EXAM 2 BIO 29 FOR SECOND MIDTERM

MATERIAL, TEXTBOOK, SELF KNOWLEDGE FOR LECCTURE 5

LECTURE 5- INTO TO THERMODYNAMICS & HOW ENZYMES WORK
What level of biology is this lecture in?
atoms, organelle, cell,
what is an enzyme?
Enzyme- are macromolecules that act like catalysis, that increase or change the rate of a
chemical reaction w/o being consumed in the reaction
-

can work in reverse/ backwards

are designed for specificity

How do Enzymes work?

Enzymes are simple machines
o Like ALL simple machines is NEED AN EXTERNAL ENERGY
SOURCE
What is the power source for enzymes?
The energy comes from the ENVIROMENT
-- however, coupled reaction drive UNFAVOABLE REACTIONS to completion
ALL ENZYMES ARE PROTIENS BUT NOT ALL PROTEINS ARE
ENZYMES
CLASSES & FUNCTIONS OF PROTEINS
-

Each enzyme has a specific function.

Organisms (humans) do not want proteins that can do more than one function
why?
o Could make too many proteins that are not needed.

STRUCTURAL PROETINS
- Make Elastic flexible fibers
- They form the cytoskeletons of eukaryotes cells
- Hold tissues of animal cell together

GLOBULAR PROTEINS
- Are protein machines
- Each machine has a UNQIUE purpose.
- Enzymes are GLOBULAR proteins
-Enzymes needs a molecule to bind to them for the reaction to happen
-

This molecule is called a substrate.

Substrate- the molecule that the enzymes acts on
o The enzymes can fold around the substrate
The location where the substrate binds to the enzymes is called the --active site

the active site NEARLY EXACT MATCHES the surface of the substrate.

However there are look-alike that can prevent the reactants form happening:
Inhibitors and regulators

Inhibitor- look alike substrates that affect the reaction of an enzyme.

2types of inhibitors

competitive inhibitors- look alike substrate that compete for admission into the
active site. enters the active site and prevents the CORRECT substrate of doing
it job.

Non-competitive inhibitors- does not bind in the active site but rather another
part of the enzyme- to stop the reaction.
o cause a distortion of the shape

REGULATION

Allosteric Regulation- change an enzymes shape and the functioning of it active

site by binding elsewhere

Covalent regulation- a molecule that covalently binds to the enzyme ex- PO43-

Enzymes stays in close contact with the substratesthat can direct and
facilitate a reaction

An enzyme DOES NOT CHANGE the amount of free energy (G) released or
absorbed

free energy- the portion of a system energy that can perform work when temp and
pressure are uniform throughout the system.
-

ENZYMES HAVE OPTIMUM pH & TEMPERATURE

Enzymes can be controlled by non-substrate molecules

a) cofactor- any NON-PROTEIN molecule or ion that is required for the

functioning of
an enzyme.
How does co-factors works
o they bind tightly or loosely to the enzyme or bind to the substrate
o crucial function in the catalysis.
b) coenzyme- an ORGANIC molecule serving as a cofactor.
-

Allosteric molecule can trigger or lock in changes in enzymes shape.

ENZYMES ALSO REGULATE METABOLIC REACTION.

o They do this through feedback and feed forward

Feedback- regulate metabolism.

o There are enzymes to help regulate the chemical reactions (metabolism)
o One specific enzymes for EACH REACTION
o In a feedback the enzyme report the amount of product of the reaction from the
beginning of the reaction to the end.
o HOWEVER IN A FEEDFOWARD the enzyme from the end of the reaction
report back to the beginning of the reaction.
o Negative- stops
o Positive- speeds up the reaction.
-

Positive is rare compare to negative feedback.

THERMODYNAMICS & ENGERGETICS

G= H - TS
G change in total energy
H (work) change in Enthaply
S change in Enthropy
T is mostly constant
Exergonic- spontaneous
-

Free energy decreases

Energy is release
The system become more stable
G is NEGATIVE

Endergonic non-spontaneous

Free energy increases

Energy is absorbed
The system become less stable
Work is converted and stored into free energy
G is POSITIVE

Hydrolysis- reaction that water use to break down covalent bonds

- Is a exergonic reaction
- b/c energy is being release in the bonds
ATP : Interacelluar Energy Currency
-

the energy is store in the bonds between the phostate group.

Hydrolysis of ATP realeases MORE ENERGY than other Hydrolysis

Reactions
-

ATP is a reusable Store of Chemical Energy

How is ATP created?

- Two ways to make ATP
o Substrate chain phoslorlation- giving a PO43- to a ADP
o done by the catalyst called kinase
o Elertrachemical grandiat- ( oxidative phosphorylation) a molecule is
oxidizes and the energy is use to ATP. Happen in the e- transport exchange
o Use the delta pH in the membrane
o Or a proton gradient in the membrane
o A proton gradient is created by using the energy released from the NADH.
The proton then goes through the ATP synthesis
LECTURE 6- INTO TO CELL ANATOMY
CELLS ARE COMPLEX MACHINES
Complex machine- is a device that can convert work into another form of energy
Work- is the conversion of energy into movement.
So how do cells and organelle related to a complex machine?
- Organelles are like organs for the cell
- Just like a complex machine it converts the work into another form of energy
for the cell.
THE DEFINATION OF A CELL, LIFE, AND ORGAISM
ALL LIVING ORGANISM SHOW

1.
2.
3.
4.

metabolism/ use energy

grow
reproduce
response to stimuli

THIS IS WHAT SEPARTE A LIVING THING FROM A NON-LIVING THING

Groups of Organisms
o Domains of Organism
A) Arehea B) Bacteria C) Eukarya
- Animal
-Plants
- Fungi

The types of Eukarya are called the

KINGDOMS.

FOUR MAJOR CLASSES OF EUKARYOTES MIRCOSCOPIC

1. Protozoa-

PARAMECIUM

EUGLENA

2. the Amoebas

AMOEBA
3. the FUNGI

DICTYOSTELIUM

SACCHAROMYCES

ASPERGILLUS

4. the Algae

DIATOM

CHLAMYDOMONAS

TWO KINDS OF CELLS

1. Eukaryote- have internal membrane all appear to have a single ancestor
2. prokaryote- have NO internal membrane or internal compartments.

EUKARYOTE ORGANELLE
Plasma membrane
- separates the cell from the environment
- define the area
- if the cells does not have a plasma membrane it is considered DEAD
- ANYTHING OUTSIDE THE MEMBRANE IS NONLIVING
- ANYTING INSIDE THE MEMBRANE IS ALIVE
THE NUCLUESDOUBLE MEMBRANE- INFO CENTRL

The nucleus stores the DNA and transcript of

RNA
Nuclear envelope- encloses the nucleus that
separates it from the cytoplasm.
--DOUBLE MEMBRANE is the membrane
-- member the membrane is made out of lipids.
w/in the nucleus the DNA is organized into
chromosomes--- carry the genetic info.
Chromosomes are made up of chromatin
protein that surround the nucleous
Humans have 46 chromosomes23 in sex
cells.

RIBOSOME
- Is the site for the conversion of mRNA to protein.
- Has two parts
o Large 50S and Small 30S
- Each part bind to the RNA to form a protein translation complex

Function: PROTEIN SYNTHESIS

CHAPEROIN
- Fold misfolded proteins
- That allows them to reach their correct conformation
- The proteins enters misfolded and comes out in it correct formation

PROTEASOME
- Shreds misfolded proteins
- Allows them to be recycle
- The interior is lined with proteolytic enzymes
- Why doesnt it just goes through the Chaperoin
o b/c it cannot regain it shape at all
ENDOPLASMIC RETICULUM (ER) DOUBLE MEMBRANE.

The ER is continues with the

nuclear envelop.
-It exports proteins to different areas of the cells
FUNTION OF THE ROUGH ER.
o Have ribosomes attached to it.
o The ribosomes make proteins.
o Glycoprotiens- proteins that have
carbohydrates covalently bonded to them.

The ER is wavy because it need

a large surface area. Therefore
the wavyness increase the
surface area.
Also where Ca is store.
2types- SMOOTH AND
ROUGH ER.
Rough is first.

o also have vesicle that is use for transport. (In both I think)
FUNCTION OF THE SMOOTH ER
o synthesis with lipids mostly to detoxify drug and poison
o metabolism of carbohydrates
GOLGI APPARATUSSHIPPING AND RECEIVING CENTER POST OFFICE .

After thing leave the ER from

the transport vesicles goes to
Gogi
The product r then modified
and is send to different
locations.
Looks like & is consist of
flattened sac called cistemae
However the sacs r not
connected

F. LYSOMES
Lysosmes are membranous sacs that
has enzymes for DIGESTION.
Stores digestive store
Degrades food polymers to monomers
Defective organelles and sometimes
whole cells.
Work beast in acidic environment.

Mitochondrion- DOUBLE MEMBRANE POWEROUSE OF THE CELL .

The cell energy factory

Where cellular respiration and metabolic

processes occur ( will be discuss later).
ATP is generated- where energy come from.
ATP ( adenosine triphosphate) the energy is
released when the bonds between the PO43- is
broken.

Transfer e- from NADH to oxygen that

creates a pH gradient.
The gradient powers the ATP synthesis
o Function- cell respiration

The mitochondrion has 2 MEMBRANES

The outer is smooth
The inner is folded and called cristae
Cristae- the interfolding of the inner membrane of
the mitochondrion.
The space bet. The 2 membranes (membrane
space) has an acidic level.

--in the INNER MEMBRANE there is the Mitochondria Matrix

o The matrix has a pH of neural or basic
o Contains the mitochondrial DNA and free ribosome
o The enzymes in the matrix catalyze some steps of cellular respiration.
o The metabolic reaction in the Matrix is the Krebs cycle or the Citric Acid.
o Krebs Cycle cellular energy and e- transfer chain ( will be explain later)
CYTOSKELETON- a network of fibers extending throughout the cytoplasm
o Functions- support & intra- cellular
3 components of the cytoskeleton
o Microtubules (thickest) , microfilament (thinnest) , intermediate filaments
(fibers)
o MICROTUBULES grow out a centrosome a region near the nucleus
microtubule organizing center
3 different systems
- Actin- transport
o Import vesicles from the exterior to the center of the cell
o Keeps the plasma membrane from bulging and rupturing
- Mircotubule- transport
o Used to export vesicles away from the nucleus to the outer edges of the
cell
- Keratin support networks
Centrosome
- center of the microtubule network
- provided the expansive push needed to separate the chromosomes during
animals cell division
- only in animal cells

PLANTS CELLS DO NOT NEED CENTROSOME B/C DURING CELL

DIVISION

FLAGELLA (prokaryote)- The flagella and cilla are protein filaments that extends from the plasma
membrane.
- Is in the OUTSIDE ENVIROMENT
- Function: to move the cell.
FLAGELLA (eukaryote)
- are microtubles structure
- are ATP powered for movement
- move cells forward in a whip-like strokes
- NOT FOUND IN PLANTS CELLS
EXTRACELLUALAR MATRIX
o Animal cells are protected by a matrix of flexible protein fibers.
o The fibers can be coated with sugar chain
o The sugar chain increase water retention around the cell
VACUOLE
o Osmotic pressure balance
o Mineral storage and organic storage.
o Storage of waste
o Function: digestion, storage, waste disposal, water balance, plant cell growth,
protection

PLANT WALL
o External to the plasma membrane
o Is a DEAD material
o Useful for defense
o Plants use carbohydrates & oxidized aromatic amino acids
CHLORPLAST- 2 MEMBRANE
o Energy factory in the PLANT CELL (photosynthetic eukaryote cell )
o The light reactions happens in the thylakoid membrane
o The dark reactions happen in the stroma

o Contains green pigment

o Function in the photosynthesis production of sugar
o Inside the inner layer
o There are thylakoids
o Enclose the luman system of vesicles
o Thylakoids looks like flattended sacsthe sacs are called granum.
o Where photosynthesis happens
o Stroma- is the fluid outside the thylakoids.
o Have free ribosome and the chloroplast DNA

B
C

F
G

D
H

A- ocular lense magnifies the images usually by ten-folds (eye piece)

B. specimen stage where the specimence is placed for observation.
C. Condenser- it function is to focus light
D- Iris diaphragm- control the amount of light entering the objective lens.
E- Objective lens- allows different magnification
F- course/fine focus knob the course focus knobs focuses by going up and down. The
Fine focus knob focuses by 4 times, increasing magnification and

G- light source- control the amount of light.

H- knob- controls the intensity of light.

Resolution Limits
Units of observation
Eye

SI units
0.1mm

Light (bright filed microscope)

0.2 um

Transmission EM

0.1 nm

Scanning EM

3-5 nm

Atomic Force microscope

0.1 nm

Microbiology- the study of living objects smaller than a human eye can see.

Cells vs Viruses
o Viruses are NON-LIVING organism
o They can not reproduce, respond to stimuli, grow, use energy
o UNLESS THEY ARE OUTSIDE OF A HOST
o When they are inside of a host they fulfill all of the qualities a livinf
organism can do.

o
o
o
o

The human red blood cell is 6-8 um. T4 bacteriophage is 225 nm.
Adenovirus is 90 nm. Tobacco mosaic virus is 250 nm.
E. coli is 2 um.
The E. coli would be a beach ball, all the viruses will be a peanut

History of Microbiology
Girolamo Fracastoro (1483- 1553)
o The first to say in public that disease are cause by organism that we can not see
o THE GERM THEORY
o But cannot test his hypothesis
Robert Hooke (1635-1703)
o Coined the word CELL
o Defined the word CELL
o FIRST to study biological material under the microscope
Antony van Leeuwenhoek (1632-1723)
o Observe living things in pond water
o And dental plaque
o First to find single cell prokaryote and bacteria
Schleiden
o Plants are made up of cells
Schwann
o Animals are made up of cells
Louis Pasteur (1822- 1895)
o Demonstrated chirality of carbon compounds (1849)
o Refuted Theory of Spontaneous Generation (1862)
o Invented a sterilization technique called Pasteuiazation
LECTURE 7- PLANT ANATOMY (chapters 35,36,38)
Nonvascular Plants (Bryophytes)
Phylum Hepatophyta- liverworts--- 9,000

Phylum Amthocerophyta Hornworts 100

Phylum Bryophytamosses15,000
Vascular Plant
Seedless Vascular Plants
Phylum Lycophyta Lycophytes 1,200
Phylum Pterophyta Pterophyta 12,000
Seed Plants
Gymmnoperns ( seed born w/o fruit)
Phylum GInkgophyta Ginkgo 1
Phylum Cycadophyta Cycads 130
Phylum Gnetophyta Gnetophytes 75
Phylum Coniferophyta Conifers600
Angiosperms ( seed born w/ plats)
Phylum Anthophyta Flowering Plants 250,000
Types of Plants
Moss
-

have a lacking ability to move water through the xylem and phloem
that why they are small

dont produce flowers, seeds, or pollens

have a vascular tissue

Ferns

Gymnosperms
- no flower or fruit are produce
Angiosperms
- MOST DIVERSE GROUP
- Present of flowers , fruit, and pollen
Plants Tissues
- Dermal tissues
o Protective, connective
o Epidermis and endodermis
o Cortex
-

Ground Tissues

o Multifunctional
-

Vascular Tissue(respiratory tissue)

o Transport of nutrients
o Xylem
o Phloem

Plants Organs:
- ROOTS
- STEM
- LEAVE
- (FLOWERS)

Roots- is mostly dermal and ground

- extracts water and ions from the soil
- blocks toxic ions from reaching other part of the plant
- storage area for excess carbohydrates
- penetrate the soil
Structure
- root cap-protects the growing tip
-

apical Meristem- creates new cells for the root cap and the main root.

Expansion of small cells into long cells.

o The cell just gets longer
o Also in this area excretion of protons into the cell wall
o Helps propel the root through the soil
o Expansion provide growth in roots

- Root hair and lateral roots harvest water and nutrients from the soil.
Function
- Anchorage
o Keeps the plants firmly to the ground
o Hold it upright
-

Acquisition of Water
o Roots hair use osmotic pressure to draw water

Acquisition of Inorganic Nutrients

o Root hair acquire water soluble nutrients

Storage of Photosynthetic Products

o stores extra carbohydrates in roots to rebuild leaves every spring

Excretion
- excretion of acid allows hydrolysis of pectins that holds wall microfibrils
2gether
- excretion of acid creates a pH electrical/chemical gradient

channel protein use the pH gradient

Water Transport in Roots

- flow in three ways
1. Symplastic Transport- water and other molecule is transported through the
plasmodesmata network
2. Apoplastic Transport water & other molecule that travel through the pores
cell walls
3. Transmembrane Transport a combination of both.
Roots Shield Against Toxic Minerals
-

Both nutrients and toxic minerals can use Apoplastic Transport

But doesnt use Symplastic Transport

Casparian Strip is a ring of cells in the roots that block passive transport of
material such as toxins
Blocks Apoplastic Transport of molecule

Roots Adaptation
Tap Root System
- Useful for tall plants
- Aid in anchorage
- Central root is a direct extension of the main stem
Fibrous Root System
- No central root
- Useful for dry environment
Aerial Root
- Adapted to capture nutrients from rain

Buttress Root
- Add support for tall plants
Pnematophores
- Growth in Anaerobic Soils (lack of Oxygen)
Prop Roots
- Extra support for tall plants
Storage Roots
- Specialized for storage.

Stems is mostly vascular tissue

main function to transport nutrients through the plant.
- Main area for transport throughout the plant
- Support the plant upright
- Has the xylem and phloem
- Xylem-dead cell functions to transport water and ionsupwardPASSIVE
- Phloem-dead cell function as transport of sugarsdownwards-- ACTIVE
- Cell expansion drives growth in stems
Stems: Adaptations
- Reproductive
o Specialized for Asexual reproduction
-

Storage
o Bulbs and tubers store H2O & nutrients

Tendrils
o Adaptation for anchorage
o Good for windy environment

Photosynthetic
o Stem are main organs of photosynthetic in Cactus & Succulents
Composed of Nodes and Internodes
o - Nodes- where the leaves are attach
o Internode- the place bet. The nodes
o Auxiliary bud- structure that can form a lateral shout known as a branch
-

branches and buds emerge from nodes.

Inter node are supportive sections

Leaves ground and vascular

- Water loss happen here
Structure
- Blade- expanded part of a leaf

Petiole - stalk that joins the blade to the stem

Vein conductive tissues for transport into and out of leaf

Webbing ground and dermal tissue between veins

Stipules- small appendages sometimes present at the petiole base

Auxiliary bud- organ that can be mobilize to form a new leaf. (not part of the
leaf)

Types of Leaves
1. simple leaf

2. Compound Leaf

Able to count the amount

3. Doubly Compound Leaf

Difficult to count the amount

TISSUE ORGANIZATION OF LEAVES
o Has a epidermal barrier epidermis
o In the epidermis there is the stomata
o Stomata- a pore that allow gas exchange bet, the surrounding air and
photosynthetic cells inside the leaf
Basically- regulate the CO2 uptake
Where water is evaporated water is only evaporated at the
leaves.
o In the stomata there are two guard cells.
Guard cells- regulate the opening and closing of the stomata.
o The ground tissues of a leaf is called mesophyll
o Mesophyll- bet. The upper and lower epidermal layer.

Surface of a Leaf
- the stomata are on the surface
- have guard cells
o Guard cells- regulate the opening and closing of the stomata.
Guard cells control gas exchange
ATP-driven K+ pumps bring water inside the guard cells that cause
them to open to let the water out and let CO2 to enter.

Leaf Function
- Capture light
-

Capture Carbon dioxide

o Use NADPH & ATP to convert CO2 into carbohydrates

Biosynthetic Factory
o Primary Metabolites
- Sugars, lipids
o Secondary Metabolites
- Alkaloids, Tannins, etc.
o Hormones
- Coordinate Plant Behavior

Environment Sensor
o Day length sensor
o Water pressure sensor

Leaf Adaptation
- Bracts
o Brightly pigmented to help organism locate reproductive organs.
-

Reproductive
o Asexual reproduction

Spines
o Defensive, Anti-Predator, Ouch

Storage
o Water, nutrients, or both

Tendrils
o Adaptations for anchorage

o Good for windy environment

o Help anchor
Other purpose for leaves
- Attract insects (bracts)
- Storage
- Gas exchange (guard cells and stomata)
Water transport from root to Leaf
Loss of water atmosphere creates a water gradient
Evaporation from the leaves creates a pull on other water molecules
H bonds allows evaporation to pull water to leaves

Meristematic Tissues: How Plants Grow

- Meristematic tissues- type of ground tissue that divides quickly and
differentiates into other types.
Similar to stem cell tissue
Plants grow outward from aprical buds
o Cambium meristematic stem tissue
Located beneath dermal layer divides rapidly inwards and
outwards
The plants then become WIDER
-

Vascular Cambium- adds layers of vascular tissue called secondary xylem

(wood) and secondary phloem

Cork Cambium- adds layers of secondary tissue forming the periderm

Bark on woody plant

Flowers: Structure & Function

Flower- is a speacialized leaf organ dedicated to sexual reproduction

1- Stamen- pollen producing reproductive organ

2. Anther- it conatin a chamber called microsporangia (pollen sak) that produces pollen.
3. Fillament- the stalk portion of the stamen
4. Stigma- the sticky part of the flowers carpeltraps pollen grain
5. style the stalk of a flower carpel, with the ovary at the base
6. ovary-the portion of a carpel in which the egg containing ovules develop
7. carpel- the ovule-producing organ of a flower
8. Sepal-enclose and protects a flower bud before it opens
9. Petal- a modify leaf of a flowering plants that attracts insects to them
10. ovule- contains the eggs
Four Cycle
1. sepal
2. petal
3. stamen
4. carpel
Types of Anigiosperm Flowers
Simple
Aggregate

one ovary

many ovaries/flower

Compund
- many flowers/ stem

Accessory
- one ovary

Parts of Fruit look in lecture

Sepals
Seed
Receptacle

Type of Edible Angiosperm Fruits

- simple
- aggregate
- compound
- accessory
Types of Fruit
-

Nut
o In woody plants

Berry
o From edible ovary or accessory tissue

Burr
o Encased in woody ovary designed to entangle fur

Achene
o Fruit designed for air dispersal with wings or hair

Naked
o Released w/o end osperm

Distribution of Seeds
-

By animals
o Ingestion
o Attachment

by wind
o achene

by water
o like a coconut

Lecture 8- Photosynthesis
-photosynthesis powers the world directly or in directly.
- we all live off the product of the sun
-photosynthesis- is the process that convert solar (photon) into chemical energy.
o Happens in plants, algae, certain protests and some prokaryotes
o These organism also feeds the world
o Reaction:
o 6CO 2 + 6H20 + LIGHT ENERGY C6H12O6 + 6O2
The green is part of the DARK REACTIONS
Plants
o The chloroplast is the organelle responsible for light trapping, energy conversion,
+ oxygen release.
o All land plants arose from photosynthetic ancestors even though some does not
use photosynthetic
-

plants are photoautotrophs

o photoautotrophs- gets energy from light and sustain themselves without
eating another organism. (gets Carbon from the air not other)

plants that are photoautotroph using the energy of the sun to make
organic molecule.

The Role of Light in the Biosphere

the electromagnetic spectrum is a range of light that carries energy and
radiation
Visible Light is the light with the right wavelength for photosynthesis
o This light drive photosynthesis
o The higher the frequency the shorter the wavelength (more energy)
Why is Visible Light the Valuable to Photosynthesis
Visible light lies at the middle of the electromagnetic spectrum meaning it has
medium energy.
Why is this important?
o Too low energy no e- will be releases (radio, IR)
o Medium energya gentle releases of e- (visible light)
o Too MUCH energythe e- are destroyed (x-rays, gamma rays)

Photosynthetic Pigments: Light Absorption

Pigments- are substances that absorbs visible light in the chloroplast.
o Different pigments absorb different wavelength
o Ex: leaves are green because it absorbs red and blue light very well but
green light very poorly.
The green light either bounces off or goes right through it.
2 types of photosynthetic pigments of the plants
Chlorophyll a- participates directly in light reactions
Absorbs blue-violet and red photons very
well
Chlorophyll b- absorbs the accessory pigments.
Absorbs the green-blue and red-orange
photons.
o Chlorophyll are green pigment for the same reason
why leaves are green
Are found in the thylakoid
o There another pigment that is found in plants Carotene
Carotene- an accessory pigment either yellow or orange, in the
chloroplast of plants.

Absorbs light wavelength that the chlorophyll can not

absorbs.
o This way it widens the spectrum of colors the can
drive photosynthesis

THIS IS ALL FOUND ON THE CHROROPLAST ORGANELLE IN A PLANT CELL

Chloroplast vs. Mitochondria
Like the mitochondria the chloroplast creates a pH gradient to make ATP.
Provide the cell with energy
chloroplast are green for the same reason as why leaves are green and
chlorophyll.

Why are the other colors absorbed more than green ?

oxygen
oxygen produce is related to the absorption of light.
Best absorbed colors produce the most O2
Red and blue has the most amount of O2. GREEN HAS THE LEAST
AMOUNT

Chloroplast- the Light Trapping Oragnelle

-

Chloroplast are solar-powered chemical factories.

The thylakoid transform the light energy into the chemical energy of ATP and
NADPH
The activated Chl reacts with the Plastoquione (PQ) and
Plastocyanin (PC)

the e-traps the photon and than converts it to work (complex machine)
o move it away from the Mg2+ nucleus. (a chlorophyll has a Mg2+ center)

when the Chl absorbs light it gets excited and needs to get to ground state.
o 3 ways of returning to ground state
- Fluorescence- release energy usually of a the longer wavelength
-

Resonance Energy Transfer Vibration energy is transfer to

another

Transfer of e- to another molecule

LIGHT REACTIONS happens in the chloroplast

--When photon hit the chlorophyll in the thylakoid membrane it get excited and then the
one next get excited and so on & so on. UNTIL that energy (the cause of the excitement)
hit SPECIAL PAIR of chlorophyll
o The special pair of chlorophyll gives off an eThe green is the chlorophyll
Photosytem consists of a
reaction-center complex
surrounding by light-harvesting
complexes.
The loss of e- is replaced by the
e- form the splitting of water

Linear E- flow in photosynthesis -the celluar respiration exchange in the chloroplast.

This diagram is know as the Z- scheme

The e- from chlorophyll a molecule to the primary electron acceptor.
o Light hit the pigment molecule and the chlorophyll get excited and pass it on
to other chlorophyll ( as stated before)
o Then that energy reaches the special pair in PHTOSYSTEM 2( is call
photosystem 2 because it was discovered 2nd )
o The special pair in Phtosystem 2 is call P680 it absorbed light at 680
wavelength very well.
o P680 then get excited and give off an eo ALSO HAPPENING THE PS2 an enzymes is catalyzes the splitting of water
into 2 eo Those e- from the splitting of water is given to P680 one by one
(remember two are given off) when it lose it e- in it excited state.
o SO WHAT HAPPEN TO THE E- THAT WAS GIVEN OFF BY THE P680?
o The e- is then carried by the plastoquinione (PQ) and brings it to the
CYTOCHROME COMPLEX
o The cytochrome complex is another complex.
o As the is going through this complex the energy falls that provide
energy for the synthesis of ATP
o Meanwhile the electron it then taken up by the plastocyamin(PC) (sit
on topn the Cytochrome complex ) and carry the e- to PS ONE.
o When the e- enters PS 1 the special pair P700 ( absorbs 700nm photo very
well)
o The P700 then get excited getting the e- and gives off an e- as well.
o That given off e- is then passes through a series of redox reaction from PS 1
down a second e- transport chain through the protein FERREDOXIN (Fd)

o Then the e enter the NADP+ REEDUCUTION. Where the NADP+ is turn to
NADPH.
o Making this molecule have higher energy than water and the e- are
more ready for the Calvin Cycle (dark reactions)
o The H+ that was given off from PS 1 and PS 2 in the thlakoid space goes to the
ATP synthase. Similar to the ATP synthase to the mitochondria.

THIS IS THE LIGHT REACTION:

THE PRODUCTS ARE ATP , O2, and NADPH
The Dark Reactions
- The Calvin Cycle converts CO2 to organic molecule.
- The cycle builds sugars from smaller molecules by using ATP and the
reducing power of e- carried by NADPH to make C-C and C-H bonds from
O=C=O

The CARBON enter the cycle ONE AT A TIMEbut needs 3 to pass

Phase 1- Carbon Fixation
carboxylationribulose biphosphate rubisco is a C5 sugar that is attached to
EACH CO2 molecule.
The product of this is a SIX CARBON that is unstable making it split in half
which forms 2 3- phosphoglercerate. (PGA) REMEMBER PER CO2
Phase 2- REDUCTION
each 3- biphosphoglercerate gets a PO43- form an ATP- PER (2 ATP per CO2
6CO2)
then a pair of e- from NADPH that makes 3- biphosphoglercerate lose a PO43becoming G3P- EACH (2 NADPH PER 3-biphospoglercerate)
o in the diagram it show for EVERY THREE MOLECULE CO2 that enters
the cycle there is ONE MOLECULE of G3P
o in phase 2 glocose is given off.
o LOST OF ONE CARBON
PGA to G3P
Phase 3- Regeneration of he CO2 ACCEPTOR- RUBP
-- the rest of the 5 CARBONS it combines together with the use of ATP.
o 1 ATP per 5 CARBONS.
--regeneration of the CO2 acceptor (RuBP)
however there is a problem with RuBisCO
o it can do both carboxylation & oxygenation.
o How is this a problem
o It can take the product of C5 and break it down to a point that it is useless.
Meaning that the energy use in the Calvin Cycle was useless.
Therefore the cycle has to be repeat again.
REMEMBER THREE (3) CO2 MUST PASS INORDER FOR G3P is produce.

Questions
What is the significance of the dark reaction?
o Produce of sugars G3P
Where does the O2 come from?
o The splitting of water.
Carbon Fixation of C4 Plants
o CO2 is trapped by PEP-Carboxylase instead of REUBISCO
o Unlike REUBISCO it does not bind to O2
o Cause one more ATP
o The tissue are organized to funnel photosynthate from the mesophyll to vein
effciently
o Have other cells surrounding it.
o Spatial Separation

C4 Plants conduit CO2 fixation and ATP/ NADPH production in

different tissue to minimize photorespiration

CAM Plants
o The CO2 is trapped at night by crassulic acid
o Does not required NADPH or ATP
o This minimizes water loss in dry environment.
o Mostly found in dry environments
o Temporal Separation
CAM plants conducts CO2 fixation and ATP/NADPH production
at different times to minimizes water loss
Photosynthesis in Bacteria
1. Free living chloroplast
o Remember bacteria does not have internal membrane so they dont really
have chloroplast
2. Water or hydrogen sulfide split (H2S)
3. Bacteria that Photosynthesize include:
o Cyanobacteria & Proclorophytes
o Green & Purple sulfur-producing bacteria
o Green & Purple non-sulfur bacteria
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