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Energetics- Chapters 6 & 7 (plus some of Ch. 3,
"Biochemistry")
last updated on 09/30/2008
"Energy for Life" = Enzymes, Photosynthesis, and Cellular Respiration
Energy Transfers in Nature = the flow of energy through an ecosystem:
"All living things must change food into energy" Ch. 7
Involved the conversion of food (potential, stored chemical energy) into usable Energy
(to do work). Remember some of that chemical (carb) energy is "lost" as it is passed up
the trophic levels...do you know why?
A Marine Energy Pyramid
The study of these energy conversions involves the fusion of several branches of science: biochemistry,
organic chemistry, physics...
ENERGY
process: Cellular respiration
where: mitochondria of ALL cells
product: energy molecules (ATP)
FOOD
process: Photosynthesis
where: chloroplasts of plants and some
microorganisms
product: Glucose (simple sugar)
ATP= adenosine triphosphate
~ = high-energy phosphate bonds
see page 55
monosaccharide
disaccharide
energy is released by breaking off terminal
phosphate groups
ATP-P = ADP
polysaccharide
ADP-P= AMP
the molecule can also be re-charged
(phosphorylated) with the addition of energy
AMP+P= ADP
ADP+P=ATP
These, and all other chemical reactions in living cells (and organisms) are regulated by
ENZYMES
Read page 57 in Chapter 3 !!!
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Enzymes are globular proteins in living systems that mediate metabolic reactions
Metabolism: the series of energy exchanges and chemical reactions that occur in living
systems (cells, organisms).
catabolic activities = breakdown of larger molecules into smaller; AB==> A + B
anabolic activities = synthesis of larger molecules from smaller ones; C + D ==> CD
check it out enzyme analogy
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Enzymes act as catalysts (push, or speed up, chemical reactions)
Enzymes lower the heat (ACTIVATION ENERGY) of reactions to enable chemical bonds
to form or break more easily
(Example of AB==> A + B)

Enzymes act upon specific substrates (there are thousands of different enzymes in the
body to mediate thousands of different reactions)
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Enzymes have an active site that fits with their substrate in a "lock-and-key"
fashion = "specificity"
o sometimes, to get a good "fit", enzymes require a vitamin or mineral to fit
into the active site: COENZYME
o "Induced Fit Hypothesis" a change in the shape of an enzyme allowing
it to react more effectively with a substrate.
Enzymes mediate the reaction in the substrate but do not take part in the
reaction themselves, so enzymes can be re-used again and again
Enzymes can be DENATURED when their 3-D active site is warped by heat or
drastic pH changes (acid)
Enzymes can be temporarily inhibited (turned on/off) by certain molecules, so
reactions are controlled
Some classes of enzymes:
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Proteases
Lipases
Amylases (sucrase, lactase, etc.)
most enzyme names end in -ane
the substrate upon which they act
or
-ase suffix, and most are named after
PHOTOSYNTHESIS
(text reference: Chapter 6)
I. Introduction:
The process of making glucose from inorganic substances is called photosynthesis.
Certain types of bacteria, called cyanobacteria, contain thylakoids that carry on the
processes of photosynthesis.
1st photosynthetic organisms 3 to 3.5 billion years old probably responsible for
changing the earth's atmosphere (use CO2 and H2O to synthesize glucose and O2)
CO2 + H2O -----light--- chlorophyll----> C6H12O6 + O2
II. The Nature of Light
Isaac Newton - discovered prism divides white light into the visible light spectrum
James Maxwell - discovered light (visible) is only a small part of a larger electromagetic
spectrum
1 nm (nanometer) = 10-9 m
variation in this WAVELENGTH (
) makes different lights
all light travels at approx. 300,000 km/sec
Albert Einstein: (1905) proposed that light travels in both waves and particles "photons
" (packets of energy)
Photons for different light are inversely energetic to the wavelength ex: Violet light has
short l, but large amounts of energy in each photon.
III. How Plant Pigments Work
Pigments absorb light of certain wavelengths (reflect some wave lengths back, or
transmit other wavelengths). Different pigments absorb light energy at different
wavelengths = absorption spectrum
Pigments tend to absorb the most opposite color light (see color
wheel) http://www.cs.berkeley.edu/~sequin/CS184/IMGS/Colorwheel.GIF
In plants, chlorophyll a is directly involved in the transformation of light energy into
chemical energy
Chlorophyll is a large molecule with a central Magnesium atom held in a porphyrin ring
(like Fe in hemoglobin)
Most photosynthetic cells also contain chlorophyll b and/or carotenoids (red, orange,
yellow) => most prevalent is beta-carotene, called "accessory pigments"
The presence of the " secondary" pigments allow photosynthetic cells to capitalize on
the greatest range of

When pigments absorb light, electrons within the pigment molecules are boosted
to a higher energy level
IV. The Chloroplast
here's the way it's laid out: animation
A. The structure of the chloroplast- similar in structure to the mitochondria:
surrounded by 2 membranes that are separates by an intermembrane space
3rd layer inside: grana (stacks of thylakoids), surrounded by a dense solution:
the stroma
B. Thylakoid: the structural unit of photosynthesis is usually a form of a flattened
sac, or vesicle. These form the internal membranes of a chloroplast (can be up to
500,000 chloroplasts per square mm of leaf surface)
Excellent website to explain photosynthesis and chloroplasts CLICK HERE
V. The Stages of Photosynthesis
A. REQUIREMENTS FOR PHOTOSYNTHESIS
Photosynthesis requires carbon dioxide, water, and sunlight. The carbon dioxide
and water provide the necessary elements to make glucose, while light is the
energy source for the process.
In all photosynthetic organisms, two separate sets of chemical reactions make up
the whole photosynthetic process. The first step is called the light dependent
reaction (light reaction). The second step is called the light independent reaction
(dark reaction).
A simplified equation:
CO2 + H2O--------> C6H12O6 + O2
LEAF ANATOMY
o
o
Water is taken in through the roots and travels up the XYLEM to the
leaves
CO2 taken in through STOMATA in leaf
B. LIGHT REACTION
1. Chlorophyll and other Pigments
Light must be absorbed to be used by living organisms. Pigments absorb light.
Different pigments absorb different ë wavelengths. White pigment absorbs no
light; black pigment absorbs all light; chlorophyll, a green pigment, absorbs red,
blue and violet light. The green color is not absorbed, but is reflected back to our
eyes.
Different organisms use different pigments in photosynthesis.
a. Chlorophyll a The main pigment involved in the conversion of light energy to
chemical energy in photosynthesis; blue-green color
Accessory pigments:
b. Chlorophyll b Similar to chlorophyll a; greenish-yellow pigment
c. Carotenoids/xanthophylls: are yellow, red and orange. Beta-carotene is a
carotenoid.
The green chlorophyll in plants masks the color of the carotenoids. Thus, we can
only see the carotenoids when the leaf stops producing chlorophyll in the fall.
Carotenoids absorb light energy of different wavelengths than chlorophyll. These
pigments can pass the energy from the light to chlorophyll a.
online chromatography (pigment separation) lab
2. Thylakoids (CHLOROPLAST ANATOMY online)
Chlorophyll appears in association with sheet-like membrane structures called
thylakoids. A thylakoid is a flattened sac or vesicle that makes up part of the
organelles called chloroplasts in eukaryotic plant cells. Within the thylakoid
membrane there are approximately 200-300 chlorophyll molecules. In the
thylakoid membrane there are two types of chlorophyll molecules.
a. Light Antennas
Light Antennas gather light energy. When the light strikes the molecule, it
vibrates. Because the molecules are tightly packed together, the excitation of the
molecules spreads rapidly from molecule to molecule until it reaches the reaction
center. The reaction center releases electrons into the electron transport chain.
b. Reaction Center
When any molecule absorbs light, its electrons become excited and are boosted
to a higher energy state. In photosynthetic cells, an excited molecule will pass its
energy to an adjacent molecule. The passing of energy to the adjacent molecule
continues until the energy reaches the reaction center.
Because the chlorophyll molecules are neatly lined up the high energy electrons
pass easily from the excited reaction centers to the electron transport chains.
Electron transport chains are chains of molecules that pass electrons from
molecule to molecule. There are two types of electron transport chains in the light
reaction.
A. "Light-Dependent Reactions" (aka Energy-Capturing Rxns)need light
energy to occur
Plants trap light energy when electrons from excited chlorophyll to be boosted to
higher energy levels and passed down a series of steps (Photosystems I and II).
To see DIAGRAM click this link.
The "excited" electrons in chlorophyll ----> Water molecules are broken down.
Oxygen is given off. The two hydrogen atoms go different paths. Energy is used
to form ATP from ADP, and to reduce NADP+ to NADPH.
Occurs in the thylakoids.
B. "Light-Independent Reactions"(aka the Carbon-Fixing Rxns, or the
"dark" rxns.)are enzymatic; can take place in/out of light, but need the products
of light rxns to work
o
CO2 is taken in through STOMATA in leaf
o
o
o
Energy in the form of ATP & NADPH (from previous set of rxns) used to
reduce carbon (from CO2) into sugar molecules ("carbon fixation")
Occurs in the stroma.
Now, CO2 goes through the Calvin Cycle. The starting (and ending) compound
is a 5-C sugar with 3 phosphates attached =RuBP (Ribulose biphosphate). Click
here for DIAGRAM.
CO2 binds to RuBP ------------> RuBPCO2
which then splits into 2 molecules of PGAL (phosphoglyceraldehyde) 3-C* each
(enzyme: RuBP carboxylase, or "rubisco")
* = this is why the Calvin Cycle is sometimes called the "three carbon pathway")
6 turns of the cycle = one 6-C molecule of sugar (glucose)
overall equation:
6RuBP + 6 CO2 + 18 ATP + 12 NADPH + 12 H+ + 12 H2O
ends up as
6RuBP + glucose + 18 Pi + 18ADP + 12 NADP+ + H2O (liberated)
The PGAL can be combined to form the following products: glucose, cellulose,
maltose, starch, fatty acids,amino acids, and other molecules. RuBP is also
reformed through a series of complicated reactions.
This is not an efficient process. Less than 1% of the light energy that reaches the
chloroplast is found in thecarbohydrates produced.
C. PHOTOSYNTHETIC PHOSPHORYLATION
The phosphorylation of ADP to ATP (as the electrons are passed down ETC) is a
chemiosmotic process. The two electron transport chains contain cytochromes.
The electron carriers and the enzymes are embedded in the membrane of the
thylakoids, or chloroplasts, which is impermeable to H+ ions.
In this energy producing mechanism (chemiosmotic coupling) two events occur:
a proton gradient is established, and potential energy stored in the gradient is
released and captured in the formation of ATP from ADP and a phosphate.
There is an electrochemical gradient of potential energy established as protons
are pumped through the thylakoid membrane. They use energy released as
electrons pass down the chain. ADP is phosphorylated to ATP as protons flow
down their gradient through ATP synthetase complexes.
The H+ are pumped out of the stroma and into the thylakoid space. When the H+
flow down the gradient, they move from the thylakoid space back into the stroma
where ATP is synthesized.
The potential energy comes from a difference of pH and the difference of
electrical charge across the membrane. In fact the pH on the inside of the
thylakoid membrane is around 5, while the pH on the outside of the thylakoid
membrane is about 8. The protons flow through a channel and neutralize
negative charges on the other side of the membrane, releasing energy. The
channel is provided by a large enzyme called ATP synthetase. This complex,
composed of two factors known as Fo and. Fl, are embedded in the membrane.
ATP synthetase has sites for ADP and ATP and catalyzes the formation of ATP
from ADP and phosphate. It is not known whether it takes two, three or four H +
ions passing through the ATP synthetase complex to form an ATP molecule.
STILL CONFUSED? Check out Photosynthesis tutorials online!
Tutorials: check out some photosynthesis animations
Photosynthesis, the movie
Cellular Respiration
(text reference Chapter 7)
C6H12O6 + O2 ------------------------> CO2 + H2O+ ATP (energy)
enzymes
The breakdown of the sugar takes place through a series of chemical reactions.
This takes place in the mitochondria. Other living organisms have developed
numerous and different fermentation pathways.
Step 1:GLYCOLYSIS
Takes 6-C glucose (C6H1206 ) and breaks it down into two molecules of
pyruvate, or pyruvic acid, (a three carbon compound). This occurs in the
cytoplasm of the cell.
cool glycolysis animation
Step 2: OXIDATION: further breakdown of pyruvic acid; the energy released
and the electrons boosted can be used to phosphorylate even more ATP
Pyruvic acid can take one of 2 main pathways
I. Aerobic ( with O2)
The Oxidationof Pyruvic Acid
Breaks down pyruvic acid to CO2 + H2O + ATP (the oxidation of food
molecules within the cell)
2 stages:
1. The Krebs Cycle
Takes place in the presence of oxygen (aerobic)
2. The Electron Transport Chain
In eukaryotic cells, takes place in the MITOCHONDRIA
"cristae" - 2 inner membranes, folded to increase surface area for reactions
"matrix"- dense solution of enzymes, coenzymes, water, etc. found within the
cristae
OR...
II. Anaerobic ( without O2)-several ways...produces minimal ATP =
"FERMENTATION"
with other byproducts:
a. Pyruvate will be converted to alcohol (ethanol) and carbon dioxide. This is
called alcohol fermentation and is the basis of our wine, beer and liquor industry.
---> ethanol
example: grapes ( with yeast " blooms") crushed; sugar in grape juice is
metabolized by yeast cells without O2 until all sugar is used up (12- 17% alcohol)
="fermentation"
b. The pyruvate will be converted to lactic acid. This is called lactic acid
fermentation. Lactic acid is what makes your muscles burn during prolonged
exercise, this process is also used to make yogurt.
---> lactic acid (or one of several organic acids)
Produced by a variety of microorganisms + animal cells+ muscle fatigue (low
pH).
When O2 goes up & ATP demand is reduced, lactic acid is converted back into
pyruvic acid
FLOW CHART DIAGRAM below: