day
1300
How many grams does the typical adult human body contain
50 g ATP/ADP
ATP-ADP cycle
- revolving door through which energy passes during its transfer from catabolic to anabolic pathways
- using energy from catabolic reactions in the cell, ATP is regenerated by the addition of a phosphate group to ADP in three diff ways
1. substrate level phosphorylation
2. oxidative phosphorylation
3. photophosphorylation
ATP-ADP cycle summary
Substrate level phosphorylation
- transfer of a high-energy PO4- from a phosphorylated compounds to ADP
Oxidative phosphorylation
- energy released by transferring clectrons from one compound (oxidation) to another (reduction) along an electron trasnport chain to a final acceptor (such as oxygen) is used to create a proton gradient and hence to synthesize ATP
photophosphorylation
- light causes chlorophyll to release excited electrons and the energy from this electron trasnfer of chlorphyll through a system of carrier molecules is used to reate a proton gradient and hence to synthesize ATP (as well as other energy sources)
Redox reactions
chemical reactions that transfer electrons between reactants (donor and acceptor) are called oxidation-reduction reactions
Fe3+ + Cu+ –> Fe2+ + Cu2+
can be divided in two 2 half reactions:
Fe3+ + e- –> Fe2+
Cu+ –> Cu2+ + e-
Other ways for electron transfer to occur in redox reactions:
- hydrogen atoms
AH2 –> A + 2e- + 2H+
AH2 + B –> A + BH2
- hydride ion (H-) has 2 electrons
- direct combination with oxygen: which acts as an electron acceptor that is covelantly incorporated into the product (oxidation of a hydrocarbon to an alcohol)
Dehydrogenations in biological systems
NAD/NADP-dependent reactions
NAD(P) binding in dehydrogenases
where does binding occur?
- Rossman fold
FAD/FMN-dependent reactions
Redox potential
- when two redox pairs are together in solution, electron trasnfer from the electron donor of one pair to the electron acceptor of the other may proceed spontaneously
- the tendency for such a reaction depends on the relative affinity of the acceptor of each redox pair for electrons
- the redox potential (or electromotive force, emf) Enot, a measure (in volts) of this affinity, can be determined experimentally using the:
H+ + e- –> 1/2 H+
as a reference (arbitrarily assigned as Enot = 0.00V)
Using electrochemical cell
Half-cell that takes electrons from the standard hydrogen cell is assigned a positive E not ( a negative E not when it donates electrons)
Quantification of REdox potential
- redox potential depends not only on the chemical species present, but also on their activities, approximated by their concnetrations
- the standard redox potential Enot related to the actual redox otential E at any concentration of oxidized and reduced species in a living cell nu the Nernst equation
E0 at pH 7 and 250c
ΔG = -nF ΔE
