Chapter 1-9 Recapture – MT1
Chapter 1 – Photosynthetic Animals
Animals can be photosynthetic or non-photosynthetic. Elysia Chlorotica is a sea slug that is
photosynthetic and is invertebrate. Snail and slugs are very similar. It is found in the eastern seaboard
and is primarily aquatic based, although there is potential for other factors to play a role.
The animal is brown with red pigment segments and has no chloroplasts in the early stages of life. It
feeds on algae early in life, and then eventually turns green from all the chlorophyll that is has
consumed over time.
Elysia will become the model for most lectures.
Elysia has a very interesting relationship with its food in that they are extremely specialized. There is one
food source for one animal. The animal is a eukaryote, and all components are digested except the
chloroplasts. The more chloroplasts that are retained, the more green Elysia will become.
The relationship is specifically denoted as endosymbiosis. The process is known more specifically as
Kleptoplasty, which means literally, “stolen plastid.” In this case, the plastid is the fully chloroplast.
It is important to note that there are other types of plastids in biology other than chloroplasts. The
chloroplasts are continuously kept in the sea slug.
Carbon (reduced organic matter and molecules) and energy obtained from an outside source.
Heterotrophs are organisms that gain energy through this system. The energy released from this process
leads to the ability to live. (Utilization)
Obtaining inorganic forms of carbon (CO 2 from direct energy sources and utilizes them.
Photoautotrophs utilize sunlight as the primary energy source, whereas Chemoautotrophs utilize
chemicals as their primary energy source.
Elysia is very unique in that it is entire autotrophic due to the chloroplasts. That said, it is very important
to remember that there are many organisms that can fall into both the Heterotrophic and Autotrophic
Elysia’s food source is Vaucheria litorea which is filamentous yellow - green algae (Xanthophyceae).
It is a eukaryote that has a single tube that holds chloroplasts. It has mitochondria, rough and small ER
and a nuclear envelope. Measuring Photosynthesis
We have the ability to measure photosynthesis in a specific set of chloroplasts. What would we measure
in the plant to determine the rate of photosynthesis? We could potentially measure the amount of
Oxygen release. We can conversely measure the intake of the Carbon Dioxide consumed.
In most slugs, the time that chloroplasts can be kept is very short (about 10 days). However, in the case
of Elysia, there is a much more efficient system that can keep the chloroplasts for up to (about 75 days),
and the overall functionality is much better than that of the all other slugs.
The rate of decrease in functionality for most slugs is remarkable in that is drops from about 0.6 to 0.1 in
a matter of 10 days, followed by the apoptotic initiation. However, in Elysia, there is only a drop from
0.8 to about 0.65 over the period of 75 full days, followed by the apoptotic initiation.
Why does photosynthesis in normal chloroplasts decrease so quickly in all environments, whereas
kleptoplastic chloroplasts stay maximized?
The life cycle of Elysia is based around the system fully where the primary food source is Vaucheria.
Without the presence of the specific food source, the life cycle will be very different. This is a fully
obligate system that can be very quickly disrupted.
Elysia is also a hermaphrodite and shows all necessary properties such as both male and female
components. However, it does not mate with itself like those individuals that are simultaneously
monoecious. It still has to find a mate, and goes through sexual recombination and meiosis. The eggs are
laid in the spring and surprisingly do not have chloroplasts present when born. They must go through
the same system of slowly eating their way up to the chloroplast integration.
There is a fully 1 year cycle, where in the spring the eggs are laid, they go through the summer, fall and
winter months, and then lay their eggs again. As soon as an adult lays their eggs, they immediately die.
The whole population is immediately reduced at the same time due to the death all in the same season.
The interesting thing about the death pattern is the fact that Elysia is full of viruses, in all types of cells,
and the integration begins early in life. The viruses are unique again in that they are retroviruses, similar
to HIV, where reverse transcription is necessary for host infection. The only difference in the case is that
these viruses are locked in the cells for good. They are known as ERV’s (Endogenous Retroviruses). They
are unsure of how to infect new hosts. Through the process of continuous infection, they eventual kill
Humans are completely filled with ERV’s and at this current point in time, we are unsure if they actually
kill us or not. They are continuously infecting us, but not to the point where the apoptotic system is
engaged. The ERV’s are part of our genome, and are very similar to Elysia and Vaucheria.
How does Elysia maintain chloroplasts photosynthetically competent for so long?
How Elysia bring chloroplasts into its cells?
How is gene expression regulated in Elysia? Chapter 2 – The Origin of Life
The earth was formed at 12:01 am on January 1 , 6.4 billion years ago.
March 2 - 3.8 billion years ago, there was a lot of evidence supporting that there was prokaryotic cells
in existence. That said, it is most likely accurate in saying that there was some life form approximately 4
billion years ago, (0.2 billion years before the prokaryotic findings).
April 28 – O2has developed in the atmosphere – 2.7 billion years ago
Oxygen came in after the first life forms were found, which leads us to believe that some cells were able
to live without cellular respiration.
June 13 – 2.2 billion years ago, standard eukaryotic cells have formed.
August 12 – 1.4 billion years ago, more complex versions of the previous cells have developed over
time and are now expressing various higher level thinking.
October 15 – 6 million years
Homo sapiens st
In the closing of the year, on December 31 at 11:59 pm, Homo sapiens are brought into existence. This
translates into about 150, 000 years, which is a significant jump in time from all other components of
There are only 3 domains of life on Earth today:
We believe that all three domains and all subspecialties belong to LUCA. (Last Universe Common
Ancestor). This is a common idea among all plants, with the idea that there is a common idea.
All living things have the presence of:
2. Genetic Information
3. Deoxyribonucleic Acid
5. Adenosine Triphosphate(ATP)
7. Triad of the Genome – DNA, RNA, Protein It is important to note that all of these components did not just all of a sudden happen in one single
Life has evolved pretty fast, in that it only took 6.5 billion years. This is really nothing long compared to
the time it would have taken to the earth to form fully and then cool.
Stromatolites are made from cyanobacteria in aquatic environments. The have been found up to 3.5
billion years ago. This clearly indicated that over 3.5 billion years ago, there were some filamentous
In order to make life, we must have the following:
1. Abiotic Synthesis – Proteins, Carbs, Fats – in the simplest forms
2. Heritable Information – Not always DNA – Could have been something else.
3. Formation of Cells
There are 3 stages of the earth:
1. Geophysics Stage – Were the conditions right for developing life as we know it. What was the
composition of the earth and the atmosphere
2. Chemical Stage – How were the building blocks of the earth developed through chemical
reactions that occur with synthesis?
3. Biological Stages – How did the building blocks organize into living cells?
We know lots of information about the easy stuff in the first two stages, but we have very little
knowledge of the last stage.
What were the conditions of earth before time in Primordial soup? The early atmosphere was composed
of Water, Hydrogen, Methane, Nitrate, and Sulfuric Acid. Is there everything necessary to make proper
life in the early years with the soup? The atmosphere was also reductive, as opposed to oxidizing. There
were also the presence of many energy sources such as UV light, lightening, etc.
The whole setup of this environment has created a perfect environment for life to form.
Can we make organic molecules from inorganic molecules? Stanley Miller worked under Urey’s lab and
attempted to create amino acids and such. The reaction worked perfectly. He achieved the synthesis of
amino acids, sugars, Purines and Pyrimidines. It is important to note that these are all monomers, which
means they are singular. Proteins however are polymers (many).
Is abiotic synthesis possible today? Yes, Oxygen gas is extremely electronegative, and can help create
these difficult reactions. Chirality
A chiral molecule is one that is not superimposable on its mirror image. These are extremely important
and can be represented by your hands. Biological examples are:
1. Two enantiomers
3. Chemical and Physical Properties
Thalidomide was a drug for pregnant women who were getting sick. The problem that aroused was the
deformations due to the amount of drug present during birth (1960’s). There is a chemical equilibrium
that is attempted to be reached by converting Teratogen to Antiemetic in our bodies, but one of the
forms causes serious birth defects. The problems occurred because the drug was Chirality.
In the Miller-Urey experiment, there was a racemic mixture formed which means that there is a balance
that is attempted to be made between two elements in perfect 50/50 ratio. In biology, this is a problem
because most systems are homochiral, and have serious problems when actually developed.
It is important to note that homochirality and racemic mixtures cannot co-exist. Biology only allows for
one form to be created. There is never a mixture of the two naturally.
Homochirality is essential to the evolution of life. The specificity of life requires that there is
homochirality. LUCA at some point must have decided that not both chiral forms can be used, and
therefore by random chance omitted the other stream of information.
1. Random Chance
2. Extra-terrestrial Origin
a. The Murchison Meteorite contains 7 amino acids and does have express homochirality.
1. The development of the DNA, RNA and protein triad is extremely important
2. The synthesis of polymers are very difficult, as we are currently only familiar with monomers
3. The first cells are extremely different than the cells we see today. The building blocks are much
different than the final results.
Remember that the transfer of information from mRNA to Protein goes through a specific set of
processes. These processes are known as transcription and translation. The questions raised about the
dogma are based around the basis of how LUCA was able to create the Dogma from things that did not
exist. Did proteins come before mRNA, or did they coexist? This is an extremely difficult question to
answer, as there is no set true 100% correct explanation.
We believe that the intermediate molecule…RNA…We believe that RNA linear sequences could be the
answers to all the dogmas system of pattern. The information, structure and catalytic role of RNA
however is quite difficult to understand. That said, it is important to note that RNA is unique in that it
can fold much easier than its later component, DNA. The reason RNA can fold is because of the lack of double stranded structure and hydrogen bonding. The
RNA folding leads to proteins which allow for a variety of different functions based on the type and
number of folds.
Ribosomes are extremely important, and we can confirm this because even LUCA has the presences of
RNA through Ribosomes. Ribosomes are traditionally an ancient organelle, as they have been found in
the most simple and most archaic species on earth. It is important to understand that older cells were
made up 67% by RNA and only 33% protein.
A Ribozyme is an enzyme that catalyzes RNA reactions. It is an RNA molecule. A ribozyme has a catalytic
ability and is known as an enzyme, but IS NOT A PROTEIN!
A ribozyme is a 3 dimensional structure. The ribozymes are able to self-splice introns and exons in order
to catalyze their own excisions.
Ribosome aminotransferase activity is catalyzed by the RNA component of the Ribosome.
We believe that there was initially a system where RNA brought amino acids together in order to form
proteins through the process that we now know as translation. Many years ago, they were much more
basic. Enzymes can catalyze reactions much better than that of RNA, which is why there was a shift
towards Protein synthesis.
There are only 4 nucleotides that make up RNA, but in the case of proteins, there are 8 essential and 12
non-essential amino acids that can come together to form way more combinations.
Remember that the dogma states that DNA comes before RNA. In a small amount of time, RNA will
break down if it is left in the environment because it isn’t very stable. However, DNA has the ability to
stay very structured due to its double stranded features.
Due to the fact that genetic information needs to be secure, it is kept in the DNA form with the double
helical structure. Again, in this case, there is the double stranded complimentary casing that ensures if
there are any mistakes, they will be corrected for.
1. How do we go from monomers to polymers (abiotic systems)?
2. How did the first cells come about?
It is possible that the transition from Monomers to Polymers can be achieved through the presence of
clay particles (montmorillonite). Since there is such a great surface area of clay, it is thought that the
charge present is enough of an energy source to get the job done.
Micelles are cells that have a single layer of phospholipids, whereas a vesicle has a variety of layers.
Remember that the polar head groups of the bilayers will face outwards towards the aqueous
environment. The important concept between Micelle and Vesicles are that the transferred process is Spontaneous.
There is no energy required. Also, the speed of the reaction can be speed up by catalysts such as the clay
The most important concept of a cell is the fact that is plays a role as a physical barrier that creates two
very different environments. The internal cell is very different than the outside environment.
The fundamental aspects are much more important than they seem, and play a large role in biology.
Chapter 3 – The Drake Equation
What is the probability of aliens coming to earth?
The Hubble Deep Field takes pictures of our universes, and captures all of the galaxies through the Milky
Way. Andromeda M31 is a galaxy similar to that of the Milky Way. The speed of light is 1.1 billion km/h,
which translates to 9 x 10 km.
There are no objects that can travel faster than the speed of light, so it would be way too difficult to
travel to distance planets and galaxies. That said, we can focus our time on getting to the nearest star
The nearest star to our galaxy is called Proxima Centauri. It is relative close compared to the rest of the
galaxy, as it is only 4.22 light years away. Our space shuttle can go about 31, 000km/hr. which means we
could get to the star in about 150, 000 years. Space travel is not an option at this point in time.
If there are intelligent life forms out in the galaxy, we could interact with them by monitoring radio
waves from earth that of which can travel the speed of light making it possible to transfer information
much faster than the space shuttle.
The radio astronomy system is the most efficient method of sound travel at this point in time.
SETI – Search for Extraterrestrial Intelligence – Computer based program that can help detect radio
waves from a far distance, similar to that of satellites.
The Drake Equation
The drake equation utilizes s set of data about the Galaxy and other information to determine the
chance of other inhabitable life forms that could be present. Each component is equally valuable, but
may not bring as great of a chance to the table. Ns = 100 billion
Fp = 0.5(50billion stars)
Kepler Mission was to detect planets in the environment. It is in space, but does not move at all. It looks
at about 150, 000 stars. It analyzes each star to determine if there is a planet. It measures the decrease
in brightness in the star when a planet moves between the star and the Kepler satellite. Most of the
planets orbit binary systems. Planets naturally form when the star condenses and is produced itself.
Ne = 2
Mass and distance from the parent star are the two critical factors that determine if the planet is
habitable. The habitable zone is a temperature zone only encompasses earth as the temperature is just
right (Goldilocks Theory).Venus and Mars may have been able to have habitable conditions at some
point, but it is left unproven.
With all of these values so far, 100 billion planets could support life.
Mars is very dirt dry and does not have any water sources, which we take for granted. We believe that
water is directly correlated to the ability of a planet to sustain life. In Water, oxygen is more
electronegative and causes H O to be polar. The Hydrogen is slightly positively charged, while Oxygen is
slightly negatively charged.
Water should be a gas in earth atmosphere, but due to the Hydrogen bonding, there is the liquid form
most often. Water has high cohesion, heat capacity, and heat of vaporization. Water is also extremely good at solvating solutes. Water shields the electrostatic shells created between two ions in a mixture.
Did water exist on other planets in our solar system? Geological evident shows that water most likely
was present on Mars at some point in time. There are some significant proofs on mars that explain that
water would have been present. On mars, it took 4 days for water to sublimate.
Europa and Titan are two moons in our solar system that may have existed at some point in time. There
is no clear evidence of life anywhere else but on earth.
Fl = 1
What fraction of the planetary systems actually develops life? All plants that are capable of developing
life do so. This is very hard to calculate, but we assign a value that is most reasonable. This only occurs if
the planet is in the habitable zone.
The drake equation now starts to shake.
Fi = 0.1
Fc = 0.1
In both variables, there is the need for both intelligent and communicating life. That said, we assume
that each variable represents 10% of the full populations.
At this point, the value of n is 1 billion planets with intelligent communicating life.
We are extremely interested in the civilizations that are technologically advanced that are still currently
in existence. There may have been intelligent life that has existed in the past, which is an extremely
How old is our communicating civilization? It is approximately 0.0000001 of the full N value. When the
calculation is complete, we develop a N value equaling 100. There are 100 planets today that are able to
communicate. This is under the assumption that the lifetime is about 1000 years.
That said, if the lifetime is extremely long (100 million years), than the N value would be about 10
Enrico Fermi explains that if there are so many intelligent communicating life form inhabited planets,
then why haven’t we heard anything yet. The explanation for this is based around a few plausible
1. We are unable to detect the planets
a. Distances are too great
b. If N=100, it would take us 10, 000 years for us to pick up radio signals.
c. If N=100, 000, 000, then the time between planets would be 10 light years.
d. We are technologically incompatible
2. No other civilizations exist. We may be alone. Chapter 4 – Fundamentals of Biochemistry
Biological Function is the most important concept of biology.
There are two competing ideas
1. Take a living creature and break it apart and look for the fundamental components
2. We look at the organism as a whole and trying to look at inside information through genetics.
Through biochemistry, we address the function of the cell and proteins specifically from the aspect of
biological function, which is the basis of idea one.
Through genetic, we address the concept of genes and how they interact in our bodies to produce a
It is important to note however that we do not need to isolate ourselves into one of these two streams
and can rather take an approach of Molecular Biology and look at both proteins and gene integrated
into each other’s biological structure and functionality.
By opening the field of Molecular Biology, we can connect both genetics and biochemistry.
If we understand proteins, we will understand how biology works. Protein structure and function is the
pinnacle to all of the cells function.
Abundance is extremely important with proteins, because from a numerical standpoint, the raw
abundance of any given protein will change the functionality overall. If abundance in increased, the
overall function is.
If abundance is so important, we should look at the steps involved with controlling abundance. There
are two systems in our bodies that work hand in hand to create control among the protein.
1. Transcriptional Control
a. We can control abundance through converting genes in DNA to mRNA
2. Translational Control
a. We can control abundance through limiting recruitment of Ribosomes and tRNA
3. Post Transcriptional Control
a. We can regulate this process by decaying the mRNA before Translation
4. Post Translational Control
a. This is an extremely complex system, but it occurs after Translation
Abundance vs. Activity
The pure abundance of proteins is not the same as the activity. There can be a large abundance of
proteins in pure numbers, but the overall activity can be regulated to high or low performance.
All types of control act differently, but the end goal is the regulation of the amount of function that
occurs from the synthesis of a new protein. Constitutive Expression – The gene is always turned on and is always making the same level of protein
Induced Expression – The gene is usually on, and is kept on through a manual mechanism
Repressed Expression – The gene is usually on, and is shut off through a manual mechanism
Northern RNA blot Analysis
Most of the time, there is a correspondence between the amount of transcription/translation that
occurs, and the respective abundance that pertains to it. We would like to look at the numerical values
for protein abundance, which can be achieved by using the Northern blot analysis.
We take a variant of cells or tissue, and we isolate the RNA from each tube, and we run it on a gel
through electrophoresis. We then separate the RNA through size, which is taken care of through the
electrophoresis. 97% of the RNA in a cell is rRNA. mRNA is not as frequently seen.
In a normal human, there are 30, 000 different types of RNA, and we wish to look at a specific one of
those types. We want to evaluate the abundance of that one RNA.
We then transfer the RNA to a membrane of nylon. We must know what gene we are looking for in
order to calculate the abundance. We use a radioactive probe that is a single stranded piece of DNA. If
we incubate them together, they will anneal to the RNA that we are interested in. The creation will be
Homologous and Single stranded.
If we lay a film on the blot again, we can see the exposed blot on an x-ray film.
A western blot works the same way as the above steps, but we do not use a radioactive probe, as we are
not looking for complimentary base pairing in RNA. We use an antibody instead to help pair up the
necessary proteins we are looking for. You can purchase these antibodies in order to use the Western
blot. If an antibody is unknown, we can also create one.
When we look at a gene with mRNA in yeast, we look at the induction of genes. In 24 degrees, the yeast
is able to work properly and does have gene 1 active. However, if we incubate them to 40 degrees, we
see the induction of gene 1 in large abundances. This represents increased Transcript Abundance in the
If we then focus our attention to the proteins, we can see that a variety of proteins will act differently.
Protein one for example may be induced, while Protein 2 is Constitutive.
We can differentiate between a protein and a peptide. They are fairly similar, and are created through
jamming Amino acids together. Remember that an Amino acid is based on a variable component plus an
amino N group and a Carboxylic Acid (=O, -OH) group. The peptide backbone is the linear component of
the Carboxylic Acid and N group that does not include the non-functional R group. Amino Acids
For amino acids, there are polar and non-polar based charged groups. The non-polar group is really
interesting because it affects and induces the hydrophobic effect. This effect is the tendency chemically
for a molecule to avoid water.
Functionally, this is extremely important.
There are 4 types of proteins
a. Primary proteins are fairly linear with no bonding to fold over. A typical protein in this
case if 500 amino acids.
a. Produced by regular interactions between the backbones
b. There are alpha helix and beta sheet that can form(only 2 types)
a. This structure is based on 3D folding through the R groups binding together. Hydrogen
bonding is extremely important along with hydrophobic and ionic bonding. Disulfide
bridges are unique, as they form standardized SS bonds.
a. We will not look at this protein right now, but it is based on the combination of the
above 3 types of proteins
A tertiary structure is where we can easily distinguish between a peptide and a protein. A peptide goes
through the primary and secondary stages with no function which defines itself, but in the third stage,
there is the potential for a switch over to a protein that has a specified function.
The correct conformation is extremely important, as this will alter the overall function. The functional
state of a protein is called the Native conformation. To be functional, the protein cannot be rigid. This
requires some of the bonds to be weak, with allows flexibility. A flexible protein is functional.
Extremophiles are organisms that function well in environments that are extreme (Extremely hot/cold).
Most proteins require a specified shape at the tertiary level. The big question is how a Primary protein
makes its way into the correct conformation for a tertiary level protein. This question was unknown for
a long time, but was discovered in 1972 by Christian Anfinsen.
From a three dimensional structure, we can add Urea and we will get the breaking of bonds to get back
to the primary stage. This is known as denaturing. At this point, we wish to figure out how to get back to
the Native state. We simply remove the Urea, and we get the refolding of tertiary functional proteins.
The refolded state is over 90% accurate.
Protein folding is spontaneous! This process occurs naturally and does not require any energy. There is
not ATP or other chemicals required. Protein folding depends solely on the primary sequence of the
initial protein. There is no outside help required. The rate at which this process happens is nearly
instantaneous. Levinthal Paradox
There is a system involved in checking the confirmations that a protein should be in. The system is
extremely efficient, and reduces the amount of time required. Without a system like this, proteins
would take millions of years to be categorized, which is longer than the age of the universe.
What drives protein folding? With the concept of free energy, we can deduce that the newly synthesized
peptide has way more energy than the native confirmation. If we add energy (urea), we can force the
system backward, and if we remove urea, there will be a spontaneous shift towards the Native
conformation. Secondary structure and the hydrophobic effect both play a role in determining the
This overall process is known as energy funneling, as we are taking an extremely high energy primary
protein and funneling the energy away so that can get a low energy final native conformation. We wish
to be in the most stable state possible with respect to proteins. In the native conformation, the unstable
hydrophobic sections are buried in the protein to ensure that there is no instability.
Predicting protein folding is extremely important. We cannot currently predict how the proteins will
fold, but we are attempting to overcome these proteins.
In this system, we lose the tertiary structure. The most important concept is that there is a loss of native
1. Heat breaks weak bonds
2. pH disrupts ionic bonds
3. Organic solvent quickly break bonds
4. Urea is the best way to denature proteins.
Consequences of Denaturation
By denaturing proteins, we normally expose the hydrophobic amino acids. We also sometime increase
the risk of misfolding and the amount of aggregation.
Folding a protein at 0.1 mg/ml, spontaneity occurs, and the folding occurs extremely easily. This is
known as VITRO.
In VIVO, There is a large concentration (300mg/ml) of the protein. This leads to Macro-molecular
crowding, where there are so many proteins trying to fold that errors occur. This can disrupt the normal
folding sequence which leads to misfolding (like FKBP13).
Chaperones are molecules that help folding proteins through the dogma to the finalized stable form.
They help stabilize the non-native forms from time to time. In a cell, an unfolded protein goes into a
capsule with a chaperone, where the folding occurs, and then is released. This system is exclusively ATP
dependant. Chapter 5 – Energy and Thermodynamics
Thermodynamics is the study of energy and its transformation. Entropy and Enthalpy are the two most
important aspects of thermodynamics. Respiration and Photosynthesis is heavily based on
thermodynamics and the rules associated with it.
Why do you need to eat food?
Everyone needs to consume a large number of calories from proteins, carbs and lipids regardless of
expenditures. Energy is defined as the capacity to do work.
There are a variety of types of work.
1. Motion - Things that move
2. Kinetic – Electrons moving
3. Potential – Energy in the structure and position of an object.
4. Chemical - Chemical bonds in the system
There are three types of Thermodynamic systems.
The system is the object of interest. This is the thing we wish to look at. The universe conversely, is
everything else that the system can exchange energy and matter.
1. Isolated – No energy or matter exchange
2. Closed – Only energy can exchange
3. Open – Both energy and matter can be exchanged
The earth is the example of a closed system because only energy is exchange. There is very little physic
matter based exchanges that occur.
First Law of Thermodynamics
The total amount of energy in the universe is constant. That said, the states that the energy is in can be
changed all the time. Niagara Falls is an extremely useful example of this as the energy is constantly
being changed in states. Hydro is energy made from hydroelectric power. The water goes through a
transformation through turbines where it moves mechanical turbines, making new forms of energy that
is then sent off to our houses.
Transformations are not 100 percent conservation all the time
Second Law of Thermodynamics
Every energy transformation in the world increases the disorder of the universe, which is measured in
the form of Entropy. Entropy is a measure of inefficiency too. In a car, energy is used to make a car
move, but there is also energy lost through heat in the car’s engine. The efficiency is not every perfect.
All energy transformations are not equally beneficial.
The disorder of an isolated system always increases regardless. Physical objects always break down.
There is no stopping this process from happening, and it will continuously break down at the same rate
without any additional catalyst.
The reason photosynthesis and cellular respiration is not 100 percent efficient is because proteins are
continuously breaking down in our bodies. This is caused from Entropic problems. It requires 2000 proteins to keep a chloroplast alive while is takes nearly 3000 proteins to keep a mitochondria alive. If
we isolate the organelles, there is no longer a supply of proteins, and they will eventually decay.
Can a reaction occur spontaneously? A spontaneous reaction occurs without any external power or
energy. There is not requiring for energy input. That said, the rate of which the reaction occur is
Reactions occur spontaneously when:
1. Products have lower potential energy than the reactants(Exothermic, negative delta H)
2. Products have less order than the reactants.(delta S is positive)
Gibbs Free energy is known as free energy. This is the amount of energy that can actually be used.
Remember delta G is based on Enthalpy and Entropy, along with the temperature in the system.
If delta G is negative, then we have an exergonic reaction and there will be a spontaneous completion.
If delta G is positive, then we have an endergonic reaction and there will be a non-spontaneous
If a reaction undergoes a phase change, there is an increase in entropy. (Solid to liquid, liquid to gas)
These reactions will also be spontaneous in nature because there are exothermic properties and there is
These two factors lead to the reaction being exergonic.
The melting of ice is spontaneous. There is no energy required for it to occur. (Provided that room
temperature is present as a condition). There is a strong amount of negative delta G. The reaction is
actually endothermic. That said, water has slightly different properties than most systems. There are 4
combinations of enthalpy and entropy both positively and negatively.
Free Energy, Stability and Work Capacity
All three terms are somewhat interchangeable with each other by definition. There is more free energy,
less stability and a greater work capacity. In the opposite case, there is less free energy, more stability
and less work capacity.
ATP – Adenosine Triphosphate
ATP hydrolysis is extremely important in biological systems. There is a component of ATP that is very
similar to a nucleic acid, which opens the question as to how it was developed. Why is it that ATP is a
better form of energy then just adenosine (nucleotide)? The answer lays in the actual triphosphate
component meaning that there are 3 phosphates. There is a large exergonic reaction when a phosphate
is ripped off through hydrolysis. When the triphosphate is broken down, we have the presences of an
inorganic phosphate on its own.
ATP breaking down into ADP releases the actual energy that was previously stored in the system. In a
system of water, ATP would break down into ADP and then would release heat into the water. ATP hydrolysis is extremely reactive and spontaneously, but it rarely occurs. The rate of reaction is also
extremely slow, which raises some concerns biologically.
That said, energy is used to drive other reactions, so there must be a way to harness energy from the
ATP. Through energy coupling, we can utilize ATP. In the case of creating glutamine from glutamic acid
and ammonia, there is an endergonic reaction. Because endergonic reactions are non-spontaneous, we
can couple it with an exergonic reaction provided by ATP which cancel each other out and come up
There is always more energy in the phosphorylated forms of elements. In the synthesis of Glutamine,
there is a positive outcome where the reaction occurs better and has a lower negative delta G value
creating exergonic synthesis.
All of the reactions in our bodies require enzymes to help out. In the coupling, there is Glutamine and
ATP in extremely close proximity, which causes water to be absent. There is actually no hydrolysis,
because water isn’t present, but rather the terminal phosphate, is transferred to the Glutamate. The
single phosphate is never made in with ATP. It is a simple transfer. ATP hydrolysis should be called ATP
In any isolate system, there is a point where the delta G value will fall to zero as all the free energy has
been used up. This is known as equilibrium because there is no way to go past this point, and causes the
greatest amount of stability. If humans ever reach delta G=0, we will be dead. An open system will
never reach equilibrium.
Life and the Second Law
Does life actually go against the second law of thermodynamics? The world is an extremely ordered
looking place, yet it is said that we have an extreme amount of entropy. Life does not actually go against
the second law because we are in an open system, and the second law only applies to closed systems.
We can make systems more ordered simply by inducting energy into it which causes balance. The heat
given off by living things is tremendous, and this ends up increasing the disorder in the environment. We
tend to keep the entropy of our bodies low so that we can eat. By eating, we are constantly reducing the
amount of entropy in our bodies. This requires constant energy flow. Remember that our bodies never
stop transcribing proteins. Living things are islands of low entropy in a sea of high entropy.
Chapter 6 – Enzymes
Remember that spontaneity has nothing to do with the rate of r12ction. Enzym20 allow for reactions to
be significantly sped up. The rate change is approximately 10 to about 10 . This is a significant
increase in rate of reaction.
Also note that a catalyst is an enzyme that speeds up a reaction without being consumed itself. A
catalyst is typically a protein that will carry out this same function. An enzyme can make a spontaneous occur faster, but cannot make a non-spontaneous reaction occur any faster. In order for an endergonic