Diversity of Life Notes

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 order 1.
Harness and utilize energy 2.
Reproduce (heritable genetic information) 3.
Respond to stimuli 4.
Homeostasis 5.
Growth and develop 6.
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 environments
Adapt 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 DNA 2.
System of information transfer (DNA, RNA, PROTEIN) 3.
system of protein assembly using ribosomes and mRNA, tRNA, 4.
ATP as source for chemical energy 5.
Metabolic pathway to generate ATP 6.
Proteins: Major structure and catalytic molecule 7.
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) Genus
2) 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 Life
September-20-13 7:59 PM
BIOA01 Module 1 (revized) pgina 1
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
DNA repair (Base uracil is replaced with thymine).
CHP3 The Origins & Chemical Building Blocks of Life
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 compartment
System 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 did
evolved the capacity for aerobic respiration
How did life evolve?
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
Extreme temperature
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*
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
Replication 1.
Segregation 2.
Cytokinesis 3.
Asexual method of reproduction: Binary fission
Rapid reproduction and mutation 1.
Conjugation (transfer via pilus)
Transformation (from surroundings)
Transduction (bacteriophages carry gnes from host cell to another)
Genetic recombination 2.
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)
Metabolic diversity
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 the
human body
Beneficial effects
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 envelope
Presence 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 chloroplast a.
Derived only from pre-existing mitochondria and chloroplasts b.
Divide by binary fission c.
Reproduction 2.
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 cells
Used 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 similar to cyanobacteria

Mitochondrial RNA most similar to proteobacteria
Sequence analysis 6.
Evidence supporting theory of endosymbiosis:
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
Proteins then delivered to other regions of the cell witin small vesicles
Rough ER
Endoplasmic reticulum (little net)
Nucleus
CHP2 Eukaryotic cells (I)
Cisternae formed by a single membrane(enclosed space called ER lumen)
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
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 cell 1.
Drives cell motility (motor protein-driven movement, kinesin molecule *walking*, ATP
dependent process)
2.
Filopodia
Microvilli
Forms cell surfaces structures which probe the environment 3.
Movement of cargo inside the cell 4.
Separation of chromosomes
Cytokinesis
Cell division 5.
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
-Cilia beat in oarlike stroke which moves fluids over the cell surface
CHP2 Eukaryotic cells (II)
-Cilia beat in oarlike stroke which moves fluids over the cell surface
it is composed of cellulose fibres
embedded in branched carbohydrate network
Perforated by small channels (plasmodesmata)- all ions and small molecules to move
between cells
Cell wall (supports and protects)

Site of photsynthesis
molecules in thylakoid membrane absorb light energy
Enzymes in stroma use this energy to make carbohydrates
Chloroplast
Large vesicles- perfomr specialized functions: organelle
90% of the cell volume may be occupied by one or more central vacoules
Surrounded by a tonoplast (membrane)- contains transport proteins to move materian
in and out
Salts
Sugars
Pigments
Waste products
Storage functions
Central vacuole
Specialized structures of plant cells
Lysosomes
Centrosomes (with centrioles)
Flagella (present in some plant sperm)
Animals cell
Chloroplasts
Central vacuole
Cell wall
Plasmodesmata
Plant cells
Comparison of plant and animal cells
Importance of membranes for living organisms:
Provides internal environment 1.
concentration of molecules inside of cells 2.
selectively permeable 3.
Singer.Nicolson Fluid Mosaic Model (1972
Proteins not necess. mobile while phospholipids are.
Plasma membrane (phospholipid bilayer) in which relatively disperse membrane proteins (not
relatively diffuse) could freely diffuse.
Phospholipd structure
Polar Hydrophilic head (water loving) composed of glycerol, phosphate group + polar unit
Hydrophobic tail (hate) composed of fatty acid chains (Hydrocarbon, it can modify fluidity by
ultering saturation)
Amphipathic (philic/phobic)
Hydrophobic effect: Tendency of POLAR molecules to exclude hydrophobic molecules
Micelle, single layer
Liposome, double layer
Planar bilayer
This nature enables to self assemble into structures within aqueous env.
Frye-Edidin experiment
Marked membrane proteins of human cells with fluorescent markers. and same with mouse cells.
They fuse two cells together to create hybrid cell. At first proteins segregated and then they mixed
(moved, fussing).
-All fatty acid are initially sinthesized as saturated molecules (viscous membrane)
-Enzymes (desaturases) changes saturation. If unsaturated the membrane becomes more
fluid. (increasing spaces between molecules)
Membrane fluidity is dependent on fatty acid composition and temperature.
Bacteria, archea, protist, plants
Organisms can regulate fatty acid saturation by regulating proportion of unsaturated fatty acids by
regulation desaturase transcript
Structure: philic(towards aquous env.)/phobic
Sterols(act as buffers) influence membrane fluidity
at low tem: disrupt fatty acid association
at high tem: restrain mov of molecule
Plasma membrane proteins
Traverse lipid bilayer
-Extracellular (sticks out) recognition, it has binding site
-Transmembrane(embedded in bilayer) stretch of 17-20 nonpolar aminoacids that form
alpha helix in the membrane.
distinct domains
Integral membrane proteinsn(EXPAND):
CHP5 Cell Membranes
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
transport 1.
Enzymatic activity 2.
Signal transduction (recognition of signals) 3.
Attachment 4.
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 from

hydrophobic 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
symport (ions moving in same direction but against concentration gradient)
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.
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 contents
are 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!
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
In order for organisms to display order, their surroundings have to have lower order
CHP4 Energy and Enzymes
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 down
there 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 hydrolysis
The 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 unchanged when 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 of proteins 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
Expose reactant to altered charge environment (alter substrate to favour catalysis)
Enzymes induce transition state by:
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 of phosphatases, 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
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 a fixed amount of energy that is inversely related
to its wavelength) that have wave-like characteristics
release of energy obtain by absorption of photon
electron 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.

Photosynthesis
Glucose
Glycolysis
Pyruvate
Aerobic Anaerobic
(Cellular Resp) (fermentation)
CHP7 Photosynthesis
September-20-13 11:57 AM
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 ATP 4.
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 (more
potential energy), then that molecule undergoes reduction using NADPH to produce
G3P
Reduction to carbohydrate G3P
Regeneration of RUBP
The G3P left over from the kelvin cycle is going to be the starting point
(Refer to diagram!)
Occurs in chloroplast sotroma
Calvin Cycle (light independent)
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
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 ETC 2.
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 CO
2
and leaves in the form of sugar.
The cycle spends ATP as an energy source and consumes NADPH
2
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 fixation adds 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, CO
2
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 NADPH
2
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 CO
2
, thereby completing the cycle.
3.
For every three molecules of CO
2
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
NADPH
2
. The light reactions sustain the Calvin cycle by regenerating the ATP and NADPH
2
.
CHP7 Photosynthesis II
NADPH
2
. The light reactions sustain the Calvin cycle by regenerating the ATP and NADPH
2
.
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 inhibitor
Rubisco 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 of
oxygen (oxygenation occurs 1/3)
Reaction occurs in:
chloroplasts 1.
RuBP+ O2 glycolate + 3PG
glycolate diffuses into peroxisome converted to glycine 2.
in mitochondria glycine converted to serine and CO2 is released 3.
This significantly reduces photosynthetic efficiency
Leaf anatomy and photorespiration
Large surface area
Waxy cuticle
Surface pores (stomata)
Leaf anatomy
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 spatialseparation
2. 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 malate
iii. 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
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
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
CHP6 Cellular respiration (FINISH)
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 energy 1.
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 of
pyruvate 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
Only occurs in aerobic pathway
Oxidative phosphorylation
CHP6 Cellular respiration II
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 UQ 2.
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 synthesis 3.
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

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 3 1.
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 3 2.
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 aerobes 1.
Can switch between fermentation and full oxidative pathway
Facultative anaerobes 2.
Require O2-free environment to survive
O2 can be toxic- reactive oxygen species (ROS) are powerful oxidizing agents
Obligate (strict) anaerobes 3.
Organisms differ in metabolic pathway (ability to use oxygen)

Diversity of Life Notes

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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

How is all life on earth related?

Anoxygenic photosynthesis, Evolution of oxygenic pho, produce O2.

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

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

Chloroplasts RNA most similar to cyanobacteria

Some genes relocated to nucleus through HGT)

Why do both mitochondria and chloroplasts still retain a genome?

Nucleolus: site of rRNA synthesis

Maintain cell shape

The cytoskeleton is composed of three main types of fibres:

Cell wall (supports and protects)

-Channel proteins: Hydrophilic pathways (Molecules are protected from

All things obey the laws of thermodynamics

Competitive inhibition (active site) shaote resemble substrate

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

Integration of two processes:

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

Requires coordinated gene expression of chloroplast and nuclear genome

Electron transport and chemiosmosis can be uncoupled

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