Todays Plan: 2/25/16

Bellwork: Wrap-up glycolysis and do

the pyruvate processing step (15
mins)
Comparing Photosynthesis and
Respiration activity (45 mins)
Respiration notes (the rest of class)
Todays Plan: 2/26/16
Bellwork: Wrap up ETC (15 mins)
Floating Disc Lab (the rest of class)
Todays Plan: 2/29/16
Bellwork: Notes on Light Reactions
(20 mins)
White-boarding lab (40 mins)
Finish photosynthesis notes (the rest
of class)
Todays Plan: 3/9/15
Bellwork: Watch video if you havent
already and plan your variable with
your group, also design your data
chart (20 mins)
Photosynthesis leaf disc lab (45 mins)
Finish photosynthesis notes (the rest
of class)
Todays Plan: 3/10/15
Bellwork: Test your last variable (30
mins)
While youre waiting on the last
variable, look at the demo
respirometer and make sense of the
data/lab write-up
Finish photosynthesis notes (the rest
of class)
Todays Plan: 3/2/16
Bellwork: Go over tomorrow and Test
Q&A (10 mins)
Unit 3 Test (the rest of the period)
Energy
Capacity to cause change
Kinetic
Energy associated with relative motion of objects
Thermal Energy
Energy associated w/ random movement of atoms or
molecules
Potential
Energy that matter possesses b/c of location or structure
Chemical Energy
Potential energy available for release in a chemical reaction
Free Energy
Portion of system's energy that can perform work when
temp/pressure are uniform
Laws of Thermodynamics
1st Law:
Energy is constant-can be neither created
or destroyed
Can be converted from one form to another
2nd Law
Every energy transfer or transformation
increase the entropy of the universe
Entropy=disorder or randomness
Offset by biological processes that maintain or
increase order
(a) First law of (b) Second law of thermodynamics
thermodynamics
Capturing & storing free energy
Autotrophs=
Photosynthetic-capture energy from
sunlight
Chemosynthetic-capture energy from
small inorganic molecules
Heterotrophs=
Metabolize carbs, lipids & proteins
Fermentation-produces alcohol & lactic
acid (organic molecules)
Catabolic Pathways and Energy
Metabolism manages material & energy resources of
the cell
Breaks down complex molecules & puts together simple
molecules
Some molecules have potential energy because of the
arrangement of their atoms
Breaking these molecules down (catabolism) releases
this energy
Electron-transfer is responsible for much of this energy
release:Redox rxns
e- acceptor is reduced
e- donor is oxidized
Sometimes, the e- is not completely removed, but shared
differently ex: Oxygen gas to Water in cellular respiration
(Oxygen is reduced)
Figure 9-4

Electrons Electrons
pulled closer pulled farther
to C; from O;
C is reduced O is oxidized

Potential
energy increases
6 CO2 6 H2O Input of 6 O2
(carbon dioxide) (water) energy Glucose (oxygen)

Glucose has four more

CH2O groups like the
one above
Figure 9-1

ATP consists of three phosphate groups, ribose, and adenine.

Adenine

Phosphate groups

Ribose

Energy is released when ATP is hydrolyzed.

ATP Water
ADP Inorganic Energy
phosphate
NAD+
Hydrogen atoms are good candidates for e-
transfer as the energy of the electron is
reduced when transferred to other atoms,
like Oxygen
NAD+ is a coenzyme intermediate that
temporarily accepts Oxygen (step reactions
release more energy than if e- transfer
happened all at once)
As Hydrogens are stripped from glucose by
dehydrogenases (2 at a time), 2 e- and 1
p+ get transferred to NAD+ to make
NADH+H+
Later, in the e- transport chain, the
Hydrogens will be released from the
molecule
Figure 9-7

NAD+ NADH
(electron carrier)
Oxidized Reduced
Reduction

Oxidation
Nicotinamide Nicotinamide
Phosphate Phosphate
Oxidized Reduced
Ribose Ribose

Phosphate Phosphate
Adenine Adenine

Ribose Ribose
Cellular Respiration-Overview
3 steps:
Glycolysis-glucose is halved to form 2 pyruvate, which
will lose a Carbon and be attached to Coenzyme A
prior to step 2, becoming Acetyl CoA (cytoplasm)
Krebs (Citric Acid) Cycle-For each acetyl CoA, this is a
series of reactions generating 1 ATP (substrate-level
phosphorylation) and Hydrogen carriers
(mitochondrial matrix)
Electron Transport chain-Hydrogen Carriers will be
stripped of their H+ and e-, causing the synthesis of
mass quantities of ATP-oxidative phosphorylation
(inner mitochondrial membrane)
Figure 9-8
Figure 9-10

Enzyme
ATP
ADP

Phosphorylated
substrate
Glycolysis
Literally means sugar-splitting
Glucose is cleaved to form pyruvate
2 ATP are consumed in the process
(during the energy investment phase
at the onset), but 4 ATP are
generated via substrate-level
phosphorylation (during the energy
payoff phase later), yielding a net
gain of 2 ATP
Figure 9-13l

All 10 reactions of
glycolysis occur
in cytosol

GLYCOLYSIS
What goes in:

Glucose Glucose- Fructose- Fructose-

6-phosphate 6-phosphate 1,6-bisphosphate

What comes out:

Glycolysis begins with an energy-

investment phase of 2 ATP
Figure 9-13r

The 2 indicates that glucose

has been split into two 3-carbon sugars

Pyruvate

During the energy payoff phase, 4 ATP are produced for a net
gain of 2 ATP
Figure 9-16

Cristae are sacs of inner

membrane joined to the
rest of the inner membrane
by short tubes

Matrix
Cristae

Inner
membrane
Intermembrane
space
Outer membrane
The Krebs Cycle
Also called the citric acid cycle
Once Pyruvate enters the mitochondrion, its carboxyl
group is removed and is oxidized so that NADH are
formed. The remaining molecule is attached to
coenzyme A to become acetyl CoA, which enters the
Krebs cycle
The point is not so much to produce ATP (only 1 is
produced per acetyl CoA), but to strip the acetyl CoA
of electrons to reduce NAD+ and FAD so that the e-
transport chain can happen.
By the end of this, were done oxidizing glucose. The
rest of respiration is about generating ATP with our
hydrogen carriers
Figure 9-17
Figure 9-19
The two red
THE KREBS CYCLE carbons enter
the cycle via
acetyl CoA

Pyruvate
Acetyl CoA Citrate Isocitrate
In each turn of the
cycle, the two
blue carbons are
converted to CO2

All 8 reactions of the

Krebs cycle occur in the -Ketoglutarate
mitochondrial matrix,
Oxaloacetate outside the cristae

In the next cycle, this

red carbon becomes
a blue carbon Succinyl CoA
Malate

Succinate
Fumarate
Electon Transport Chain (ETC)
This is a collection of molecules
(flavoprotein, iron-sulfur protein, coenzyme
Q, and cytochromes)embedded in the inner
membrane of the mitochondria
NADH and FADH2 drop off their Hydrogens,
which pass electrons to these embedded
molecules.
H+ builds up outside of the membrane
which drives chemiosmosis as it powers the
ATP synthase rotor to generate ATP
Final e- acceptor is Oxygen
Figure 9-22

The electron transport

chain takes place in the
inner membrane and
cristae of the mitochondrion

FMN: Nucleotide with a flavin-

containing group
Fe S: Protein with an iron-
sulfur group
Cyt: Protein with a heme
group (a cytochrome)
Q: Ubiquinone
Figure 9-25b
The FO unit is the base; the F1 unit is the knob.

THE STRUCTURE OF ATP SYNTHASE

Intermembrane H + H + H + H +
H+ H+
space H+ H+ + H+
H+ + H +
H
H +
H H+
H+
H+ H+ H
+

H+ FO unit

Stalk
Mitochondrial
matrix H+

F1 unit

ADP + Pi ATP
Figure 9-24

Occurs in the inner membrane

of the mitochondrion
Anaerobic respiration
When Glycolysis occurs, the presence
or absence of oxygen determines
whether or not the Krebs cycle will
proceed.
In the absence of oxygen,
fermentation occurs in stead
Less efficient, only 2 ATP produced
Plants=alcoholic fermentation
Animals=lactic acid fermentation
Figure 9-27
Fermentation pathways allow cells to regenerate NAD+
for glycolysis.

Fermentation Intermediate accepts

by-product electrons from NADH

Lactic acid fermentation occurs in humans.

2 Pyruvate

No intermediate;
pyruvate accepts
electrons from NADH
2 Lactate

Alcohol fermentation occurs in yeast.

2 Pyruvate

2 Ethanol 2 Acetylaldehyde
Versatility of catabolism
Various other biomolecules can be
metabolized through the processes of
aerobic respiration
Proteins are broken into amino acids which
can enter any of the steps of this process
Fats are digested into glycerol and fatty
acids
Glycerol can go through glycolysis
Fatty acids go through beta oxidation where
theyre broken into 2-carbon sequences and can
enter the Krebs cycle as Acetyl CoA
Figure 9-29
Anabolic Processes
Some of the intermediate molecules
from aerobic respiration are used
directly
Amino acids are also synthesized by
siphoning molecules away from the
Krebs Cycle
Some AAs, however, are essential,
meaning that the body cant make them
and needs them from food
Figure 9-30

Pathway for synthesis Fats Phospholipids

of RNA, DNA

Fatty acids

Glycogen Several intermediates

Glucose Pyruvate Acetyl CoA KREBS used as substrates in
or starch CYCLE
GLYCOLYSIS amino acid synthesis

Lactate
(from fermentation)
Feedback Regulation
When ATP drops, the cell works hard to
catabolize fats and carbohydrates to re-
supply the cell with ATP
Respiration and heart rate increase to supply
more oxygen
One enzyme in glycolysis,
Phosphofructokinase, is inhibited by ATP
and stimulated by AMP, so as ATP
accumulates, respiration slows
Its also sensitive to citrate from the Krebs cycle,
which allows the rates of glycolysis and the
Krebs cycle to synchronize
Figure 9-20

These steps are

also regulated via
feedback inhibition,
This step by ATP and NADH
is regulated Citrate
by ATP

Acetyl CoA
Oxaloacetate
Photosynthesis
The process where autotrophs convert light
energy from the sun to chemical energy (in
carbohydrates) for the heterotrophs in the
food chain
Is another redox process, like respiration,
and is responsible for carbon fixation
Done exclusively in the chloroplast
Thylakoids-membrane discs that are stacked in
grana (site of the 1st stage of photosynthesis)
Stroma-fluid that surrounds thylakoids (site of
the 2nd stage of photosynthesis)
Figure 10-2

Leaves contain millions of chloroplasts.

Cell

Chloroplasts

Chloroplasts are highly structured, membrane-rich organelles.

Outer membrane

Inner membrane

Thylakoids

Granum

Stroma
The stages of Photosynthesis
Light (dependent) Reactions (On the
Thylakoid membrane)
Is an electron tranport chain that harnesses light
energy into ATP and Hydrogen carriers
Involves photolysis of water and exciting
chlorophyll molecules
Calvin Cycle (In the stroma)
Also called the Dark reactions or Light-
Independent Reactions
This is where carbon fixation occurs and the
sugars are built
About Light and Pigments
Light occurs in waves along an electromagnetic
spectrum
Wavelength is the distance between crests of the
wave
Visible light spectrum lies between 380 and 750 nm
and is responsible for color
Light can be absorbed, reflected, or transmitted
Pigments absorb light for photosynthesis, but absorb
best at different wavelengths, which broadens the
spectrum for ps.
Chlorophyll a-primary pigment for photosynthesis
(blue green)
Chlorophyll b-accessory pigment (olive green)
Carotenoids-accessory pigment (yellow and orange)
Figure 10-4
Wavelengths (nm)

Gamma Ultra- Micro- Radio

rays X-rays Infrared waves waves
violet

Shorter Longer
wavelength wavelength
Visible light
nm

Higher Lower
energy energy
Figure 10-6a

Different pigments absorb different wavelengths of light.

Chlorophyll b Chlorophylls absorb blue and red

light and transmit green light
Chlorophyll a
Carotenoids absorb blue
Carotenoids and green light and
transmit yellow, orange,
or red light
The Light Reactions
Begins with the excitement of Chlorophyll by photons of light
An electron gets raised from ground to excited state
Sometimes, with pigments, the e- drops back to ground and releases heat or light
(fluorescence)
Photosystem II
A protein complex (reaction center complex) that is surrounded light harvesting
complexes consisting of pigment molecules
As photons are absorbed in the light harvesting complex, the energy is transferred
from pigment to pigment until it reaches a pair of chlorophyll a molecules (P680)
within the reaction center complex
These pigments pass the excited electron to the primary e- acceptor
Photolysis occurs, splitting water to give off Oxygen gas, Hydrogen Ions, and
e-s
The e-s are given to the P680+ pair
The buildup of H+ will eventually drive the synthesis of ATP, just as they did in the
ETC of respiration
The e-s pass through the P680 pair, to the e- acceptor, and then to an ETC to
Photosystem I
Photosystem I
Contains a pair of chlorophyll a called P700 that excite the e- and sends it through
another ETC
At the end of that ETC, NADP+ accepts the electrons to become NADPH
The ATP and NADPH formed here power the Calvin Cycle
Figure 10-11

FLUORESCENCE or RESONANCE or REDUCTION/OXIDATION

Electron drops back down to Energy in electron is transferred to nearby pigment. Electron is transferred to
lower energy level; heat and a new compound.
fluorescence are emitted.
Higher Electron
acceptor
Reaction
center
Energy of electron

Photon

Photon Fluorescence
e
Heat

e e

Lower Chlorophyll molecule Chlorophyll molecules in antenna complex Reaction center

Figure 10-15

4e ETC

Higher 2 NADP+ + 2 H+

Pheophytin ETC
Ferredoxin
4e
PQ
Energy of electron

Cytochrome 4 Photons 2 NADPH

complex

4 Photons PC
ATP
produced via P700
proton-motive force Photosystem I
P680
Photosystem II

Lower 4e
2 H2O 4 H+ + O2
Cyclic Electron Flow
This is an alternate path for the light
reactions to take (in photsynthetic
bacteria that dont have Photosystem
II)
In this path, Photosystem I is used,
but not Photosystem II
Figure 10-16

Higher
Ferredoxin
Energy of electron

PQ Photon
Cytochrome
complex

PC

ATP P700
produced via
proton-motive
force
Lower Photosystem I
The Calvin Cycle
The ATP and NADPH generated by the Light Reactions
are used here in the stroma
Occurs in 3 Phases
Carbon Fixation-Carbon Dioxide is added to RuBP
(Ribulose Bisphosphate), a 5-carbon sugar. This is
catalyzed by RuBP carboxylase
Reduction-Phosphates from ATP are attached to the
molecule from step 1 and electrons from NADPH are
donated, reducing the molecule to glyceraldehyde-3-
phosphate (G3P, PGAL), the sugar that will eventually
be converted to glucose (think of it as of a glucose
molecule)
Regeneration of RuBP-the remaining carbon
backbones are rearranged and phosphorylated by
ATP to form RuBP. This will allow the cycle to start
over again
Figure 10-19

The Calvin cycle has three phases. The reaction occurs in a

cycle.
Carbons are symbolized as
3 CO2 red balls to help you follow
them through the cycle

3 P P 6 P
RuBP Fixation of 3-phosphoglycerate
carbon dioxide
3 ADP + 3 Pi
All three phases of the 6 ATP
Calvin cycle take place in
the stroma of chloroplasts 3 ATP 6 ADP + 6 Pi
Regeneration of Reduction of
Fixation: 3 RuBP + 3 CO2 6 3-phosphoglycerate RuBP from G3P 3-phospho-
glycerate
Reduction: 6 3-phosphoglycerate + 6 ATP + 6 NADPH 6 G3P to G3P
6 NADPH
Regeneration: 5 G3P + 3 ATP 3 RuBP 6 NADP+ + 6 H+
6 P
5 G3P G3P

1 G3P
Alternative Mechanisms of Carbon
Fixation
Evolved in plants living in hot, arid environments to help plants
conserve water
Most plants are C3 plants, b/c RuBP breaks into 3 Carbons
On hot days, the Stomates are closed to prevent water loss, but this
means less Carbon Dioxide and less Photosynthesis
In that instance, plants switch to photorespiration, which fixes Oxygen
in place of CO2. This, however, is counterproductive as it consumes ATP
A different mechanism is needed for plants that constantly live in hot
environments
C4 Plants
These plants have bundle-sheath cells surrounding their veins
Calvin cycle only occurs in the bundle-sheath cells, but Carbon-fixation
occurs in the mesophyll cells, creating 4C compounds (by PEP
Carboxylase) that are fed to the bundle sheath cells and the Calvin
Cycle through the plasmodesmata
Bundle sheath cells release CO2 back to the mesophyll cells
CAM Plants
Exists in water-storning plants (succulents)
Plants open stomates at night and close them during the day (opposite
of other plants)
Carbon dioxide collected at night are stored as organic acids in a
process called crassulacean acid metabolism (CAM)
Figure 10-21
Leaf surfaces contain stomata.

Leaf surface

Guard cells Pore Stoma

Carbon dioxide diffuses into leaves through stomata.

Interior of leaf

O2
H2 O

Leaf surface

Photosynthetic Extracellular CO2 Stoma

cells space
Figure 10-23
C4 plant Leaf surface
Mesophyll cells contains
PEP carboxylase

Bundle-sheath cells
contain rubisco

Vascular tissue

CO2
Mesophyll
cells

C4 C4 compound
PEP cycle

C3
Bundle-sheath
compound CO2 cells

Calvin 3PG
RuBP cycle

Vascular
Sugar tissue
Figure 10-24
C4 plants CAM plants

CO2 stored in one cell CO2 stored at night

CO2 CO2

C4 C4
cycle cycle
Organic Organic
acid acid

CO2 CO2

Calvin Calvin
cycle cycle

G3P G3P
and used in another. and used during the day.