Although we and other biologists will often only consider one direction of a reaction, keep in mind that catalysts do not determine the direction of a reaction- they simply allow the reaction to occur in whichever direction is energetically favorable

It means that the cell can control metabolic flux by controlling the availability of catalysts.

Each variable group on an amino acid gives that amino acid specific chemical properties (acidic, basic, polar, or nonpolar). This gives each amino acid R group different chemical properties

The carboxyl group of one amino acid and the amino group of the incoming amino acid combine, releasing a molecule of water and creating the peptide bond.

Each amino acid is attached to another amino acid by a covalent bond, known as a peptide bond,

There are 20 genetically encoded amino acids available to the cell to build in proteins and all of these contain the same core sequence: N-C-C- where the first ("alpha") C will always carry the R group and the second will have a double (ketone) bond to oxygen

Each amino acid has the same core structure, which consists of a central carbon atom, also known as the alpha (α) carbon, bonded to an amino group (NH2), a carboxyl group (COOH), and a hydrogen atom.

Amino acids are the monomers that make up proteins.

Again, Dr. Britt will only quiz you on what goes into the Calvin cycle, its first step, and what comes out.

Six molecules of both ATP and NADPH are used up in the process, helping to drive the reactions and produce the electrons required to reduce the incoming CO2. The "spent" molecules (ADP and NADP+) return to the nearby thylakoids to be recycled back into ATP and NADPH.

Ribulose-1,5-bisphosphate (RuBP) is composed of five carbon atoms and includes two phosphates.

In the stroma of plant chloroplasts, in addition to CO2, two other components are present to initiate the light-independent reactions:

The biological pathway that leads to carbon fixation in green plants and cyanobacteria is called the Calvin Cycle and is a reductive pathway (consumes energy and electrons) which leads to the reduction of CO2 to G3P.

"Carbon Fixation", the incorporation of inorganic carbon (CO2) into organic molecules

while those organisms that require organic sources of carbon, such as glucose or amino acids, are referred to as heterotrophs

Organisms that can obtain all of their required carbon from an inorganic source (CO2) are referred to as autotrophs,

It is at this step that light energy is transformed into the more stable form of chemical energy. All of the subsequent redox reactions are involved in pumping protons or in delivering that e- to NADP.

The Calvin cycle takes place in the stroma, conveniently located vis a vis the ATP- and NADPH-producing thylakoids

The captured energy is transferred from chlorophyll to chlorophyll until ...eventually... (after about a millionth of a second), it is delivered to the reaction center. Up to this point, only energy has been transferred between molecules, not electrons. In other words, no new bonds have formed.

Both photosystems have the same basic structure; a number of antenna proteins to which chlorophyll molecules are bound surround the reaction center where the photochemistry takes place. Each photosystem is serviced by this light-harvesting complex, which passes energy from sunlight to the reaction center;

These two types are simply called photosystem II (PSII, carrying P680) and photosystem I (PSI, carrying P700), and were named (confusingly) in the order of their discovery. The two complexes differ on the basis of what they oxidize (that is, their source of electrons) and what they reduce (the place to which they deliver their energized electrons). Working in tandem, these two photosystems can power the production of both NADPH and ATP.

In oxygenic photosynthesis, two types of pigment are found embedded in the thylakoid membrane (in plants) or the bacterial inner membrane (in cyanobacteria).

oxygenic photosynthesis is more complex than the "sulfur-genic" photosynthesis described above, requiring two different reaction centers, with different reduction potentials.

The overall function of "light-dependent" reactions of photosynthesis is to transform solar energy into chemical compounds, in the form of NADPH and ATP. This energy supports the "light-independent" reactions and fuels the assembly of sugar molecules.

In non-cyclic photophosphorylation electrons are removed from the photosystem, as they end up in NADPH after moving through an electron transport chain

As in the green sulfur bacteria example above, the step that transfers light energy into the biomolecule takes place in a multiprotein, multipigment complex called a photosystem

This NADPH will be used for carbon fixation. Thus in order to keep generating NADPH there's needs to be a source of electrons to refill the "electron hole" in bacteriochlorophyll

In an electron transport chain analogous to that of respiration, the electron is passed exergonically from carrier to carrier. The redox reaction at one of the carriers powers a proton pump, pushing protons into a higher concentration compartment. Eventually the electron is used to reduce bacteriochlorophyllox (making a complete loop) and the whole process can start again.

This electron must come from an external source with a lower reduction potential than the (ground state) pigment and depending on the reduction potential of that pigment there are different possible sources that might be employed, including H2O, reduced sulfur compounds such as SH2, and even elemental S0

The visible light seen by humans as white light is composed of a rainbow of colors, each with a characteristic wavelength.

However, the electron energized by light might have an alternative fate: it might descend through a different series of carriers (without pumping protons) and instead be deposited onto a close relative of NAD+ called NADP. Addition of 2 e- generates NADPH, which is going to be used to build sugars from CO2

This electrochemical gradient generates a proton motive force whose concentration gradient can then be coupled to the endergonic production of ATP, via ATP synthase (again, just as in respiration).

For example, as you can see in the Table below, the ground state pigment at the reaction center of PSII (the "chlorophyll a" in P680) cannot reduce anything listed in the table- it is the weakest reducing agent described there (even weaker than H2O!).

While in the excited state, the pigment has a much lower reduction potential (E˚', it moves upward on our electron tower, it becomes a stronger reducing agent) and can donate these unstable, high potential energy electrons to carriers with greater E˚'

"unexcited", or "ground state"

The first step of the process involves the absorption of a photon by a pigment molecule. Light energy is transferred to the pigment and promotes electrons into an excited state.

Photophosphorylation probably evolved relatively shortly after electron transport chains and anaerobic respiration.

Photophosphorylation is the process of transferring the energy from light into ATP.

Because the energy changed the reduction potential such that the molecule is now a stronger e- donor, this high-energy e- can be transferred exergonically to an appropriate e- acceptor. In other words, the excited state can be involved in a redox reactions. This is a photochemical reaction

When an atom absorbs a photon of light, an electron acquires that energy, leaving its ground (lowest potential energy) orbital and moving up to a higher energy orbital. This is an unstable situation.

Each type of pigment can be identified by the specific pattern of wavelengths it absorbs from visible light. This characteristic is known as the pigment's absorption spectrum.

Carotenoids are the red/orange/yellow pigments found in nature. They are found in fruit

This ring structure is chemically related to the structure of heme compounds that also coordinate a metal and are involved in oxygen binding and/or transport in many organisms. Different chlorophylls are distinguished from one another by different "decorations"/chemical groups on the porphyrin ring

There are five major chlorophyll pigments named: a, b, c, d, and f. Chlorophyll a is related to a class of more ancient molecules found in bacteria called bacteriochlorophylls. Chlorophylls are structurally characterized by ring-like porphyrin group that coordinates a metal ion.

If a plant were able to absorb 100% of incident photons, what color would it be? What if a variant of the same species of plant lacked a pigment required to absorb red light?

green plants appear green because they reflect, rather than absorb, most of the photons at a combination of wavelengths that we perceive as green

At the center of the biological interactions with light are groups of molecules we call organic pigments.

Signaling interactions are largely responsible for perceiving changes in the environment

A specific "color" of light has a characteristic wavelength.

The distance between peaks in a wave is referred to as the wavelength and is abbreviated with the Greek letter lambda (Ⲗ

NAD+ is used by the cell to "pull" electrons off of compounds and to carry them to other locations within the cell, thus they are called electron carriers

The oxidation of, or removal of an electron from, a molecule (whether accompanied with the removal of an accompanying proton or not) results in a change of free energy for that molecule - matter, internal energy, and entropy have all changed in the process.

Each of these two types of molecules is involved in energy transfer that involve different classes of chemical reactions. It's interesting that while one class of carrier delivers electrons (and energy), the other delivers phosphates (and energy), but both include an adenine nucleotide(s).

In this course we will examine two major types of molecular recyclable energy carriers: (1) nicotinamide adenine dinucleotide (NAD+), a close relative nicotinamide adenine dinucleotide phosphate (NADP+), and flavin adenine dinucleotide (FAD2+) and (2) nucleotide mono-, di- and triphosphates, with particular attention paid to adenosine triphosphate (ATP).

Each individual carrier in the pool can exist in one of multiple distinct states: it is either carrying a "load" of energy, a fractional load, or is "empty".

Keep in mind that a positive ΔE0' gives you a negative ΔG

Using the Nerst equation essentially corrects for the  number of electrons per transfer (here n = 2) and puts things into units biologists can use, and copes with the directionality (sign) for us. F has units of kJ*/volt, E has units of (Volts), so we end up with kJ, a unit of energy.

here n is the number of electrons involved in each transfer, and F is a constant that is a positive number

E0' values and to help us predict the direction of electron flow between potential electron donors and acceptors.

Different compounds, based on their structure and atomic composition, have intrinsic and distinct attractions for electrons. This quality is termed reduction potential or E0’ and is a relative quantity (relative by comparison to some “standard” reaction).

By convention we analyze and describe redox reactions with respect to reduction potentials (E0'), a term that quantitatively describes the "ability" of a compound to gain electrons.

If you consider a generic redox reaction and reflect back on the thermodynamic lectures, what factor will determine whether a redox reaction will proceed in a particular direction spontaneously, and what might determine its rate?

Sometimes a redox tower will list compounds in order of decreasing redox potentials (high values on top and low values on the bottom). Our towers do not- we list (reduced vs. oxidized state) molecule pairs with negative values (highly negative E˚') up top and positive ones (highly positive E˚') towards the bottom. Does presenting the data this way change the redox potential of a compound?

The electron tower is a tool that ranks different common half reactions based on how likely they are to donate or accept electrons.

The amount of energy transferred in a redox reaction is associated with the difference between each half reactions' reduction potential, E0

Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions.

The ETC produces a proton gradient. No ATP is directly generated in this process. However, the proton gradient is then used by the cell (among other things) to run an enzyme called ATP synthase which catalyzes the reaction ADP + Pi --> ATP. This method of ATP production (called oxidative respiration) results in additional- many additional- ATPs being produced.

The process of fermentation results in the reduction of pyruvate to form lactic acid and the oxidation of NADH to form NAD+.

We can generalize the process by describing it as the returning of electrons to a derivative of the molecule that they were once removed from, usually to restore pools of an oxidizing agent. This, in short, is fermentation.