Chapter 5

Ground Rules of Metabolism

BIO 121
Instructor: Dr. Marisa Khoo
Chapter 5: Big Ideas

Cellular respiration

ATP ATP

How Enzymes Function

Energy and the Cell

Membrane transport
ENERGY AND THE CELL

Cellular respiration

ATP ATP
 Energy and the World of life
• Cells are small units, a chemical factory,
housing thousands of chemical reactions
• The result of reactions is maintenance of the cell,
manufacture of cellular parts, and replication
• Energy is the capacity to do work and cause
change
 Energy and the World of life
• Kinetic energy is the energy of motion.
• Kinetic energy performs work by transferring
motion to other matter
• For example, water moving through a turbine
generates electricity
• Heat, or thermal energy, is kinetic energy
associated with the random movement of atoms
 Energy and the World of life
• Potential energy is energy stored in the
location or structure of matter and includes
chemical energy.

• An example of potential energy is water

behind a dam
• Chemical energy is potential energy because of its
energy available for release in a chemical reaction
 First law of thermodynamics:
• Energy cannot be created or destroyed
– Total amount of energy in the universe is constant
– Energy can be converted from one form to
another.
– E.g. Chemical energy converted to kinetic energy
• ATP has potential energy
• Energy in ATP transfer to actin/myosin
(microfilaments on muscle cells) for contraction
• Some energy converted to thermal energy (heat
loss)
 Second law of thermodynamics:
• Energy transfers or
transformations increase
entropy, with some energy
being lost as heat.
– Entropy = measure of how
much energy of a system is
dispersed.
• All organisms keep on
losing energy.
• Life can maintain its
organization only because
it is being continually
resupplied with energy!
 Fuel Energy conversion Waste
products
Heat
energy

Carbon
Gasoline
dioxide
+ Combustion +
Kinetic energy
of movement

Water
Oxygen
Energy conversion in a car
Heat
energy

Cellular respiration
Carbon
Glucose dioxide
+ ATP ATP +

Oxygen Energy for cellular work Water

Energy conversion in a cell
© 2018 Pearson Education Ltd.
 Chemical reactions either release or
store energy
• An exergonic reaction is a chemical reaction
that releases energy
• This reaction releases the energy in covalent
bonds of the reactants
• Burning wood releases the energy in glucose,
producing heat, light, carbon dioxide, and water
• Cellular respiration also releases energy and heat
and produces products but is able to use the
released energy to perform work
 Reactants

Amount of
Potential energy

Energy energy released

of molecules

Products
 Chemical reactions either release or
store energy
• An endergonic reaction requires an input of
energy and yields products rich in potential
energy
• The reactants contain little energy in the
beginning, but energy is absorbed from the
surroundings and stored in covalent bonds of the
products
• Photosynthesis makes energy-rich sugar
molecules using energy in sunlight
 Products
Potential energy

Energy Amount of
energy required
of molecules

Reactants
Exergonic and Endergonic Reactions
 Energy’s one way flow
• Energy flows from the environment into living
organisms, and then back to the environment. The
flow drives a cycling of materials among producers
and consumers.
• Energy is not recycled
- In from the sun; into and out of ecosystem
• All living things harvest external energy
• Producers and consumers use energy to assemble
rearrange and dispose of substance.
• Substances cycle among organisms over time.
 One-Way
Energy
Flow ENERGY OUT
Energy continually
flows from the sun.
ENERGY IN
Sunlight energy reaches
environments on Earth.
Producers of nearly all
ecosystems secure some
and convert it to stored
forms of energy. They
and all other organisms
convert stored energy
to forms that can drive producers
cellular work. ENERGY OUT
NUTRIENT With each conversion,
CYCLING there is a one-way flow of
a bit of energy back to the
consumers environment. Nutrients
cycle between producers
and consumers.
Fig. 5.4, p. 75
Energy’s one way flow
A Energy In
Sunlight reaches environments on Earth.
Producers in those environments capture
some of its energy and convert it to other
forms that can drive cellular work.

PRODUCERS

B Some of the energy

captured by producers
ends up in the tissues
of consumers.

CONSUMERS

C Energy Out
With each energy transfer, some energy
escapes into the environment, mainly as
heat. Living things do not use heat to drive
cellular work, so energy flows through the
world of life in one direction overall.
 Energy in the molecules of life
• ATP, adenosine triphosphate, is the energy
currency of cells.
• It is composed of adenine (a nitrogenous base),
ribose (a five-carbon sugar), and three phosphate
groups.
• ATP powers nearly all forms of cellular work.
• The transfer of a phosphate group from ATP is
involved in chemical, transport, and
mechanical work.
Energy in the molecules of life

adenine

three phosphate
groups

ribose
 ATP shuttles chemical energy and
drives cellular work
• Hydrolysis of ATP releases energy by transferring its
third phosphate from ATP to some other molecule
– Bonds between phosphate groups hold a lot of energy
– When a phosphate group is transferred via the process of
phosphorylation, energy is transferred along with it. In the
process, ATP energizes molecules

Triphosphate H2O Diphosphate

Adenosine P P P Adenosine P P + P + Energy

ATP ADP Phosphate

ATP synthesis ATP ATP hydrolysis
requires energy releases energy

Energy from Energy for

cellular respiration cellular work
ADP + P
HOW ENZYMES FUNCTION
 How do enzymes work?
• Metabolism requires enzymes
• In a process called catalysis, an enzyme makes a reaction
run much faster than it would on its own
• Enzymes are catalysts
• Catalysts speed reaction rates by lowering
activation energy.
• Activation energy- Minimum energy needed to
start a reaction
• Catalysts are unchanged by the reaction
• Most are proteins
Activation energy
 Enzyme structure
• Enzymes have unique 3-dimensional shapes
• The shape is critical to their roles as biological
catalysts.
• As a result of its shape, an enzyme substrate fits
specifically in its active site.
• Active site
• Small cleft in enzyme’s surface where reactions occur
• Substrate binds to enzyme in the active site and a
reaction takes place
• Specific - recognizes specific substrates.
1 The enzyme is available
with an empty active site
Active site Substrate
(sucrose)
2 The substrate
enters the active
site, which enfolds
the substrate with
an induced fit
Enzyme
Glucose (sucrase)

Fructose
H2O

4 The products
are released
3 The substrate
is converted
to products
 How do enzymes work?
• How enzymes lower activation energy:
- By concentrating substrate molecules
- By orienting substrates to favor reaction
- By inducing fit between substrate and active site
- By excluding water from active site (Water can
interfere with reactions)
• Activation energy allows enzyme to bring substrate
to transition state  Product results
 Induced fit model
• The active site of an enzyme is more flexible and can be
changed by the substrate binding to it.
• The analogy is like a hand fitting into a glove.
• The glove adjusts in shape and size to fit various sized
hands within a certain range.
 Enzyme activity
• Environmental factors (e.g., pH, temperature,
salt) influence an enzyme’s shape and function
– Each enzyme functions best in a particular range of
conditions that reflect the environment in which it
evolved
– Eg: Most human enzyme work best at pH 6-8.
– Too much or too little salt can interfere with hydrogen
bonds that holds an enzyme in its 3D shape.
– Different salinity may change enzyme shape
 Enzyme activity
• The enzyme pepsin digests proteins in the
very acidic (pH 2) stomach environment
- Pepsin denatures above pH 5.5
- Pepsin becomes inactivated when the
stomach’s contents pass into the small intestine
(pH 9)
• The enzyme trypsin continues protein
digestion in the small intestine at the higher
pH
Enzyme activity
 Cofactors and Coenzymes
• Many enzymes require a non-protein
cofactor/coenzyme to assist them in their
reaction.
• Cofactors - inorganic molecules that help
enzymes to act e.g (metallic ions) Zn2+,
Ca2+, Mg2+
• Coenzymes: small organic molecules (e.g
vitamin) that help enzymes to act.
 Metabolic pathways
• Metabolic pathway: series of enzyme-
mediated reactions by which cells build,
remodel, or break down an organic molecule
– Linear pathway: reactions run straight from
reactant to product
– Cyclic pathway: the last step regenerates a
reactant for the first step
 Metabolic pathways
Linear pathway Cyclic pathway
reactant

enzyme 1 reactant product

enzyme 1
intermediate enzyme 3

enzyme 2 intermediate intermediate

intermediate

enzyme 3
enzyme 2
product
 Controls over metabolism
• What mechanisms help cells regulate the
production of substances?
– Regulatory molecules or ions that bind directly to
an enzyme’s active site
– Binding of an allosteric regulator (outside of the
active site) alters the shape of an enzyme in a way
that enhances or inhibits its function
– Feedback inhibition: The end product of a series
of enzymatic reactions often inhibits the activity
of one of the enzymes in the series.
Controls over metabolism-Allosteric
regulator
Controls over metabolism-Feedback
inhibition
 REDOX reaction
• The bonds of organic molecules hold a lot of
energy that can be released in a reaction with
oxygen
• To facilitate burning, cells break organic
molecules apart in small, manageable steps
– Most of these steps are oxidation–reduction
reactions (redox reactions; electron transfers)
– In a typical redox reaction, one molecule accepts
electrons (it becomes reduced) from another
molecule (which becomes oxidized)
 REDOX reaction
• Oxidation–reduction (redox) reactions
– Electron transfers used in metabolic pathways
– Oxidation  loss electrons/energy
– Reduction  gain electrons/energy
REDOX reaction
Main metabolic pathways
MEMBRANE TRANSPORT
 Diffusion and membranes
• Concentration of a substance
– Number of atoms or molecules in a given volume
• Concentration gradient of a substance
– A difference in concentration between two regions
• Diffusion: spontaneous spreading of molecules or
ions
– Essential for substances to move into, through, and
out of cells
• What affects the rate of diffusion?
– Size, temperature, concentration, charge, and
pressure
 Selective permeability
•Lipid bilayers are selectively permeable
•Water can cross, but ions and most polar molecules cannot
How substances cross membrane?
 Osmosis
• Osmosis
– The diffusion of water across a selectively permeable
membrane
– Water molecules follow their concentration gradient,
influenced by solute concentration
• If a membrane, permeable to water but not to a
solute, separates two solutions with different
concentrations of solute, water will cross the
membrane, moving down its own concentration
gradient, until the solute concentration on both
sides is equal.
Osmosis
 Tonicity
• Tonicity is a term that describes the ability of
a surrounding solution to cause a cell to gain
or lose water.
• Tonicity is dependent on the concentration of a non-
penetrating solute on both sides of the membrane
• Cells shrink in a hypertonic solution.
• Cells swell in a hypotonic solution.
• Isotonic solutions  two solutions with the
same tonicity
 Hypotonic solution Isotonic solution Hypertonic solution
(lower solute levels) (equal solute levels) (higher solute levels)
H2O
H2O H2O H2O
Animal cell

Lysed Normal Shriveled

Plasma H2O
H2O H2O membrane
Plant cell

Turgid (normal) Flaccid Shriveled (plasmolyzed)

 Turgor pressure
• Plasmolysis occurs in plants when the soil or
water around them contains high concentrations
of salts or fertilizers
• Turgor: pressure that a fluid exerts against a
structure
– Also called osmotic pressure
– When enough pressure builds up inside a plant cell,
water stops diffusing into its cytoplasm
• If the turgor inside the cells decreases, the plant
wilts
Turgor pressure
Turgor pressure
A Osmotic pressure
keeps plant
parts erect. These
cells in an iris
petal are
plump with
cytoplasm.

B Cells from a
wilted iris petal. The
cytoplasm shrank,
and the plasma
membrane moved
away from the wall.
 Transport proteins can facilitate
diffusion across membranes
• Hydrophobic substances easily diffuse across a
cell membrane.
• However, polar or charged substances do not
easily cross cell membranes.
• Instead, polar or charged substances move across
membranes with the help of specific transport
proteins, called facilitated diffusion, which
– does not require energy and
– relies on the concentration gradient.
 Transport proteins can facilitate
diffusion across membranes
• Transport proteins help specific substances
diffuse across the membrane down their
concentration gradients and thus requires no
input of energy.
• The very rapid diffusion of water into and out
of certain cells is made possible by a protein
channel called an aquaporin.
 Cells expend energy in the active
transport of a solute
• In active transport, a cell must expend energy
to move a solute against its concentration
gradient.
• The energy molecule ATP supplies the energy
for most active transport.
• The mechanism alters the shape of the
membrane protein through phosphorylation
using ATP
 Extracellular Fluid

Cytoplasm

Figure 5.28 The sodium–potassium pump.

This transport protein (gray) actively transports sodium ions (Na+) from cytoplasm to
extracellular fluid, and potassium ions (K+) in the other direction. The transfer of a phosphate
group ( P ) from ATP provides energy required for transporting the ions against their
concentration gradient.
 Requires no energy Requires energy
Passive transport Active transport
Diffusion Facilitated Osmosis Higher solute
diffusion Higher water concentration
Higher solute concentration concentration

Solute

Water
Lower solute Lower water Lower solute
concentration concentration concentration
 Membrane trafficking
• A cell uses two mechanisms for moving large
molecules across membranes
• Exocytosis is used to export bulky molecules, such
as proteins or polysaccharides
• Endocytosis is used to import substances useful to
the livelihood of the cell
• In both cases, material to be transported is
packaged within a vesicle that fuses with the
membrane
Exocytosis and endocytosis transport large
molecules across membranes
Exocytosis and endocytosis transport large
molecules across membranes
• There are two kinds of endocytosis.
1. Phagocytosis is the engulfment of a particle by
the cell wrapping cell membrane around it,
forming a vacuole.
2. Receptor-mediated endocytosis is where
receptors in a receptor-coated pit interact with a
specific protein, initiating formation of a vesicle
Phagocytosis
EXTRACELLULAR CYTOPLASM
FLUID
Pseudopodium

“Food” or
other particle
Food
vacuole

Receptor-mediated endocytosis
Coat protein
Coated
Receptor vesicle

Coated
Specific pit
molecule