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BioChemistry CH 3: Energy & Enzymes

Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Derived from content by David Knuffke.
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Brian Berning

on 7 October 2013

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Transcript of BioChemistry CH 3: Energy & Enzymes

Energy & Enzymes
Theory
&
Laws of Thermodynamics
First:
Second:
Energy can not be created or destroyed!
Entropy of the Universe increases!
Cellular Energy Theory:
Gibbs Free Energy:
Kinetic & Potential Energy
Organisms are energy processing systems.
Energy from the Sun, or from Chemical Bonds is used to undertake cellular/organismal work

Work
: Anything that requires atoms to be moved around through cellular actions (aka: "everything you do")
Both are useful to organisms for different purposes.
Both contribute to phenomena at all levels of organization in the Universe.
A Measurement of the amount of "useful" energy that a system (like a cell) can use for performing work.

At the cellular level, the major biological source of energy is from the rearranging of atoms to from higher energy compounds to lower energy compounds.
Exergonic Reactions:
Endergonic Reactions:
Release energy (matter is converted from higher energy arrangements to lower energy arrangements) .
Will happen spontaneously, once they are initiated.
Change in free energy is NEGATIVE.
Require energy input to occur (matter is converted from lower energy arrangements to higher energy arrangements) .
Can not occur spontaneously.
Change in free energy is POSITIVE.
G
=
H
-
T S
G = Free Energy
H = Enthalpy (energy stored in a substance)
T = Temperature
S = Entropy
Life is Highly Ordered
Life Requires Energy Input
Organisms use the energy they convert to power cellular/organismal processes that decrease their overall entropy (or at least delay its increase). This process increases the entropy of their surroundings.
A highly ordered living system uses energy input to maintain/increase order
ATP!
The Return of Kinetics
Adenosine Tri-Phosphate
The short term energy storage/release molecule of choice in cells
tens of millions made and used per second per cell
The bonds between phosphate groups in nucleoside tri-phosphates (like ATP) are relatively unstable.
Much more free energy is released when the bonds between them are broken than is required by the cell to initiate their cleavage.
Energy!
ATP
ADP
Much of the work done by cellular proteins is mediated by the addition and removal of
Phosphate groups from ATP by proteins to other proteins (kinases and phosphatases).
Metabolism
Refers to the sum total of all chemical reactions that take place in an organism.

Energy from
catabolic
reactions (ex: respiration) is used to power the synthesis of ATP from ADP and Phosphate groups.

ATP (and other NTP's) is used to power the
anabolic
Reactions that require chemical energy.
Reaction Coupling
Refers to linking an exergonic process with a cellular process.


If an endergonic process requires less free energy than an exergonic process produces, coupling those two reactions allows for maximum efficiency, and an overall negative delta G.
The Reaction Profile
All reactions require an input of energy (the "
activation energy
") to make the breaking of current chemical bonds energetically favorable (the "
transition state
").

The relationship between the energy of the products and the energy of the reactants is what determines if a reaction is exergonic or endergonic.
Catalysts!
effect of catalyst
Any substance that increases the rate of a chemical reaction while not participating in the reaction.

Lowers the activation energy of a reaction.

Reusable (since they don't participate).
Enzymes!
Organization:
Biological catalysts.

Proteins and some RNA molecules (examples?)
How do they do it?
Enzymes interact with reactants ("
substrate
")

Cause breaking/formation of particular atomic bonds to be more energetically favorable.

This work is localized to an area of the enzyme called the "
active site
".
Induced Fit
The shape of the active site of an enzyme is shape-specific for a particular substrate.

The binding of a substrate to the active site induces the necessary conformational change of the enzyme to catalyze the reaction.
Reactants
Enzyme-Substrate
Complex
Enzyme
Products
Examples:
The active site is localized to a small area of the enzyme
Peroxidase
Found in plants.

Breaks down hydrogen peroxide and aids in defense against pathogens.
Evolutionary Considerations:
Rubisco!
Attaches carbon dioxide to sugar precursor molecules in photosynthesis.

50% of all protein found in a chloroplast.
Co-factors
Most enzymes require accessory compounds many of which you are familiar with as ("
vitamins
") or metal ions (aka "
minerals
") in order to be functional.
Magnesium ion (
green
) associated with rubisco's active site.
An iron ion (
dark red
) is visible in the peroxidase's active site.
Evolution plays a central role in enzyme structure and function.

Various studies have been conducted to investigate the effect of evolution on enzymes.

These include:
analysis of enzyme genes (sequence comparison).
Artificial selection of enzyme activity in laboratory settings.
Ethnographic/Demographic studies of enzyme genotypes and enzymatically determined phenotypes.
Variation + Natural Selection = Adaptation
Regulation:
Enzymatic function can be stimulated or inhibited by factors in the cell.
Competitive Interactions
Non-Competitive Interactions
vs.
A molecule other than the substrate binds to the active site.
Regulation is accomplished without occupying the active site.
Allosteric Site:
Stimulate or inhibit enzyme activity by causing a conformational change in the enzyme.
Activation:
Inhibition:
Binding of an activator molecule can stabilize the enzyme in an active conformation.
Binding of an inhibitor molecule can stabilize the enzyme in an inactive conformation.
Constant Oscillation
Active
Inactive
Activator
Inhibitor
Binding of a substrate molecule to an active subunit of an enzyme can also trigger stabilization of the active conformation in all subunits ("
cooperativity
")
Important enzymes for cell death (apoptosis and necrosis).

Data from an experiment to determine if caspase enzymes can have an allosteric site.

The active and inactive forms of caspase 1 were already known.

Hypothesis: Allosteric inhibition of caspase 1 will lock the enzyme in an inactive conformation.
"-ase"
A common nomenclature suffix for enzymes.
prefix: usually refers to enzyme's substrate
Ex. Caspase
Compartmentalization
Localization of specific enzymes (and the reactions they mediate) within compartments of the cell allow for more control over when and where particular metabolic reactions occur in eukaryotes
Environmental Infuence:
Like all proteins, enzyme structure (and therefore function) can be effected by the conditions of the enzyme's environment.

There are three major environmental conditions that effect enzyme structure and function
1. Temperature 2. pH

3. Concentration (enzyme, substrate, cofactors)
Feedback:
Many metabolites have regulatory effects on enzymes that catalyze the metabolic pathways that result in the production of those metabolites.
More PE, Less KE
Less PE, More KE
Practice
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