11 Aug 2016
School
Department
Course
Professor
BIOL 201 – Cell Biology and Metabolism C. Aikins
Notes I: Topic 1 - 10 (Vesicular transport) Winter 2011
1
Topic 1 – Introduction
Introduction to Metabolism
E. coli is great at growing and dividing
To grow, requires carbon source (glucose), NH4
+, PO4
3-, salts
Must convert these into amino acids, nucleotides, lipids, sugars, vitamins (coenzymes), macromolecules (DNA, RNA,
proteins, polysaccharides)
Converts glucose small molecules (pyruvate) through a glycolytic cycle
• Generates some ATP
With the help of NH4
+ & PO4
3-, convert pyruvate into nucleotides, amino acids, lipids, etc.
• These other biosynthesis mechanisms are endergonic and anabolic
♦ Anabolic builds up new molecules
♦ Endergonic consumed energy (from ATP)
Conversion of pyruvate to carbon dioxide is called the Kreb’s or TCA Cycle
• Generates a lot of ATP
Overall conversion of glucose to carbon dioxide and ATP is catabolic and exergonic
• Catabolic breaks down the glucose molecules
• Exergonic releases energy (captured in the form of ATP)
Breakdown of glucose and synthesis of new compounds occurs through interconnected pathways involving many
different reactions
Metabolism the chemical reactions that occur in a cell
Cellular reactions are governed by the same rules that govern all chemical reactions
Each reaction is catalyzed by a specific enzyme
Organisms devote much of their genome to specifying metabolic proteins
We will focus on a few central pathways critical for cellular energy conversions
Topic 2 – Energy and Biological Systems
Introduction
Energy the ability to do work
Can be classified into two general categories; kinetic and potential
More concerned about potential energy when discussing biological organisms, which includes
• Energy residing within chemical bonds
• Energy regarding concentration gradients
• Energy in the form of charge separations across membranes
Energy can be converted from one form to another
Will discuss how the cytoskeleton uses energy to move the cell
Chemical reactions that occur in cells are governed by the same rules that govern all chemical reactions
The key energetic principles that govern reactions include
2
Equilibrium
Free energy
Standard free energy
Chemical Equilibrium
All chemical reactions are reversible, to some degree
Consider the reaction A + B C + D
The rates at which the forward and reverse reactions may differ
At equilibrium, the rate forwards equals the rate reverse
The rate at which any given reaction occurs depends on several factors
Concentration
Rateforward = k1[A][B]
Ratereverse = k2[C][D]
At equilibrium, k1[A][B] = k2[C][D]
• Can generate an equilibrium constant,
C
[ ]
D
[ ]
A
[ ]
B
[ ]
=k1
k2
=keq
♦ The constant, keq, is an intrinsic characteristic of the reaction
Consider A ⇌ B
• Rateforward = k1[A]
• Ratereverse = k2[B]
• at equilibrium,
B
[ ]
A
[ ]
=keq
A reaction will proceed in the direction that favours an approach to equilibrium
EXAMPLE: If the equilibrium constant for the reaction A⇄B id 0.5 and the initial concentration of A is 25mM and [B] =
12.5 mM then
B
[ ]
A
[ ]
=0.5 =keq
, thus it is at equilibrium
Gibbs Free Energy
Free Energy (G) the energy in a system that is capable of doing work
Consider: reactants products
∆G = Gproducts - Greactants
Reaction will only proceed if ∆G < 0 (ie rp)
∆G > 0 reaction can proceed from right to left
Depends on the conditions of the reaction
If ∆G = 0, reaction is at equilibrium
∆G is influenced by temperature, pressure, concentrations of reactants and products, pH
Standard Free Energy
3
∆G0’ ∆G under standard conditions, concentrations of reactants and products are both 1M
Standard conditions 1 atm pressure, 25°C (298°K), pH = 7.0
Given A + B C + D
ΔG=ΔG'+2.303RT log C
[ ]
D
[ ]
A
[ ]
B
[ ]
⎛
⎝
⎜
⎞
⎠
⎟
For a reaction at equilibrium, ∆G = 0
•
0=ΔG'+2.303RT log C
[ ]
D
[ ]
A
[ ]
B
[ ]
⎛
⎝
⎜
⎞
⎠
⎟
ΔG'=−2.303RT log C
[ ]
D
[ ]
A
[ ]
B
[ ]
⎛
⎝
⎜
⎞
⎠
⎟ =−1362log keq
( )
• thus, ∆G0’ is a function of keq and also a measure of how much work the given rxn can do
• 1.362 (kcal/mol), 1362 (cal/mol)
If keq is large, the reaction will favour the production of the products
• ∆G0’ is negative
If keq is small, the reaction will favour the production of the reactants
• ∆G0’ is positive
The true determinant of which way the reaction will favour is the free energy, ∆G
It takes into account the concentrations of the reactants and products at the given moment
The standard free energy change is an indication of the energy released or consumed during a reaction
If ∆G0’ is negative, the reaction is exergonic (energy releasing)
Given A B (equal concentrations), the reaction would favour the production of B
If ∆G0’ is positive, the reaction is endergonic (energy consuming)
Given A B (equal concentrations), the reaction would favour the production of A
∆G0’ (AB) = – ∆G0’ (BA)
All reactions can proceed in either the forward or reverse directions depending on the relative concentrations of
the reactants and products
Standard free energy values are additive
Important to metabolism, how we couple energetically unfavourable rxns with energetically favourable ones
Consider A B C
∆G0’ (AC) = ∆G0’ (AB) + ∆G0’ (BC)
Catalysis
For a reaction to occur, reacting species must pass through a higher energy state, the “transition state”
When the bonds in the reactants must be broken
If, say the temperature rises high enough, (or other energy is put in) the rxn may occur spontaneously
Must pass through a critical state in order to move to products (transition state)
Catalysts act to accelerate the rates of reactants, lowers activation energy
Act by reducing the ∆G0 between the reactants and the transition state
They DO NOT change any other thermodynamic parameter
Enzymes
Are specific catalysts for biological reactions