Cellular and Molecular Biology
Part II – Dr. Mbungu
1-29-03
Macromolecules of Life:
- When we talk about the macromolecules of life, the first ones that comes to mind are
carbohydrates. The formula for carbs is CH2O. These molecules are used to give a cell energy and
is also used in the membrane.
- Lipids are also important macromolecules of life.
- Proteins
- Nucleotides.
When we are talking about macromolecules of life, we are talking about these 4 types of molecules.
Carbohydrates (overview):
- These molecules come in different forms. When you have molecules with between 3 to 8 carbons,
they are called monosacharride. The simplest monosacharide is glyceraldehydes. It is a triose (3carbon sugar). Erythrose is a tetrose, ribose is a pentose, glucose and fructose are hexoses.
- Carbon atoms adjoin to a number of other atoms. Since carbon can join with different
atoms/groups or the same atoms. If the carbon atom is bound to 4 different atoms/groups, it is said
to be chiral. When you have a chiral carbon, you are suggesting that you can have isomers. If there
is no chirality, you cannot have isomerism. The number of isomers can be determined by the
formula 2n, with n being the amount of chiral centers. If you look at glucose for example, you see
that carbon #5 is joined to 4 different groups. This is considered to be the chiral center.
- Glucose and fructose have the same structural formula, but they are isomers. The carbonyl carbon
is on position number 1 in glucose and position number 2 in fructose. Glucose is thus an aldehyde
and fructose is a ketone. You can also have isomers with the OH group at the chiral carbon to the
left or to the right (type L- or D- respectively). In the body, the cells can only use one type, L or D.
It uses D glucose, but it cannot use L glucose. This is because the enzymes have sterioisometry. If
an enzyme recognizes only the d-form, it will not recognize the L form.
The ring structure and Polymers
- This is the most common conformation of sugars. When glucose folds in solution, carbon number
one, which has the carbonyl group will come very close to carbon number 5 so that the hydroxyl
group of carbon number 5 can get close enough to react with the carbonyl carbon. When the
reaction takes place, you end up forming a ring structure. All that happens in the reaction is that
you form a bond and create an extra OH group.
- If this group is facing up, the molecule will have different reactions than if it was down. So these
are 2 different isomers that are called anomers. The beta anomer is formed when the hydroxyl
group is pointing up, and alpha when it is pointing down. What will happen is that the hydroxyl
group of one glucose can react with another hydroxyl group from another glucose and form a
glycosidic bond. If you form a long chain of glucose in the alpha form, you will form alpha
amylose or amylopectin etc. These are starches. Amylopectin is the most common form in plants.
Amylopectin is branched while amylose is a straight chain. We have enzymes that can digest this.
- If the glucose is beta, you form a different arrangement. This leads to the formation of cellulose.
This cannot be digested in humans because we don’t have enzymes to digest the beta form.
- Glycogen is also a polymer of alpha glucose. Glycogen is extensively branched. It is formed in
animals, not plants. This is the kind of starch you store in the liver. Glycogen and amylopectin
look very similar, but found in different organisms.
Glucose is the most common monosaccharide in the body.
*Suppose you have 2 molecules. E.g. an amino acid threonine. You will find that threonine has 2 chiral
carbons and thus 4 isomers. If you look at those isomers, there will be maybe only 2 isomers that differ
only at 1 point. These are called epimers.*
There are 3 sugars that are very common and are very important in the body:
1. Glucose
2. Galactose
3. Fructose
These are all monosachharides. They are all C6H12O6. They are all isomers that are used for different
things in the cells.
- If you form a glycosidic bond between 2 glucose molecules, you loose a molecule of water. This
process is condensation. What you end up forming is a dissacharide – maltose.
- If you take glucose and galactose, you form lactose
- If you react glucose and fructose, you get sucrose
Fructose is a very popular sugar in the dieting industry because it is twice as sweet as glucose. To
sweeten something with glucose, you only need half as much. When you take fructose in the body, you
have enzymes that can convert fructose into glucose. The body can only use glucose, so the fructose
gets converted.
2-5-03
LIPIDS
- One of the things that is common with lipids is that all of them are insoluble in water and soluble
in organic solvents.
- Lipids are important in the body for different reasons. When you look at the chemical
characteristics of a lipid. We are going to look at what happens when you react a lipid with an
alcohol.
- The most common Lipids are carboxylic acid. If you react COOH with OH, the carboxylic acid
will release OH, and the OH will release hydrogen. This will form an ester and water. The bond
between the two reactants is called an ester linkage. Plants have different scents depending on
what kind of esters it has.
Common carboxylic acids in nature:
- Myristic Acid (14)
- Palmitic acid (16)
- Palmitoleic acid (16)
- Stearic acid (18)
- Oleic acid (18)
- Linoleic acid (18)
- Linolenic acid (18)
The number within parentheses indicates the number of carbons.
Some fatty acids are saturated, others are unsaturated. Unsaturated Fatty acids are those with double
bonds between the carbons. Those with 1 double bond are called monounsaturated. Those with more
are polysaturated.
If you look at the structure of a saturated lipid, you will see that it is straight. If you have an
unsaturated fatty acid, there will be a kink in the chain.
This can be in the cis or trans form, meaning hydrogens in the same direction or in opposite directions.
The most common form is the cis configuration. This makes lipids into oils. Oils have a cis
configuration and they are liquid at room temperature. Those that are solid at room temperature are
usually in the trans forms.
Linoleic and linolenic acids are not made in the body in high enough quantities. Therefore, these have
to be taken in your diet. These kinds of Fatty acids are considered essential.
If you react glycerol with a carboxylic acid, you form a molecule with ester linkages. Since glycerol
has 3 OH groups, you can form ester linkages with three carboxylic acids. This resulting molecule is a
triacylglyceride. This is the most common form of lipid in your diet.
If instead of using a carboxylic acid at the 3rd OH group, you react it with a phosphoric acid, the
molecule becomes a phospholipid. On the phosphate group you can introduce different groups that
give different products. You can have choline, ethanolamine, serine, a sugar etc joined to the
phosphate group to give the phospholipid its distinctive character. If you use choline, the molecule will
become phosphotidyl choline, if you use ethanolamine, the molecule will become phosphatidyl
ethanolamine etc.
Glycerol (most common) is not the only molecule that you can use to form a phospholipid.
Sphingosine can also be used to make a lipid. If you react it with a carboxylic acid, it will react with
the amine group on the sphingosine to form an amide bond. But you still leave an OH free to react with
other molecule. The molecule formed is called ceramide. The OH can be joined with a molecule of
sugar so form a glycolipid. If phosphoric acid is used, you can form a phospholipid.
Cholesterol.
- Made up of 3 cyclohexane rings and 1 cyclopentane rings.
- Very important in making steroids and hormones in the body
If you analyzed a cell membrane for the types of lipids present, you will find that the sphingomyelin are
mostly found on the outside of the cell. If you look at phosphotidyl choline, you will find it on the outside
mostly. If you look at phosphatidylethanolamine you will see that it is mostly on the inside. If you look at
phosphatidylserine, you see that it is found on the inside. Different cells may have more of one type of
lipids than the other. Nervous tissue is more likely to have more sphingolipids.
Functions of Lipids:
- Membrane Structure. The lipid has a long hydrocarbon tail. On 1 of the R group, you will have a
polar group. The long tail will be mostly hydrophobic. The polar part will be hydrophobic. The
whole molecule is called amphiphatic. Amphi means 2 sides. Amphiphatic means that 1 side will
stay in water and the other won’t. Because of this, if you take a phospholipid and shake it up in the
water, you can form a micelle. The tails go to the inside (hydrophobic) and the head will be on the
surface (hydrophilic). Because of this characteristic, the membrane of a cell is a bilayer. Water is
on the outside surface (exoplasmic) and the inside surface of the cell (cytoplasmic face). This
makes the bilayer form a necessity allowing for the hydrophilic parts to be with the water.
- Cell signaling. Phospholipids are very important for second messengers. Enzymes can cut parts of
the membrane, the cell can then process it and use it as a second messenger.
- Energy. You get more energy from a lipid than from a carbohydrate (gram for gram). There are
some reasons why the body prefers carbohydrates, which we will see later.
- Insulation and protection. Certain tissues in the body are coated with a fatty layer. This is very
important for protecting the tissue. Studies have shown that if a woman looses too much fat, this
can compromise the ability to have children.
- Transport of lipophilic molecule. E.g. vitamin A is not water-soluble. If we didn’t have lipids, we
could not transport it in the body and you would suffer from vitamin A deficiency.
(1 day missing)
2-10-03
The structure of glucose.
The carbon atoms in the molecule of glucose are numbered from 1-6. We begin numbering from the end
with the functional group. The functional group is a carbonyl carbon that is part of an aldehyde group. It
can be converted into a ring structure and anomers can be formed.
All the bonds in a glucose molecule represent energy. If you break a bond, you release energy. We are
going to look at how this happen.
Free energy (G).
Reactions can have a negative or positive free energy change. If it is negative, it is called exergonic. These
reactions are favorable. If the delta G is positive, it is endergonic and not favorable. For you to drive an
endergonic reaction in a cell, it needs to be coupled with an exergonic so that the energy released is used to
drive the enderonic reaction.
A food molecule has bonds. If you oxidize this food molecule, you release energy. This process has a
negative delta G. There are other molecules called activated carrier molecules. As you release this energy
from oxidizing the food, the activated carrier molecules take the energy and bring it to a place where it can
converts molecules available in the cell into molecules needed by the cell. In most of the reactions in a cell,
the activated carrier molecule is ATP.
If you look at the overall reaction for the hydrolysis of ATP, you see that you produce ADP and Pi and the
delta G is –7.3 kcal/mol. This is a highly exergonic reaction. The energy released is used for chemical
synthesis.
The reason ATP has so much energy is because it has 3 phosphate groups. These each have negative
charges, making it unstable.
Other activated carrier molecules are NADP+, NAD, FAD. They all work in the same way.
If you take a molecule of glucose and burn it you release a lot of energy (2840kJ). The end product would
be CO2 and H2O. If you did this, this energy would be lost as heat. The cell controls this process so that
you release the energy step by step so that most of the energy can be caught and taken up by the activated
carrier molecule. This happens in the process of glycolysis.
GLYCOLYSIS
“glyco” means sugar. “Lysis” is breaking down. Glycolysis is the process by which the cell breaks down
glycolysis step by step with the end product being pyruvate.
You start out with a molecule of glucose. This molecule is not very reactive. You need to activate it. To
activate it, you need to phosphorylate it. This is done by ATP. The ATP donates a phosphate group to
carbon number 6 with the help of an enzyme called hexokinase. The result is then glucose-6-phosphate.
This is an aldehyde that must be converted into a ketone. And aldehyde has a carbonyl carbon on the last
carbon. A ketone has the carbonyl carbon in the chain. The carbonyl carbon must be moved to a place
inside the chain. The molecule becomes fructose-6-phosphate. This is mediated by the enzyme,
phosphoglucomutase. Once you have fructose-6-phosphate, you have to phosphorylate it at carbon number
1, to produce fructose-1,6-bisphosphate. The enzyme that does this is phosphofructokinase (PFK). This is a
very important enzyme. It is the key regulatory enzyme in this process. This molecule of fructose-1,6bisphosphate can be broken into 2 molecules. When this is broken down, you get glyceraldehydes-3phosphate (aldehyde) and dihydroxyacetonephosphate (DHAP (ketone)). The body cannot use ketones for
energy. The body must convert the ketone to the aldehyde with the enzyme triose isomerase. The product
now is 2 glyceraldehyde-3-phosphate. This glyceraldehydes-3-phophate is then converted to 1,3
bisphophoglycerate. This reaction releases energy. NAD takes this energy and becomes NADH. The
1,3bisph.. is then converted to 3-phosphoglycerate. This process releases enough energy to phosphorylate
ADP, which becomes ATP (there are actually 2 formed per glucose). This is called substrate-level
phosphorylation. There is another process of forming energy where you have to use a membrane. In
glycolysis you do not need a membrane. The 3-phosphoglycerate is then converted to 3-phosphopyruvate,
which is then converted to pyruvate, while phosphorylating ADP to form another ATP (2).
So, the process of glycolysis uses 2 ATP and forms 4 ATP. The net result of glycoslysis is 2 molecules of
ATP. There is also a production of 2 molecules of NADH. This might seem like a little, but it sets the stage
for some other processes to make more energy. In addition to this, the intermediates can be used to
synthesize other necessary molecules.
The fate of pyruvate.
There are 3 things that can happen with pyruvate:
1. Krebbs cycle (When O2 is available)
2. Homolactic fermentation. NADH converts pyruvate to lactate. The advantage to that is that you
can form NAD+, which can allow glycolysis to continue. The problem is that you accumulate
lactic acid in the body and this causes your muscles to feel sore. When O2 becomes available, the
lactate can then be converted into pyruvate, which can go through the Krebbs cycle.
3. Yeast is a facultative anaerobes. It can survive with or without O2. First you release a CO2 from
pyruvate, to form a 2-carbon molecule (acetylaldehyde). This can receive an electron from NADH.
When you reduce an aldehyde you get an alcohol. When NADH donates its electrons to
acetylaldehyde, you get ethanol. This is metabolism in the absence of O2.
Evolutionists say that glycolysis is the first process that evolved to generate energy when no O2 was
available.
2-12-03
If there is O2 available, the process moves from the cytosol to the mitochondrion. The pyruvate is brought
into the mitochondria. It has an outer and an inner membrane. The inner mitochondrial membrane is folded.
The folds are called crystae. The folding increases surface area so that you have more surface/space to
carry out respiration. If you look at the mitochondria of a plant with those in the flight muscle of a bird, you
will see that the mitochondria in the flight muscle is much more folded.
Krebs cycle.
Pyruvate is a 3-carbon molecule. If you have O2 available, pyruvate is transported into the mitochondria.
There are 3 enzymes that form a complex called pyruvate dehydrogenase. One of the enzymes is a
decarboxylase. It takes a molecule of pyruvate and remove 1 molecule of CO2. The molecule then becomes
an acetate. This is a 2-carbon molecule. Another enzyme within the same complex removes the hydrogen
atoms and associated electrons, and gives those electrons to NAD, reducing it to NADH. The acetate is
then combined with a coenzyme A and the product is acetyl coA. To form a bond between an acetyl and a
coA, you form a thioester bond. These bonds have a lot of energy. When you break this bond, it released a
lot of free energy. Acetyl coA is thus a very high-energy molecule. This combines with another 4-carbon
molecule called oxaloacetate. The thioester bond is broken, which releases enough energy to drive the
endergonic process of bring oxaloacetate and Acetyl coA together. The product is citrate. Citrate is
converted into isocitrate, which gets converted to something else etc. Some of the steps are oxidation ATP,
which requires the release of electrons (and associated proton (H)). NAD gets converted into NADH. FAD
gets converted into FADH2. (Follow through the Krebs cycle and memorize steps)
There is one step where energy is released by substrate-level phosphorylation. GTP is formed by this
process. This GTP molecule converts ADP to ATP, with the release of GDP.
Every molecule of pyruvate produces 3 NADH and 1 FADH2, which gives reducing power. This reducing
power is used to generate energy in the electron transport chain.
How many NADH’s are produced in glycolysis for every molecule of glucose? 4
How many NADH’s are produced for every acetylcoA? 4
The outer membrane of the mitochondria is very permeable to molecules, but those molecules can’t cross
the inner membrane. Transport proteins are required for this. The NADH that is produced in the cytosol
cannot find its way in the inner membrane. A shuttle system is necessary to transport it into the
mitochondria. The NADH donates its electrons onto another molecule, which gives them to oxaloacetate.
When it takes these electrons, it becomes malate. The malate goes through a cycle and becomes
oxaloacetate. The malate carries the electrons in from the NADH into the mitochondria.
On the inner membrane, there are a number of protein complexes that are at different energy levels from
high to low. When the electrons come in they will be donated to the first complex. When you accept
electrons you become reduced. When it becomes reduced, the complex passes the electrons to the next
complex, the next complex passes it to the next complex etc. They are moving in a linear fashion and is
called electron transport. There are places where when an electron moves from 1 place to the next, energy
is released. This energy that is released is used to pump H+ from the mitochondria matrix to the
intermembrane space. There are 3 of these places in the electron transport chain where protons are pumped
into the intermembrane space. When these protons accumulate in the space, you are creating an electrical
gradient. Not only are you creating and electrical gradient, but also a chemical gradient. So there is an
electrochemical gradient, which is called the proton motive force. There is one enzyme on the membrane
where these protons can pass through. This enzyme is ATP synthetase. As they go through this protein, the
energy will be used to make ATP from ADP and ATP. This method of forming ATP is called
chemiosmosis. This chemiosmotic process is very different from substrate-level phosphorylation.
As these electrons are moving down the ETC, the last electron acceptor is oxygen. So this method of
forming ATP is called oxidative phosphorylation. The O2 combines with hydrogen to produce water.
Cyanide blocks the O2 from receiving electrons and will stop respiration. 2,4-dinitrophenol makes the inner
membrane permeable to protons. So ATP is not made.
Electrons from NADH moves all the way through the ETC. There are 3 places in the ETC where there is
enough energy to produce ATP. Electrons that come from FADH2 don’t start at the beginning of the ETC.
FADH does not give its electrons to the first step. NADH produces 3 ATP. FADH produces only 2 ATP.
So, 8 NADH’s are produced in the citric acid cycle. 4 NADH’s are produced in glycolysis. 2 FADH’s are
produced. You can then calculate how many ATP’s are made.
When you are sleeping the body does not need much ATP. Glycolysis is inhibited when the cell does not
need much energy. The enzymes that control these processes are subject to allosteric regulation. When you
are sleeping, if you are making ATP, it can build up. When this ATP levels build up, it can bind to a
allosteric site on an enzyme necessary for glycolysis, slowing down glycolysis. Citrate is also a negative
regulator of the enzymes. One of the enzymes in this process is phosphofructokinase.
If you have too much ADP or AMP, they can bind to an allosteric site on the enzyme, increasing its
activity. Gycolysis will then speed up.
The process responds to the energetic needs of the cell. This is not only happening with
phosphofructokinase, but also enzymes in the krebs cycle and other enzymes necessary for respiration.
When you are breaking down fats, you can take it through a series of steps. Through this series of steps,
you release NADH and FADH. When this happens, these molecules are taken to the Krebs cycle and ETC.
In the process of breaking down fats, you break down 2 carbons at a time. This is called beta oxidation. The
2 carbons form the acetyl for the Krebs cycle. A fat of 16 carbons can make up to 131 ATP. This is why
metabolizing fats produce so much energy.
When proteins are metabolized, the first thing you do is remove the amino group. A carbohydrate remains.
Depending on how many carbons it has, it will enter glycolysis and Krebs cycle at different places. You
cannot really say how many molecules of ATP you will form from the metabolism of proteins.
2-19-03
Metabolism
1. Catabolism: Processes that generate energy in the body. Beginning with complex molecules and
producing simple molecules.
a. Glycolysis
b. Kreb Cycle
c. Electron transport system (ETS)
2. Anabolism: The process by which simple molecules are combined to produce complex molecules.
Requires energy
a. E.g. CO2 + H2O O2 + Sugars (Photosynthesis) Energy comes from the sun.
i. All organisms depend on the energy from the sun through plants. When a
carnivore eats an omnivore, the energy is transferred to the carnivore.
Photosynthesis
This anabolic process takes place in the chloroplast. If you look at a leaf, you see that you have the upper
and lower epidermis. Then you have the palasade and mesophyll cells. These cells have chloroplast in
them. If you look at the chloroplast structure, you can make comparisons with the mitochondria. There are
people that think that in evolution, chloroplast and mitochondria come from the same source.
Chloroplasts have an inner and an outer membrane just like mitochondria. The inner membrane of the
mitochondria was folded, but not in the chloroplast. The outer membrane is permeable, but the inner
membrane is not so permeable (like mitochondria). H2O, O2 and CO2 can cross the inner membrane. It’s a
barrier for all other molecules, which require transport molecules. In the chloroplasts, there is a 3rd
membrane, which is called the thylakoid membrane. So, chloroplasts have 3 membranes, as opposed to 2 in
the mitochondria. The thylakoid membrane is organized (folded) to form the grana. Inside the thylakoid
membrane compartments, you find the thylakoid space/lumen. Outside the thylakoid, we find the stroma.
Different processes occur on the thylakoid membranes, stroma and thylakoid spaces.
The photosynthetic pigment in the plant is chlorophyll. This pigment is located in the thylakoid membrane.
It is made up of a porphorin ring with a centrally located magnesium and a hydrophobic tail region. The
porphorin ring is structurally similar to that in the heme group of hemoglobin, except for an iron in the
center.
Photosynthesis is driven by sunlight. Light has 2 characteristics: Wave properties and particle properties.
As a wave, when light travels it has wavelengths, which can be determined. As particles, it contains energy.
This energy is carried by particles called photons. The smaller the wavelength, the more energy the light
contains. Chlorophyll can absorb energy from the photons. When this energy is taken up, the electrons of
chlorophyll will be excited to a higher energy level and the molecule is said to be photoexcited. There are
other pigments in plants, which give plants the different shades of color. E.g. beta caroteins give the plant
an orange look. In the fall, when photosynthesis starts decreasing and chlorophyll gets broken down, the
leaves start expressing the other pigments like beta caroteins and they get an orange color. Each pigment in
a plant, whether chlorophyll, caroteine or something else, has its own absorption spectra.
If you look at the thylakoid membrane, you see that you have chlorophyll molecules organized into light
harvesting complexes:
1. Antenna Complex: If you have a leaf and light is hitting the leaf, some of the molecules of
chlorophyll are part of the antenna complex. These chlorophyll molecules receive light from the
sun and pass it on to the other chlorophyll in the antenna complex and eventually to the reaction
center chlorophyll.
2. Reaction Center: There are 2 molecules of chlorophyll A at the reaction center.
3. Photosystems (I and II). The difference between the 2 systems is the wavelengths that they are
sensitive to. PSII is sensitive to light of 680nm. PSI is sensitive to light of 700nm.
When light enters it hits the antenna of PSII and PSI. When the reaction center in PSII receive energy from
other chlorophyll, the electrons are excited, and the electrons are passed to cytochromes. When chlorophyll
molecules in the reaction center of PSI, it passes the energy on to ferrodoxin, then the energy is passed to
NADP reductase. The reaction center chlorophyll in PSI gets electrons from plastocyanin, which gets it
from other proteins in the membrane that received electrons from PSII. As it gives off its electrons it
becomes oxidized so much that it can oxidize water to generate O2. This is called Photolysis or the Hill
reaction.
Within the antenna you can have different pigments. Since every pigment only receives light from 1
wavelength, you can then harvest energy from different wavelengths of light.
In the mitochondria, when NAD donated electrons to the cytochromes, the energy was used to pump
protons from the matrix to the intermembrane space. They then created the proton motive force. They went
back through the matrix through ATP synthase, in the process, yielding ATP.
As the electrons are moved from the reaction center and they are going through the electron transport
proteins, energy is released and used to pump protons from the stroma to the thylakoid space, concentrating
protons in the thylakoid space and generating a proton motive force. They can then go back into the stroma
through the ATP synthase. In ATP in the mitochondria is called F0F1, and the one in the chloroplast is
CF0F1 and are very similar. This produces ATP in the stroma. This, of course, can not take place unless
there is light so these are called the light stages of photosynthesis, and yield ATP and NADPH.