Questioning the cell theory using atypical examples, including striated muscle,
giant algae and aseptate fungal hyphae.
To test the cell theory you should look at the structure of as many living organisms as
you can, using a microscope. In each case you should ask the question, "Does the organism or tissue fit the trend stated in the cell theory by consisting of one or more cells?"
In humans they have an average length of about 30 mm, whereas other human cells are mostly less than 0.03 mm in length. Instead of having one nucleus they have many, sometimes as many as several hundred.
Three atypical examples are worth considering:
● Striated muscle is the type of tissue that we use to change the position of our body. The building blocks of this tissue are muscle fibres, which are similar in some ways to cells. They are surrounded by a membrane and are formed by division of pre-existing cells. They have their own genetic material and their own energy release system. However muscle fibres are far from typical. They are much larger than most animal cells.
● Fungi consist of narrow thread-like structures called hyphae. These hyphae are usually white in colour and have a fluffy appearance. They have a cell membrane and, outside it, a cell wall. In some types of fungi the hyphae are divided up into small cell-like sections by cross walls called septa. However, in aseptate fungi there are no septa. Each hypha is an uninterrupted tube-like structure with many nuclei spread along it.
● Algae are organisms that feed themselves by
photosynthesis and store their genes inside nuclei, but they are simpler in their structure and organization than plants. Many algae consist of one microscopic cell. There are vast numbers of these unicellular algae in the oceans and they form the basis of most marine food chains. Less common are some algae that grow to a much larger size, yet they still seem to be single cells. They are known as giant algae. Acetabularia is one example. It can grow to a length of as much as 100 mm, despite only having one nucleus. If a new organism with a length of 100 mm was discovered, we would certainly expect it to consist of many cells, not just one.
Multicellular organisms have properties that emerge from
the interaction of their cellular components.
Some unicellular organisms live together in colonies, for example a type of alga called Volvox aureus. Each colony consists of a ball made of a protein gel, with 500 or more identical cells attached to its surface. Although the cells are cooperating, they are not fused to form a single cell mass and so are not a single organism.
Organisms consisting of a single mass of cells, fused together, are multicellular. One of the most intensively researched multicellular organisms is a worm called Caenorhabditis elegans. The adult body is about one millimetre long and it is made up of exactly 959 cells. This might seem like a large number, but most multicellular organisms have far more cells. There are about ten million million cells in an adult human body and even more in organisms such as oak trees or whales.
Although very well known to biologists, Caenorhabditis elegans has no common name and lives unseen in decomposing organic matter. It feeds on the bacteria that cause decomposition. C. elegans has a mouth, pharynx, intestine and anus. It is hermaphrodite so has both male and female reproductive organs. Almost a third of the cells are neurons, or nerve cells. Most of these neurons are located at the front end of the worm in a structure that can be regarded as the animal's brain.
Although the brain in C. elegans coordinates responses to the worm's environment, it does not control how individual cells develop. The cells in this and other multicellular organisms can be regarded as cooperative groups, without any cells in the group acting as a leader or supervisor. It is remarkable how individual cells in a group can organize themselves and interact with each other to form a living organism with distinctive overall properties. The characteristics of the whole organism, including the fact that it is alive, are known as emergent properties.
Emergent properties arise from the interaction of the component parts of a complex structure. We sometimes sum this up with the phrase: the whole is greater than the sum of its parts. A simple example of an emergent property was described in a Chinese philosophical text written more than 2,500 years ago: "Pots are fashioned from clay. But it's the hollow that makes the pot work." So, in biology we can carry out research by studying component parts, but we must remember that some bigger things result from interactions between these components.
Differentiation involves the expression of some genes and not others in a cell's genome.
There are many different cell types in a multicellular organism but they all have the same set of genes. The 220 cell types in the human body have the same set of genes, despite large differences in their structure and activities. To take an example, rod cells in the retina of the eye produce a pigment that absorbs light. Without it, the rod cell would not be able to do its job of sensing light. A lens cell in the eye produces no pigments and is transparent. If it did contain pigments, less light would pass through the lens and our vision would be worse. While they are developing, both cell types contain the genes for making the pigment, but these genes are only used in the rod cell.
This is the usual situation - cells do not just have genes with the instructions that they need, they have genes needed to specialize in every possible way. There are approximately 25,000 genes in the human genome, and these genes are all present in a body cell. However, in most cell types less than half of the genes will ever be needed or used.
When a gene is being used in a cell, we say that the gene is being expressed. In simple terms, the gene is switched on and the information in it is used to make a protein or other gene product. The development of a cell involves switching on particular genes and expressing them, but not others. Cell differentiation happens because a different sequence of genes is expressed in different cell types. The control of gene expression is therefore the key to development.
An extreme example of differentiation involves a large family of genes in humans that carry the information for making receptors for odorants - smells. These genes are only expressed in cells in the skin inside the nose, called olfactory receptor cells. Each of these cells expresses just one of the genes and so makes one type of receptor to detect one type of odorant. This is how we can distinguish between so many different smells. Richard Axel and Linda Buck were given the Nobel Prize in 2004 for their work on this system.
The capacity of stem cells to divide and differentiate along different pathways is necessary in embryonic development. It also makes stem cells suitable for therapeutic uses.
A new animal life starts when a sperm fertilizes an egg cell to produce a zygote. An embryo is formed when the zygote divides to give two cells. This two-cell embryo divides again to produce a four-cell embryo, then eight, sixteen and so on. At these early stages in embryonic development the cells are capable of dividing many times to produce large amounts of tissue. They are also extremely versatile and can differentiate along different pathways into any of the cell types found in that particular animal. In the 19th century, the name stem cell was given to the zygote and the cells of the early embryo, meaning that all the tissues of the adult stem from them.
Stem cells have two key properties that have made them one of the most active areas of research in biology and medicine today.
● Stem cells can divide again and again to produce copious quantities of new cells. They are therefore useful for the growth of tissues or the replacement of cells that have been lost or damaged.
● Stem cells are not fully differentiated. They can differentiate in different ways, to produce different cell types.
Embryonic stem cells are therefore potentially very useful. They could be used to produce regenerated tissue, such as skin for people who have suffered burns. They could provide a means of healing diseases such as type 1 diabetes where a particular cell type has been lost or is malfunctioning. They might even be used in the future to grow whole replacement organs - hearts or kidneys, for example. These types of use are called therapeutic, because they provide therapies for diseases or other health problems.
There are also non-therapeutic uses for embryonic stem cells. One possibility is to use them to produce large quantities of striated muscle fibres, or meat, for human consumption. The beef burgers of the future may therefore be produced from stem cells, without the need to rear and slaughter cattle.
It is the early stage embryonic stem cells that are the most versatile. Gradually during embryo development the cells commit themselves to a pattern of differentiation. This involves a series of points at which a cell decides whether to develop along one pathway or another. Eventually each cell becomes committed to develop into one specific cell type. Once committed, a cell may still be able to divide, but all of these cells will differentiate in the same way and they are no longer stem cells.
Small numbers of cells remain as stem cells, however, and they are still present in the adult body. They are present in many human tissues, including bone marrow, skin and liver. They give some human tissues considerable powers of regeneration and repair. The stem cells in other tissues only allow limited repair - brain, kidney and heart for example.
Use of stem cells to treat Stargardt's disease and one other named condition.
There are a few current uses of stem cells to treat diseases, and a huge range of possible future uses, many of which are being actively researched. Two examples are given here: one involving embryonic stem cells and one using adult stem cells.
The full name of this disease is Stargardt's macular dystrophy. It is a genetic disease that develops in children between the ages of six and twelve. Most cases are due to a recessive mutation of a gene called ABCA4. This causes a membrane protein used for active transport in retina cells to malfunction. As a consequence, photoreceptive cells in the retina degenerate. These are the cells that detect light, so vision becomes progressively worse. The loss of vision can be severe enough for the person to be registered as blind.
Researchers have developed methods for making embryonic stem cells develop into retina cells. This was done initially with mouse cells, which were then injected into the eyes of mice that had a condition similar to Stargardt's disease. The injected cells were not rejected, did not develop into tumours or cause any other problems. The cells moved to the retina where they attached themselves and remained. Very encouragingly, they caused an improvement in the vision of the mice.
In November 2010, researchers in the United States got approval for trials in humans. A woman in her 50s with Stargardt's disease was treated by having 50,000 retina cells derived from embryonic stem cells injected into her eyes. Again the cells attached to the retina and remained there during the four-month trial. There was an improvement in her vision, and no harmful side effects.
Further trials with larger numbers of patients are needed, but after these initial trials at least, we can be optimistic about the development of treatments for Stargardt's disease using embryonic stem cells.
This disease is a type of cancer. All cancers start when mutations occur in genes that control cell division. For a cancer to develop, several specific mutations must occur in these genes in one cell. This is very unlikely to happen, but as there are huge numbers of cells in the body, the overall chance becomes much larger. More than a quarter of a million cases of leukemia are diagnosed each year globally and there are over 200,000 deaths from the disease.
Once the cancer-inducing mutations have occurred in a cell, it grows and divides repeatedly, producing more and more cells. Leukemia involves the production of abnormally large numbers of white blood cells. In most cancers, the cancer cells form a lump or tumour but this does not happen with leukemia. White blood cells are produced in the bone marrow, a soft tissue in the hollow centre of large bones such as the femur. They are then released into the blood, both in normal conditions and when excessive numbers are produced with leukemia. A normal adult white blood cell count is between 4,000 and 11,000 per mm^3 of blood. In a person with leukemia this number rises higher and higher. Counts above 30,000 per mm^3 suggest that a person may have leukemia. If there are more than 100,000 per mm^3 it is likely that the person has acute leukemia.
To cure leukemia, the cancer cells in the bone marrow that are producing excessive numbers of white blood cells must be destroyed. This can be done by treating the patient with chemicals that kill dividing cells. The procedure is known as chemotherapy. However, to remain healthy in the long term the patient must be able to produce the white blood cells needed to fight disease. Stem cells that can produce blood cells must be present, but they are killed by chemotherapy. The following procedure is therefore used:
● A large needle is inserted into a large bone, usually the pelvis, and fluid is removed from the bone marrow.
● Stem cells are extracted from this fluid and are stored by freezing them. They are adult stem cells and only have the potential for producing blood cells.
● A high dose of chemotherapy drugs is given to the patient, to kill all the cancer cells in the bone marrow. The bone marrow loses its ability to produce blood cells.
● The stem cells are then returned to the patient's body. They re-establish themselves in the bone marrow, multiply and start to produce red and white blood cells.
In many cases this procedure cures the leukemia completely.
Ethics of the therapeutic use of stem cells from specially created embryos, from the umbilical cord blood of a new-born baby and from an adult's own tissues.
Stem cells can be obtained from a variety of sources.
● Embryos can be deliberately created by fertilizing egg cells with sperm and allowing
the resulting zygote to develop for a few days until it has between four and sixteen cells. All of the cells are embryonic stem cells.
● Blood can be extracted from the umbilical cord of a new-born baby and stem cells obtained from it. The cells can be frozen and stored for possible use later in the baby's life.
● Stem cells can be obtained from some adult tissues such as bone marrow.
Stem cell research has been very controversial. Many ethical objections have been raised. There are most objections to the use of embryonic stem cells, because current techniques usually involve the death of the embryo when the stem cells are taken. The main question is whether an early stage embryo is as much a human individual as a new-born baby, in which case killing the embryo is undoubtedly unethical.
When does a human life begin? There are different views on this. Some consider that when the sperm fertilizes the egg, a human life has begun. Others say that early stage embryos have not yet developed human characteristics and cannot suffer pain, so they should be thought of simply as groups of stem cells. Some suggest that a human life truly begins when there is a heartbeat, or bone tissue or brain activity. These stages take place after a few weeks of development. Another view is that it is only when the embryo has developed into a fetus that is capable of surviving outside the uterus.
Some scientists argue that if embryos are specially created by in vitro fertilization (IVF) in order to obtain stem cells, no human that would otherwise have lived has been denied its chance of living. However, a counterargument is that it is unethical to create human lives solely for the purpose of obtaining stem cells. Also, IVF involves hormone treatment of women, with some associated risk, as well as an invasive surgical procedure for removal of eggs from the ovary. If women are paid for supplying eggs for IVF this could lead to the exploitation of vulnerable groups such as college students.
We must not forget ethical arguments in favour of the use of embryonic stem cells. They have the potential to allow methods of treatment for diseases and disabilities that are currently incurable, so they could greatly reduce the suffering of some individuals.
Prokaryotes have a simple cell structure without compartments.
All organisms can be divided into two groups according to their cell structure. Eukaryotes have a compartment within the cell that contains the chromosomes. It is called the nucleus and is bounded by a nuclear envelope consisting of a double layer of membrane. Prokaryotes do not have a nucleus.
Prokaryotes were the first organisms to evolve on Earth and they still have the simplest cell structure. They are mostly small in size and are found almost everywhere - in soil, in water, on our skin, in our intestines and even in pools of hot water in volcanic areas.
All cells have a cell membrane, but some cells, including prokaryotes, also have a cell wall outside the cell membrane. This is a much thicker and stronger structure than the membrane. It protects the cell, maintains its shape and prevents it from bursting. In prokaryotes the cell wall contains peptidoglycan. It is often referred to as being extracellular.
As no nucleus is present in a prokaryotic cell its interior is entirely filled with cytoplasm. The cytoplasm is not divided into compartments by membranes - it is one uninterrupted chamber. The structure is therefore simpler than in eukaryotic cells, though we must remember that it is still very complex in terms of the biochemicals that are present, including many enzymes.
Organelles are present in the cytoplasm of eukaryotic cells that are analogous to the organs of multi-cellular organisms in that they are distinct structures with specialized functions. Prokaryotes do not have cytoplasmic organelles apart from ribosomes. Their size, measured in Svedberg units (S) is 70S, which is smaller than those of eukaryotes.
Part of the cytoplasm appears lighter than the rest in many electron micrographs. This region contains the DNA of the cell, usually in the form of one circular DNA molecule. The DNA is not associated with proteins, which explains the lighter appearance compared with other parts of the cytoplasm that contain enzymes and ribosomes. This lighter area of the cell is called the nucleoid - meaning nucleus-like as it contains DNA but is not a true nucleus.
Membrane proteins are diverse in terms of structure,
position in the membrane and function.
Cell membranes have a wide range of functions. The primary function is to form a barrier through which ions and hydrophilic molecules cannot easily pass. This is carried out by the phospholipid bilayer. Almost
all other functions are carried out by proteins in the membrane.
Functions of membrane proteins
- Hormone binding sites (also called hormone receptors), for example the insulin
- Immobilized enzymes with the active site on the outside, for example in the small intestine.
- Cell adhesion to form tight junctions between groups of cells in tissues and organs.
- Cell-to-cell communication, for example receptors for neurotransmitters at synapses.
- Channels for passive transport to allow hydrophilic particles across by facilitated diffusion.
- Pumps for active transport which use ATP to move particles across the membrane.
Because of these varied functions, membrane proteins are very diverse in structure and in their position in the membrane. They can be divided into two groups.
● Integral proteins are hydrophobic on at least part of their surface and they are therefore embedded in the hydrocarbon chains in the centre of the membrane. Many integral proteins are transmembrane - they extend across the membrane, with hydrophilic parts projecting through the regions of phosphate heads on either side.
● Peripheral proteins are hydrophilic on their surface, so are not
embedded in the membrane. Most of them are attached to the surface
of integral proteins and this attachment is often reversible. Some have a single hydrocarbon chain attached to them which is inserted into
the membrane, anchoring the protein to the membrane surface.
Membranes all have an inner face and an outer face and membrane proteins are orientated so that they can carry out their function correctly. For example, pump proteins in the plasma membranes of root cells in plants are orientated so that they pick up potassium ions from the soil and pump them into the root cell.
The protein content of membranes is very variable, because the function of membranes varies. The more active a membrane, the higher is its protein content. Membranes in the myelin sheath around nerve fibres just act as insulators and have a protein content of only 18%.
The protein content of most plasma membranes on the outside of the cell is about 50%. The highest protein contents are in the membranes of chloroplasts and mitochondria, which are active in photosynthesis and
respiration. These have protein contents of about 75%.
The fluidity of membranes allows materials to be taken into cells by endocytosis or released by exocytosis.
A vesicle is a small sac of membrane with a droplet of fluid inside. Vesicles are spherical and are normally present in eukaryotic cells.
They are a very dynamic feature of cells. They are constructed, moved around and then deconstructed. This can happen because of the fluidity of membranes, which allows structures surrounded by a membrane to change shape and move.
To form a vesicle, a small region of a membrane is pulled from the rest of the membrane and is pinched off. Proteins in the membrane carry out this process, using energy from ATP.
Vesicles can be formed by pinching off a small piece of the plasma membrane of cells. The vesicle is formed on the inside of the plasma membrane. It contains material that was outside the cell, so this is a method of taking materials into the cell. It is called endocytosis. Figure 1 shows how the process occurs.
Vesicles taken in by endocytosis contain water and solutes from outside the cell but they also often contain larger molecules needed by the cell that cannot pass across the plasma membrane. For example, in the placenta, proteins from the mother's blood, including antibodies, are absorbed into the fetus by endocytosis. Some cells take in large undigested food particles by endocytosis. This happens in unicellular organisms including Amoeba and Paramecium. Some types of white blood cells take in pathogens including bacteria and viruses by endocytosis and then kill them, as part of the body's response to infection.
Evidence from Pasteur's experiments that spontaneous generation of cells and organisms does not now occur on Earth.
Louis Pasteur made a nutrient broth by boiling
water containing yeast and sugar. He showed that if this broth was kept in a sealed flask, it remained unchanged, and no fungi or other organisms appeared. He then passed air though a pad of cotton wool in a tube, to filter out microscopic particles from the air, including bacteria and the spores of fungi. If the pad of cotton wool was placed in broth in a sealed flask, within 36 hours, there were large number of microorganisms in the broth and mould grew over its surface.
The most famous of Pasteur's experiments
involved the use of swan-necked flasks. He placed samples of broth in flasks with long necks and then melted the glass of the necks and bent it into a variety of shapes, shown in figure 3.
Pasteur then boiled the broth in some of the flasks to kill any organisms present but left others unboiled as controls. Fungi and other organisms soon appeared in the unboiled flasks but not in the boiled ones, even after long periods of time. The broth in the flasks was in contact with air, which it had been suggested was needed for spontaneous generation, yet no spontaneous generation occurred. Pasteur snapped the necks of some of the flasks to leave a shorter vertical neck. Organisms were soon apparent in these flasks and decomposed the broth.
Pasteur published his results in 1860 and subsequently repeated them with other liquids
including urine and milk, with the same results. He
concluded that the swan necks prevented organisms from the air getting into the broth or other liquids and that no organisms appeared spontaneously. His
experiments convinced most biologists, both at the time of publication and since then.
Mitosis is division of the nucleus into two genetically 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.
Before mitosis can occur, all of the DNA 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 correlation between smoking and incidence of cancers.
A correlation in science is a relationship between two variable factors. The relationship between smoking and cancer is an example of a correlation. There are two types of correlation. With a positive correlation, when one factor increases the other one also increases; they also decrease together. With a negative correlation, when one factor increases the other decreases.
There is a positive correlation between cigarette smoking and the death rate due to cancer.
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 of the survey also show huge increases in the death
rate due to cancers of the mouth, pharynx, larynx and lung. This
is expected as smoke from cigarettes comes into contact with each
of these parts of the body, but there is also a positive correlation
between smoking and cancers of the esophagus, stomach, kidney, bladder, pancreas and cervix. Although the death rate due to other cancers is not significantly different in smokers and non-smokers, smokers are several times more likely to die from 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 different chemical substances. Twenty of these have been shown in experiments to cause tumours in the lungs of
laboratory animals or humans. There is evidence that at least forty other chemicals in cigarette smoke are carcinogenic. This leaves little doubt that smoking is a cause of cancer.
Life is based on carbon compounds including
carbohydrates, lipids, proteins and nucleic acids.
Living organisms use four main classes of carbon compound. They have
different properties and so can be used for different purposes.
Carbohydrates are characterized by their composition. They are composed of carbon, hydrogen and oxygen, with hydrogen and oxygen in the ratio of two hydrogen atoms to one oxygen, hence the name carbohydrate.
Lipids are a broad class of molecules that are insoluble in water, including steroids, waxes, fatty acids and triglycerides. In
common language, triglycerides are fats if they are solid at room temperature or oils if they are liquid at room temperature.
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).
Drawing molecular diagrams of glucose, ribose, a saturated fatty acid and a generalized amino acid.
There is no need to memorize the structure of many different molecules but a biologist should be able to draw diagrams of a few of the most important molecules.
Each atom in a molecule is represented using the
symbol of the element. For example a carbon
atom is represented with C and an oxygen atom
with O. Single covalent bonds are shown with a
line and double bonds with two lines.
Some chemical groups are shown with the
atoms together and bonds not indicated. Table 1 gives examples.
- The formula for ribose is C5H1 0O5
- The molecule is a fve-membered ring with a side chain.
- Four carbon atoms are in the ring and one forms the side chain.
- The carbon atoms can be numbered starting with number 1 on the right.
- The hydroxyl groups (OH) on carbon atoms 1 , 2 and 3 point up,
down and down respectively.
- The formula for glucose is C6H12O6
- The molecule is a six-membered ring with a side chain.
- Five carbon atoms are in the ring and one forms the side chain.
- The carbon atoms can be numbered starting with number 1 on the right.
- The hydroxyl groups (OH) on carbon atoms 1 , 2, 3 and 4 point down, down, up and down respectively, although in a form of glucose used by plants to make cellulose the hydroxyl group on carbon atom 1 points upwards.
Saturated fatty acids
- The carbon atoms form an unbranched chain.
- In saturated fatty acids they are bonded to each other by single bonds.
- The number of carbon atoms is most commonly between 1 4 and 20.
- At one end of the chain the carbon atom is part of a carboxyl group
- At the other end the carbon atom is bonded to three hydrogen atoms.
- All other carbon atoms are bonded to two hydrogen atoms.
- A carbon atom in the centre of the molecule is bonded to four
- an amine group, hence the term amino acid;
- a carboxyl group which makes the molecule an acid;
- a hydrogen atom;
- the R group, which is the variable part of amino acids.
Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.
Cohesion refers to the binding together of two molecules of the same
type, for 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 useful for water transport in plants. Water is sucked
through xylem vessels at low pressure. The method can only work if
the water molecules are not separated by the suction forces. Due to
hydrogen bonding this rarely happens and water can be pulled up to the
top of the tallest trees - over a hundred metres.
Hydrogen bonds can form between water and other polar molecules,
causing water to stick to them. This is called adhesion. This property is
useful in leaves, where water adheres to cellulose molecules in cell walls. If water evaporates from the cell walls and is lost from the leaf via the network of air spaces, adhesive forces cause water to be drawn out of the nearest xylem vessel. This keeps the walls moist so they can absorb carbon dioxide needed for photosynthesis.
Water has several thermal properties that are useful to living organisms:
- High specifc heat capacity. Hydrogen bonds restrict the motion of water molecules and increases in the temperature of water require hydrogen bonds to be broken. Energy is needed to do this. As a result, the amount of energy needed to raise the temperature of water is relatively large. To cool down, water must lose relatively large amounts
of energy. Water's temperature remains relatively stable in comparison to air or land, so it is a thermally stable habitat for aquatic organisms.
- High latent heat of vaporization. When a molecule evaporates
it separates from other molecules in a liquid and becomes a vapour
molecule. The heat needed to do this is
called the latent heat of vaporization. Evaporation therefore has a cooling effect. Considerable
amounts of heat are needed to evaporate water, because hydrogen
bonds have to be broken. This makes it a good evaporative coolant. Sweating is an example of the use of water as a coolant.
- High boiling point. The boiling point of a substance is the highest
temperature that it can reach in a liquid state. For the same reasons that
water has a high latent heat of vaporization, its boiling point is high. Water is therefore liquid over a broad range of temperatures - from 0'C
to 1 00'C. This is the temperature range found in most habitats on Earth.
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. If a nonpolar molecule is surrounded by water molecules, hydrogen bonds
form between the water molecules, but not between the nonpolar molecule
and the water molecules. If 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, if they are in contact with each other, more hydrogen bonds can form between water molecules.
This is not because they are water-fearing: 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 form larger and larger groups. The forces that cause nonpolar molecules to join together into groups in water are known as hydrophobic interactions.
Methods oftransport of glucose, amino acids, cholesterol, fats, oxygen and sodium chloride in blood in relation to theirsolubility in water.
Blood transports a wide variety of substances,
using several methods to avoid possible problems
and ensure that each substance is carried in large enough quantities for the body's needs.
Sodium chloride is an ionic compound that is
freely soluble in water, dissolving to form sodium ions (Na+) and chloride ions (Cl) , which are carried in blood plasma.
Amino acids have both negative and positive
charges. Because of this they are soluble in water but their solubility varies depending on the R group, some of which are hydrophilic while others are hydrophobic. All amino acids are soluble enough to be carried dissolved in blood plasma.
Glucose is a polar molecule. It is freely soluble in water and is carried dissolved in blood plasma.
Oxygen is a nonpolar molecule. Because of the small size of the molecule it dissolves in water but only sparingly and water becomes saturated with oxygen at relatively low concentrations. Also, as the temperature of water rises, the solubility of oxygen decreases, so blood plasma at 37'C can hold much less dissolved oxygen than water at 20'C or lower. The amount of oxygen that blood plasma can transport around the body is far too little to provide for aerobic cell respiration. This problem is overcome by the use of hemoglobin in red blood cells. Hemoglobin has binding sites for oxygen and greatly increases the capacity of theblood for oxygen transport.
Fats molecules are entirely nonpolar, are larger than oxygen and are insoluble in water. They are carried in blood inside lipoprotein complexes. These are groups of molecules with a single layer of phospholipid on the outside and fats inside. The hydrophilic phosphate heads of the phospholipids
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.
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
functions are very different. This is due to differences in the type of glucose used to make them and in the type of linkage between glucose molecules.
Glucose has five -OH groups, any of which
could be used in condensation reactions, but only three of them are actually used to link to make polysaccharides. The most common link is
between the -OH on carbon atom 1 and the -OH on carbon atom 4. The -OH on carbon atom 6 is used to form
side branches in some polysaccharides.
Glucose can have the -OH group on carbon atom 1 pointing either upwards or downwards. In alpha
glucose (alpha-glucose) the -OH group points downwards
but in beta glucose (beta-glucose) it points upwards. This small difference has major consequences for
polysaccharides made from glucose.
Cellulose is made by linking together beta-glucose molecules. Condensation reactions link carbon atom 1 to carbon atom 4 on the next -glucose. The -OH groups on carbon atom 1 and 4 point in opposite
directions: up on carbon 1 and down on carbon 4. To bring these -OH groups together and allow a condensation reaction to occur, each beta-glucose
added to the chain has to be positioned at 180' to the previous one. The glucose subunits in the chain are oriented alternately upwards and downwards.
The consequence of this is that the cellulose molecule is a straight chain, rather than curved.
Cellulose molecules are unbranched chains of
beta-glucose, allowing them to form bundles with hydrogen bonds linking the cellulose molecules. These bundles are called cellulose microfbrils.
They have very high tensile strength and are used as the basis of plant cell walls. The tensile strength of cellulose prevents plant cells from bursting, even when very high pressures have developed inside the cell due to entry of water by osmosis.
Starch is made by linking together alpha-glucose
molecules. As in cellulose, the links are made by condensation reactions between the -OH groups on
carbon atom 1 of one glucose and carbon atom 4 of the adjacent glucose. These -OH groups both point downwards, so all the glucose molecules in starch can be orientated in the same way. The
consequence of this is that the starch molecule is curved, rather than straight. There are two forms of starch. In amylose the chain of alpha-glucose molecules is unbranched and forms a helix. In amylopectin the chain is branched, so has a more globular shape.
Starch is only made by plant cells. Molecules of both types of starch are hydrophilic but they are too large to be soluble in water. They are therefore useful in cells where large amounts of 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 of glucose and therefore of energy in seeds and storage organs such as potato cells. Starch is made as a temporary store in leaf cells when glucose is being made faster by photosynthesis than it can be exported to other parts of the plant.
Glycogen is very similar to the branched form of
starch, but there is more branching, making the
molecule more compact. Glycogen is made by
animals and also some fungi. It is stored in the
liver and some muscles in humans. Glycogen has
the same function as starch in plants: it acts as
a store of energy in the form of glucose, in cells
where large stores of dissolved glucose would
cause osmotic problems. With both starch and
glycogen it is easy to add extra glucose molecules or remove them. This can be done at both ends of an unbranched molecule or at any of the ends in a branched molecule. Starch and glycogen molecules do not have a fixed size and the number of glucose molecules that they contain can be increased or decreased.
Scientifc evidence for health risks oftrans-fats and saturated fats.
There have been many claims about the effects of different types of fat on human health. The main concern is coronary heart disease (CHD) .
In this disease the coronary arteries become partially blocked by fatty
deposits, leading to blood clot formation and heart attacks.
A positive correlation has been found between saturated fatty acid intake and rates of CHD in many research programs. However, fnding
a correlation does not prove that saturated fats cause the disease. It could be another factor correlated with saturated fat intake, such as low amounts of dietary fbre, that actually causes CHD.
There are populations that do not fit the correlation. The Maasai of Kenya for example have a diet that is rich in meat, fat, blood and milk. They therefore have a high consumption of saturated fats,
yet CHD is almost unknown among the Maasai.
Diets rich in olive oil, which contains cis-monounsaturated fatty acids, are traditionally eaten in countries around the Mediterranean. The
populations of these countries typically have low rates of CHD and it has been claimed that this is due to the intake of cis-monounsaturated
fatty acids. However, genetic factors in these populations, or other aspects of the diet such as the use of tomatoes in many dishes could explain the CHD rates.
There is also a positive correlation between amounts of trans-fat consumed and rates of CHD. Other risk factors have been tested, to see if they can account for the correlation, but none did. Trans-fats
therefore probably do cause CHD. In patients who had died from CHD, fatty deposits in the diseased arteries have been found to contain high
concentrations of trans-fats, which gives more evidence of a causal link.
Living organisms synthesize many diferent proteins with
a wide range of functions.
Other groups of carbon compounds have important roles in the cell, but none can compare with the versatility of proteins. They can be compared to the worker bees that perform almost all the tasks in a hive. All of the
functions listed here are carried out by proteins.
- Catalysis - there are thousands of different enzymes to catalyse
specifc chemical reactions within the cell or outside it.
- Muscle contraction - actin and myosin together cause the
muscle contractions used in locomotion and transport around the body.
- Cytoskeletons - tubulin is the subunit of microtubules
that give animals cells their shape and pull on chromosomes during mitosis.
- Tensile strengthening - fbrous proteins give tensile strength needed in skin, tendons, ligaments and blood vessel walls.
- Blood clotting - plasma proteins act as clotting factors that cause
blood to turn from a liquid to a gel in wounds.
- Transport of nutrients and gases - proteins in blood help
transport oxygen, carbon dioxide, iron and lipids.
- Cell adhesion - membrane proteins cause adjacent animal cells to stick to each other within tissues.
- Membrane transport - membrane proteins are used for facilitated diffusion and active transport, and also or electron transport during cell respiration and photosynthesis.
- Hormones - some such as insulin, FSH and LH are proteins, but hormones are chemically very diverse.
- Receptors - binding sites in membranes and cytoplasm for hormones, neurotransmitters, tastes and smells, and also
receptors for light in the eye and in plants.
- Packing of DNA - histones are associated with DNA in eukaryotes and help chromosomes to condense during mitosis.
- Immunity - this is the most diverse group of proteins, as cells can make huge numbers of different antibodies.
There are many biotechnological uses for proteins including enzymes
for removing stains, monoclonal antibodies for pregnancy tests or insulin for treating diabetics. Pharmaceutical companies now produce many different proteins for treating diseases. These tend to be very
expensive, as it is still not easy to synthesize proteins artifcially. Increasingly, genetically modifed organisms are being used as microscopic protein factories.
Every individual has a unique proteome.
A proteome is all of the proteins produced by a cell, a tissue or an organism. By contrast, the genome is all of the genes of a cell, a tissue or
an organism. To find out how many different proteins are being produced, mixtures of proteins are extracted from a sample and are then separated by gel electrophoresis. To identify whether or not a particular protein is present, antibodies to the protein that have been linked to a fluorescent marker can be used. If the cell fluoresces, the protein is present.
Whereas the genome of an organism is fixed, the proteome is variable
because different cells in an organism make different proteins. Even in a single cell the proteins that are made vary over time depending on the cell's activities. The proteome therefore reveals what is actually happening in an organism, not what potentially could happen.
Within a species there are strong similarities in the proteome of all
individuals, but also differences. The proteome of each individual is unique, partly because of differences of activity but also because of small differences in the amino acid sequence of proteins. With the possible exception of identical twins, none of us have identical proteins, so each of us has a unique proteome. Even the proteome of identical twins can become different with age.
Temperature, pH and substrate concentration afect the rate of activity of enzymes.
Enzyme activity is afected by temperature in two ways
- In liquids, the particles are in continual random motion. When a liquid is heated, the particles in it are given more kinetic energy. Both enzyme and
substrate molecules therefore move around faster at higher temperatures and the chance of a substrate molecule colliding with the active site of the
enzyme is increased. Enzyme activity therefore increases.
- When enzymes are heated, bonds in the enzyme vibrate more and the chance of the bonds breaking is increased. When bonds in the enzyme break, the structure of the enzyme changes, including the
active site. This change is permanent and is called denaturation. When an enzyme molecule has been denatured, it is no longer able to catalyse reactions. As more and more enzyme molecules in a
solution become denatured, enzyme activity falls. Eventually it stops altogether, when the enzyme has been completely denatured. So, as temperature rises there are reasons for both increases and decreases in enzyme activity.
The pH scale is used to measure the acidity or alkalinity of a solution.
The lower the pH, the more acid or the less alkaline a solution is. Acidity is due to the presence of hydrogen ions, so the lower the pH, the higher the hydrogen ion concentration. The pH scale is logarithmic. This means that reducing the pH by one unit makes a solution ten times more acidic. A solution at pH 7 is neutral. A solution at pH 6 is slightly acidic; pH 5 is ten times more acidic than pH 6, pH 4 is one hundred times more acidic than pH 6, and so on.
Most enzymes have an optimum pH at which their activity is highest. If the pH is increased or decreased from the optimum, enzyme activity decreases and eventually stops altogether. When the hydrogen ion concentration is higher or lower than the level at
which the enzyme naturally works, the structure of the enzyme is altered, including the active site. Beyond a certain pH the structure
of the enzyme is irreversibly altered. This is another example of
Enzymes do not all have the same pH optimum - in fact, there is a wide range. This reflects the wide range of pH environments in
which enzymes work. For example, the protease secreted by Bacillus licheniformis has a pH optimum between 9 and 1 0. This bacterium
is cultured to produce its alkaline-tolerant protease for use in
biological laundry detergents, which are alkaline.
Immobilized enzymes are widely used in industry.
In 1897 the Buchner brothers, Hans and Eduard, showed that an extract of yeast, containing no yeast cells, would convert sucrose into alcohol. The door was opened to the use of enzymes to catalyse chemical processes outside living cells.
Louis Pasteur had claimed that fermentation of sugars to alcohol could only occur if living cells were present. This was part of the theory of vitalism, which stated that substances in animals and plants can only be made under the infuence of a "vital spirit" or "vital force". The artificial synthesis of urea had provided evidence against vitalism, but the Buchners' research provided a clearer falsification of the theory.
More than 500 enzymes now have commercial uses. Some enzymes are used in more than one type of industry.
The enzymes used in industry are usually immobilized. This is
attachment of the enzymes to another material or into aggregations, so that movement of the enzyme is restricted. There are many ways of doing this, including attaching the enzymes to a glass surface, trapping them in an alginate gel, or bonding them together to form enzyme aggregates of up to 0.1 mm diameter.
Enzyme immobilization has several advantages.
- The enzyme can easily be separated from the products of the reaction, stopping the reaction at the ideal time and preventing
contamination of the products.
- After being retrieved from the reaction mixture the enzyme may be recycled, giving useful cost savings, especially as many enzymes are very expensive.
- Immobilization increases the stability of enzymes to changes in temperature and pH, reducing the rate at which they are degraded and have to be replaced.
- Substrates can be exposed to higher enzyme concentrations than with dissolved enzymes, speeding up reaction rates.
Drawing simple diagrams of the structure of single nucleotides and of DNA and RNA, using circles, pentagons and rectangles to represent phosphates, pentoses and bases.
The structure of DNA and RNA molecules can be shown in diagrams using simple symbols for the subunits:
- circles for phosphates;
- pentagons for pentose sugar;
- rectangles for bases.
The base and the phosphate are linked to the pentose sugar. The base is linked to C1 - the carbon atom on the right hand side of the pentose sugar. The phosphate is linked to C5 - the carbon atom on the side chain on the upper left side of the pentose sugar.
To show the structure of RNA, draw a polymer of nucleotides, with a line to show the covalent bond linking the phosphate group of each nucleotide to the pentose in the next nucleotide. The phosphate is linked to C3 of the pentose - the carbon atom that is on the lower left.
If you have drawn the structure of RNA correctly, the two ends of the polymer will be different. They are referred to as the 3' and the 5' terminals.
- The phosphate of another nucleotide could be linked to the C3 atom of the 3' terminal.
- The pentose of another nucleotide could be linked to the phosphate of the 5' terminal.
To show the structure of DNA, draw a strand of nucleotides, as with RNA, then a second strand alongside the first. The second strand should be run in the opposite direction, so that at each end of the DNA molecule, one strand has a C3 terminal and the other a C5 terminal. The
two strands are linked by hydrogen bonds between the bases. Add letters or names to indicate the bases. Adenine (A) only pairs with thymine (T)
and cytosine (C) only pairs with guanine (G).
Use of Taq DNA polymerase to produce multiple copies of DNA rapidly by the polymerase chain reaction (PCR).
The polymerase chain reaction (PCR) is a technique used to make many copies of a selected
DNA sequence. Only a very small quantity of the DNA is needed at the start. The DNA is loaded into a PCR machine in which a cycle of steps repeatedly doubles the quantity of the selected DNA. This involves double-stranded DNA being separated into two single strands at one stage of
the cycle and single strands combining to form
double-stranded DNA at another stage.
The two strands in DNA are held together by hydrogen bonds. These are weak interactions,
but in a DNA molecule there are large numbers of them so they hold the two strands together
successfully at the temperatures normally encountered by most cells. If DNA is heated to a
high temperature, the hydrogen bonds eventually break and the two strands separate. If the DNA is then cooled hydrogen bonds can form, so the strands pair up again. This is called re-annealing.
The PCR machine separates DNA strands by heating
them to 95'C for fifteen seconds. It then cools the DNA quickly to 54'C. This would allow re-annealing of parent strands to form double-stranded DNA. However, a large excess of short sections of single-stranded DNA called primers is present. The primers bind rapidly to target sequences and as a large excess of primers is present, they prevent the
re-annealing of the parent strands. Copying of the single parent strands then starts from the primers.
The next stage in PCR is synthesis of double-
stranded DNA, using the single strands with primers as templates. The enzyme Taq DNA polymerase is used to do this. It was obtained from
a bacterium, Thermus aquaticus, found in hot springs, including those of Yellowstone National Park. The temperatures of these springs range from 50'C to
80'C. Enzymes in most organisms would rapidly
denature at such high temperatures, but those of
Thermus aquaticus, including its DNA polymerase, are adapted to be very heat-stable to resist denaturation.
Taq DNA polymerase is used because it can resist
the brief period at 95'C used to separate the DNA strands. It would work at the lower temperature of 54'C that is used to attach the primers, but
its optimum temperature is 72'C. The reaction mixture is therefore heated to this temperature for
the period when Taq DNA polymerase is working.
At this temperature it adds about 1 ,000 nucleotides per minute, a very rapid rate of DNA replication.
When enough time has elapsed for replication of the selected base sequence to be complete,
the next cycle is started by heating to 95'C. A cycle of PCR can be completed in less than two minutes. Thirty cycles, which amplify the DNA by a factor of a billion, take less than an hour.
With the help of Taq DNA polymerase, PCR allows the production of huge numbers of copies of a selected base sequence in a very short time.
Production of human insulin in bacteria as an example of the universality of the genetic code allowing gene transfer between species.
Diabetes in some individuals is due to destruction of cells in the pancreas that secrete the hormone insulin. It can be treated by injecting insulin into
the blood. Porcine and bovine insulin, extracted from the pancreases of pigs and cattle, have both been widely used. Porcine insulin has only one
difference in amino acid sequence from human
insulin and bovine insulin has three differences. Shark insulin, which has been used for treating diabetics in Japan, has seventeen differences.
Despite the differences in the amino acid sequence between animal and human insulin, they all bind to the human insulin receptor and cause lowering
of blood glucose concentration. However, some diabetics develop an allergy to animal insulins, so it is preferable to use human insulin. In 1982 human insulin became commercially available for the first time. It was produced using genetically
modified E. coli bacteria. Since then methods of production have been developed using yeast cells and more recently safflower plants.
Each of these species has been genetically modified by transferring the gene for making
human insulin to it. This is done in such a way that the gene is transcribed to produce mRNA and the mRNA is translated to produce harvestable quantities of insulin. The insulin produced has exactly the same amino acid sequence as if the gene was being transcribed and translated in human cells.
This may seem obvious, but it
depends on each tRNA with a
particular anticodon having the same amino acid attached
to it as in humans. In other words, E. coli, yeast and safflower (a prokaryote, a
fungus and a plant) all use the same genetic code as
humans (an animal) . It is fortunate for genetic engineers that all organisms, with very few exceptions, use the same genetic code as it makes gene transfer possible between widely differing species.
Use of anaerobic cell respiration in yeasts to produce ethanol and carbon dioxide in baking.
Yeast is a unicellular fungus that occurs naturally in habitats where glucose or other sugars are available, such as the surface of fruits. It can respire either aerobically or anaerobically. Anaerobic cell respiration in yeast is the basis for production of foods, drinks and renewable energy.
Bread is made by adding water to four, kneading the mixture to make dough and then baking it. Usually an ingredient is added to the dough to create bubbles of gas, so that the baked bread has a lighter texture. Yeast is often this ingredient. After kneading, the dough is kept warm to encourage the yeast to respire. Any oxygen in the dough is soon used up so the yeast carries out anaerobic cell respiration. The carbon dioxide produced by anaerobic cell respiration cannot escape from the dough and forms bubbles. The swelling of the dough due to the production of bubbles of carbon dioxide is called rising. Ethanol is also produced by anaerobic cell respiration, but it evaporates during baking.
Bioethanol is ethanol produced by living organisms, for use as
a renewable energy source. Although any plant matter can be utilized as a feed stock and various living organisms can be used to convert the plant matter into ethanol, most bioethanol is
produced from sugar cane and corn (maize), using yeast. Yeast
converts sugars into ethanol in large fermenters by anaerobic
respiration. Only sugars can be converted, so starch and cellulose must first be broken down into sugars. This is done using enzymes. The ethanol produced by the yeasts is purified by distillation and various methods are then used to remove water from it to improve its combustion. Most bioethanol is used as a fuel in vehicles, sometimes in a pure state and sometimes mixed with
Changes to the Earth's atmosphere, oceans and rock
deposition due to photosynthesis.
Prokaryotes were the first organisms to perform photosynthesis, starting
about 3,500 million years ago. They were joined millions of years later by algae and plants, which have been carrying out photosynthesis ever since.
One consequence of photosynthesis is the rise in the oxygen concentration of the atmosphere. This began about 2,400 million years ago (mya), rising to 2% by volume by 2,200 mya. This is known as the Great Oxidation Event.
At the same time the Earth experienced its first glaciation, presumably due to a reduction in the greenhouse effect. This could have been due to the rise in oxygenation causing a decrease in the concentration of methane in the atmosphere and photosynthesis causing a decrease in carbon dioxide concentration. Both methane and carbon dioxide are potent greenhouse gases.
The increase in oxygen concentrations in the oceans between 2,400 and 2,200 mya caused the oxidation of dissolved iron in the water, causing it to precipitate onto the sea bed. A distinctive rock formation was produced called the banded iron formation, with layers of iron oxide alternating with other minerals. The reasons for the banding are not yet fully understood. The banded iron formations are the most important iron ores, so it is thanks to photosynthesis in bacteria billions of years ago that we have abundant supplies of steel today.
The oxygen concentration of the atmosphere remained at about 2% from 2,200 mya until about 750-635 mya. There was then a significant rise to 20% or more. This corresponds with the period when many groups of multicellular organisms were evolving.
Temperature, light intensity and carbon dioxide concentration are possible limiting factors on the rate of photosynthesis.
The rate of photosynthesis in a plant can be affected by three
● light intensity;
● carbon dioxide concentration.
Each of these factors can limit the rate if they are below the optimal level. These three factors are therefore called limiting factors. According to the concept of limiting factors, under any combination of light intensity, temperature and carbon dioxide concentration, only one of the factors is actually limiting the rate of photosynthesis. This is the factor that is furthest from its optimum. If the factor is changed to make it closer to the optimum, the rate of photosynthesis increases, but changing the other factors will have no effect, as they are not the limiting factor.
Of course, as the limiting factor is moved closer to its optimum, while keeping the other factors constant, a point will be reached where this factor is no longer the one that is furthest from its optimum and another factor becomes the limiting factor. For example, at night, light intensity is presumably the limiting factor for photosynthesis. When
the sun rises and light intensity increases, temperature will usually take over as the limiting factor. As the temperature increases during the morning, carbon dioxide concentration might well become the
Energy losses between trophic levels restrict the length of food chains and the biomass of higher trophic levels.
Biomass is the total mass of a group of organisms. It consists of the cells and tissues of those organisms, including the carbohydrates and other carbon compounds that they contain. Because carbon compounds have chemical energy, biomass has energy. Ecologists can measure how much energy is
added per year by groups of organisms to their biomass. The results are calculated per square metre of the ecosystem so that different trophic levels
can be compared. When this is done, the same trend is always found:
the energy added to biomass by each successive trophic level is less. In secondary consumers, for example, the amount of energy is always less per year per square metre of ecosystem than in primary consumers.
The reason for this trend is loss of energy between trophic levels.
● Most of the energy in food that is digested and absorbed by organisms in a trophic level is released by them in respiration for use in cell activities. It is therefore lost as heat. The only energy available to organisms in the next trophic level is chemical energy in carbohydrates and other carbon compounds that have not been used up in cell respiration.
● The organisms in a trophic level are not usually entirely consumed by organisms in the next trophic level. For example, locusts
sometimes consume all the plants in an area but more usually only parts of some plants are eaten. Predators may not eat material from the bodies of their prey such as bones or hair. Energy in uneaten material passes to saprotrophs or detritivores rather than passing to organisms in the next trophic level.
● Not all parts of food ingested by the organisms in a trophic level are digested and absorbed. Some material is indigestible and is egested in feces. Energy in feces does not pass on along the food chain and
instead passes to saprotrophs or detritivores.
Because of these losses, only a small proportion of the energy in the biomass of organisms in one trophic level will ever become part of the biomass of organisms in the next trophic level. The figure of 10% is often quoted, but the level of energy loss between trophic levels is variable. As the losses occur at each stage in a food chain, there is less and
less energy available to each successive trophic level. After only a few
stages in a food chain the amount of energy remaining would not be
enough to support another trophic level. For this reason the number of
trophic levels in food chains is restricted.
Biomass, measured in grams, also diminishes along food chains, due
to loss of carbon dioxide and water from respiration and loss from the food chain of uneaten or undigested parts of organisms. The biomass of higher trophic levels is therefore usually smaller than that of lower
levels. There is generally a higher biomass of producers, the lowest
trophic level of all, than of any other trophic level.
Production of an annotated diagram of the digestive system
The part of the human body used for digestion
can be described in simple terms as a tube through which food passes from the mouth to the anus. The role of the digestive system is to break down the diverse mixture of large carbon compounds in food, to yield ions and smaller
compounds that can be absorbed. For proteins,
lipids and polysaccharides digestion involves
several stages that occur in different parts of
Digestion requires surfactants to break up lipid
droplets and enzymes to catalyse reactions.
Glandular cells in the lining of the stomach
and intestines produce some of the enzymes.
Surfactants and other enzymes are secreted
by accessory glands that have ducts leading
to the digestive system. Controlled, selective
absorption of the nutrients released by digestion
takes place in the small intestine and colon, but
some small molecules, notably alcohol, diffuse through the stomach lining before reaching the small intestine.
Mouth: Voluntary control of eating and swallowing. Mechanical digestion of food by chewing and mixing with saliva, which contains lubricants and enzymes that start starch digestion
Esophagus: Movement of food by peristalsis from the mouth to the stomach
Stomach: Churning and mixing with secreted water and acid which kills foreign bacteria and other pathogens in food, plus initial stages of protein digestion
Small intestine: Final stages of digestion of lipids, carbohydrates, proteins and nucleic acids, neutralizing stomach acid, plus absorption of nutrients
Pancreas: Secretion of lipase, amylase and protease
Liver: Secreation of surfactants in bile to break up lipid droplets
Gall Bladder: Storage and regulated release of bile
Large intestine: Re-absorption of water, further digestion especially of carbohydrates by symbiotic bacteria, plus formation and storage of feces
Processes occurring in the small intestine that result in the digestion of starch and transport of the products of digestion to the liver.
Starch digestion illustrates some important processes including catalysis, enzyme specificity and membrane permeability. Starch is a macromolecule, composed of many α-glucose monomers linked together in plants by condensation reactions. It is a major constituent of plant-based foods such as bread, potatoes and pasta. Starch molecules cannot pass through membranes so must be digested in the small intestine to allow absorption.
All of the reactions involved in the digestion of starch are exothermic, but without a catalyst they happen at very slow rates. There are two types of molecule in starch:
● amylose has unbranched chains of α-glucose linked by 1,4 bonds;
● amylopectin has chains of α-glucose linked
by 1,4 bonds, with some 1,6 bonds that make the molecule branched.
The enzyme that begins the digestion of both
forms of starch is amylase. Saliva contains
amylase but most starch digestion occurs in the
small intestine, catalysed by pancreatic amylase.
Any 1,4 bond in starch molecules can be broken
by this enzyme, as long as there is a chain of at
least four glucose monomers. Amylose is therefore digested into a mixture of two- and three-glucose fragments called maltose and maltotriose.
Because of the specificity of its active site, amylase
cannot break 1,6 bonds in amylopectin. Fragments
of the amylopectin molecule containing a
1,6 bond that amylase cannot digest are called
dextrins. Digestion of starch is completed by
three enzymes in the membranes of microvilli
on villus epithelium cells. Maltase, glucosidase
and dextrinase digest maltose, maltotriose and
dextrins into glucose.
Glucose is absorbed into villus epithelium cells
by co-transport with sodium ions. It then moves by facilitated diffusion into the fluid in interstitial spaces inside the villus. The dense network of capillaries close to the epithelium ensures that glucose only has to travel a short distance to enter the blood system. Capillary walls consist of a single layer of thin cells, with pores between adjacent cells, but these capillaries have larger
pores than usual, aiding the entry of glucose.
Blood carrying glucose and other products of
digestion flows though villus capillaries to venules in the sub-mucosa of the wall of the small intestine. The blood in these venules is carried via the hepatic portal vein to the liver, where excess glucose can be absorbed by liver cells and converted to glycogen for storage. Glycogen is similar in structure to amylopectin, but with more 1,6 bonds and therefore more extensive branching.
There is a separate circulation for the lungs.
There are valves in the veins and heart that ensure a one-way flow,
so blood circulates through arteries, capillaries and veins. Fish have a
single circulation. Blood is pumped at high pressure to their gills to be
oxygenated. After flowing through the gills the blood still has enough pressure to flow directly, but relatively slowly, to other organs of the
body and then back to the heart. In contrast, the lungs used by mammals for gas exchange are supplied with blood by a separate circulation.
Blood capillaries in lungs cannot withstand high pressures so blood is pumped to them at relatively low pressure. After passing through the capillaries of the lungs the pressure of the blood is low, so it must return to the heart to be pumped again before it goes to other organs. Humans therefore have two separate circulations:
● the pulmonary circulation, to and from the lungs
● the systemic circulation, to and from all other organs, including the heart muscles.
Figure 7 shows the double circulation in a simplified form. The pulmonary circulation receives deoxygenated blood that has returned from the systemic circulation, and the systemic circulation receives blood
that has been oxygenated by the pulmonary circulation. It is therefore essential that blood flowing to and from these two circulations is not mixed. The heart is therefore a double pump, delivering blood under different pressures separately to the two circulations.
Causes and consequences of occlusion of the
One of the commonest current health problems is atherosclerosis, the
development of fatty tissue called atheroma in the artery wall adjacent
to the endothelium. Low density lipoproteins (LDL) containing fats and
cholesterol accumulate and phagocytes are then attracted by signals
from endothelium cells and smooth muscle. The phagocytes engulf the
fats and cholesterol by endocytosis and grow very large. Smooth muscle cells migrate to form a tough cap over the atheroma. The artery wall bulges into the lumen narrowing it and thus impeding blood flow.
Small traces of atheroma are normally visible in children's arteries
by the age of ten, but do not affect health. In some older people atherosclerosis becomes much more advanced but often goes unnoticed until a major artery becomes so blocked that the tissues it
supplies become compromised.
Coronary occlusion is a narrowing of the arteries that supply blood
containing oxygen and nutrients to the heart muscle. Lack of oxygen
(anoxia) causes pain, known as angina, and impairs the muscle's
ability to contract, so the heart beats faster as it tries to maintain blood circulation with some of its muscle out of action. The fibrous cap covering atheromas sometimes ruptures, which stimulates the
formation of blood clots that can block arteries supplying blood to the
heart and cause acute heart problems.
The causes of atherosclerosis are not yet fully understood. Various factors have been shown to be associated with an increased risk of
atheroma but are not the sole causes of the condition:
● high blood concentrations of LDL (low density lipoprotein)
● chronic high blood glucose concentrations, due to overeating,
obesity or diabetes
● chronic high blood pressure due to smoking, stress or any
● consumption of trans fats, which damage the endothelium of the artery.
There are also some more recent theories that include microbes:
● infection of the artery wall with Chlamydia pneumoniae
● production of trimethylamine N-oxide (TMAO) by microbes in
Causes and consequences of lung cancer.
Lung cancer is the most common cancer in the
world, both in terms of the number of cases and
the number of deaths due to the disease. The specific causes of lung cancer are considered here.
● Smoking causes about 87% of cases. Tobacco
smoke contains many mutagenic chemicals. As
every cigarette carries a risk, the incidence of
lung cancer increases with the number smoked
per day and the number of years of smoking.
● Passive smoking causes about 3% of cases. This
happens when non-smokers inhale tobacco
smoke exhaled by smokers. The number of
cases will decline in countries where smoking is banned indoors and in public places.
● Air pollution probably causes about 5% of
lung cancers. The sources of air pollution that are most significant are diesel exhaust fumes,
nitrogen oxides from all vehicle exhaust fumes
and smoke from burning coal, wood or other
● Radon gas causes significant numbers of cases in some parts of the world. It is a radioactive gas that leaks out of certain rocks such as granite. It accumulates in badly ventilated
buildings and people then inhale it.
● Asbestos, silica and some other solids can cause lung cancer if dust or other particles of them are inhaled. This usually happens on construction
sites or in quarries, mines or factories.
The consequences of lung cancer are often very severe. Some of them can be used to help diagnose the disease: difficulties with breathing, persistent
coughing, coughing up blood, chest pain, loss of
appetite, weight loss and general fatigue. In many patients the tumour is already large when it is discovered and may also have metastasized, with secondary tumours in the
brain or elsewhere. Mortality rates are high.
Only 15% of patients with lung cancer survive for more than 5 years. If a tumour is discovered
early enough, all or part of the affected lung may
be removed surgically. This is usually combined
with one or more courses of chemotherapy. Other patients are treated with radiotherapy. The minority of patients who are cured of lung cancer, but have lost some of their lung tissue, are likely to continue to have pain, breathing difficulties, fatigue and also anxiety about the possible return of the disease.
In chemiosmosis protons diffuse through ATP synthase
to generate ATP.
The mechanism used to couple the release of energy by oxidation to ATP
production remained a mystery for many years, but is now known to be
chemiosmosis. This happens in the inner mitochondrion membrane. It
is called chemiosmosis because a chemical substance (H+) moves across
a membrane, down the concentration gradient. This releases the energy needed for the enzyme ATP synthase to make ATP. The main steps in the
process are as follows
●NADH + H+ supplies pairs of hydrogen atoms to the first carrier in the
chain, with the NAD+ returning to the matrix.
● The hydrogen atoms are split, to release two electrons, which pass from carrier to carrier in the chain.
● Energy is released as the electrons pass from carrier to carrier, and
three of these use this energy to transfer protons (H+) across the inner mitochondrial membrane, from the matrix to the intermembrane space.
● As electrons continue to flow along the chain and more and more
protons are pumped across the inner mitochondrial membrane, a
concentration gradient of protons builds up. This proton gradient is a store of potential energy.
● To allow electrons to continue to flow, they must be transferred to a terminal electron acceptor at the end of the chain. In aerobic
respiration this is oxygen, which briefly becomes •O2, but then combines with two H+ ions from the matrix to become water.
● Protons pass back from the intermembrane space to the matrix
through ATP synthase. As they are moving down the concentration
gradient, energy is released and this is used by ATP synthase to
Absorption of light by photosystems generates
Chlorophyll and the accessory pigments are grouped together in large light-harvesting arrays called photosystems. These photosystems are
located in the thylakoids, an arrangement of membranes inside the
chloroplast. There are two types of light-harvesting arrays, called
Photosystems I and II. In addition to light-harvesting arrays, the
photosystems have reaction centres.
Both types of photosystem contain many chlorophyll molecules, which absorb light energy and pass it to two special chlorophyll molecules in
the reaction centre of the photosystem. Like other chlorophylls, when
these special chlorophyll molecules absorb the energy from a photon of
light an electron within the molecule becomes excited. The chlorophyll
is then photoactivated. The chlorophylls at the reaction centre have
the special property of being able to donate excited electrons to an
Rather confusingly, Photosystem II, rather than Photosystem
I, is where the light-dependent reactions of photosynthesis begin. The electron acceptor for this photosystem is called plastoquinone. It collects two excited electrons from Photosystem II and then moves away to another position in the membrane. Plastoquinone is hydrophobic, so although it is not in a fixed position, it remains within the membrane.
Absorption of two photons of light causes the production
of one reduced plastoquinone, with one of the chlorophylls
at the reaction centre having lost two electrons to a plastoquinone molecule. Photosystem II can repeat this process, to produce a second reduced plastoquinone, so the chlorophyll at the reaction centre has lost four electrons and
two plastoquinone molecules have been reduced.
Annotation of a diagram to indicate the adaptations of a
chloroplast to its function.
There is a clear relationship between the structure of the chloroplast
and its function.
1. Chloroplasts absorb light. Pigment molecules, arranged
in photosystems in the thylakoid membranes, carry out light
absorption. The large area of thylakoid membranes ensures that
the chloroplast has a large light-absorbing capacity. The thylakoids
are often arranged in stacks called grana. Leaves that are brightly
illuminated typically have chloroplasts with deep grana, which allow more light to be absorbed.
2. Chloroplasts produce ATP by photophosphorylation. A proton gradient is needed. This develops between the inside and outside of the thylakoids. The volume of fluid inside the thylakoids is very small, so when protons are pumped in, a proton gradient
develops after relatively few photons of light have been absorbed,
allowing ATP synthesis to begin.
3. Chloroplasts carry out the many chemical reactions of the
Calvin cycle. The stroma is a compartment of the plant cell in which the enzymes needed for the Calvin cycle are kept together with their substrates and products. This concentration of enzymes and substrates
speeds up the whole Calvin cycle. ATP and reduced NADP, needed for
the Calvin cycle, are easily available because the thylakoids, where they are produced, are distributed throughout the stroma.
Plant hormones control growth in the shoot apex.
A hormone is a chemical message that is produced and released in one part of an organism to have an effect in another part of the organism. Auxins are hormones that have a broad range of functions including initiating the growth of roots, influencing the development of fruits and regulating leaf development. The most abundant auxin is indole-3-acetic acid (IAA). IAA has a role in the control of growth in the shoot apex. Among other effects, IAA promotes the elongation of cells in stems. IAA is synthesized in the apical meristem of the shoot and is transported down the stem to stimulate growth.
At very high concentrations, it can
Axillary buds are shoots that form at the junction, or node, of the stem and the base of a leaf. As the shoot apical meristem grows and forms leaves, regions of meristem are left behind at the node. Growth at these nodes is inhibited by auxin produced by the shoot apical meristem. This is termed apical dominance. The further distant a node is from the
shoot apical meristem, the lower the concentration of auxin and the less likely that growth in the axillary bud will be inhibited by auxin. In addition, cytokinins, hormones produced in the root, promote axillary bud growth. The relative ratio of cytokinins and auxins determine whether the axillary bud will develop. Gibberellins are another category
of hormones that contribute to stem elongation.
The switch to flowering is a response to the length of light and dark periods in many plants.
Long-day plants flower in summer when the nights have become short
Short-day plants flower in the autumn (fall), when the nights have become long enough.
Observations of flowering suggested that the trigger for this in some plants might be a particular day length, but experiments have shown
that it is the length of darkness that matters, not the length of daylight.
A pigment was discovered in leaves that plants use to measure the length of dark periods. It is called phytochrome and is unusual as it can switch between two forms, PR
● When PR absorbs red light of wavelength 660 nm it is converted into PFR
.● When PFR absorbs far-red light, of wavelength 730 nm, it is converted
to PR. This conversion is not of great importance as sunlight contains more light of wavelength 660 nm than 730 nm, so in normal sunlight phytochrome is rapidly converted to PFR
.● However, PR is more stable than PFR, so in darkness PFR very gradually changes into PR.
Further experiments have shown that PFR is the active form of phytochrome and that receptor proteins are present in the cytoplasm to which PFR but not PR
● In long-day plants, large enough amounts of PFR remain at the end of short nights to bind to the receptor, which then promotes transcription of genes needed for flowering.
● In short-day plants, the receptor inhibits the transcription of the
genes needed for flowering when PFR binds to it. However, at the end of long nights, very little PFR remains, so the inhibition fails and the
Antigens on the surface of red blood cells stimulate antibody production in a person with a different blood group.
Blood groups are based on the presence or absence of certain types of antigens on the surface of red blood cells. Knowledge of this is important in the medical procedure called transfusion where a patient is given blood from a donor. The ABO blood group and the Rhesus (Rh) blood group are the two most important antigen systems in blood transfusions as mismatches between donor and recipient can lead to an immune response.
In figure 3, the differences between the three A, B and O phenotypes are displayed. All three alleles involve a basic antigen sequence called antigen H.
In blood type A and B, this antigen H is modified by the addition of an additional molecule. If the additional molecule is galactose, antigen B results. If the additional molecule is N-acetylgalactosamine, antigen A results. Blood type AB involves the presence of both types of antigens.
If a recipient is given a transfusion involving the wrong type of blood, the result is an immune response called agglutination followed by hemolysis where red blood cells are destroyed and blood may coagulate in the vessels.
Blood typing involves mixing samples of blood with antibodies. Figure 5 shows the result of a blood group test showing reactions between blood types (rows) and antibody serums (columns). The first column shows the blood's appearance prior to the tests. There are four human blood types: A, B, AB and O. Type A blood has type A antigens (surface proteins) on its blood cells. Type B blood has type B antigens. Mixing type A blood with anti-A+B serum causes an agglutination reaction, producing dense red dots that are different from the control in the first column. Type B blood undergoes the same reaction with anti-B serum and anti A+B serum. AB blood agglutinates in all three anti-serums. Type O blood has neither the A or B antigen, so it does not react to the serums.