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Metabolism 1: Cellular Energetics
Transcript of Metabolism 1: Cellular Energetics
Transformations ARE ALLOWED! Any closed system will tend toward a state of maximum entropy.
True for the Universe as a whole.
Portions of the Universe can still function as "open" systems.
Energy (and the matter that accompanies it) can be used to decrease an open system's entropy. 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 Biological Systems use Exergonic Reactions to provide the free energy necessary for endergonic reactions. Living systems are not the only systems in the universe that require energy conversion to function. 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 Open & Closed Systems Closed systems inexorably tend toward an absence of free energy.
They reach at a state of equilibrium between inputs and outputs.
Closed Inevitably Dull Open Open systems will not reach equilibrium as long as the processes of the system recieve inputs and produce outputs.
There is no inherent limit to the complexity of an open system, provided there is enough input to allow for that complexity
Usually Interesting 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.
Complex Enzyme Products Examples: The active site is localized to a small area of the enzyme Topoisomerase: Involved in minimizing mechanical stress on DNA during replication.
Makes a temporary cut in the helix.
Blue: 2 polypeptide chains.
Orange: DNA Double-Helix
Purple: Active site. 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. A manganese ion (dark green) is visible in the topoisomerase 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.
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 Interactions "Other-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 on 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 enviornment.
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. Big Questions: Big Questions: Make Sure You Can: Make Sure You Can: How do living systems adhere to the constraints of the Universe?
How can a living system maintain order in a Universe of increasing entropy? How do living systems control their metabolism?
How do living systems carry out a wide variety of specific chemical reactions?
Explain how living systems adhere to the first and second laws of thermodynamics.
Explain how living systems can increase in order even though the Universe is moving toward a state of maximum entropy.
Compare endergonic and exergonic reactions.
Compare open and closed systems.
Explain how ATP allows for cellular work.
Explain the effect of a catalyst on a reaction profile.
Explain how enzymes function as catalysts.
Explain the induced fit model of enzyme function.
Provide examples of enzyme-catalyzed reactions in biological systems.
Explain the relationship between enzyme structure and function.
Explain the major modes of regulation of enzyme activity. * there are a few exceptions (e.g. stellar fusion), which don't matter for us More PE, Less KE Less PE, More KE Life is an open system! Equilibrium = Death Practice