diversity of life notes

8/11/2019 Diversity of Life Notes

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Biology is the study of life.

*Liquid water is the fundamental prerequisite for the development of life*

Earth is ~ 4.6 Billion years old and lies within the habitable zone around the sun. (this is the position were heat

from the sun allows water to exist in liquid state)

In order to be considered alive it must have the 7 characteristics:

But what is life?

Display order1.

Harness and utilize energy2.

Reproduce (heritable genetic information)3.

Respond to stimuli4.

Homeostasis5.

Growth and develop6.

This characteristics are "emergent" (there is a hierarchy of interactions where simpler things do not

have the properties found in higher levels)

Evolve (adapt to change) *Key for diversity*7.

Diversity and unity through evolution

Theory of evolution through natural selection (single common ancestor)

Charles darwin (natural selection, 1859) created a unifying framework

Diversity

Live in diff environmentsAdapt to changing environments

Differences enables them to:

Reproduction with potential for errors, errors lead to evolution.

Cell theory: cells come from pre-existing cells, all organisms are composed by it. Cells are the basic unit of

life

How is all life on earth related?

Cells (Lipid bilayer)1.

Genetic system based on DNA2.

System of information transfer (DNA, RNA, PROTEIN)3.

system of protein assembly using ribosomes and mRNA, tRNA,4. ATP as source for chemical energy5.

Metabolic pathway to generate ATP6.

Proteins: Major structure and catalytic molecule7.

How is life on earth unifyied?

Classifications are made on the basis of share features (structure/function)

Taxonomy (classification of life) developed by Linnaeus in 1735

1) Genus2) Species

All organisms have 2 parts for their scientific name (in italics)

Phylogeny (geneological relationship)

Tree of life (still in progress)

CHP3 Biology and The Tree of LifeSeptember-20-13 7:59 PM

BIOA01 Module 1 (revized) pgina 1


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How important molecules for life came to be?

Is hypothesized that they came to be in 4 main stages

1st stage Abiotic synthesis of monomers (NOT SYNTHESIZED BY LIVING ORGANISMS) :

Primordial atmosphere contained large quantities of H2, CO2, NH3 (ammonia),CH4 (methane)

1) Oparin-Haldane hypothesis: reducing atmosphere where molecules in premordial atmosphere

contained abundance of electrons and H2, reacting with one another producing larger more complex

molecules)

Because there was no oxygen, there was no ozone layer, therefore, UV light + lighting provided the

energy needed for the formation of the molecules

Note: Today's atmosphere is considered oxidizing due to large amounts of oxygen present (because

of its affinity it accepts the electrons and reduces chances for complex macromolecules to form)

Miller-Urey experiment was the first to demonstrate the abiotic formation of important molecules

can be easily produced in the laboratory

2)Deep sea vents: Release superheated nutrient rich water, as well as reduced molecules

(CH4,NH3,H2S) which created a geochemical gradient that with the extreme pressures of the

environment gave rise to the building macromolecules of life.

"Carbon chondrites"- rich in organic molecules

Clay hypothesis charged layers of clay allows for molecular adhesion forces to bring

monomers together (clay stores potential energy) It also accelerates formation of lipid

vesicles

2nd stage Polymerization

3) Extraterrestrial Origins (Panspermia): organic molecules tha came from meteorites

one of the key attributes of a modern cell is that it has a membrane-defined

comparment, where it provides a distinction from external environment and the

concentration of key molecules within the membrane creates better chances for the

formation of more complex molecules.

3rd stage Protobionts (similar to lisosomes which are lipid vesicles with lipid bilayer similar to

cell membrane)

Protobionts are capable of simple reproduction and metabolism all within a selectively

permeable membrane.

4th stage Central Dogma

Ribozymes: a group of RNA molecules that could themselves act as a catalyst. They are

single stranded molecules that can fold into very specific shapes on intramolecular

hydrogen bonding or base pairing. (critical for reacting with substrate molecules)

Are the steps from DNA to RNA to ribosomes for the formation of proteins which is aid by

enzymes (which are proteins) but... there were no proteins! so wth, how did it happen then?

"RNA world" from RNA to RNA, protein to DNA,RNA,PROTEIN

FROM MACROMOLECULES TO LIFE

From RNA world to DNA world.

Why DNA? DNA is more stale, better at storaging information and is double stranded which aids in

CHP3 The Origins & Chemical Building Blocks of LifeSeptember-20-13 7:59 PM



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DNA repair (Base uracil is replaced with thymine).

more variety (22 diff amino acids, compare to 4 nucleotides)

Aminoacids interact chemically with each other giving rise to many many combinations

grater rate of catalysis (10-100x greater)

From RNA catalyst to Proteins.

Membrane defined compartmentSystem to store information

way to harness and utilize energy

The model of the origin of life must explain:

Early protobionts used molecules present in the environment for growth and replication

Heterotrophs (other-feeding)- they obtain carbon from organic molecules and produce

C02

Anoxygenic photosynthesis, Evolution of oxygenic pho, produce O2.

Autotrophs (self-feeding) obtain carbon from inorganic molecules (CO2)

*Primordial heterotrophs did not survive the change in environment and those who didevolved the capacity for aerobic respiration

How did life evolve?



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Lack of membrane-enclosed organelles

Including extreme habitats too hostile for most organisms

remarkable diversity

Thrive almos everywhere

Appear simple in structure compared to eukaryotic cells

Have the greates metabolic diversity of all organisms

Important for food production

Some responsible for disease, some essential for health

most familiar to us

Bacteria

Discovered around 40 years ago, not wll known

Share some cellular features with bacteria, some with eukaryotes, some unique

Live in very extreme conditions

Archea

Classified into two domains that differ in structure, physiology and biochemistry

Are unicellular

Sphere (coccus)

Rod (Bacillus)

Spiral (spirillus)

Common shapes:

Are very small (1 to 10 um)

Morphology

The Gram Stain

It differentiate bacterial based on their cellwall

constituent. Gram positive bacteria(purple) consist of

thick layer of Peptidoglycan, while gram negative (Pink) consist

of thin layer of Peptidoglycan, and a thick layer of

Lipopolysaccharide.

Layer that lies outside of cell wall which consists of many polysaccharides.

Dessication

It protects bateria frome external environment

Sticky capsule protects many prokaryotic cells.

Cell structure

Cell wall

cell membrane

capsule(layer of

polysaccharides

pili

flagella

External:DNA packed into nucleoid

plasmids

ribosomes

lack of internal membrane

boud organelles

semblance of cytoskeleton

Internal:

peptoglycon layer (peptide + sugar)

Cell wall(it maintance shape, provides

protection and prevents from

bursting in hypotonic

environments )

Primary component is

peptidoglycan (polymer of

modified sugars cross linked by

short polypeptides)

Some contain outer membrane(Which contains

lopopolysaccharide (LPS) which

provides more protection

and immune recognition

cell walls allow to classify

bacteria acording to differences

CHP20 *Tree of life- Prokaryotes*September-20-13 9:58 PM



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Extreme temperature

Invading viruses*

Antibiotics

Considered a virulence factor (helps to evade detection by immune cells)

Pili and flagella

Aids attachment of bacteria to hosts surfaces, required for colonization during infection,

required to initiate formation of biofilm

Conjugative (Sex) pili allow transfer of plasmids between bacteria (one methor for horizontal

transfer HGT

Pilius (singular)- a hairlike appendage found on the surface of many bacteria

Primary role in locomotion

sensory to external environment (chemicals and temp)

Prokaryotic and Eukaryotic flagella differ in protein composition, structure, and mechanism of

propulsion

Flagella (sensory and locomotive)- cell surface appendage -"Whip-like" motion

Ring of DNA (Single circular DNA molecule= chromosome)

Packed into nucleoid region

no nucleolus

no nuclear membrane

Small genome

Genome

May also have smaller rings of DNA called plasmids, which provide resistance to antibiotics, and that

replicate independently of the chromosome (Can be transferred between bacteria via pili)

Smaller than eukaryotic ribosomes

Protein synthesis similar to eukaryotes

Bacteria ribosomes sensitive to antibiotics, archaeal and eukaryotic are not

Archaeal ribosomes shame some similarities with eukaruotic ribosomes

Ribosomes (spreed throughout)

Produces exact copies of parent and it can result in rapid population growth

Replication1.

Segregation2.

Cytokinesis3.

Asexual method of reproduction: Binary fission

Rapid reproduction and mutation1.

Conjugation (transfer via pilus)

Transformation (from surroundings)

Transduction (bacteriophages carry gnes from host cell to another)

Genetic recombination2.

Promoting genetic diversity

Antibiotic binds to enzymes. mutations cause binding site of enzyme to change which does not

allow antibiotic to work

Pathogenic bacteria and antibiotic resistance

attachment of bacteria, growth and divide (Communicate), produce extracellular polymer

substance (encapsulates, for protection) , attachment of other organisms.

Bio films (communities)



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Autotrophs (Self-feeding)- Energy from inorganic carbon

Organisms are grouped according to source of carbon, also by source of energy

Heterotrophs (other feeding)- energy from organic carbon

Phototrophs (light as energy source) photoautotrophs & photoheterotrophs

Chemotrophs (oxidize inorganic or organic substances) chemoautotrops &chemoheterotrophs

Metabolic diversity

Biogeochemical cycles-

Pathway by which a chemical element moves

ex. Bacteria and archea are able to do nitrogen fixation which is the only mechanism of

replenishing the nitrogen resources. (all organisms rely on them)

through an ecosystem

Exotoxins -Leak from or are secreted

(Are proteins)

Outer membrane of all

gram-negative bacteria

Endotoxins- The lipid A portion of LPS

They cause about half of all human diseases

BUT only a small fraction of bacteria are

pathogenic(cause disease by secreting toxins)

Harmful effects

~100 quadrillion bacteria cells

Bacteria cover every inch of thehuman body

Beneficial effects



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Most widely held hypothesis: derived from infolding of a prokaryotic cell plasma membrane,

inclosing the DNA

Origin of endomembrane system

Separation od DNA and cytoplasm by a nuclear envelopePresence of membrane-bound compartments with specialized metabolic and synthetic functions

Distinguising features

Morphology (similarities between shape of bacterium, mitochondrion and chloroplast)1.

A cell cannot sinthesize a mitochondrion or chloroplasta.

Derived only from pre-existing mitochondria and chloroplastsb.

Divide by binary fissionc.

Reproduction2.

Genetic information (Contein their own circular DNA)3.

Transcription and translation: Contain complete machinery for transcription and translation -

ribosomes similar to bacterial's

4.

Have electron transport chains similar to prokaryotic cellsUsed to generate chemical energy

Swallowed up into inner membrane

In prokaryotes, ETC in plasma membrane

Electron transport:5.

Ribosomal RNA sequency firmly establishes mitochondria and chloroplasts belong on the

bacteria tree of life

Chloroplasts RNA most s imilar to cyanobacteria

Mitochondrial RNA most similar to proteobacteria

Sequence analysis6.

Evidence supporting theory ofendosymbiosis:

What happened to the genes of human mitochondrial genome? (only 37)

Some genes were lost (redundant with nuclear genes)

In order to centralize genetic information

90% of proteins required for mitochondrial and chloroplast function are encoded by genes

found in the nucleus

Some genes relocated to nucleus through HGT)

Endosymbiosis and Horizontal Gene Transfer

Gene transfer not yet complete

Retained genes encode for proteins involved in electron transport chain- Tight regulation may be

difficult in genes are in the nucleus

Why do both mitochondria and chloroplasts still retain a genome?

OVERVIEW OF AN ANIMAL CELL

DNA organized into chromosomes (Single DNA molecule+proteins-> Chromatin (the complex

combination of DNA, RNA, and protein that makes up chromosomes)

Nucleolus: site of rRNA synthesis

Pore complex regulates entry and exit (RNA, Proteins, macromolecules)

Nuclear envelope is a double membrane(inner, outer + nuclear pore)

The nucleus

Proteins which function in cytosol

Free ribosomes in cytosol

Insertion in membranes

Packaging organeless

Export from the cell

Proteins destined for

Ribosomes bound to ER

Ribosomes: Protein factories

Cisternae formed by a single membrane(enclosed space called ER lumen)

Interconnected network of membranous channels and vesicles called cisternae

Ribosomes stud membrane surfaces facing cytoplasm

Proteins enter the lumen where they are chemically modified

Rough ER

Endoplasmic reticulum (little net)

Nucleus

CHP2 Eukaryotic cells (I)September-21-13 5:44 PM



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Ribosomes stud membrane surfaces facing cytoplasm

Proteins enter the lumen where they are chemically modified

Proteins then delivered to other regions of the cell witin small vesicles

Rough ER

Synthesizes lipids

Detoxifies drugs and poisons

Stores calcium ions

Smooth ER

Proteins enter via vesicles at the Cis face

Modifies ER products

Manufactures certain macromolecules

Sorts and packages for transport

and exit via the Trans face

The Golgi Complex (sorting machinery)

Digest macromelules

Acidic pH

Lysosomes (Membranous sac of hydrolytic enzymes)

Phagocytosis (The engulfing and ingestion of bacteria or other foreign bodies by phagocytes)

Important role in:

Site of cellular respiration

ATP- generating reactions occur in the cristae and matrix

Mitochondria



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Tubulin: diameter of an alpha-tubulin and a beta-tubulin.

It is a hallow tube, which wall consists of 13 columns of tubulin

Maintain cell shape

Cell motility

Chromosome movement during cell division

Organelle movement.

Functions:

Microtubules (biggest) Interior 15nm, exterior 25 nm with +/- ends

Maintain cell shape

Anchorage of nucleus and some other organelles

Formation on nuclear lamina

Functions:

Intermediate filaments Fibrous proteins coiled and supercoiled into thick cables (Tissue

specific proteing composition) 8-12nm, non-polar

Maintain cell shape

Changes in cell shape

Cell motility

Cell division(Muscle contraction)

Functions:

Microfilaments (smallest) Two interwined strands of actin(each a polymer of actin subunits)

5-7 nm with +/- ends which provides dynamic change of structure

The cytoskeleton is composed of three main types of fibres:

Provides structural integrity to the cell1.

Drives cell motility (motor protein-driven movement, kinesin molecule *walking*, ATP

dependent process)

2.

Filopodia

Microvilli

Forms cell surfaces structures which probe the environment3.

Movement of cargo inside the cell4.

Separation of chromosomes

Cytokinesis

Cell division5.

The cytoskeleton

Comprise part of the microtubules organizing centre (MTOC)

Involved in microtubule 'spindle' organization during cell division

Flagella and cilia arise from centrioles

It is made up of 9 sets of three microtubules

Centrioles

Motile structures extending from cell surface

Similar in structure except cilia usually shorter and often numerous on cells

Dynein motor proteins slide the microtubules over each other to produce movement

Flagella and cilia

-Flagella moves in S-waves which propels the cell through watery medium

CHP2 Eukaryotic cells (II)September-21-13 10:30 PM



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alpha helix in the membrane.

-Intracellular, comunication within cell for change

Associated with outer or inner side.

Held to membrane by proteins or lipids

Peripheral membrane proteins

Functions

transport1.Enzymatic activity2.

Signal transduction (recognition of signals)3.

Attachment4.

Transport (across plasma membrane)1.

Hydrophobic nature restricts free movement of molecules

Diffusion (From high to low concentration, the rate depends on concentration gradient.

larger gradient, faster diffusion)

Osmosis: Diffusion of WATER across selectively permeable membrane from a

solution of lesser solute concentration to a solution of greater solute

concentration.

a) Simple : movement without involvement of a transporter, rate depends on molecular

size and lipid solubility.

Aquaporin: Very narrow- single file movement of water. very specific for

water.

Voltage-gated channel: Critical movement for most ions from high to low.

produced in a change in the 3D shape. Important for nerve conduction and

muscle contraction

-Channel proteins: Hydrophilic pathways (Molecules are protected fromhydrophobic core of bilayer), transport of water and ions

Both transmembrane protein*

-Carrier proteins (grab and transport) specific substrate that binds to molecule

that causes protein to change conformation allowing molecule to be release into

intracellular region. From high to low.

b) Facilitated: carried out by transmembrane proteins

Passive: Movement of substance across a membrane without useing energy

Rate of diffusion dependent on concentration gradient.

-For simple diffusion: as long as there is a concentration gradient the rate of transport continues to increase

-For facilitated diffusion: concentration differs across the membrane and as the concentration is increased

you reach a plato (flat, saturation) because carrier molecules are used up.

Transport Kinetics( chart) :

H pumps, Ca, Na/K (View ppt)

Primary. (protein that does transporting, and hydrolyses ATP to power transport

directly) the move positively charged ions (+)

Secondary transport proteins using ion concentration gradient from primary active

transport to drive transport to a diff molecule

Active: require energy, movement against concentration gradient (Low to high) Large

proportion of cell ATP goes towards active transport (fundamental for cell activity: uptake of

nutrients, removal of waste, maintenance of intracellular concentration of ions)

02 can diffuse, but many other molecules are not able.



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symport (ions moving in same direction but against concentration gradient)

Antiport(moving in opposite directions against concentration gradient )

For further clarification refer to ppt pg 32 chart.

other mechanisms for transport

Exocytosis (transport material out of the cell): Vesicles that will fuse in membrane and the contentsare going to be taken outside.

Pinocytosis -(drinking) envagination of molecules, internal vesicle in cell.

Repetor-mediated- transmembrane proteins specific that binds and triggers rignal in cell and

causes invagination and causes vesicle to be pulled in the cell.

Endocytosis

Anchoring junctions

Tigh junction

Gap junction

Membrane proteins function in intercellular joining

membrane proteins respond to environmental stimuli. Specific binding site with causes activation of

protein on cytoplasmic domain. which triggers a signaling cascade (enzymatic reactions)n

phospholiration reaction.

Add textbook notes!



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The energy of life

Metabolic Patways

Growth

Reproduction

movement

ability to respond to stimuli

Cells are maniature factories-hundreds of biochemical reactions that collectively accomplish the

activities of life:

Living organisms must be able to harness and utilize energy

They occur in highly regulated steps

Compartmentalized

product of one reaction is a reactnt of the next reaction

Each Step is catalyzed by a specific enzyme

Regulated by feedback reaction that as control mechanisms

Metabolism: Total of all chemical reactions that occur in an organism or a specific set of reactions

Anabolic (Energy is consumed)

Synthesis of amino acids

Proteins

Photosyntesis

Build complex molecules from simpler ones

Catabolic (Energy is released)

Cellular respiration

degradative reactions: complex molecules broken down into simpler molecules

Two types of reactions

Metabolism manages the materian and energy resources of the cell

Kinetic Energy: Energy in motion

Stored energy can be found in chemical bonds, concentration gradients, change

imbalances (often called, chemical potential energy)

Potential Energy: energy of structure or position (or stored)

Potential energy can be converted to Kinetic energy

Energy: the capacty to do work (causes change)

1st law: energy can be transferred and transformed, but it canot be created or destroyed

2nd law: Every energy transfer or transformation increases the entropy of the universe

(disorder)

All things obey the laws of thermodynamics

To decrease entropy, increase energy (internally)

The Increase heat, increase entropy (Externally)

Thermodinamics: The study of energy and its transformations

CHP4 Energy and EnzymesSeptember-17-13 10:23 PM



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In order for organisms to display order, their surroundings have to have lower order

G=H-TS , where H is total energy or enthalpy and S is entropy

Free energy (G): Energy that can do work

Exorgenic (expontaneous) Release free energy. -G (heat)

Endorgenic (Non-expontaneous) Require free energy. +G

Reaction types

In order to break bond we to form products we use energy, therefore, when bonds are broken downthere is a release of energy.

It requires increasing amounts of energy to add phosphate groups.

Releases free nergy

ADP + Pi (inorganic phosphate) Exergonic

The breakdown of ATP in aqueous environments:

Both products are negatively charged which causes repulsion that favors hydrolysisThe realize of terminal phosphate is energetically favored

The release of the inorganic phosphate increases disorder of the system

Higg free energy release is due to 3 factors:

ATP: Adenosine Triphosphate (very unstable, high potential energy) Ribose sugar, nucleotide

Adenine, 3 phosphate groups.

Enzymes required are driven by catalysis (they bring molecules in close contact)

Free energy transferred to reactants through transfer of terminal phosphate group

(Phosphorylation)

Endergonic reactions of living organism are made possible by coupling reactions (The exergonic

release of energy when ATP is converted into ADP +Pi is used to drive this endergonic reaction)

ATP Synthesis is endergonic

Spontaneous reactions occurs without the input of energy

Therodynamically unstable reactions (Free energy is negative)

Rate of reaction can be altered by enzymes

Kinetically unstable reactions (reactants will rapidly convert to products)

Laws of thermodynamics do not tells us about the rate of reaction

Activation energy Ea : Initial energy investment to start a reaction

Catalyst are chemical agents able to speed up rate of reactions

Molecules then move into transition state where their bonds are unstable

Enzymes combine with reactants but release unchangedwhen reaction is complete. they have

specificity (specific substrates, and substrate interacts with the active site of the enzyme , Site

for catalysis)

Enzymes are a specialized group ofproteins that catalyze reactions ( by lowering activation energy),They do not alter the change in free energy of the reaction

Substrate binds to enzyme and form enzyme-substrate complex

Enzyme catalyzes breakage of bonds (products are released

Enzyme can catalyze another reaction

Catalytic cycle of enzyme:

Co-factor: non- protein that alters activity of enzyme (metals: iron, copper, zinc, manganese)

Bring reacting molecules together

Enzymes induce transition state by:



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Expose reactant to altered charge environment (alter substrate to favour catalysis)

Change the shape of the substrate

In the presence of excess substrate, rate is proportional to amount of enzyme

At limiting amounts of enzyme and increasing amounts of substrate, rate reaches maximum

(enzyme saturated)

Competitive inhibition (active site) shaote resemble substrate

Noncompetitive (binds to allosteric site) changes shape so substrate cant bind.

non-substrate molecules hat bind to enzyme reduce its activity

Enzyme inhibitors lower rate of catalysis

reversible binding

High or low affinity(strength) state for binding.

Allosteric regulation: Allows for rapid changes in activity

Added to enzymes (phosphorylation) called protein Kinases

Removal of phosphate (dephospho) carried out by enzymes called protein phosphatases

Covalent modification: Can activate or inactivate enzyme

Regulation of enzyme activity

Temp: increase in temp, increase in reaction (at high temp proteins denature, so rate of

reactions decreases)

Ph: Optimal at Ph of 7, Ph affects charged groups in amino acids of enzymes

Tempt and Ph

In the presence ofphosphatases, dephospho reaction takes around 10ms

In the absence of enzyme, the reaction could take 1 trillion years to occur

Add textbook notes!

Reversible phosphorylation of proteins is a central mechanism of signal transduction



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Light energy stored as chemical energy in bonds of carbs

Anabolic, metabolic pathways build complex molecules and store energy

Photosynthesis:

(produce Carbohydrate and oxygen)

Occurs in photoautotrophs, self feeding users of light

Conversion of CO2 into organic molecules using light energy

Majority of carbon fixation comes about thorugh photosynthesis in

other organisms (other than plants, page 5)

Light reaction: Captures light energy to synthesize ATP & NADPH

Calvin cycle: Electrons and protons of NADPH and energy convert of ATP convert CO2 into

carbohydrates.

Integration of two processes:

It can also be further simplified but sugar is represented by the general formula for

carbohydrates : [CH2O]

It can be symplified by cancelling waters in booth sides

6 CO2 + 12 H20 + Light Energy --> C6H12O6 + 6O2 +6H20

Equation:

Previously thought to be from splitting of CO2 but C.B. van Niel challenged the idea and studied

bacteria that does not produce oxygen

O2 derived from the splitting of H2O

CO2 + 2 H2X --> [CH2O] + H20+2X

In those organisms where there is no production of oxygen(anoxygenic photosynthetic pathway), the

general formula for photosynthesis is

Why is photosynthesis important?

Glucose is major product of photosynthesis (food, source of energy)

All the organic molecules are direct or indirect products of photosynthesis

Reduced carbon is source of carbon for lipids, proteins, nucleic acids

stroma (liquid surrounding tylakoids) are enzymes that catalyse reactions of the calvin cycle

inside of chloropast inner and outer membrane, within there are the talakoids( group of tylakoids

is called granum, grana)

Thalakoid membrane (light reaction): proteins, pigments, electro transfer carriers, ATP synthase

(component that carry out the light reaction)

Photosynthesis takes place in chloroplast

Light energy

Light energy comes in packets called photons (contain afixed amount of energy that is inversely related

to its wavelength) that have wave-like characteristics

release of energy obtain by absorption of photonelectron is transfer to an electron accepting molecule , becomes oxidized

electron can transfer energy to pigment molecule and go back to ground state (inductive

resonance)

How do we absorb energy? Electron from ground to excited state.

PhotosynthesisGlucose

Glycolysis

Pyruvate

Aerobic Anaerobic

(Cellular Resp) (fermentation)

CHP7 PhotosynthesisSeptember-20-13 11:57 AM



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Caratenoid does not absorb yellow

Chlorophyll does not absorb green

Pigment molecules have absorptions within visible spectrum from 400 to 700

Absorption can be measured and displayed in an action spectrum

occurs in thylokoid membranes and involves Photosystems (assemblies of pigment-proteins)

Light energy absorbed by photosystem 2, pigments go to excited state through

inductive resonance, causes reduction of primary acceptor

1.

Ass electrons passes along ETC (Plastoquinone PQ to Cytochrome complex to

pastocyanin) PQ picks up hygrogen ions from stroma into lumen of tylakoid.

2.

Light energy absorbed by photosystem 1 causes reduction of primary acceptor, an

electron is passed to Ferredoxin then electrons are held by NADP+ reductase complex,

NADP+ reductase to NADPH (using 2 electrons and one proton)

3.

Proton gradient drives ATPase synthase complex: ADP+Pi to form ATP4.

Generation of oxygen occrus when water is split in order to reduce photosystem 2.

Chlorophyll P680 (Photosystem 2) Absorb ligh with shorter wavelength (higher energy) than

Clorophyll P700 (Photosystem 1)

Occurs in thylokoids in chloropasts

Electrons pass along series of oxidizing agents

Electros passed down an energy gradient (energy released)

From stroma into lume of thylokoid

Energy used to actively transport H+ AGAINST concentration gradient

Leads to production of ATP through PHOTOPHOSPHORYLATION.

H+ flow back into stroma using facilitated diffusion through channel proteins ATP Synthase

chemiosmosis ATP synthesis

Reduces NADP+ to NADPH

Reactants: Light, ADP +Pi,NADP+, H2O

Products: ATP and NADPH+H+, O2

Uses both photosystem with 2 electron transport chains

1) non- cyclic (linear) electron flow

Reactants: Light, ADP+Pi

Products: ATP

Uses only photosystem 1 (Flow of electron switches after ferredoxin, wich prevents

reduction of NADP+ and produces only ATP)

Compensates for greater ATP requirement in Calvin-Benson Cycle

2) Cyclic electron flow

Light reaction

1 Carbon joins with RuBP (Ribulose 1,5- bisphosphate) catalized by Rubisco which

produces two molecules of 3PG (3-Phosphoglycerate)

Carbon fixation of CO2 to 3PG

3PG undergoes phosphorylation (from ATP to ADP) and the Pi is added (morepotential energy), then that molecule undergoes reduction using NADPH to produce

G3P

Reduction to carbohydrate G3P

Regeneration of RUBP

(Refer to diagram!)

Occurs in chloroplast sotroma

Calvin Cycle (light independent)



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The G3P left over from the kelvin cycle is going to be the starting point

it uses the products of the light reactions, it also uses more ATP than NADPH (extra

ATP is produced in the cyclic electron flow in the light reaction)

Artificial photosynthesis

Harnessing light energy

Who is using the metabolic pathway?1.

Where are the reactions taking place?2.

What are the reactants and products?3.

What is happening to carbon compunds?4.

What is happening to free energy leves?5.

What is happening to ATP?6.

What is happening to energy carriers (NADP)?7.

How is the pathway regulated?8.

Suggestion questions



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Absorption spectrum of pigment molecules

P680 (P2) has an absorption maximum of 680nm

P700 (P1) has absorption maximum of 700 nm

(Both still have a spectrum, they are both chlorophyll molecules- absoption difference due to

association with proteins and therefore electron distribution)

Light energy absorbed by PII causes oxidation of P680 and reduction of primary acceptor.1.

e- is passed along ETC2.

Light energy absorbed by PI causes oxidation of P700 and reduction of primary acceptor. The

electron is passed to Ferredoxin, and then held by NADP+ reductase complex. NADP+ is the

reduced to NADPH (using 2e- and one proton)

3.

Proton gradient drives ATPase synthase complex (ADP+Pi=ATP)4.

PII uses light energy to split water.

This splitting is carried out by oxygen complex (manganese-oxygen-calcium cluster)

*Oxygenic photosynthesis is the result of the development of photosystem II*

Cyclic electron flow, electrons are passed down into ETC creating a chemical gradient that dives ATP

synthase (only ATP is produced)

The Calvin cycle

The Calvin cycle is a metabolic pathway found in the stroma of the chloroplast in which carbon

enters in the form of CO2 and leaves in the form of sugar.

The cycle spends ATP as an energy source and consumes NADPH2 as reducing power for adding high

energy electrons to make the sugar. There are three phases of the cycle

Rubisco

Most important enzyme in the biosphere

Converts ~ 100 billion tonnes of CO2 annually

Rubisco acts as a carboxylase

catalyzes CO2 fixationadds CO2 to RuBP to form 3PG

accounts for ~50% of the total protein content of plant leaves

MOST ABUNDANT PROTEIN IN THE WORLD

WHY? Catalytically VERY slow! Only 3-10 molecules of CO2 per second

Carbon Fixation, CO2 is incorporated into a five-carbon sugar named (RuBP). The enzyme

which catalyzes this first step is rubisco. It is the most abundant protein in chloroplasts and probably

the most abundant protein on Earth.

1.

Large subunit encoded by chloroplast genome (synthesized in stroma)

Small subunid encoded by nuclear genome (synthesized in cytosol, imported into

chloroplast, associates with large subunit)m

Requires coordinated gene expression of chloroplast and nuclear genome

Synthesis of rubisco:

The product of the reaction is a six-carbon intermediate which immediately splits in half to

form two molecules of 3-phosphoglycerate.

Reduction, ATP and NADPH2 from the light reactions are used to convert 3PG to G3P , the

three-carbon carbohydrate precursor to glucose and other sugars.

2.

Regeneration, more ATP is used to convert some of the of the pool of G3P back to RuBP, the

acceptor for CO2, thereby completing the cycle.

3.

For every three molecules of CO2 that enter the cycle, the net output is one molecule of (G3P).

For each G3P synthesized, the cycle spends nine molecules of ATP and six molecules of

CHP7 Photosynthesis IISeptember-26-13 3:58 PM



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NADPH2. The light reactions sustain the Calvin cycle by regenerating the ATP and NADPH2.

C3 pathway of photosynthesis

The problem with Rubisco

not only catalytically very slow... BUT the active site of Rubisco can also bind O2

O2 is competitive inhibitorRubisco acts as an oxygenase (carbon loss, no net gain, oxygen gain)as well as a carboxylase (carbon

gain)

Product of O2 binding is a two-carbon compound

requires ATP to convert it to CO2 for export

= PHOTORESPIRATION

How does this occur, and how can it be minimized?

Photorespiration

Light-dependent reactions (light energy transferred to ATP and NADPH

Light indendent reactions (CO2 released instead of being fixed into sugars)

Rubisco has higher affinity for CO2 than O2 but normal atmospheric conditions have abundance ofoxygen (oxygenation occurs 1/3)

Reaction occurs in:

chloroplasts1.

RuBP+ O2glycolate + 3PG

glycolate diffuses into peroxisomeconverted to glycine2.

in mitochondria glycine converted to serine and CO2 is released3.

This significantly reduces photosynthetic efficiency

Leaf anatomy and photorespiration

Large surface area

Waxy cuticle

Leaf anatomy



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Surface pores (stomata)

Delicate balance between minimizing water loss and regulating was exchange

Stomata regulates gas exchange

oxygenase function (and photorespiration) favoured in C3 plants under certain conditions:

1. high temperatures

2. low CO2 concentrations

3. high O2 concentrations

stomata close to reduce water loss

CO2 levels drop

O2 accumulates

reduces gas exchange

when hot (and dry)

solubility of CO2 and O2 decreases with increased temperature

as T increases, photorespiration takes away a greater proportion of carbon above 35C this can

result in 50% energy lost through photorespiration

Adaptations to minimize photorespiration

dominant form of inorganic carbon in aqueous environment is bicarbonate anion (HCO3-)

ATP-dependent pump

bicarbonate converted to CO2by carbonic anhydrase

CO2diffuses into chloroplast

Algae Pump CO2 into cells

Increased CO2 concentration out-competes O2

Alternative Photosynthetic Pathways

Plants that have evolved in tropical / sub-tropical areas have developed alternative pathways

Leaf anatomy modified to compensate for allosteric character of Rubisco

1. C4 Pathway uses spatialseparation2. CAM Pathway uses temporalseparation

1. C4 Pathway

C4 plants bypass photorespiration

C4 pathway raises [CO2] relative to [O2] so carboxylase function is favoured by Rubisco

lacks oxygenase activity

high affinity for CO2

Uses alternative enzyme = PEP carboxylase

i. PEP carboxylase in mesophyll

ii. chloroplasts fixes CO2 into 4-C oxaloacetate, then reduced to malateiii. Malate transported into bundle sheath cells

pyruvate converted to PEP requires ATP

iv. Malate oxidized to pyruvate to produce high [CO2] locally that enter Calvin-Benson Cycle



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2. CAM Pathway

= (Crassulacean Acid Metabolism)

Operate like C4 plants but use temporal separation

Stomata close during day

Prevents water loss and cuts off exchange of gases

Malate diffuses into cytosol where it is oxidized to pyruvate and CO2is released in high

concentration

carboxylase activity of Rubisco favoured

maximizes efficiency of Calvin Cycle



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Chemiosmotic ATP Synthesis

in Photosynthesis

- electron flow from light through pigment molecules provides energy for ATP synthesis= PHOTOPHOSPHORYLATION

in Cellular Respiration

- electron flow from oxidation of glucose through glycolysis / pyruvate oxidation / citric acid cycle

provides energy for ATP synthesis

= OXIDATIVE PHOSPHORYLATION



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CHP6 Cellular respiration (FINISH)September-26-13 4:30 PM



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Pyruvate oxidation and the citric acid cycle

Oxidative phosphorylation

Aerobic respiration permits the complete oxidation of glucose to energy trapped in ATP

Glycolysis happens in the cytoplasm of all cells

Matrix

Reactions removing electrons (pyruvate oxidation, citric acid cycle)

Inner membrane

Electron transfer

ATP synthesis by ATP synthase

Mithochondria

Product of glycolysis (pyruvate still contains useable energy)

Occurs only in aerobic pathway

Occurs in mitochondria matrix (In Eukaryotes)

Occurs in plasma membrane (in prok)

Multistep reaction catalyzed by enzyme complex Pyruvate dehydrogenase complex

Pyruvate is oxidized to acetate and converted to acetyl group which releases 1 CO2 per pyruvate and energy1.

Energy is captured when NAD+ is reduced to NADH+H+2.

Remaining energy captured when acetyl group combines with coenzyme A yielding Acetyl-CoA (Product ofpyruvate oxidation) .

3.

Pyruvate oxidation

completes oxidation of pyruvate to CO2

Only occurs in aerobic patway

In cytoplasm in prokaryotes

Occurs in mitochondrial matrix in eukaryotes

8 steps, each catalyzed by specific enzyme

First step: Acetyl group of Acetyl-CoA(2C) combines with oxaloacetate (4C), forming citrate (6C)

Next 7 steps decompose citrate back to oxaloacetate (cyclic) with relese of 2x CO2

NADH and FADH2 produced relay electrons to the ETC

Citric acid cycle (Krebs cycle)

NADH and FADH2 account for most of the energy extracted so far

The electron carriers donate electrons to ETC

ETC creates a proton-motive force (ATP synthesis via oxidative phosphorylation)

Occurs in mitochondrial inner membrane (Eukaryotes) and plasma membrane in prokaryotes

Oxidative phosphorylation

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Only occurs in aerobic pathway

Electros passed down from NADH and FADH2 to O2

Recycling process involving electron transfer via energy carriers (NADH+H+/FADH2)

Respiratory chain (ETC)1.

Active transport of H+ out of matrix (against concentration/charge gradient) at complex I and IV and by UQ2.

Electrochemical gradient

Proton-motive force (PMF)

Source of potential energy

Establishes gradient of proton concentration and electric charge

Chemiosmosis

Facilitated diffusion through proton channel (ATP synthase complex) back into matrix coupled to ATP synthesis3.

Oxidative phosphorylation: Electron Transport and chemiosmosis

Basal unit forms a channel for H+ to pass freely

Proton-motive force propels protons through channel- down the concentration gradient

Binding of protons to headpiece causes rotation that catalyzes the formation of ATP

Smallest molecular rotary motor know

ATP synthase (molecular motor)

Electron transport and chemiosmosis ATP synthesis are separate and distinct processes

Mechanisms prevent formation of proton-motive force

Possible to have high electron transport without ATP synthesis

Some organisms alter the expression of uncoupling proteins as a means of regulating body temperature (eg.

Hibernating animals)

Electron transport and chemiosmosis can be uncoupled



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Rates of glycolysis and citric acid cycle can be regulated

ATP

ADP

NAD+

NADH+H+

on allosteric enzymes

-Reactions are increased or decreased by actions of:

Allosteric control

How are metabolic pathways regulated?

Control point in Glycolysis at reaction 31.

Involves glycolytic enzyme phosphofructokinase

Enzyme inhibit by abundant ATP from oxidative

phosphorylation (Slows down glycolysis)

Enzyme activated by abundant ADP (which speeds up glycolysis)

Control point in citric acid cycle at reaction 32.

Involves citric acid cycle enzyme isocitrate dehydrogenase

Enzyme inhibit by ATP and NADH+H

Enzyme activated by ADP and NAD+

Regulation in glycolysis and cellular respiration

Many archea, bacteria, and most eukaryotes

Absolute requirement for oxygen

Huge energy demands not met by glycolysis/fermentation

Strict aerobes1.

Can switch between fermentation and full oxidative pathway

Facultative anaerobes2.

Require O2-free environment to survive

O2 can be toxic- reactive oxygen species (ROS) are powerful oxidizing agents

Obligate (strict) anaerobes3.

Organisms differ in metabolic pathway (ability to use oxygen)

diversity of life notes

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