1.4 MeMbrAne trAnsPort
expimal dig Figure 16 Replicates are needed for each
treatment in a rigorous experiment
Experimental design: accurate quantitative
measurements in osmosis experiments are essential.
An ideal experiment gives results that have only one reasonable
interpretation. Conclusions can be drawn from the results without any
doubts or uncertainties. In most experiments there are some doubts
and uncertainties, but if the design of an experiment is rigorous, these
can be minimized. The experiment then provides strong evidence for
or against a hypothesis.
This checklist can be used when designing an experiment:
Results should if possible be quantitative as these give stronger
evidence than descriptive results.
Measurements should be as accurate as possible, using the most
appropriate and best quality meters or other apparatus.
Repeats are needed, because however accurately quantitative
measurements are taken biological samples are variable.
All factors that might affect the results of the experiment must be
controlled, with only the factors under investigation being allowed
to vary and all other factors remaining constant.
After doing an experiment the design can be evaluated using this
checklist. The evaluation might lead to improvements to the design
that would have made the experiment more rigorous.
If you have done an osmosis experiment in which samples of plant
tissue are bathed in solutions of varying solute concentration, you
can evaluate its design. If you did repeats for each concentration of
solution, and the results were very similar to each other, your results
were probably reliable.
Designing osmosis experiments Figure 17 Micrograph of red onion cells placed
in salt solution
Rigorous experimental design is needed to produce
reliable results: how can accurate quantitative 43
measurements be obtained in osmosis experiments?
The osmolarity of plant tissues can be investigated in many ways.
Figure 1 7 shows some red onion cells that had been placed in a
sodium chloride solution. The following method can be used to
observe the consequences of osmosis in red onion cells.
1 Peel off some epidermis from the scale of a red onion bulb.
2 Cut out a sample of it, about 5 5mm.
3 Mount the sample in a drop of distilled water on a microscope
slide, with a cover slip.
1 CELL BIOLOGY
4 Observe using a microscope. The cytoplasm should fll the space
inside the cell wall, with the plasma membrane pushed up against it.
5 Mount another sample o epidermis in sodium chloride solutions
with concentration o 0.5mol dm-3 or 3%. I water leaves the cells
by osmosis and the volume o cytoplasm is reduced, the plasma
membrane pulls away rom the cell wall, as shown in Figure 1 7.
Plant cells with their membranes pulled away rom their cell walls
are plasmolysed and the process is plasmolysis.
This method can be used to help design an experiment to fnd out the
osmolarity o onion cells or other cells in which the area occupied by
the cytoplasm can easily be seen. The checklist in the previous section
can be used to try to ensure that the design is rigorous.
Preventing osmosis in excised tissues and organs
Tissues or organs to be used in medical procedures must be bathed in a solution
with the same osmolarity as the cytoplasm to prevent osmosis.
Animal cells can be damaged by osmosis. bathed in solutions with ( a) the same osmolarity,
Figure 1 8 shows blood cells that have been ( b) higher osmolarity and ( c) lower osmolarity.
a) b) c)
Figure 18 Blood cells bathed in solutions o diferent solute concentration
In a solution with higher osmolarity (a hypertonic used, which is called normal saline. It has an
solution) , water leaves the cells by osmosis so osmolarity o about 300 mOsm (milliOsmoles) .
their cytoplasm shrinks in volume. The area
o plasma membrane does not change, so it Normal saline is used in many medical
develops indentations, which are sometimes called procedures. It can be:
crenellations. In a solution with lower osmolarity
(hypotonic) , the cells take in water by osmosis saely introduced to a patients blood system
and swell up. They may eventually burst, leaving via an intravenous drip.
ruptured plasma membranes called red cell ghosts.
used to rinse wounds and skin abrasions.
Both hypertonic and hypotonic solutions thereore
damage human cells, but in a solution with same used to keep areas o damaged skin moistened
osmolarity as the cells (isotonic) , water molecules prior to skin grats.
enter and leave the cells at the same rate so they
remain healthy. It is thereore important or used as the basis or eye drops.
any human tissues and organs to be bathed in
an isotonic solution during medical procedures. rozen to the consistency o slush or packing
Usually an isotonic sodium chloride solution is hearts, kidneys and other donor organs that
have to be transported to the hospital where
the transplant operation is to be done.
44
1.5 tHe orIGIn of cells
Figure 19 Donor liver packed in an isotonic medium, surrounded by isotonic slush. There is a worldwide shortage of donor
organs in most countries it is possible to register as a possible future donor
1.5 th igi
Understanding Applications
Cells can only be ormed by division o Evidence rom Pasteurs experiments that
pre-existing cells. spontaneous generation o cells and organisms
does not now occur on Earth.
The frst cells must have arisen rom
non-living material. Nature of science
The origin o eukaryotic cells can be explained Testing the general principles that underlie the
by the endosymbiotic theory. natural world: the principle that cells only come
rom pre-existing cells needs to be verifed.
Cell division and the origin of cells
Cells can only be ormed by division o pre-existing cells.
Since the 1 880s there has been a theory in biology that cells can only be
produced by division of a pre-existing cell. The evidence for this hypothesis
is very strong and is discussed in the nature of science panel below.
The implications of the hypothesis are remarkable. If we consider the
trillions of cells in our bodies, each one was formed when a previously
45
1 CELL BIOLOGY
toK existing cell divided in two. Beore that all o the genetic material in
the nucleus was copied so that both cells ormed by cell division had a
Wha d we gain, and wha d we le, nucleus with a ull complement o genes. We can trace the origin o cells
when we name mehing? in the body back to the frst cell the zygote that was the start o our
lives, produced by the usion o a sperm and an egg.
When Dr Craig Venters team
announced that they had succeeded Sperm and egg cells were produced by cell division in our parents. We
in transplanting the synthetic genome can trace the origins o all cells in our parents bodies back to the zygote
rom one bacterium into another rom which they developed, and then continue this process over the
bacterium in the journal Science some generations o our human ancestors. I we accept that humans evolved
ethicists responded by questioning rom pre-existing ancestral species, we can trace the origins o cells back
the language o calling it the creation through hundreds o millions o years to the earliest cells on Earth.
o a synthetic cell: There is thereore a continuity o lie rom its origins on Earth to the cells
in our bodies today.
The science is ying 30,000 eet over
the publics understanding ... Scientists In 201 0 there were reports that biologists had created the frst artifcial
can be their own worst enemy by using cell, but this cell was not entirely new. The base sequence o the D NA
words like clone or synthetic lie. o a bacterium ( Mycoplasma mycoides) was synthesized artifcially, with a
ew deliberate changes. This DNA was transerred to pre-existing cells
Glenn Mcgee, funde f Ameican o a dierent type o bacterium ( Mycoplasma capricolum) , which was
Junal f biehic eectively converted into Mycoplasma mycoides. This process was thereore
an extreme orm o genetic modifcation and the creation o entirely
Frankly, hes describing it in a way new cells remains an insuperable challenge at the moment.
thats drumming up controversy more
than characterising it accurately. His Aciviy
claim that weve got the frst sel-
replicating lie orm whose parent is a the l f silphium
computer, thats just silly.
The Greek coin in fgure 2 depicts a Silphium plant, which grew in a small part
It misuses the word parent. The o what is now Libya and was highly prized or its medicinal uses, especially
advance here needs to be described as a birth control agent. It seems to have been so widely collected that within a
in sane and accurate ways. What ew hundred years o the ancient Greeks colonizing North Arica it had become
he's managed to do is synthesise a extinct. Rather than arising again spontaneously, Silphium has remained extinct
genome much larger than any genome and we cannot now test its contraceptive properties scientifcally. How can we
thats been synthesised rom scratch prevent the loss o other plants that could be o use to us?
beore.
Gegy Kaenick, Haing Iniue
reeach schla
Figure 2 An ancient Greek coin, showing Silphium
Figure 1 Synthetic Mycoplasma bacteria
46
1.5 tHe orIGIn of cells
Spontaneous generation and the origin of cells
Veriying the general principles that underlie the natural world: the principle that
cells only come rom pre-existing cells needs to be verifed.
Spontaneous generation is the ormation o living Some biologists remained convinced that
organisms rom non-living matter. The Greek spontaneous generation could occur i there
philosopher and botanist Theophrastus reported was access to the air. Louis Pasteur responded
that a plant called Silphium had sprung up rom soil by carrying out careully designed experiments
where it was not previously present and described with swan-necked fasks, which established
this as an example o spontaneous generation. beyond reasonable doubt that spontaneous
Aristotle wrote about insects being ormed rom generation o lie does not now occur. Pasteurs
the dew alling on leaves or rom the hair, fesh or experiments are described in the next section o
aeces o animals. In the 1 6th century the German- this sub-topic.
Swiss botanist and astrologer Paracelsus quoted
observations o spontaneous generation o mice, Apart rom the evidence rom the experiments
rogs and eels rom water, air or decaying matter. o Pasteur and others, there are other reasons
or biologists universally accepting that cells only
It is easy to see how ideas o spontaneous come rom pre-existing cells:
generation could have persisted when cells and
microorganisms had not been discovered and the A cell is a highly complex structure and no
nature o sexual reproduction was not understood. natural mechanism has been suggested or
From the 1 7th century onwards biologists carried producing cells rom simpler subunits.
out experiments to test the theory that lie could
arise rom non-living matter. Francesco Redi No example is known o increases in the
showed that maggots only developed in rotting number o cells in a population, organism or
meat i fies were allowed to come into contact tissue without cell division occurring.
with it. Lazzaro Spallanzani boiled soup in eight
containers, then sealed our o them and let the Viruses are produced rom simpler subunits
others open to the air. Organisms grew in the but they do not consist o cells, and they can
containers let open but not in the others. only be produced inside the host cells that
they have inected.
Spontaneous generation and Pasteurs experiments
Evidence rom Pasteurs experiments that spontaneous generation o cells and
organisms does not now occur on Earth.
Louis Pasteur made a nutrient broth by boiling then melted the glass o the necks and bent it into
water containing yeast and sugar. He showed that a variety o shapes, shown in gure 3.
i this broth was kept in a sealed fask, it remained
unchanged, and no ungi or other organisms Pasteur then boiled the broth in some o the
appeared. He then passed air though a pad o fasks to kill any organisms present but let others
cotton wool in a tube, to lter out microscopic unboiled as controls. Fungi and other organisms
particles rom the air, including bacteria and the soon appeared in the unboiled fasks but not in
spores o ungi. I the pad o cotton wool was the boiled ones, even ater long periods o time.
placed in broth in a sealed fask, within 36 hours, The broth in the fasks was in contact with air,
there were large number o microorganisms in which it had been suggested was needed or
the broth and mould grew over its surace. spontaneous generation, yet no spontaneous
generation occurred. Pasteur snapped the necks o
The most amous o Pasteurs experiments some o the fasks to leave a shorter vertical neck.
involved the use o swan-necked fasks. He placed Organisms were soon apparent in these fasks and
samples o broth in fasks with long necks and decomposed the broth.
47
1 CELL BIOLOGY
Pasteur published his results in 1 860 and rom the air getting into the broth or other liquids
subsequently repeated them with other liquids and that no organisms appeared spontaneously. His
including urine and milk, with the same results. He experiments convinced most biologists, both at the
concluded that the swan necks prevented organisms time o publication and since then.
Figure 3 Drawings o Pasteurs Origin o the frst cells
swan-necked fasks
The frst cells must have arisen rom non-living material.
I we trace back the ancestry o cells over billions o years, we must
eventually reach the earliest cells to have existed. These were the frst
living things on Earth. Unless cells arrived on Earth rom somewhere
else in the universe, they must have arisen rom non-living material.
This is a logical conclusion, but it gives perhaps the hardest question o
all or biologists to answer: how could a structure as complex as the cell
have arisen by natural means rom non-living material?
It has sometimes been argued that complex structures cannot arise by
evolution, but there is evidence that this can happen in a series o stages
over long periods o time. Living cells may have evolved over hundreds
o millions o years. There are hypotheses or how some o the main
stages could have occurred.
1. Production of carbon compounds such as 2. Assembly of carbon compounds into
sugars and amino acids polymers
Stanley Miller and Harold Urey passed steam A possible site or the origin o the frst carbon
through a mixture o methane, hydrogen and compounds is around deep-sea vents. These are
ammonia. The mixture was thought to be cracks in the Earths surace, characterized by
representative o the atmosphere o the early gushing hot water carrying reduced inorganic
Earth. Electrical discharges were used to simulate chemicals such as iron sulphide. These chemicals
lightning. They ound that amino acids and other represent readily accessible supplies o energy, a
carbon compounds needed or lie were produced. source o energy or the assembly o these carbon
compounds into polymers.
ammonia
water vapour (NH3)
methane (CH4) electrode
hydrogen
(H2)
condenser
cold
water in
cooled water containing
organic compounds
Figure 5 Deep sea vents
sample taken for
chemical analysis
Figure 4 Miller and Ureys apparatus
48
1.5 tHe orIGIn of cells
3. Formation of membranes 4. Development of a mechanism for
inheritance
I phospholipids or other amphipathic carbon
compounds were among the frst carbon Living organisms currently have genes made o
compounds, they would have naturally assembled D NA and use enzymes as catalysts. To replicate
into bilayers. Experiments have shown that these DNA and be able to pass genes on to ospring,
bilayers readily orm vesicles resembling the enzymes are needed. However, or enzymes to
plasma membrane o a small cell. This would have be made, genes are needed. The solution to this
allowed dierent internal chemistry rom that o conundrum may have been an earlier phase in
the surroundings to develop. evolution when RNA was the genetic material.
It can store inormation in the same way as
DNA but it is both sel-replicating and can itsel
act as a catalyst.
Figure 6 Liposomes
Endosymbiosis and eukaryotic cells Aiviy
The origin o eukaryotic cells can be explained by the Wh did i bgi?
endosymbiotic theory.
Erasmus Darwin was
The theory o endosymbiosis helps to explain the evolution o Charles Darwins
eukaryotic cells. It states that mitochondria were once ree-living grandather. In a poem
prokaryotic organisms that had developed the process o aerobic cell entitled The Temple o
respiration. Larger prokaryotes that could only respire anaerobically Nature, published in 1803,
took them in by endocytosis. Instead o killing and digesting the he tells us how and where
smaller prokaryotes they allowed them to continue to live in their he believed lie to have
cytoplasm. As long as the smaller prokaryotes grew and divided as ast originated:
as the larger ones, they could persist indefnitely inside the larger cells.
According to the theory o endosymbiosis they have persisted over Organic Lie began
hundreds o millions o years o evolution to become the mitochondria beneath the waves ...
inside eukaryotic cells today. Hence without parent by
spontaneous birth
The larger prokaryotes and the smaller aerobically respiring ones were Rise the frst specks o
in a symbiotic relationship in which both o them benefted. This is animated earth
known as a mutualistic relationship. The smaller cell would have been
supplied with ood by the larger one. The smaller cell would have Has Erasmus Darwins
carried out aerobic respiration to supply energy efciently to the larger hypothesis that lie began in
cell. Natural selection thereore avoured cells that had developed this the sea been alsifed?
endosymbiotic relationship.
49
The endosymbiotic theory also explains the origin o chloroplasts.
I a prokaryote that had developed photosynthesis was taken in by
a larger cell and was allowed to survive, grow and divide, it could
have developed into the chloroplasts o photosynthetic eukaryotes.
Again, both o the organisms in the endosymbiotic relationship would
have benefted.
1 CELL BIOLOGY
Activity original ancestral evolution of the
prokaryote nucleus
Bangiomorpha and the
origins of sex. evolution of evolution of evolution of
photosynthesis aerobic respiration linear chromosomes,
The frst known eukaryote mitosis and meiosis
and frst known
multicellular organism is endocytosis produces
Bangiomorpha pubescens. mitochondria
Fossils o this red alga
were discovered in 1,200 endocytosis
million year old rocks to produce
rom northern Canada. It is chloroplasts
the frst organism known
to produce two dierent evolution of evolution of
types o gamete a larger plant cells animal cells
sessile emale gamete
and a smaller motile male plant cell animal cell
gamete. Bangiomorpha is ( e u ka ry o ti c) (eukaryotic)
thereore the frst organism
known to reproduce Figure 7 Endosymbiosis
sexually. It seems unlikely
that eukaryote cell
structure, multicellularity
and sexual reproduction
evolved simultaneously.
What is the most likely
sequence or these
landmarks in evolution?
Although no longer capable of living independently, chloroplasts
and mitochondria both have features that suggest they evolved from
independent prokaryotes:
They have their own genes, on a circular DNA molecule like that of
prokaryotes.
They have their own 70S ribosomes of a size and shape typical of
some prokaryotes.
They transcribe their DNA and use the mRNA to synthesize some of
their own proteins.
They can only be produced by division of pre-existing mitochondria
and chloroplasts.
50
1.6 cell dIVIsIon
1.6 c ivii
Understanding Applications
Mitosis is division o the nucleus into two The correlation between smoking and incidence
genetically identical daughter nuclei. o cancers.
Chromosomes condense by supercoiling Skills
during mitosis.
Identifcation o phases o mitosis in cells
Cytokinesis occurs ater mitosis and is dierent viewed with a microscope.
in plant and animal cells.
Determination o a mitotic index rom a
Interphase is a very active phase o the cell micrograph.
cycle with many processes occurring in the
nucleus and cytoplasm. Nature of science
Cyclins are involved in the control o the Serendipity and scientifc discoveries: the
cell cycle. discovery o cyclins was accidental.
Mutagens, oncogenes and metastasis are
involved in the development o primary and
secondary tumours.
The role of mitosis Figure 1 Hydra viridissima with a small
new polyp attached, produced by asexual
Mitosis is division o the nucleus into two genetically reproduction involving mitosis
identical daughter nuclei.
The nucleus of a eukaryotic cell can divide to form two genetically
identical nuclei by a process called mitosis. Mitosis allows the cell to
divide into two daughter cells, each with one of the nuclei and therefore
genetically identical to the other.
B efore mitosis can occur, all of the D NA in the nucleus must be
replicated. This happens during interphase, the period before mitosis.
Each chromosome is converted from a single DNA molecule into two
identical DNA molecules, called chromatids. During mitosis, one of these
chromatids passes to each daughter nucleus.
Mitosis is involved whenever cells with genetically identical nuclei are
required in eukaryotes: during embryonic development, growth, tissue
repair and asexual reproduction.
Although mitosis is a continuous process, cytologists have divided the
events into four phases: prophase, metaphase, anaphase and telophase.
The events that occur in these phases are described in a later section of
this sub-topic.
51
1 CELL BIOLOGY
Activity Interphase
There is a limit to how many times Interphase is a very active phase o the cell cycle with
most cells in an organism can undergo many processes occurring in the nucleus and cytoplasm.
mitosis. Cells taken rom a human
embryo will only divide between The cell cycle is the sequence o events between one cell division
40 and 60 times, but given that and the next. It has two main phases: interphase and cell division.
the number o cells doubles with Interphase is a very active phase in the lie o a cell when many
each division, it is easily enough to metabolic reactions occur. S ome o these, such as the reactions o
produce an adult human body. There cell respiration, also occur during cell division, but DNA replication
are exceptions where much greater in the nucleus and protein synthesis in the cytoplasm only happen
numbers o divisions can occur, such during interphase.
as the germinal epithelium in the
testes. This is a layer o cells that During interphase the numbers o mitochondria in the cytoplasm increase.
divides to provide cells used in sperm This is due to the growth and division o mitochondria. In plant cells and
production. Discuss how many times algae the numbers o chloroplasts increase in the same way. They also
the cells in this layer might need to synthesize cellulose and use vesicles to add it to their cell walls.
divide during a man's lie.
Interphase consists o three phases, the G phase, S phase and G2 phase.
1
In the S phase the cell replicates all the genetic material in its nucleus, so
that ater mitosis both the new cells have a complete set o genes. Some
do not progress beyond G1, because they are never going to divide so do
not need to prepare or mitosis. They enter a phase called G0 which may
be temporary or permanent.
G2 Supercoiling of chromosomes
Mitosis Chromosomes condense by supercoiling during mitosis.
Cytokinesis During mitosis, the two chromatids that make up each chromosome must
be separated and moved to opposite poles o the cell. The DNA molecules
SEach of the PHASEINTER G1 in these chromosomes are immensely long. Human nuclei are on average
less than 5 m in diameter but DNA molecules in them are more than
chromosomes 50,000 m long. It is thereore essential to package chromosomes into
is duplicated Cellular contents, much shorter structures. This process is known as condensation o
apart from the chromosomes and it occurs during the frst stage o mitosis.
chromosomes
are duplicated. Condensation occurs by means repeatedly coiling the DNA molecule to
make the chromosome shorter and wider. This process is called supercoiling.
G0 Proteins called histones that are associated with DNA in eukaryote
chromosomes help with supercoiling and enzymes are also involved.
Figure 2 The cell cycle
Phases ofmitosis
Identifcation o phases o mitosis in cells viewed with a microscope.
There are large numbers o dividing cells in the To be able to identiy the our stages o mitosis,
tips o growing roots. I root tips are treated it is necessary to understand what is happening
chemically to allow the cells to be separated, they in them. Ater studying the inormation in this
can be squashed to orm a single layer o cells on a section you should be able to observe dividing
microscope slide. Stains that bind to DNA are used cells using a microscope or in a micrograph and
to make the chromosomes visible and stages o assign them to one o the phases.
mitosis can then be observed using a microscope.
52
1.6 cell dIVIsIon
Prophase Interphase chromosomes are Prophase nucleoli visible
visible inside the nuclear membrane in the nucleus but no
The chromosomes become individual chromosomes
shorter and atter by coiling. To centromere MTOC
become short enough they have
to coil repeatedly. This is called microtubules
supercoiling. The nucleolus breaks
down. Microtubules grow rom
structures called microtubule
organizing centres (MTOC) to orm
a spindle-shaped array that links
the poles o the cell. At the end o
prophase the nuclear membrane
breaks down.
chromosome nuclear envelope
consisting of two disintegrates
sister chromatids
spindle
microtubules
Early prophase Late prophase
Metaphase Metaphase mitotic spindle
plate equator
Microtubules continue to grow Metaphase chromosomes
and attach to the centromeres aligned on the equator and not Metaphase
on each chromosome. The two inside a nuclear membrane
attachment points on opposite
sides oeach centromere allow the
chromatids oa chromosome to
attach to microtubules rom diferent
poles. The microtubules are all put
under tension to test whether the
attachment is correct. This happens
by shortening othe microtubules at
the centromere. Ithe attachment is
correct, the chromosomes remain on
the equator othe cell.
Anaphase Daughter
chromosomes
At the start o anaphase, each separate
centromere divides, allowing
the pairs o sister chromatids to Anaphase two groups of V-shaped Anaphase
separate. The spindle microtubules chromatids pointing to the two poles
pull them rapidly towards the
poles o the cell. Mitosis produces
two genetically identical nuclei
because sister chromatids are
pulled to opposite poles. This
is ensured by the way that the
spindle microtubules were
attached in metaphase.
53
1 CELL BIOLOGY
Telophase Telophase tight groups of Interphase nucleoli visible
chromosomes at each pole, new inside the nuclear membranes
The chromatids have reached cell wall forming at the equator but not individual chromosomes
the poles and are now called
chromosomes. At each pole the
chromosomes are pulled into a
tight group near the MTOC and
a nuclear membrane reforms
around them. The chromosomes
uncoil and a nucleolus is formed.
By this stage of mitosis the cell is
usually already dividing and the
two daughter cells enter interphase
again.
Cleavage furrow
Nuclear envelope
forming
Telophase
data-base questions: Centromeres and telomeres
Figure 3 and the other micrographs on the preceeding pages show
cells undergoing mitosis. In gure 3, DNA has been stained blue. The
centromeres have been stained with a red fuorescent dye. At the
ends o the chromosomes there are structures called telomeres. These
have been stained with a green fuorescent dye.
1 Deduce the stage o mitosis that the cell was in, giving reasons
or your answer. [3]
2 The cell has an even number o chromosomes.
a) State how many chromosomes there are in this cell. [1 ]
b) Explain the reason or body cells in plants and animals [2]
having an even number o chromosomes.
Figure 3 Cell in mitosis c) In the micrograph o a cell in interphase, the centromeres
54 are on one side o the nucleus and the telomeres are on
the other side. Suggest reasons or this. [2]
d) An enzyme called telomerase lengthens the telomeres, by
adding many short repeating base sequences o DNA. This
enzyme is only active in the germ cells that are used to
produce gametes. When DNA is replicated during the cell
cycle in body cells, the end o the telomere cannot be replicated,
so the telomere becomes shorter. Predict the consequences or
a plant or animal o the shortening o telomeres. [2]
1.6 cell dIVIsIon
The mitotic index
Determination o a mitotic index rom a micrograph.
The mitotic index is the ratio between the number o cells in mitosis
in a tissue and the total number o observed cells. It can be calculated
using this equation:
Mitotic index = _number _o cells in_mitosis
total number o cells
Figure 4 is a micrograph o cells rom a tumour that has developed
rom a Leydig cell in the testis. The mitotic index or this tumour can
be calculated i the total number o cells in the micrograph is counted
and also the number o cells in meiosis.
To fnd the mitotic index o the part o a root tip where cells are
prolierating rapidly, these instructions can be used:
Obtain a prepared slide o an onion or garlic root tip. Find Figure 4 Cells undergoing mitosis in a Leydig
and examine the meristematic region, i.e. a region o rapid cell division. cell tumour
Create a tally chart. Classiy each o about a hundred cells in this
region as being either in interphase or in any o the stages o mitosis.
Use this data to calculate the mitotic index.
Cytokinesis Figure 5 Cytokinesis in ( a) fertilized sea urchin
egg (b) cell from shoot tip of Coleus plant
Cytokinesis occurs ater mitosis and is diferent in plant
and animal cells.
Cells can divide ater mitosis when two genetically identical nuclei are
present in a cell. The process o cell division is called cytokinesis. It
usually begins beore mitosis has actually been completed and it happens
in a dierent way in plant and animal cells.
In animal cells the plasma membrane is pulled inwards around the
equator o the cell to orm a cleavage urrow. This is accomplished using
a ring o contractile protein immediately inside the plasma membrane
at the equator. The proteins are actin and myosin and are similar to
proteins that cause contraction in muscle. When the cleavage urrow
reaches the centre, the cell is pinched apart into two daughter cells.
In plant cells vesicles are moved to the equator where they use to orm
tubular structures across the equator. With the usion o more vesicles
these tubular structures merge to orm two layers o membrane across the
whole o the equator, which develop into the plasma membranes o the
two daughter cells and are connected to the existing plasma membranes at
the sides o the cell, completing the division o the cytoplasm.
The next stage in plants is or pectins and other substances to be
brought in vesicles and deposited by exocytosis between the two new
membranes. This orms the middle lamella that will link the new cell
walls. Both o the daughter cells then bring cellulose to the equator and
deposit it by exocytosis adjacent to the middle lamella. As a result, each
cell builds its own cell wall adj acent to the equator.
55
1 CELL BIOLOGY
Cyclins and the control of the cell cycle
Cyclins are involved in the control o the cell cycle.
Each o the phases o the cell cycle involves many important tasks. A
group o proteins called cyclins is used to ensure that tasks are perormed
at the correct time and that the cell only moves on to the next stage o
the cycle when it is appropriate.
Cyclins bind to enzymes called cyclin-dependent kinases. These kinases
then become active and attach phosphate groups to other proteins in the
cell. The attachment o phosphate triggers the other proteins to become
active and carry out tasks specifc to one o the phases o the cell cycle.
There are our main types o cyclin in human cells. The graph in fgure 6
shows how the levels o these cyclins rise and all. Unless these cyclins reach
a threshold concentration, the cell does not progress to the next stage o the
cell cycle. Cyclins thereore control the cell cycle and ensure that cells divide
when new cells are needed, but not at other times.
concentration
G1 phase S phase G2 phase mitosis
Cyclin D triggers cells to move from G0 to G1 and from G1 into S phase.
Cyclin E prepares the cell for DNA replication in S phase.
Cyclin A activates DNA replication inside the nucleus in S phase.
Cyclin B promotes the assembly of the mitotic spindle and other tasks
in the cytoplasm to prepare for mitosis.
Figure 6
Discovery of cyclins
Serendipity and scientifc discoveries: the discovery o cyclins was accidental.
During research into the control o protein synthesis Further research revealed other cyclins and
in sea urchin eggs, Tim Hunt discovered a protein confrmed what Hunt had suspected rom an early
that increased in concentration ater ertilization then stage that cyclins are a key actor in the control
decreased in concentration, unlike other proteins o the cell cycle. Tim Hunt was awarded a Nobel
which continued to increase. The protein was being Prize or Physiology in 2001 to honour his work
synthesized over a period o about 30 minutes and in the discovery o cyclins. His Nobel Lecture can
then soon ater was being broken down. Further be downloaded rom the internet and viewed.
experiments showed that the protein went through In it he mentions the importance o serendipity
repeated increases and decreases in concentration several times because he had not set out to
that coincided with the phases o the cell cycle. The discover how the cell cycle is controlled. This
breakdown occurred about ten minutes ater the discovery is an example o serendipity a happy
start o mitosis. Hunt named the protein cyclin. and unexpected discovery made by accident.
56
1.6 cell dIVIsIon
tumur frmai a ar Aiviy
Mutagens, oncogenes and metastasis are involved in the car rarh
development o primary and secondary tumours.
Tumours can orm in any tissue at any
Tumours are abnormal groups o cells that develop at any stage o lie in age, but the skin, lung, large intestine
any part o the body. In some cases the cells adhere to each other and (bowel) , breast and prostate gland are
do not invade nearby tissues or move to other parts o the body. These particularly vulnerable. Cancer is a
tumours are unlikely to cause much harm and are classifed as benign. major cause o death in most human
In other tumours the cells can become detached and move elsewhere populations so there is a pressing
in the body and develop into secondary tumours. These tumours are need to fnd methods o prevention
malignant and are very likely to be lie-threatening. and treatment. This involves basic
research into the control o the cell
Diseases due to malignant tumours are commonly known as cancer cycle. Great progress has been made
and have diverse causes. Chemicals and agents that cause cancer are but more is needed.
known as carcinogens, because carcinomas are malignant tumours.
There are various types o carcinogens including some viruses. All Who should pay or research into
mutagens are carcinogenic, both chemical mutagens and also high cancer?
energy radiation such as X-rays and short-wave ultraviolet light. This is
because mutagens are agents that cause gene mutations and mutations
can cause cancer.
Mutations are random changes to the base sequence o genes. Most
genes do not cause cancer i they mutate. The ew genes that can
become cancer-causing ater mutating are known as oncogenes. In a
normal cell oncogenes are involved in the control o the cell cycle and
cell division. This is why mutations in them can result in uncontrolled
cell division and thereore tumour ormation.
Several mutations must occur in the same cell or it to become a tumour
cell. The chance o this happening is extremely small, but because
there are vast numbers o cells in the body, the total chance o tumour
ormation during a lietime is signifcant. When a tumour cell has been
ormed it divides repeatedly to orm two, then our, then eight cells and
so on. This group o cells is called a primary tumour. Metastasis is the
movement o cells rom a primary tumour to set up secondary tumours
in other parts o the body.
Smoking and cancer
The correlation between smoking and incidence o
cancers.
A correlation in science is a relationship between two variable
actors. The relationship between smoking and cancer is an example
o a correlation. There are two types o correlation. With a positive
correlation, when one actor increases the other one also increases;
they also decrease together. With a negative correlation, when one
actor increases the other decreases.
There is a positive correlation between cigarette smoking and the
death rate due to cancer. This has been shown repeatedly in surveys.
table 1 shows the results o one o the largest surveys, and the longest
57
1 CELL BIOLOGY
continuous one. The data shows that the more cigarettes smoked per
day, the higher the death rate due to cancer. They also show a higher
death rate among those who smoked at one time but had stopped.
The results o the survey also show huge increases in the death
rate due to cancers o the mouth, pharynx, larynx and lung. This
is expected as smoke rom cigarettes comes into contact with each
o these parts o the body, but there is also a positive correlation
between smoking and cancers o the esophagus, stomach, kidney,
bladder, pancreas and cervix. Although the death rate due to other
cancers is not signifcantly dierent in smokers and non-smokers,
table 1 shows smokers are several times more likely to die rom all
cancers than non-smokers.
It is important in science to distinguish between a correlation and a
cause. Finding that there is a positive correlation between smoking
and cancer does not prove that smoking causes cancer. However,
in this case the causal links are well established. Cigarette smoke
contains many dierent chemical substances. Twenty o these
have been shown in experiments to cause tumours in the lungs o
laboratory animals or humans. There is evidence that at least orty
other chemicals in cigarette smoke are carcinogenic. This leaves little
doubt that smoking is a cause o cancer.
caue o death etween 1951 Mortaity rate per 100,000 men/year
and 2001
lieong former current moker (igarette/day)
(sampe ize: 34,439 mae non-moker igarette
dotor in britain) moker 114 1524 25
All cancers 360 466 588 747 1,061
Lung cancer 17 68 131 233 417
Cancer of mouth, pharynx, 9 26 36 47 106
larynx and esophagus
All other cancers 334 372 421 467 538
Table 1 from British Medical Journal 328(7455) June 24 2004
58
1.6 cell dIVIsIon
daa-ba qui: The efect o smoking on health
One o the largest ever studies o the eect o death was recorded or each o the doctors who died
smoking on health involved 34,439 male British during this period. The table below shows some
doctors. Inormation was collected on how much o the results. The fgures given are the number o
they smoked rom 1 951 to 2001 and the cause o deaths per hundred thousand men per year.
typ f ia n-mkr 114 1524 >25 igar
igar igar pr ay
Respiratory (diseases o the lungs 107
and airways) pr ay pr ay 471
1,037
Circulatory (diseases o the heart and 8 237 310
blood vessels) 6
20 1,447 1,671 1,938
Stomach and duodenal ulcers
11 33 34
Cirrhosis o the liver 13 22 68
22 6 18
Parkinsons disease
1 Deduce whether there is a positive correlation 4 Discuss whether the data proves that
between smoking and the mortality rate smoking is a cause o cirrhosis o the
due to all types o disease. [2 ] liver. [3]
2 Using the data in the table, discuss whether the 5 The table does not include deaths due to
threat to health rom smoking is greater with cancer. The survey showed that seven types
respiratory or with circulatory diseases. [4] o cancer are linked with smoking. Suggest
3 Discuss whether the data suggests that smoking three cancers that you would expect [3]
smoking to cause.
a small number o cigarettes is sae. [3]
59
1 CELL BIOLOGY
Questions c) Explain the dierence in area o the inner
and outer mitochondrial membranes. [3]
1 Figure 7 represents a cell rom a multicellular
organism.
d) Using the data in the table, identiy two o
the main activities o liver cells. [2]
3 In human secretory cells, or example in the lung
and the pancreas, positively charged ions are
pumped out, and chloride ions ollow passively
through chloride channels. Water also moves rom
the cells into the liquid that has been secreted.
Figure 7 In the genetic disease cystic brosis, the chloride
channels malunction and too ew ions move
a) Identiy, with a reason, whether the cell is out o the cells. The liquid secreted by the cells
becomes thick and viscous, with associated
(i) prokaryotic or eukaryotic; [1 ] health problems.
(ii) part o a root tip or a nger tip; [1 ] a) State the names o the processes that:
(iii) in a phase o mitosis or in interphase. [1 ] (i) move positively charged ions out o
b) The magnication o the drawing is 2,500 . the secretory cells [1 ]
(i) Calculate the actual size o the cell. [2] (ii) move chloride ions out o the [1 ]
secretory cells.
(ii) Calculate how long a 5 m scale
bar should be i it was added to the ( iii) move water out o the secretory cells. [1 ]
drawing. [1 ] b) Explain why the fuid secreted by people
c) Predict what would happen to the cell i it was with cystic brosis is thick and viscous. [4]
placed in a concentrated salt solution or one
hour. Include reasons or your answer. [3] 4 The amount o D NA present in each cell
nucleus was measured in a large number
2 Table 2 shows the area o membranes in a rat o cells taken rom two dierent cultures o
liver cell. human bone marrow (gure 8).
Membrane component Area (m2) a) For each label (I, II and III) in the Sample B
Plasma membrane 1,780 graph, deduce which phase o the cell cycle
Rough endoplasmic reticulum the cells could be in; i.e. G1 , G2 or S. [3]
Mitochondrial outer membrane 30,400
7,470 b) Estimate the approximate amount o DNA
per nucleus that would be expected in the
ollowing human cell types:
Mitochondrial inner membrane 39,600 (i) bone marrow at prophase [2]
Nucleus 280 (ii) bone marrow at telophase.
Lysosomes 100
Other components Sample A Sample B
18,500 3 (non-dividing cell culture) 3 (rapidly dividing cell culture)
2 I
2
1
Table 2 Number of cells (in thousands) III
Number of cells (in thousands) 1
a) Calculate the total area o membranes in the
II
liver cell. [2]
b) Calculate the area o plasma membrane as 5 10 15 5 10 15
a percentage o the total area o membranes DNA/pg per nucleus DNA/pg per nucleus
in the cell. Show your working. [3 ] Figure 8
60
2 Molecular BIoloGY
Intdtin hydrogen and oxygen are used to supply and
store energy. Many proteins act as enzymes to
Water is the medium for life. Living organisms control the metabolism of the cell and others
control their composition by a complex web have a diverse range of biological functions.
of chemical reactions that occur within this Genetic information is stored in DNA and can
medium. Photosynthesis uses the energy in be accurately copied and translated to make the
sunlight to supply the chemical energy needed proteins needed by the cell.
for life and cell respiration releases this energy
when it is needed. Compounds of carbon,
2.1 Molecules to metabolism
undstnding appitins
Molecular biology explains living processes in Urea as an example o a compound that is
terms o the chemical substances involved. produced by living organisms but can also be
artifcially synthesized.
Carbon atoms can orm our bonds allowing a
diversity o compounds to exist. Skis
Lie is based on carbon compounds Drawing molecular diagrams o glucose, ribose, a
including carbohydrates, lipids, proteins and saturated atty acid and a generalized amino acid.
nucleic acids.
Identifcation o biochemicals such as
Metabolism is the web o all the enzyme carbohydrate, lipid or protein rom
catalysed reactions in a cell or organism. molecular diagrams.
Anabolism is the synthesis o complex Nt f sin
molecules rom simpler molecules including
the ormation o macromolecules rom Falsifcation o theories: the artifcial synthesis
monomers by condensation reactions. o urea helped to alsiy vitalism.
Catabolism is the breakdown o complex
molecules into simpler molecules including the
hydrolysis o macromolecules into monomers.
61
2 MOLECULAR BIOLOGY
Figure 1 A molecular biologist at work in the Molecular biology
laboratory
Molecular biology explains living processes in terms
o the chemical substances involved.
The discovery o the structure o DNA in 1 953 started a revolution in
biology that has transormed our understanding o living organisms. It
raised the possibility o explaining biological processes rom the structure
o molecules and how they interact with each other. The structures are
diverse and the interactions are very complex, so although molecular
biology is more than 50 years old, it is still a relatively young science.
Many molecules are important in living organisms including one as
apparently simple as water, but the most varied and complex molecules
are nucleic acids and proteins. Nucleic acids comprise DNA and RNA.
They are the chemicals used to make genes. Proteins are astonishingly
varied in structure and carry out a huge range o tasks within the
cell, including controlling chemical reactions o the cell by acting as
enzymes. The relationship between genes and proteins is at the heart
o molecular biology.
The approach o the molecular biologist is reductionist as it involves
considering the various biochemical processes o a living organism
and breaking down into its component parts. This approach has been
immensely productive in biology and has given us insights into whole
organisms that we would not otherwise have. Some biologists argue
that the reductionist approach o the molecular biologist cannot explain
everything though, and that when component parts are combined there
are emergent properties that cannot be studied without looking at the
whole system together.
O Synthesis of urea
C Urea as an example o a compound that is produced by
H N NH living organisms but can also be artifcially synthesized.
22 Urea is a nitrogen-containing compound with a relatively simple
molecular structure (fgure 2) . It is a component o urine and this was
Figure 2 Molecular diagram of urea where it was frst discovered. It is produced when there is an excess
o amino acids in the body, as a means o excreting the nitrogen
rom the amino acids. A cycle o reactions, catalysed by enzymes, is
used to produce it ( fgure 3 ) . This happens in the liver. Urea is then
transported by the blood stream to the kidneys where it is fltered out
and passes out o the body in the urine.
Urea can also be synthesized artifcially. The chemical reactions used
are dierent rom those in the liver and enzymes are not involved, but
the urea that is produced is identical.
ammonia + carbon dioxide ammonium carbamate
urea + water
About 1 00 million tonnes are produced annually. Most o this is used
as a nitrogen ertilizer on crops.
62
2.1 Molecules to MetabolisM
CO2 + NH3 urea
enzyme 1 arginase
carbamoyl phosphate
ornithine
enzyme 2
citrulline arginine
aspartate fu m a ra t e
enzyme 3 enzyme 4
argininosuccinate
Figure 3 The cycle of reactions occurring in liver cells that is used to synthesize urea
urea and the alsifcation o vitalism
Falsifcation o theories: the artifcial synthesis o urea helped to alsiy vitalism.
Urea was discovered in urine in the 1 720s and was organic compounds could be as well. Whlers
assumed to be a product o the kidneys. At that achievement was evidence against the theory
time it was widely believed that organic compounds o vitalism. It helped to alsiy the theory, but it
in plants and animals could only be made with the did not cause all biologists to abandon vitalism
help o a vital principle. This was part o vitalism immediately. It usually requires several pieces o
the theory that the origin and phenomena o lie evidence against a theory or most biologists to
are due to a vital principle, which is dierent rom accept that it has been alsifed and sometimes
purely chemical or physical orces. Aristotle used controversies over a theory continue or decades.
the word psyche or the vital principle a Greek
word meaning breath, lie or soul. Although biologists now accept that processes
in living organisms are governed by the same
In 1 828 the German chemist Friedrich Whler chemical and physical orces as in non-living
synthesized urea artifcially using silver matter, there remain some organic compounds
isocyanate and ammonium chloride. This was that have not been synthesized artifcially. It is
the frst organic compound to be synthesized still impossible to make complex proteins such
artifcially. It was a very signifcant step, because as hemoglobin, or example, without using
no vital principle had been involved in the ribosomes and other components o cells. Four
synthesis. Whler wrote this excitedly to the years ater his synthesis o urea, Whler wrote
Swedish chemist Jns Jacob Berzelius: this to Berzelius:
In a manner of speaking, I can no longer Organic chemistry nowadays almost
hold my chemical water. I must tell you drives one mad. To me it appears like a
that I can make urea without the kidneys primeval tropical forest full of the most
of any animal, be it man or dog. remarkable things; a dreadful endless
jungle into which one dare not enter, for
An obvious deduction was that i urea had been there seems no way out.
synthesized without a vital principle, other
63
2 MOLECULAR BIOLOGY
ativity carbon ompounds
crbon ompounds Carbon atoms can orm our bonds allowing a diversity
o compounds to exist.
Can you fnd an example
o a biological molecule Carbon is only the 1 5th most abundant element on Earth, but it can be
in which a carbon atom is used to make a huge range of different molecules. This has given living
bonded to atoms o three organisms almost limitless possibilities for the chemical composition and
other elements or even our activities of their cells. The diversity of carbon compounds is explained
other elements? by the properties of carbon.
Titin is a giant protein that Carbon atoms form covalent bonds with other atoms. A covalent bond
acts as a molecular spring is formed when two adjacent atoms share a pair of electrons, with one
in muscle. The backbone o electron contributed by each atom. Covalent bonds are the strongest type of
the titin molecule is a chain bond between atoms so stable molecules based on carbon can be produced.
o 100,000 atoms, linked by
single covalent bonds. Each carbon atom can form up to four covalent bonds more than
most other atoms, so molecules containing carbon can have complex
Can you fnd an example structures. The bonds can be with other carbon atoms to make rings
o a molecule in your or chains of any length. Fatty acids contain chains of up to 20 carbon
body with a chain o over atoms for example. The bonds can also be with other elements such as
1,000,000,000 atoms? hydrogen, oxygen, nitrogen or phosphorus.
Carbon atoms can bond with just one other element, such as hydrogen in
methane, or they can bond to more than one other element as in ethanol
(alcohol found in beer and wine) . The four bonds can all be single
covalent bonds or there can be two single and one double covalent bond,
H for example in the carboxyl group of ethanoic acid (the acid in vinegar) .
HCH methane
H classifying arbon ompounds
HH Lie is based on carbon compounds including
H C C O H ethanol carbohydrates, lipids, proteins and nucleic acids.
HH Living organisms use four main classes of carbon compound. They have
different properties and so can be used for different purposes.
H
O Carbohydrates are characterized by their composition. They are composed
of carbon, hydrogen and oxygen, with hydrogen and oxygen in the ratio of
HCC ethanoic acid two hydrogen atoms to one oxygen, hence the name carbohydrate.
OH
H
HHHHHHHHHHHHHHHHH O Lipids are a broad class of
molecules that are insoluble in
HC C C C C C C C C C C C C C C C C C water, including steroids, waxes,
fatty acids and triglycerides. In
OH common language, triglycerides
HH H H HHHHHHH are fats if they are solid at room
temperature or oils if they are
linolenic acid an omega-3 fatty acid liquid at room temperature.
Figure 4 Some common naturally-occurring carbon compounds
Proteins are composed of one or more chains of amino acids. All of the
amino acids in these chains contain the elements carbon, hydrogen, oxygen
and nitrogen, but two of the twenty amino acids also contain sulphur.
Nucleic acids are chains of subunits called nucleotides, which contain
carbon, hydrogen, oxygen, nitrogen and phosphorus. There are two types
of nucleic acid: ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) .
64
2.1 Molecules to MetabolisM
Drawing molecules
Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a
generalized amino acid.
There is no need to memorize the structure o atom is represented with C and an oxygen atom
many dierent molecules but a biologist should with O. Single covalent bonds are shown with a
be able to draw diagrams o a ew o the most line and double bonds with two lines.
important molecules.
Some chemical groups are shown with the
Each atom in a molecule is represented using the atoms together and bonds not indicated. Table 1
symbol o the element. For example a carbon gives examples.
Name of group Full structure Simplied notation
hydroxyl OH OH
amine NH2
carboxyl H COOH
N
H
H
O
C
O
H
methyl CH CH3
H
Table 1
Ribose OH
The ormula or ribose is C5H10O5 5
The molecule is a fve-membered ring with a side chain.
HCH
Four carbon atoms are in the ring and one orms the side chain.
The carbon atoms can be numbered starting with number 1 on the right. O OH
The hydroxyl groups (OH) on carbon atoms 1 , 2 and 3 point up, 4CH H C1
HH
down and down respectively.
3 C C2
Glucose
OH OH
The ormula or glucose is C6H12O6
The molecule is a six-membered ring with a side chain. Ribose
Five carbon atoms are in the ring and one orms the side chain.
The carbon atoms can be numbered starting with number 1 on the right. 6 CH2OH
The hydroxyl groups (OH) on carbon atoms 1 , 2, 3 and 4 point
5C O C
down, down, up and down respectively, although in a orm o HH OH
glucose used by plants to make cellulose the hydroxyl group on H 1C
carbon atom 1 points upwards. 4 C OH
C
HO C
2
3
H OH
Glucose
65
2 MOLECULAR BIOLOGY
Saturated fatty acids O OH
C
The carbon atoms form an unbranched chain.
In saturated fatty acids they are bonded to each other by single bonds. HCH
The number of carbon atoms is most commonly between 1 4 and 20. HCH
At one end of the chain the carbon atom is part of a carboxyl group HCH
At the other end the carbon atom is bonded to three hydrogen atoms. HCH
All other carbon atoms are bonded to two hydrogen atoms. HCH
HCH
Amino acids HCH
HCH
A carbon atom in the centre of the molecule is bonded to four HCH
different things: HCH
HCH
an amine group, hence the term amino acid; HCH
HCH
a carboxyl group which makes the molecule an acid; HCH
HCH
a hydrogen atom;
H
the R group, which is the variable part of amino acids.
Full molecular diagram o a
R R O saturated atty acid
HO
CH3 (CH2) n C
NCC N2N C COOH
HO H OH
H H Simplifed molecular diagram
full molecular diagram o a saturated atty acid
simplied molecular diagram
Molecular diagrams o an amino acid
Identifying molecules
Identifcation o biochemicals as carbohydrate, lipid or protein rom molecular
diagrams.
The molecules of carbohydrates, lipids and
proteins are so different from each other that it is
usually quite easy to recognize them.
Proteins contain C, H, O and N whereas
carbohydrates and lipids contain C, H and O
but not N.
Many proteins contain sulphur (S) but
carbohydrates and lipids do not.
Carbohydrates contain hydrogen and oxygen Figure 5 A commonly-occurring biological molecule
atoms in a ratio of 2:1 , for example glucose
is C6H12O6 and sucrose (the sugar commonly
used in baking) is C12H22O11
Lipids contain relatively less oxygen than
carbohydrates, for example oleic acid (an
unsaturated fatty acid) is C18H34O2 and the
steroid testosterone is C19H28O2
66
2.1 Molecules to MetabolisM 67
Metbolism
Metabolism is the web of all the enzyme catalysed
reactions in a cell or organism.
All living organisms carry out large numbers o dierent chemical
reactions. These reactions are catalysed by enzymes. Most o them
happen in the cytoplasm o cells but some are extracellular, such as the
reactions used to digest ood in the small intestine. Metabolism is the
sum o all reactions that occur in an organism.
Metabolism consists o pathways by which one type o molecule is transormed
into another, in a series o small steps. These pathways are mostly chains o
reactions but there are also some cycles. An example is shown in fgure 3.
Even in relatively simple prokaryote cells, metabolism consists o over
1 ,000 dierent reactions. Global maps showing all reactions are very
complex. They are available on the internet, or example in the Kyoto
Encyclopedia o Genes and Genomes.
anbolism
Anabolism is the synthesis of complex molecules from
simpler molecules including the formation ofmacromolecules
from monomers by condensation reactions.
Metabolism is oten divided into two parts, anabolism and catabolism.
Anabolism is reactions that build up larger molecules rom smaller ones.
An easy way to remember this is by recalling that anabolic steroids
are hormones that promote body building. Anabolic reactions require
energy, which is usually supplied in the orm o ATP.
Anabolism includes these processes:
Protein synthesis using ribosomes.
DNA synthesis during replication.
Photosynthesis, including production o glucose rom carbon dioxide
and water.
Synthesis o complex carbohydrates including starch, cellulose and
glycogen.
ctbolism
Catabolism is the breakdown of complex molecules
into simpler molecules including the hydrolysis of
macromolecules into monomers.
Catabolism is the part o metabolism in which larger molecules are
broken down into smaller ones. Catabolic reactions release energy and
in some cases this energy is captured in the orm o ATP, which can then
be used in the cell. Catabolism includes these processes:
Digestion o ood in the mouth, stomach and small intestine.
Cell respiration in which glucose or lipids are oxidized to carbon
dioxide and water.
Digestion o complex carbon compounds in dead organic matter by
decomposers.
2 MOLECULAR BIOLOGY
2.2 Water
understnding applictions
Water molecules are polar and hydrogen bonds Comparison of the thermal properties of water
form between them. with those of methane.
Hydrogen bonding and dipolarity explain Use of water as a coolant in sweat.
the adhesive, cohesive, thermal and solvent
properties of water. Methods of transport of glucose, amino acids,
cholesterol, fats, oxygen and sodium chloride
Substances can be hydrophilic or hydrophobic. in blood in relation to their solubility in water.
Ntre of science
Use theories to explain natural phenomena:
the theory that hydrogen bonds form between
water molecules explains waters properties.
HH Hydrogen bonding in wter
O
Water molecules are polar and hydrogen bonds form
tends to small between them.
pull the positive
electrons charge + A water molecule is ormed by covalent bonds between an oxygen atom
slightly on each and two hydrogen atoms. The bond between hydrogen and oxygen
in this hydrogen involves unequal sharing o electrons it is a polar covalent bond. This
direction atom is because the nucleus o the oxygen atom is more attractive to electrons
than the nuclei o the hydrogen atoms (fgure 1 ).
Corresponding negative charge
2- on oxygen atom Because o the unequal sharing o electrons in water molecules, the
hydrogen atoms have a partial positive charge and oxygen has a partial
Figure 1 Water molecules negative charge. B ecause water molecules are bent rather than linear,
the two hydrogen atoms are on the same side o the molecule and orm
water molecule one pole and the oxygen orms the opposite pole.
hydrogen bond Positively charged particles (positive ions) and negatively charged
particles (negative ions) attract each other and orm an ionic bond.
Figure 2 The dotted line Water molecules only have partial charges, so the attraction is less but it
indicates the presence of is still enough to have signifcant eects. The attraction between water
an intermolecular force molecules is a hydrogen bond. Strictly speaking it is an intermolecular
between the molecules. This orce rather than a bond. A hydrogen bond is the orce that orms when
is called a hydrogen bond a hydrogen atom in one polar molecule is attracted to a slightly negative
atom o another polar covalent molecule.
Although a hydrogen bond is a weak intermolecular orce, water
molecules are small, so there are many o them per unit volume o water
and large numbers o hydrogen bonds (fgure 2) . Collectively they give
water its unique properties and these properties are, in turn, o immense
importance to living things.
68
2.2 Water
Hydrogen bonds and the properties of water
Use theories to explain natural phenomena: the theory that hydrogen bonds form
between water molecules explains waters properties.
There is strong experimental evidence or hydrogen It might seem unwise to base our understanding
bonds, but it remains a theory that they orm o the natural world on something that has not
between water molecules. Scientists cannot prove been proven to exist. However this is the way
without doubt that they exist as they are not directly that science works we can assume that a theory
visible. However, hydrogen bonds are a very useul is correct i there is evidence or it, i it helps to
way o explaining the properties o water. They predict behaviour, i it has not been alsifed and
explain the cohesive, adhesive, thermal and solvent i it helps to explain natural phenomena.
properties o water. It is these distinctive properties
that make water so useul to living organisms.
Properties of water
Hydrogen bonding and dipolarity explain the cohesive,
adhesive, thermal and solvent properties of water.
Cohesive properties
Cohesion reers to the binding together o two molecules o the same
type, or instance two water molecules.
Water molecules are cohesive they cohere, which means they stick to
each other, due to hydrogen bonding, described in the previous section.
This property is useul or water transport in plants. Water is sucked
through xylem vessels at low pressure. The method can only work i
the water molecules are not separated by the suction orces. Due to
hydrogen bonding this rarely happens and water can be pulled up to the
top o the tallest trees over a hundred metres.
Adhesive properties
Hydrogen bonds can orm between water and other polar molecules,
causing water to stick to them. This is called adhesion. This property is
useul in leaves, where water adheres to cellulose molecules in cell walls.
I water evaporates rom the cell walls and is lost rom the lea via the
network o air spaces, adhesive orces cause water to be drawn out o
the nearest xylem vessel. This keeps the walls moist so they can absorb
carbon dioxide needed or photosynthesis.
Thermal properties
Water has several thermal properties that are useul to living organisms:
High specifc heat capacity. Hydrogen bonds restrict the motion o
water molecules and increases in the temperature o water require
hydrogen bonds to be broken. Energy is needed to do this. As a result,
the amount o energy needed to raise the temperature o water is
relatively large. To cool down, water must lose relatively large amounts
o energy. Waters temperature remains relatively stable in comparison
to air or land, so it is a thermally stable habitat or aquatic organisms.
High latent heat o vaporization. When a molecule evaporates
it separates rom other molecules in a liquid and becomes a vapour
molecule. The heat needed to do this is called the latent heat o
69
2 MOLECULAR BIOLOGY
toK vaporization. Evaporation therefore has a cooling effect. Considerable
amounts of heat are needed to evaporate water, because hydrogen
How do scientic explanations difer bonds have to be broken. This makes it a good evaporative coolant.
rom pseudo-scientic explanations? Sweating is an example of the use of water as a coolant.
Homeopathy is a practice where High boiling point. The boiling point of a substance is the highest
remedies are prepared by dissolving temperature that it can reach in a liquid state. For the same reasons that
things like charcoal, spider venom water has a high latent heat of vaporization, its boiling point is high.
or deadly nightshade. This mother Water is therefore liquid over a broad range of temperatures from 0 C
tincture o harmul substance is diluted to 1 00 C. This is the temperature range found in most habitats on Earth.
again and again to the point where a
sample rom the solution is unlikely to Solvent properties
contain a single molecule o the solute.
It is this ultra-dilute solution that is Water has important solvent properties. The polar nature of the water
claimed to have medicinal properties. molecule means that it forms shells around charged and polar molecules,
The properties are reerred to as the preventing them from clumping together and keeping them in solution.
memory o water. Despite the large Water forms hydrogen bonds with polar molecules. Its partially negative
number o practitioners o this practice, oxygen pole is attracted to positively charged ions and its partially
no homeopathic remedy has ever been positive hydrogen pole is attracted to negatively charged ions, so both
shown to work in a large randomized dissolve. Cytoplasm is a complex mixture of dissolved substances in
placebo-controlled clinical trial. which the chemical reactions of metabolism occurs.
Hydrophilic and hydrophobic
Substances can be hydrophilic or hydrophobic.
The literal meaning of the word hydrophilic is water-loving. It is used to
describe substances that are chemically attracted to water. All substances
that dissolve in water are hydrophilic, including polar molecules such
as glucose, and particles with positive or negative charges such as
sodium and chloride ions. Substances that water adheres to, cellulose for
example, are also hydrophilic.
Some substances are insoluble in water although they dissolve in other
solvents such as propanone (acetone) . The term hydrophobic is used to
describe them, though they are not actually water-fearing. Molecules
are hydrophobic if they do not have negative or positive charges and are
nonpolar. All lipids are hydrophobic, including fats and oils
Figure 3 When two nonpolar molecules in water come into contact, weak interactions form
between them and more hydrogen bonds form between water molecules
70
2.2 Water
I a nonpolar molecule is surrounded by water molecules, hydrogen bonds
orm between the water molecules, but not between the nonpolar molecule
and the water molecules. I two nonpolar molecules are surrounded by
water molecules and random movements bring them together, they behave
as though they are attracted to each other. There is a slight attraction
between nonpolar molecules, but more signifcantly, i they are in contact
with each other, more hydrogen bonds can orm between water molecules.
This is not because they are water-earing: it is simply because water
molecules are more attracted to each other than to the nonpolar molecules.
As a result, nonpolar molecules tend to join together in water to orm larger
and larger groups. The orces that cause nonpolar molecules to join together
into groups in water are known as hydrophobic interactions.
comparing water and methane
Comparison o the thermal properties o water with
those o methane.
The properties o water have already been described. Methane is a
waste product o anaerobic respiration in certain prokaryotes that live
in habitats where oxygen is lacking. Methanogenic prokaryotes live
in swamps and other wetlands and in the guts o animals, including
termites, cattle and sheep. They also live in waste dumps and are
deliberately encouraged to produce methane in anaerobic digesters.
Methane can be used as a uel but i allowed to escape into the
atmosphere it contributes to the greenhouse eect.
Water and methane are both small molecules with atoms linked by
single covalent bonds. However water molecules are polar and can
orm hydrogen bonds, whereas methane molecules are nonpolar and
do not orm hydrogen bonds. As a result their physical properties are
very dierent.
The data in table 1 shows some o the physical properties o methane
and water. The density and specifc heat capacity are given or
methane and water in a liquid state. The data shows that water has
a higher specifc heat capacity, higher latent heat o vaporization,
higher melting point and higher boiling point. Whereas methane is
liquid over a range o only 22 C, water is liquid over 1 00 C.
Popy Mhn W
Formula CH HO
Molecular mass
4 2
16 18
1g per cm3
Density 0.46g per cm3 4.2 J per g per C
2,257 J/g
Specifc heat capacity 2.2 J per g per C
0 C
Latent heat o vaporization 760 J/g 100 C
Melting point 182 C
Boiling point 160 C Figure 4 Bubbles of methane gas, produced by
prokaryotes decomposing organic matter at
Table 1 Comparing methane and water the bottom of a pond have been trapped in ice
when the pond froze
71
2 MOLECULAR BIOLOGY
cooling the body with sweat There are methods o cooling other than sweating,
though many o these also rely on heat loss due
Use of water as a coolant in sweat. to evaporation o water. Panting in dogs and birds
is an example. Transpiration is evaporative loss
Sweat is secreted by glands in the skin. The sweat o water rom plant leaves; it has a cooling eect
is carried along narrow ducts to the surace o the which is useul in hot environments.
skin where it spreads out. The heat needed or the
evaporation o water in sweat is taken rom the
tissues o the skin, reducing their temperature.
Blood fowing through the skin is thereore
cooled. This is an eective method o cooling
the body because water has a high latent heat o
vaporization. Solutes in the sweat, especially ions
such as sodium, are let on the skin surace and
can sometimes be detected by their salty taste.
Sweat secretion is controlled by the hypothalamus
o the brain. It has receptors that monitor blood
temperature and also receives sensory inputs rom
temperature receptors in the skin. I the body is
overheated the hypothalamus stimulates the sweat
glands to secrete up to two litres o sweat per hour.
Usually no sweat is secreted i the body is below
the target temperature, though when adrenalin is
secreted we sweat even i we are already cold. This
is because adrenalin is secreted when our brain
anticipates a period o intense activity that will
tend to cause the body to overheat.
Transport in blood plasma
Methods of transport of glucose, amino acids, cholesterol, fats, oxygen and
sodium chloride in blood in relation to their solubility in water.
Blood transports a wide variety o substances, Glucose is a polar molecule. It is reely soluble in
using several methods to avoid possible problems water and is carried dissolved in blood plasma.
and ensure that each substance is carried in large
enough quantities or the bodys needs. Oxygen is a nonpolar molecule. Because o the
small size o the molecule it dissolves in water but
Sodium chloride is an ionic compound that is only sparingly and water becomes saturated with
reely soluble in water, dissolving to orm sodium oxygen at relatively low concentrations. Also, as
ions (Na+) and chloride ions (Cl-) , which are the temperature o water rises, the solubility o
carried in blood plasma. oxygen decreases, so blood plasma at 37 C can
hold much less dissolved oxygen than water at
Amino acids have both negative and positive 2 0 C or lower. The amount o oxygen that blood
charges. Because o this they are soluble in water plasma can transport around the body is ar too
but their solubility varies depending on the R little to provide or aerobic cell respiration. This
group, some o which are hydrophilic while others problem is overcome by the use o hemoglobin in
are hydrophobic. All amino acids are soluble red blood cells. Hemoglobin has binding sites or
enough to be carried dissolved in blood plasma. oxygen and greatly increases the capacity o the
blood or oxygen transport.
72
2.3 carbohydrates and liPids
Fats molecules are entirely nonpolar, are larger phospholipid
than oxygen and are insoluble in water. They are protein
carried in blood inside lipoprotein complexes. cholesterol
These are groups of molecules with a single layer triglyceride
of phospholipid on the outside and fats inside. The
hydrophilic phosphate heads of the phospholipids Figure 5 Arrangement of molecules in a lipoprotein complex
face outwards and are in contact with water in
the blood plasma. The hydrophobic hydrocarbon
tails face inwards and are in contact with the
fats. There are also proteins in the phospholipid
monolayer, hence the name lipoprotein.
Cholesterol molecules are hydrophobic, apart
from a small hydrophilic region at one end. This
is not enough to make cholesterol dissolve in
water and instead it is transported with fats in
lipoprotein complexes. The cholesterol molecules
are positioned in the phospholipid monolayers, with
the hydrophilic region facing outwards in the region
with the phosphate heads of the phospholipids.
2.3 c p
understnding applictions
Monosaccharide monomers are linked Structure and unction o cellulose and starch
together by condensation reactions to orm in plants and glycogen in humans.
disaccharides and polysaccharide polymers.
Scientifc evidence or health risks o trans-ats
Fatty acids can be saturated, monounsaturated and saturated ats.
or polyunsaturated.
Lipids are more suitable or long-term energy
Unsaturated atty acids can be cis or trans storage in humans than carbohydrates.
isomers.
Evaluation o evidence and the methods used
Triglycerides are ormed by condensation rom to obtain evidence or health claims made
three atty acids and one glycerol. about lipids.
Ntre of science Skills
Evaluating claims: health claims made about Use o molecular visualization sotware to
lipids need to be assessed. compare cellulose, starch and glycogen.
Determination o body mass index by
calculation or use o a nomogram.
73
2 MOLECULAR BIOLOGY
toK carbohydrates
iw cmpeng paradgms gve Monosaccharide monomers are linked together by
dferen explanans a phenmenn, condensation reactions to orm disaccharides and
hw can we decde whch s crrec? polysaccharide polymers.
Thomas Kuhn, in his book The Structure o Glucose, ructose and ribose are all examples o monosaccharides. The
Scientifc Revolutions adopted the word structure o glucose and ribose molecules was shown in sub-topic 2.1 .
paradigm to reer to the rameworks that Monosaccharides can be linked together to make larger molecules.
dominate the interpretation oinormation
in a scientifc discipline at a particular Monosaccharides are single sugar units.
point in time. The paradigm impacts the
kinds oquestions that are supposed to D isaccharides consist o two monosaccharides linked together. For
be asked. example, maltose is made by linking two glucose molecules together.
Sucrose is made by linking a glucose and a ructose.
Nutritionism is the reductionist paradigm
that the presence oindicator nutrients Polysaccharides consist o many monosaccharides linked together.
are the key determinant ohealthy Starch, glycogen and cellulose are polysaccharides. They are all made
ood. Even highly processed ood may by linking together glucose molecules. The dierences between them
be advertised as healthy depending are described later in this sub-topic.
on the degree to which it contains
healthy nutrients. Words like carbs, When monosaccharides combine, they do so by a process called
vitamins and polyunsaturated at have condensation (fgure 1 ) . This involves the loss o an OH rom one
entered the everyday lexicon. Some molecule and an H rom another molecule, which together orm
argue that this aligns consumer anxiety H2O. Thus, condensation involves the combination o subunits and
with the commercial interests oood yields water.
manuacturers.
Linking together monosaccharides to orm disaccharides and
An alternative paradigm or determining polysaccharides is an anabolic process and energy has to be used to do it.
the healthiness oood is argued or by ATP supplies energy to the monosaccharides and this energy is then used
Michael Pollan in his book In Deense o when the condensation reaction occurs.
Food. It argues that ood quality should
be determined by cultural tradition which H HH H Monosaccharides, C6H12O6
tended to look at ood more holistically: e.g. glucose, fructose, galactose
HO OH HO OH
The sheernovelty and glamoro Disaccharide, C12H22O11
the Western diet, with its seventeen H2O e.g. maltose, sucrose, lactose
thousand new ood products every year
and the marketing power thirty-two Condensation Hydrolysis
billion dollars a year used to sell us (water removed) (water added)
those products, has overwhelmed the
orce otradition and let us where we HH
now fnd ourselves: relying on science
and journalism and government and HO O OH
marketing to help us decide what to eat Glycosidic
bond
Michael Pollan, In Deense oFood: An
Eater's Maniesto Condensation Hydrolysis
HH
Polysaccharide
e.g. starch, glycogen
HO O O O OH
Figure 1 Condensation and hydrolysis reactions between monosaccharides and
disaccharides
74
2.3 carbohydrates and liPids
Imaging carbohydrate molecules
Use of molecular visualization software to compare
cellulose, starch and glycogen.
The most widely used molecular visualization software is JMol, which
can be downloaded free of charge. There are also many websites that
use JMol, which are easier to use. Suggestions of suitable websites are
available with the electronic resources that accompany this book.
When JMol software is being used, you should be able to make these
changes to the image of a molecule that you see on the screen:
Use the scroll function on the mouse to make the image larger
or smaller.
Left click and move the mouse to rotate the image.
Right click to display a menu that allows you to change the style
of molecular model, label the atoms, make the molecule rotate
continuously or change the background colour.
Spend some time developing your skill in molecular visualization and
then try these questions to test your skill level and learn more about
the structure of polysaccharides.
Questions
1 Select glucose with the ball and stick style with a black background.
What colours are used to show carbon, hydrogen and [2]
oxygen atoms?
2 Select sucrose with sticks style and a blue background.
What is the difference between the glucose ring and the [1 ]
fructose ring in the sucrose molecule?
3 Select amylose, which is the unbranched form of starch, with
the wireframe style and a white background. If possible select a
short amylose chain and then a longer one.
What is the overall shape of an amylose molecule? [1 ]
How many glucose molecules in the chain are linked to [1 ]
only one other glucose?
4 S elect amylopectin, with the styles and colours that you prefer.
Amylopectin is the branched form of starch. Zoom in to look
closely at a position where there is a branch. A glucose molecule
must be linked to an extra third glucose to make the branch.
What is different about this linkage, compared to the [1 ]
linkages between glucose molecules in unbranched parts
of the molecule?
How many glucose molecules are linked to only one other Figure 2 Images of sugars using molecular
visualization software (a) fructose,
glucose in the amylopectin molecule? [1 ] (b) maltose, (c) lactose
75
2 MOLECULAR BIOLOGY
5 Select glycogen. It is similar but not identical to the
amylopectin orm o starch.
What is the dierence between glycogen and amylopectin? [1 ]
6 Select cellulose.
How is it dierent in shape rom the other polysaccharides? [1 ]
7 Look at the oxygen atom that orms part o the ring in each
glucose molecule in the chain.
What pattern do you notice in the position o these oxygen
atoms along the chain?
Polysaccharides
Structure and function of cellulose and starch in plants and glycogen in humans.
Starch, glycogen and cellulose are all made by linking
together glucose molecules, yet their structure and
unctions are very dierent. This is due to dierences
in the type o glucose used to make them and in the
type o linkage between glucose molecules.
Glucose has fve OH groups, any o which Figure 3 Glucose molecule
could be used in condensation reactions, but
only three o them are actually used to link to
make polysaccharides. The most common link is
between the OH on carbon atom 1 (on the right
hand side in molecular diagrams o glucose) and
the OH on carbon atom 4 (shown on the let
hand side) . The OH on carbon atom 6 (shown
at the top o molecular diagrams) is used to orm
side branches in some polysaccharides.
Glucose can have the OH group on carbon atom 1
pointing either upwards or downwards. In alpha
glucose (-glucose) the OH group points downwards
but in beta glucose (-glucose) it points upwards.
This small dierence has major consequences or
polysaccharides made rom glucose.
Cellulose is made by linking together -glucose Figure 4 Cellulose
molecules. Condensation reactions link carbon atom
1 to carbon atom 4 on the next -glucose. The OH Cellulose molecules are unbranched chains o
groups on carbon atom 1 and 4 point in opposite -glucose, allowing them to orm bundles with
directions: up on carbon 1 and down on carbon 4. hydrogen bonds linking the cellulose molecules.
To bring these OH groups together and allow a These bundles are called cellulose microfbrils.
condensation reaction to occur, each -glucose They have very high tensile strength and are used
added to the chain has to be positioned at 1 80 to as the basis o plant cell walls. The tensile strength
the previous one. The glucose subunits in the chain o cellulose prevents plant cells rom bursting,
are oriented alternately upwards and downwards. even when very high pressures have developed
The consequence o this is that the cellulose inside the cell due to entry o water by osmosis.
molecule is a straight chain, rather than curved.
76
2.3 carbohydrates and liPids
Starch is made by linking together -glucose Figure 5 Starch
molecules. As in cellulose, the links are made by
condensation reactions between the OH groups on glycogen it is easy to add extra glucose molecules
carbon atom 1 o one glucose and carbon atom 4 or remove them. This can be done at both ends
o the adjacent glucose. These OH groups both o an unbranched molecule or at any o the ends
point downwards, so all the glucose molecules in a branched molecule. Starch and glycogen
in starch can be orientated in the same way. The molecules do not have a fxed size and the
consequence o this is that the starch molecule is number o glucose molecules that they contain
curved, rather than straight. There are two orms o can be increased or decreased.
starch. In amylose the chain o -glucose molecules
is unbranched and orms a helix. In amylopectin the
chain is branched, so has a more globular shape.
Starch is only made by plant cells. Molecules o both
types o starch are hydrophilic but they are too large
to be soluble in water. They are thereore useul
in cells where large amounts o glucose need to be
stored, but a concentrated glucose solution would
cause too much water to enter a cell by osmosis.
Starch is used as a store o glucose and thereore o
energy in seeds and storage organs such as potato
cells. Starch is made as a temporary store in lea cells
when glucose is being made aster by photosynthesis
than it can be exported to other parts o the plant.
Glycogen is very similar to the branched orm o
starch, but there is more branching, making the
molecule more compact. Glycogen is made by
animals and also some ungi. It is stored in the
liver and some muscles in humans. Glycogen has
the same unction as starch in plants: it acts as
a store o energy in the orm o glucose, in cells
where large stores o dissolved glucose would
cause osmotic problems. With both starch and
Figure 6 Glycogen
lipids
Triglycerides are formed by condensation from three fatty
acids and one glycerol.
Lipids are a diverse group o carbon compounds that share the property
o being insoluble in water. Triglycerides are one o the principal groups
o lipid. Examples o triglycerides are the at in adipose tissue in humans
77
2 MOLECULAR BIOLOGY
and the oil in sunfower seeds. Fats are liquid at body temperature
(37 C) but solid at room temperature (20 C) whereas oils are liquid at
both body temperature and room temperature.
A triglyceride is made by combining three atty acids with one glycerol
(see gure 7) . Each o the atty acids is linked to the glycerol by a
condensation reaction, so three water molecules are produced. The
linkage ormed between each atty acid and the glycerol is an ester bond.
This type o bond is ormed when an acid reacts with the OH group in
an alcohol. In this case the reaction is between the COOH group on a
atty acid and an OH on the glycerol.
Triglycerides are used as energy stores. The energy rom them can be
released by aerobic cell respiration. Because they do not conduct heat
well, they are used as heat insulators, or example in the blubber o
Arctic marine mammals.
Glycerol Fatty acids H Triglyceride (fat)
H
H CO H HO C (CH2) n CH3 H C O C (CH2)n CH3
O
H CO H O Condensation
C O C (CH2)n CH3
H CO H HO C (CH2) n CH3 (water removed) H O
H
O C O C (CH2)n CH3
HO
HO C (CH2) n CH3 H
O Ester bond
3H2O
Figure 7 Formation of a triglyceride from glycerol and three fatty acids
enrgy storag
Lipids are more suitable for long term energy storage in humans than carbohydrates.
Lipids and carbohydrates are both used or energy greater because ats orm pure droplets in
storage in humans, but lipids are normally used cells with no water associated, whereas each
or long-term energy storage. The lipids that are gram o glycogen is associated with about two
used are ats. They are stored in specialized groups grams o water, so lipids are actually six times
o cells called adipose tissue. Adipose tissue is more ecient in the amount o energy that
located immediately beneath the skin and also can be stored per gram o body mass. This
around some organs including the kidneys. is important, because we have to carry our
There are several reasons or using lipids energy stores around with us wherever we go.
rather than carbohydrates or long-term It is even more important or animals such as
energy storage: birds and bats that fy.
The amount o energy released in cell Stored lipids have some secondary roles
respiration per gram o lipids is double that could not be perormed as well by
the amount released rom a gram o carbohydrates. Because lipids are poor
carbohydrates. The same amount o energy conductors o heat, they can be used as
stored as lipid rather than carbohydrate heat insulators. This is the reason or much
thereore adds hal as much to body mass. o our stored at being in sub-cutaneous
In act the mass advantage o lipids is even adipose tissue next to the skin. Because at
78
2.3 carbohydrates and liPids
is liquid at body temperature, it can also act can be broken down to glucose rapidly and
as a shock absorber. This is the reason or then transported easily by the blood to where
adipose tissue around the kidneys and some it is needed. Fats in adipose tissue cannot be
other organs. mobilized as rapidly. Glucose can be used either
in anaerobic or aerobic cell respiration whereas
Glycogen is the carbohydrate that is used ats and atty acids can only be used in aerobic
or energy storage, in the liver and in some respiration. The liver stores up to 1 50 grams
muscles. Although lipids are ideal or long- o glycogen and some muscles store up to
term storage o energy, glycogen is used or 2% glycogen by mass.
short-term storage. This is because glycogen
d- qu: Emperor penguins 0.4 0.5
8.0
During the Antarctic winter emale Emperor 6.8 14.3
penguins live and eed at sea, but males have 12 . 0 18.2
to stay on the ice to incubate the single egg the captive before
emale has laid. Throughout this time the males 0.4 0.8
eat no ood. Ater 1 6 weeks the eggs hatch
and the emales return. While the males are 7.7 captive after
incubating the eggs they stand in tightly packed
groups o about 3 , 0 0 0 birds. To investigate the 11.8 0.4
reasons or standing in groups, 1 0 male birds wild before
were taken rom a colony at Pointe Geologie in 6.9 14.4
Antarctica. They had already survived 4 weeks 17.3
without ood. They were kept or 1 4 more
weeks without ood in enced enclosures 2.2
where they could not orm groups. All other
conditions were kept the same as in the wild wild after
colony. The mean air temperature was 1 6 . 4 C .
The composition o the captive and the wild Key
birds bodies was measured beore and ater the water
1 4-week period o the experiment. The results lipid
in kilograms are shown in fgure 8. protein
other substances
a) Calculate the total mass loss or each [2]
group o birds.
i) wild Figure 8
ii) captive
b) Compare the changes in lipid content o the
captive birds with those o the birds living
ree in the colony. [2]
c) Besides being used as an energy source, state
another unction o lipid which might be
important or penguin survival. [1 ]
79
2 MOLECULAR BIOLOGY
Body mass index
Determination of body mass index by calculation or use
of a nomogram.
The body mass index, usually abbreviated to BMI, was developed
by a B elgian statistician, Adolphe Quetelet. Two measurements are
needed to calculate it: the mass o the person in kilograms and their
height in metres.
BMI is calculated using this ormula:
BMI = _mass in k_ilograms
(height in metres) 2
Units or BMI are kg m-2
BMI can also be ound using a type o chart called a nomogram. A
straight line between the height on the let hand scale and the mass
on the right hand scale intersects the BMI on the central scale. The
data based questions on page 81 include a BMI nomogram.
BMI is used to assess whether a persons body mass is at a healthy
level, or is too high or too low. Table 1 shows how this is done:
actvty bMi sttu
below 18.5 underweight
etmtng ody ft 18.524.9 normal weight
prcntg 25.029.9 overweight
To estimate body fat 30.0 or more obese
percentage, measure the
thickness of a skinfold in Table 1
millimetres using calipers in
these four places: In some parts o the world ood supplies are insufcient or are unevenly
distributed and many people as a result are underweight. In other parts
Front of upper arm o the world a likelier cause o being underweight is anorexia nervosa.
Back of upper arm This is a psychological condition that involves voluntary starvation and
Below scapula loss o body mass.
Side of waist
The measurements are Obesity is an increasing problem Measuring body mass. What was this
added and then analysis in some countries. Excessive ood persons body mass index if their height
tools available on the internet intake and insufcient exercise was 1.80 metres?
can be used to calculate cause an accumulation o at in
the estimate. adipose tissue. The amount o body
at can be estimated using skinold
Figure 9 Measuring body fat calipers (fgure 9) . Obesity increases
with skinfold callipers the risk o conditions such as
coronary heart disease and type 2
diabetes. It reduces lie expectancy
signifcantly and is increasing
the overall costs o health care in
countries where rates o obesity
are rising.
80
2.3 carbohydrates and liPids
d qu: Nomograms and BMI b) Suggest two ways in which the woman
Use fgure 1 1 to answer these questions.
1 a) State the body mass index o a man could reduce her body mass. [2]
who has a mass o 75 kg and a height 4. Outline the relationship between height
o 1 .45 metres. [1 ] and BMI or a fxed body mass. [1 ]
b) Deduce the body mass status o this man. [1 ]
2 a) State the body mass o the person standing body mass/kg height/cm
on the scales on the previous page. [1 ] 150
140 125
b) The person has a height o 1 .8 metres.
130
Deduce their body mass status. [1 ] 130
120 body mass index
3 a) A woman has a height o 1 50 cm and 110 135
140
a BMI o 40. Calculate the minimum 50 145
100
amount o body mass she must lose to 95
90 40
reach normal body mass status. Show
85
all o your working. [3]
80 150
75 30 155
70
65 160
60 20 165
55 170
50
45 175
180
40 185
10
35 190
195
30 200
205
25 210
Figure 10 Jogger Figure 11
Fatty acids
Fatty acids can be saturated, monounsaturated or
polyunsaturated.
The basic structure o atty acids was described in sub-topic 2.1 . There is
a chain o carbon atoms, with hydrogen atoms linked to them by single
covalent bonds. It is thereore a hydrocarbon chain. At one end o the
chain is the acid part o the molecule. This is a carboxyl group, which
can be represented as COOH.
The length o the hydrocarbon chain is variable but most o the atty acids
used by living organisms have between 1 4 and 20 carbon atoms. Another
variable eature is the bonding between the carbon atoms. In some atty
81
2 MOLECULAR BIOLOGY
O OH O OH O OH acids all o the carbon atoms are linked by single covalent bonds,
C C C but in other atty acids there are one or more positions in the chain
where carbon atoms are linked by double covalent bonds.
H CH H CH H CH
H CH H CH H CH I a carbon atom is linked to adjacent carbons in the chain by single
H CH H CH H CH bonds, it can also bond to two hydrogen atoms. I a carbon atom
H CH H CH H CH is linked by a double bond to an adjacent carbon in the chain,
H CH H CH H CH it can only bond to one hydrogen atom. A atty acid with single
H CH H CH H CH bonds between all o its carbon atoms thereore contains as much
H CH H CH H CH hydrogen as it possibly could and is called a saturated fatty acid.
H CH Fatty acids that have one or more double bonds are unsaturated
H CH CH CH because they contain less hydrogen than they could. I there is
H CH CH CH one double bond, the atty acid is monounsaturated and i it has
H CH H CH H CH more than one double bond it is polyunsaturated.
H CH CH H CH
H CH CH H CH Figure 1 2 shows one saturated atty acid, one monounsaturated
H CH H CH H CH and one polyunsaturated atty acid. It is not necessary to remember
H CH CH H CH names o specifc atty acids in IB B iology.
CH H CH
H H CH H unsatrated fatty acids
H CH
H Unsaturated fatty acids can be cis or trans isomers.
palmitic acid linolenic acid palmitoleic acid In unsaturated atty acids in living organisms, the hydrogen atoms
saturated are nearly always on the same side o the two carbon atoms that
polyunsaturated monounsaturated are double bonded these are called cis-atty acids. The alternative
is or the hydrogens to be on opposite sides called trans-atty
non-essential all cis cis acids. These two conormations are shown in fgure 1 4.
essential non-essential
In cis-atty acids, there is a bend in the hydrocarbon chain at the
omega 3 omega 7 double bond. This makes triglycerides containing cis-unsaturated
atty acids less good at packing together in regular arrays than
Figure 12 Examples of fatty acids saturated atty acids, so it lowers the melting point. Triglycerides
with cis-unsaturated atty acids are thereore usually liquid at room
temperature they are oils.
Trans-atty acids do not have a bend in the hydrocarbon chain at
the double bond, so they have a higher melting point and are solid
at room temperature. Trans-atty acids are produced artifcially by
partial hydrogenation o vegetable or fsh oils. This is done to produce
solid ats or use in margarine and some other processed oods.
HH H Figure 14 Fatty acid stereochemistry (a) trans (b) cis
CC CC
cis H
trans
Figure 13 Double bonds
in fatty acids
82
2.3 carbohydrates and liPids
Health risks of fats Figure 15 Triglycerides in olive oil
contain cis-unsaturated fatty acids
Scientifc evidence or health risks o trans-ats and
narrowed fatty plaque causing
saturated ats.
lumen of artery thickening of the artery lining
There have been many claims about the eects o dierent types o at
on human health. The main concern is coronary heart disease (CHD) .
In this disease the coronary arteries become partially blocked by atty
deposits, leading to blood clot ormation and heart attacks.
A positive correlation has been ound between saturated atty acid
intake and rates o C HD in many research programs. However, fnding
a correlation does not prove that saturated ats cause the disease. It
could be another actor correlated with saturated at intake, such as
low amounts o dietary fbre, that actually causes CHD.
There are populations that do not ft the correlation. The Maasai o
Kenya or example have a diet that is rich in meat, at, blood and
milk. They thereore have a high consumption o saturated ats,
yet CHD is almost unknown among the Maasai. Figure 1 7 shows
members o another Kenyan tribe that show this trend.
Diets rich in olive oil, which contains cis-monounsaturated atty acids,
are traditionally eaten in countries around the Mediterranean. The
populations o these countries typically have low rates o CHD and it
has been claimed that this is due to the intake o cis-monounsaturated
atty acids. However, genetic actors in these populations, or other
aspects o the diet such as the use o tomatoes in many dishes could
explain the CHD rates.
There is also a positive correlation between amounts o trans-at
consumed and rates o CHD. Other risk actors have been tested, to
see i they can account or the correlation, but none did. Trans-ats
thereore probably do cause CHD. In patients who had died rom CHD,
atty deposits in the diseased arteries have been ound to contain high
concentrations o trans-ats, which gives more evidence o a causal link.
layer of muscle outer coat of artery
and elastic bres
Figure 16 Artery showing fatty plaque
Figure 17 Samburu people of Northern Kenya. Like the Maasai, the Samburu have
a diet rich in animal products but rates of heart disease are extremely low
83
2 MOLECULAR BIOLOGY
evaluating th halth risks of foods
Evaluating claims: health claims made about lipids need to be assessed.
Many health claims about oods are made. In similar controlled experiments with humans. It
some cases the claim is that the ood has a health might be possible to select matched groups o
benet and in other cases it is that the ood is experimental subjects in terms o age, sex and
harmul. Many claims have been ound to be alse health, but unless identical twins were used they
when they are tested scientically. would be genetically dierent. It would also be
almost impossible to control other variables such
It is relatively easy to test claims about the eects as exercise and ew humans would be willing
o diet on health using laboratory animals. Large to eat a very strictly controlled diet or a long
numbers o genetically uniorm animals can be bred enough period.
and groups o them with the same age, sex and state
o health can be selected or use in experiments. Researchers into the health risks o ood must
Variables other than diet, such as temperature and thereore use a dierent approach. Evidence is
amount o exercise, can be controlled so that they obtained by epidemiological studies. These involve
do not infuence the results o the experiment. Diets nding a large cohort o people, measuring their
can be designed so that only one dietary actor varies ood intake and ollowing their health over a
and strong evidence can thus be obtained about the period o years. Statistical procedures can then
eect o this actor on the animal. be used to nd out whether actors in the diet
are associated with an increased requency o a
Results o animal experiments are oten particular disease. The analysis has to eliminate
interesting, but they do not tell us with certainty the eects o other actors that could be causing
what the health eects are on humans o a actor the disease.
in the diet. It would be very dicult to carry out
Nature of science question: using volunteers in experiments.
D uring the S econd World War, experiments humans, cannot synthesize ascorbic acid. During
were conducted both in England and in the US trial periods with various intakes o vitamin C,
using conscientious objectors to military service concentrations in blood plasma and urine were
as volunteers. The volunteers were willing to monitored. The guinea-pigs were then killed and
sacrice their health to help extend medical collagen in bone and skin was tested. The collagen
knowledge. A vitamin C trial in England involved in guinea-pigs with restricted vitamin C had less
20 volunteers. For six weeks they were all given cross-linking between the protein bres and
a diet containing 70 mg o vitamin C. Then, or thereore lower strength.
the next eight months, three volunteers were
kept on the diet with 70 mg, seven had their 1 Is it ethically acceptable or doctors or
dose reduced to 1 0 mg and ten were given no scientists to perorm experiments on
vitamin C. All o these ten volunteers developed volunteers, where there is a risk that the
scurvy. Three- centimetre cuts were made in health o the volunteers will be harmed?
their thighs, with the wounds closed up with
ve stitches. These wounds ailed to heal. There 2 Sometimes people are paid to participate in
was also bleeding rom hair ollicles and rom the medical experiments, such as drug trials. Is
gums. Some o the volunteers developed more this more or less acceptable than using unpaid
serious heart problems. The groups given 1 0 mg volunteers?
or 70 mg o vitamin C ared equally well and did
not develop scurvy. 3 Is it better to use animals or experiments or are
the ethical objections the same as with humans?
Experiments on requirements or vitamin C have
also been done using real guinea-pigs, which 4 Is it acceptable to kill animals, so that an
ironically are suitable because guinea-pigs, like experiment can be done?
84
2.3 carbohydrates and liPids
anlysis of dt on helth risks of lipids
Evaluation of evidence and the methods used to obtain the evidence for health
claims made about lipids.
An evaluation is defned in IB as an assessment o How widely spread is the data? This is shown
implications and limitations. Evidence or health by the spread o data points on a scattergraph
claims comes rom scientifc research. There are or the size o error bars on a bar chart. The
two questions to ask about this research: more widely spread the data, the less likely it
is that mean dierences are signifcant.
1 Implications do the results o the research
support the health claim strongly, moderately I statistical tests have been done on the data,
or not at all? do they show signifcant dierences?
2 Limitations were the research methods used The second question is answered by assessing the
rigorous, or are there uncertainties about methods used. The points below reer to surveys
the conclusions because o weaknesses in and slightly dierent questions should be asked to
methodology? assess controlled experiments.
The frst question is answered by analysing the How large was the sample size? In surveys it is
results o the research either experimental usually necessary to have thousands o people
results or results o a survey. Analysis is usually in a survey to get reliable results.
easiest i the results are presented as a graph or
other type o visual display. How even was the sample in sex, age, state o
health and lie style? The more even the sample,
Is there a correlation between intake o the the less other actors can aect the results.
lipid being investigated and rate o the disease
or the health beneft? This might be either a I the sample was uneven, were the results
positive or negative correlation. adjusted to eliminate the eects o other actors?
How large is the dierence between mean Were the measurements o lipid intake and
(average) rates o the disease with dierent disease rates reliable? Sometimes people in a
levels o lipid intake? Small dierences may survey do not report their intake accurately
not be signifcant. and diseases are sometimes misdiagnosed.
d- qu: Evaluating evidence from a health survey
The Nurses Health Survey is a highly respected Health Study. American Journal of Epidemiology,
survey into the health consequences o many 1 61 :672679. doi:1 0.1 093/aje/kwi085
actors. It began in 1 976 with 1 21 ,700 emale
nurses in the USA and Canada, who completed a To asse ss the eects o trans- ats on rates
lengthy questionnaire about their liestyle actors o CHD, the participants in the survey were
and medical history. Follow- up questionnaires divided into ive groups according to their
have been completed every two years since then. trans-at intake. Quintile 1 was the 20% o
participants with the lowest intake and quintile
Details o the methods used to assess diet and 5 was the 20% with the highest intake. The
diagnose coronary heart disease can be ound average intake o trans-ats or each quintile
by reading a research paper in the American was calculated, as a percentage o dietary
Journal o Epidemiology, which is reely available energy intake. The relative risk o CHD was
on the internet: Oh, K, Hu, FB, Manson, JE, ound or each quintile, with Quintile 1
S tamper, MJ and Willett, WC . ( 2 005 ) D ietary assigned a risk o 1 . The risk was adjusted or
Fat Intake and Risk o Coronary Heart Disease dierences between the quintiles in age, body
in Women: 2 0 Years o Follow-up o the Nurses mass index, smoking, alcohol intake, parental
85
2 MOLECULAR BIOLOGY
history o CHD, intake o other oods that relative risk of CHD 1.6
aect CHD rates and various other actors. 1.4
Figure 1 8 is a graph showing the percentage 1.2
o energy rom trans-ats or each o the ive 1.0
quintiles and the adjusted relative risk o 0.8
CHD. The eect o trans-at intake on relative 0.6
risk o CHD is statistically signiicant with a 0.4
conidence level o 99%. 0.2
1 Suggest reasons or using only emale nurses 0
1
in this survey. [3] 1.5 2.0 2.5 3.0
percentage of energy from trans-fats
2 State the trend shown in the graph. [1 ]
3 The mean age o nurses in the fve quintiles Data for graph
1.3 1.6 1.9
was not the same. Explain the reasons or % of energy from 1.0 1.08 1.29
t ra n s - fa t
adjusting the results to compensate or the 2.2 2.8
Relative risk of 1.19 1.33
eects o age dierences. [2] CHD
4 Calculate the chance, based on the statistical
tests, o the dierences in CHD risk being due Figure 18
to actors other than
trans-at intake. [2]
5 Discuss evidence rom the graph that other
actors were
having some eect on rates o CHD. [2]
data-base questions: Saturated fats and coronary heart disease
Populations E. Finland
ranked W. Finland
by % calories as Zutphen
saturated fat USA
Slavonia
Belgrade
Crevalcor
Zrenjanin
Dalmatia
Crete
Montegiorgio
Velika
Rome
Corfu
Ushibuka
Tanushimaru
% Calories as 22 19 19 18 14 12 10 10 9 9 9 9 8 7 3 3
saturated fat
Death CHD 992 351 420 574 214 288 248 152 86 9 150 80 290 144 66 88
rate/ All 543 1080 1078 1027 764 1248 1006
100,000 causes 1727 1318 1175 1088 1477 509 1241 1101 758
yr 1
Table 2 [5]
1 a) Plot a scattergraph o the data in table 2. [2]
b) Outline the trend shown by the scattergraph. [2]
2 Compare the results or: [2]
[4]
a) East and West Finland;
b) Crete and Montegiorgio.
3 Evaluate the evidence rom this survey or saturated ats as a cause o coronary heart disease.
86
2.4 Proteins
2.4 P
understnding applictions
Amino acids are linked together by Rubisco, insulin, immunoglobulins, rhodopsin,
condensation to orm polypeptides. collagen and spider silk as examples o the
range o protein unctions.
There are twenty diferent amino acids in
polypeptides synthesized on ribosomes. Denaturation o proteins by heat or deviation o
pH rom the optimum.
Amino acids can be linked together in any
sequence giving a huge range o possible Skills
polypeptides.
Draw molecular diagrams to show the ormation
The amino acid sequence o polypeptides is o a peptide bond.
coded or by genes.
Ntre of science
A protein may consist o a single polypeptide or
more than one polypeptide linked together. Patterns, trends and discrepancies: most but
not all organisms assemble polypeptides rom
The amino acid sequence determines the three- the same amino acids.
dimensional conormation o a protein.
Living organisms synthesize many diferent
proteins with a wide range o unctions.
Every individual has a unique proteome.
amino cids nd polypeptides
Amino acids are linked together by condensation to orm
polypeptides.
Polypeptides are chains of amino acids that are made by linking together
amino acids by condensation reactions. This happens on ribosomes by
a process called translation, which will be described in sub-topic 2.7.
Polypeptides are the main component of proteins and in many proteins
they are the only component. Some proteins contain one polypeptide
and other proteins contain two or more.
The condensation reaction involves the amine group (- NH2) of one amino
acid and the carboxyl group (- C OOH) of another. Water is eliminated, as
carboxyl amino peptide bond
group group
H H condensation H OH H O
H O H O (water removed) H
NCC 1 N C C N CCNCC
H OH H OH H OH
RR R R
amino acid amino acid
H2O
Figure 1 Condensation joins two amino acids with a peptide bond
87
2 MOLECULAR BIOLOGY
in all condensation reactions, and a new bond is ormed between the two
amino acids, called a peptide bond. A dipeptide is a molecule consisting
o two amino acids linked by a peptide bond. A polypeptide is a molecule
consisting o many amino acids linked by peptide bonds.
Polypeptides can contain any number o amino acids, though chains
o ewer than 20 amino acids are usually reerred to as oligopeptides
rather than polypeptides. Insulin is a small protein that contains two
polypeptides, one with 21 amino acids and the other with 30. The largest
polypeptide discovered so ar is titin, which is part o the structure o
muscle. In humans titin is a chain o 34,350 amino acids, but in mice it is
even longer with 35,21 3 amino acids.
Drawing peptide bonds
Draw molecular diagrams to show the ormation o a peptide bond.
To orm a dipeptide, two amino acids are linked by There is chain o atoms linked by single covalent
a condensation reaction between the amine group bonds orming the backbone o the oligopeptide,
o one amino acid and the carboxyl group o the with a repeating sequence o - N- C- C-
other. This is shown in fgure 1 . A hydrogen atom is linked by a single bond
The peptide bond is the same, whatever R to each nitrogen atom in the backbone and
group the amino acid carries. To test your skill an oxygen atom is linked by a double bond to
at showing how peptide bonds are ormed, try one o the two carbon atoms.
showing the ormation o a peptide bond between The amine (- NH2) and carboxyl (- COOH)
two o the amino acids in fgure 2. There are groups are used up in orming the peptide
sixteen possible dipeptides that can be produced
rom these our amino acids. bond and only remain at the ends o the
chain. These are called the amino and carboxyl
You could also try to draw an oligopeptide o our terminals o the chain.
amino acids, linked by three peptide bonds. I you The R groups o each amino acid remain and
do this correctly, you should see these eatures:
project outwards rom the backbone.
OH COOH H H
H CH H CH H CH
H2N C COOH H CH H2N C COOH H2N C COOH
H2N C COOH H
H H
serine H alanine glycine
glutamic acid
Figure 2 Some common amino acids
The diversity of amino acids
There are twenty diferent amino acids in polypeptides
synthesized on ribosomes.
The amino acids that are linked together by ribosomes to make
polypeptides all have some identical structural eatures: a carbon atom
in the centre o the molecule is bonded to an amine group, a carboxyl
group and a hydrogen atom. The carbon atom is also bonded to an R
group, which is dierent in each amino acid.
88
2.4 Proteins
Twenty dierent amino acids are used by ribosomes to make acvy
polypeptides. The amine groups and the carboxyl groups are used up in
orming the peptide bond, so it is the R groups o the amino acids that scuvy
give a polypeptide its character. The repertoire o R groups allows living
organisms to make and use an amazingly wide range o proteins. Some Ascorbic acid (vitamin C) is
o the dierences are shown in table 1 . It is not necessary to try to learn needed to convert proline
these specifc dierences but it is important to remember that because into hydroxyproline, so
o the dierences between their R groups, the twenty amino acids are ascorbic acid deciency
chemically very diverse. leads to abnormal collagen
production. From your
Some proteins contain amino acids that are not in the basic repertoire knowledge o the role o
o twenty. In most cases this is due to one o the twenty being modifed collagen, what efects do
ater a polypeptide has been synthesized. There is an example o you expect this to have?
modifcation o amino acids in collagen, a structural protein used to Test your predictions by
provide tensile strength in tendons, ligaments, skin and blood vessel researching the symptoms
walls. Collagen polypeptides made by ribosomes contain proline o ascorbic acid deciency
at many positions, but at some o these positions it is converted to (scurvy) .
hydroxyproline, which makes the collagen more stable.
Nine R groups are hydrophobic Eleven R groups are hydrophilic
with between zero and nine Four Seven R groups can become charged
carbon atoms
Three R Six R groups hydrophilic Four R groups act as Three R groups act as
groups contain do not contain R groups are an acid by giving up a a base by accepting a
polar but never proton and becoming proton and becoming
rings rings negatively charged
charged positively charged
Table 1 Classifcation o amino acids
amino cids nd origins
Patterns, trends and discrepancies: most but not all organisms assemble
polypeptides rom the same amino acids.
It is a remarkable act that most organisms make will always avour organisms that use them
proteins using the same 20 amino acids. In some and do not use other amino acids.
cases amino acids are modifed ater a polypeptide
has been synthesized, but the initial process o All lie has evolved rom a single ancestral
linking together amino acids on ribosomes with species, which used these 20 amino acids.
peptide bonds usually involves the same 20 Because o the way that polypeptides are
amino acids. made by ribosomes, it is difcult or any
organism to change the repertoire o amino
We can exclude the possibility that this trend is acids, either by removing existing ones or
due to chance. There must be one or more reasons adding new ones.
or it. Several hypotheses have been proposed:
Biology is a complicated science and discrepancies
These 20 amino acids were the ones produced are commonly encountered. Some species have
by chemical processes on Earth beore the origin been ound that use one o the three codons that
o lie, so all organisms used them and have normally signal the end o polypeptide synthesis
continued to use them. Other amino acids might (stop codons) to encode an extra non-standard
have been used, i they had been available. amino acid. For example, some species use UGA
to code or selenocysteine and some use UAG to
They are the ideal 20 amino acids or making code or pyrrolysine.
a wide range o proteins, so natural selection
89
2 MOLECULAR BIOLOGY
dt-bse questios: Commonality of amino acids
1 a) Discuss which o the three hypotheses or use o the same
20 amino acids by most organisms is supported by the
evidence. [3]
b) Suggest ways o testing one o the hypotheses. [2]
2 Cell walls o bacteria contain peptidoglycan, a complex carbon
compound that contains sugars and short chains o amino acids.
Some o these amino acids are dierent rom the usual repertoire
o 20. Also, some o them are right-handed orms o amino acids,
Figure 3 Kohoutek Comet 26 diferent whereas the 20 amino acids made into polypeptides are always the
amino acids were ound in an articial comet
produced by researchers at the Institut let-handed orms. Discuss whether this is a signifcant discrepancy
dAstrophysique Spatiale (CNRS/France) ,
which suggests that amino acids used by the that alsifes the theory that living organisms all make polypeptides
rst living organisms on Earth may have come
rom space using the same 20 amino acids. [5]
ativity Polypeptide diversity
clultig polypeptie iversity Amino acids can be linked together in any sequence
giving a huge range of possible polypeptides.
number number of possible
of mio mio i sequees Ribosomes link amino acids together one at a time, until a polypeptide is
ully ormed. The ribosome can make peptide bonds between any pair o
is 201 amino acids, so any sequence o amino acids is possible.
202 400
1 The number o possible amino acid sequences can be calculated starting
with dipeptides (table 2) . Both amino acids in a dipeptide can be any
2 o the twenty so there are twenty times twenty possible sequences
(202) . There are 20 20 20 possible tripeptide sequences (203) . For
3 8,000 a polypeptide o n amino acids there are 20n possible sequences.
4 The number o amino acids in a polypeptide can be anything rom 20 to
206 64 million tens o thousands. Taking one example, i a polypeptide has 400 amino
acids, there are 20400 possible amino acid sequences. This is a mind-
10.24 trillion bogglingly large number and some online calculators simply express it as
infnity. I we add all the possible sequences or other numbers o amino
Table 2 Calculate the missing values acids, the number is eectively infnite.
Figure 4 Lysozyme with nitrogen o amine Genes and polypeptides
groups shown blue, oxygen red and sulphur
yellow. The active site is the clet upper let The amino acid sequence of polypeptides is coded for
by genes.
90
The number o amino acid sequences that could be produced is
immense, but living organisms only actually produce a small raction o
these. Even so, a typical cell produces polypeptides with thousands o
dierent sequences and must store the inormation needed to do this.
The amino acid sequence o each polypeptide is stored in a coded orm
in the base sequence o a gene.
Some genes have other roles, but most genes in a cell store the amino
acid sequence o a polypeptide. They use the genetic code to do this.
Three bases o the gene are needed to code or each amino acid in
the polypeptide. In theory a polypeptide with 400 amino acids should
require a gene with a sequence o 1 ,200 bases. In practice genes are
2.4 Proteins
always longer, with extra base sequences at both ends and sometimes
also at certain points in the middle.
The base sequence that actually codes for a polypeptide is known to
molecular biologists as the open reading frame. One puzzle is that
open reading frames only occupy a small proportion of the total DNA
of a species.
Proteins and polypeptides Figure 5 Integrin embedded in a membrane
(grey) shown olded and inactive and open
A protein may consist o a single polypeptide or more than with binding sites inside and outside the cell
one polypeptide linked together. indicated (red and purple)
Some proteins are single polypeptides, but others are composed of two acvy
or more polypeptides linked together.
Molecular biologists are
Integrin is a membrane protein with two polypeptides, each of which investigating the numbers o
has a hydrophobic portion embedded in the membrane. Rather like the open reading rames in selected
blade and handle of a folding knife the two polypeptides can either be species or each o the major
adjacent to each other or can unfold and move apart when it is working. groups o living organism. It is
still ar rom certain how many
Collagen consists of three long polypeptides wound together to form genes in each species code or
a rope-like molecule. This structure has greater tensile strength than a polypeptide that the organism
the three polypeptides would if they were separate. The winding actually uses, but we can
allows a small amount of stretching, reducing the chance of the compare current best estimates:
molecule breaking. Drosophila melanogaster,
Hemoglobin consists of four polypeptides with associated non-polypeptide the ruit fy, has base
structures. The four parts of hemoglobin interact to transport oxygen sequences or about 14,000
more effectively to tissues that need it than if they were separate. polypeptides.
num f exmpl bckgud Caenorhabditis elegans, a
plyppd nematode worm with less
than a thousand cells, has
Enzyme in secretions such as nasal mucus and about 19,000.
1 lysozyme tears; it kills some bacteria by digesting the
Homo sapiens has base
peptidoglycan in their cell walls. sequences or about 23,000
dierent polypeptides.
2 integrin Membrane protein used to make connections
between structures inside and outside a cell. Arabidopsis thaliana, a
small plant widely used in
Structural protein in tendons, ligaments, skin research, has about 27,000.
3 collagen and blood vessel walls; it provides high tensile
Can you nd any species with
strength, with limited stretching. greater or lesser numbers o
open reading rames than these?
Transport protein in red blood cells; it binds
4 hemoglobin oxygen in the lungs and releases it in tissues with 91
a reduced oxygen concentration.
Table 3 Example o proteins with diferent numbers o polypeptides
Protein conformations
The amino acid sequence determines the three-dimensional
conormation o a protein.
The conformation of a protein is its three-dimensional structure. The
conformation is determined by the amino acid sequence of a protein
and its constituent polypeptides. Fibrous proteins such as collagen
2 MOLECULAR BIOLOGY
Figure 6 Lysozyme, showing how a polypeptide are elongated, usually with a repeating structure. Many proteins are
can be folded up to form a globular protein. globular, with an intricate shape that oten includes parts that are helical
Three sections that are wound to form a helix or sheet-like.
are shown red and a section that forms a sheet
is shown yellow. Other parts of the polypeptide Amino acids are added one by one, to orm a polypeptide. They are
including both of its ends are green always added in the same sequence to make a particular polypeptide. In
globular proteins the polypeptides gradually old up as they are made,
to develop the fnal conormation. This is stabilized by bonds between
the R groups o the amino acids that have been brought together by
the olding.
In globular proteins that are soluble in water, there are hydrophilic
R groups on the outside o the molecule and there are usually
hydrophobic groups on the inside. In globular membrane proteins there
are regions with hydrophobic R groups on the outside o the molecule,
which are attracted to the hydrophobic centre o the membrane.
In fbrous proteins the amino acid sequence prevents olding up and
ensures that the chain o amino acids remains in an elongated orm.
Denaturation of proteins
Denaturation of proteins by heat or pH extremes.
The three-dimensional conormation o proteins Extremes o pH, both acidic and alkaline, can
is stabilized by bonds or interactions between R cause denaturation. This is because charges on R
groups o amino acids within the molecule. Most groups are changed, breaking ionic bonds within
o these bonds and interactions are relatively the protein or causing new ionic bonds to orm.
weak and they can be disrupted or broken. This As with heat, the three-dimensional structure
results in a change to the conormation o the o the protein is altered and proteins that have
protein, which is called denaturation. been dissolved in water oten become insoluble.
There are exceptions: the contents o the stomach
A denatured protein does not normally return are normally acidic, with a pH as low as 1 .5, but
to its ormer structure the denaturation is this is the optimum pH or the protein-digesting
permanent. Soluble proteins oten become enzyme pepsin that works in the stomach.
insoluble and orm a precipitate. This is due to
the hydrophobic R groups in the centre o the
molecule becoming exposed to the water around
by the change in conormation.
Heat can cause denaturation because it causes Figure 7 When eggs are heated, proteins that were dissolved
vibrations within the molecule that can in both the white and the yolk are denatured. They become
break intermolecular bonds or interactions. insoluble so both yolk and white solidify
Proteins vary in their heat tolerance. Some
microorganisms that live in volcanic springs or in
hot water near geothermal vents have proteins
that are not denatured by temperatures o 80 C
or higher. The best known example is D NA
polymerase rom Thermus aquaticus, a prokaryote
that was discovered in hot springs in Yellowstone
National Park. It works best at 80 C and because
o this it is widely used in biotechnology.
Nevertheless, heat causes denaturation o most
proteins at much lower temperatures.
92
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