Chapter 6: Energy and Metabolism Flashcards
Thermodynamics
branch of chemistry concerned with energy changes
Energy
the capacity to do work
Kinetic energy
energy of motion
Potential energy
stored energy
What is the most convenient way of measuring energy?
heat energy
One calorie
the heat required to raise the temperature of one gram of water 1 degree C
Does breaking bonds between atoms require or release energy?
require energy
Oxidation
when an atom or molecule loses an electron
Reduction
when an atom or molecule gains an electron; more energy than oxidized form
First Law of Thermodynamics
- energy cannot be made or destroyed
- energy can change from one form to another
- the total amount of energy in the universe is constant
What happens to some of the energy when it is converted
it leaves as heat (random motion of molecules)
Where do organisms acquire energy from to carry out cellular work?
- the sun
- chemical bonds
Work
anything that requires atoms to be moved around by cellular reaction
Gibbs Free Energy
a measurement of the amount of “useful” energy that a system can use for doing work
Where does most of the biological source of energy come from at a cellular level?
rearranging of atoms from higher energy compounds to lower energy compounds
Formula for change in free energy
Δ G = ΔH -TΔS
G = free energy
H = Enthalpy (energy stored in a substance)
T = Temperature
S = Entropy
Exergonic reactions
- release of energy (matter converted from higher energy arrangements to lower energy arrangements)
- happens spontaneously
- change in free energy is negative
- more free energy
- less stable
- greater work capacity
Example of exergonic reaction
Cellular respiration
- glucose is being broken down to make ATP
- energy is being released
C6H12O6 + O2 –> 36ATP + CO2 + H2O
Endergonic reactions
- require the input of energy to occur (matter is converted from lower energy arrangements to higher energy arrangements)
- does NOT occur spontaneously
- change in free energy is positive
- less free energy
- more stable
- less work capacity
Example of endergonic reaction
Photosynthesis
ATP + CO2 + H2O –> C6H12O6 + O2
How do biological systems use exergonic reactions?
- provide the free energy needed to undergo endergonic reactions
Second Law of Thermodynamics
- any closed system will tend toward a state of maximum entropy (randomness)
- parts of the universe can still function as an “open” system
- energy can be used to decrease entropy
How is life highly ordered?
- organisms use the energy they convert to power cellular processes that can decrease or delay overall entropy
- increases entropy of surroundings
- organism uses energy input to maintain/increase order
Closed systems
- inexorably tend toward an absence of free energy
- they reach at a state of equilibrium between input and outputs
- inevitably dull
Open systems
- will not reach equilibrium as long as the processes of the system receive inputs and produce outputs
- usually inputs
- life is an open system
- no limit to complexity of open system
When does an organism reach equilibrium?
when it is dead
Cellular Energy Theory: ATP
- the short term energy storage/release molecule of choice in cells
- tens of millions are made and used per second
- the bonds between phosphate groups in nucleotide triphosphates (like ATP) are relatively unstable
- more free energy is released when bonds between them are broken than is required by the cell to initiate their cleavage
What is ATP responsible for?
- making sugars
- supplying activation energy for chemical reactions
- actively transporting substances across membranes
- building block for RNA molecules
How does ATP hydrolysis drive endergonic reactions?
- cells use exergonic reactions to provide the energy needed to synthesize ATP from ADP + Pi–> the hydrolysis of ATP (exergonic) provides energy for endergonic reactions, like muscle contraction, to occur
How are endergonic cellular reactions driven?
- coupling to the exergonic hydrolysis of two terminal phosphates –> the bonds holding the terminal phosphates together are easily broken to release energy
Cellular proteins
- assist in the cellular energy theory process of breaking bonds of ATP
- 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 phosphates; enzymes)
Metabolism
the sum total of all chemical reactions that take place in an organism
How is the synthesis of ATP from ADP and phosphate groups powered?
by energy from catabolic reactions (respiration)
What powers anabolic reactions that require chemical energy?
ATP and other nucleotide triphosphates
Catbolism
- reactions that make energy by breaking down molecules
- exergonic, energy-releasing processes
Anabolism
- reactions that expend energy to build up molecules
- endergonic, energy-consuming processes
Reaction coupling
- 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/graph
- all reactions need an input of energy (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 endergonic or exergonic
Catalysts
- any substance that increases the rate of a chemical reaction while not participating in the reaction
- lowers activation energy of the reaction
- reusable
Enzymes
- biological catalysts
- proteins and some RNA molecules
- “ase” is a common suffix for enzymes
- prefix usually refers to the substrate
How do enzymes work?
- interact with reactants (substrates)
- 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 a specific shape for a specific substrate
- binding of substrate to active site induces conformational change of enzyme to catalyze the reaction
Active site
clefts or pockets on an enzymes surface where the substrate binds to and the reaction is carried out –> forms enzyme-substrate complex
Examples of enzymes
- topoisomerase: minimizes mechanical stress on DNA during replication
- rubisco: attaches carbon dioxide to sugar precursor molecules in photosynthesis
- 50% of all protein found in a chloroplast
Co-factors
- most enzymes need accessory compounds like vitamins or metal ions (minerals) in order to function
Co-enzyme
- nonprotein organic molecule
- vitamins
- modified nucleotides
Enzyme regulation
can be stimulated or inhibited by factors in the cell
Competitive Interactions
a molecule other than the substrate binds to the active site
Non-competitive Interactions
- regulation is accomplished without occupying the active site
- noncompetitive inhibitors bind to enzyme in a place other than active site, change the enzyme shape, which stops the substrate from binding
Allosteric Site
- chemical on/off switches
- binding of substrate to this site can switch an enzyme between its active and inactive configuration
Allosteric Interactions
- other site
- stimulate or inhibit enzyme activity by causing a conformational change in the enzyme
Allosteric inhibitor
a substance that binds to allosteric sites and reduces enzyme activity
Allosteric activator
a substance that binds to allosteric sites to keep enzymes in their active configuration and increases enzyme activity
Cooperativity
- binding of a substrate molecule to an active subunit of an enzyme can trigger the stabilization of the active conformation in all subunits
Activation
- binding of an active molecule can stabilize an enzyme in an active conformation
Inhibition
- binding of an inhibitor molecule can stabilize the enzyme in an inactive conformation
Compartmentalization
localization of specific enzymes (and the reactions they mediate) within compartments of the cell allow for more control over where/when certain metabolic reactions occur in eukaryotes
Effect of temperature on enzyme activity
- increases until optimal temperature, usually around body/environment temp
Optimal temperature of a typical human enzyme
37 degrees Celsius
Optimal temperature of a thermophilic (heat tolerant) bacteria
77 degrees Celsius
Effect of pH on enzyme activity
usually optimal around 6-8
Optimal pH for pepsin (stomach enzyme)
2
Optimal pH for trypsin (intestinal enzyme)
8
Effect of substrate concentration on enzyme activity
- as substrate concentration increases, so does the enzyme activity until it hits a saturation point, where there are more substrates than enzymes available to bind to
Feedback (inhibition)
- many metabolites have regulatory effects on enzymes that catalyze the metabolic pathways that result in the product of those metabolites
- the end-product of the pathway binds to an allosteric site on the enzyme that catalyzes the first reaction in the pathway
