Chapter 1-Light and Life

Light serves 2 functions: 1) a source of energy that directly or indirectly sustains virtually all organisms.
2) light provides organisms with info about the physical world that surrounds them

- Wavelength: distance between 2 successive peaks

- Light: most commonly defined as the por on of the electromagnetic spectrum that humans can
detect with their eyes o 400-700 nm o Light has no mass o Particle-wave duality: light is a
wave of protons
▪ Inverse relationship: the longer the wavelength, the lower the energy of the
photons it contains
▪ Photons: stream of energy particles
- Although light has no mass, it is s ll able to interact with matter and cause change o When
a photon of light hits an object, the photon has 3 possible fates: 1) reflected off object 2)
transmitted through object or 3) absorbed by object
- A major class of molecules that are very efficient at absorbing photons are called PIGMENTS o
3 types: 1) chlorophyll a (involved in photosynthesis) 2) retinal (involved in vision) and
3)indigo (in jeans) o They can absorb photons easily because: they have a region
where carbon atoms are covalently bonded to each other with alternating single and
double bonds (conjugated system) which results in the delocalization of electrons…means
the electrons are available to interact with a photon of light
o Pigments absorb light at different wavelengths
▪ Differs in the amount of excited states a pigment has
o Photon absorption is related to the concept of colour
▪ A pigments colour is the result of photons of light that it DOES NOT absorb
- The basic light-sensing system is termed the PHOTORECEPTOR.
o Most common photoreceptor is rhodopsin (basis of vision in animals) o Each rhodopsin
molecule consists of a protein called opsin that binds a single pigment molecule called
retinal. Opsins are membrane proteins that s pan a membrane multiple times and form
a complex with the retinal molecule at the centre
o Absorption of a photon of light causes the retinal pigment molecule to change shape.
This change triggers alterations to the opsin protein which triggers downstream events,
including alterations in intracellular ion concentrations and electrical signals.
- Eyespot:
o In organisms such as plants, algae, and invertebrates o Light sensitive structure o
Within chloroplast of the cell o Photoreceptors of the eyespot allow the cell to sense
light direction and intensity
o Does not play a role in photosynthesis
o Light absorption by the eyespot is linked to the swimming response by a signal
transduction pathway
o In plants: a photoreceptor called phytochrome senses the light environment
 ▪ Present in the cytosol
▪ Phytochrome becomes active and initiates a signal transduction pathway that
reaches the nucleus
▪ Critical for the normal developmental process activated when seedlings are
exposed to light
- The eye can be defined as the organ animals use to sense light
O The process of vision requires not only a n eye to focus and absorb incoming light but also a
brain or at least a simple nervous system that interprets signals sent from the eye
▪ We see with our brain, not with our eyes
o Simplest eye: ocellus
▪ The photoreceptor cell is actually a modified nerve cell that contains thousands
of individual photoreceptor molecules
▪ In flatworms o
Compound eyes:
▪ Common in insects
▪ Built of hundreds of individual units called OMMATIDIA fi ed closely together
▪ Incoming light gets focused onto a bundle of photoreceptor cells by the
ommatidia
▪ Brain receives a mosaic image of the world
▪ Good at detecting movement
o Single-lens eye:
▪ Most vertebrates including humans
▪ Light enters through the transparent cornea; a lens concentrates the light and
focuses it onto a layer of photoreceptor cells at the back of the eye, the retina.
The photoreceptor cells of the retina send information to the brain through the
op c nerve.
- The photoreceptor cells that line the human retina can be damaged by exposure to bright light
o Photo-oxidative damage: the absorption of excess light energy can result in excited
electrons reacting with O2, producing what are called reactive oxygen species
o Ionizing radiation: photons at these wavelengths are energetic enough to remove an
electron from an atom resulting in the forma on of ions
o Dimers: damage to structure of DNA resulting in change of shape of the double helix
and prevents its replica on.
- Many organisms synthesize melanin, a pigment that strongly absorbs ultraviolet light o
Humans synthesize melanin in specialized skin cells called melanocytes
▪ Melanin synthesis increases upon skin exposure, which results in the brown
colour of a suntan
▪ People with high melanin levels who live in regions that do not receive
abundant sunlight are susceptible to vitamin D deficiency
● Some ultraviolet radiation is good to synthesize vitamin D
 - Circadian Rhythms o Circa=around diem=day
o Governed by an internal biological clock
o Free running: run along me independently of external conditions
o A biological clock is built around a small set of so-called clock genes and clock proteins
▪The expression of these genes and proteins is autoregulatory: they control their
own abundance
o Presence of biological clock enhances an organism’s ability to survive under ever-
changing environments by giving them the ability to anticipate or predict when a
change will occur.
o Photoperiod: when organisms keep track of the changing seasons in part by being able
to measure day length
o Suprachiasmatic nucleus (SNC): central clock which regulates the timing of clocks in
peripheral issues
▪ Receives direct light inputs through the op c nerve of the eyes s o that it can be
reset periodically
- Pollination involves the movement of pollen from anthers (male parts) of one flower, to the
stigma (female parts) of the same or other flowers to effect fertilization and production of fruit
and seeds
O Plants that use animals as pollinators must obtain the correct candidates
o Bees and some insects can see ultraviolet regions o f the electromagnetic spectrum and are
particularly attracted to flowers that strongly reflect ultraviolet radiation
- Camouflage is used for concealment from either predators or prey
O Colour, pattern and behaviour
- The presence of artificial light disrupts the orientation of nocturnal animals
- With decreasing light levels, we first lose our ability to see colour, followed by our ability to
distinguish shapes
o Rod receptors, which do not perceive different colours, are about 100 m as sensitive to light
as cone receptors
- Bioluminescence: make their own light
O Chemical energy in the form of ATP is used to excite an electron in a substrate molecule
from the ground state to a higher excited state, and when the electron returns to the ground
state, the energy is released as a photon of light
o Used to attract mate or prey, camouflage and communication
o Has not been reported in land plants or higher vertebrates

Chapter 2- the cell: an overview

- Cell theory
o All organisms are composed of one or more cells
o The cell is the basic structural and functional unit of all living organisms
 o Cells arise only from the division of pre-existing cells
- If cells are broken open, the property of life is lost
- Cells are bounded by the PLASMA MEMBRANE
O Bilayer made of lipids with embedded protein molecules
o Hydrophobic barrier
o Semi permeable…maintains the specialized internal ionic and molecular environments
required for cellular life
- Central region of the cell
O Contains DNA molecules
O Genes: segments of DNA that code for individual proteins
O Contains proteins that help maintain the DNA structure and enzymes that duplicate DNA
and copy its information into RNA -
Cytoplasm:
o Contains organelles, cytosol and cytoskeleton o Cell’s vital ac vi es occur in the
cytoplasm o Organelles: small, organized structures important for cell function o
Cytosol: aqueous solution containing ions and various organic molecules o
Cytoskeleton: protein-based framework of filamentous structures that, among other
things, helps maintain proper cell shape and plays key roles in cell division and
chromosome segregation from cell genera on to cell genera on - Prokaryotic cells:
o Three common shapes: spherical, rodlike and spiral
o Does not contain a nucleus
o Has a nucleoid: DNA-containing central region of the cell that has no boundary
membrane separa ng it from the cytoplasm
o Individual genes in the DNA molecule encode the info required to make proteins.
▪ This info is copied into mRNA (messenger RNA)
▪ Ribosomes: use the info in the mRNA to assemble amino acids into proteins
o Contains a cell wall-provides rigidity and protects cell
▪ Cell wall is coated with an external layer of polysaccharides called GLYCOCALYX
● When its diffused and loose=slime layer
● When its gela nous and firm=capsule
● Helps protect cells from physical damage and desicca on and may
enable a cell to a ach to a surface
o Plasma membrane: contains most of the molecular systems that metabolize food
molecules into the chemical energy of ATP
o Most cellular functions occur either on t he plasma membrane or in the cytoplasm
o Flagella: long, threadlike protein fibres that rotate in a socket in the plasma membrane
and cell wall to push the cell through a liquid medium
o Pili: hair-like shape of protein extending from cell that helps to a ach the cell to surfaces
- Eukaryotic cells
o Divided into four major groups: protists, fungi, animals and plants o Defined as having cells
where DNA is contained within a membrane-bound compartment called the nucleus
o Cytosol: participates in energy metabolism and molecular synthesis and performs
specialized functions in support and motility
o The nucleus is separated from the cytoplasm by the NUCLEAR ENVELOPE, which consists
of 2 membranes, one layered just inside the other and separated by a narrow space
(lamins are found on the inner surface)
o Embedded in the nuclear envelope are many hundreds of nuclear pore complexes
▪ Large, cylindrical structure formed of many types of proteins called the
nucleoporins
▪ Exchanges components between the nucleus and cytoplasm and prevents the
transport of material not meant to cross the nuclear membrane
▪ Nuclear pore: path for the assisted exchange of large molecules such as proteins
and RNA molecules
▪ Some proteins need to be imported into the nucleus
● These are distinguished by the presence of a special, short amino acid
sequence called a nuclear localization signal
▪ Nucleoplasm: liquid or semi-liquid substance within the nucleus
▪ Chroma n: takes up most of the space in the nucleus-combination of DNA and
proteins
o Each individual DNA molecule with its associated proteins is a EUKARYOTIC
CHROMOSOME
▪ Chroma n: refers to any collection of eukaryotic DNA molecules with their
associated proteins
▪ Chromosome: refers to a one complete DNA molecule with its associated
proteins
o Nucleoli: mass of small fibres and granules
▪ From a round the genes coding for the rRNA molecules of ribosomes
o Ribosomes:
▪ Eukaryotic ribosomes are larger than prokaryotic
▪ They use info in mRNA to assemble amino acids into proteins
▪ Many ribosomes are attached to membranes
● Most are attached to the ER
o Endomembrane system
▪ Collection of interrelated membranous sacs that divide the cell into functional
and structural compartments
▪ Includes nuclear envelope, endoplasmic reticulum and golgi complex
▪ Synthesis and modification of proteins and their transport into membranes and
organelles, synthesis of lipids, detoxification of some toxins
 ▪ Membranes of the system are connected either directly (physically) or indirectly
(vesicles)
● Vesicles: small membrane-bound compartments that transfer
substances between parts of the system
o Endoplasmic reticulum:
▪ Extensive interconnected network of membranous channels and vesicles called
CISTERNAE
▪ Each cisternae is formed by a single membrane that surrounds an enclosed
space called the ER lumen.
▪ 2 ER: rough and smooth
● Rough: many ribosomes that stud its outer surface
● Proteins made on ribosomes a ached to the ER enter the ER lumen,
where they fold into their final form
o Chemical modifications of these proteins occur in the lumen o Proteins are then
delivered to other regions of the cell
o For most proteins made on the rough ER, the next destination is the Golgi complex,
which packages and sorts them to delivery to their final destinations.
● Smooth: membranes have no ribosomes a ached to their surfaces
● Has various functions in the cytoplasm
● Synthesis of lipids and break down of toxins
▪ Rough and smooth ER are often connected
▪ The relative proportions of rough and smooth ER reflect cellular activities
in protein and lipid synthesis
o Golgi complex
▪ Consists of a stack of flattened, membranous sacs known as cisternae
▪ Not interconnected
▪ Receives proteins that were in the ER and transported in vesicles. When vesicles
contact the CIS face of the complex (side facing the nucleus), they fuse with
the golgi membrane and release their contents directly into the cisternal.
● Here they are chemically modified
▪ The modified proteins are transported within the Golgi to the TRANS face of the
complex (faces the plasma membrane), where they are sorted into vesicles that
bud off the margins of the Golgi
▪ Membrane of a vesicle that fuses with the plasma membrane becomes part
of the membrane….used to expand the surface of the cell during cell growth.
● Used in exocytosis
o Lysosomes
▪ Small, membrane-bound vesicles that contain more than 30 hydroly c enzymes
for the diges on of many complex molecules, including proteins, l ipids, nucleic
acids and polysaccharides
 ▪ Found in animals but not plants
▪ Central vacuole is the equivalent in plants
▪ Assume variety of sizes and shapes
▪ Are formed from the Golgi complex
▪ Very acidic compared to pH of cytosol….this difference reduces the risk to the
viability of the cell should the enzymes be released from the vesicle
▪ Can digest several types of materials
▪ Autophagy: digest organelles that are not func oning correctly
▪ Phagocytosis: process in which some types of cells engulf bacteria or other
cellular debris to break them down
● Phagocytes use this (white blood cells)
▪ Lysosomal storage disease: hydroly c enzymes normally found in lysosome is
absent
● Result: substrate of that enzyme accumulates in the lysosomes and
eventually interferes with normal cellular ac vi es
o Mitochondria
▪ Membrane-bound organelles in which cellular respira on occurs
▪ Generate most of the ATP in the cell
▪ Requires oxygen
▪ Outer mitochondrial membrane: smooth and covers outside of the organelle
▪ Inner mitochondrial membrane: surface are is expanded by folds called cristae
▪ Mitochondrial matrix: innermost compartment
▪ Contains DNA and ribosomes that resemble the equivalent structures in
bacteria
● This suggests that mitochondria originated from ancient bacteria that
became permanent residents of the cytoplasm during the evolu on of
eukaryo c cells
o Cytoskeleton
▪ Interconnected system of protein fibres and tubes that extends throughout the
cytoplasm
▪ 3 major types: microtubules, intermediate filaments and microfilaments
▪ Microtubules:
● Smallest
● Dimers are organized head-to-tail in each filament, giving the
microtubule a polarity oContains a 1 (plus) end and 2 (minus) end
● Dynamic-changing lengths as required by their func on
● Change length by addi on or removal of tubulin dimers o
Adding or detaching occurs more rapidly at the 1 (plus) end
 ● Many of the cytoskeleton microtubules in animal cells are formed and
radiate outward from a site called the CELL CENTRE or CENTROSOME
● At its midpoint=centrioles
● Microtubules that radiate from the centrosome anchor the ER, Golgi
complex, lysosomes, secretory vesicles and mitochondria in posi on o
Also provides tracks along which vesicles move from the cell
interior to the plasma membrane
● Animal cell movements are generated by “motor” proteins that push
or pull against microtubules o One end is firmly fixed
o Other end has reac ve groups that “walk” along another microtubule
by making an a achment, forcefully swivelling a short distance, and then
releasing
o Motor proteins that walk along microfilaments are called
MYOSINS and the ones that walk on microtubules are called
DYNEINS and KINESINS
● Intermediate filaments o Only found in mul cellular
organisms o Tissue specific in their protein composi on o
Providing structural support in man cells and ssues
● Microfilaments o Largest o Consists of 2 polymers of ac n
subunits wound around each other in a long helical spiral o
Asymmetrical in shape o Have polarity o Have 1(plus) end and 2
(minus) end o Best known as one of the 2 components of the
contrac le elements in muscle fibres of vertebrates
o Involved in the ac vely flowing mo on of cytoplasm called cytoplasmic
streaming
▪ When animal cells divide, microfilaments are
responsible for dividing the cytoplasm
o Flagella: propel a cell through a watery medium o Cilia: move fluids over
the cell surface
- Specialized structures of plant cells o Chloroplasts:
▪ Sites of photosynthesis
▪ Members of a family of plant organelles called PLASTIDS
● Amyoplasts: colour-less plas ds that store starch, a product of
photosynthesis
● Chromoplasts: contain red and yellow pigments and are responsible for
the colours of ripening fruits or autumn leaves
● All plas ds contain DNA genomes and molecular machinery for gene
expression and the synthesis of proteins on ribosomes
▪ Contain outer and inner boundary membrane
 ● These two boundary membranes completely enclose an inner
compartment called the STROMA
● Within the stroma is a third membrane system that consists of fla ened
sacs called THYLAKOIDS.
o In higher plants, the thylakoids are stacked one on top of the other forming
GRANA
o Thylakoid membranes contain molecules that absorb light energy and
convert it to chemical energy is photosynthesis
▪ Primary molecule absorbing light is chlorophyll-green
pigment present in chloroplast
o Central vacuole
▪ Large vesicles
▪ Membrane that surrounds the central vacuole called the TONOPLAST, contains
transport proteins that move substances into and out of the central
vacuole
▪ As plant cells mature, they grow primarily by increases in the pressure and
volume of the central vacuole
o Cell wall
▪ Extracellular structure because it is located outside the plasma membrane
▪ Provide support to individual cells, contain t he pressure produced in the central
vacuole and protect cells against invading bacteria and fungi
- Specialized cells in animals o Cell adhesion molecules: bind cells together
o Cell junc ons: seal the spaces between cells and provide direct communica on between
cells
o Extracellular matrix (ECM): supports and protects cells and provides mechanical linkages
o Cell adhesion:
▪ Glycoproteins embedded in the plasma membrane
▪ Bind to specific molecules on other cells
▪ As an embryo develops into an adult, the connec ons made by cell adhesion
become permanent and reinforced by cell junc ons
o Cell junc ons:
▪ Anchoring junc on: adjoin cells adhere at a mass of proteins anchored beneath
their plasma membrane by many intermediate filaments
▪ Tight junc on: form between adjacent cells by fusion of plasma membrane
proteins on their outer surfaces
● Seal ght enough to prevent leaks and of ions or molecules between cells
▪ Gap junc on: cylindrical arrays of proteins form direct channels that a llow small
molecules and ions to flow between the cytoplasm of adjacent cells
o ECM
▪ Primary func on is protec on and support
 ▪ Glycoproteins are the main component
▪ Collagen: forms fibres with great tensile strength and elas city

Chapter 3 – Defining life and its origins (3.4b,3.4e,3.5)

- Heterotrophs: organisms that obtain carbon from organic molecules o Earliest forms of life
- Autotrophs: obtain carbon from the environment in an inorganic form, most o en carbon
dioxide.
o Eg. Plants and other photosynthe c organisms
- All present day organisms can be categorized into one of 3 domains: Archae, Bacteria and
Eukarya o Archaea are more closely related to eukaryotes than to
bacteria
- All life forms currently on Earth share a remarkable set of common a ributes:
o 1) cells made of lipid molecules brought together forming a bilayer o 2) a gene c
system based on DNA o 3) a system of informa on transfer-DNA to RNA to protein o
4) a system of protein assembly from a pool of amino acids to transla on using
messenger RNA (mrna) and transfer RNA (trna) using ribosomes
o 5) reliance on proteins as the major structural and cataly c molecule o 6) use of ATP as
the molecule of chemical energy o 7) the breakdown of glucose by the metabolic
pathway of glycolysis to generate ATP o *the fact that these 7 a ributes are shared by all
life on Earth suggests that all present-day organisms descended from a common
ancestor
o LUCA: the original life form from which all archaea, bacteria and eukaryotes are
descended
▪ Last Universal Common Ancestor
- Present-day eukaryo c cells have 2 major characteris cs that dis nguish them from archaea and
bacteria o 1) separa on of DNA and cytoplasm by a nuclear envelope o 2)
presence in the cytoplasm of membrane-bound compartments with specialized metabolic and
synthe c func ons
- A large amount of evidence indicates that mitochondria and chloroplasts are actually descended
from a prokaryote: mitochondria came from aerobic bacteria and chloroplast came from
cyanobacteria o Endosymbiosis: state that the prokaryo c ancestors of modern mitochondria
and chloroplast were engulfed by larger prokaryo c cells, forming a mutually
advantageous rela onship called a SYMBIOSIS
▪ Slowly over me the host cell and the endosymbionts became inseparable parts
of the same organism
- 6 lines of evidence suggest that mitochondria and chloroplast have dis nct prokaryo c characteris
cs o 1) Morphology: same shape to that of archaea and bacteria o 2) Reproduc on: mitochondria
and chloroplast are derived from pre-exis ng mitochondria and chloroplast. They divide by
binary fission, which is how bacteria and archaea divide
 o 3) Gene c informa on: Both mitochondria and chloroplast contain t heir own DNA, which
contains protein-coding genes that are essen al for organelle func on
o 4) Transcrip on and transla on: Both chloroplast and mitochondria contain a complete
transcrip on and transla on machinery
o 5) Electron transport: Both have ETCs and it is contained in the inner membrane o
6) Sequence analysis: sequencing of the RNA that makes up the ribosomes of
chloroplasts and mitochondria firmly establishes that they belong on the bacterial
branch
- Genome: defined as the complete complement of an organism’s gene c material -
Horizontal Gene Transfer (HGT) (development of the nucleus):
o Change in loca on of the gene-the nucleus as opposed to the mitochondria o
Chain of events:
▪ 1) some of the genes that were within the protomitochondrion or
protochloroplast were lost
▪ 2) many of the genes within them were relocated to the nucleus o
Pertains to any movement of genes between organisms other than to offspring -
Development of the endomembrane system:
o Most widely held hypothesis is that it is derived from the infolding of the plasma
membrane
- Increased complexity requires increased energy
- Unlike a true mul cellular organism, a cell colony is a group of cells that are all o f one type:
there is no specializa on in cell structure or func on

Chapter 4-Energy and Enzymes

- Life (chemical+physical) are energy-driven processes.

o We detect it through its ability to do work o Energy: capacity to do work o
Energy can exist in many different forms, including heat, chemical, electrical
and mechanical forms.
- Energy can be grouped into 2 types:
1) Kine c energy: energy possessed by an object because it is in mo on.
a. Falling rock, kicked football, flow of electrons
b. Photons of light are also a form of kine c energy
2) Poten al energy: stored energy-the energy an object has because of its loca on or
chemical structure.
a. A boulder at the top of a cliff

Thermodynamics-the study of energy and its transforma ons

o System: object being studied

 a. Isolated: one that does not exchange ma er or energy with its surroundings.
Eg thermos bo le
b. Closed: can exchange energy but not ma er with its surroundings. E.g
greenhouse or earth.
c. Open: both energy and ma er can move freely between the system and its
surroundings. Eg ocean.
o Surrounds: everything outside the system o Universe: total of the system and the
surroundings
- First Law of thermodynamics: energy can be transformed from one form into another or
transferred from one place to another, but it cannot be created or destroyed. Also called the
“principle of the conserva on of energy”. Eg Niagara Falls.
- Each me energy is transformed from one form into another, some of the energy is lost and
unavailable to do work.
o Eg heat: energy associated with random molecular movement.
o In most cases, heat cannot be harnessed to do work; instead, it is simply lost to the
environment.
o The unsuable energy that is produced during energy transforma ons results in an
increase in the disorder or randomness of the universe=ENTROPY
- Second Law of thermodynamics: the total disorder of a system and its surroundings always
increases.
o Systems will move spontaneously toward arrangements with greater disorder-greater
entropy
o It takes energy to maintain low entropy
- Does life obey second law of thermodynamics: yes o Living things bring in energy and ma er
and use them to generate order out o f disorder.
o Some food supplies muscles but most food energy is used to simply maintain our cells in
their highly ordered state.
o Living things give off heat and carbon dioxide which increases the entropy of the
surroundings.
▪ The entropy of a system is allowed to decrease as long as the entropy of the
universe as a whole increases.
- Spontaneous reac ons: a reac on will occur. May proceed slowly or quickly.
o 2 factors are needed to determine whether a reac on is spontaneous:
1) The change in energy content of a system
a. Reac ons tend to be spontaneous if the products have less poten al energy
than the reac ons.
i. The poten al energy in a system is called ENTHALPY or H
ii. Endothermic: products have more poten al energy than reactants
iii. Exothermic: reactants have more poten al energy than products
 2)Change in entropy

b. Reac ons tend to be spontaneous when the products are less ordered than
the reactants.
i. Generally, changes from solid to liquid etc increase entropy.
Changes from liquid to solid etc decrease entropy
ii. Eg. Glass of ice: mel ng ice at 25C is endothermic but spontaneous
because of increase in entropy.
- Free energy : por on of a system’s energy that is available to do work (G) o In living
organisms, free energy accomplishes the chemical and physical work involved in ac vi es such as
the synthesis of molecules, movement, and reproduc on.
o G=Gfinal state-Gini al state o G=H-TS
▪ H=change in enthalpy
▪ S=change in entropy
▪ T in absolute temperatue=+273.16
▪ Free energy change as a system goes from the ini al to the final state is the sum
of the changes in energy content and entropy
o For a reac on to spontaneous, G has to be nega ve ( free energy of products must be less
than t hat of reactants=exergonic (catabolic).
o Systems that have high free energy are less stable than systems that h ave less free
energy.
- Chemical equilibrium: the point at which there is no longer any overall change in the concentra
on of products and reactants o The point of equilibrium is related to the G for the reac on. Eg
some reac ons have G close to 0 and are thus readily reversible.
o Free energy of the system are lower when the products are “contaminated” or diluted
by some molecules of reactant than when the system is made up of pure produce
because the mixture has higher entropy.
- Metabolism: defined as the sum of all of the chemical reac ons that t ake place within an
organism. Ending of one reac on is the beginning of another. o Exergonic reac on:
releases free energy…G is nega ve o Endergonic reac on: consumes free energy…G is posi ve
o Catabolic pathway: energy is released by the breakdown of complex molecules to
simpler compounds. Eg cellular respira on
o Anabolic pathway: consume energy to build complicated molecules from simpler ones;
o en called biosynthe c pathways. Eg photosynthesis or synthesis of macromolecules.
o Both catabolic and anabolic can be made up of both exergonic and endothermic reac
ons.
o Living organisms are defined as having a –G and reach equilibrium when they die.

ATP
 - ATP consists of a five-carbon sugar (ribose), linked to the nitrogenous base adenine and a
chain of 3 phosphate groups
- Breakdown of ATP in an aqueous solu on is a HYDROLYSIS reac on that liberates free energy and
results in f orma on of ADP and inorganic phosphate.
- High free energy of hydrolysis of ATP is due to 3 factors:
1) Both products of hydrolysis reac on carry a nega ve charge, and the repulsion between
these ionic products favours hydrolysis.
2) Release of terminal phosphate allows greater opportunity for hydra on and thi is an energe
cally favoured state.
3) Inorganic phosphate group can exist in a wide variety or resonance forms, not all of
which are available when it is bonded.
*The high free energy of hydrolysis is simply due to the large difference in the usable
energy content of the reactants (high) as compared to the products (low).

- How do cells harness the high free energy available in ATP to do cellular work?

- energy coupling: the exergonic release of energy when ATP is converted to ADP and Pi is used
to drive an endergonic reac on.
- The reason that energy is not simply lost as heat when ATP is broken down is that ATP is not
actually hydrolyzed during energy-coupling reac ons.
- ATP is a renewable resource that is made by recombining ADP and Pi. - ATP cycle: con nued
breakdown and resynthesis of ATP.

Laws of thermodynamics do not tell us anything about the speed of a reac on

- A reac on is “thermodynamically unstable” if the free energy change of the reac on is nega ve.
- In a “kine cally unstable” reac on, the reactants will rapidly be converted into p roducts.
Ac va on energy: ini al energy investment required to start a reac on
Transi on state: molecules that gain the necessary ac va on energy, where bonds are u
nstable and are ready to be broken.

Why using heat to speed up reac on is bad idea:

- High temperatures destroy the structural components of cells
- Increase in temperature would speed up all possible chemical reac ons in a cell, thus the cri cal
regula on of metabolic pathways would be lost.

Catalyst: chemical agent that speeds up rate of reac on without taking part in reac on

- Most common biological catalyst: enzyme.

Ac va on energy represents a real KINETIC barrier that prevents spontaneous reac ons from proceeding
quickly.
 - Enzymes increase rate of reac on by lowering this barrier.
- Enzymes make it possible for a greater propor on of reactant molecules to a ain the ac va on
energy.
- Although they lower ac va on energy, they do not alter change in free energy, only
difference is path the reac on takes.
In enzyma c reac ons, an enzyme combines briefly with reac ng molecules and is released unchanged
when the reac on is complete.

- Reactant that an enzyme acts on is called enzyme’s substrate.

- Enzymes are specific
- Substrate interacts with only a very small region of the enzyme=ac ve site…where catalysis takes
place.
- Induced –fit hypothesis: enzymes are flexible. Just before substrate binding, enzyme changes its
shape so that the ac ve site becomes even more precise in its ability to bind substrate.
- Because enzymes are released unchanged they can con nue doing this process.
- Cofactor: nonprotein group that binds very precisely to enzyme, o en metals.
o Essen al for cataly c ac vity o Organic
cofactors are called coenzymes.

Enzymes increase the rate of reac on by increasing the number of substrate molecules that a ain the
transi on state conforma on.

- Bringing the reac ng molecules together o Reac ng molecules can assume the transi on
state only when they collide; binding to an enzyme’s ac vie site brings reactants together in the
right orienta on for catalysis to occur.
- Exposing the reactant molecule to altered charge environments that promote catalysis o
In some systems, the ac ve site of the enzyme may contain ionic groups whose posi ve and
nega ve charges alter the substrate in a way that favours catalysis
- Changing the shape of a substrate molecule o The ac ve site may strain or distort substrate
molecules into a conforma on that mimics the transi on state.

Rate of catalysis is propor onal to the amount of enzyme: As enzyme concentra on increases, the rate of
product forma on increases. In this system, what is limi ng the rate of reac on is the amount of enzyme
in the reac on mixture.

- At very low concentra ons, substrate molecules collide so infrequently with enzyme
molecules that the reac on proceeds slowly.
- As enzyme molecules approach max rate, increasing substrate concentra on has smaller and
smaller effect and rate of reac on levels off=at this point the enzyme is said to be saturated with
substrate.

The rate at which an enzyme can catalyze a reac on can be lowered by enzyme inhibitors, which a re
non-substrate molecules that bind to an enzyme and decrease its ac vity. Some inhibitors work by
binding to the ac ve site of an enzyme, whereas other inhibitors bind to cri cal sites located
elsewhere in the structure of the enzyme.

- Compe ve inhibitor: competes with normal substrate for access to the ac ve site o If
concentra on of inhibitor is high enough, reac on may stop completely.
- Noncompe ve inhibitor: specific molecules inhibit enzyme ac vity that bind somewhere else
on enzyme.
o Decreases enzyme ac vity because upon binding it changes the conforma on of enzyme,
reducing ability to bind to substrate.
- Reversible inhibitors: binding of inhibitors to enzyme is weak and readily reversible, with
enzyme ac vity returning to normal following inhibitor release.
- Irreversible inhibitors: strong bind to enzyme through covalent bonds that enzyme is
completely disabled.
o Can only be overcome by cell synthesizing more of par cular enzyme. o
E.g an bio cs

It is important for metabolism to work efficiently

- A typical cell contains thousands of enzymes, for each enzyme that synthesizes a specific
molecule there is usually another enzyme that catalyzes the reverse reac on.
o If both enzymes are ac ve in same cell compartment at same me, 2 processes would run
simultaneously in opposite direc ons and have no overall effect other than was
ng energy.

To limit (the above) from happening there are two major mechanisms that directly regulate enzyme
ac vity:

1) Allosteric regula on: enzyme ac vity is controlled by the reversible binding of a

regulatory molecule to the allosteric site, a loca on on the enzyme outside the ac ve site.
i. Because these molecules alter enzyme ac vity by binding at sites separate from
the ac ve site, their ac ons are non compe ve. See page 87.
ii. High affinity state (ac ve form): enzyme binds strongly to its substrate
iii. Low affinity state (inac ve form): enzyme binds weakly to its substrate.
iv. Allosteric inhibitor: converts an allosteric enzyme from high to low affinity state
v. Allosteric ac vator: converts it from low to high affinity state.
- Allosteric inhibitors are a product of the metabolic pathway they regulate o If
product is in excess…effect of inhibitor slows or stops enzyma c ac vity o If
product is scars…effect of inhibitor slows to allow product to accumulate.
o This (above0 is called FEEDBACK INHIBITION
2) Covalent modifica on: some enzymes are o en completely inac ve and are ac vated only when
their structure changes by covalent modifica on. OR some enzymes are always ac ve and are
made inac ve by covalent modifica on.
 i. Phosphoryla on vs dephosphoryla on
ii. Proteoly c cleavage: some enzymes are synthesized in cataly cally inac ve forms
that are ac vated a er the protein is shortened slightly by an enzyme called
PROTEASE.
The ac vity of most enzymes is strongly altered by changes in pH and temperature. Characteris cally,
enzymes reach maximal ac vity within a narrow range of temperature or pH; at levels outside this
range, enzyme ac vity drops off.

- Most enzymes have a pH op mum near the pH of the cellular contents, about pH 7.
- Effects of temperature:
o Temperature has a general effect on chemical reac ons of all kinds. As temp increases,
rate of chemical reac ons increases.
o Temp has a more specific effect on all proteins. As temp rises, kine c mo ons of amino
acid chains of an enzyme increase, along with strength and frequency of collisions. At
some point, these disturbances become strong enough to denature the enzyme.
o In range 0C to 40C, reac on rate doubles for every 10C increase in temp. o Above
40C, enzyme starts to denature, falls to zero at 60C. o Peak enzyme ac vity:
40C-50C

Chapter 5 (5.2-5.7)

- Fluid mosaic model: model proposes that membranes are not rigid with molecules locked into
place but rather consist of proteins within a mixture of lipid molecules the consistency of olive
oil.
o The mosaic aspect of the fluid mosaic model refers to the fact that most membranes
contain an assortment of different types of proteins.
▪ Because they are larger than lipid molecules, proteins move more slowly in the
fluid environment of the membrane.
- Phospolipids: forms lipid bilayer o Consists of a head group a ached to two long chains of
carbon and hydrogen called a FATTY ACID.
o They are amphipathic: fa y acid part is hydrophobic (water fearing…nonpolar) and
phosphate-containing head is hydrophilic (water loving…polar).
- Fluidity of lipid bilayer is influenced by 2 factors:
o 1) the type of fa y acids that make up the lipid molecules
▪ Saturated: linear, pack ghtly together, rigid
▪ Unsaturated: double bonds (can’t pack ghtly together), FLUID o
2) temperature
▪ The more unsaturated a group of lipid molecules, the lower the temperature
has to be for gelling to occur (forming semisolid…liquid to solid).
o For most membrane systems, the normal fluid state is achieved by a mixed popula on
of saturated and unsaturated fa y acids.
- Keeping membranes in a fluid state is absolutely essen al to cell func on.
o Temp too low: can inhibit func ons
o Temp too high: membrane leakage.
- Most organisms can ac vely adjust the fa y acid composi on of their membranes so that proper
fluidity is m aintained over a broad temperature range.
o Unsaturated fa y acids are produced during fa y acid biosynthesis through the ac on of a
group of enzymes called DESATURASES.
▪ Desaturases act on saturated fa y acids by catalyzing a reac on that removes two
hydrogen atoms from neighbouring carbon atoms and introducing a double
bond.
▪ The more desaturases, the more fluid the membrane…used when temperature
drops.
▪ Like many proteins, desaturase abundance i s regulated at the level of gene
transcrip on, which results in changes to desaturase transcript (MRNA)
abundance.
o Sterols also influence membrane fluidity
▪ Found in animal cells but not in plants
▪ Act as buffers
▪ At high temps: they help restrain the movement of lipid molecules
▪ At low temps: they disrupt fa y acids from associa ng by occupying space
between lipid molecules thus slowing the transi on to the nonfluid gel state.
- Two major types of proteins are associated with membranes: integral and peripheral
membrane proteins.
- Membrane proteins can be separated into 4 major func onal categories:
o Transport: a protein may provide a hydrophilic channel that allows movement of a
specific compound.
o Enzyma c ac vity: a number of enzymes are membrane proteins.
o Signal transduc on: Membranes o en contain receptor proteins on their outer surface
that bind to specific chemicals such as hormones. On binding, these receptors trigger
changes on the inside surface of the membrane that lead to transduc on of the
signal through the cell.
o A achment/recogni on: on inside + outside surface of membrane…act as a achment
points for a range of cytoskeleton elements, as well as components involved in cell to
cell recogni on.
- Proteins that are embedded in the phospholipid bilayer are called Integral Membrane Proteins
o A subset of integral membrane proteins that traverse the en re lipid bilayer are
referred to as “transmembrane proteins”.
▪ Because the transmembrane proteins interact with both the aqueous sides of
the membrane and the hydrophobic core, it has domains with different
polarity.
 ● Domain that interacts with lipid bilayer (hydrophobic core) is mostly
non polar…this forms a secondary structure called an “alpha helix”
● Domain that interacts with aqueous sides on either side of membrane is
mostly polar.
o Primary structure: amino acid sequence of a protein o Ter ary structure: folding due to
R group interac ons o Fourth structure: more than one polypep de.
o How to tell if it is a transmembrane protein: stretches of non polar amino acids.
▪ Most transmembrane proteins span the membrane more than once.
- Peripheral membrane proteins: are posi oned on the surface of a membrane and do not
interact with the hydrophobic core of the membrane o Are held to membrane by noncovalent
bonds
o Are found on cytoplasmic side of the plasma membrane and form part of the
cytoskeleton
o They are made up of polar and non polar amino acids.

Passive membrane transport

- The hydrophobic nature of membranes severely restricts the free movement of many
molecules into and out of cells and from one compartment to another.
- Passive transport: movement of a substance across a membrane without the need to expend
chemical energy such as ATP o Diffusion drives passive transport o Above absolute zero (-
273C) molecules are in constant mo on o Driving force behind diffusion is an increase in
entropy
▪ When in ini al state (one region with more molecules than other) molecules are
more ordered and in a state of lower entropy. As diffusion occurs, when
molecules are disturbed, entropy increases.
▪ As it reaches maximum disorder, molecules release free energy, which can
accomplish work
o Rate of diffusion depends on the concentra on difference (concentra on
gradient). ▪ The larger the gradient, the faster the rate of diffusion.
- Simple diffusion (passive): movement of molecules directly across a membrane without
the involvement of a transporter.
o Depends on : molecular size and lipid solubility o Molecules that use this
are : O2, CO2, steroid hormones, water or glycerol.
▪ Membrane is prac cally impermeable to charged molecules.
o Slow but never plateaus
- Facilitated diffusion (passive): diffusion o f molecules across a membrane through the aid of a
transporter.
o Carried out by two transport proteins: channel and carrier o Channel proteins: form
hydrophilic pathways in the membrane through which molecules can pass.
 ▪ Diffusion of water is facilitated by water-specific transport proteins called
AQUAPORINS.
● Very narrow
● Specific for water
● Show presence of posi ve charges in centre of channel that are thought
to repel the transport of protons.
▪ Gated channel: these transporters can switch between open, closed and
intermediate states and are cri cal to the movement of most ions.
● Gates are open or closed by changes in voltage across membrane.
o Carrier proteins: each carrier protein binds a single specific solute and transports it
across the lipid bilayer….UNIPORT.
▪ Carrier protein undergoes conforma onal changes that progressively move the
solute binding site from one side of the membrane to the other, thereby
transpor ng the solute.
o Is quick and can plateau.
- Osmosis: diffusion of water molecules across a selec vely permeable membrane.
o Hypotonic: more concentra on in cell than o ut…water comes in…cell swells
o Hypertonic: more concentra on out of cell…water comes out…cell shrinks

Ac ve Membrane Transport

- Ac ve transport: transport of molecules across a membrane against a concentra on

gradient (movement from LOW to HIGH concentra on) requires expenditure of energy.
- 3 main func ons of ac ve transport:
1) Uptake of essen al nutrients from the fluid surrounding cells even when their concentra
ons are lower than in cells
2) Removal of secretory or waste materials from cells or organelles even when the
concentra on of those materials is higher outside the cells or organelles
3) Maintenance of H, Na, K and Ca
- Membrane poten al: voltage across a membrane.
- Primary ac ve transport: the same protein that transports a substance also hydrolyses ATP to
power the transport directly - Sodium-potassium pump:
o Pushes 3 Na+ ions out of the cell and two K+ ions into the cell in the same pumping
cycle o Inside of cell becomes nega vely charged o Voltage: electrical poten al
difference across the plasma membrane results from this difference in charge as well as
from unequal distribu on of ions across the membrane created by passive transport.
- Electro-chemical gradient: both a concentra on difference of ions and an electrical charge
difference on the two sides of the membrane o Store energy that is used for other transport
mechanisms…aka secondary ac ve transport.
- Secondary ac ve transport: the transport is indirectly driven by ATP….extension of primary ac ve
transport.
 o Occurs by 2 mechanisms:
1) Symport: the cotransported solute moves through the membrane channel in the
same direc on as the driving ion known as COTRANSPORT….both ion and molecule
move in same direc on.
2) An port: the driving ion moves through the membrane channel in one direc on,
providing the energy for the ac ve transport of another molecule in the opposite
direc on known as EXCHANGE DIFFUSION….ion and molecule move in opposite
direc ons.
Exocytosis vs Endocytosis

- Eukaryo c cells import and export larger molecules by endocytosis and exocytosis.
o Both require energy
- Exotysosis: secretory vesicles move through the cytoplasm and contact the plasma membrane.
o Vesicle fuses with plasma membrane, releasing the vesicle’s contents to the cell exterior.
- Endocytosis: trap in depressions that bulge inward from the plasma membrane.
o Depression then pinches off as an endocy c vesicle o Bulk phase endocytosis:
extracellular water is taken in along with any molecules that happen to be in solu on in
the water
▪ No binding by surface receptors takes place o Receptor mediated
endocytosis: molecules to be taken in are bound to the outer cell surface by receptor
proteins. Receptors recognize and bind only certain molecules from the solu on
surrounding the cell. A er binding, receptors collect into depression in plasma
membrane called COATED PIT because of network of proteins that coat and reinforce the
cytoplasmic side. o Phagocytosis is eg

Signal Transduc on

1) Recep on: binding of a signal molecule with a specific receptor of target cells is termed
recep on. Target cells have receptors that are specific for the signal molecules.
a. Found on plasma membrane
2) Transduc on: process whereby the signal recep on triggers other changes within the cell
necessary to cause the cellular response in transduc on.
a. Signalling cascade
3) Response: transduced signal causes a specific cellular response.
- Membrane receptors recognize and bind signal molecules are integral membrane proteins that
extend through the en re membrane.
o Specifc
o Molecular structure of that receptor changes so that it transmits the signal through
the plasma membrane, ac va ng the cytoplasmic end of the receptor protein.
 - A common characteris c of signalling mechanisms is that the signal is relayed inside the cell by
PROTEIN KINASES, enzymes that transfer a phosphate group from ATP to one o r more sites on
par cular proteins.
o Ac ve only when called upon
o Act in a chain, catalyzing a series of phosphoryla on reac ons called a
PHOSPHORYLATION CASCADE, to pass along a signal.
o Last protein in cascade is Target Protein.
- Effects of protein kinases in the signal transduc on pathways are balanced and reversed by
another group of enzymes called PROTEIN PHOSPHATASES, which remove phosphate groups
from target proteins.
o Most of the protein phosphatases are con nuously ac ve in cell
Why not have receptor ac va on lead directly to response?

- Signal transduc on pathways amplify the original signal.

- Amplifica on: an increase in the magnitude of each step as a signal transduc on pathway
proceeds.
o Generally, the more enzyme-catalyzed steps in a response pathway, the greater the
amplifica on.
- Cyclic AMP Signal Transduc on Pathway
1) Signaling molecule binds to a receptor
2) Receptor conforma onal change ac vates G protein
3) Ac vated G protein travels and ac vates adenylyl cyclase
4) Ac vated adenylyl cyclase catalyzes the conversion of ATP to cyclic AMP
5) Cyclic AMP binds to and ac vates protein kinase A
6) Ac vated protein kinase A phosphorylates other proteins in the cell

Chapter 6-Cellular Respira on

Cellular Respira on: collec on of metabolic reac ons within cells that breaks down food molecules to
produce ATP.

o Transform the poten al energy found in food molecules into a form that can be used for
metabolic processes.
- Life and its systems are driven by a cycle of electron flow that is powered by light in
photosynthesis and oxida on in cellular respira on
- An electron that is farther away from the nucleus contains more energy than an electron that is
more closely held by the nucleus o Electrons that from the covalent C-H bond are
equidistant from both atomic nuclei-not being strongly held by either.
▪ Can be easily removed
 ▪ Fat is almost en rely C-H bonds, while proteins and carbohydrates contain
varying amounts of other atoms including oxygen
- The more electronega ve an atom, the greater the force that holds the electrons to the atom,
and, therefore, the greater the energy required to remove the electrons.
- Oxidized: when molecules lose electrons - Reduced: when molecules gain electrons -
Concept of redox reac ons:
1) Although many oxida on reac ons involve o xygen, others, including a number involved in
cellular respira on, do not.
2) The gain or loss of an electron in a redox reac on is not always complete
- Cellular respira on is controlled combus on o Combus on of glucose releases energy
as electrons are transferred to oxygen, reducing it to water, and the carbon in glucose is
converted to carbon dioxide.
o Energy of C-H bonds is not liberated suddenly, producing heat, but is slowly released in
a stepwise fashion, with the energy being transferred to other molecules.
o Dehydrogenases: group of enzymes that facilitate the transfer of electrons from food to
a molecule that acts as an energy carrier or shu le
▪ Most common energy carrier: NAD+