Photon: Packet of sunlight. Has both particle and wave properties.
Pigments: Any substance that absorbs light.
Solar radiation has a variety of wavelengths: Visible light fuels photosynthesis
• T.E. Engelmann’s Experiment:
Hypothesis: If light can be separated spatially into component wavelengths,
oxygen concentration would be highest where the wavelengths involved in
photosynthesis are present.
• Pigments have colour but the colour you see is the reflected wavelength not the
• Photosynthesis depends on the wavelengths the photons absorbed by special light
capturing molecules (pigments), not the reflected. Absorption begins energy transfer
• Lightcatching part of pigment molecule alternates between single and double bonds.
These bonds have electrons that can be excited and moved to another (higher) energy
level when they absorb light.
Electron excitation is first step to photosynthesis.
• Variety of photosynthetic pigments that absorb different wavelengths
Colour of pigment is the wavelength that is reflected back that you can see.
Black pigments absorb all kinds of wavelengths
White and lighter pigments are really picky. They reflect almost all back.
Photosynthetic pigments have their own characteristic absorption spectra.
Ex. Chlorophyll (Green pigment) absorbs all wavelengths except green
Chlorophylls: Main pigments that absorb light from two nongreen regions.
Accessory pigments: Trap photons in other wavelengths and transfer the energy to main
Photosystem function: Accessory pigments
Most pigments in photosystem are accessory or harvester pigments.
When excited they transfer energy to adjacent pigment molecules
Each transfer uses energy (But energy also available for photosynthesis)
Photosystem: Reaction Center_
Energy is reduced to level that can be captured by molecule of chlorophyll a.
This Chlorophyll molecule is reaction center of a ‘photosystem’: Collection of pigments
Reaction center accepts energy and transfers to nonpigment molecule in ETC. Two stages of photosynthesis: Light vs. Dark reactions
Pigments in chloroplast membranes absorb light energy and give up electrons that enter
ETC to produce ATP and NADPH.
Pigments that give up electrons get replaced electrons from split water molecule and O is 2
released as waste product.
ETC: Electron transport chain: Adjacent to pigment system and is embedded in membrane.
Acceptor molecule in chain transfers electron from pigment reaction center to next
molecule in chain.
As electrons pass energy that is released is used to make ATP.
Arrangement of chlorophyll and other pigments packed into thylakoid.
Eukaryotic plants have two photosystems: I and II.
I: Uses chlorophyll a, in form P700.
II: Uses different form of chlorophyll a, as P680. Second to be discovered.
Difference between I and II?
PS I produces reducing power (H+) which is added to carbon dioxide in dark cycle
to make glucose
PSII produces ATP, O an2 electrons used to replenish electrons lost from
Light independent: Dark Reactions
Synthesizes organic carbon
Can proceed in the dark using ATP and NADPH from light reactions.
Takes place in stoma (nonmembrane part of chloroplast)
Called ‘CalvinBenson’ Cycle
Cyclic reaction pathway
Produce: Glucose + ADP + NADP+
Summary: Photons > Pigments > Electrons > ATP/NADPH > Sugars
Gases diffuse through small pores in leaves called stomata. Leaves loose too much water when
stomata are open, problem for plants in hot areas.
Two types of dark cycles evolved for this: C3 and C4 (For desert plants since more
efficient at water conservation).
C3: Called this because CO2 first incorporated into 3carbon compound. Occurs everywhere in
leaf. More efficient under cool and moist conditions and normal light, requires less machinery.
C4: CO2 first incorporated into 4carbon compound. Takes place in inner cell. Better for dry
places. Faster. Stomata not open as much.
All respiration (in organisms) begins with glycolysis, which proceeds without oxygen in cell
cytoplasm. Not an efficient ATP producer though.
In absence of oxygen, fermentation begins (anaerobic) and occurs in cytoplasm. Not efficient ATP
maker as well.
When oxygen is present, Krebs cycle + ETC activated. ETC occurs in membrane of
mitochondrion. Very efficient ATP producer.
Starts with glycolysis in cytoplasm
Completed in cell mitochondria
Step 1: Glycolysis: Splits 1 molecule of glucose into 2 pyruvates: Generates 2 ATP and 2 NADPH
(for transfer of H+ and e) in the process.
Step 2: Krebs cycle: Generates 2 ATP and lots of reducing power (H+ and e) as NADH and
FADH , 2O is 2 ste product.
Step 3: ETC: Uses reducing power producing 32 ATP. Electrons and H+ are transferred to oxygen
to produce water.
TOTAL ATP: 36 molecules. (2 in gly., 2 in Krebs, 32 in ETC)
Role of Coenzymes:
NAD+ and FAD accept electrons and hydrogen and are converted to NADH and
FADH i2 first 2 steps
They deliver electrons and hydrogen icons ‘stripped’ from glucose to the ETC
which produces ATP
Glycolysis: 2 stages
1) Energy requiring steps
Energy from 2 ATP activates glucose and its sixcarbon derivatives
2) Energyreleasing steps
Products of first part are split into 3C pyruvates
4 ATP and 2 NADH form
2 Net produced ATP (2 in, 4 out net)
Glycolysis: Multiple steps
First and second stages of glycolysis actually involve 9 steps (glucose > 2 Pyruvate)
These steps basically rearrange the C and P atoms in sequence. Each step requires specific
Second stage Reactions: Aerobic Respiration: (LEO THE LION SAYS GER)
1) Preparatory reaction begins with pyruvate
3 carbon pyruvate is converted to 2C ‘acetyl unit’ and one CO . 2 +
NAD is reduced to NADH (this is production of reducing power)
2) Krebs Cycle
Acetyl units are oxidized to CO 2
NAD and FAD are reduced to NADH and FADH
Overall reactants per pyruvate molecule: Overall Products per pyruvate molecule:
1 AcetylCoA 1 Coenzyme A
3 NAD + 2 CO2
1 FAD 3 NADH
1 ADP and 1 P i 1 FADH 2
Results of stage 2:
All carbon molecules end up as CO 2
Coenzymes (FAD, NAD ) are reduced (they pick up electrons and hydrogen to shuttle to
One molecule of ATP forms per pyruvate
4 – C oxaloacetate regenerates to acetylcoenzyme A for reuse in next cycle.
MAIN FUNCTION OF STAGES (ABOVE): TO PRODUCE REDUCING POWER (i.e. electrons
and Hydrogen for ETC chain).
Electron transport chain and phosphorylation: Stage 3
• Occurs in mitochondrial membrane.
• Coenzymes NADH and FADH deliver e2ectrons to ETC
• Electron transfer sets up H+ ion gradient across mitochondrial membrane (gradient
is temporary form of stored energy, like water behind a dam for electricity).
• Flow of H+ down the gradient powers ATP formation from ADP and P i
• Main function to produce ATP
Chemiosmotic model of Energy storage: ETC’s H ion gradient across mitochondrial membrane
creates temporary energy storage.
The H ion gradient powers ATP production.
Importance of oxygen:
• Electron transport ‘phosphorylation’ (i.e. creation of ATP from ADP and P by the i
ETC) requires presence of oxygen at the end of transfer chain to accept the electron.
• Oxygen takes spent electrons from ETC and combines with H to form water.
Electrons cannot accumulate in cell, that’s why electron acceptor (O ) is 2ssential to
• No oxygen
• Produce less ATP than aerobic pathways
• Two types: o Fermentation (2 kinds)
o Anaerobic electron transport
Used by: Single celled organisms, bacteria and yeast. Multicellular organisms are obligate
anaerobes (cannot survive without O )2
• Begins with glycolysis
• Does not break glucose down completely (to CO an2 H O) 2
• Yields only 2 ATP and some reducing power
• Steps that follow glycolysis are only there to regenerate NAD+ for reuse in
2 kinds of fermentation:
1) Lactate: Fermenters produce lactate (lactic acid) from pyruvate.
2) Alcoholic: Fermenters produce ethanol. Used to make beer, wine and what not.
Why does lactic acid build up in muscles?
As oxygen is limited (when working out we try to breath faster) body temporarily
switches to anaerobic, converting pyruvate into lactate. Working muscle cells can continue
anaerobic energy production at high rates in short time.
• Similar to oxygen based system but does not use oxygen
• Carried by certain bacteria
• ETC is in the bacterial plasma (outer) membrane.
• Final electron acceptors are inorganic (nitrate and sulfate) not2O
• ATP yield is much lower than from oxygen, slightly higher than fermentation
Cells: Cell structure and Function • Cell is a smallest unit having properties of life such as selforganization and self
• Life exists because cells divide and grow.
• Cell can survive on its on
• Highly organized for metabolism
• Senses and responds to environment
• Has potential to reproduce
Why so small?
> As size increases it takes more time to get external compounds into and around the cell.
Also distance from membrane to cell center grows.
> To overcome this cardiovascular systems have been dedicated as transport systems
Two types of cells:
1) Prokaryotic (Evolved first):
Have no internal membranebound organelles
2) Eukaryotic (Evolved from prokaryotes)
Has membranebound organelles and specialized organelles for specialized
Both cells have plasma (outer) membrane, region where DNA is stored and cytoplasm (cellular
• DNA is not in membranebound nucleus
• Smallest and simplest
• No membranebound organelles, no internal membrane
• First to evolve
• 2 groups:
o Archaebacteria (live in extreme habitats)
o Eubacteria (more common and widespread)
Both differ from each other in metabolic abilities, composition of membranes and
structure of ribosomes.
• Prokaryotic structure:
o Pilus: Hair like structure on surface, helps grip and used to exchange genetic
o Flagellum: Whip like appendage used for locomotion
o Cytoplasm: Cellular substance outside nucleus
o Plasma membrane: outer membrane of cell
o Cell wall: Outer layer of bacteria exposed to outside environment
o DNA: Genetic information
• Nucleoid – Central region in bacteria where DNA is concentrated but its not a true
nucleus. Imaginary structure, no physical boundary enclosing it.
Eukaryotic Cells: • Have complex internal structure. Have nucleus and organelles and a cytoskeleton.
• Evolved from simpler prokaryotic cells (e.g. bacteria)
Cell wall, central vacuole and chloroplast are only found in plant cells not animal cells.
• Function of nucleus: Keeps DNA protected and separated from metabolic
o To also isolate DNA related functions into a smaller chamber for better control and
• DNA is organized into distinctive chromosomes (while prokaryotic cells contain
only 1 circular DNA molecule and a bunch of different circlets of DNA called plasmids)
• Eukaryotic DNA Has complex proteins called histones
• Eukaryotic nucleus:
o Chromatin: Complex of nucleic acids and proteins, primarily histones that
condenses to form chromosomes during division
o Nuclear envelope is structure around nucleus
o Nucleoplasm is liquid surrounding chromosomes
o Nucleolus is a knot of specialized chromatin that manufactures ribosomes
Ribosomes: Site of protein synthesis:
• Copies of DNA are made using different sugar (Ribose) to make RNA.
• 3 kinds of RNA
o Ribosomal RNA (rRNA) become ribosomes which are sites for protein synthesis
o Messenger RNA (mRNA) travels to ribosomes where they dictate the specific
sequence of amino acids.
o Transfer RNA (tRNA) transport specific amino acids to their proper positions as
specified by mRNA on ribosome during protein synthesis.
Cytomembrane system (C.M):
• C.M. system is group of related organelles (E.R, Golgi bodies, Vesicles) in which
lipids are assembled and new polypeptide chains are modified.
• After manufacturing products are sorted and shipped via the ER to various
Endoplasmic Reticulum: ER –
• Cannels continuous with nuclear membrane
• Extends throughout cytoplasm
• Two regions visible – rough (with ribosomes) and smooth (no ribosomes)
• Adds finishing touches on proteins and lipids
• Packages finished material for shipment
• Material arrives and leaves in vesicles Vesicles:
• Membranous sacs that move around in cytoplasm. Sites of digestion. Formed by
pinching of membranes in ER, Golgi bodies and outer membranes
• Two kinds:
o Lysosomes: contain enzymes that break down cellular components
o Peroxisomes: contain enzymes that rid cell of toxic hydrogen peroxide (by product