Download Assignment 5 Bioenergy/ Photosynthesis

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Working in groups of two to four and armed with a textbook or some other reliable source,
answer the following questions concerning enzyme function and photosynthesis (Chapters 5 & 6).
This assignment is worth 30 points with the possible points for each question in parenthesis. The
following sites may help you answer and understand the questions.
http://www.biology-pages.info/E/Enzymes.html
http://www.microtack.com/html/enzyme1.htm
http://www.ucl.ac.uk/~ucbcdab/enzass/inhibition.htm
1. (5) Define the following terms that relate to an enzyme: activation energy, active
site, conformation, denaturation, and coenzyme/cofactor binding site?
Enzymes are proteins and therefore must be folded or conformed into a specific shape to be
functional. Their function is to assist the occurrence of the necessary biological reactions within
the parameters (limits) (pH, O2 concentrations, CO2 concentrations, temperature, etc.) of normal
biological function. Enzyme folding or conformation includes the opening of a portion of the
protein called the active site. This site is designed to bind to reactant molecules called substrate.
Once the reactants are bound, forming an enzyme-substrate complex (or E-S C) via usually
hydrogen bonds or ionic interactions, the enzyme can change its conformation to move the
reactants into a position to react (e.g. split the reactant apart, put two reactants together, or
change the reactivity or shape of the reactant). The amount of energy required for the reaction to
proceed without an enzyme is called the activation energy and enzymes lower this amount of
energy by being able to bind to the substrate and then change their conformation to force the
reaction. Denaturation of a protein is a process by which some factors, like temperature or pH,
affect the shape of a protein by breaking or disrupting the bonds (H-bonds, R-R interactions, or
ionic interactions) of the protein. In the case of an enzyme, denaturation changes the shape of the
active site. After denaturation the enzyme cannot react with the substrate and the reaction will
not proceed. Another binding site on the enzyme located at a distance from the active site, called
the cofactor/coenzyme site, binds either to a vitamin or a mineral. Once the vitamin or mineral is
bound the active site shape is altered, either to open the site or to close the site. In this way
vitamins and minerals are necessary for regulating normal enzyme function.
2. (5) How are enzymes inhibited by competing molecules and by non-competing molecules?
If another molecule has a similar enough shape to the substrate it can partially bind to the
active site of an enzyme and thereby compete with the actual substrate for binding to the active
site. This is called competing (competitive) inhibition of an enzyme. At this point it comes down to
concentration or a numbers game. If there are more competitors than substrate then the enzyme
will be blocked from binding to the substrate but if more substrate is available then the reaction
will proceed because the enzyme “sees” the substrate more often than the competitor (This is just
random bumping into each other not a seek and destroy mission.). This problem can usually be
rectified by providing an increase in the amount or concentration of the normal substrate molecule
and increase the likelihood of the enzyme bumping into substrate rather than the inhibitor.
If another molecule binds to the cofactor/coenzyme site then the situation is exceedingly dire
to normal enzyme and organism function. This is called non-competing (non-competitive)
Biology& 100
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Class Assignment 5
inhibition. When something binds to the cofactor/coenzyme site it can bind tighter than the usual
cofactor/coenzyme. This action blocks this regulatory site and shuts down the enzyme by altering
the enzymes conformation and thus the active site so that the substrate can’t bind to the active site
at all. Since it doesn’t deal with concentration of substrate then the only way to correct this
situation is to destroy the enzyme and build a new enzyme and eliminating the non-competitive
inhibitor. This takes time and could result in the death of the organism depending on how many of
the enzymes for that reaction are affected. Some poisons have this effect and this is why they
must be eliminated or neutralized as quickly as possible from the body before the enzymes of cells
are affected.
3. (5) Draw a graph that would represent enzyme function at various temperatures and various pH
levels?
Explain why the graphs give the bell shaped appearance? Enzymes function best in an optimal
pH or temperature environment causing the graph of activity to take on a bell shaped curve. The
shape of the curve relates to the degree of denaturation of the enzyme caused by the
environmental change.
4. (5) Describe the concept of energy coupling reactions in regards to ATP usage?
Adenosine Tri-Phosphate (ATP) coupling reactions involve combining one reaction say A + B
that is energetically unfavorable at normal biological parameters with a reaction that will add some
energy to the reaction. To accomplish this reaction an ATP molecule donates a P (represents
energy) to one reactant which energizes this reactant, we will call A, to react with another reactant
called B forming a new molecule called AB. Once the reaction has taken place the P is released and
the product AB is formed. The P (often written as Pi) can then be recombined with an Adenosine
Di-Phosphate (ADP) to make another ATP with the addition of more energy. The AB that was
produced can be used however the cell wants.
These web sites may be helpful to your understanding of photosynthesis.
http://www.ftexploring.com/me/photosyn1.html
https://www.khanacademy.org/science/biology/photosynthesis-in-plants/introduction-to-stages-ofphotosynthesis/v/photosynthesis
Biology& 100
Mr. Brumbaugh
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Class Assignment 5
5. (5) Describe the light dependent reactions of photosynthesis in five steps or less.
A. Sunlight strikes two separate chlorophyll based photosynthetic pigment systems (remarkably
called Photosystem I (PSI) and Photosystem II (PSII)) which excite two electrons within a
core magnesium atom of each pigment system (labelled P680 and P700 in the figure below
the numbers refer to the wavelength of light that best stimulates electron excitation). The
pigment chlorophyll houses the magnesium in both systems.
B. The excited electrons of each system are passed through an Electron Transport Chain (ETC)
associated with the different photosystems. The first chain associated with PSII generates an
ATP molecule as the electrons are passed down the chain and the electrons are passed to the
second pigment system (PSI). A second electron chain associated with PSI reduces a
Nicotinamide Adenine Dinucleotide Phosphate (NADP+) molecule by giving the electrons from
the second pigment system to NADP+ to form NADPH + H+. Where did the H+ come from to
complete this transfer?
C. The hydrogen that associates with the NADP+ comes from the splitting of a water molecule to
replace the electrons lost from the first pigment system (PSII). Remember PSII gave its
electrons to the second pigment system (PSI). The H+ ion moves across the thylakoid
membrane where the cytochrome complexes are embedded to cause a build-up of potential
energy. This gradient energy is allowed to dissipate back across the membrane via a protein
complex called ATP Synthase (or I can make ATP doggoneitase) to yield an ATP molecule from
ADP and Pi.
D. The oxygen from the water is given off as waste to either be used by plant cells mitochondria
in cellular respiration or to the atmosphere via leaf stomata.
These reactions occur in pigments called chlorophyll embedded into the thylakoid membrane
of a chloroplast’s grana. How does the oxygen get out of the plant? It can either be used by the
plant cells mitochondria to act as the final electron acceptor in cell respiration or released out of
the leaf through the stomata.
Biology& 100
Mr. Brumbaugh
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Class Assignment 5
6. (5) Describe the light independent reactions (Calvin cycle or dark reactions) of photosynthesis) in
five steps or less. Divide the Calvin cycle into two halves: Molecule building and Rearrangement.
A. An enzyme named “Rubisco” (see figure below) combines 3CO2 molecules from the
atmosphere (via the leaf stomata) with 3 molecules of RuBP (Ribulose BiPhosphate) that is
already inside the stroma of a chloroplast to form six molecules called 3-PGA or 3phosphoglycerate (carbon fixation).
B. 12ATP’s from the light reactions are used to energize (open or break) the CO2’s. 2 ATP per
each CO2 because two bonds need to be broken.
C. This opens the CO to accept the H+ from 6NADPH + H+. These steps generate 6 molecules of
Glyceraldehyde 3-Phosphate (6G3P) (Molecule building).
D. The G3P’s are separated and one of the G3P’s is used to build other molecules like glucose,
lipids, amino acids or anything the plant cell needs, while the rest (5G3P’s) are rearranged
(Rearrangement) back into the 3 RuBP’ s that is needed to start the cycle again. The
rearrangement steps cost 3 more ATP’s
These reactions occur via enzymes embedded into the chloroplast’s stroma. What limits the
rate of these reactions? The availability of CO2, RuBP, ATP, NADH + H+ (from the light dependent
reactions), and rubisco activity would limit the rate of reaction by the Calvin cycle enzymes.
Biology& 100
Mr. Brumbaugh
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Class Assignment 5