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Lecture 2

BIOL 1201 Lecture Notes - Lecture 2: Escherichia Coli, Electrochemical Gradient, Cytosine


Department
Biological Sciences
Course Code
BIOL 1201
Professor
Moroney, James
Lecture
2

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Study Guide #2 for Biology 1201, section 4 2013
Chapter 8, pages 142-161
Metabolism, metabolites
The totality of an organism’s chemical reaction is called metabolism.
The degradative processes are catabolism. These processes release energy.
Anabolic pathways consume energy to build complicated molecules from simpler
ones
Cellular respiration is a catabolic process
Where is energy required in the cell? This is a hard concept to grasp. It is needed to
build the cell, maintain the cell, make and keep ion gradients etc.
Energy is required in all parts of the cell
STRUCTURE OF ATP AND ITS ROLE IN THE CELL (FIGURE 8.8); ATP cycle
(Figure 8.11)
ATP contains the sugar, ribose, a nitrogenous base called adenine, and three
phosphates all negatively charged (the bonds between the phosphates can be
broken down by hydrolysis)
ATP is a nucleotide
oThe ATP cycle: occurs mostly in the mitochondria ATP regeneration is
done by the addition of a phosphate to ADP. The free energy required to
phosphorylate ADP comes from catabolic processes in the cell. This
shuttling of inorganic phosphate energy is the ATP cycle
The ATP cycle is endergonic
How ATP drives chemical work and mechanical work (Figures 8.9 and 8.10)
With help of specific enzymes, the cell is able to use the energy released by ATP
hydrolysis directly to drive chemical reactions, that would by themselves be
endergonic
Transport work: ATP phosphorylates transport proteins

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Mechanical work: ATP binds noncovalently to motor proteins and is then
hydrolyzed which releases ADP and a phosphate. Another ATP can then bind. (it
walks along the cytoskeleton)
Chemical work: energy coupling using ATP hydrolysis
Enzymes, activation energy, catalysis (Figures 8.14 and 8.15)
An enzyme is an activation molecule that acts as a catalyst. Enzymes lower the
activation energy of a reaction.
Enzymes are proteins and depend on their shape for activity
Activation energy: the energy required to contort the reactant molecules so the
bonds can break
Factors Affecting Enzyme Activity
oTemperature and pH
oCofactors- Non protein “helpers” (inorganic metals, vitamins)
oEnzyme inhibitors- competitive inhibition is when the active site is
blocked; noncompetitive inhibition is when the inhibitor binds away from
the active site changing protein shape
oallosteric regulation- regulatory molecules, either activators or inhibitors,
bind to specific regulatory sites affecting the shape and function of the
enzyme
The reactant an enzyme acts on is referred to as the enzymes substrate.
Catalysis:
oSubstrates enter the active site; enzyme changes shape such that its active
site enfolds the substrate (induced fit)
oSubstrates are held in active site by weak interactions, such as hydrogen
and ionic bonds
oActive site can lower activation energy and speed up a reaction by:
Acting as a template for substrate orientation
Stressing the substrates and stabilizing the transition state
Providing a favorable micro environment

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Participating directly in the catalytic reaction
oSubstrates are converted to products
oProducts are released
oActive site is available for two new substrate molecules
Chemical energy is a form of potential energy
Favorable versus unfavorable reactions; Exergonic and endergonic reactions (Figure
8.6)
Exergonic reaction: energy released; spontaneous; favorable
oProducts have less free energy than the reactants
oSpontaneous does not mean rapidly
oExample: Glucose + O2 to CO2 and water, ATP reverting to ADP
Endergonic reaction: energy required; nonspontaneous; unfavorable
o Example: ATP cleavage to ADP and Pi
Coupled reactions (Figure 8.9),
Energy coupling: the use of an exergonic process to drive an endergonic one. ATP
is responsible for mediating most energy coupling
Example: Glutamate + NH3 Glutamine (unfavorable)
ATP ADP+ Pi (favorable)
The coupled reaction:
Glutamate + NH3 +ATP Glutamine + ADP+Pi
Enzymes lower activation energy (8.13) they DO NOT make an unfavorable reaction
favorable.
Feedback inhibition (Figure 8.21)
A metabolic pathway is switched off by the inhibitory binding of its end product
to an enzyme that acts early in the pathway.
Most common way enzymes are regulated
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