ENERGY IN BIOLOGY

3.1 Life and the Flow of Energy

Learning Outcomes:
1. Describe the different forms of energy.

1. Summarize the two laws of thermodynamics and how these laws

apply to cells.
3.1 Life and the Flow of Energy
Energy is the ability to do work or bring about a change. In order to
maintain their organization and carry out metabolic activities, cells as well as
organisms need a constant supply of energy. This energy allows living organisms
to carry on the processes of life, including growth, development, response to
stimuli, metabolism, and reproduction.
The majority of organisms get their energy from organic nutrients produced
by photosynthesizers (algae, plants, and some bacteria). Therefore, life on Earth
is ultimately dependent on solar energy.
Forms of Energy
Energy occurs in two forms: kinetic and potential. Kinetic energy is the
energy of motion, as when a ball rolls down a hill or a moose walks through
grass. Potential energy is stored energy—its capacity to accomplish work is not
being used at the moment. The food we eat has potential energy because it can
be converted into various types of kinetic energy. Food is specifically called
chemical energy because it contains energy in the chemical bonds of organic
molecules. When a moose walks, it has converted chemical energy into a type of
kinetic energy called mechanical energy.
Two Laws of Thermodynamics
Figure 6.1 illustrates the flow of energy in a terrestrial ecosystem. Through
photosynthesis, plants capture a small portion of the incoming solar energy. This is
stored in the chemical bonds of organic molecules, such as carbohydrates. When
plants use their carbohydrates (through cellular respiration), some of the energy
dissipates as heat. In an ecosystem, plants serve as the food source for other
organisms, such as moose. The cellular respiration pathways in the moose use
these carbohydrates as energy, once again releasing energy as heat. All living
organisms metabolize organic nutrient molecules, and eventually, all the captured
solar energy dissipates as heat. Therefore, energy flows through an ecosystem. It
does not recycle.
 Two laws of thermodynamics explain why energy flows in ecosystems and in
cells. The first law of thermodynamics explains the ability of organisms to convert
chemical energy to mechanical energy:

During photosynthesis, plant cells use solar energy to convert energy-poor

molecules, such as carbon dioxide and water, to energy-rich molecules, such as
carbohydrates. As we have seen, not all of the captured solar energy is used to form
carbohydrates; some becomes heat:
 Obviously, plant cells do not create the energy they use to produce
carbohydrate molecules. That energy comes from the sun. The energy from the
sun is not destroyed in the process because heat is also a form of energy.
Similarly, a moose uses the energy derived from carbohydrates to power its
muscles. And as its cells use this energy, none is destroyed, but some becomes
heat, which dissipates into the environment:
The second law of thermodynamics, therefore, applies to living systems.

The heat released during photosynthesis (from the plant) and cellular
respiration (from both the plant and moose) dissipates into the environment.
This energy is no longer usable— that is, it is not available to do work. With
transformation upon transformation, eventually all usable forms of energy
become heat that is lost to the environment. Heat that dissipates into the
environment cannot be captured and converted to one of the other forms of
energy.
 As a result of the second law of thermodynamics, no process requiring a
conversion of energy is ever 100% efficient. Much of the energy is lost in the
form of heat. In automobiles, the gasoline engine is between 20% and 30%
efficient in converting chemical energy into mechanical energy. The majority of
energy is obviously lost as heat. Cells are capable of about 40% efficiency, with
the remaining energy given off to their surroundings as heat.
Cells and Entrophy
The second law of thermodynamics can be stated another way: Every energy
transformation makes the universe less organized and more disordered. The
term entropy is used to indicate the relative amount of disorganization. Because
the processes that occur in cells are energy transformations, the second law
means that every process that occurs in cells always does so in a way that
increases the total entropy of the universe. Then, too, any one of these
processes makes less energy available to do useful work in the future.
 Above figure illustrates the second law of thermodynamics. The second law of
thermodynamics tells us that glucose tends to break apart into carbon dioxide and
water (Fig. a). Why? Because glucose is more organized, and therefore less stable,
than its breakdown products. Also, hydrogen ions on one side of a membrane tend
to move to the other side unless they are prevented from doing so (Fig. b). Why?
Because when they are distributed randomly, entropy has increased. As an analogy,
you know from experience that a neat room (Fig. c) is more organized but less stable
than a messy room, which is disorganized but more stable. How do you know a neat
room is less stable than a messy room? Consider that a neat room always tends to
become more messy.
 Cellular processes, such as the synthesis of glucose and ion transport across
a membrane, are possible because cells have the ability to obtain an input of
energy from an outside source. This energy ultimately comes from the sun. Life
depends on a constant supply of energy from the sun because the ultimate fate
of all solar energy in the biosphere is to become randomized in the universe as
heat. A living cell remains organized because it functions to maintain a constant
flow of energy.
Cell cycle
The cell cycle
Key Concepts

● The cell cycle, or cell division cycle, comprises the succession of events
that culminates in the asexual reproduction of a eukaryotic cell.
● The cell cycle is divided into two main parts: interphase and M phase.
● Interphase is subdivided into three phases: gap phase 1 (G1), synthesis
(S), and gap phase 2 (G2).
● M phase, which follows interphase, consists of mitosis (nuclear division)
and cytokinesis (cell division).
● The proteins that regulate DNA synthesis, mitotic entry, and mitotic exit
appear to be well conserved throughout eukaryotic evolution.

https://www.accessscience.com/content/cell-cycle/116150
The cell cycle ● The succession of events that culminates in the asexual reproduction
of a eukaryotic cell; also known as the cell division cycle.
● The eukaryotic parent cell doubles its volume, mass, and complement
of chromosomes, then sorts its doubled contents to opposite sides of
the cell, and finally divides in half to yield two genetically identical
offspring.
● This idea fits well with the behavior of many unicellular organisms;
however, for multicellular organisms, the daughter cells may differ from
their parent cell and from each other in terms of size, shape, and
differentiation state.

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The cell cycle ● The time required for completion of a eukaryotic cell cycle varies
enormously from cell to cell.
● Embryonic cells that do not need to grow between divisions can
complete a cell cycle in as little as 8 min, whereas cycling times of 10–
24 h are typical of the most rapidly dividing somatic cells (that is, the
cells of the body of an organism except the germ cells).
● Many somatic cells divide much less frequently: liver cells divide about
once a year, and mature neurons never divide. Such cells may be
thought of as temporarily or permanently withdrawing from the cell
cycle.

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The eukaryotic phases
● The cell cycle is divided into two main parts:
1. Interphase - During interphase, the cell grows and replicates
its chromosomes. Interphase accounts for all but an hour or
two of a 24-h cell cycle, and is subdivided into three phases:
a. gap phase 1 (G1)
b. synthesis (S)
c. and gap phase 2 (G2)
1.M phase - which consists of mitosis (nuclear division) and
cytokinesis (cell division).

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The Interphase
G1 phase
Gap phase 1 (G1) begins at the completion of mitosis and cytokinesis and
lasts until the beginning of S phase. This phase is generally the longest of
the four cell cycle phases and is quite variable in length. During this phase,
the cell chooses either to replicate its deoxyribonucleic acid (DNA) or to
exit the cell cycle and enter a quiescent state (the G0 phase). Late in G1
phase, the cell becomes committed to replicating its DNA. In mammalian
cells, the time at which this commitment occurs is called the restriction
point.

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The Interphase
S phase
Replication of the chromosomes is restricted to one specific portion of
interphase, called S phase (DNA synthesis phase), which typically lasts
about 6 h. In mammalian cells, the start of S phase (the actual initiation of
DNA synthesis) takes place several hours after the cell has committed to
carrying out DNA synthesis. During S phase, each chromosome replicates
exactly once to form a pair of physically linked sister chromatids. In
animal cells, a pair of centrioles is also duplicated during S phase.

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The Interphase
G2 phase
The portion of interphase that follows S phase is called gap
phase 2 (G2). Some cells can exit the cell cycle from G2
phase, just as they can from G1 phase.

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The Interphase
M phase
M phase includes the overlapping processes of mitosis and cytokinesis. Mitosis is
divided into five stages:

1. prophase,
2. prometaphase,
3. metaphase,
4. anaphase,
5. and telophase.

Cytokinesis usually begins during anaphase and ends at a point after the completion of
mitosis. At the end of cytokinesis, the parent cell has formed its two G1 phase progeny,
and the cell is ready to repeat the cycle.

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The control cycle
● The network of proteins that regulate DNA synthesis (G1/S), mitotic
entry (G1/M), and mitotic exit (the transition from mitotic metaphase to
anaphase and then out of mitosis) appears to be well conserved
throughout eukaryotic evolution.
● At the heart of these cell cycle transitions is the periodic activation and
inactivation of cyclin-dependent protein kinases (CDK). In addition, in
multicellular eukaryotes, pathways regulating entry into and exit from
the cell cycle entrain these central cyclin-dependent kinases to extrinsic
signals.

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The control cycle
Cell cycle entry

● In multicellular eukaryotes, most cells spend most of their time in the quiescent G0
state. In response to peptide growth factors, cells initiate a signal transduction
cascade that culminates in entry into G1 phase. Components of these mitogenic
signaling pathways include receptor tyrosine kinases [such as the epidermal growth
factor (EGF) receptor], small G-proteins (such as Ras), and signal-relaying protein
kinases (such as MAP kinase).
● Many components of these mitogenic signaling pathways are capable of causing
malignant transformation when overexpressed or inappropriately activated. The
cancer-causing forms of these proteins are termed oncoproteins, and their genes
are termed oncogenes.

https://www.accessscience.com/content/cell-cycle/116150
The control cycle
The events of the cell cycle must occur in the correct order, even if the steps take longer
than normal.

1. The red stop signs in represent three checkpoints when the cell cycle possibly
stops. Researchers have identified proteins called cyclins that increase and
decrease as the cell cycle continues. The appropriate cyclin has to be present for
the cell to proceed from the G1 stage to the S stage and from the G2 stage to the
M stage.
2. The first checkpoint during G1 allows the cell to determine whether conditions
are favorable to begin the cell cycle. The cell needs to assess whether there are
building blocks available for duplication of the DNA and if the DNA is intact. DNA
damage can stop the cell cycle at the G1 checkpoint.
The control cycle
The events of the cell cycle must occur in the correct order, even if the steps take longer
than normal.

4. In mammalian cells, the p53 protein stops the cycle at the G1 checkpoint when DNA is
damaged. First, the p53 protein attempts to initiate DNA repair, but if that is not possible,
the cell enters G0 phase and undergoes apoptosis.

5. The cell cycle stops at the G2 checkpoint if DNA has not finished replicating. This
prevents the initiation of the M stage before completion of the S stage. Also, if DNA is
damaged, stopping the cell cycle at this checkpoint allows time for the damage to be
repaired. If repair is not possible, apoptosis occurs.
The control cycle The events of the cell cycle must occur in the correct order, even if the steps take longer
than normal.

6. Another cell cycle checkpoint occurs during the mitotic (M) stage. The cycle stops if the
chromosomes are not going to be distributed accurately to the daughter cells.

● These checkpoints are critical for preventing cancer development. A damaged cell
should not complete mitosis, but instead should undergo apoptosis.
● Mammalian cells tend to enter the cell cycle only when stimulated by an external
factor. Growth factors are hormones that are received at the plasma membrane.
These signals set into motion the events that result in the cell entering the cell
cycle. For example, when blood platelets release a growth factor, skin fibroblasts
in the vicinity are stimulated to finish the cell cycle so an injury can be repaired.
The Proto-oncogenes and Tumor
Suppressor GenesTwo types of genes control the movement of a cell through the cell cycle:

1. Proto-oncogenes: encode proteins that promote the cell cycle and

prevent apoptosis. They are often likened to the gas pedal of a car
because they cause cells to continue through the cell cycle.
2. Tumor suppressor genes - encode proteins that stop the cell cycle
and promote apoptosis. They are often likened to the brakes of a car
because they inhibit cells from progressing through the cell cycle
Apoptosis
Apoptosis is the process of programmed cell death. It is
used during early development to eliminate unwanted
cells; for example, those between the fingers of a
developing hand. In adults, apoptosis is used to rid the
body of cells that have been damaged beyond repair.
Apoptosis also plays a role in preventing cancer. If
apoptosis is for some reason prevented, it can lead to
uncontrolled cell division and the subsequent
development of a tumor.
The end.
Metabolism &
Enzymes
From food webs to the life of a
cell
energy

energy

energy
 Flow of energy through
▪ Life is built on chemical reactions
life
◆ transforming energy from one form to
another organic molecules →
ATP & organic molecules
organic molecules →
sun ATP & organic
molecules

solar energy →
ATP & organic molecules
 Metabolis
m▪ Chemical reactions of life
◆ forming bonds between molecules
▪ dehydration synthesis
▪ synthesis
▪ anabolic reactions
◆ breaking bonds between molecules
▪ hydrolysis
▪ digestion
▪ catabolic reactions

That’s why
they’re called
AP Biolo y anabolic steroids!
Examples
▪ dehydration synthesis (synthesis)
enzyme

H2O

▪ hydrolysis (digestion)

enzyme +

H2O
Examples
▪ dehydration synthesis (synthesis)

enzyme

▪ hydrolysis (digestion)

enzyme
Chemical reactions &
▪ Some chemical reactions release energy
energy
◆ exergonic digesting molecules=
LESS organization=
◆ digesting polymers lower energy state
◆ hydrolysis = catabolism

▪ Some chemical reactions require

input of energy
◆ endergonic building molecules=
MORE organization=
◆ building polymers higher energy state
◆ dehydration synthesis = anabolism
Endergonic vs. exergonic reactions
exergonic endergonic
- energy released - energy invested
- digestion - synthesis

+ΔG

-ΔG

ΔG = change in free energy = ability to do work

 Energy &
▪ Organisms require energy to live
life
◆ where does that energy come from?
▪ coupling exergonic reactions (releasing energy)
with endergonic reactions (needing energy)

+ + energy
digestion

synthesis

+ + energy
 What drives
▪ If reactions are “downhill”, why don’t
reactions?
they just happen spontaneously?
◆ because covalent bonds are stable bonds
Why don’t stable
starch polymers
spontaneously
digest into their
monomers?

A
Activation
▪ Breaking down large molecules
energy
requires an initial input of
energy
◆ activation energy
◆ large biomolecules are stable

◆ must absorb energy to break bonds

cellulose CO2 + H2O + heat

energy
Too much activation energy for
▪ Activation energy
life
◆ amount of energy needed to
destabilize the bonds of a molecule
◆ moves the reaction over an “energy hill”

glucose Not a match!

That’s too much
energy to expose
living cells to!
Reducing Activation
▪ Catalysts
energy
◆ reducing the amount of energy
to start a reaction
uncatalyzed reaction Pheeew…
that takes a lot
less energy!
catalyzed reaction

NEW activation energy

reactant

product
y
 Catalysts
▪ So what’s a cell got to do to reduce
activation energy?
◆ get help! … chemical help… ENZYMES

Call in the
ENZYMES!

ΔG

ogy
Enzymes
▪ Biological catalysts
◆ proteins (& RNA)
◆ facilitate chemical reactions
▪ increase rate of reaction without being consumed
▪ reduce activation energy
▪ don’t change free energy (Δ G) released or
required
◆ required for most biological reactions
◆ highly specific
▪ thousands of different enzymes in cells
◆ control reactions
of life
 Enzymes vocabulary
substrate
▪ reactant which binds to enzyme
▪ enzyme-substrate complex: temporary association
product
▪ end result of reaction
active site
▪ enzyme’s catalytic site; substrate fits into active site

active site
substrate products

enzyme
Properties of
▪ Reaction specific
enzymes
◆ each enzyme works with a specific substrate
▪ chemical fit between active site & substrate
⬥H bonds & ionic bonds
▪ Not consumed in reaction
◆ single enzyme molecule can catalyze
thousands or more reactions per
second
▪ enzymes unaffected by the reaction
▪ Affected by cellular conditions
◆ any condition that affects protein structure
▪ temperature, pH, salinity
 Naming
▪conventions
Enzymes named for reaction they catalyze
◆ sucrase breaks down sucrose
◆ proteases break down
◆ proteins lipases break
down lipids
◆
DNA polymerase builds DNA
▪ adds nucleotides
to DNA strand
◆
pepsin breaks down
proteins
(polypeptides)
Lock and Key model
▪ Simplistic model of In biology…
enzyme action Size
doesn’t matter…
◆ substrate fits into 3-D Shape matters!
structure of enzyme’
active site
▪ H bonds between
substrate & enzyme
◆ like “key fits into lock”
Induced fit
▪ More accurate model of enzyme action
model
◆ 3-D structure of enzyme fits substrate
◆ substrate binding cause enzyme to
change shape leading to a tighter
fit
▪ “conformational change”
▪ bring chemical groups in position to catalyze
reaction
How does it
▪ Variety of mechanisms to lower
work?
activation energy & speed up reaction
◆ synthesis
▪ active site orients substrates in correct
position for reaction
⬥enzyme brings substrate closer together
◆ digestion
▪ active site binds substrate & puts stress on
bonds that must be broken, making it easier
to separate molecules
Factors that Affect Enzymes

2007-2008
Factors Affecting Enzyme
▪ Enzyme concentration
Function
▪ Substrate concentration
▪ Temperature
▪ pH
▪ Salinity
▪ Activators
▪ Inhibitors

catalase
Enzyme
concentration What’s
happening here?!

reaction rate

enzyme concentration
 Factors affecting enzyme
▪ Enzyme concentration
function
◆ as ↑ enzyme = ↑ reaction rate
▪ more enzymes = more frequently collide with
substrate
◆ reaction rate levels off
▪ substrate becomes limiting factor
▪ not all enzyme molecules can find substrate
reaction rate

APogy
enzyme concentration
Substrate
concentration What’s
happening here?!

reaction rate

substrate concentration
 Factors affecting enzyme
▪ Substrate concentration
function
◆ as ↑ substrate = ↑ reaction rate
▪ more substrate = more frequently collide with
enzyme
◆ reaction rate levels off
▪ all enzymes have active site engaged
▪ enzyme is saturated
▪ maximum rate of reaction
reaction rate

substrate concentration
Temperatur
e What’s
happening here?!

reaction rate

37°
temperature
Factors affecting enzyme function
▪ Temperature
◆ Optimum T°
▪ greatest number of molecular collisions
▪ human enzymes = 35°- 40°C
⬥body temp = 37°C
◆ Heat: increase beyond optimum T°
▪ increased energy level of molecules disrupts
bonds in enzyme & between enzyme & substrate
⬥H, ionic = weak bonds
▪ denaturation = lose 3D shape (3° structure)
◆ Cold: decrease T°
▪ molecules move slower
▪ decrease collisions between enzyme & substrate
 Enzymes and
▪ Different enzymes function in
temperature
different organisms in different
environments hot spring
human enzyme bacteria enzyme
reaction rate

37°C 70°C
temperature (158°F)
How do ectotherms do
it?
 p
H What’s
happening here?!

pepsin trypsin
reaction rate

pepsin

trypsin

01 2 3 4 5 6 7 8
9 10 11 12 13 14
pH
Factors affecting enzyme
▪ pH
function
◆ changes in pH
▪ adds or remove H+
▪ disrupts bonds, disrupts 3D shape
⬥acids
disrupts attractions between charged amino

⬥affect 2° & 3° structure

⬥denatures protein
◆ optimal pH?
▪ most human enzymes = pH 6-8
⬥depends on localized conditions
⬥pepsin (stomach) = pH 2-3
⬥trypsin (small intestines) = pH 8
0 1 2 3 4 5 6 7 8 9 10 11
Salinity
What’s
happening here?!

reaction rate

salt concentration
Factors affecting enzyme
▪ Salt concentration
function
◆ changes in salinity
▪ adds or removes cations (+) & anions (–)
▪ disrupts bonds, disrupts 3D shape
⬥acids
disrupts attractions between charged amino

⬥affect 2° & 3° structure

⬥denatures protein
◆ enzymes intolerant of extreme salinity
▪ Dead Sea is called dead for a reason!
 Compounds
▪ Activators
which help
Fe in
enzymes
cofactors
◆ hemoglobin
▪ non-protein, small inorganic
compounds & ions
⬥Mg, K, Ca, Zn, Fe, Cu
⬥bound within enzyme molecule
◆ coenzymes
▪ non-protein, organic molecules
⬥tobind temporarily or permanently
enzyme near active site

▪ many vitamins Mg in
⬥NAD (niacin; B3) chlorophyll
⬥B2)
FAD (riboflavin;

⬥Coenzyme A
Compounds which regulate
▪ Inhibitors
enzymes
◆ molecules that reduce enzyme activity
◆ competitive inhibition

◆ noncompetitive inhibition

◆ irreversible inhibition

◆ feedback inhibition
 Competitive
▪ Inhibitor & substrate “compete” for active site
Inhibitor
◆ penicillin
blocks enzyme bacteria use to build cell walls
◆ disulfiram (Antabuse)
treats chronic alcoholism
▪ blocks enzyme that
breaks down alcohol
▪ severe hangover & vomiting
5-10 minutes after drinking
▪ Overcome by increasing substrate
concentration
◆ saturate solution with substrate
so it out-competes inhibitor
for active site on enzyme
 Non-Competitive
▪Inhibitor
Inhibitor binds to site other than active site
◆ allosteric inhibitor binds to allosteric site
◆ causes enzyme to change shape
▪ conformational change
▪ active site is no longer functional binding site
⬥keeps enzyme inactive
◆ some anti-cancer drugs
inhibit enzymes involved in DNA synthesis
▪ stop DNA production
▪ stop division of more cancer cells
◆
cyanide poisoning
irreversible inhibitor of Cytochrome C,
an enzyme in cellular respiration
▪ stops production of ATP
Irreversible
▪ Inhibitor permanently binds to enzyme
inhibition
◆ competitor
▪ permanently binds to active site
◆ allosteric
▪ permanently binds to allosteric site
▪ permanently changes shape of enzyme
▪ nerve gas, sarin, many insecticides
(malathion, parathion…)
⬥cholinesterase inhibitors
■ doesn’t breakdown the neurotransmitter,
acetylcholine
Allosteric
▪ Conformational changes by regulatory
regulation
molecules
◆ inhibitors
▪ keeps enzyme in inactive form
◆ activators
▪ keeps enzyme in active form

y Conformational Allosteric regulation

Efficiency
▪ Organized groups of enzymes
◆ enzymes are embedded in membrane
and arranged sequentially
▪ Link endergonic & exergonic reactions
Whoa!
All that going on
in those little
mitochondria!

y
Feedback
▪
Inhibition
Regulation & coordination of production
◆product is used by next step in pathway
◆ final product is inhibitor of earlier step
▪ allosteric inhibitor of earlier enzyme
▪ feedback inhibition
◆ no unnecessary accumulation of product

A→B→ C→D→ E→F→G

→
→

→
→

→
enzyme
en enzyme enzyme enzyme
Xzyme
1 2
enzyme
3 4 5 6

allosteric inhibitor of enzyme 1

 threonine
Feedback
▪ inhibition
Example
◆ synthesis of amino
acid, isoleucine from
amino acid, threonine
◆ isoleucine becomes
the allosteric inhibitor
of the first step in the
pathway
▪ as product
accumulates it
collides with enzyme
more often than
substrate does
isoleucine
 Cooperativit
y▪ Substrate acts as an activator
◆ substrate causes conformational
change in enzyme
▪ induced fit
◆ favors binding of substrate at 2nd site
◆ makes enzyme more active & effective
▪ hemoglobin

Hemoglobin
▪ 4 polypeptide chains
▪ can bind 4 O2;
▪ 1st O2 binds
▪ now easier for other
3 O2 to bind