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Week 5
Last week, we talked about energy and how chemical reactions in biology are often
endergonic (energy storing) or exergonic (energy releasing). Let’s look at the
endergonic and exergonic reaction a little more closely. Here is a picture showing an
exergonic reaction going from left to right.
Lactose is a disaccharide. When it is broken down into glucose and galactose it releases
energy (and is therefore exergonic). Notice that the energy is actually released and stored
by the breaking and forming of a covalent bond. In fact, the covalent bond is very
important for energy storage. Notice that it takes energy to get up the first part of the hill.
But once you are over the hill, you should notice that more overall energy is released
(that is what makes it an exergonic reaction.) Let’s think of it this way: Imagine you
have put a rubber band around both of your hands. When you pull your hands apart, the
rubber band stretches. It takes energy to try and separate your hands when you have the
rubber band around them. If you really stretch them far, the rubber band will eventually
break and all the energy will be released at once. This energy required to break the
rubber band or get the car up the first part of the hill is called the activation energy. The
activation energy is the energy required to make the reaction occur.
Now if you look at the picture below, you will notice that the hill is smaller. This is
because an enzyme is being used. An enzyme is a special type of protein that has a very
specific shape that is able to fit onto specific molecules. The enzyme weakens the bond
and makes it easier to break the bond. They lower the activation energy. If you think
back to our rubber band idea, you can think of an enzyme as a pair of scissors that makes
a small nick or cut in the rubber band so that the rubber band breaks easier when you pull
your hands apart. Enzymes are VERY important in biology. Nearly every chemical
reaction we will look at is controlled by enzymes. In fact, we will soon learn that genetic
diseases are directly related to incorrect enzymes that either don’t do what they are
supposed to, or, they do something new that they should have never done!
Cellular Respiration:
When food is eaten, an animal (such as a rabbit, snake or even a human) receives energy
stored in the chemical bonds of the food. But how is the energy stored in the chemical
bonds turned into energy that can be used by living organisms? Well, it turns out that the
energy stored in the chemical bonds of the food you eat is transformed into energy stored
in a special molecule called ATP. Making ATP is the main goal of cellular respiration.
Cellular respiration can be summarized by the chemical equation:
C6H12O6 + ADP + 6O2
Enzymes
6CO2 + 6H20 + ATP
This type of reaction involves two kinds of chemical processes called oxidation and
reduction. When something is oxidized, it loses electrons. When something is reduced,
it gains electrons (think about the fact that electrons are negative and that makes more
sense). In this reaction, Glucose (C6H12O6 ) is oxidized and the oxygen is reduced.
Oxidation and reduction always occur together and these are thus called Redox
reactions.
There are many steps in cellular respiration. Cellular respiration can be divided into four
parts: 1) Glycolysis 2) PDC (pyruvate dehydrogenase complex) 3) Krebs Cycle and 4)
Electron Transport Chain. The first step, glycolysis, takes place in the cytoplasm of
the cell (the area between the cell membrane and the organelles). Glycolysis has many,
many, MANY steps. Each step also has an enzyme. We won’t learn all the steps.
Instead (for all four parts) we will only focus on the inputs and outputs of each and the
main goal of each. Skip ahead to the SUMMARY CHART to see what you really need
to know. Referring to the chart as you read this section is also a good idea.
Step 1-GLYCOLYSIS: The inputs of glycolysis are glucose and NAD+ (a molecule that
can “hold” high energy electrons.) The outputs of glycolysis are Pyruvic Acid (which
gets converted into Acetyl-Coenzyme A before the Krebs Cycle), NADH and some ATP.
The main goal of glycolysis is to break down glucose and to store the high energy
electrons in the bonds to make NADH. Think of NADH as a high energy electron
shuttle. Those electrons are going to be very important later on.
Now remember, don’t get blown away by the above figure, but you do need to know the
inputs and outputs of each step AND the main goal of each step.
Step 2-PDC: The PDC is a series of reactions that basically take pyruvic acid, cut off one
of the carbon dioxides (and release it as CO2), and attach another molecule called
coenzyme-A. This molecule, (the pyruvic acid missing a carbon and the coenzyme-A)
make a molecule called acetyl Coenzyme-A. This series of reactions is used to transport
this molecule into the mitochondria for the rest of the steps. Many text books will refer
to this step as the “intermediate step” or “the in between step”.
Step 3-The Krebs Cycle: The Krebs Cycle inputs include Acetyl-Coenzyme A and
NAD+. The outputs of Krebs include ATP, CO2 and NADH. The Krebs cycle takes
place in the inner membrane space of the mitochondria. Here is the Krebs cycle:
You will notice that some ATP is made and some Carbon Dioxide comes out of the
process. But again, the main goal here is to make NADH. You will notice that FADH2 is
also made. You don’t need to worry about knowing the difference between NADH and
FADH2. For our purposes, you can assume they work the same way.
Step 4-The Electron Transport Chain: In the Electron Transport Chain, we finally get
to use all that NADH that we made. Remember, NADH is holding onto a high energy
electron. That, and the fact that it has an extra hydrogen, is really the difference between
it and NAD+. You should notice two things right away in the electron transport chain.
First, that it takes place along the inside membrane of the mitochondria. This membrane
is similar to the plasma membrane or cell membrane that we learned about earlier. It is
made up of phospholipids. You should also notice the series of proteins that are
embedded within this membrane. These are important. What happens is this: The high
energy electrons in NADH are going to be passed to these proteins. Each time the
electron is passed from protein to protein, it gives off a little bit of energy. Some of that
energy escapes as heat as you should already know. But some of that energy is used to
pump an H+ (also from the NADH) across this inner membrane. This is a type of active
transport (because it requires energy to do). After all the NADH molecules have passed
their high energy electrons on, you end up with a big pile of H+ on the outside of this
inner membrane. A special protein then allows the H+ to flow through them. This is
kind of like a waterfall. This “hydrogen waterfall” releases a tremendous amount of
energy (again, some escapes as heat). This energy is used to take a phosphate and stick it
onto ADP to make ATP. This is how the majority of ATP (about 32 of the 36 molecules)
is made.
What happens to that electron as it gets passed down? At the end of the chain, an
oxygen, which has a strong affinity for electrons, grabs onto it. The oxygen also pulls in
some hydrogen ions as they float through the “waterfall”. Combining the oxygen, the
electron, and the hydrogen forms water. So, by the process of cellular respiration, one of
the things you make is water. You can also see now why you need oxygen. It is what we
call the final electron acceptor in the electron transport chain. Here is a simple little chart
to help you remember the most important things for each step.
SUMMARY CHART:
Step
Input
Output
Main Goal
Glycolysis
Glucose, NAD+,
ADP
NADH, ATP,
Pyruvic Acid
Make NADH
PDC
Pyruvic Acid,
Coenzyme- A,
NAD+, ADP
Acetyl-Coenzyme
A, CO2,
Make NADH
Krebs Cycle
Acetyl CoenzymeA, NAD+, ADP
NADH, ATP, CO2
Make NADH
Electron Transport
Chain
NADH, Oxygen
ATP, Water
Make ATP
*Note that Pyruvic Acid gets turned into Acetyl Coenzyme-A between glycolysis and
the Krebs cycle. Also, some CO2 is produced between these steps as well.
Don’t forget, THE MAIN GOAL OF CELLULAR RESPIRATION is to make ATP.
Coming Up….(but you need to know at least this part
for this coming quiz!)…
Similar to the chemical reactions of cellular respiration, photosynthesis is a very
important set of reactions involved with transforming energy. Photosynthesis can be
broken down into two main parts: The Light Reactions and the Dark Reactions (or the
Calvin Cycle). In the light reactions, plants use sunlight and a special chemical called
chlorophyll to basically make two energy rich products, one is ATP and the other a
chemical called NADPH. NADPH is sort of like NADH (found in cellular respiration)
and is holding onto high energy electrons. During the light reactions, plants also split
water to get some electrons that are needed to run the light reactions. When plants split
the water, they make Oxygen.
During the dark reactions, plants use the energy in the NADPH and ATP that they made
during the light reactions (along with carbon dioxide and an enzyme that is called
Rubisco (rubisco is short for a very long name). The enzyme basically glues carbon
dioxide molecules together. In the end, the dark reactions make glucose. Thus,
photosynthesis is really the opposite of cellular respiration.
Plants are not the only organisms that do photosynthesis. There are some single-celled
organisms, for example, called protozoans (look back to week 3) that can do
photosynthesis. But, plants are by far the most important photosynthesizers (if that is
even really a word) because there are so many of them.
Most plants have two important types of tissue that are used to transport food and water
throughout the plant. These are called the phloem (used to transport food) and the xylem
(used to transport water). Food (glucose) is generally made up in the leaves and then
excess food is sent down the phloem to the roots for storage. When the plant later needs
that stored energy, it travels back up the phloem to the various other cells of the plant.
Water is obtained via the roots and travels up the xylem to the various parts of the plant.
ASSIGNMENT #5 – Print this sheet off and turn it in with your lab next week. This
sheet of paper goes on top (then the lab).
1) The final electron acceptor in the electron transport chain of cellular respiration is?
A) Carbon Dioxide (CO2)
B) Oxygen (O2)
C) Water (H2O)
D) Sodium (Na+)
E) Glucose
2) Pushing a rock up a hill would be similar to a:
A) Exergonic Reaction
B) Endergonic Reaction
3) Which plant tissue is used for transporting water throughout a plant?
A) Xylem
B) Phloem
4) Which of the following is an enzyme that is used in the dark reactions of
photosynthesis?
A) Chlorophyll
B) DNA Polymerase
C) RNA Polymerase
D) Rubisco
E) Glucase
5) Which of the following molecules is an output of glycolysis?
A) Carbon Dioxide
B) Glucose
C) NADH
D) NADPH
E) Water
6) What is a catalyst?
7) Explain the difference between figure 6.7a and 6.7b.
8) What is meant by energy efficiency and what happens to the other energy that is not
“efficient”?
9) Explain where the energy is or how it is stored in an energy rich molecule.
10) What are metabolic pathways?
Words that you may be asked to define or use in fill-in-the blank types of questions:
Endergonic, Exergonic, Energy, Activation Energy, Enzyme, Substrate, Active Site,
inhibitor, Glycolysis, PDC, Krebs Cycle, Electron Transport Chain, NADH, NAD+,
ADP, ATP, Oxygen, Water, ATP Synthase, Pyruvic acid, Coenzyme A, AcetylCoenzyme A, Carbon Dioxide, Photosynthesis, Chlorophyll, Xylem, Phloem, Rubisco,
Light Reactions, Dark Reactions, Calvin Cycle, Cytoplasm, inner and outer
mitochondrial membrane, Mitochondria, Glucose, Oxidation, Reduction, Redox
Reactions