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Metabolism
Metabolism: all of the chemical reactions in an
organism
Metabolic pathways: series of chemical reactions
that either build complex molecules or break down
complex molecules

Substrate Intermediate Intermediate Product

Enzyme 1 Enzyme 2 Enzyme 3

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 Metabolic Pathways
There are two types of metabolic pathways

Catabolic Pathways Anabolic Pathways

Pathways that Pathways that
release energy by consume energy to
breaking down build complicated
complex molecules molecules from
into simpler simpler compounds
compounds

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Metabolic Pathways

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 Energy
● Energy: the ability to do work
● Organisms need energy to survive and function
○ A loss in energy flow results in death

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 Energy
● Kinetic energy: energy associated with motion
○ Thermal energy: energy associated with the
movement of atoms or molecules
● Potential energy: stored energy
○ Chemical energy: potential energy available for
release in a chemical reaction

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 Laws of Thermodynamics
The study of energy transformations in matter is
called thermodynamics
● The laws apply to the universe as a whole

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 Laws of Thermodynamics
1st Law:
● Energy cannot be created or destroyed
● Energy can be transferred or transformed

The chemical
(potential) energy
stored in the nut
will be transformed
into kinetic energy
for the squirrel to
climb the tree
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 Laws of Thermodynamics
2nd law:
● Energy transformation increases the entropy
(disorder) of the universe
● During energy transfers or transformations, some
energy is unusable and often lost as heat
As the squirrel
climbs the tree
some energy is
released as heat

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 Misconception Check
Cells create organized structures by taking in less
organized starting materials (ie make proteins from
amino acids). If this is true, how do cells not violate
the 2nd law of thermodynamics?
Answer: after the squirrel
ate the nut, catabolic
reactions turned complex
molecules into simpler ones.
As the squirrel climbs it is
also releasing CO2 and H2O
which increases entropy
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 Misconception Check
In comparison to early life on Earth, organisms today
are highly organized and complex. How does this
increase in organization over time not violate the 2nd
law of thermodynamics?

Answer: the entropy of

organisms may decrease,
as long as the total
entropy of the universe
increases

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 Free Energy
Since the laws of thermodynamics apply to the
universe as a whole, scientists use a concept called
free energy to determine the likelihood of reactions
in organisms, or if the reactions are energetically
favorable
ΔG = ΔH - TΔS

ΔS: change in
ΔG: change in ΔH: change in entropy
free energy total energy
T: absolute
temp (K)
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 Free Energy
The free energy change of reactions determine
whether or not the reaction occurs spontaneously

Based on free energy changes,

chemical reactions can be classified No outside
as exergonic or endergonic input of
energy is
required

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 Free Energy
ΔG＜0
Exergonic reactions:
Reaction is spontaneous
reactions that
release energy
● I.e. Cellular
respiration (-686
kcal/mol)

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 Free Energy
ΔG＞0
Endergonic reactions: Reaction is not spontaneous
reactions that absorb Absorbs free energy
energy
● I.e. Photosynthesis
● (+686 kcal/mol)

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 Cells and Energy
● Living cells have a constant flow of materials in and
out of the membrane
○ Cells are not at equilibrium (if so they would be
dead)
● Cell’s perform three kinds of work
○ Mechanical: movement (i.e. beating cilia, movement
of chromosomes, contraction of muscle cells)
○ Transport: pumping substances across membranes
against spontaneous movement
○ Chemical: synthesis of molecules (ie building
polymers from monomers)
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 ATP
Adenosine triphosphate: molecule that organisms
use as a source of energy to perform work

Structure:

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 ATP
● ATP couples exergonic reactions to endergonic
reactions to power cellular work
○ Exergonic process drives the endergonic process
● Organisms obtain energy by breaking the bond
between the 2nd and 3rd phosphate in a
hydrolysis reaction
○ ATP → ADP
● Phosphorylation: the released phosphate moves
to another molecule to give energy

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Hydrolysis of ATP

energy

Comes from the lowering of free

energy NOT from the bond itself
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 Regeneration of ATP
● ADP can be regenerated to ATP via the ATP cycle
(p.153 in book, Fig. 8.12)

ATP + H2O

Energy Energy
from for
exergonic ADP + Pi cellular
process work

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Rate of Metabolic Reactions
The laws of thermodynamics tell us if a reaction is
spontaneous, but it does not describe the rate of the
reaction
● Some spontaneous reactions move so slowly that
it would be impossible for cells to utilize them
efficiently
○ The hydrolysis of sucrose to glucose would take
nearly 1000 years to happen spontaneously!
Think Pair Share
If it takes nearly 1000 years for the
hydrolysis of sucrose, then how is it Enzymes
possible that cells do this each day
without waiting 1000 years?
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 Enzymes
Enzymes: macromolecules that
catalyze (speed up) reactions by
lowering the activation energy
● Are not consumed by the
reaction
● Type of protein
● Enzyme names end in -ase

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 Enzyme Structure
The enzyme acts on a reactant called a substrate

Active site: area for substrate to bind

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 Enzyme Function
Substrates are held in active
Substrates
Active site site by weak interactions
open

Enzyme-substrate complex

Products released
Substrates converted to
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 Induced Fit
Induced fit: enzymes will change the shape of their
active site to allow the substrate to bind better

Enzyme-substrate complex
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 Enzyme Catabolism

Enzyme helps break down complex molecules

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 Enzyme Anabolism

Enzyme helps build complex molecules

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 Effects on Enzymes
Enzymes are proteins, which means their 3D shape
can be affected by different factors.
● The efficiency of enzymes can be affected by:
○ Temperature
○ pH
○ Chemicals

Remember:
A change in shape means a change in function

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 Effects on Enzymes
Optimal conditions: the conditions (temperature and pH)
that allow enzymes to function optimally (at their best)

● The rate of enzyme activity increases with

temperature (due to collision) up to a certain point
○ After a certain point, the enzyme will denature
● Enzymes function best at a specific pH
○ Being outside the normal pH range can cause
hydrogen bonds in the enzyme to break,
changing the shape of the enzyme

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 Optimal Temperature
Optimal Temp

Enzyme 1
Rate of reaction

Enzyme 2
Enzyme 3

0 20 40 60 80 100
Temperature (°C)
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 Enzyme cofactors
“non protein helpers”
● Cofactors: non protein molecules that assist
enzyme function (catalytic activity)
○ Inorganic cofactors consist of metals
○ Can be bound loosely or tightly
○ Holoenzyme: an enzyme with the cofactor
attached
● Coenzymes: Organic cofactors
○ Ex: vitamins- important in nutrition because they
act as coenzymes or raw materials from which
coenzymes are made.
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 Enzyme Inhibitors
● Enzyme inhibitors: reduce the activity of specific
enzymes
○ Inhibition can be permanent or reversible
■ Permanent: inhibitor binds with covalent bonds
● Example: toxins and poisons
■ Reversible: inhibitor binds with weak
interactions

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 Enzyme Inhibitors
Competitive inhibitors: reduce enzyme activity by
blocking substrates from binding to the active site
● Inhibition can be reversed with increased substrate
concentrations

Substrate
Competitive inhibitor
Active site

Enzyme Enzyme

Normal substrate binding Competitive Inhibition

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 Enzyme Inhibitors
Noncompetitive inhibitors: bind to an area other than the
active site (allosteric site), which changes the shape of
the active site preventing substrates from binding
● Type of allosteric inhibition

Substrate

Active site

Enzyme Enzyme
Noncompetitive
inhibitor
Normal substrate binding Noncompetitive Inhibition
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Regulation of Chemical Reactions
● A cell must be able to regulate its metabolic
pathways
● How?
○ Control where and when enzymes are active
○ Switch genes that code for enzymes on or off

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 Allosteric Regulation
● Allosteric enzymes have two binding sites
○ 1 active site
○ 1 allosteric site (regulatory site, site other than the
active site)

Active site

Active site
Allosteric site

Allosteric site

Enzyme © Getting Down With Science

Multi-subunit enzyme
 Allosteric Regulation
● Allosteric regulation: molecules bind (noncovalent
interactions) to an allosteric site which changes
the shape and function of the active site
○ May result in inhibition (by an inhibitor) or
stimulation (by an activator) of the enzymes
activity

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 Allosteric Regulation: Activator
● Allosteric activator: substrate binds to allosteric
site and stabilizes the shape of the enzyme so
that the active sites remain open
Active site

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 Allosteric Regulation: Inhibitor
● Allosteric inhibitor: substrate binds to allosteric
site and stabilizes the enzyme shape so that the
active sites are closed (inactive form)
Active site

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Allosteric Regulation: Cooperativity
● Cooperativity: substrate binds to one active site
(on an enzyme with more than one active site)
which stabilizes the active form
○ Considered allosteric regulation since binding at
one site changes the shape of other sites

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 Feedback Inhibition
Sometimes, the end product of a metabolic pathway
can act as an inhibitor to an early enzyme in the
same pathway
Intermediate
Product
Enzyme 1 Enzyme 2
Active site
inactive

Substrate
Pathway continues once the Product binds to allosteric
product is used up by the cell site on Enzyme 1
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 Practice FRQ
The common cold is a viral infection that affects the
upper respiratory tract. Symptoms include a cough,
runny nose, and fever. a) Identify what happens to
the body when it has a fever. b) Explain why having
a fever is beneficial in fighting off the virus. c)
Explain why having a long-term fever (3+ days) can
be dangerous to the human body.

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 Practice FRQ
The human body needs vitamins to function
properly. For example, a deficiency in vitamin B 12
leads to muscle weakness and fatigue because the
body is unable to produce red blood cells. a)
Explain how vitamins function in the body and why
they are necessary.

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