Metabolism – Chapter 8 - Chemical reactions in life
Latin
• Allo - other
• Ana – to build
• Cata – break down
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Endo - inside
Exo - outside
Kine - moving
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Lyse - split
Thermo - heat
Terms
• Activation energy
• Active site
• Allosteric enzyme
• Anabolic
• Biennial
• Catabolic
• Coenzymes
• Cofactors
• Competitive inhibition
• Cooperativity
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Diapause
Endergonic
Energy coupling
Endothermy
Enthalpy
Entropy
Exergonic
Exothermy
Enzyme
Feedback inhibition
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Free energy
Gibb’s equation
Induced fit
Inhibitors
Multi-enzyme complex
Non-competitive
inhibition
Substrate
Thermodynamics
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College Board: Learning Objectives: Metabolism
4.B.1 – Interactions between molecules affect their structure and function
a. Change in the structure of a molecule may result in a change in the function of the system.
b. The shape of enzymes, active sites and interaction with specific molecules are essential for the basic
functioning of the enzyme.
Evidence of student learning is a demonstrated understanding of each of the following:
1. For an enzyme-mediated reaction to occur, the substrate must be complimentary to the surface properties
(shape and charge) of the active site. In other words, the substrate must fit into the enzyme’s active site.
2. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters
the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors
or coenzymes are present and bind to the appropriate sites on the enzyme.
No specific cofactors or coenzymes are within the scope of the course and the AP exam.
c. Other molecules and the environment in which the enzyme acts can enhance or inhibit enzyme activity.
Molecules can bind reversibly or irreversibly to the active or allosteric sites changing the activity of the
enzyme.
d. The change in function of an enzyme can be interpreted from data regarding the concentration of product or
substrate as a function of time. These representations demonstrate the relationship between an enzyme’s
activity, the disappearance of substrate, and/or presence of a competitive inhibitor.
2.A.1 – All living systems require constant input of free energy
a. Life requires a highly ordered system
1. Order is maintained by constant input of free energy into the system
2. Loss of order or free energy results in death
3. Increased disorder and entropy are offset by biological processes that maintain or increase order
a. Living systems do not violate the second Law of Thermodynamics which states that entropy increases over
time.
Evidence of student learning is a demonstrated understanding of each of the following:
1. Order is maintained by coupling reactions that increase entropy (and so have negative changes in
free energy) with those that decrease entropy (and so have positive changes in free energy)
2. Energy input must exceed free energy lost to entropy to maintain order and power cellular processes
3. Energetically favorable exergonic reactions such as ATP-ADP, have a negative change in free energy
can be used to maintain or increase order in a system by being coupled with reactions that have
positive free-energy change.
b. Organisms use free energy to maintain organization, grow and reproduce
Evidence of student learning is a demonstrated understanding of each of the following:
1. Organisms use various strategies to regulate body temperature and metabolism.
To foster student understanding of this concept instructors may choose an illustrative example such as:
 Endothermy – (use of thermal energy to maintain homeostasis)
 Ectothermy – (use of external temperature to regulate and maintain temperature)
 Elevated floral temperatures in some plants
2. Reproduction and rearing of offspring requires free energy beyond that used for maintenance and
growth. Different organisms use various reproductive strategies in response to energy availability.
To foster student understanding of this concept, instructors may choose an illustrative example such as:
 Seasonal reproduction in animals and plants
 Life-history strategy (biennials, reproductive diapause)
3. There is a relationship between metabolic rate per unit body mass and the size of multicellular
organisms – generally, the smaller the organisms, the higher the metabolic rate.
4. Excess acquired free energy vs required free energy expenditure results in energy storage or growth
5. Insufficient acquired free energy vs required results in loss of mass and ultimately death
c. Changes in free energy availability can result in changes in population size
d. Changes in free energy availability can result in disruptions to an ecosystem
To foster student understanding of this concept, instructors can choose an illustrative example such as:
 Change in the producer level can affect the size and number of other trophic levels
 Change in energy resource levels such as sunlight can affect all trophic levels
Notes:
Thermodynamics
• 1st law – energy cannot be created or destroyed. energy can be transformed, but does not go away
• 2nd law – Entropy; as energy is transformed it becomes less usable. Energy becomes more random (less
useful) because heat is given off as energy is transformed. 90% is lost in living systems (10% rule)
– Entropy increases as energy is transformed. Ie. Stuff goes from order to disorder.
• ‘Free’ Energy; ‘Free’ = ‘usable’
– Organisms absorb free (usable) energy from light. They convert light energy into potential chemical
energy in chemical bonds (especially C-H); entropy of the environment increases.
– Cells/organisms maintain their organization by increasing the entropy (disorder) of the universe/Earth.
• Gibbs “Free” Energy - ΔG = ΔH – TΔS – a mathematical formula for measuring energy
• H – Enthalpy (the amount of usable energy in the system)
• T – Temperature in Kelvin (273 + C⁰)
• S - Entropy (disorder created when something is broken down)
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Two types of Energy: Potential and Kinetic Energy
• Potential energy – stored; energy is stored in C-H covalent bonds (also the energy stored by being in a
certain position)
• Kinetic – Movement; molecules move; cells move or move stuff (spindle fibers)
Chemical reactions: Two kinds:
• Exergonic – release of energy; products have less energy than the reactants – ex. fire, respiration, hydrolysis
• Endergonic – absorption (storage) of energy; products have more energy than the reactants – ex.
Photosynthesis, dehydration synthesis
– Energy coupling*** – cells combine an Exergonic reaction with an Endergonic reaction. An exergonic
reaction releases stored energy which is absorbed by the endergonic reaction.
• Ex. ADP-ATP cycle; ATP is produced by cell to produce energy for the cell. ATP*** - energy
‘currency’ of cells; the phosphate bond is easily broken/formed which is what makes it useful as an
energy source****
• Examples of work performed by cells: (list examples)
Metabolism – total of all chemical reactions of cells (organisms)
• Anabolism – reactions that build; store energy by assembling macromolecules (photosynthesis), Endergonic
• Catabolism – reactions that break down; release energy (digestion, respiration), Exergonic
Activation Energy – chemical reactions are random collisions of molecules
• Activation energy – energy that is needed to begin a chemical reaction (usually heat)
– Transition state - reactants absorb energy
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Rate of Reactions: Three factors affect rate of reaction in cells:
1. Temperature – molecules in motion, the faster they move, the faster they collide
2. Energy that is provided by the cell (in the form of ATP)
3. Enzymes – catalysts that reduce activation energy and so accelerate chemical reactions
• Most are globular proteins with specific conformational shape** and can only catalyze one
specific reaction
• Either anabolic or catabolic
• DNA controls the cell’s activities by storing the code for protein (enzymes)****
– Enzyme Structure:
• Substrate – reactant/molecule that the enzyme acts upon
• Active site – area where the substrate attaches to the enzyme
– How Enzymes Work
• Specificity – the substrate fits as a ‘Lock and Key’
• Induced fit model - enzyme changes shape when the substrate attaches to the active site
making it easier for bonds to form or break
– Factors That Affect Enzyme Activity:
• Correct environmental conditions - pH, heat, salinity (break ____ bonds)
• Presence or absence of certain chemicals determines if the reaction takes place
• Cofactors – minerals or co-enzymes (vitamins) that ‘help’ the enzyme
• Inhibitors - resemble substrate and can block active site
• Ex. Cyanide is a poison because it competes with catalase
• Inhibitors are produced by the cell to slow or stop reactions
• Allosteric enzymes – some enzymes have a place away from the active site that
controls the overall shape of the enzyme. In order to function, a cofactor first has
to bind to the allosteric site. This changes the shape of the enzyme to its
conformational (functional) shape and then the enzyme can work. An inhibitor may
bind to the allosteric site and change the shape so that it doesn’t work.
• Cooperativity – one substrate molecule can bind to an active site changing the shape so that
more can bind. Cooperativity enables it so that only it requires a small concentration of
substrate to activate enzyme. Ex. Phosphofructokinase, Hemoglobin
• Feedback Inhibition – the final product at the end of a chain of reactions blocks the first
enzyme in the chain which stops the chain of reactions. Useful to stop reactions when
enough product has been formed.
• Cells are organized – cells form Multi-enzyme complexes – a series of enzymes are
positioned in a specific location in a membrane. This forms an ‘assembly line’ making a
process go faster; Ie. Inner membrane of mitochondria, chloroplasts
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Organisms use free energy to maintain organization, grow and reproduce:
• Organisms use various strategies to regulate temperature:
• Ectothermy – use external temperature to regulate and maintain temperature (‘cold-blooded’)
• Endothermy – use their own thermal energy to maintain homeostasis (birds, mammals)
• Smaller endothermic organisms have a really high metabolic rate because they lose so much heat
energy to the air/water; this is due to the higher SA/V ratio
• Organisms use various reproductive strategies in response to energy availability.
• Seasonal reproduction in animals and plants; reproduce in spring when plants begin to grow or later
in the summer when there is less competition
• Life-history strategy (biennials, reproductive diapause).
– Biennials – take two years to grow
– Diapause – eggs and/or development stop due to adverse conditions (insects, plants)
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A change that disrupts the amount of free energy available (ie. Sunlight) in an ecosystem may have catastrophic
effects on all other trophic levels:
– If the grasses don’t grow, mouse population is reduced, coyote population is then affected, etc.
– Reduced biodiversity