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Chapter 8 Notes: An Introduction to Metabolism

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on 20 October 2014

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Transcript of Chapter 8 Notes: An Introduction to Metabolism

Introduction: The Energy of Life
8.1: An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics
Metabolism: totality of an organism’s chemical reactions. Manages the material and energy resources of the cell.
Organization of the Chemistry of Life into Metabolic Pathways
A specific molecule is altered in a series of steps, creating a certain product.
Each step of the pathway is catalyzed by a specific enzyme.
Mechanisms that regulate enzymes balance metabolic supply and demand.
Catabolic/breakdown pathways
: release energy by breaking down complex molecules into simpler compounds.
A major pathway of catabolism is cellular respiration: sugar, glucose, and other organic fuels are broken down in the presence of oxygen into carbon dioxide and water.
Pathways can have more than one starting molecule and/or product.
Energy that was stored in the organic molecules becomes available to do the work of the cell.
Ex: ciliary beating or membrane transport.
Anabolic/biosynthetic pathways
: consume energy to build complicated molecules from simpler ones.
Ex: synthesis of a protein from amino acids.
Energy released from the
downhill
reactions of
catabolic pathways
can be stored and used to drive the
uphill
reactions of
anabolic pathways
.
Bioenergetics: study of how energy flows through living organisms.
8.4 Enzymes speed up metabolic reactions by lowering energy barriers
Enzyme: a macromolecule that acts as a catalyst
Catalyst: a chemical agent that speeds up a areaction without being consumed by the reaction.
Enzymes are specific. Enzymes have a shape-match with their substrates.

8.5 Regulation of Enzyme Activity helps control metabolism
If a cell’s metabolic pathways were not tightly regulated, it will be disasterous.
A cell regulates metabolism by:
switching on or off the genes that encode specific enzymes.
or by regulating the activity of enzymes.
8.3 ATP Powers Cellular Work by coupling exergonic reactions to endergonic reactions
Three main works of a cell:
Chemical: breaking down ( catabolism )or building up ( anabolism )
Transport work: in and out of the cell membrane
Mechanical Work: movement

Chapter 8 Notes: An Introduction to Metabolism
Energy Coupling: exergonic process --> drive an endergonic one

Hydrolysis : adding water to break the bond between phosphate
exergonic
Energy released --> chemical change to a lower state of free energy ( given to the outside / other molecule )

The energy from ATP : endergonic!!
the loss phosphate is transferred to some other molecule/reactant → phosphorylation
The Regeneration of ATP:
The Laws of Energy Transformation
Thermodynamics
: study of energy transformations that occur in a collection of matter is called a system (matter under study) and surroundings (everything outside system
First Law of Thermodynamics
: energy can be transferred and transformed, but it cannot be created or destroyed
Second Law of Thermodynamics
: Every energy transfer or transformation increases the entropy of the universe

More about First Law and Second Law
First Law
Also called
principle of conservation of energy
: energy is never destroyed, just converted into different forms throughout the universe
Second Law
During every energy transfer/transformation, some energy becomes unusable energy. In most energy transformations, more usable forms of energy are at least partly converted to heat
Heat is only usable when there is a temperature difference
If temp. is uniform, heat can only warm the body of matter

Increased entropy is apparent in physical aspect, but increased entropy in universe is less apparent (either in increasing heat or less ordered forms of matter
Spontaneous: process that can occur w/o input of energy
Nonspontaneous: process that needs energy added to system
Biological Order and Disorder
Living systems increase entropy of surroundings since they create ordered structures from less organized materials and vice versa
Loss of chemical energy is accounted for by heat generated during metabolism
Energy flows into ecosystem as light and exits as heat
Entropy of system decreases as long as total entropy of universe increases
Energy: the capacity to cause change.
Life depends on the ability of cells to transform energy from one form into another.
Kinetic energy: the relative motion of objects.
Moving objects can perform work by imparting motion to other matter.
Heat/thermal energy: kinetic energy associated with the random movement of atoms or molecules.
An non-moving object may still possess energy.
Potential energy: energy that matter possesses because of its location or structure.
Molecules possess energy because of the arrangement of their atoms.
Chemical energy: potential energy available for release in a chemical reaction.
Complex molecules are high in chemical energy.
Catabolic reaction: atoms are rearranged and energy is released, resulting in lower-energy breakdown products.
The structures and biochemical pathways of cells enable them to release chemical energy from food molecules, powering life processes.
Organisms are energy transformers.
Form of Energy
Nonspontaneous process
Spontaneous process
8.2: The free-energy change of a reaction tells us whether or not the reaction occurs spontaneously
Free-Energy Change, deltaG
Gibbs Free Energy (Free Energy): the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system
deltaG=deltaH - TdeltaS
deltaG<0 is spontaneous; deltaG > or = 0 is nonspontaneous
Effects of Temperature and pH on Enzymes
Rate of enzymatic activity increases with temperature; however when it reaches a certain limit it drops sharply.
Many enzymes require nonprotein helpers, called cofactors, for catalytic activity.
Inhibitors reduce enzyme function. There are two kinds of inhibitors.

Inhibition of Enzyme Activity
Continued
deltaG = G final state - G initial state
negative deltaG system in final state is less likely to change and is more stable than initial
Free energy can also measure a system’s instability (tendency to change to a more stable state)
Less stability=more stability; high concentration=low concentration
Maximum stability=equilibrium

Free Energy and Metabolism
Exergonic reaction: net release of free energy, negative deltaG; loss of free energy
Endergonic reaction: absorbs free energy from its surroundings, positive deltaG
Reactions in isolated system reach equilibrium
Cell that has reached equilibrium is dead; therefore metabolism is never at equilibrium
Key to maintain lack of equilibrium is that product of reaction does not accumulate, but becomes reactant of next step
Activation Energy (EA)
Activation Energy: initial investment of energy for starting a reaction
Every chemical reaction between molecules involves bond breaking and bond forming.
Enzymes lower the amount of EA needed, so the reaction rate is faster.
Exergonic
Endergonic
Substrate Specificity of Enzymes
Substrate: reactant an enzyme acts on
Enzyme-substrate complex: The enzyme binds to a substrate, or substrates.
Active site: region on the enzyme where the substrate binds
Induced fit
repositions chemical groups of active sites to enhance their catalytic ability for chemical reactions



Small molecules are assembled into polymers, which are hydrolyzed later as needed.
In multicellular organisms: many cells export chemical products that are used in other parts of the organism.
Cellular respiration extracts the energy stored in sugars and other fuels.
Cells apply this energy to perform various types of work.
Ex: transport of solutes across the plasma membrane.
Bioluminescence: cells convert the energy stored in certain organic molecules to light.
Metabolic activities carried out by a cell are precisely coordinated and controlled.
The Active Site is the enzyme's catalytic center.
In an enzymatic reaction, the substrate binds to the active site of the enzyme
The enzyme’s active site can lower an EA barrier by
Orienting substrates correctly
Straining substrate bonds / tension
Providing a favorable microenvironment
Covalently bonding to the substrate
Allosteric Regulation
results in the inhibition or stimulation of an enzyme’s activity
occurs when a protein’s function at one site is affected by the binding of a regulatory molecule to a separate site.
Allosteric Activation and Inhibition

Most allosterically regulated enzymes are constructed of two or more polypeptide chains.

Cooperativity:
is a form of allosteric regulation that can amplify enzyme activity.


Feedback Inhibition
During feedback inhibition, a metabolic pathway is switched off by the end product and it binds with an enzyme, shutting down the pathway
Cell Metabolism
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