I do not understand how to solve for part a of question 1, I

Question # 00085540 Posted By: kimwood Updated on: 07/27/2015 02:43 AM Due on: 08/26/2015
Subject Biology Topic Biochemistry Tutorials:
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Biological Sciences 103
Spring, 2015
K. Hilt

Homework #3

Know:
a) the components and their functions in the electron transport chain of mitochondria
b) how ATP synthase works
c) the components and their functions in photosynthesis; the concepts of the Calvin cycle
d) the reactions for biosynthesis of palmitic acid
Assigned problems in Biochemical Calculations (Segel):
Oxidation and reduction:
read pages 172 174
examples 3-12, 3-13, and 3-14 on pages 175 - 179

View the following two animations:
1) ATPase Scene 2 which shows ATP synthase as a molecular motor, synthesizing ATP.
www.evolusie.co.za/anim_ATPase3_flv.htm

2) Powering the Cell: Mitochondria at http://multimedia.mcb.harvard.edu/ which illustrates several
things, including ATP synthase and translocation of ATP and ADP across the inner mitochondrial
membrane.
Note: both animations will require either Apple Quicktime Player and/or Flash Macromedia
Plugin. Both may be downloaded for free from the web.

1.
A student has 35 ml of a crude extract of pig heart. They want to determine how many total I.U.s of
malate dehydrogenase they have in the extract. They take 0.1 ml of the extract and add it to 400 µl of 20 mM
MOPS, pH 7.4 (dilution A). After mixing gently, they take 400 µl of dilution A and add it to 800 µl of 20 mM
MOPS, pH 7.4 (dilution B). They then run the assay that is listed below:
400 μl
10 μl
10 μl
30 μl

20 mM MOPS, pH 7.4
10 mM NADH (in H2O)
25 mM oxaloacetate (in H2O)
of dilution B of their MDH solution, in 20 mM MOPS, pH 7.4

They mix everything gently together and then measure the ΔA340/Δ time. Their measured ΔA340/20 sec.
was -0.065.
a) How many total I.U.s of MDH were in the crude extract?
b) Why did you mix gently?
c) Which of the above enzyme assay components should be kept on ice? Why? Which components
should not be kept on ice? Why?

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Read the following blog from Nova (http://www.pbs.org/wgbh/nova/blogs/physics/2014/03/quantum-life/)
concerning excitons in photosynthesis.
QUANTUM PHYSICS

Quantum Biology: Better Living Through Quantum Mechanics
By Seth Lloyd on Mon, 10 Mar 2014

A quantum computer is a serious piece of hardware. My colleagues and I build quantum computers from
superconducting systems, quantum dots, lasers operating on nonlinear crystals, and the like. Although the part of a
quantum computer that actually performs the calculation is too small to be seen even under a microscope, the
apparatus used to address and control the quantum computer typically takes up an entire laboratory full of
equipment. In order to keep their sensitive components shielded from the environment, many quantum computers
have to operate at very low temperatures, sometimes a few thousandths of a degree above absolute zero.

So in the spring of 2007 when the New York Times reported that green sulphur-breathing bacteria were performing
quantum computations during photosynthesis, my colleagues and I laughed. We thought it was the most crackpot
idea we had heard in a long time. Closer examination of the paper, published in Nature, however, showed that
something decidedly non-crackpot was going on.

It's not easy being quantum. Credit: wagaboodlemum/Flickr, under a Creative Commons license.

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Photosynthesis converts light from the Sun into chemically useful energy inside cells. In photosynthesis, particles of
light called photons are absorbed by light-sensitive molecules called chromophores (light carriers in ancient
Greek), which are arranged in a tightly bound structure called an antenna photocomplex. When a photon is
absorbed, a quantum particle of energy called an exciton is generated. (An exciton isnt a particle in the traditional
sense, but it acts enough like a particle that physicists find it useful to treat it as one. Such mathematical likenesses
are called quasi-particles.) The exciton hops from chromophore to chromophore inside the photocomplex until it
arrives at the reaction center, an agglomeration of molecules that take in the exciton and transform its energy into a
form that the living system can put to use to perform cellular metabolism, grow, and reproduce. The great majority
of the energy used by living systems once came from photosynthesis: Every calorie that you consume came originally
from excitons that hopped through the antenna photocomplex of a photosynthetic organism.

By zapping complexes of photosynthetic molecules with lasers, the authors of the paper were able to show that the
excitons use quantum mechanics to make their journey through the photocomplex more efficient. The experimental
evidence was strong and compelling. The authors also speculated that the excitons were performing a particular
quantum computation algorithm called a quantum search, in which the wave-like nature of propagation allows the
excitons to zero in on their target. As it turns out, the excitons were performing a different kind of quantum
algorithm called a quantum walk, but the crackpot fact remained: Quantum computation was helping the bacteria
move energy from point A to point B.

How could tiny bacteria be performing the kind of sophisticated quantum manipulations that it takes human beings
a room full of equipment to perform? Natural selection is a powerful force. Photosynthetic bacteria have been
around for more than a billion years, and during that time, if a little quantum hanky panky allowed some bacteria to
process energy and reproduce more efficiently than other bacteria, then quantum hanky panky stuck around for the
next generation. Nature is also the great nanotechnologist. Living systems operate on the basis of molecular
mechanisms, where atoms and energy are channeled systematically through molecular complexes within the cell.
The molecules in turn are assembled using the laws of quantum mechanicsquantum weirdness is always lurking
just around the chemical corner. These quantum changes can either help or hinder energy transport. Natural
selection ensures that the role of quantum weirdness in cellular energy transport is a beneficial one.

How can quantum weirdness assist in energy transport? The answer lies in a phenomenon called wave-particle
duality. Wave-particle duality means that waveslight and soundare at bottom composed of particlesphotons
and phonons. Conversely, things that we think of as particles, such as electrons, atoms, or for that matter soccer
balls, have waves associated with them.

The quantum wave of a soccer ball is about the same size as the ball itself, and doesnt extend halfway down the
soccer field (although the ball can sometimes seem to be on Lionel Messis left and right foot at the same time). But
the wave corresponding to a particle can be much larger than the particle itself. While a single exciton consists of an
excited electron within a chromophore, the wave corresponding to a propagating exciton can extend over many
chromophores.

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Does that make sense? Of course not! Quantum mechanics is fundamentally strange and counterintuitive: Quantum
particles dont behave like soccer balls.

To see how the wavelike nature of excitons can assist in their propagation, first visualize a classical kind of exciton
dynamics. Imagine that each chromophore is a lilypad, and the exciton is a frog hopping randomly between
neighboring lilypads. The frog starts at the edge of the circular lilypond. How long does it take to get to the ponds
center? Because the frog is hopping from lilypad to lilypad at random, it sometimes moves towards the center of the
pond, but it is equally likely to move to the left or right, or even backward. The frog will land on a substantial fraction
of all the lilypads in the pond on its way to the center. The number of hops the frog has to take to get to the center is
proportional to the number of lilypads in the pond.

Now consider a quantum frog. The frogs initial wave is circularly symmetric at the edge of the lilypond and
propagates inward, like a backward version of the wave created when you drop a stone in the center of a pond. The
time it takes for the wave to travel from the shore to the center of the pond is proportional to the radius of the
lilypond. But the radius of the lilypond goes as the square root of the number of lilypads in the pond, because the
number of lilypads is proportional to the area of the pond, i.e., the radius squared. The wavelike nature of
propagation in quantum mechanicsthe quantum hophas the potential to get the frog to the center of the pond
much more quickly than the classical hop. So, for example, if the frog hops once a minute, and a classical frog takes
100 minutes to get to the center, then the quantum frog takes only 10 minutes.

In green sulphur-breathing bacteria, the antenna photocomplex through which the excitons propagate is like the
lilypond for the quantum frog: The waves corresponding to the excitons are spread out over many chromophores,
and wavelike propagation allows excitons to move more quickly from chromophore to chromophore than classical
hopping would allow.

Together with Alan Aspuru-Guzik and Patrick Rebentrost at Harvard, my MIT colleague Masoud Mohseni and I
constructed a general theory of how quantum walks in photosynthesis can use the wavelike nature of quantum
mechanics to attain maximum efficiency. It turns out that wavelike transport is not always the best strategy. To
understand why, suppose that the lilypond is full of rocks sticking up out of the water. As the wave moves through
the pond, it scatters off the rocks. As a result, the wave never reaches the middle of the pond, which remains calm
and protected. This is a phenomenon called destructive interference. Although the wave can propagate a short
distance, eventually the random waves scattered off the rocks interfere with the overall waves propagation,
effectively stopping it in its tracks. The quantum frog becomes completely stuck: A classical hopping strategy would
have been more efficient. In the antenna photocomplex, the rocks are microscopic irregularities and molecular
disorder that scatter the quantum wave as it tries to pass through.

By constructing detailed quantum mechanical models, my collaborators and I were able to identify the optimal
strategy for the interplay between wavelike propagation and classical hopping in photosynthesis. Over short
distances, the wavelike propagation is more effective than random hopping. The exciton travels like a wave right up

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to the distance at which destructive interference causes it to get stuck. At this point, the fact that living systems are
hot, wet environments comes into play: The environment effectively gives the exciton a whack that gets it unstuck
and makes it perform a classical hop, which frees up the exciton to propagate again. (The technical term for this
whack is decoherence.) Then the process repeats. The wave propagates until it gets stuck; the environment gives it
a whack; the exciton hops. Eventually, the exciton reaches the reaction center in the minimum possible time.
Expressed in terms of our quantum frog, the rule is simple: Wave until you get stuck, then hop.

The birds, the bees, and the fruit flies

Photosynthetic plants and bacteria are masters of the minutiae of quantum mechanics, manipulating quantum
coherence and decoherence to attain almost 100% energy transport efficiency. If quantum hanky panky is so
effective, are there other living beings that take advantage of quantum effects to live better and have more offspring?
Only in the case of photosynthesis have scientists actually found the smoking gun (or maybe the smoking photon).
However, there are several other organisms in which quantum mechanisms apparently play an important role.

European robins are sensitive to the Earths magnetic field, which helps them during migration. Do they have a tiny
compass in their heads, a piece of magnetite that swivels back and forth to point out magnetic north? Apparently
not. Instead the evidence suggests another light-activated quantum mechanism. A photon excites an electron, which
swivels around in the Earths magnetic field; the rate at which the electron decays from its excited state depends on
how far it has swiveled. Since the robins need light to detect magnetic north, the next time you see a flock of them
stumbling around at night, you know what is going on.

I smell a quantum

Quantum mechanics may also be involved in the sense of smell. Scientists have long believed that smell operates via
a lock and key mechanism, an idea Linus Pauling first proposed more than 50 years ago. The molecule to be
sniffedthe odorantlocks into a receptor in the olfactory apparatus that can only fit that particular key. The
receptor then unlocks or changes its configuration, leading to a flow of ions sufficiently large to trigger a neuron to
fire.

The problem with this model is that olfactory receptors are not very specific: They can be unlocked by many different
keys. This has led some researchers to propose that the receptors are sensitive not only to the shape of the odorant
molecule, but to its vibrational frequenciesthat is, its sound. The combination of shape and sound provides a
unique signature for the molecule. For the vibrational theory of smell to hold, however, the underlying dynamics of
the molecule in the receptor must be intrinsically quantum mechanical: The receptor must respond to individual
phononsquasi-particles of soundgenerated by the molecule. Experiments show that fruit flies are indeed
sensitive to vibrational frequencies of molecules, supporting the hypothesis of quantum smell. When trained to
sense a molecule with a particular vibrational frequency they are attracted to it like flies tophonons.

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Who is quantum?

Where else might quantum mechanics play a role in life? Because light is made up of photons, interactions between
living systems and light represent a good place to look. Our eyes are capable of detecting single photons by a highly
quantum mechanical mechanism: A molecule in the retina absorbs a single photon, and uses its energy to release the
flow of tens of thousands of ions, stimulating a neural response. Neural impulses in the brain are probably too
coarse and classical to support the wave-like quantum dynamics that hold sway in photosynthesis, but at the level of
individual synapses, the neurotransmitter binding mechanism might well benefit from the same types of quantum
dynamics that apparently enhance smell.

As scientists delve deeper into the details of molecular dynamics in living systems, they are likely to see more
examples of quantum mechanics at work. We dont yet know exactly what aspects of biology benefit from quantum
mechanics. But we do know one thing: The unquantized life is not worth living.

Go Deeper
Editors picks for further reading

Nature: Physics of life: The dawn of quantum biology
In this Nature news feature, asks whether quantum biology should be treated as a new scientific discipline.

World Science Festival: Quantum Biology
In this 90-minute webcast, Seth Lloyd, Thorsten Ritz, and Paul Davies discuss the intersection of biology and
quantum mechanics.

Tell us what you think on Twitter, Facebook, or email.

Seth Lloyd
Seth Lloyd was the first person to develop a realizable model for quantum computation and is working with a variety
of groups to construct and operate quantum computers and quantum communication systems. Dr. Lloyd is the
author of over a hundred and fifty scientific papers, and of "Programming the Universe" (Knopf, 2004). He is
currently professor of quantum-mechanical engineering at MIT.

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