Bioenergetics
Graphing Tuesday
• Create a line graph with 2 y axes.
• These are fake numbers @ hunting in Summer
Shade!
Year
# Hunters
Year
# Deer
2000
150
2000
8,000
2001
200
2001
7,800
2002
125
2002
3,000
2003
100
2003
2,500
2004
300
2004
3,000
2005
350
2005
3,250
2006
355
2006
4,500
Stem Cell Review
• 1. What is a stem cell? _____________
________
• 2. List the 2 types of stem cell: ______
________
• 3. Which stem cell is controversial? Why?
• 4. Where do they get adult stem cells from?
Review
•
•
•
•
Potential vs. Kinetic Energy
List 4 macromolecule types
How are these made/destroyed?
Functions of Each Macromolecule.
Metabolism
• The sum of all chemical reactions occurring
in an organism.
• Catabolism- breaking down. EXERGONIC.
Releases stored potential energy/heat.
• Anabolism- building up. ENDERGONIC.
Absorbs energy/heat from environment.
• Anabolism and Catabolism are an example of
ENERGY COUPLING…2 different
processes united by common energy.
Energy (E)
• Kinetic- energy of movement, usually e- or
protons in Biology.
• Potential- energy of position, usually in the
chemical bonds of e-/p in Biology.
• Cell Respiration releases energy (KE),
Photosynthesis allows capture of E from
great E source (PE)
Potential Energy vs. Kinetic
Energy
Thermodynamics
• Study of heat and its properties.
• First Law of Thermodynamics: energy
cannot be created/destroyed just
transformed/transferred.
• Second Law of Thermodynamics: every
energy transfer increases entropy
(disorder).
• Most organized at conception, as you move
towards death you become more
organized…evolution?
Thermodynamics
LE 8-3
Sunlight is high quality E, Heat is low
quality E
Heat
Chemical
energy
First law of thermodynamics
CO2
H2O
Second law of thermodynamics
Gibbs “Free” Energy- ability to
work (make ATP/GTP)
•
Δ G = ΔH – TΔ S
• G- Gibbs “free” energy
• H – Enthalpy (Total usable energy in the system)
• T – Temperature in Kelvin (273 + C⁰)
• S- Entropy (Disorder created by something being
broken down)
• Δ – Change in a variable over time
Unstable (Capable of work)=LIVING
vs.
Stable (no work)=DEAD
G < 0
A closed hydroelectric system
G = 0
LE 8-6a
Catabolism if G is negative, e.g. cell respiration. There is free
energy to do work
Free energy
Reactants
Amount of
energy
released
(G < 0) Final-initial E
Energy
Products
Progress of the reaction
Exergonic reaction: energy released
LE 8-6b
Anabolism if G is positive, then it cannot do work, energy is bound
up (photosynthesis=endergonic)
Free energy
Products
Energy
Reactants
Progress of the reaction
Endergonic reaction: energy required
Amount of
energy
required
(G > 0)
Remember
• Not all energy can be used…
• Lots is lost to heat, some to waste
(defacation)
Types of work
performed by
living cells
Pi
P
Motor protein
Protein moved
Mechanical work: ATP phosphorylates motor proteins
Membrane
protein
ADP
+
Pi
ATP
Pi
P
Solute transported
Solute
Transport work: ATP phosphorylates transport proteins
P
NH2
Glu
+
NH3
+
Pi
Glu
Reactants: Glutamic acid
and ammonia
Product (glutamine)
made
Chemical work: ATP phosphorylates key reactants
ATP
ATP
• The 3 PO4 make it very unstable. This
instability allows it to do lots of work.
Phosphorylation
ATPADP +Pi
ADP +Pi ATP
G=-13J
G=13J
Exergonic, can do work
Endergonic, can’t do work
Phosphorus Cycle
Initially in rocks, rocks
weather, P then in soil
or inwater to be used
by producers to make
phospholipids,
DNA/RNA, proteins.
U2,D1
Data Set 1 Picture
Enzyme Review
• Protein function is caused by
structure…sequence of _ _ and how they
are _.
• All major processes in cells involve
proteins.
• Suffix of most proteins:_
• Proteins are catalysts: speed up and control
rate of reactions.
Enzyme Review
• Enzymes are not consumed in the reaction.
Benefit?
• Enzymes used to be described as “lock and
key” now they are said to be “induced fit”
or “fits like a glove”
• H bonds responsible for induced fit
Enzymes Lower EA
• Energy of Activation is the energy required
to get the molecules lined up and ready for
a reaction to take place (metabolism).
• Because the molecules are sitting in the
enzyme in position, it reduces all the time
and energy of them “naturally” coming
together.
• Enzymes also eliminate the need for heat to
move the molecules faster…we won’t
incinerate ourselves during metabolism 
.
Free energy
Course of
reaction
without
enzyme
EA
without
enzyme
EA with
enzyme
is lower
Reactants
Course of
reaction
with enzyme
G is unaffected
by enzyme
Products
Progress of the reaction
.
Substrate
Active site
Enzyme
Enzyme-substrate
complex
Enzymatic Process
• Active Site- location of chemical reactions
between enzyme and substrate.
• Enzyme Substrate Complex- caused by
induced fit. Held together by H bonds,
ionic bonds, and Van der Waals.
• The amino acid R groups perform the
reaction.
R groups of Amino Acids
.
Substrates enter active site; enzyme
changes shape so its active site
embraces the substrates (induced fit).
Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds.
Substrates
Enzyme-substrate
complex
Active
site is
available
for two new
substrate
molecules.
Enzyme
Products are
released.
Substrates are
converted into
products.
Products
Active site (and R groups of
its amino acids) can lower EA
and speed up a reaction by
• acting as a template for
substrate orientation,
• stressing the substrates
and stabilizing the
transition state,
• providing a favorable
microenvironment,
• participating directly in the
catalytic reaction.
3 Factors that Affect Enzymes
•
•
•
•
1. Temperature
2. Salinity
3.pH
*They all affect the 2*structure of proteins
by altering the H bonds.
• If a protein unwinds it is said to be __
• Type of protein that prevents misfolding_
Enzyme Inhibitors
• These will slow or stop the rate of reactions
• 1. Competitive Inhibitors- compete with
substrate for active site, bind to active site,
and SLOW reactions down.
• 2. Non-competitive Inhibitors- bind
somewhere to the enzyme, change the
active site completely, and STOP reactions.
• Inhibitors can be classified as reversible
(Antabuse) or irreversible (Sarin-nerve gas)
A substrate can
bind normally to the
active site of an
enzyme.
Substrate
Active site
.
Enzyme
Normal binding
A competitive
inhibitor mimics the
substrate, competing
for the active site.
Competitive
inhibitor
Competitive inhibition
A noncompetitive
inhibitor binds to the
enzyme away from the
active site, altering the
conformation of the
enzyme so that its
active site no longer
functions.
Noncompetitive inhibitor
Noncompetitive inhibition
Allosteric Enzymes
“Allo” different, “stery” shape
• Enzymes that will change shape, thus being
turned off or on.
• Inhibitor molecules turn the enzyme off
• Feedback Inhibition or Negative Feedback
Loop-prevents wasting energy
• Activator molecules turn the enzyme on
Feedback
Inhibition or
Negative Feedback
Initial substrate
(threonine)
Active site
available
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Enzyme 2
Active site of
enzyme 1 can’t
bind
Intermediate B
theonine
pathway off
Enzyme 3
Isoleucine
binds to
allosteric
site
Intermediate C
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)
Cooperativity
• One active site helps other active sites on
the same molecule.
• RBC-4 part molecule, each part carries O.
When Part 1 fills with O the next part does
…and RBC deliveer O in the same way.
• This is an example of cell
efficiency/specializatino, conservation of
E, and regulation.
Proteins involved
in constructing a
red blood cell
Quaternary
Structure
Polypeptide
chain
b Chains
Iron
Heme
Polypeptide chain
Collagen
a Chains
Hemoglobin
Bioenergetics
• Enzymes are needed in all efficient energy
reactions.
• Two energy reactions we will focus on:
• Photosynthesis- anabolic, endergonic, +G
• Cell Respiration-catabolic, exergonic, -G
Remember
• Electrons are a source of E
• CHOs come from H20 and CO2 by plant’s
chloroplast
• E in a molecule is directly related to # H
present.
• Autotrophs =
• Heterotrophs =
Autotroph - Plants
Autotroph - Algae
Autotroph - Phytoplankton
Autotroph - Bacteria
Heterotroph - Animal
Heterotroph - Fungus
Photosynthesis
• Chlorophyll- light absorbing protein
pigment that reflects green light. Found in
plants, algae, and blue-green bacteria.
• Chloroplast- organelle that contains grana
(thylakoids) and stroma
Chloroplast
Chloroplast Parts
• Thylakoids- contain chlorophyll. Site of
Light reaction. Purpose is to make ATP &
NADPH.
• Grana- stacks of thylakoids
• Stroma- watery area @ thylakoids. Site of
light independent (Calvin Cycle). Purpose
is to use ATP & NADPH to make glucose
using CO2
Photosynthesis chemical reaction
(Remember… conservation of matter.)
• 6 CO2 + 6 H2O  C6H12O6 + 6 O2
+ Heat
Photosynthesis
• Take radiant energy and convert into
chemical energy (ATP & NADPH)
• Take chemical energy (ATP & NADPH)
and turn it into potential chemical energy
(carbohydrate). Sugar creation is done by
catabolism.
Photosynthesis Light Reaction
Photosynthesis Calvin Cycle
Sunlight Terminology
Electromagnetic Spectrum
Absorption vs. Reflection
Sunlight
•
•
•
•
High quality E
Sunlight travels in waves.
Each color has a wavelength
Red light has the longest wavelengths
• Least energy of the white light
• Blue light has the shortest wavelengths
• Most energy of the white
• Units of light are called photons
Chloroplasts REFLECTING
Green Light
White
light
Refracting
prism
Chlorophyll
solution
Photoelectric
tube
Galvanometer
0
Slit moves to
pass light
of selected
wavelength
Green
light
100
The high transmittance
(low absorption) reading
indicates that chlorophyll
absorbs very little green
light.
Chlorophyll ABSORBING
Blue light to power
photosynthesis
White
light
Refracting
prism
Chlorophyll
solution
Photoelectric
tube
0
Slit moves to
pass light
of selected
wavelength
Blue
light
100
The low transmittance
(high absorption) reading
indicates that chlorophyll
absorbs most blue light.
Chloroplasts absorbing the blue and
the red light waves. The green is
NOT being absorbed.
Light Absorption vs. Reflection
• Absorbed light = used light (red and blue0
• Reflected light- unused light (green light)
in plants
Chlorophyll Molecule
(How many electrons are in Mg’s outer shell?)
Hint: Look at the Periodic Table.
Absorbed Light
• Light is absorbed by pigments:
• Chlorophyll A-main one
• Chlorophyll B- help A
• Carotenoids- reflects orange, red, yellow,
help A
• Photosystems- groups of pigments in the
thylakoid membrane
• Photosystem I: makes ATP & NADPH
• Photosystem II: makes ATP
Photosystem and collecting
sunlight energy.
Where are the photosystems
located?
Synthesis Question (U2, D6)
• Question: The word “photosynthesis”
means the “the process of using light to
make”. What is made in the process is the
organic macromolecule sugar
(carbohydrate). In no more than three
sentences, justify the meaning of
photosynthesis by briefly telling what colors
of light are involved in the process, what the
light is converted into, and what are those
molecules purpose. (5 Points)
•
•
•
•
•
1pt. Discussion of the red and blue colors
of white light being absorbed by plants.
1pt. Discussion of converting the light
energy into ATP and NADPH or chemical
energy molecules
1pt. Discussion of ATP and NADPH
(Chemical energy molecules) being used to
make sugar.
1pt. Correct use of scientific terms.
1pt. Answer has no more than three
sentences. (Following Directions.)
Remember
• Cells have a high SA:V ratio. Why? SA:V
ratio also high for mitochondria and
chloroplast.
• Valence electrons involved in bonding.
Light Dependent Reactions of
Photosynthesis
• * Turns radiant energy into chemical
energy __ & __.
• Takes place in the light, on thylakoid
membrane.
• Uses photosystems either in a cyclic
electron flow or a non-cyclic electron flow.
• There are 1000s of photosystems per each
thylakoid. Benefit? SA:V?
Non-cyclic electron flow
Cyclic electron flow
Photosynthesis
• 1. Sunlight strikes the Photosystem II, 2
H2O enters Photosystem II.
• 2. O2 is released from PII as waste, and
2H+, 2 E- are left.
• 3. H+ is in the stroma, and the e- move
using a carrier protein, Cytochrome C,
down the primary electron transport chain.
• 4. Light also strikes Photosystem I causing
it to lose electrons and move down another
primary electron transport chain.
• 5. e-from PI, move towards enzyme, to
NADP+ Reductase this enzyme reduces
NADP+ into NADPH.
• Redox Reactions- 2 molecules exchanging e-
• 6. Redox reactions cause e- to move down
ETC
• 7. As e- move down the ETC, they power
proton pumps (H+) with their kinetic energy.
• 8. H+ actively pumped from stroma into the
thylakoid which causes a change in pH, and
the concentration gradient is established. (air
in balloon)
• 9. This [gradient] is the potential energy that
will make ATP using the enzyme ATP
Synthetase Complex (complex=many
proteins) through anabolic phosphorylation.
(air leaving balloon)
• The quantities are mind boggling. A hectare (e.g.
a field 100 m by 100 m) of wheat can convert as
much as 10,000 kg of carbon from carbon dioxide
into the carbon of sugar in a year, giving a total
yield of 25,000 kg of sugar per year.
• There is a total of 7000 x 109 tonnes of carbon
dioxide in the atmosphere and photosynthesis
fixes 100 x 109 tonnes per year. So 15% of the
total carbon dioxide in the atmosphere moves into
photosynthetic organisms each year.
H+ (protons) being pumped into the
thylakoid to “build” potential energy.
Photosynthesis
Energy Coupling
• Using energy from the proton pump to
make energy in the form of ATP.
• Active transport sets up [gradient],
diffusion creates the ATP
• Making ATP in photosynthesis is called
chemiosmosis.
Data set 2 picture (U2,D7)
Review
Remember
• 1. Law of Conservation of Mass- Matter is
neither created or destroyed…just
transferred/ transformed.
• CHO are energy storage molecules for
quick release.
• C is the backbone of the 4 biomolecules.
• Primary source of C is CO2 from air.
Light Independent ReactionsCalvin Cycle
• Uses ATP and NADPH to perform carbon
fixation (make sugar from CO2).
• 1. CO2 enters through the stomata, CO2
diffuses through c.m. and membrane of
chloroplast into the stroma.
• 2. 3CO2 molecules will be added to RuBPa five carbon molecule.
• 3. Immediately the 6C molecule breaks into
2 3C molecules (6 3C molecules total).
Calvin Cycle step 1
• 4. Use 6 ATP & 6 NADPH to bend each
3C sugars. (6 3C sugars).
• The bent 3C sugars are then 6 molecules of
G3P.
• 5. 1G3P goes into making glucose, the
other 5 G3Ps go back into the Calvin
Cycle.
• 6. Using 3 ATP they are converted into 3
molecules of RuBP
Making Glucose
• One G3P per turn of the cycle.
• Takes 2 turns to make one glucose.
• Takes 9 ATP and 6NADPH per turn…
18 ATP and 12 NADPH per glucose.
• The glucose is used for food, and excessis
stored in starch to be used in cell
respiration or making cell walls.
Photorespiration
• Uses O2 to fix carbon instead of CO2.
• This is a last resort to stay alive, when the
stomata are closed off to prevent H20 loss.
• In C3 plants this will quickly lead to death.
• In C4 plants there is extra enzymes to grab
CO2, and photosynthesis occurs in the
inner leaf cells. These plants are adapted
for hot weather…corn, cotton, summer
flowers.
CAM Plants
• Crussulacean Acid Metabolism- utilize
CO2 stored as Crussulacean Acid because
stomata only open at night. The C. acid is
broken down in the day, and releases CO2
for Calvin Cycle.
• Desert plants, succulents, bromeliads, etc.
• CAM Plants prevent transpiration.
Transpiration
• Transpiration dictates available energy…
• Deserts have lots of transpiration
…minimal photosynthesis…minimal E.
• Rainforests have little transpiration…lots
of photosynthesis…lots of E…bigger food
webs.
Competition vs. Evolution
• Each plant type (C3, C4, CAM) have its
own niche.
• A niche prevents competition thus
conserving E.
• The more E conserved the more spent of
reproducing, thus highly populating the
area.
• Is this competition or evolution? Justify in
3 sentences.
Remember…
• Law of Conservation of Matter…
• Second Law of Thermodynamics- all E
initiates from the sun (high quality), and
ends up in entropy (low quality/disorder).
• Carbon skeletons for 4 biomolecules
Energy Flow and Matter
Cycling
Tertiary
consumers
Microorganisms
and other
detritivores
Detritus
Secondary
consumers
Primary consumers
Primary producers
Heat
Key
Chemical cycling
Energy flow
Sun
Carbon Cycle
1. All C starts in atm.
2. Photosynthesis fixes CO2 to
sugar.
3. Sugars used by consumers
in cell respiration and
release CO2.
4. Fossil fuel burning also
releases CO2 into atm.
CO2 in atmosphere
Photosynthesis
Cellular
respiration
Burning of
fossil fuels
and wood
Carbon compounds
in water
Higher-level
Primary consumers
consumers
Detritus
Decomposition
Ecosystems
• All the interacting communities is a given
area, also involves abiotic factors.
• Important Abiotic factors:
•
•
•
•
Temp.
Water
Nutrient cycling
Energy flow
Trophic Structure “troph=feed”
• These are feeding relationships.
• Second Law- with each level E is lost to
entropy.
• All E eventually lost to heat.
• Matter also flows through the trophic
levels, never created/ destroyed…think
geochemical cycles
Food Web vs. Chain
Energetic Hypothesis/ Pyramid of
Numbers
• Energetics Hypothesis- there are short food
chains because of the 10% rule.
• 90% of all energy consumed by the
organisms is lost to heat/ maintenance
before eaten by the next trophic level.
Food chains and the 10% Rule of
Energy
10% Rule
Plant material
eaten by caterpillar
200 J
67 J
Feces
100 J
33 J
Growth (new biomass)
Cellular
respiration
Primary Productivity
• Total amount of sunlight turned into
chemical energy by photosynthesis.
• Global Energy Budget- amount of sunlight
used for photosynthesis.
• Photosynthesis produces 170 billion tons of
sugar annually.
• Using only 1% of solar energy.
Productivity of the Earth
(Based on Chlorophyll Density)
Red And Yellow areas have the highest
productivity…so where are they located?
Net Primary Productivity
• Gross Primary Productivity- total E
produced
• R- E used by autotrophs
• NPP usually = 10%. It is the E available to
next trophic level.
•
NPP = GPP - R
Data Set 3 picture U2,D9