Chapter 1 - Light and Life
Impressionism - art movement in 19th century characterized my use of small visible
brush strokes that emphasized light and color rather than lines to deﬁne object. Ex.
Claude Monet. Uses unmixed pure colors. ex. putting yellow and blue in pure form on
the canvas so they mingle in the eyes of the viewer and create the impression of green.
Painted in open air, because they thought they could catch the sunlight
Cataract - vision-deteriorating disease where lens becomes opaque because of
progressive degeneration of a protein that makes up the lens. Opaqueness absorbs
certain wavelengths of light and decreases transmittance of blue light. World appears
1.1 The Physical Nature of Light
Two functions of light: energy source and vision (info about surroundings). Ex. alga
Chlomydomonas reihardtii has in each cell a chloroplast to make energy and a eyespot
(light sensor) that senses light direction and light intensity.
- In both functions: light needs to be captured.
What is Light?
- Sun: by turning hydrogen into helium it converts matter into energy.
- Energy is given off as electromagnetic radiation that travels at the speed of light.
- moves in two waves, electrical and one magnetic which orient at 90 degrees to each
- distinguished by their wavelength, the distance between two successive peaks.
- the portion of the electromagnetic spectrum that humans can detect with their eyes.
From 400nm (blue) - 700nm (red).
- Outside these portions - wavelengths are not called light but ultraviolet and infrared
- light - can also be described as stream of energy particles called photons, which have
no mass but precise amount of energy.
- amount of energy is inversely related to wavelength in a photon. Blue light has shorter
wavelengths and higher energy than red light.
Light interacts with matter
1) reﬂected off the object
2) transmitted through the object
3) absorbed by the object.
- for most objects all three come in place, but for organisms absorption must occur. - Pigment: the molecule that can absorb photons of light. Pigments differ in the
wavelengths they can absorb. Ex. chlorophyll a, retinal, indigo (jeans) etc.
- Pigments differ but one critical feature is common to light absorption: a conjugated
system - a region where carbon atoms are covalently bonded with alternating single
and double bonds - results in delocalization of electrons and the electrons are not
closely associated with particular atoms therefore can interact with the photon of light.
Why Chlorophyll is Green
- Absorption - occurs when energy of a photon is transferred to an electron of the
pigment molecule. A photon excites an electron from ground state to excited state.
- To be absorbedA : single photon can only excite a single electron and energy of
photon must match energy difference between ground state and excited state.
Color of pigment - determined by the wavelengths it cannot absorb. Chlorophyll is
green because it can absorb blue and red light but not green. Green photons are
reﬂected or transmitted and responsible for the color.
Action spectrum: a plot of the effectiveness of different wavelengths of light on a
biological process. Ex. red and blue more effective for photosynthesis.
Light as Source of Energy
- the excited state electron is a source of potential energy. Ex. photosynthetic electron
transport to synthesize energy-rich compounds NADPH and ATP..
- Other energy is used to synthesize biological molecules such as lipids etc.
Light as a Source of Information
- not every organism sees the world the same.
Rhodopsin, a Highly Conserved Photoreceptors
Photoreceptor: most basic light-sensing system.
Ex. Rhodopsin - most common photoreceptor. - basis of vision in animals but also a
light sensing unit of the eyespot in many organisms. Made of protein, opsin and retinal.
- Absorption of light causes retinal pigment to change shape that triggers alternations in
opsin which triggers downstream events.
- Photoreceptor cells - in our eyes are rods and cones that line the retina.
Sensing Light Without Eyes
- Ex. plants, algae, invertebrates, and even some prokaryotes.
- Eyespot - in the chloroplast in a region closely associated with cell membrane. It
doesn’t play a role in photosynthesis instead has photoreceptors that allow the cell to
sense light direction and intensity.
Phototaxis: the bodily movement of an organism in response to light, either towards it
or away from it.
Light absorption by the eyespot triggers cascades of events to send electrical signals. - In plants - we have a phytochrome as a photoreceptor, senses light environment and
is critical for photomorphogenesis, the normal developmental process activated when
seedlings are exposed to light.
- Phytochrome - when activated initiates a signal transduction pathway that reaches
the nucleus that signal for many genes, many of which are proteins involved in
- organ of animals to sense light.
- When compared to other organism the eye needs the brain for vision. They are
thought that they have co-evolved
1) Ocellus - simplist eye
- consists of up to 100 photoreceptor cells lining a cup or pit. Each ocellus is covered on
one side by a layer of pigment cells that blocks most of the light rays arriving from the
opposite side of the animal.
- Ocelli occur in variety of animals, including insects, arthropods, and molluscs.
** “Image-forming eyes” are two types: compound eyes and single-lens eyes****
2) Compound Eyes
- common in arthropods.
- Each contains hundreds to thousands of ommatidia (Omma = eye), units ﬁtted closely
- Each ommatidium samples only a small part of the visual ﬁeld as light entering is
focused onto a bundle of photoreceptor cells.
- Brain receives signals as a mosaic image.
3) Single - lens Eyes - camera eyes
- light enters through cornea, lens concentrates light and layer of photoreceptors at back
of eye, the retina records image.
Darwin and the Evolution of the Eye
- Theory of Natural Selection
- Darwin proposes that the eye as it exists in humans and other animals did not appear
suddenly but evolved by variation and natural selection over time from a simple,
- Starting with a patch of light-sensitive cells on skin
- *** remember that the eye is no good unless the brain improves at the same time,
allowing for more advanced neural processing.
Light Can Damage Biological Molecules - only electromagnetic spectrum from 400nm - 700nm is used for photosynthesis,
vision, phototaxis, navigation, and many other light-driven processes
- Is it a coincidence? - George Wald says NO. It is because these wavelengths are the
most dominant ones reaching Earth’s surface.
- Shorter wavelengths - absorbed in ozone layer
- Longer wavelengths - absorbed by water vapour, and CO2 in atmosphere.
- Another reason - shorter wavelengths have too much energy that would destroy the
chemical bonds of molecules or even oxidize them producing ions (ionizing radiation).
Longer ones would not supply enough energy and are more readily absorbed by
Damage by Light: Direct Effects
- All organisms that are exposed to sunlight - have developed mechanisms to help
or prevent light-induced damage or repair it.
- Ex. in photosystems of chloroplasts - there is unavoidable damage to the proteins
etc. but over time repair mechanisms have been developed. On top of that, all
photosynthetic organisms have carotenoids that protect by absorbing excess light and
dissipating energy as heat.
- If plant doesn’t have carotenoids, it will turn white when in light because the chlorophyll
becomes oxidized and the light-harvesting capabilities become destroyed.
Damage by Light: Indirect Effects
- Ultraviolet rays accompany light therefore light indirectly has damaging effects from
the ultraviolet rays.
- Ultraviolet Rays - between blue light and X-ray on the spectrum - between 200nm -
- The ozone protects from the most harmful UV-C but the UV-B and UV-A reach us.
- UV rays can damage proteins and molecules by ionizing them - particularly vulnerable
- in DNA - interaction between UV and nucleotide can form a “dimer” - can change the
shape of the double-helix structure and prevent replication and hinder gene
- Organisms have developed mechanisms for this - fur or avoidance for animals but in
humans, they have melanin.
- Melanin - pigment that absorbs UV rays. It absorbs preferentially photons of
electromagnetic spectrum in the UV region. Melanocytes synthesize melanin and
generally people in sunnier areas have more melanin.
- Not all UV radiation is absorbed by melanin - we need some for vitamin D synthesis
Role of Light in Ecology and Behavior
- Adaptations for photosynthetic organisms by adjustments in light-harvesting properties
of pigments and in animals often leads to unique colorations for attraction or
protection. Using Light to Tell Time: Circadian Rhythms
- sleep- wake cycle, metabolic processes, cell division, body temp., locomotion, cell
division and looking for food and mating - determined by the 24 hour day
- Physiological and behavioral responses geared by Earth’s day-night cycle are called
circadian rhythms (circa=around, diem=day)
- Deﬁning characteristic of circadian rhythms - they are NOT direct responses to
changes in external light, but can be “free-running” without daily input, but they are
monitored by the circadian rhythm instead. Ex. DNA synthesis at night - so light does
not destroy it or photosynthesis right before dawn etc.
- Central biological clock controlling circadian rhythms - found within the
suprachiasmatic nucleus, a region in the hypothalamus.
- Suprachiasmatic nucleus - receives light inputs directly from the eye via optic nerve,
and uses it to set the biological clock and in turn regulates processes including
melatonin secretion from pineal gland that which controls sleep-wake cycle as its
synthesis is active at nighttime but not during the day.
- Conditions can interfere with normal circadian cycling -jet lag, some plants show
seasonal activities as well as daily cycles including migration, hibernation, ﬂowering,
Avoiding Detection: Camouﬂage
- works when animal fails to distinguish another from the background. Ex. peppered
Using Colour as Signals
- Animals often use bright colours to signal that they are distasteful and/ or armed and
- Key is that the signal must be received so perception plays a role
- Other signals - like sounds, odour etc. Some mimic the warning signals of the others.
- Flowers colours to guide pollination
Light in Aquatic Habitats
- Water attenuates light rapidly and almost no light penetrates below about 150m.
- Longer wavelengths are better selectively scattered and absorbed than shorter
- Therefore, below 30m light is monochromatic and solely blue wavelengths.
- Fish closer to the surface, are very colorful, while deep sea ﬁsh tend to have black
backs and silver underbodies
Ecological Light Pollution
- Rapid proliferation of artiﬁcial lighting that illuminates public buildings, streets and
signs has resulted in “light pollution”, which has transformed the nighttime environment
over signiﬁcant portions of Earth’s surface.
- presence of artiﬁcial light disrupts orientation in nocturnal animals that are accustomed
to operating in the dark. Ex. turtles you put their eggs in areas depending on light or
migrating birds etc. Life in the Dark
- with dimmer light- we ﬁrst lose our ability to see color then shapes.
- Nocturnal animals see very well in dim light.
- Evolution has lead that they don’t even have functional eyes anymore. Ex. the blind
mole rat. His eyes are small and covered by layers of tissue. However the
photoreceptors of the eye remain functional but brain is dramatically reduced. This
allows the setting of their biological clocks and control of circadian rhythms
Organisms Making Their Own Light: Bioluminescence
- Many organisms are bioluminescent: they produce their light.
- Bioluminescence occurs - chemical energy in the form of ATP excites an electron in
a substrate molecule to a higher excited state, and when the electron returns to the
ground state, the energy is released as a photon of light.
- Very efﬁcient and only 5% are given off as heat compared to 95% of regular light.
- They use light to attract their mates, for camouﬂage, to attract prey or to communicate
- Bioluminescence has NOT been reported in land plants or higher vertebrates.
What is Life
- Note: types of atoms and molecules found in living things do not differ from those
found in nonliving forms of matter.
- Living cells obey the same fundamental laws of chemistry and physics as does the
abiotic (nonliving) world
Seven Characteristics that All Forms of Life Share
- These seven are common to all forms of life.
1) Display order: arranged in highly ordered manner, with cell being the unit.
2) Harness and utilize energy
4) Respond to stimuli - make adjustments to their structure, function, and behavior in
response to changes to the external world.
5) Exhibit homeostasis - regulate to remain constant
6) Growth and development
7) Evolve - change over the course of generations
Virus - exhibits properties of life, but are based on its ability to infect living cells. They
have their own nucleic acids but need another organism to make proteins. Therefore
most scientists don’t consider a virus alive.
The Fundamental Unit of Life Is a Cell
- Scientists using light microscopes where able to yield 3 generalizations about the
organization of living organisms - the 3 together became the tenets of the cell theory:
1) All organisms are composed of one or more cells
- Prokaryotes - only a single cell - unicellular organisms
2) The cell is the smallest unit that has the properties of life
3) Cells arise only from the growth and division of preexisting cells - new cells can only
rise from the division of preexisting ones (not through DNA and RNA)
The Origins of Information and Metabolism
- Very Important: the development of a system for the storage, replication, and
translation of information for protein synthesis and the development of metabolic
The Origin of Information System
- DNA - all organisms have it. Large, double-stranded helix, contains instructions for
- Info. in DNA is copied onto RNA, which directs the production of protein molecules
- Enzymes are needed to catalyze the replication of DNA, the transcription of DNA into
RNA and the translation of RNA into protein.
- Changes in DNA are what contribute to evolution over generations.
Ribozymes Are Biological Catalysts that Are Not Proteins
- a group of RNA molecules that could themselves act as catalysts to make the process
of information ﬂow from DNA to RNA to protein.
- Ribozymes can catalyze reactions on the precursor RNA molecules that lead to their
own synthesis as well as on unrelated RNA molecules.
- what makes RNA act as catalysts is their shape: single-stranded that can fold in very
speciﬁc shapes (like protein functions)
- This suggests that early life may have existed in an “RNA world”, where it could serve
as a carrier of info. and a catalyst
- First cells - might have contained only RNA, which self-replicated and catalyzed
reactions critical for survival
- Hypothesis - small number of RNA molecules evolved that could catalyze the
formation of very simple proteins, independent of the ribosome.
- Modern ribosome - key intermediate role as an intermediate between RNA and
protein, composed of 2/3 RNA and 1/3 proteins.
- The RNA of the ribosomes - is what catalyzes the incorporation of amino acids.
Ribosome may be considered a time of ribozyme.
- However, proteins are way more versatile and are even made out of 20 different amino
acids while RNA is made only of 4 nucleotides.
DNA is favored over RNA for storage because:
1) Each strand is chemically more stable because of the presence of deoxyribose
instead of ribose
2) Base uracil in RNA replaced by thymine in DNA. Uracil is easily recognized as
damaged cytosine and can be repaired. 3) double-stranded shape gives DNA to repair a mutation through the complementary
Development of Energy-Harnessing Reaction Pathways
- Oxidation-reduction reactions - were probably the ﬁrst. Oxidize food molecules, use
energy to reduce other molecules.
- In primitive cells - electrons removed in an oxidation would have been transferred
directly to the substance reduced in a one-step process.
- However this in not efﬁcient and has high waste
- Evolution led to multistep processes and slow oxidation. Ex. cellular respiration
- This is a efﬁcient stepwise energy release which opened the ETC.
- ATP became established as the coupling agent linking energy-releasing reactions to
those requiring energy
- Two forms of life based on two fundamentally distinct types of cells: prokaryotic and
- Earliest evidence of life: stromatolites - fossilized remains of structures formed by
- Modern-day Stromatolites - formed by action of photosynthetic prokaryotes called
cyanobacteria (sophisticated metabolism suggests evolution)
Panspermia Hypothesis -life on earth could have had an extraterrestrial origin. Two
points support this:
1) Given that primordial Earth had to cool after being formed, many argue that the
window for the development of life is very narrow
2) Life is far more resilient than previously thought. E.g. Extremophiles (mostly
prokaryotes) and simple eukaryotes can survive in very harsh conditions.
Prokaryotes - the simpler organisms and are earliest form of life.
Prokaryotes Have Properties Common to All Cells
- Prokaryotes found in two domains:
They do not have a nucleus which makes them distinct from eukaryotes but
posses fundamental features:
a) All have a selectively permeable plasma membrane
b) Cytoplasm consists of:
- cytosol - mostly water, salts and organic molecules.
- protein complexes that allows passage in plasma membrane - in the photosynthetic
prokaryotes they are the sites if photosynthetic ETC c) DNA organized in chromosomes - but structure is distinctively different. In
prokaryotes which lack a nucleus the DNA is found in a central region of the cell,
d)Rely like the eukaryotes on ribosomes for synthesis of proteins and undergo
transcription and translation.
Prokaryotes Display Remarkable Diversity
- few micrometers in length and a micrometer in diameter - 10x smaller than eukaryotic
- much less internal membrane organization
- able to use a variety of substance as energy and carbon sources and to synthesize
almost all their required organic molecules from simple inorganic raw materials
- biochemically more versatile than eukaryotes
- abundant and live in almost all regions of Earth’s surface, from antarctic to hot springs
Oxygenic Photosynthesis and the Rise of Atmospheric Oxygen
- earliest prokaryotes relied on anaerobic metabolism as atmosphere lacked molecular
- Then eventually started using oxygen
- Cyanobacteria: harness electrons from water and oxidizes water resulting in the
formation of O2 and over millions of years accumulated in the atmosphere
- + oxygenic photosynthesis which also releases O2 - another huge advantage afforded
- rise in atmospheric O2 led quite rapidly to the evolution of prokaryotic cells, which are
able to undergo aerobic respiration.
Characteristics that distinguishes them from prokaryotes:
- separation of DNA and cytoplasm by a nuclear envelope
- presence of membrane bound compartments with specialized functions in cytoplasm:
mitochondria, chloroplasts, endoplasmic reticulum, Golgi complex and others
- highly specialized motor (contractile) proteins that move cells and internal cell parts
The Endomembrane (within membrane) System Is Derived from the Plasma
- collection of interrelated membranous sacs that divide the cell into functional and
structural compartments called organelles.
- Major membrane components: Nuclear envelope, ER, and Golgi Complex.
- Infolding of the plasma membrane is believed to be responsible for the evolution of all
of these structures
- Pockets of plasma membrane may have extended inward and surrounded the
nuclear region - the membranes are physically connected or indirectly by vesicles, small membrane-
bound compartments that transfer substances between parts of this system
1) Nuclear envelope: controls movement of proteins and RNA molecules into and out
2) Endoplasmic Reticulum: an extensive interconnected network of membranous
channels and vesicles.
- Rough ER - has ribosomes on outer surface. Proteins synthesized here are destined
for the plasma membrane or for release outside the cell. Proteins are synthesized on
surface then enter the lumen to get folded into ﬁnal form then delivered within vesicles
to join with the Golgi complex.
- Smooth ER - no ribosomes. Serves various functions - synthesis of lipids that become
part of cell membranes.
- Proteins that are freely suspended in cytosol remain there, pass nuclear pores to enter
nucleus or become part of organelles or structures.
3) Golgi Complex: consists of a stack of ﬂattened membranous sacs and is usually
located between the rough ER and plasma membrane
- receives proteins from ER and here they undergo further chemical modiﬁcations.
- Golgi also regulates the movement of several types of proteins. Some are excreted
from the cell, other embedded in membrane and others placed in lysosomes.
Theory of Endosymbiosis Suggests that Mitochondria and Chloroplasts Evolved
from Ingested Prokaryotes
- Another clear characteristic of eukaryotes are energy-transducing organelles:
chloroplast and mitochondrion.
- Theory states: the prokaryotic ancestors of modern mitochondria and chloroplasts
were engulfed by large prokaryotic cells, forming a mutually advantageous relationship
called a symbiosis and over time the host cell and the endosymbionts became
inseparable parts of the same organism
- Key factor is thought to be the rise in O2
- mitochondria came from free-living aerobic prokaryotic cells.
- chloroplasts came from cyanobacteria because they are photosynthetic
- all eukaryotic cells contain mitochondria and only plants and algae contain both
mitochondria and chloroplasts.
Several Lines of Evidence Support the Theory of Endosymbiosis
1) Morphology - mitochondria resemble aerobic prokaryotes and chloroplasts resemble
2) Reproduction - mitochondria and chloroplasts can also be only derived from
mitochondria or chloroplasts by binary ﬁssion
3) Genetic information - have their own DNA that codes for the proteins essential for
the organelle’s function. However they have less genes because some have located
themselves in the nucleus.
4) Transcription and Translation - they contain complete transcription and
translational machinery, including a variety of enzymes and the ribosomes necessary for synthesis of proteins encoded by their DNA. And their ribosomes are similar to
those in prokaryotes.
5) Electron Transport - can generate energy in the form of ATP through the presence
of their own ETC like prokaryotes.
The Cytoskeleton Supports and Moves Cell Structure
- maintains shape and internal organization of each type of cell
- it is the interconnected system of protein ﬁbers and tubes that extends throughout the
- reinforces membrane and function in movement.
In animal cells it is made of:
1) Microtubules - microscopic hollow tubes
2) Intermediate ﬁlaments - ﬁbers that occur singly, in parallel bundles and in interlinked
networks either alone or in combo with microtubules and microﬁlaments.
3) Microﬁlaments - thin ﬁbers consisting of two rows of protein subunits wound around
each other in a long spiral
Eukaryotic cell movements - generated by “motor” proteins that push or pull along
microtubules and microﬁlaments.
- attached on one side to a cell structure, such as a vesicle or microtubule or
microﬁlament and other side walks along by making an attachment.
- ATP supplies the walking
Sperm tails - depend solely on microtubules for whipping motion
Amoeboid motion, cytoplasmic streaming, contraction of muscle cells - use solely
During cell division - microtubules and microﬁlaments are active - chromosomes
divide and move by microtubules and cytoplasm is divided by microﬁlaments.
The Flagella of Eukaryotes and Prokaryotes Are Not Evolutionary Related
- they are long, hair-like structures that project from the cell surface and function in cell
- common on single-celled prokaryotes and numerous eukaryotic cells
- they superﬁcially look the same and serve same function, the ﬂagella of prokaryotes
and eukaryotes are structured differently.
Ex. ﬂagellum of bacteria - made of a single protein called ﬂagellin, and propels the
bacteria like a boat.
Ex. ﬂagella of a eukaryote constructed of microtubules and movement is whiplike. The Evolution of Proteins and DNA
Chapter 3 - Selection, Biodiversity and Biosphere
Biodiversity - measured as the number of species of organisms, reﬂects the reality that
life on Earth exists from the ocean ﬂoor to well into the atmosphere.
- How to group organisms is a challenge.
- We can take a taxonomic deﬁnition depending on how we deﬁne “type” of organism -
consider the number of organisms in each kingdom.
- We are quite accurate with the numbers of large observable organisms like mammals,
birds, and ﬂowering plants, but not so accurate about microscopic organisms. Ex. very
rough numbers of soil fungi and aquatic prokaryotes.
The Hierarchy of Life - from larger to small
1) Biosphere - All regions of Earth’s crust, waters, and atmosphere that sustain life
2) Ecosystem - Group of communities interacting with their shared physical
3) Community - Populations of all species that occupy the same area
4) Population - Group of individuals of the same kind (that is, the same species) that
occupy the same area
5) Multicellular organism - Individual consisting of interdependent cells
6) Cell - Smallest unit with the capacity to live and reproduce, independently or as part
of a multicellular organism.
Now going away from taxonomic categories
We can group by how organisms get their carbon!!
1) Autotrophs - most plants, which synthesize organic carbon using inorganic carbon
CO2. (Auto=self, troph= nourishment)
2) Heterotrophs - all animals are hetrotrophs. Obtain carbon from organic molecules
either from living hosts or in products, wastes or remains of dead organisms.
We can group by organisms source of energy!!
1) Chemotrophs (chemo=chemical, troph=nourishment) - obtain energy by oxidizing
inorganic or organic substances.
2) Phototrophs - obtain energy from light
Now we can combine and group organisms by carbon and energy source
1) Chemoautotroph - Found in some bacteria and archaeans; not found in eukaryotes.
Carbon from inorganic CO2 and energy from oxidation of molecules
2) Chemoheterotroph - Found in some bacteria and archaeans, and also in proteins,
fungi, animals and plants. Carbon from organic molecules and energy from oxidation
of molecules 3) Photoautotroph - Found in some photosynthetic bacteria, in some proteins and in
plants. Carbon from inorganic CO2 and energy from light
4) Photoheterotroph - Found in some photosynthetic bacteria. Carbon from Organic
molecules and energy from light.
- Prokaryotes - show greatest diversity and they are the only representatives of
chemoautotrophs and photoheterotrophs.
- occurs when phenomenon affects survival of organisms.
- Antibiotics - bacteria becoming resistant
- Selection is the major force responsible for evolution and biodiversity
- Genetic variation
The tree of Life
- Darwin envisioned the history of life as a tree. Branching points represent the origins
of new lineages; branches that do not reach the top represent extinct groups.
- the area occupied by life on Earth
- physical enviornment and abiotic factors ex. sunlight, rain etc. inﬂuence evolution and
- Abiotic factors contribute to region’s climate
Earth’s spherical shape causes the intensity of incoming radiation to vary from the
equator to the poles.
- At the equator - sun’s rays hit at 90 degrees - shortest distance
- At poles - travels at an oblique direction
Seasonality: Weather Through the Year
- Earth is tilted on its axis at a ﬁxed position of 23.5 degrees from the perpendicular to
the plane on which it orbits the sun.
- Tilt produces seasonal variation
- tropics receive small seasonal changes
Air Circulation: Wind Patterns
Ocean Currents ETC.
- The diversity of living organisms is also affected by interactions among organisms. - Most important interaction: Competition - by consuming each other and by
parasitism (one organism beneﬁts from the other - a type of symbiotic relationship)
- mutualism - both organisms beneﬁt.
Trophic Interactions: Movements of Energy, Biomass and Numbers
Chapter 5 - Membranes and Transport
Why It Matters
Cystic Fibrosis - caused by mutations to a single gene that codes for a protein called
CFTR, that usually acts as a membrane transport protein that pumps Cl- out and a
series of events that promote keeping the mucus lining moist.
Overview of the Structure of Membranes
- key evolution development - plasma membrane.
- Membrane is selectively permeable.
- subsequent development of internal membranes allowed for compartmentalization of
processes and increased complexity. Ex. nuclear envelope
The Fluid Mosaic Model of Membranes
- Model proposes that membranes are not rigid with molecules locked into place but
consist of ﬂuid lipid molecules in which proteins are embedded and ﬂoat freely.
- lipid molecules of all biological membranes are bilayers, which vibrate, ﬂex back and
forth, spin around their axis, move sideways etc. within the same bilayer half.
- Rarely does a lipid molecule ﬂip-ﬂop between the two layers
- this makes it dynamic
- Proteins move slower because they are bigger
- small number of proteins anchor cytoskeleton ﬁlaments to the membrane
- number of proteins and lipids have carbs linked to them, forming glycoproteins and
- proportions of lipids and protein vary for type of membrane
- Important characteristic - proteins on one layer are different than the ones on other
half of bilayer. - called membrane asymmetry.
- Ex. hormones and growth factors bind to receptor proteins found only on the external
surface of plasma membrane. Binding causes change in different protein components
on inner surface of membrane which lead to signal transduction within the cell.
Experimental Evidence in Support of the Fluid Mosaic Model
2 pieces of evidence
1) Membranes Are Fluid - like oil. Ex. proteins started mixing in experiment.
2) Membrane Asymmetry
The Lipid Fabric of a Membrane
- underlying fabric of all membranes - lipid molecules. - organisms can adjust the types of lipids in membrane so it doesn’t become too stiff or
1) Phospholipids Are the Dominant Lipids in Membranes
- two fatty acid “tails”
- linked to one of several types of alcohols or amino acids by a phosphate group
- critical property - phospholipids are amphipathic - fatty acid chains are hydrophobic
(nonpolar) and phosphate head is hydrophilic (polar)
- when added to aqueous solution, phospholipids form a bilayer. Occurs spontaneous
and doesn’t require anything, because hydrophobic fatty acids aggregate and polar
head associate with water.
- Arrangement is favored because they represent the lowest energy state and is more
likely to occur.
- Dependent on how densely the lipid molecules can pack
- And this is inﬂuenced by: lipid molecules composition and temperature.
- saturated fatty acids have a straight shape allowing them to pack tightly
- unsaturated are less straight causing loose packing
- Very low temp.- closely packed forming a viscous semiliquid gel as a membrane
- membrane adjusts according to situation.
Organisms Can Adjust Fatty Acid Composition
- maintenance of ﬂuid state is crucial.
- Too low temp. - can result in really tight packing and no permeability.
- Too high temp. - increase permeability that can also cause problems.
- Therefore we use the saturated vs unsaturated ratio to ﬁx it. Ex. prokaryotes can
survive in such harsh conditions because they can alter this ratio.
- Unsaturated fatty acids produced through desaturases (introduce double bonds),
because all fatty acids are essentially synthesized as saturated molecules.
- Transcript abundance of a desaturase gene increases as temperature is lowered -
resulting in increase of unsaturated fatty acids.
- Sterols also have an inﬂuence on membrane ﬂuidity - cholesterol found in membranes
of animal cells but not in plants or prokaryotes.
- Sterols act as membrane buffers: at high temps, they restrain movement of lipid
molecules (reducing ﬂuidity). At low temps, disrupt fatty acids from associating by
occupying space between, thus slowing transition to nonﬂuid gel state.
- determines function of membrane and makes it unique
Key Functions of Membrane Proteins
- can be separated into 4 major functional categories that can all be even found in
one membrane: 1) Transport- provide hydrophilic channel that allows movement of speciﬁc compound
2) Enzymic Activity - ex. respiratory and photosynthetic electron transport chains.
3) Signal Transduction - have receptor proteins that when molecules bind to them, it
triggers change on inside surface that lead to transduction of the signal through cell
4) Attachment/ recognition - proteins exposed to internal and external act as
attachment points for a range of cytoskeleton elements and components involved in
Membrane Proteins can be classiﬁed into two categories:
1) Integral Membrane Proteins
2) Peripheral Membrane Proteins
Integral Membrane Proteins
- embedded in phospholipid bilayer
- all have at least one region that interact with the hydrophobic core.
- most integral proteins are transmembrane proteins - span the entire membrane bilayer
- to interact with hydrophobic core, the proteins consist of predominantly non-polar
amino acids usually coiled in alpha helices
- to tell that its a transmembrane protein - check primary amino acid sequence of the
Peripheral Membrane Proteins
- positioned on the surface of the membrane and do not interact with the hydrophobic
core of membrane.
- they are held by noncovalent bonds (hydrogen bonds and ionic bonds) by integrating
with exposed portions of integral proteins and lipid molecules
- most peripheral proteins are on cytoplasmic side
- Some are part of cytoskeleton, such as microtubules, microﬁlaments etc.
- they do not interact with hydrophobic core
Passive Membrane Transport
- movement of a substance across a membrane without the need to expend chemical
Based on Diffusion - from high to low due to an increase in entropy (disorder).
- Rate of diffusion depends on difference or concentration gradient.
Two Types of Passive Transport:
1) Simple Diffusion - overall size and charge determine the ease of moving across.
- small non-polar or molecules with no charge can usually pass easily, even water or
glycerol that are polar can still diffuse through
- practically impermeable to charged molecules ex. Cl-, Na+ and PO4-, because the
charge prevents them from entering the hydrophobic core.
2) Facilitated Diffusion - speeds up movement of needed compounds, like water, amino acids, sugars and ions
by protein complexes that span the membrane.
- movement still occurs across a concentration gradient and transport ceases when
concentration gradient is at zero.
Two Groups of Transport Proteins Carry Out Facilitated Diffusion
- Facilitaed diffusion is carried out by integral proteins called transport proteins that
extend entirely through the membrane.
Two types are:
1) Channel proteins - forms hydrophilic pathways through which water and ions can
pass. So the molecules do not have to interact with hydrophobic core
- Gated channels - (channel proteins) that facilitate the transport of ions ex. Na+, K+,
Ca2+ etc. The gates may be opened or closed by changes in voltage across the
membrane. Found in all eukaryotes. In animals, they are responsible for nerve
2) Carrier Proteins - also form passageways through the lipid bilayer. Each binds to
speciﬁc single solute and transports it across the bilayer.
- This is called uniport transport - a single solute carrier-mediated transfer.
- Here the carrier protein after binding undergoes conformational changes that move the
binding site from one end to the other. This property disiguishes carrier proteins from
How can you determine if a compound is transported by facilitated diffusion and
not just simple diffusion?
- First facilitated diffusion is much faster
- Second facilitated diffusion can be saturated like an enzyme. Membrane has a limited
amount of transporters. See graph!! It reaches a plateau.
- In simple diffusion, the whole membrane surface is the transporter. Rate is slower but
it never reaches a plateau.
Osmosis: The Passive Diffusion of Water
- passive transport of water from a solution of lesser solute concentration to a solution of
greater solute concentration
- Can occur through simple diffusion or facilitated diffusion by water-speciﬁc transport
proteins called aquaporins, found in all organisms. ( single-ﬁle movement of water
- movement dictated by solute concentration.
- Hypotonic - solution with lesser solute concentration around cell causes water to
moves inside cell and swell
- Hypertonic - solution with higher solute concentration around cell causes water to
move out and cell shrinks.
- Isotonic - equal concentration of solute.
- animal cells must constantly pump Na+ out by active transport so water doesn’t make
cell burst. Active Membrane Transport
- substances are pushed against their concentration gradients through an energy-
Active Transport Requires Energy
- estimated that 25% of cell’s ATP are for active transport.
Two Kinds of Primary Active Transport
1) Primary Active Transport - the same protein that transports a substance also
hydrolyzes ATP to power the transport directly.
2) Secondary Active Transport - transport is indirectly driven by ATP hydrolysis. Here
the transport proteins don’t break down ATP, instead use a favorable concentration
gradient of ions, built up by primary active transport, as their energy source of
transport for a different ion or molecule.
Primary Active Transport Moves Positively Charged Ions
- All move positively charged ions across.
- The gradient established is essential to cellular life.
- Ex. H+ pump: push hydrogen ions from cytoplasm to the cell exterior. Pump
temporarily bind a phosphate group removed from ATP during pumping cycle.
- Ex. Ca2+ pump: in eukaryotes, pushes Ca2+ out of cell and from cytosol into vesicles
- Ex. Na+/K+ pump: pushes 3 Na+ out and 2 K+ in therefore positive ions accumulate
outside. Causes a membrane potential due to a electrical potential difference.
(electrochemical gradient) - store energy that is used for other transport mechanisms.
Secondary Active Transport Moves Both Ions and Organic Molecules
- use concentration gradient of an ion established by a primary pump as their energy
- Ex. animal cells use high outside/ low inside Na+.
- Here the transfer of the solute is always coupled with the transfer of the ion supplying
the driving force
Secondary active transport occurs by two mechanisms:
1) Symport - he contransport solute moves through the membrane channel in the same
direction as the driving ion ( phenomenon called cotransport)
2) Antiport - driving ion moves through the membrane channel in one direction,
providing the energy for the active transport of another molecule in the opposite
direction. (phenomenon called exchange diffusion)
Exocytosis and Endocytosis
- Eukaryotic cells import and export larger molecules by endocytosis and exocytosis.
- Also contribute to back- and- forth ﬂow of membranes between endomembrane
system and the plasma membrane.
- Both processes require energy. Exocytosis Releases Molecules to the Outside by Means of Secretory Vesicles
- secretory vesicles move through cytoplasm and contact plasma membrane
- vesicle membrane fuses with plasma membrane and releases the content to the cell
- Plant cells also use this - to secrete carbs to build a strong cell wall.
Endocytosis Brings Materials into Cell in Endocytic Vesicles
- substances are trapped in pitlike depressions that bulge inward from the plasma and
pinches off as a vesicle.
- This takes place in most eukaryotic cells by one of two distinct related pathways:
1) Bulk-phase endocytosis (pinocytosis): extracellular water is taken in along with
any molecules that were in it.
- No binding by surface receptors takes place
2) Receptor-mediated Endocytosis: the molecules are bound to the outer cell surface
by receptor proteins, which are integral proteins
- receptor proteins recognize and bind only to certain molecules
- Then receptors collect into a depression in the plasma membrane called coated pit
because clathrin coat and reinforce the cytoplasmic side
- Vesicles form and pinch off than rapidly loses its clathrin
- May fuse with lysosome - enzymes thre digest the contents into molecular products
that can get transported by transport proteins
- Ex. LDL- carry cholesterol and then cell uses receptor-mediated endocytosis to take it
*** Some cells can take in aggregates of molecules by a process related to receptor-
mediated endocytosis - called phagocytosis
- Surface receptors bind molecules on the substances.
- Cytoplasmic lobes extend, surround and engulf the materials forming a pit that pinches
off and sinks in cytoplasm as large endocytic vesicle
Chapter 8 - Cell Communication
Chapter 21 - Prokaryotes
The Full Extent of Prokaryote Diversity Is Unknown
- only a fraction have been identiﬁed and the ones studied are the ones that researchers
are able to grow in cultures and media.
Prokaryotes Make Up Two of the Three Domains of Life
The 3 domains are: Archaea, Bacteria and Eukarya.
- Prokaryotes account for Archaea and Bacteria. - Bacteria are the most known to us, while Archaea were only discovered 40 years ago.
- Archaea share futures that are common in bacteria and eukarya but have their own
unique features as well.
- Archaea live under very extreme conditions that even bacteria cannot live under
Prokaryote Structure and Function
- they are the smallest organisms in the world; 1- 2 um long, but they dominate life on
Earth and their biomass exceeds that of animals and may be greater than plant life.
- Prokaryotes are more diverse than Eukaryotes
Prokaryotic Cells Appear Simple in Structure Compared with Eukaryotic Cells
- 3 common cell shapes: spiral, spherical (coccoid) and cylindrical. And some Archaea
are even squared.
- appear simple than eukaryotic cell
- chromosome is not contained in a membrane-bound nucleus but is packed into an
area of the cell called nucleoid.
- they have no cytoplasmic organelles equivalent to mitochondria, ER, Golgi complex.
- simplicity is fooling: prokaryotes have cytoskeleton not homologous to eukaryote but
serving some of the same functions and have more sophisticated organization.
- genome of most consist of single, circular DNA molecule and some have a linear
- Many have circles of DNA called plasmids - contain genes for nonessential but
beneﬁcial functions such as antibiotic resistance. Plasmids replicate separately of
chromosomes and can be transferred from one cell to another (antibiotic resistance is
readily shared) - horizontal gene transfer.
- Contain ribosomes: Bacterial ribosomes are smaller than eukaryotic ribosomes but
uses the same protein synthesis mechanism
- Archaeal ribosomes resemble those of bacteria in size but differ in structure and use
a combo of bacterial and eukaryotic processes. Therefore antibiotics don’t disturb
Prokaryotic Cell Walls
- Most have a cell wall that lies outside of plasma membrane
- Primary component of it in bacteria is peptidoglycan - a polymer of sugars and amino
acids that forms linear chains and peptide cross-linkages between the chains provide
strength and rigidity.
- Penicillin works against the cross-linkages.
Two Bacteria groups based on their gram stain procedure used as identiﬁcation
- cells are stained with violet and rinsed with ethanol and counterstained with safranin.
1) Gram-positive cells - cells that retain the violet color and has single thick
peptidoglycan layer 2) Gram-negative cells - do not retain the violet but retain the safranin and has two
distinct layers, a thin peptidoglycan outside of the plasma membrane and an outer
membrane external to this layer
- the outer layer contains lipopolysaccharides (LPS) - this layer protects gram-negative
cells. E.g. from penicillin
Archaea have cell walls made of molecules related to peptidoglycan but are assembled
from proteins or polysaccharides.
- gram stain doesn’t work on them
- many prokaryotes are surrounded by a layer of polysaccharides known as a capsule.
- Capsule - “sticky and play important role in protection from temp, bacteria, antibiotics,
Flagella and Pili
- Many prokaryotes can move actively most commonly via ﬂagella - whip-like extension
of a cell wall.
- Prokaryotic ﬂagella are very different from eukaryotic ﬂagella in structure and
1) Prokaryotic ﬂagella - made of rigid helical proteins and rotate like a propeller on a
2) Archean ﬂagella - superﬁcially similar to bacterial and carry out same function but
they differ on which components they are made of and are coded for by different
- Some prokaryotes have pili
Pili : “hair” extending from cell walls that allow bacterial cell to adhere to each other and
act as conduit for transfer of plasmids. Some enable bacteria to bind to animal cells and
some can conduct electricity.
** Prokaryotic cells are simpler and less structurally diverse than eukaryotic cells but are
more diverse metabolically.
Prokaryotes Have the Greatest Metabolic Diversity of All Organisms
*** Remember that organisms can be grouped in 4 modes of nutrition based on
sources of energy and carbon.
Ex. photoautotrophs like green plants - light as energy and CO2 as carbon source
Ex. chemoheterotrophs like animals, fungi and humans - organic molecules for
energy and carbon
*** The two other modes are only found in prokaryotes
- Photoheterotrophs - use light as energy and organic molecules as carbon source
- Chemoautotrophs - “lithotrophs” (rock-eaters) - oxidation of inorganic substances
for energy and CO2 as carbon source.
Chemolithotrophs - thrive in habitats such as deep-sea hydrothermal vents and rely on
plants ability and other photoautotrophs to capture light energy. - Some prokaryotes use Oxygen as ﬁnal electron acceptor - called aerobes.
- Aerobes may be obligate - cannot survive without oxygen
- Some prokaryotes use metals instead - called anaerobes - Only prokaryotes are
capable of using metals.
- Obligate anaerobes - are poisoned by oxygen and survive either by fermentation or
- Facultative anaerobes - use O2 when present, but under anaerobic conditions they
use fermentation or anaerobic respiration.
*** Prokaryotes are more diverse in their fermentation reactions.
Prokaryotes Play Key Roles in Biogeochemical Cycles
- because they metabolize such as wide range of substrates
- Biogeochemical cycle - pathway by which a chemical element moves through the
- prokaryotes are crucial in the transformation of these elements
Ex. Nitrogen Cycle
- largest nitrogen source is the atmosphere (80%) but most organisms cannot break the
triple bond in them. Prokaryotes are the only ones that can break this bond and
convert N2 into forms that can be used - known as nitrogen ﬁxation - N2 is reduced to
ammonia that quickly ionizes to ammonium which prokaryotes use to produce
nitrogen-based molecules like amino acids and nucleic acids.
- Not all bacteria convert ﬁxed nitrogen directly into organic molecules, some carry out
nitriﬁcation - ammonium to nitrate, which is taken up by plants and fungi that
incorporate it into organic molecules and animals eat it.
Asexual Reproduction Can Result in Rapid Population Growth
- normal mode of reproduction for prokaryotes - by binary ﬁssion - under favorable
conditions one cell becomes two etc.
- some can double in only 20 minutes
- they have highest mutation rates
Pathogenic Bacteria Cause Diseases by Different Mechanisms
- Some bacteria produce Exotoxins - toxic proteins that leak from the bacterium. Ex. in
- Other bacteria cause disease through endotoxins - natural components of the outer
membrane of Gram-negative bacteria. When gram-negative cell lyses -
lipopolysaccharides of outer membrane are released and exposure to lipid A, a
component of the layer causes endotoxic shock
- Endotoxins overstimulate the immune response. Ex. salmonella.
The Domain Archaea
- ﬁrst ones were isolated from extreme environments therefore they were called -
- Others have been found in less extreme environments - They share some cellular features with eukaryotes and some with bacteria and have
some unique ones.
Archaea Have Some Unique Characteristics
- lipid molecules in archaeal plasma membranes are unlike of others. Different linkage
between glycerol and hydrophobic tails (tails are isoprenes not fatty acids). Some
lipids have polar heads at both ends.
- this makes them more resistant to disruption making them better suited for extreme E.
- cell walls are also more resistant than bacteria’s and can survive being boiled in strong
- Many are chemoautotrophs and some are chemoheterotrophs
- None have been shown to be pathogenic
Molecular Studies Reveal Three Evolutionary Branches in the Archaea - based on
different rRNA sequence
- found in various extreme conditions. They include:
a) Methanogens: live in low oxygen environments and represent 1/2 known Archaea.
- obligate anaerobes and live in oxgen-lacking sediments of swamps, lakes, marshes
and sewage works, cattle, sheep, in intestines of dogs and humans
- generate energy by converting various substrates like CO2, H, acetate into methane
gas which is released in atmosphere
b) Halophiles - salt-loving.
- Extreme Halophiles live in highly saline environments (dead sea and salted preserved
- most are aerobic chemoheterotrophs
- extreme ones - some use light as secondary energy source, supplementing the
c) Extreme thermophiles
- live in extremely hot environments (hot springs and ocean ﬂoor hydrothermal vents)
- optimal temperature range: 70-95 degrees
- some belong to euryachaeota but most belong to crenarchaeota
- inlcude most of the extreme thermophiles - the most thermophilic member dies below
90 degrees and grows optimally at 106.
a) Psychrophiles - cold-loving - between -10 to -20 degrees. Found in the Antarctic and
b) Mesophilic members - comprise large part of plankton found in cool, marine waters,
where they are food sources for other marine organisms. 3) Korarchaeota - recognized solely on the basis of DNA samples from marine and
terrestrial hydrothermal environments. Only group not grown in cultures.
- nothing is known about their physiology
- they are the oldest archaeal lineage
Chapter 4 - Energy and Enzymes
- Life relies on catalysts called enzymes to speed up the rates of reaction without the
need for an increase in temperature ( because life needs a certain temp to operate)
** Phosphatases - catalyze removal of phosphate groups from a range of molecules -
are the fastest catalyzed reactions.
- the reverse is called phosphorylation and is a central mechanism of intracellular
- life requires temperatures that are relatively low (below 100 C)
Energy and the Laws of Thermodynamics
- energy cannot be weighed directly - we can detect it by its ability to do work - deﬁned
as capacity to do work.
Energy Exists in Different Forms and States
- including heat, chemical, electrical and mechanical energy.
- the forms can be converted readily from one to another. Ex. photosynthesis converts
light into chemical energy in forms of sugars and organic molecules.
Energy can be grouped into 2 different states:
1) Kinetic Energy: energy of an object in motion. Ex. waves of ocean
2) Potential Energy: stored energy. Energy an object has because of its location or
chemical structure. Ex. a boulder at top of cliff, glucose or gasoline etc. Due to their
atomical structure - sometimes called chemical potential energy. The Laws of Thermodynamics Describe the Energy Flow in Natural Systems
- Thermodynamics: study of energy and its transformation.
- system: object studied
- surroundings: outside of system
3 types of systems:
1) isolated: one that does not exchange matter or energy with its surroundings. Ex.
2) open: both energy and matter can move freely between the system and the
surroundings. - living organisms
3) closed: can exchange energy but not matter with its surroundings. ex. the Earth.
The First Law of Thermodynamics: energy can be transferred from one place to
another but cannot be created or destroyed. Also called “The principle of the
conservation of energy”. Ex. Niagara Falls.
The Second Law of Thermodynamics: each time energy is transformed from one
form into another some of the energy is lost and unavailable to do work. Ex. machines
are never 100% efﬁcient. Also applies to living organisms. Released in heat.
- Unusable energy that is produced during energy transformations results in an increase
in the disorder or randomness of the universe - called entropy - the measure of
disorder is basis of 2nd law.
- Can be stated as: the total disorder (entropy of a system and its surroundings always
increases. - this why a car can’t stay new etc.
Life and the Second Law of Thermodynamics
- Life is highly ordered. - it takes energy to maintain low entropy. Life is an open system
and (living organisms) - exchange energy and matter thus keeping their order. Ex.
replaced damaged skin cells etc.
- However entropy should be increasing - absolutely but as long as the entropy of the
universe as a whole increases the system of an organism is allowed to decrease.
Free Energy and Spontaneous Reactions
- Spontaneous Reactions: chemical and physical reaction will occur without energy
input. (here no description of rate)
Energy Content and Entropy Contribute to Making a Reaction Spontaneous
- 2 Factors to determine whether a reaction is spontaneous
1) Reactions tend to be spontaneous if the products have less potential energy than the
- Enthalpy: potential energy in a system - Endothermic: H. Reactions that absorb energy - the products have more potential
energy than the reactants
- Exothermic: processes that release energy - produces large amounts of heat -
products have less potential energy than reactants.
- Ex. Process of ice melting is spontaneous
2) Reactions tend to be spontaneous when the products are less ordered than the
- spontaneous when entropy of products is greater than entropy of reactants.
- Ex. increase in entropy in glass of ice water that melts the ice - ice molecules are more
ordered than water.
- solid ---> liquid ----> gas result in an increase in entropy.
Change in Free Energy Indicates Whether a Reaction is Spontaneous
*** energy is lost as an increase in entropy occurs
- Free Energy: the portion of a system’s energy that is available to do work. delta G.
delta G = delta H - T delta S
H - change in enthalpy
S - change in the entropy over course of reaction
T - absolute temp in kelvin
- free energy changes as a system goes form initial to ﬁnal states is the sum of the
changes in energy content and entropy.
- For a reaction to be spontaneous - delta G has to be negative.
- interplay between entropy and enthalpy to determine whether it will occur
- also remember that free energy of the ﬁnal state compared to initial state also is
represented by delta G.
- concentration gradient: exists across a membrane is less stable and contains more
free energy than after diffusion
Life and Equilibrium
- Equilibrium = maximum stability
- Chemical equilibrium - a state in which the reaction does not stop but rather a state
in which the rate of the forward reaction equals the rate of backward reaction.
- as reaction moves toward equilibrium - free energy becomes progressively lower.
- the more negative free energy the further toward completion the reaction will move
before equilibrium is established
- many reactions in organisms never reach equilibrium because they are open systems
- products don’t accumulate and steady supply of reactants.
- overall free energy is always negative in organisms Look at Exergonic vs Endergonic rxns graphs pg. 78
Metabolic Pathways Consist of Exergonic and Endergonic Reactions
Exergonic reaction: releases free energy - delta G is negative because the products
contain less free energy than the reactants
Endergonic reaction: products contain more free energy than the reactants and delta
G is positive.
Metabolic pathways are a series of these reactions
- Catabolic pathway - energy is released by breaking down of complex molecules to
simpler compounds. Ex. cellular respiration - negative delta G
- Anabolic pathway - consumes energy to build complicated molecules from simpler
ones. Ex. photosynthesis or synthesis of macronutrients. - positive delta G
The Energy Currency of the Cell: ATP
ATP Hydrolysis Releases Free Energy
- high-energy phosphate groups
- ATP is made of ﬁve carbon sugar, ribose, linked to nitrogenous base adenine, and 3
phosphate groups - energy comes from the phosphate arrangements
- highly unstable and the removal of one or two is spontaneous - reaction is called
hydrolysis ---> ADP and Pi and further hydrolysis produces AMP
ATP and Energy Coupling
- release energy and you want to harness it. How do you couple hydrolysis to an
- Process called Energy coupling: ATP is brought in close contact with a reactant
molecule involved in an endergonic reaction and when ATP is hydrolyzed the terminal
phosphate group is transferred to reactant molecule (phosphorylation of reactant to
make it less stable)
- you need an enzyme to bring ATP closer
- process is spontaneous and has - delta G.
Regeneration of ATP
- Endergonic reaction ADP +Pi
- needs energy from the exergonic breakdown of complex molecules that contain free
energy. The Roles of Enzymes in Biological Reactions
- Laws don’t tell anything about speed of reaction - just because it is spontaneous
doesn’t mean it will proceed rapidly.
The Activation Energy Represents a Kinetic Barrier
- to break bonds you need to make molecule unstable which needs energy - this initial
energy required to start up process is called Activation Energy
- The transition state: where bonds are unstable and are ready to be broken
What provides the activation energy?
- molecules in chemical rxn are in constant motion (at temp. above absolute zero) and
slowly gain more energy to reach the transition state.
- But you need to increase the number of molecules that enter transition state than the
free energy released may be enough to get the remaining reactants. Ex. propane
torch. - spark is what provide molecules of propane with the energy to reach transition
- Chemists use heat to provide the energy needed to reach transition state but it can
destroy components because of heat or it can speed up all processes in a cell (not
Enzymes Accelerate Reactions by Reducing the Activation Energy
- Use a catalyst and you don’t have to increase the temp.
- it speeds up reaction and takes part in it.
- most common catalysts are enzymes
- Enzymes lower the barrier of Activation energy and make it possible for greater # of
reactants to attain Ea.
- Remember that enzymes DO NOT alter free energy of the reaction. Therefore they
cannot make an endergonic reaction proceed spontaneously but only an exergonic
- For endergonic you can use ATP hydrolysis but not enzyme alone.
Enzymes Combine with Reactants and Are Release Unchanged
- the reactant that an enzyme acts on is called enzyme’s substrate
- the substrate only interacts with enzyme’s active site - place where catalysis occurs -
lock an key hypothesis but now we have the induced-ﬁt hypothesis to show that
enzymes are not rigid and can change conformation so active site becomes more
- Many enzymes require cofactors - nonprotein group that binds very precisely to the
- Organic cofactors are called coenzymes. Enzymes Reduce the Activation Energy by Inducing Transition State
- Enzymes function by increasing the number of reactant molecules that acquire the
transition state conformation.
- Enzymes can do that through 3 major mechanisms:
1) Bringing the reacting molecules together. Reactants can only assume transition state
if they collide. Binding to active site brings them together in the right orientation for
2) Exposing the reactant molecule to altered charge environments that promote
3) Changing the shape of a substrate molecule. Active site strain may distort substrate
molecules into a conformation that mimics the transition state.
Conditions and Factors that Affect Enzyme Activity
The Inﬂuence of Enzyme and Substrate Concentrations on the Rate of Catalysis
Chapter 6 - Cellular Respiration
The Chemical Basis of Cellular Respiration
- energy in biosphere enters through photosynthesis - trap light energy and make
organic molecules that contain free energy
- cellular respiration extracts this free energy through slow-oxidizing energy-rich
Food as Fuel
- abundance of hydrogen in form of carbon-hydrogen bonds is key. - because the
electron is far from the equally as far from the nucleus.
- Oxygen rich molecules contain less potential energy because of its strong
The Principle of Redox
- oxidation: loss of electrons (e-) and molecules afterwards is said to be oxidized. -
linked to a reduction reaction
- being reduced - gaining an electron
- never have one without the other
- Oxygen’s high electronegativity makes it the ideal ﬁnal electron acceptor. (reduced) -
but many reactions use other atoms. - sometime redox reactions are not complete and electron is shared between two
Cellular Respiration is Controlled Combustion
- series of steps make it possible to lose the least energy
- the oxidation of food molecules occurs in presence of dehydrogenases that facilitate
the transfer of electrons from food to a molecule that acts as an energy carrier or
shuttle. Ex of carrier ---> NAD+ removes two hydrogen atoms from substrate molecule
and transfers two electrons but only one proton to become completely reduced to
- Other proton from NAD+ is simply released
Cellular Respiration: An Overview
3 Parts of Cellular Respiration
1) Glycolysis - in cytosol
- glucose to two pyruvates and ATP from substrate-level phosphorylation
- some ATP and NADH
2) Citric Acid in Mitochondrion and ATP from substrate-level phosphorylation
- Acetyl-CoA which is formed from oxidation of pyruvate enters a metabolic cycle where
it is completely oxidized to CO2.
- ATP and NADH
3) Electron transfer system and oxidative phosphorylation in mitochondrion.
- NADH is oxidized and liberated electrons pass along an ETC until they are transferred
to O2 producing water.
- Free energy released establishes a proton gradient across a membrane and remaining
ATP is synthesized.
- In prokaryotes glycolysis and Krebs Cycle occur in cytosol and ETC on internal
membranes derived from plasma membrane.
- Eukaryotes Krebs cycle and ETC occur in mitochondrion
- composed of 2 membranes which together deﬁne two compartments: the
intermembrane space and matrix (interior aqueous environment)
- Prokaryotes do not have mitochondria Glycolysis
- 10 sequential enzyme-catalyzed reactions that lead to the oxidation of glucose into 2
- Most ancient pathway. Supported by: universality, no requirement for O2, occurring in
cytosol and doesn’t require ETC.
Reactions of Glycolysis
- 2 phases: Energy Investment Phase (2 ATP used up) and Energy Payoff Phase - 4
ATP and 2 NADH produced.
- Other products are 2 pyruvates and 2 H2O.
1) Glucose receives a phosphate group from ATP (phosphorylation reaction) - enzyme
hexokinase ----> glucose-6-phosphate.
2) Glucose-6-phosphate is rearranged into its isomer fructose-6-phosphate.
(isomerization reaction) - enzyme phosphoglutamase.
3) Phosphorylation again of fructose-6-phosphate (enzyme: Phosphofructokinase)
4) Fructose -1,6-phosphate is split into glyceraldehyde-3-phosphate (G3P) and DAP
5) The DAP produced is converted into G3P, giving a total of two of these molecules per
molecule of glucose (isomerization reaction)
6) 2 electrons and 2 protons are removed from G3P - some of energy is trapped by
phosphate group from the cytosol and electrons and 1 proton are accepted by NAD+
and other proton is released in cytosol.
7) Phosphoglyceratekinase (substrate-level phosphorylation reaction) to produce 2 ATP.
8) Mutase reaction - shifting of a chemical group to another within same molecule
9) Enolase (redox reaction) and 2 waters are produced
10) Pyruvatekinase (substrate-level phosphorylation) produces 2 ATP
***Substrate-level phosphorylation is also used to produce ATP in Citric Cycle. Pyruvate Oxidation and the Citric Acid Cycle
- 75% of energy is still there.
Bridging Glycolysis and the Citric Acid Cycle
- Citric Acid Cycle is localized in mitochondrial matrix so pyruvate must pass through