Topic 2 – Molecular Biology
Essential Idea
Living organisms control their composition by a complex web of chemical
reactions.
Molecules to metabolism
Chemical Elements and Water
The most common elements in living things are Carbon, Hydrogen, Oxygen and Nitrogen. These form the
basic structure of many important organic chemicals such as carbohydrates, lipids, proteins and nucleic acids.
A variety of other elements are also needed, including Sulphur, Calcium, Phosphorus, Iron and Sodium. For
example:





Sulphur is an important element in many proteins, where it forms sulphur bridges between amino acids
to hold a protein together
Calcium is a major constituent in bones, teeth, the shells of molluscs etc, where it helps to add strength
Phosphorous is an important constituent of phospholipids of cell membranes
Iron is found in haemoglobin in the blood
Sodium ions are important in the functioning of the nervous system (the sodium potassium pump)
Water
Water has very distinctive properties that make it very unique and which make it so important to living
organisms. One of the most important features is its polarity. An oxygen atom has 6 electrons in its outer shell.
In a water molecule it shares an electron with each of two hydrogen atoms. However, it is not a symmetrical
arrangement (see diagram below); the remaining 4 electrons move to one end of the oxygen atom and, since
electrons are negatively charged, this end becomes negative. The hydrogen atoms each have one electron, which
they share with the oxygen atom. This means that the proton (which is positive) is positioned at the opposite end
of the molecule. The result is a molecule that has a weak negative charge at the oxygen end and a weak positive
charge at each of the hydrogen ends.
From: www.progressivegardens.com/
From: www.morris.umn.edu
This polarity means that the negative ends of water molecules are attracted to the positive ends of other water
molecules. These weak bonds are known as hydrogen bonds and they are also found in some other molecules
(e.g. the bonds holding two strands of DNA together are hydrogen bonds, which is why they can be easily
separated during replication and protein synthesis).
The attraction between water molecules gives it strong cohesive properties, meaning that water sticks together.
The surface tension of water is due to this, as is the viscosity (thickness) of water, allowing insects to walk on
its surface and fish to swim through it (making it useful as a transport medium). Another feature of this is that
the water molecules take a lot more energy to evaporate (making it a good coolant for sweat) gives it a high
specific heat capacity (meaning that it does not change temperature easily). The polarity of water means that
many substances will dissolve in it, making it a good solvent and therefore useful as a medium for metabolic
reactions (chemical reactions in the body). Nearly all the chemical reactions in an organism occur in solution.
Methane is a similar sized molecule to water and it is composed of single covalent bonds, so one could predict
that they would have similar properties. However, the polarity of water molecules gives them very different
properties to non-polar methane molecules as seen below.
Property
Formula
Molecular mass
Density
Specific heat capacity
Latent heat of vaporization
Melting point
Boiling point
Methane
CH4
16
0.46 g per cm3
2.2 J per g per °C
760 J/g
-182 °C
-160 °C
Water
H2O
18
1 g per cm3
4.2 J per g per °C
2,257 J/g
0 °C
100 °C
Carbon Compounds
A carbon atom has a valency of 4, which means it can combine with up to 4 other atoms. They form strong
covalent bonds, which means they share electrons. Covalent bonds are strong bonds, meaning that carbon
compounds are usually quite stable molecules. This makes them useful for the formation of the big, complex
organic compounds found in living things. Organic compounds are any compounds made of carbon that are
found in living organisms (except hydrogencarbonates and oxides of carbon).
In general terms, we can think of organic compounds as the substances that are only created by living organisms
and inorganic compounds as those that might be found in a place with no living organisms (like on the moon).
In living organisms we have a variety of complicated compounds such as sugars, proteins and fats, but if you
went to a planet with no life, you would only find much simpler compounds each containing only a few atoms.
(e.g. sodium chloride, carbon dioxide, iron sulphate etc).
It was once thought that organic compounds could only be made by organisms. This gave rise to the idea of
vitalism, that there was some vital ‘spark’ of life that made living things inherently different. This idea
remained for thousands of years until in 1828 scientists found a way to synthesis the organic compound urea.
The idea of vitalism quickly lost credibility and is little heard of today. It is now widely accepted that the
chemical processes in living things are the same as those occurring in non-living matter.
A full molecular diagram shows the relative positions of all the atoms in a molecule. It is a 2D diagram of a
3D structure. A simplified diagram is often used instead, which only shows the parts of the molecule that are
involved in reactions. The Carbon atoms and most of the hydrogen atoms are often not included.
Glucose – full molecular diagarm
Glucose – simplified diagram
You need to be able to identify and draw some of the most important organic compounds. Note that some of the
diagrams (such as amino acids and fatty acids) have a generalized structure, which varies between different
types of molecule.
Glucose
Ribose
Amino acid (general structure)
Glycerol
Fatty acid (saturated full structure)
Fatty acid (general structure)
Saturated fats are considered particularly bad for your health; they have fatty acid chains with no double bonds
between the carbon atoms (as in the example below). Monounsaturated fatty acids have a single double bond,
while polyunsaturated fatty acids have many.
Stearic acid (right) is a saturated fatty acid.
It has no double bonds between the carbon
atoms
Oleic acid is a monounsaturated fatty acid.
It has a single double bond between two
carbon atoms.
Unsaturated fatty acids can have their double bond arranged in two different ways, depending on how the
double bond is formed. In trans fatty acids the double bond forms in such a way that the fatty acid is fairly
straight. In cis fatty acids the double bond attaches in a way that forms a kink in the chain (see diagram below).
This affects the way the fatty acids arrange themselves – for example, it is difficult to fit as many kinked cis
fatty acids into a small space.
Trans and cis forms of a fatty acid (oleic acid) (from: en.wikipedia.org)
Metabolism
Metabolism is the web of all enzyme-catalysed reactions in a cell or organism. In some cases it involves
building up smaller molecules into bigger ones, while in others it involves the breakdown of larger molecules
into smaller ones.
Anabolism
Anabolism is the synthesis of complex molecules from simpler molecules including the formation of
macromolecules from monomers by condensation reactions. Examples include: protein synthesis using
ribosomes, DNA synthesis during replication, photosynthesis and synthesis of complex carbohydrates (such as
starch, cellulose and glycogen) from simple sugars.
Condensation reactions
Many of the molecules shown above can be joined together in a condensation reaction. A condensation reaction
occurs when two molecules join together to produce a new molecule plus a molecule of water from the H and
OH that needed to be removed.
In the diagram below we can see how two amino acids can join to form a dipeptide and a water molecule. The
OH from the amino acid on the left is removed and the H from the amino acid on the right is removed. The two
amino acids are then able to join. The H and OH combine to make H2O.
From: www.umanitoba.ca/.../lab2/biolab2_4
A very similar process occurs to join dipeptides into polypeptides, monosccharides into disaccharides or
polysaccharides, or to join three fatty acids to glycerol to make a lipid.
Catabolism
Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of
macromolecules into monomers. It includes the digestion of food, cell respiration, and the breakdown of larger
macromolecules (such as glycogen) into smaller particles (such as glucose).
Hydrolysis reactions
Hydrolysis is the reverse of a condensation reaction. When a molecule is split into two, an H and an OH are
required. These come from the addition of a water molecule. The diagram below shows molecules of lactose
and water being split to produce molecules of galactose and glucose.
www.indiana.edu
Carbohydrates, Lipids and Proteins
Carbohydrates, lipids and proteins are similar in having a carbon ‘backbone’ with hydrogen and oxygen atoms
attached. However, they vary in the quantities of these three elements and whether other elements are attached.
Of the three, carbohydrates have the highest oxygen content. Sugars and fatty acids are both comprised of C, H
and O, but fatty acids only have oxygen atoms at one end of the molecule. Proteins and polypeptides are easily
recognized by the high amounts of Nitrogen, with one N atom found in each amino acid. Some amino acids also
have a Suphur atom.
Carbohydrates – only C, H, and O roughly in proportion 1:2:1 (H:O always 2:1)
Lipids – mostly C and H, with a bit of O at one end
Proteins – C, H, O, and N, with some S
Carbohydrates
Monosaccharides and disaccharides
In the diagrams above we can see that simple sugars, such as glucose and ribose, have carbon atoms joined into
a ring by an oxygen atom. Any carbohydrate with a single ring like this is called a monosaccharide. Other
examples include galactose and fructose. More complex carbohydrates with two rings, such as maltose, lactose
and sucrose, are known as disaccharides.
Glucose – is the main source of energy to make ATP molecules during respiration. It is a monosaccharide.
Fructose – is a monosaccharide and the main sugar found in fruits.
Lactose – is a disaccharide and the main sugar found in milk. It is formed from a condensation reaction between
a glucose and a galactose molecule.
Sucrose – is a disaccharide comprised of a glucose and a fructose molecule. Sugars are transported around
plants in the phloem in the form of sucrose.
Maltose – is a disaccharide formed from two glucose molecules, produced from the breakdown of starch.
Polysaccharides
Those with more than two rings, such as starch, glycogen and cellulose, are called polysaccharides. Most of
these form very long chains, or branched chains. Polysaccharides are mostly used for structure (such as
cellulose in plant cell walls or chitin in fungal cell walls and insect exoskeletons), or for energy storage (such as
starch and glycogen).
Cellulose – is the main constituent of plant cell walls.
Glycogen – glucose is hard to store because it is soluble, so animals convert it into long chains of glycogen,
which is less soluble and can be stored more easily.
Starch – starch is the equivalent polysaccharide in plants. It is used as a store of energy. Like glycogen, it can
easily be broken down into glucose.
The above polysaccharides are all made from the condensation of glucose molecules. The differences between
them are in the type of glucose used (mainly where the OH and H parts are attached), and the degree to which
they form chains or branches.
Alpha D glucose is the same at Beta D glucose, except
that the H and OH on the right hand side are the
opposite way around. This means they form a different
structure when they join up to make a polysaccharide
(see below)
Starch and glycogen have a similar structure. They both
have long unbranched chains, known as amylose, and
branched chains, known as amylopectin. The diagram on the
right above shows an unbranched amylose chain.
The diagram on the right below shows a branched chain of
amylopectin. Glycogen is similar to amylopectin, but it
branches much more frequently.
The relative proportions of amylose and amylopectin in starch varies between different plant species, but
typically is about 20 to 25 % amylose and 75 to 80 % amylopectin.
A benedict’s test can be used to test for reducing sugars. The ring structures found in carbohydrates sometimes
open up when in solution and when this occurs it causes reduction of the benedict’s solution making it change
colour. This occurs with all monosaccharides and some disaccharides, but not with polysaccharide. For
example, glucose and ribose are reducing sugars, as is the disaccharide maltose, while the disaccharide sucrose
is not. Benedict’s solution is blue. A very slight reduction by a reducing sugar turns it green, a stronger reaction
makes it pale orange, while a deeper brick orange-red colour indicates a strong reaction.
Lipids
Lipids are organic molecules characterized by their hydrophobic properties, which mean they do not combine
easily with water. There are a number of forms, such as fats, oils, waxes and steroids. You need to be able to
identify triglycerides, phospholipids and steroids from molecular diagrams.
Many lipids are in the form of a triglyceride, which are esters comprised from three fatty acid chains attached
to a glycerol molecule. Triglycerides form the main constituents of vegetable oils and animal fats.
A triglyceride
Sometimes only two fatty acid chains attach to the glycerol and a phosphate attaches in place of the third. These
are known as phospholipids and they are the main constituents of cell membranes. They have a characteristic
structure with a ‘head’ end, consisting of the glycerol and phosphate, which is polar and hydrophilic (dissolves
in water); and a ‘tail’ end, consisting of the two fatty acid chains, which are non-polar and hydrophobic (avoid
water).
A phospholipid
Steroids include many hormones (such as testosterone, and progesterone), and other important chemicals such
as cholesterol, which is a component of cell membranes. They all have a characteristic structure with four
carbon rings - three hexagons and one pentagon as shown below.
Estrogen (a steroid)
Energy storage
Lipids and carbohydrates are both used for storing energy. Sugars are very soluble, so are difficult to store
because they would affect the osmotic balance of the cell. Plants convert sugars into starch for storage and
animals convert sugars into glycogen. Starch and glycogen are less soluble than sugars, but lipids are even less
soluble, making them better for long-term storage. Lipids contain about twice the energy of equal amounts of
carbohydrate, which also makes them better as a long term energy store because there is less mass to carry.
However, carbohydrates have advantages, which make them more useful for short-term storage. Carbohydrates
are more easily broken down than lipids and the soluble products are more easily transported to where they are
required. Proteins can also be respired to produce energy, but only as a last resort when all other energy stores
have been used. In summary, immediate energy needs are met by the respiration of carbohydrates, followed by
lipids and finally proteins.
Other uses of lipids include insulation (for example Polar Bears, whales and other animals in cold countries
have thick layers of fat), phospholipids in cell membranes, steroids as hormones, waterproofing and for
buoyancy.
Proteins
The basic subunit of proteins is the amino acid. Twenty different amino acids are used to make proteins. These
amino acids are linked together by condensation reactions on ribosomes (see later section for more detail) to
form polypeptides. The twenty different amino acids can be linked together in any sequence, to form a huge
range of different polypeptides, each with its own properties. The DNA code in the genes is what determines the
arrangement and order of the amino acids in the sequence. Proteins can be formed from one or more
polypeptides. Millions of different proteins are synthesized by living organisms and there are many functions,
including:
Rubisco – an enzyme that catalyses the fixation of CO2 by ribulose bisphosphate.
Insulin – a hormone signaling for cells to convert glucose into glycogen for storage to reduce blood glucose
levels.
Immunoglobulins – also known as antibodies, they attach to antigens to bind pathogens together so that they
can be destroyed by lymphocytes.
Rhodopsin – a pigment in cones in the retina, which converts from one form to another when exposed to light,
leading to a signal being sent down a neuron.
Collagen – a fibrous protein that is mainly used for structural purposes, holding animal tissues together.
Spider Silk – a strong but elastic fibre used by spiders to build webs to trap insects, to build shelters, or even to
catch wind for dispersion.
Every individual has a unique set of genes (known as the genome), which produce a unique set of proteins
(known as the proteome).
Denaturation
The complex structure of proteins means that they are not very robust. Enzymes have a particularly complex
shape and are more prone to denaturation. Like any molecule, they vibrate when they are heated and the greater
the heat the more the vibrations. When the vibrations are too great (often between about 40 and 60°C) the
molecule starts to fall apart. This alters the shape of the active site, so it stops working. This change is usually
permanent and the enzyme will never work again. We say the enzyme has been denatured. Chemicals can also
damage enzymes and the pH is particularly important. Each enzyme has an optimum (ideal) pH where it works
best. For example, protease enzymes in the stomach work best at low (acidic) pHs, while amylase works best at
a slightly alkaline pH. If the pH is too far from the optimum conditions it can denature the enzyme.
Enzymes
Enzymes are catalysts, so they speed up chemical reactions. However, they are made from proteins making
them different from other catalysts found in inorganic chemistry. They have a very complex design that
includes an active site. This has a very specific shape, size and chemistry so that only very specific molecules
(known as substrates) can attach. The lock and key model (shown in the diagram below) shows how only
specific substrates will fit into an active site like a lock fits only one key. By contrast, many non-organic
catalysts work for many different reactions. Enzymes generally function by bringing together two subtrates to
react them together into a single product, or by breaking apart a single substrate into parts. Like other catalysts,
once the reaction is over the enzyme can be used again and again and never forms part of the product of the
chemical reaction.
From: waynesword.palomar.edu/molecu1.htm
Rate of enzyme controlled reactions
Like all chemical reactions, an increase in temperature increases the rate of reaction. This is because the
particles are all moving faster and colliding more often. The more often a substrate collides with an active site,
the faster the reaction will be. However, when temperature gets too high the enzyme is denatured, so enzymes
have optimum conditions to function; they need to be warm enough for the substrates to collide frequently with
the active sites, but not so hot that they cause denaturation. The more enzyme molecules there are the greater
the number of collisions, so an increase in enzyme concentration also increases the rate of reaction. Similarly,
an increase in substrate concentration also increases the rate of reaction. However, there is a limit, because if
you start adding huge amounts of substrate the active sites of the enzymes are working as fast as they can and so
additional substrate will not increase the rate of reaction any more. See diagrams below.
From: http://schools.moe.edu.sg/chijsjc/Biology/Enzyme/enzyme2.gif
From: www.mansfield.ohio-state.edu/.../biol1045.htm
Enzymes work best at an optimum pH, with any deviation from the optimum resulting in a lower rate of
reaction, or in extreme cases the enzyme will become denatured and the reaction will stop completely. Different
enzymes have different pHs that they work best at, so in the graph below we can see that pepsin works best in
acidic conditions (which is why the stomach is acidic), while amylase works best at around neutral and arginase
works best in alkaline conditions.
From: www2.estrellamountain.edu
Lactase
Lactose is a disaccharide sugar found in milk. Disaccharides are too big to be absorbed through the lining of the
gut, so lactose has to be broken down (digested) into monosaccharide sugars by the enzyme lactase. Wild
mammals drink milk when they are infants but not when they are adults. They do not need to keep producing
lactase because they no longer consume lactose, so the gene that makes lactase is switched off. However, for
the last few thousand years humans have farmed cows and goats to drink the milk, so they continue to consume
lactose. A recent adaptation of humans is a gene that continues to produce lactase in adults. Not everyone has
this gene and it is particularly uncommon in east Asia. Those that do not have the gene are lactose intolerant,
which means they cannot break down the lactose in milk. As a result, the lactose is not absorbed and passes
down the gut into the large intestine, where it is fermented by bacteria causing flatulence, cramps and nausea.
People with lactose intolerance can stop drinking milk, take lactase tablets or drink lactose-free milk. This is
produced by passing the milk over lactase to break down the lactose. The lactase is immobilized by attaching it
to beads, so when milk runs over the beads the lactose is broken down. A similar process of immobilized
enzymes is used in many other industries.
2.6
DNA structure
The basic unit of DNA is the nucleotide (see diagram below) which is composed of a deoxiribose sugar with a
phosphate and a base attached.
Phosphate
Sugar
Base
The nucleotides are joined together with covalent bonds between the phosphates and the sugars forming a long
strand.
DNA has two such strands that are facing in opposite directions (antiparallel, see diagram below). The two
strands are connected by hydrogen bonds between the bases.
From: www.turbosquid.com
Although the diagram shows it in a flattened form, each nucleotide is attached at a slight angle. This means that
the whole molecule is in the form of a double helix (a helix is like the shape of a spring, but it is a double helix
because there are two strands). The double helix is formed by the sugars and the phosphates, while the bases
form the connections between the two strands.
From: http://mediad.publicbroadcasting.net
Watson and Crick discovered the
structure of DNA. Other scientists had
already discovered the main components
of DNA, such as the phosphates, ribose
and bases, but they did not know how they
fitted together.
They discovered the structure by building
models of the components and fitting them
together as shown on the left.
The work was helped by another scientist
Rosalind Franklin, who was studying Xray diffraction of DNA, leading them to
the idea that it might have a helical shape.
Ultimately, the work of many scientists
was required to achieve the final model.
The bases
There are 4 bases found in DNA - Cytosine, Guanine, Adenine and Thiamine. The structure of these bases
means that Cytosine only joins with Guanine, while Adenine only joins with Thiamine. The information carried
by DNA is in the order of the bases.
2.7 DNA replication, transcription and translation
DNA replication
In topic 2 we saw how cells divide and that during anaphase of mitosis the two copies of the DNA are
separated. The DNA is copied (replicated) during the S stage of interphase. Scientists used to wonder which of
the two copies was the original and which was the copy (some thought it was a conservative process because
one of the strands was conserved intact). The main alternative hypothesis was that one of the two strands ended
up in each new DNA copy (semi-conservative).
From: http://en.wikipedia.org
Meselson and Stahl made a famous experiment to determine the answer to this question. They did this by
studying the nitrogen in DNA, which is an important component of the four bases. The most common isomer
(form) of nitrogen is N14, with another form (N15) being much rarer and a tiny bit heavier (because each atom
contains an extra neutron). They grew bacteria in a medium containing N15 for several generations to ensure that
all the nitrogen in the DNA was of this form. They then moved the bacteria to a N14 medium. This meant that
when they replicated their DNA the new strands would have N14. They then used a centrifuge (which spins to
separate molecules of different mass) to see if half of the DNA contained N14 and half N15. They found that the
DNA was all the same mass, indicating that the new strands contained equal amounts of both N14 and N15. This
disproved the theory of conservative replication, and showed that replication is semi-conservative.
From: www.nature.com
The first stage of replication involves the unwinding of the double helix and the breaking of hydrogen bonds to
separate the two strands by the enzyme helicase. New nucleotides are then added to each of the strands by the
enzyme DNA polymerase. The nucleotides are added one by one with each base attached to its
complementary base (guanine opposite cytosine and thyamine opposite adenine). In this way, the existing
strand can be used to make a complementary strand that is identical to the original one. This ensures that the
two new strands formed by DNA replication are exactly the same as the original strand.
From: http://www.ch.ic.ac.uk
Transcription and translation (Protein synthesis)
DNA carries the information to make proteins. Proteins are made from polypeptides, which are long chains of
amino acids. The R groups on the amino acids then interact in a way that folds up the polypeptide, or attaches
other polypeptides, to make the protein. Each of the polypeptides is very long, comprising hundreds and even
thousands of amino acids. For the polypeptide to fold up correctly, the sequence of amino acids must be correct,
so that every R group is in the correct place to interact with other R groups.
Transcription and translation both involve the use of RNA (Ribose Nucleic Acid). These nucleic acids are
similar to DNA, but have three main differences. The sugar in DNA is deoxyribose and the sugar in RNA is
ribose; DNA is a double strand, whereas RNA is a single strand; and the bases in DNA are C, G, A and T,
whereas in RNA they are C, G, A and U. Note that RNA has the base Uracil instead of Thiamine. The main
types of RNA are messenger RNA (mRNA, which forms during transcription and carries the information about
the gene from the DNA to the ribosome), transfer RNA (tRNA, which brings the amino acids to the ribosome,
so they can be joined up into a polypeptide), and ribosomal RNA (rRNA, which is what ribosomes are made
of).
Transcription
Proteins are synthesized on ribosomes that are on the rough endoplasmic reticulum or free in the cytoplasm.
However, the DNA is in a completely different location in the nucleus. The DNA cannot move to the cytoplasm
and the ribosomes cannot move to the nucleus, so a copy of the information on the DNA needs to be made that
can be sent to the ribosomes. The copying of the DNA is known as transcription.
Each chromosome (a strand of DNA wrapped around proteins) has
several thousand genes along its length. Each gene carries the
information to make a polypeptide (though there are a few
exceptions that have recently been discovered). To make a
polypeptide (which are used to make proteins), only a single gene
needs to be transcribed (copied).
The section of DNA carrying the code for that gene is unwound and
opened up by the enzyme RNA polymerase. One side of the DNA
is copied to make a strand of RNA. RNA polymerase adds
nucleotides using complementary base pairing with cytosine
opposite guanine, guanine opposite cytosine, adenine opposite
thiamine and uracil opposite adenine (because thiamine is not found
in RNA).
This strand of RNA (called messenger RNA or mRNA) now carries
all the information that is needed to make a polypeptide. It moves
out of the nucleus and attaches to a ribosome for translation.
Translation
Each three bases on the mRNA (a codon) codes
for a different amino acid. There are several
different transfer RNA molecules (tRNA). Each
one attaches to a particular amino acid on one
end and has a code of three bases (called the
anticodon) on the other end. The anticodon
attaches to the complementary codon on the
mRNA and in doing so it brings the correct acid
into place.
Once the first amino acid is in place another
tRNA will bring the second amino acid into
place. The two amino acids will join by forming
a peptide bond in a condensation reaction (see
condensation reactions above). The first tRNA
will now depart. Another tRNA will bring the
third amino acid, which will also join on to the
first two. The second tRNA can then detach.
This continues, with more and more amino acids
being brought to the correct place and joining up
to make the polypeptide. Once the entire
polypeptide is made (often from over 1000
amino acids) it will separate away and fold up
into a protein.
2.8 Cell Respiration
Definition - Cell respiration is the controlled release of energy from organic compounds in cells to form ATP
Large molecules tend to have more chemical energy stored in them than small molecules. Building up large
molecules from small molecules requires energy (see the next section on photosynthesis) and when large
molecules are broken down into smaller ones they tend to release energy. Organic molecules (such as
carbohydrates, nucleic acids, proteins etc) are generally very large and contain a lot of stored energy. During
respiration, these large organic molecules are broken down into simpler molecules (often inorganic molecules
such as water and carbon dioxide) and the energy released is used to build up ATP molecules from ADP and
inorganic phosphate. All living cells obtain their ATP in this way.
Glycolysis
All types of respiration in all organisms start the same way in the cytoplasm. The glucose (or other molecule
being broken down such as fat) is broken down in a series of chemical reactions (known as glycolysis if glucose
is broken down) into pyruvate. Each glucose molecule will result in the production of 4 ATP molecules during
glycolysis. Note that no oxygen is required for glycolysis.
The fate of pyruvate
What happens next depends on the circumstances, such as whether or not oxygen is present and on the organism
involved.
Anaerobic respiration in animals:
The pyruvate is converted into lactate (they used to call it lactic acid), which is similar to pyruvate but with a
slightly different structure. No extra ATP is made in this process. Because it has a similar structure, the lactate
can later be converted back to pyruvate and respired aerobically when oxygen is present. Athletes pant after a
race because they have produced lactate and now need extra oxygen to convert it back and complete the
respiration aerobically. This is known as the oxygen debt. If too much lactate builds up it is harmful and needs
to be removed. That is why humans cannot sprint for long distances, because the lactate builds up too much and
causes muscle fatigue. In slower races, the athlete can breathe quickly enough to get sufficient oxygen to the
cells for aerobic respiration and no lactate is produced.
Anaerobic respiration in plants and fungi (i.e. yeast)
In plants the pyruvate is converted into ethanol and carbon dioxide during the process of fermentation. This
also produces no extra ATP. The separation into ethanol and CO2 is not reversible, so it cannot be converted
back later. The ethanol contains a lot of energy that has to be wasted, so this is a less efficient method.
Aerobic respiration in all organisms
When oxygen is available the cell can do aerobic respiration. The pyruvate moves into the mitochondrion,
where it is broken down into CO2 and Water. The oxygen is needed to oxidize hydrogen to make H2O. A lot
more energy is released during aerobic respiration, with a single glucose molecule producing a total of 38 ATP
molecules, compared to only 4 in anaerobic respiration.
Respirometers
A respirometer can be used to
measure the aerobic respiration
of an organism or organisms.
Both sides need to be the same,
with an alkaline solution (such
as KOH) to absorb the CO2.
The organism, such as an insect
or germinating seed, is placed
on one side.
As the organism uses up the O2
it will produce CO2. However,
the CO2 is absorbed, so the
amount of O2 used up will be
recorded on the manometer. as
the other side (the control) will
not change.
It is important that no animals
are harmed in these
experiments and they must
later be returned alive to their
original environments.
From: http://mrhardy.wikispaces.com
2.9 Photosynthesis
Photosynthesis is needed to build up complex organic compounds (like amino acids, sugars, fats etc) from
simple inorganic ones (mainly H2O and CO2, though other elements such as nitrogen and sulphur are also
needed to build some organic molecules). As mentioned previously, large organic compounds generally contain
more stored chemical energy than smaller ones, so the building up of these large molecules requires energy.
This energy comes from sunlight.
Chlorophyll is the pigment found in
chloroplasts that absorbs light to provide the
energy for photosynthesis. Light from the sun
is composed of a range of wavelengths that we
see as different colours, with visible light
falling within the range of 400 to 700nm.
These wavelengths are not all used equally in
photosynthesis. The chlorophyll mainly uses
wavelengths in the blue (roughly 400 to
500nm) and red areas (roughly 600 to 700nm)
of the spectrum, so green wavelengths (roughly
500 to 600nm) are mostly reflected. That is
why plants appear green.
The absorption spectrum shows the range of
wavelengths absorbed by chlorophyll, while
the action spectrum shows the wavelengths
used in photosynthesis. The graph on the left
shows how closely the two match.
http://5e.plantphys.net
There are two main stages of photosynthesis, called the light dependent stage and the light independent stage.
H2O
→
Sunlight →
O2
↑
Light
Dependent
Stage
→
ATP
→
→
H
→
Light
Independent
Stage
↑
CO2
→ Glucose
During the light dependent stage, energy from sunlight is used to split water molecules in a process called
photolysis. The oxygen is released as a waste product and the hydrogen passes on to the next stage. Some ATP
is also made and this also passes to the next stage.
During the light independent stage CO2 is combined with hydrogen to make glucose (and other organic
molecules). The ATP from the light dependent stage helps provide the energy for this process.
Photosynthesis can be measured directly by the production
of oxygen or uptake of CO2, or indirectly by an increase in
biomass.
A plants biomass is its dry mass. Other than water, almost
all the molecules in a plant were made from photosynthesis.
So by measuring the growth of plants it is possible to record
the amount of photosynthesis they have done (assuming that
about 70% of the mass is water)
The diagram on the left shows a method used for recording
the amount of oxygen produced by an aquatic plant. The
plant produces oxygen by photosynthesis, which floats up to
the surface and fills up the test tube. The amount of oxygen
collected can then be measured.
www.ichristianschool.org/biology/eoi/eoi.htm
As with most chemical reactions, the rate of photosynthesis is controlled by temperature, because the more the
particles move the faster they react. However, photosynthesis is controlled by numerous enzymes which will
denature at high temperatures, so the rate of photosynthesis increases with temperature up to about 40 to 50°C ,
when it will stop.
Light intensity and CO2 concentration also affect the rate of photosynthesis. In both cases, the more there is the
faster the reaction. However, at higher concentrations there will be other factors limiting the rate, for example
the enzymes may be working to their maximum, so no further increase in photosynthesis will occur.
www.bbc.co.uk/.../1_food_factory2.shtml