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Biology Exam Review

Key Concepts:

Terms in this set (355)

Calculation of the magnification of drawings and the actual size of structures shown in drawings or micrographs.

When we look down a microscope the structures
that we see appear larger than they actually are. The microscope is magnifying them. Most microscopes allow us to magnify specimens by
two or three different factors. This is done by rotating the turret to switch from one objective lens to another. A typical school microscope has three levels of magnification:
● × 40 (low power)
● × 100 (medium power)
● × 400 (high power)

If we take a photo down a microscope, we can magnify the image even more. A photo taken down a microscope is called a micrograph. There are many micrographs in this book, including electron micrographs taken using an electron microscope.

When we draw a specimen, we can make the drawing larger or smaller, so the magnification of the drawing isn't necessarily the same as the magnification of the microscope.

To find the magnification of a micrograph or a drawing we need to know two things: the size of the image (in the drawing or the micrograph) and the actual size of the specimen. This formula is used for the calculation:

magnification = size of image/actual size of specimen

If we know the size of the image and the magnification, we can calculate the actual size of a specimen.

It is very important when using this formula to make sure that the units for the size of the image and actual size of the specimen are the same. They could both be millimetres (mm) or micrometres (μm) but they must not be different or the calculation will be wrong. Millimetres can be converted to micrometres by multiplying by one thousand. Micrometres can be converted to millimetres by dividing by one thousand.

Scale bars are sometimes put on micrographs or drawings, or just alongside them. These are straight lines, with the actual size that the scale bar represents. For example, if there was a 10 mm long scale bar on a micrograph with a magnification of ×10,000 the scale bar would have a label of 1 μm.
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.

Stargardt's disease
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.

Leukemia
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.
Electron microscopes have a much higher resolution than light microscopes.

If we look at a tree with unaided eyes we can see its individual leaves, but we cannot see the cells within its leaves. The unaided eye can see things with a size of 0.1 mm as separate objects, but no smaller. To see the cells within the leaf we need to use a light microscope. This allows us to see things with a size of down to about 0.2 μm as separate objects, so cells can become individually visible - they can be distinguished.

Making the separate parts of an object distinguishable by eye is called resolution.

The maximum resolution of a light microscope is 0.2 μm, which is 200 nanometres (nm). However powerful the lenses of a light microscope are, the resolution cannot be higher than this because it is limited by the wavelength of light (400-700 nm). If we try to resolve smaller objects by making lenses with greater magnification, we find that it is impossible to focus them properly and get a blurred image. This is why the maximum magnification with light microscopes is usually × 400.

Beams of electrons have a much shorter wavelength, so electron microscopes have a much higher resolution. The resolution of modern electron microscopes is 0.001 μm or 1 nm. Electron microscopes therefore have a resolution that is 200 times greater than light microscopes. This is why light microscopes reveal the structure of cells, but electron microscopes reveal the ultrastructure. It explains why light microscopes were needed to see bacteria with a size of 1 micrometre, but viruses with a diameter of 0.1 micrometres could not be seen until electron microscopes had been invented.
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.
Analysis of evidence from electron microscopy that led to the proposal of the Davson-Danielli model.

The Davson-Danielli model of membrane structure was accepted by most cell biologists for about 30 years. Results of many experiments fitted the model including X-ray diffraction studies and electron microscopy.

In the 1950s and 60s some experimental evidence
accumulated that did not fit with the Davson-Danielli model:

● Freeze-etched electron micrographs. This technique involves rapid freezing of cells and then fracturing them. The fracture occurs along lines of weakness, including the centre of membranes. Globular structures scattered through freeze-etched images of the centre of membranes were interpreted as transmembrane proteins.
● Structure of membrane proteins. Improvements in biochemical techniques
allowed proteins to be extracted from membranes. They were found to be very
varied in size and globular in shape so were unlike the type of structural protein that would form continuous layers on the periphery of the membrane. Also the proteins were hydrophobic on at least part of their surface so they would be attracted to the hydrocarbon tails of the phospholipids in the
centre of the membrane.
● Fluorescent antibody tagging. Red or green fluorescent markers were attached to
antibodies that bind to membrane proteins. The membrane proteins of some cells were tagged with red markers and other cells with green markers. The cells were fused together. Within 40 minutes the red and green markers were mixed throughout the membrane of the fused cell. This showed that membrane proteins are free to move within the membrane rather than being fixed in a peripheral layer.

Taken together, this experimental evidence
falsified the Davson-Danielli model. A replacement was needed that fitted the evidence and the model that became widely accepted was the Singer-Nicolson fluid mosaic model. It has been the leading model for over fifty years but it would be unwise to assume that it will never be superseded. There are already some suggested modifications of the model.

An important maxim for scientists is "Think it possible that you might be mistaken." Advances in science happen because scientists reject
dogma and instead search continually for better
understanding.
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
receptor.
- 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.
Particles move across membranes by simple diffusion,
facilitated diffusion, osmosis and active transport.

Osmosis is one of the four methods of moving particles across membranes.

Water is able to move in and out of most cells freely. Sometimes the number of water molecules moving in and out is the same and there is no net movement, but at other times more molecules move in one direction or the other. This net movement is osmosis.

Osmosis is due to differences in the concentration of
substances dissolved in water (solutes). Substances
dissolve by forming intermolecular bonds with water molecules. These bonds restrict the movement of the water molecules. Regions with a higher solute concentration
therefore have a lower concentration of water molecules free to move
than regions with a lower solute concentration. Because of this there
is a net movement of water from regions of lower solute concentration to regions with higher solute concentration. This movement is passive
because no energy has to be expended directly to make it occur.

Osmosis can happen in all cells because water molecules, despite being hydrophilic, are small enough to pass though the phospholipid bilayer. Some cells have water channels called aquaporins, which greatly increase membrane permeability to water. Examples are kidney cells that reabsorb water and root hair cells that absorb water from the soil.

At its narrowest point, the channel in an aquaporin is only slightly wider than water molecules, which therefore pass through in single file. Positive charges at this point in the channel prevent protons (H+) from passing through.
Structure and function of sodium-potassium pumps for active transport.

An axon is part of a neuron (nerve cell) and consists of a tubular membrane with cytoplasm inside. Axons can be as narrow as one micrometre in diameter, but as long as one metre. Their function is to convey messages rapidly from one part of the body to another in an electrical form called a nerve impulse.

A nerve impulse involves rapid movements of sodium and then potassium ions across the axon membrane. These movements occur by facilitated diffusion through sodium and potassium channels. They occur because of concentration gradients between the inside and outside of the axon. The concentration gradients are built up by active transport, carried out by a sodium-potassium pump protein.

The sodium-potassium pump follows a repeating cycle of steps that result in three sodium ions being pumped out of the axon and two potassium ions being pumped in. Each time the pump goes round this cycle it uses one ATP. The cycle consists of these steps:
1. The interior of the pump is open to the inside
of the axon; three sodium ions enter the pump and attach to their binding sites.
2. ATP transfers a phosphate group from itself to the pump; this causes the pump to change shape and the interior is then closed.
3. The interior of the pump opens to the outside of the axon and the three sodium
ions are released.
4. Two potassium ions from outside can then
enter and attach to their binding sites.
5. Binding of potassium causes release of the
phosphate group; this causes the pump to
change shape again so that it is again only
open to the inside of the axon.
6. The interior of the pump opens to the inside of the axon and the two potassium ions are released; sodium ions can then enter and bind to the pump again.
Structure and function of sodium-potassium pumps for active transport and potassium channels for facilitated diffusion in axons.

A nerve impulse involves rapid movements of
sodium and then potassium ions across the axon membrane. These movements occur by facilitated diffusion through sodium and potassium channels. Potassium channels will be described here as a special example of facilitated diffusion. Each potassium channel consists of four protein
subunits with a narrow pore between them that
allows potassium ions to pass in either direction.
The pore is 0.3 nm wide at its narrowest.

Potassium ions are slightly smaller than 0.3 nm, but when they dissolve they become bonded to a shell of water molecules that makes them too large to pass through the pore. To pass through, the bonds between the potassium ion and the surrounding water molecules are broken and bonds form temporarily between
the ion and a series of amino acids in the
narrowest part of the pore. After the potassium ion has passed through this part of the pore,it can again become associated with a shell of water molecules.

Other positively charged ions that we might expect to pass through the pore are either too large to fit
through or are too small to form bonds with the
amino acids in the narrowest part of the pore, so they cannot shed their shell of water molecules. This explains the specificity of the pump.

Potassium channels in axons are voltage gated.
Voltages across membranes are due to an imbalance of positive and negative charges across the membrane. If an axon has relatively more positive charges outside than inside, potassium channels are closed. At one stage during a nerve impulse there are relatively more positive charges inside. This causes potassium channels to open, allowing potassium ions to diffuse through. However, the channel rapidly closes again. This seems to be due to an extra globular protein subunit or ball, attached by a flexible chain of amino acids. The ball can it inside the open pore, which it does within milliseconds of the pore opening. The ball remains in place until the potassium channel returns to its original closed state.
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.

In a solution with higher osmolarity ( a hypertonic
solution), water leaves the cells by osmosis so
their cytoplasm shrinks in volume. The area
of plasma membrane does not change, so it
develops indentations, which are sometimes called crenellations. In a solution with lower osmolarity (hypotonic), the cells take in water by osmosis and swell up. They may eventually burst, leaving
ruptured plasma membranes called red cell ghosts.

Both hypertonic and hypotonic solutions therefore damage human cells, but in a solution with same
osmolarity as the cells (isotonic), water molecules enter and leave the cells at the same rate so they
remain healthy. It is therefore important for
any human tissues and organs to be bathed in
an isotonic solution during medical procedures. Usually an isotonic sodium chloride solution is used, which is called normal saline. It has an osmolarity of about 300 mOsm (milliOsmoles).

Normal saline is used in many medical procedures. It can be:
● safely introduced to a patient's blood system
via an intravenous drip.
● used to rinse wounds and skin abrasions.
● used to keep areas of damaged skin moistened
prior to skin grafts.
● used as the basis for eye drops.
● frozen to the consistency of slush for packing hearts, kidneys and other donor organs that have to be transported to the hospital where the transplant operation is to be done.
Cells can only be formed by division of pre-existing cells.

Since the 1880s 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 existing cell divided in two. Before that all of the genetic material in the nucleus was copied so that both cells formed by cell division had a nucleus with a full complement of genes. We can trace the origin of cells in the body back to the first cell - the zygote that was the start of our lives, produced by the fusion of a sperm and an egg.

Sperm and egg cells were produced by cell division in our parents. We can trace the origins of all cells in our parents' bodies back to the zygote
from which they developed, and then continue this process over the generations of our human ancestors. If we accept that humans evolved from pre-existing ancestral species, we can trace the origins of cells back through hundreds of millions of years to the earliest cells on Earth. There is therefore a continuity of life from its origins on Earth to the cells in our bodies today.

In 2010 there were reports that biologists had created the rst artificial cell, but this cell was not entirely new. The base sequence of the DNA of a bacterium (Mycoplasma mycoides) was synthesized artificially, with a few deliberate changes. This DNA was transferred to pre-existing cells of a different type of bacterium (Mycoplasma capricolum), which was effectively converted into Mycoplasma mycoides. This process was therefore an extreme form of genetic modification and the creation of entirely new cells remains an insuperable challenge at the moment.
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.
The origin of eukaryotic cells can be explained by the endosymbiotic theory.

The theory of endosymbiosis helps to explain the evolution of
eukaryotic cells. It states that mitochondria were once free-living prokaryotic organisms that had developed the process of aerobic cell respiration. Larger prokaryotes that could only respire anaerobically took them in by endocytosis. Instead of killing and digesting the smaller prokaryotes they allowed them to continue to live in their cytoplasm. As long as the smaller prokaryotes grew and divided as fast as the larger ones, they could persist indefinitely inside the larger cells. According to the theory of endosymbiosis they have persisted over hundreds of millions of years of evolution to become the mitochondria inside eukaryotic cells today.

The larger prokaryotes and the smaller aerobically respiring ones were in a symbiotic relationship in which both of them beneted. This is known as a mutualistic relationship. The smaller cell would have been supplied with food by the larger one. The smaller cell would have carried out aerobic respiration to supply energy efficiently to the larger cell. Natural selection therefore favoured cells that had developed this endosymbiotic relationship.

The endosymbiotic theory also explains the origin of chloroplasts. If 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 of photosynthetic eukaryotes. Again, both of the organisms in the endosymbiotic relationship would have benefited.

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.
Cytokinesis occurs after mitosis and is different in plant and animal cells.

Cells can divide after mitosis when two genetically identical nuclei are present in a cell. The process of cell division is called cytokinesis. It usually begins before mitosis has actually been completed and it happens in a different way in plant and animal cells.

In animal cells the plasma membrane is pulled inwards around the equator of the cell to form a cleavage furrow. This is accomplished using a ring of 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 furrow reaches the centre, the cell is pinched apart into two daughter cells.

In plant cells vesicles are moved to the equator where they fuse to form tubular structures across the equator. With the fusion of more vesicles these tubular structures merge to form two layers of membrane across the whole of the equator, which develop into the plasma membranes of the two daughter cells and are connected to the existing plasma membranes at
the sides of the cell, completing the division of the cytoplasm.

The next stage in plants is for pectins and other substances to be brought in vesicles and deposited by exocytosis between the two new
membranes. This forms the middle lamella that will link the new cell walls. Both of 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 adjacent to the equator.
Mutagens, oncogenes and metastasis are involved in the
development of primary and secondary tumours.

Tumours are abnormal groups of cells that develop at any stage of life in any part of the body. In some cases the cells adhere to each other and do not invade nearby tissues or move to other parts of the body. These tumours are unlikely to cause much harm and are classied as benign. In other tumours the cells can become detached and move elsewhere in the body and develop into secondary tumours. These tumours are
malignant and are very likely to be life-threatening.

Diseases due to malignant tumours are commonly known as cancer and have diverse causes. Chemicals and agents that cause cancer are known as carcinogens, because carcinomas are malignant tumours. There are various types of carcinogens including some viruses. All mutagens are carcinogenic, both chemical mutagens and also high 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 of genes. Most genes do not cause cancer if they mutate. The few genes that can become cancer-causing after mutating are known as oncogenes. In a normal cell oncogenes are involved in the control of the cell cycle and cell division. This is why mutations in them can result in uncontrolled cell division and therefore tumour formation.

Several mutations must occur in the same cell for it to become a tumour cell. The chance of this happening is extremely small, but because there are vast numbers of cells in the body, the total chance of tumour formation during a lifetime is significant. When a tumour cell has been formed it divides repeatedly to form two, then four, then eight cells and so on. This group of cells is called a primary tumour. Metastasis is the movement of cells from a primary tumour to set up secondary tumours
in other parts of the body.
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.
Molecular biology explains living processes in terms of the chemical substances involved.

The discovery of the structure of DNA in 1 953 started a revolution in
biology that has transformed our understanding of living organisms. It raised the possibility of explaining biological processes from the structure of 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 of tasks within the cell, including controlling chemical reactions of the cell by acting as enzymes. The relationship between genes and proteins is at the heart of molecular biology.

The approach of the molecular biologist is reductionist as it involves
considering the various biochemical processes of 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 of 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.
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.
Hydroxyl: -OH
Amine: -NH2
Carboxyl: -COOH
Methyl: -CH3

Ribose
- 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.

Glucose
- 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.

Amino acids
- A carbon atom in the centre of the molecule is bonded to four
different things:
- 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.
Water molecules are polarand hydrogen bonds form between them.

A water molecule is formed by covalent bonds between an oxygen atom
and two hydrogen atoms. The bond between hydrogen and oxygen involves unequal sharing of electrons - it is a polar covalent bond. This is because the nucleus of the oxygen atom is more attractive to electrons than the nuclei of the hydrogen atoms.

Because of the unequal sharing of electrons in water molecules, the hydrogen atoms have a partial positive charge and oxygen has a partial negative charge. Because water molecules are bent rather than linear, the two hydrogen atoms are on the same side of the molecule and form one pole and the oxygen forms the opposite pole.

Positively charged particles (positive ions) and negatively charged
particles (negative ions) attract each other and form an ionic bond. Water molecules only have partial charges, so the attraction is less but it is still enough to have signifcant effects. The attraction between water
molecules is a "hydrogen bond". Strictly speaking it is an intermolecular
force rather than a bond. A hydrogen bond is the force that forms when
a hydrogen atom in one polar molecule is attracted to a slightly negative
atom of another polar covalent molecule.

Although a hydrogen bond is a weak intermolecular force, water molecules are small, so there are many of them per unit volume of water and large numbers of hydrogen bonds. Collectively they give water its unique properties and these properties are, in turn, of immense importance to living things.
Hydrogen bonding and dipolarity explain the cohesive, adhesive, thermal and solvent properties of water.

Cohesive properties
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.

Adhesive properties
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.
Thermal properties
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.
Lipids are more suitable for long term energy storage in humans than carbohydrates.

Lipids and carbohydrates are both used for energy
storage in humans, but lipids are normally used for long-term energy storage. The lipids that are used are fats. They are stored in specialized groups of cells called adipose tissue. Adipose tissue is
located immediately beneath the skin and also around some organs including the kidneys.

There are several reasons for using lipids rather than carbohydrates for long-term energy storage:
- The amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates. The same amount of energy stored as lipid rather than carbohydrate
therefore adds half as much to body mass.
In fact the mass advantage of lipids is even greater because fats form pure droplets in cells with no water associated, whereas each gram of glycogen is associated with about two grams of water, so lipids are actually six times more efficient in the amount of energy that can be stored per gram of body mass. This is important, because we have to carry our
energy stores around with us wherever we go. It is even more important for animals such as birds and bats that fly.

- Stored lipids have some secondary roles
that could not be performed as well by
carbohydrates. Because lipids are poor conductors of heat, they can be used as heat insulators. This is the reason for much
of our stored fat being in sub- cutaneous
adipose tissue next to the skin. Because fat is liquid at body temperature, it can also act as a shock absorber. This is the reason for adipose tissue around the kidneys and some
other organs.

Glycogen is the carbohydrate that is used for energy storage, in the liver and in some muscles. Although lipids are ideal for long-term storage of energy, glycogen is used for short-term storage. This is because glycogen can be broken down to glucose rapidly and then transported easily by the blood to where it is needed. Fats in adipose tissue cannot be mobilized as rapidly. Glucose can be used either in anaerobic or aerobic cell respiration whereas fats and fatty acids can only be used in aerobic respiration. The liver stores up to 150 grams of glycogen and some muscles store up to 2% glycogen by mass.
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.
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 of
implications and limitations. Evidence for health claims comes from scientifc research. There are
two questions to ask about this research:
1. Implications - do the results of the research support the health claim strongly, moderately or not at all?
2. Limitations - were the research methods used rigorous, or are there uncertainties about the conclusions because of weaknesses in
methodology?

The first question is answered by analysing the
results of the research - either experimental
results or results of a survey. Analysis is usually easiest if the results are presented as a graph or other type of visual display.
- Is there a correlation between intake of the lipid being investigated and rate of the disease or the health beneft? This might be either a
positive or negative correlation.
- How large is the difference between mean (average) rates of the disease with different levels of lipid intake? Small differences may
not be signifcant.
- How widely spread is the data? This is shown by the spread of data points on a scattergraph or the size of error bars on a bar chart. The more widely spread the data, the less likely it
is that mean differences are signifcant.
- If statistical tests have been done on the data, do they show signifcant differences?

The second question is answered by assessing the
methods used. The points below refer to surveys and slightly different questions should be asked to
assess controlled experiments.
- How large was the sample size? In surveys it is usually necessary to have thousands of people in a survey to get reliable results.
- How even was the sample in sex, age, state of health and life style? The more even the sample, the less other factors can affect the results.
- If the sample was uneven, were the results adjusted to eliminate the effects of other factors?
- Were the measurements of lipid intake and disease rates reliable? Sometimes people in a survey do not report their intake accurately and diseases are sometimes misdiagnosed.
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 of 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 different in each amino acid.

Twenty different amino acids are used by ribosomes to make
polypeptides. The amine groups and the carboxyl groups are used up in forming the peptide bond, so it is the R groups of the amino acids that give a polypeptide its character. The repertoire of R groups allows living organisms to make and use an amazingly wide range of proteins. Some of the differences are shown in table 1 . It is not necessary to try to learn these specifc differences but it is important to remember that because of the differences between their R groups, the twenty amino acids are chemically very diverse.

Some proteins contain amino acids that are not in the basic repertoire of twenty. In most cases this is due to one of the twenty being modifed after a polypeptide has been synthesized. There is an example of modifcation of amino acids in collagen, a structural protein used to provide tensile strength in tendons, ligaments, skin and blood vessel walls. Collagen polypeptides made by ribosomes contain proline at many positions, but at some of these positions it is converted to hydroxyproline, which makes the collagen more stable.

Classification of amino acids:
- Nine R groups are hydrophobic with between zero and nine carbon atoms
- Three R groups contain rings
- Six R groups do not contain rings
- Eleven R groups are hydrophilic
- Four hydrophilic R groups are polar but never charged
- Seven R groups can become charged
- Four R groups act as an acid by giving up a proton and becoming negatively charged
- Three R groups act as a base by accepting a proton and becoming positively charged.
Denaturation of proteins by heat or pH extremes.

The three-dimensional conformation of proteins is stabilized by bonds or interactions between R groups of amino acids within the molecule. Most of these bonds and interactions are relatively weak and they can be disrupted or broken. This
results in a change to the conformation of the
protein, which is called denaturation.

A denatured protein does not normally return to its former structure - the denaturation is
permanent. Soluble proteins often become insoluble and form a precipitate. This is due to the hydrophobic R groups in the centre of the molecule becoming exposed to the water around by the change in conformation.

Heat can cause denaturation because it causes vibrations within the molecule that can
break intermolecular bonds or interactions. 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 of 80'C
or higher. The best known example is DNA polymerase from Thermus aquaticus, a prokaryote that was discovered in hot springs in Yellowstone National Park. It works best at 80'C and because of this it is widely used in biotechnology.
Nevertheless, heat causes denaturation of most
proteins at much lower temperatures.

Extremes of pH, both acidic and alkaline, can cause denaturation. This is because charges on R groups are changed, breaking ionic bonds within the protein or causing new ionic bonds to form. As with heat, the three-dimensional structure of the protein is altered and proteins that have been dissolved in water often become insoluble.
There are exceptions: the contents of the stomach
are normally acidic, with a pH as low as 1 .5, but this is the optimum pH for the protein-digesting enzyme pepsin that works in the stomach.
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.
Enzymes have an active site to which specific substrates bind.

Enzymes are globular proteins that work as catalysts - they speed up chemical reactions without being altered themselves. Enzymes are often called biological catalysts because they are made by living cells and speed up biochemical reactions. The substances that enzymes convert into products in these reactions are called substrates. A general equation for an enzyme-catalysed reaction is:

substrate __en_z_y_m_e_> product

Enzymes are found in all living cells and are also secreted by some cells
to work outside. Living organisms produce many different enzymes - literally thousands of them. Many different enzymes are needed, as
enzymes only catalyse one biochemical reaction and thousands of reactions take place in cells, nearly all of which need to be catalysed. This property is called enzyme-substrate specifcity. It is a signifcant difference between enzymes and non-biological catalysts such as the metals that are used in catalytic converters of vehicles.

To be able to explain enzyme-substrate specifcity, we must look at the mechanism by which enzymes speed up reactions. This involves the substrate, or substrates binding to a special region on the surface of the enzyme called the active site. The shape and chemical properties of the active site and the substrate match each other. This allows the substrate to bind, but not other substances. Substrates are converted into products while they are bound to the active site and the products are
then released, freeing the active site to catalyse another reaction.
Enzyme catalysis involves molecular motion and the
collision of substrates with the active site.

Enzyme activity is the catalysis of a reaction by an enzyme. There are three stages:
- The substrate binds to the active site of the enzyme. Some enzymes have two substrates that bind to different parts of the active site.
- While the substrates are bound to the active site they change into different chemical substances, which are the products of the reaction.
- The products separate from the active site, leaving it vacant for substrates to bind again.

A substrate molecule can only bind to the active site if it moves very close to it. The coming together of a substrate molecule and an active site is known as a collision. This might suggest a high velocity impact between two vehicles on a road, but that would be a misleading image and we need to think about molecular motion in liquids to understand how substrate-active site collisions occur.

With most reactions the substrates are dissolved in water around the enzyme. Because water is in a liquid state, its molecules and all the particles dissolved in it are in contact with each other and are in continual motion. Each particle can move separately. The direction of movement repeatedly changes and is random, which is the basis of diffusion in liquids. Both substrates and enzymes with active sites are able to move, though most substrate molecules are smaller than the enzyme so their movement is faster.

So, collisions between substrate molecules and the active site occur because of random movements of both substrate and enzyme. The substrate may be at any angle to the active site when the collision occurs. Successful collisions are ones in which the substrate and active site are correctly aligned to allow binding to take place.
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.
The nucleic acids DNA and RNA are polymers of nucleotides.

Nucleic acids were first discovered in material extracted from the nuclei of cells, hence their name. There are two types of nucleic acid: DNA and RNA. Nucleic acids are very large molecules that are constructed by linking together nucleotides to form a polymer.

Nucleotides consist of three parts:
- a sugar, which has fve carbon atoms, so is a pentose sugar;
- a phosphate group, which is the acidic, negatively-charged part of nucleic acids; and
- a base that contains nitrogen and has either one or two rings of atoms in its structure.

Figure 1 shows these parts and how they are linked together. The base and the phosphate are both linked by covalent bonds to the pentose sugar.

To link nucleotides together into a chain or polymer, covalent bonds are formed between the phosphate of one nucleotide and the pentose sugar of the next nucleotide. This creates a strong backbone for the molecule of alternating sugar and phosphate groups, with a base linked to each sugar.

There are four different bases in both DNA and RNA, so there are four
different nucleotides. The four different nucleotides can be linked together in any sequence, because the phosphate and sugar used to link them are the same in every nucleotide. Any base sequence is therefore
possible along a DNA or RNA molecule. This is the key to nucleic acids
acting as a store of genetic information - the base sequence is the store of information and the sugar phosphate backbone ensures that the store is stable and secure.
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).
Crick and Watson's discovery of the structure of DNA
using model-making.

Crick and Watson's success in discovering the structure of DNA was based on using the evidence to develop possible structures for DNA and testing them by model-building. Their first model consisted of a triple helix, with bases on the outside of the molecule and magnesium holding the two strands together with ionic bonds to the phosphate groups on each strand. The helical structure and the spacing between subunits in the helix fitted the X-ray diffraction pattern obtained by Rosalind Franklin.

It was difficult to get all parts of this model to fit together satisfactorily and it was rejected when Franklin pointed out that there would not be enough magnesium available to form the cross links between the strands. Another deficiency of this first model was that is that it did not take account o Chargaff's finding that the amount of adenine equals the thymine and the amount of cytosine equals the amount of guanine.

To investigate the relationship between the bases in DNA pieces of cardboard were cut out to represent their shapes. These showed that A-T and C-G base pairs could be formed, with hydrogen bonds linking the bases. The base pairs were equal in length so would it between two outer sugar-phosphate backbones.

Another flash of insight was needed to make the parts of the molecule fit together: the two strands in the helix had to run in
opposite directions - they must be antiparallel. Crick and Watson were then able to build their second model of the structure of DNA. They used metal rods and sheeting cut to shape and held together with small clamps. Bond lengths were all to scale and bond angles correct.

The model convinced all those who saw it. A typical comment was "It just looked right". The structure immediately suggested a mechanism for copying DNA. It also led quickly to the realization that the genetic code must consist of triplets of bases. In many ways the discovery of DNA structure started the great molecular biology revolution, with effects that are still reverberating in science and in society.
DNA polymerase links nucleotides together to form a new strand, using the pre-existing strand as a template.

Once helicase has unwound the double helix and split the DNA into two strands, replication can begin. Each of the two strands acts as a template for the formation of a new strand. The assembly of the new strands is
carried out by the enzyme DNA polymerase.

DNA polymerase always moves along the template strand in the same direction, adding one nucleotide at a time. Free nucleotides with each
of the four possible bases are available in the area where DNA is being replicated. Each time a nucleotide is added to the new strand, only one of the four types of nucleotide has the base that can pair with the
base at the position reached on the template strand. DNA polymerase brings nucleotides into the position where hydrogen bonds could orm,
but unless this happens and a complementary base pair is formed, the nucleotide breaks away again.

Once a nucleotide with the correct base has been brought into position and hydrogen bonds have been formed between the two bases, DNA
polymerase links it to the end of the new strand. This is done by
making a covalent bond between the phosphate group of the free nucleotide and the sugar of the nucleotide at the existing end of the new strand. The pentose sugar is the 3' terminal and the phosphate
group is the 5' terminal, so DNA polymerase adds on the 5' terminal of the free nucleotide to the 3' terminal of the existing strand.

DNA polymerase gradually moves along the template strand, assembling the new strand with a base sequence complementary to the template
strand. It does this with a very high degree of fidelity - very few mistakes are made during DNA replication.
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.
Transcription is the synthesis of mRNA copied from the DNA base sequences by RNA polymerase.

This sequence of bases in a gene does not, in itself, give any observable characteristic in an organism. The function of most genes is to specify the sequence of amino acids in a particular polypeptide. It is proteins that often directly or indirectly determine the observable characteristics of an
individual. Two processes are needed to produce a specifc polypeptide, using the base sequence of a gene. The first of these is transcription.

Transcription is the synthesis of RNA, using DNA as a template. Because RNA is single-stranded, transcription only occurs along one of the two strands of DNA. What follows is an outline of transcription:
- The enzyme RNA polymerase binds to a site on the DNA at the start of a gene.
- RNA polymerase moves along the gene separating DNA into single strands and pairing up RNA nucleotides with complementary bases
on one strand of the DNA. There is no thymine in RNA, so uracil
pairs in a complementary fashion with adenine.
- RNA polymerase forms covalent bonds between the RNA nucleotides.
- The RNA separates from the DNA and the double helix reforms.
- Transcription stops at the end of the gene and the completed RNA
molecule is released.

The product of transcription is a molecule of RNA with a base sequence that is complementary to the template strand o DNA. This RNA has a
base sequence that is identical to the other strand, with one exception - there is uracil in place of thymine. So, to make an RNA copy of the base sequence of one strand of a DNA molecule, the other strand is transcribed. The DNA strand with the same base sequence as the RNA is called the sense strand. The other strand that acts as the template and has a complementary base sequence to both the RNA and the sense
strand is called the antisense strand.
Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA.

Three components work together to synthesize polypeptides by translation:
- mRNA has a sequence of codons that specifes the amino acid sequence of the polypeptide;
- tRNA molecules have an anticodon of three bases that binds to a
complementary codon on mRNA and they carry the amino acid corresponding to that codon;
- ribosomes act as the binding site for mRNA and tRNAs and also catalyse the assembly of the polypeptide.

A summary of the main events of translation follows:
1. An mRNA binds to the small subunit of the ribosome.
2. A molecule of tRNA with an anticodon complementary to the first codon to be translated on the mRNA binds to the ribosome.
3. A second tRNA with an anticodon complementary to the second codon on the mRNA then binds. A maximum of two tRNAs can be bound at the same time.
4. The ribosome transfers the amino acid carried by the frst tRNA to the amino acid on the second tRNA, by making a new peptide bond. The
second tRNA is then carrying a chain of two amino acids - a dipeptide.
5. The ribosome moves along the mRNA so the first tRNA is released,
the second becomes the first.
6. Another tRNA binds with an anticodon complementary to the next codon on the mRNA.
7. The ribosome transfers the chain of amino acids carried by the first tRNA to the amino acid on the second tRNA, by making a new peptide bond.

Stages 4, 5 and 6 are repeated again and again, with one amino acid added to the chain each time the cycle is repeated. The process continues along the mRNA until a stop codon is reached, when the completed
polypeptide is released.

The accuracy of translation depends on complementary base pairing between the anticodon on each tRNA and the codon on mRNA. Mistakes are very rare, so polypeptides with a sequence of hundreds of amino acids are regularly made with every amino acid correct.
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
gasoline (petrol).
Lactate production in humans when anaerobic respiration is used to maximize the power of muscle contractions.

The lungs and blood system supply oxygen to most organs of the body rapidly enough for
aerobic respiration to be used, but sometimes we resort to anaerobic cell respiration in muscles. The reason is that anaerobic respiration can supply ATP very rapidly for a short period of time. It is therefore used when we need to maximize the power of muscle contractions.

In our ancestors maximally powerful muscle contractions will have been needed for survival by allowing escape from a predator or catching of prey during times of food shortage. These events rarely occur in our lives today. Instead anaerobic respiration is more likely to be used during training or sport. These are examples:
● weight lifters during the lift;
● short-distance runners in races up to 400
metres;
● long-distance runners, cyclists and rowers during a sprint finish.

Anaerobic cell respiration involves the production
of lactate, so when it is being used to supply ATP, the concentration of lactate in a muscle increases. There is a limit to the concentration that the body can tolerate and this limits how much anaerobic respiration can be done. This is the reason for the short timescale over which the power of muscle contractions can be maximized. We can only sprint for a short distance - not more than 400 metres.

After vigorous muscle contractions, the lactate
must be broken down. This involves the use of oxygen. It can take several minutes for enough oxygen to be absorbed for all lactate to be broken down. The demand for oxygen that builds up during a period of anaerobic respiration is called
the oxygen debt.
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.
Ecosystems have the potential to be sustainable over
long periods of time.

The concept of sustainability has risen to prominence recently because it is clear that some current human uses of resources are unsustainable. Something is sustainable if it can continue indefinitely.
Human use of fossil fuels is an example of an unsustainable activity. Supplies of fossil
fuels are finite, are not currently being renewed and cannot therefore
carry on indefinitely.

Natural ecosystems can teach us how to live in a sustainable way, so that our children and grandchildren can live as we do. There are three
requirements for sustainability in ecosystems:
● nutrient availability
● detoxification of waste products
● energy availability.

Nutrients can be recycled indefinitely and if this is done there should not be a lack of the chemical elements on which life is based. The waste products of one species are usually exploited as a resource by another species. For example, ammonium ions released by decomposers are
absorbed and used for an energy source by Nitrosomonas bacteria in the soil. Ammonium is potentially toxic but because of the action of these bacteria it does not accumulate.

Energy cannot be recycled, so sustainability depends on continued
energy supply to ecosystems. Most energy is supplied to ecosystems as light from the sun. The importance of this supply can be illustrated by the consequences of the eruption of Mount Tambora in 1815. Dust in the atmosphere reduced the intensity of sunlight for some months afterwards, causing crop failures globally and deaths due to starvation. This was only a temporary phenomenon, however, and energy supplies to ecosystems in the form of sunlight will continue for billions of years.
Energy released by respiration is used in living organisms and converted to heat.

Living organisms need energy for cell activities such as these:
● Synthesizing large molecules like DNA, RNA and proteins.
● Pumping molecules or ions across membranes
by active transport.
● Moving things around inside the cell, such as chromosomes or vesicles, or in muscle cells the protein fibres that cause muscle contraction.

ATP supplies energy for these activities. Every cell produces its own ATP supply.

All cells can produce ATP by cell respiration. In this process carbon
compounds such as carbohydrates and lipids are oxidized. These
oxidation reactions are exothermic and the energy released is used
in endothermic reactions to make ATP. So cell respiration transfers
chemical energy from glucose and other carbon compounds to ATP. The reason for doing this is that the chemical energy in carbon compounds such as glucose is not immediately usable by the cell, but the chemical
energy in ATP can be used directly for many different activities.

The second law of thermodynamics states that energy transformations
are never 100% efficient. Not all of the energy from the oxidation
of carbon compounds in cell respiration is transferred to ATP. The remainder is converted to heat. Some heat is also produced when ATP is
used in cell activities. Muscles warm up when they contract for example. Energy from ATP may reside for a time in large molecules when they have been synthesized, such as DNA and proteins, but when these molecules are eventually digested the energy is released as heat.
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.
Methane is produced from organic matter in anaerobic conditions by methanogenic archaeans and some diffuses into the atmosphere.

In 1776 Alessandro Volta collected bubbles of gas emerging from mud in
a reed bed on the margins of Lake Maggiore in Italy, and found that it was inflammable. He had discovered methane, though Volta did not give
it this name. Methane is produced widely in anaerobic environments, as it is a waste product of a type of anaerobic respiration.

Three different groups of anaerobic prokaryotes are involved.

1. Bacteria that convert organic matter into a mixture of organic acids,
alcohol, hydrogen and carbon dioxide.

2. Bacteria that use the organic acids and alcohol to produce acetate,
carbon dioxide and hydrogen.

3. Archaeans that produce methane from carbon dioxide, hydrogen and
acetate. They do this by two chemical reactions:
CO2 + 4H2 → CH4 +
2H2O
CH3COOH → CH4 +
CO2

The archaeans in this third group are therefore methanogenic. They
carry out methanogenesis in many anaerobic environments:

● Mud along the shores and in the bed of lakes.
● Swamps, mires, mangrove forests and other wetlands where the soil or peat deposits are waterlogged.
● Guts of termites and of ruminant mammals such as cattle and sheep.
● Landfill sites where organic matter is in wastes that have been
buried.

Some of the methane produced by archaeans in these anaerobic
environments diffuses into the atmosphere. Currently the concentration in the atmosphere is between 1.7 and 1.85 micromoles per mole. Methane produced from organic waste in anaerobic digesters is not allowed to escape and instead is burned as a fuel.
Correlations between global temperatures and carbon dioxide concentrations on Earth.

If the concentration of any of the greenhouse gases in the atmosphere changes, we can expect the size of its contribution to the greenhouse effect to
change and global temperatures to rise or fall. We can test this hypothesis using the carbon dioxide concentration of the atmosphere, because it has changed considerably.

To deduce carbon dioxide concentrations and temperatures in the past, columns of ice have been drilled in the Antarctic. The ice has built up over thousands of years, so ice from deeper down
is older than ice near the surface. Bubbles of air
trapped in the ice can be extracted and analysed
to find the carbon dioxide concentration. Global temperatures can be deduced from ratios of hydrogen isotopes in the water molecules.

Figure 5 shows results for an 800,000 year period before the present. They were obtained from an ice core drilled in Dome C on the Antarctic
plateau by the European Project for Ice Coring in
Antarctica. During this part of the current Ice Age
there has been a repeating pattern of rapid periods
of warming followed by much longer periods of
gradual cooling. There is a very striking correlation
between carbon dioxide concentration and global
temperatures - the periods of higher carbon
dioxide concentration repeatedly coincide with
periods when the Earth was warmer.

The same trend has been found in other ice cores.
Data of this type are consistent with the hypothesis that rises in carbon dioxide concentration increase the greenhouse effect. It is important always
to remember that correlation does not prove causation, but in this case we know from other
research that carbon dioxide is a greenhouse gas. At least some of the temperature variation over the past 800,000 years must therefore have been due to rises and falls in atmospheric carbon dioxide
concentrations.
Global temperatures and climate patterns are influenced by
concentrations of greenhouse gases.

The surface of the Earth is warmer than it would be with no greenhouse gases in the atmosphere. Mean temperatures are estimated to be 32°C higher. If the concentration of any of the greenhouse gases rises, more heat will be retained and we should expect an increase in global average
temperatures.

This does not mean that global average
temperatures are directly proportional to
greenhouse gas concentrations. Other factors have
an influence, including Milankovitch cycles in the
Earth's orbit and variation in sunspot activity. Even
so, increases in greenhouse gas concentrations will
tend to cause higher global average temperatures
and also more frequent and intense heat waves.

Global temperatures influence other aspects
of climate. Higher temperatures increase the evaporation of water from the oceans and
therefore periods of rain are likely to be more
frequent and protracted. The amount of rain
delivered during thunderstorms and other intense bursts is likely to increase very significantly. In
addition, higher ocean temperatures cause tropical storms and hurricanes to be more frequent and more powerful, with faster wind speeds.

The consequences of any rise in global average
temperature are unlikely to be evenly spread. Not
all areas would become warmer. The west coast
of Ireland and Scotland might become colder if
the North Atlantic Current brought less warm water from the Gulf Stream to north-west Europe. The distribution of rainfall would also be likely to change, with some areas becoming more prone to droughts and other areas to intense periods of
rainfall and flooding. Predictions about changes to weather patterns are very uncertain, but it is clear
that just a few degrees of warming would cause very profound changes to the Earth's climate patterns.
There is a correlation between rising atmospheric
concentrations of carbon dioxide since the start of the industrial revolution two hundred years ago and average global temperatures.

The graph of atmospheric carbon dioxide concentrations over the past 800,000 years indicates that there have been large fluctuations. During glaciations the concentration dropped to as low as 180 parts per million by volume. During warm interglacial periods they rose as high as 300 ppm. The rise during recent times to concentrations
nearing 400 ppm is therefore unprecedented in this period.

Atmospheric carbon dioxide concentrations were between 260 and
280 ppm until the late 18th century. This is when concentrations probably started to rise above the natural levels, but as the rise was initially very slight, it is impossible to say exactly when an unnatural rise in concentrations began. Much of the rise has happened since 1950.

In the late 18th century the industrial revolution was starting in some
countries but the main impact of industrialization globally was in the second half of the 20th century. More countries became industrialized, and combustion of coal, oil and natural gas increased ever more rapidly, with consequent increases in atmospheric carbon dioxide concentration.

There is strong evidence for a correlation between atmospheric carbon dioxide concentration and global temperatures, but as already explained, other factors have an effect so temperatures are not directly proportional to carbon dioxide concentration. Nevertheless, since the start of the industrial revolution the correlation between rising atmospheric carbon dioxide concentration and average global
temperatures is very marked.
Evaluating claims that human activities are not causing climate change.

Many claims that human activities are not causing
climate change have been made in newspapers, on
television and on the internet. One example of this is:

"Global warming stopped in 1998, yet
carbon dioxide concentrations have continued
to rise, so human carbon dioxide emissions
cannot be causing global warming."

This claim ignores the fact that temperatures on
Earth are influenced by many factors, not just
greenhouse gas concentrations. Volcanic activity and cycles in ocean currents can cause significant
variations from year to year. Because of such
factors, 1998 was an unusually warm year and
also because of them some recent years have been cooler than they otherwise would have been.

Global warming is continuing but not with equal increases each year. Humans are emitting carbon
dioxide by burning fossil fuels and there is strong
evidence that carbon dioxide causes warming, so the claim is not supported by the evidence.

Claims that human activities are not causing
climate change will continue and these claims need to be evaluated. As always in science, we should
base our evaluations on reliable evidence. There
is now considerable evidence about emissions of greenhouse gases by humans, about the effects of these gases and about changing climate patterns. Not all sources on the internet are trustworthy and we need to be careful to distinguish between
websites with objective assessments based on
reliable evidence and others that show bias.
Threats to coral reefs from increasing concentrations of dissolved carbon dioxide.

In addition to its contribution to global warming, emissions of carbon dioxide are having effects on the oceans. Over 500 billion tonnes of carbon
dioxide released by humans since the start of the industrial revolution have dissolved in the oceans.

The pH of surface layers of the Earth's oceans is
estimated to have been 8.179 in the late 18th
century when there had been little industrialization.
Measurements in the mid-1990s showed that it had fallen to 8.104 and current levels are approximately 8.069. This seemingly small change represents a 30% acidification. Ocean acidfication will become
more severe if the carbon dioxide concentration of
the atmosphere continues to rise.

Marine animals such as reef-building corals that
deposit calcium carbonate in their skeletons need to absorb carbonate ions from seawater. The concentration of carbonate ions in seawater is low, because they are not very soluble.
Dissolved carbon dioxide makes the carbonate concentration even lower as a result of some interrelated chemical reactions. Carbon dioxide
reacts with water to form carbonic acid, which
dissociates into hydrogen and hydrogen carbonate ions. Hydrogen ions react with dissolved carbonate ions, reducing their concentration.

CO2 + H2O → H2CO3 → H+ + HCO3

H+ + CO32 → HCO3

If carbonate ion concentrations drop it is more difficult for reef-building corals to absorb them to make their skeletons. Also, if seawater ceases to be a saturated solution of carbonate ions, existing
calcium carbonate tends to dissolve, so existing
skeletons of reef-building corals are threatened.
In 2012 oceanographers from more than 20
countries met in Seattle and agreed to set up a
global scheme for monitoring ocean
acidification.

There is already evidence for concerns about
corals and coral reefs. Volcanic vents near
the island of Ischia in the Gulf of Naples have
been releasing carbon dioxide into the water for thousands of years, reducing the pH of the
seawater. In the area of acidified water there are no corals, sea urchins or other animals that make
their skeletons from calcium carbonate. In their place other organisms flourish such as sea grasses and invasive algae. This could be the future of coral reefs around the world if carbon dioxide continues to be emitted from burning fossil fuels.
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
the gut.

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
The contraction of circular and longitudinal muscle layers of the small intestine mixes the food with enzymes and
moves it along the gut.

The circular and longitudinal muscle in the wall of the gut is smooth muscle rather than striated muscle. It consists of relatively short cells, not elongated fibres. It often exerts continuous moderate force,
interspersed with short periods of more vigorous contraction, rather
than remaining relaxed unless stimulated to contract.

Waves of muscle contraction, called peristalsis, pass along the intestine. Contraction of circular muscles behind the food constricts the gut to prevent it from being pushed back towards the mouth. Contraction of
longitudinal muscle where the food is located moves it on along the gut. The contractions are controlled unconsciously not by the brain but by
the enteric nervous system, which is extensive and complex.

Swallowed food moves quickly down the esophagus to the stomach in one continuous peristaltic wave. Peristalsis only occurs in one direction,
away from the mouth. When food is returned to the mouth from the
stomach during vomiting, abdominal muscles are used rather than the
circular and longitudinal muscle in the gut wall.

In the intestines the food is moved only a few centimetres at a time so
the overall progression through the intestine is much slower, allowing
time for digestion. The main function of peristalsis in the intestine is churning of the semi-digested food to mix it with enzymes and thus
speed up the process of digestion.
Enzymes digest most macromolecules in food into monomers in the small intestine.

The enzymes secreted by the pancreas into the lumen of the small intestine carry out these hydrolysis reactions:
● starch is digested to maltose by amylase
● triglycerides are digested to fatty acids and glycerol or fatty
acids and monoglycerides by lipase
● phospholipids are digested to fatty acids, glycerol and
phosphate by phospholipase
● proteins and polypeptides are digested to shorter peptides by protease.

This does not complete the process of digestion into molecules small
enough to be absorbed. The wall of the small intestine produces
a variety of other enzymes, which digest more substances. Some
enzymes produced by gland cells in the intestine wall may be secreted in intestinal juice but most remain immobilized in the plasma membrane of epithelium cells lining the intestine. They are active
there and continue to be active when the epithelium cells are abraded off the lining and mixed with the semi-digested food.
● Nucleases digest DNA and RNA into nucleotides.
● Maltase digests maltose into glucose.
● Lactase digests lactose into glucose and galactose.
● Sucrase digests sucrose into glucose and fructose.
● Exopeptidases are proteases that digest peptides by removing single amino acids either from the carboxy or amino terminal of the chain until only a dipeptide is left.
● Dipeptidases digest dipeptides into amino acids.

Because of the great length of the small intestine, food takes hours to pass through, allowing time for digestion of most macromolecules to
be completed. Some substances remain largely undigested, because humans cannot synthesize the necessary enzymes. Cellulose for example is not digested and passes on to the large intestine as one of the main components of dietary fibre.
Different methods of membrane transport are required to absorb different nutrients.

To be absorbed into the body, nutrients must pass from the lumen of the small intestine to the capillaries or lacteals in the villi. The nutrients
must first be absorbed into epithelium cells through the exposed
part of the plasma membrane that has its surface area enlarged with microvilli. The nutrients must then pass out of this cell through the plasma membrane where it faces inwards towards the lacteal and blood capillaries of the villus.

Many different mechanisms move nutrients into and out of the villus epithelium cells: simple diffusion, facilitated diffusion, active transport and exocytosis. These methods can be illustrated using two different examples of absorption: triglycerides and glucose.
● Triglycerides must be digested before they can be absorbed. The
products of digestion are fatty acids and monoglycerides, which can be absorbed into villus epithelium cells by simple diffusion as they
can pass between phospholipids in the plasma membrane.
● Fatty acids are also absorbed by facilitated diffusion as there are fatty acid transporters, which are proteins in the membrane of the microvilli.
● Once inside the epithelium cells, fatty acids are combined with
monoglycerides to produce triglycerides, which cannot diffuse back out into the lumen.
● Triglycerides coalesce with cholesterol to form droplets with a diameter of about 0.2 μm, which become coated in phospholipids and protein.
● These lipoprotein particles are released by exocytosis through the
plasma membrane on the inner side of the villus epithelium cells.
They then either enter the lacteal and are carried away in the lymph, or enter the blood capillaries in the villi.
● Glucose cannot pass through the plasma membrane by simple
diffusion because it is polar and therefore hydrophilic.
● Sodium-potassium pumps in the inwards-facing part of the plasma
membrane pump sodium ions by active transport from the cytoplasm
to the interstitial spaces inside the villus and potassium ions in the
opposite direction. This creates a low concentration of sodium ions inside villus epithelium cells.
● Sodium-glucose co-transporter proteins in the microvilli transfer
a sodium ion and a glucose molecule together from the intestinal lumen to the cytoplasm of the epithelium cells. This type of facilitated diffusion is passive but it depends on the concentration gradient of sodium ions created by active transport.
● Glucose channels allow the glucose to move by facilitated diffusion from the cytoplasm to the interstitial spaces inside the villus and on into blood capillaries in the villus.
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.
Arteries convey blood at high pressure from the ventricles to the tissues of the body.

Arteries are vessels that convey blood from the heart to the tissues of
the body. The main pumping chambers of the heart are the ventricles. They have thick strong muscle in their walls that pumps blood into the arteries, reaching a high pressure at the peak of each pumping cycle. The artery walls work with the heart to facilitate and control blood flow.
Elastic and muscle tissue in the walls are used to do this.

Elastic tissue contains elastin fibres, which store the energy that stretches
them at the peak of each pumping cycle. Their recoil helps propel the
blood on down the artery. Contraction of smooth muscle in the artery wall determines the diameter of the lumen and to some extent the rigidity of the arteries, thus controlling the overall flow through them.

Both the elastic and muscular tissues contribute to the toughness of the walls, which have to be strong to withstand the constantly changing and
intermittently high blood pressure without bulging outwards (aneurysm)
or bursting. The blood's progress along major arteries is thus pulsatile, not continuous. The pulse reflects each heartbeat and can easily be felt in arteries that pass near the body surface, including those in the wrist and the neck.

Each organ of the body is supplied with blood by one or more arteries.
For example, each kidney is supplied by a renal artery and the liver by
the hepatic artery. The powerful, continuously active muscles of the
heart itself are supplied with blood by coronary arteries.
Blood flows through tissues in capillaries with permeable walls that allow exchange of materials between cells in the tissue and the blood in the capillary.

Capillaries are the narrowest blood vessels with diameter of about
10 μm. They branch and rejoin repeatedly to form a capillary network with a huge total length. Capillaries transport blood through almost all
tissues in the body. Two exceptions are the tissues of the lens and the cornea in the eye which must be transparent so cannot contain any
blood vessels. The density of capillary networks varies in other tissues but all active cells in the body are close to a capillary.

The capillary wall consists of one layer of very thin endothelium cells, coated by a filter-like protein gel, with pores between the cells. The wall is thus very permeable and allows part of the plasma to leak out and form tissue fluid. Plasma is the fluid in which the blood cells are
suspended. Tissue fluid contains oxygen, glucose and all other substances
in blood plasma apart from large protein molecules, which cannot
pass through the capillary wall. The fluid flows between the cells in a tissue, allowing the cells to absorb useful substances and excrete waste products. The tissue fluid then re-enters the capillary network.

The permeabilities of capillary walls differ between tissues, enabling particular proteins and other large particles to reach certain tissues but not others. Permeabilities can also change over time and capillaries repair and remodel themselves continually in response to the needs of tissues that they perfuse.
Causes and consequences of occlusion of the
coronary arteries.

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
other cause
● 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
the intestine.
Pressure changes in the left atrium, left ventricle and aorta during the
cardiac cycle.

The pressure changes in the atrium and ventricle of the heart and the aorta during a cardiac cycle are shown. To
understand them it is necessary to appreciate
what occurs at each stage of the cycle. Timings assuming a heart rate of 75 beats per minute. Typical volumes of blood are shown and also an indication of the direction of blood flow to or from a chamber of the heart.

0.0 - 0.1 seconds
● The atria contract causing a rapid but
relatively small pressure increase, which pumps blood from the atria
to the ventricles, through the open
atrioventricular valves.
● The semilunar valves are closed and blood
pressure in the arteries gradually drops to
its minimum as blood continues to flow
along them but no more is pumped in.

0.1 - 0.15 seconds
● The ventricles contract, with a rapid
pressure build up that causes the atrioventricular valves to close.
● The semilunar valves remain closed.

0.15 - 0.4 seconds
● The pressure in the ventricles rises
above the pressure in the arteries so the semilunar valves open and blood
is pumped from the ventricles into the
arteries, transiently maximizing the arterial blood pressure.
● Pressure slowly rises in the atria as blood drains into them from the veins
and they fill.

0.4 - 0.45 seconds
● The contraction of the ventricular muscles
wanes and pressure inside the ventricles
rapidly drops below the pressure in the arteries, causing the semilunar valves to close.
● The atrioventricular valves remain closed.

0.45 - 0.8 seconds
● Pressure in the ventricles drops below the pressure in the atria so the atrioventricular
valves open.
● Blood from the veins drains into the atria
and from there into the ventricles, causing a slow increase in pressure.
Causes and consequences of blood clot formation in
coronary arteries.

In patients with coronary heart disease, blood clots sometimes form
in the coronary arteries. These arteries branch off from the aorta close
to the semilunar valve. They carry blood to the wall of the heart,
supplying the oxygen and glucose needed by cardiac muscle fibres for cell respiration. The medical name for a blood clot is a thrombus. Coronary thrombosis is the formation of blood clots in the coronary arteries.

If the coronary arteries become blocked by a blood clot, part of the
heart is deprived of oxygen and nutrients. Cardiac muscle cells are
then unable to produce sufficient ATP by aerobic respiration and their
contractions become irregular and uncoordinated. The wall of the heart makes quivering movements called fibrillation that do not pump blood effectively. This condition can prove fatal unless it resolves naturally or through medical intervention.

Atherosclerosis causes occlusion in the coronary arteries. Where atheroma develops the endothelium of the arteries tends to become
damaged and roughened; especially, the artery wall is hardened by deposition of calcium salts. Patches of atheroma sometimes rupture causing a lesion. Coronary occlusion, damage to the capillary
epithelium, hardening of arteries and rupture of atheroma all increase
the risk of coronary thrombosis.

There are some well-known factors that are correlated with an
increased risk of coronary thrombosis and heart attacks:
● smoking
● high blood cholesterol concentration
● high blood pressure
● diabetes
● obesity
● lack of exercise.

Of course correlation does not prove causation, but doctors
nonetheless advise patients to avoid these risk factors if possible.
Production of antibodies by lymphocytes in response to
particular pathogens gives specific immunity.

If microorganisms get past the physical barriers of the skin and invade
the body, proteins and other molecules on the surface of pathogens are
recognized as foreign by the body and they stimulate a specific immune response. Any chemical that stimulates an immune response is referred to as an antigen. The specific immune response is the production of antibodies in response to a particular pathogen. The antibodies bind to
an antigen on that pathogen.

Antibodies are produced by types of white blood cell called lymphocytes.
Each lymphocyte produces just one type of antibody, but our bodies can produce a vast array of different antibodies. This is because we have
small numbers of lymphocytes for producing each of the many types of antibody. There are therefore too few lymphocytes initially to produce enough antibodies to control a pathogen that has not previously infected the body. However, antigens on the pathogen stimulate cell division of the small group of lymphocytes that produce the appropriate type of antibody. A large clone of lymphocytes called plasma cells are produced within a few days and they secrete large enough quantities of the antibody to control the pathogen and clear the infection.

Antibodies are large proteins that have two functional regions: a hyper-variable region that binds to a specific antigen and another region that helps the body to fight the pathogen in one of a number of ways,
including these:
● making a pathogen more recognizable to phagocytes so they are
more readily engulfed
● preventing viruses from docking to host cells so that they cannot
enter the cells.

Antibodies only persist in the body for a few weeks or months and the plasma cells that produce them are also gradually lost after the
infection has been overcome and the antigens associated with it are no longer present. However, some of the lymphocytes produced during an infection are not active plasma cells but instead become memory cells that are very long-lived. These memory cells remain inactive unless the same pathogen infects the body again, in which case they become active and divide to produce plasma cells very rapidly. Immunity to an infectious disease involves either having antibodies against the pathogen, or memory cells that allow rapid production of the antibody.
Effects of HIV on the immune system and methods of transmission.

The production of antibodies by the immune system is a complex process and includes different
types of lymphocyte, including helper T-cells. The human immunodeficiency virus (HIV) invades and destroys helper T-cells. The consequence
is a progressive loss of the capacity to produce
antibodies. In the early stages of infection, the
immune system makes antibodies against HIV. If
these can be detected in a person's body, they are
said to be HIV-positive.

HIV is a retrovirus that has genes made of RNA
and uses reverse transcriptase to make DNA copies of its genes once it has entered a host cell. The
rate at which helper T-cells are destroyed by HIV varies considerably and can be slowed down by using anti-retroviral drugs. In most HIV-positive patients antibody production eventually becomes
so ineffective that a group of opportunistic
infections strike, which would be easily fought
off by a healthy immune system. Several of these are normally so rare that they are marker diseases for the latter stages of HIV infection, for
example Kaposi's sarcoma. A collection of several diseases or conditions existing together is called a syndrome. When the syndrome of conditions
due to HIV is present, the person is said to have
acquired immune deficiency syndrome (AIDS).

AIDS spreads by HIV infection. The virus only
survives outside the body for a short time and
infection normally only occurs if there is blood to blood contact between infected and uninfected people. There are various ways in which this can occur:
● sexual intercourse, during which abrasions
to the mucous membranes of the penis and vagina can cause minor bleeding
● transfusion of infected blood, or blood
products such as Factor VIII
● sharing of hypodermic needles by intravenous
drug users.
Florey and Chain's experiments to test penicillin on bacterial infections in mice.

Howard Florey and Ernst Chain formed a research team in Oxford
in the late 1930s that investigated the use of chemical substances
to control bacterial infections. The most promising of these was
penicillin, discovered by Alexander Fleming in 1928. Florey and Chain's team developed a method of growing the fungus Penicillium
in liquid culture in conditions that stimulated it to secrete penicillin. They also developed methods for producing reasonably pure samples
of penicillin from the cultures.

The penicillin killed bacteria on agar plates, but they needed to
test whether it would control bacterial infections in humans. They first tested it on mice. Eight mice were deliberately infected with
Streptococcus bacteria that cause death from pneumonia. Four of the
infected mice were given injections with penicillin. Within 24 hours
all the untreated mice were dead but the four given penicillin were
healthy. Florey and Chain decided that they should next do tests on human patients, which required much larger quantities.

When enough penicillin had been produced, a 43-year-old policeman
was chosen for the first human test. He had an acute and life-
threatening bacterial infection caused by a scratch on the face from a thorn on a rose bush. He was given penicillin for four days and his
condition improved considerably, but supplies of penicillin ran out and he suffered a relapse and died from the infection.

Larger quantities of penicillin were produced and five more patients
with acute infections were tested. All were cured of their infections,
but sadly one of them died. He was a small child who had an infection behind the eye. This had weakened the wall of the artery carrying blood to the brain and although cured of the infection, the child died suddenly of brain hemorrhage when the artery burst.

Pharmaceutical companies in the United States then began to produce penicillin in much larger quantities, allowing more extensive testing, which confirmed that it was a highly effective treatment for many previously incurable bacterial infections.
Some strains of bacteria have evolved with genes which confer resistance to antibiotics and some strains of bacteria have multiple resistance.

In 2013 the government's chief medical ofcer for England, Sally Davies,
said this:
The danger posed by growing resistance to antibiotics should be ranked along with terrorism on a list of threats to the nation. If we don't take action, then we may all be back in an almost 19th-century environment where infections kill us as a result of routine operations. We won't be
able to do a lot of our cancer treatments or organ transplants.

Strains of bacteria with resistance are usually discovered soon after the introduction of an antibiotic. This is not of
huge concern unless a strain develops multiple resistance, for example
methicillin-resistant Staphylococcus aureus (MRSA) which has infected the blood or surgical wounds of hospital patients and resists all commonly
used antibiotics. Another example of this problem is multidrug-resistant
tuberculosis (MDR-TB). The WHO has reported more than 300,000 cases
worldwide per year with the disease reaching epidemic proportions in
some areas.

Antibiotic resistance is an avoidable problem. These measures are
required:
● doctors prescribing antibiotics only for serious bacterial infections
● patients completing courses of antibiotics to eliminate infections
completely
● hospital staff maintaining high standards of hygiene to prevent cross-infection
● farmers not using antibiotics in animal feeds to stimulate growth
● pharmaceutical companies developing new types of antibiotic - no new types have been introduced since the 1980s.
External and internal intercostal muscles, and diaphragm and abdominal muscles
as examples of antagonistic muscle action.

Ventilation involves two pairs of opposite movements that change the volume and therefore the pressure inside the thorax:

Diaphragm:
Inspiration:
- Moves downwards and flattens
Expiration:
- Moves upwards and becomes more domed

Ribcage:
Inspiration:
- Moves downwards and flattens
Expiration:
- Moves downwards and inwards

Antagonistic pairs of muscles are needed to
cause these movements.

Volume and pressure changes:
Inspiration:
The volume inside the thorax increases and consequently the pressure decreases
Expiration:
The volume inside the thorax decreases and consequently the pressure increases

Movement of the diaphragm:
Diaphragm:
Inspiration:
The diaphragm contracts and so it moves downwards and pushes the abdomen wall out
Expiration:
The diaphragm relaxes so it can be pushed upwards into a more domed shape
Abdomen wall muscles:
Inspiration:
Muscles in the abdomen wall relax allowing pressure from the diaphragm to push it out
Expiration:
Muscles in the abdomen wall contract pushing the abdominal organs and diaphragm upwards

Movement of the ribcage:
External intercostal muscles:
Inspiration:
The external intercostal muscles contract, pulling the ribcage upwards and outwards
Expiration:
The external intercostal muscles relax and are pulled back into their elongated state
Internal intercostal muscles:
Inspiration:
The internal intercostal muscles relax and are pulled back into their elongated state
Expiration:
The internal intercostal muscles contract, pulling the ribcage inwards and downwards
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
organic matter.
● 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.
Causes and consequences of emphysema.

In healthy lung tissue each bronchiole leads to a group of small thin-walled alveoli. In a patient with emphysema these are replaced by a smaller number of larger air sacs with much thicker walls. The total surface area for gas exchange is considerably reduced and the distance over which diffusion of gases occurs is increased, and so gas exchange is therefore much less effective. The lungs also
become less elastic, so ventilation is more difficult.

The molecular mechanisms involved are not fully understood, though there is some evidence for
these theories:
● Phagocytes inside alveoli normally prevent lung infections by engulfing bacteria and produce elastase, a protein-digesting enzyme, to kill them inside the vesicles formed by endocytosis.
● An enzyme inhibitor called alpha 1-antitrypsin
(A1AT) usually prevents elastase and other
proteases from digesting lung tissue. In smokers, the number of phagocytes in the
lungs increases and they produce more elastase.
● Genetic factors affect the quantity and effectiveness of A1AT produced in the lungs.In about 30% of smokers digestion of proteins in the alveolus wall by the increased quantity of proteases is not prevented and alveolus
walls are weakened and eventually destroyed.

Emphysema is a chronic disease because the
damage to alveoli is usually irreversible. It causes low oxygen saturation in the blood and higher than normal carbon dioxide concentrations. As a
result the patient lacks energy and may eventually find even tasks such as climbing stairs too onerous. In mild cases there is shortness of breath during vigorous exercise but eventually even mild activity causes it. Ventilation is laboured and tends to be more rapid than normal.
Rosalind Franklin and Maurice Wilkins' investigation of DNA structure by X-ray diffraction.

If a beam of X-rays is directed at a material, most of it passes through but some is scattered
by the particles in the material. This scattering
is called diffraction. The wavelength of X-rays makes them particularly sensitive to diffraction
by the particles in biological molecules
including DNA.

In a crystal the particles are arranged in a regular
repeating pattern, so the diffraction occurs in a
regular way. DNA cannot be crystallized but the molecules were arranged in an orderly enough
array in Franklin's samples for a diffraction
pattern to be obtained, rather than random
scattering.

An X-ray detector is placed close to the sample
to collect the scattered rays. The sample can be rotated in three different dimensions to investigate
the pattern of scattering. Diffraction patterns can
be recorded using X-ray film. Franklin
developed
a high resolution camera containing X-ray film to obtain very clear images of diffraction patterns from DNA. Figure 4 shows the most famous of
these diffraction patterns.

From the diffraction pattern in figure 4 Franklin
was able to make a series of deductions about the structure of DNA:
● The cross in the centre of the pattern indicated
that the molecule was helical in shape.
● The angle of the cross shape showed the pitch
(steepness of angle) of the helix.
● The distance between the horizontal bars
showed turns of the helix to be 3.4 nm apart.
● The distance between the middle of the
diffraction pattern and the top showed that
there was a repeating structure within the molecule, with a distance of 0.34 nm between
the repeats. This turned out to be the vertical
distance between adjacent base pairs in the
helix.

These deductions that were made from the X-ray
diffraction pattern of DNA were critically important in the discovery of the structure of DNA.
DNA structure suggested a mechanism for DNA replication.

Several lines of experimental evidence came together to lead to the knowledge of the structure of DNA: molecular modelling pioneered by the Nobel prize winner Linus Pauling, X-ray diffraction patterns discerned from the careful photographs of Rosalind Franklin and the base composition studies of Erwin Chargaff. But insight and imagination played a role as well.

One of Watson and Crick's first models had the sugar-phosphate strands wrapped around one another with the nitrogen bases facing outwards. Rosalind Franklin countered this model with the knowledge that the
nitrogen bases were relatively hydrophobic in comparison to the sugar-
phosphate backbone and would likely point in to the centre of the helix.

Franklin's X-ray diffraction studies showed that the DNA helix was tightly packed so when Watson and Crick built their models, their choices
required the bases to fit together such that the strands were not too far
apart. As they trialled various models, Watson and Crick found the tight
packing they were looking for would occur if a pyrimidine was paired
with a purine and if the bases were "upside down" in relation to one
another. In addition to being structurally similar, adenine has a surplus
negative charge and thymine has a surplus positive charge so that pairing was electrically compatible. Pairing cytosine with guanine allows for the formation of three hydrogen bonds which enhances stability.

Once the model was proposed, the complementary base pairing immediately suggested a mechanism by which DNA replication could occur - one of the key requirements that any structural model would
have to address. The Watson-Crick model led to the hypothesis of semi-conservative replication.
Gene expression is regulated by proteins that bind to specific base sequences in DNA.

Some proteins are always necessary for the survival of the organism and are therefore expressed in an unregulated fashion. Other proteins need to be produced at certain times and in certain amounts; i.e., their
expression must be regulated.

Gene expression is regulated in prokaryotes as a consequence of
variations in environmental factors. For example, the genes responsible
for the absorption and metabolism of lactose by E.coli are expressed in
the presence of lactose and are not expressed in the absence of lactose. In this case, the breakdown of lactose results in regulation of gene expression by negative feedback. In the presence of lactose a repressor
protein is deactivated. Once the lactose has been broken down, the repressor protein is no longer deactivated and proceeds to
block the expression of lactose metabolism genes.

As in prokaryotes, eukaryotic genes are regulated in response to
variations in environmental conditions. Each cell of a multicellular
eukaryotic organism expresses only a fraction of its genes.

The regulation of eukaryotic gene expression is also a critical part of
cellular differentiation as well as the process of development. This is seen in the passage of an insect through its life cycle stages or in human
embryological development.

There are a number of proteins whose binding to DNA regulates
transcription. These include enhancers, silencers and promoter-proximal elements. Unlike the promoter sequence, the sequences linked to regulatory transcription factors are unique to the gene.

Regulatory sequences on the DNA which increase the rate of transcription when proteins bind to them are called enhancers. Those sequences on the DNA which decrease the rate of transcription when proteins bind to them are called silencers. While enhancers and silencers
can be distant from the promoter, another series of sequences called
"promoter-proximal elements" are nearer to the promoter and binding of proteins to them is also necessary to initiate transcription.
Eukaryotic cells modify mRNA after transcription.

The regulation of gene expression can occur at several points. Transcription,
translation and post-translational regulation occur in both eukaryotes and prokaryotes. However, most regulation of prokaryotic gene expression occurs at transcription. In addition, post-transcriptional modication of RNA is a method of gene expression that does not occur in prokaryotes.

One of the most significant differences between eukaryotes and
prokaryotes is the absence of a nuclear membrane surrounding the
genetic material in prokaryotes. The absence of a compartment in
prokaryotes means that transcription and translation can be coupled.

The separation of the location of transcription and translation into separate
compartments in eukaryotes allows for significant post-transcriptional
modification to occur before the mature transcript exits the nucleus. An example would be the removal of intervening sequences, or introns, from
the RNA transcript. Prokaryotic DNA does not contain introns.

In eukaryotes, the immediate product of mRNA transcription is
referred to as pre-mRNA, as it must go through several stages of post-
transcriptional modification to become mature mRNA.

One of these stages is called RNA splicing.
Interspersed throughout the mRNA are sequences that will not contribute to the formation of the polypeptide. They are referred to as
intervening sequences, or introns. These introns must be removed. The
remaining coding portions of the mRNA are called exons. These will be spliced together to form the mature mRNA.

Post-transcriptional modification also includes the addition of a 5' cap that usually occurs before transcription has been completed. A poly-A tail is added after the transcript has been made.
Cell respiration involves the oxidation and reduction of compounds.

Oxidation and reduction are chemical processes that always occur together. This happens because they involve transfer of electrons from
one substance to another. Oxidation is the loss of electrons from a
substance and reduction is the gain of electrons.
A useful example to help visualize this in the laboratory is in the
Benedict's test, a test for certain types of sugar. The test involves the use of copper sulphate solution, containing copper ions with a charge of two positive (Cu2+). Cu2+ often imparts a blue or green colour to solutions. These copper ions are reduced and become atoms of copper by being given electrons. Copper atoms are insoluble and form a red or orange precipitate. The electrons come from sugar molecules, which are
therefore oxidized.

Electron carriers are substances that can accept and give up electrons as required. They often link oxidations and reductions in cells. The main electron carrier in respiration is NAD (nicotinamide adenine
dinucleotide). In photosynthesis a phosphorylated version of NAD is used, NADP (nicotinamide adenine dinucleotide phosphate).

The equation below shows the basic reaction.

NAD + 2 electrons → reduced NAD

The chemical details are a little more complicated. NAD initially has one positive charge and exists as NAD+. It accepts two electrons in the
following way: two hydrogen atoms are removed from the substance that is being reduced. One of the hydrogen atoms is split into a proton and an electron. The NAD+ accepts the electron, and the proton (H+) is released. The NAD accepts both the electron and proton of the other hydrogen atom. The reaction can be shown in two ways:

NAD+ + 2H+ + 2 electrons (2e ) → NADH + H+

NAD+ + 2H → NADH + H+

This reaction demonstrates that reduction can be achieved by accepting
atoms of hydrogen, because they have an electron. Oxidation can
therefore be achieved by losing hydrogen atoms.

Oxidation and reduction can also occur through loss or gain of atoms of oxygen. There are fewer examples of this in biochemical processes,
perhaps because in the early evolution of life oxygen was absent from
the atmosphere. A few types of bacteria can oxidize hydrocarbons using
oxygen:

C7H15 CH3 + 1/2O2 → C7H15 CH2OH
n-octane n-octanol

Nitrifying bacteria oxidize nitrite ions to nitrate.
NO2 + 1/2O2 → NO3

Adding oxygen atoms to a molecule or ion is oxidation, because the
oxygen atoms have a high affinity for electrons and so tend to draw
them away from other parts of the molecule or ion. In a similar way,
losing oxygen atoms is reduction.
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
phosphorylate ADP.
The structure of the mitochondrion is
adapted to the function it performs.

There is often a clear relationship between the
structures of the parts of living organisms and the
functions they perform. This can be explained
in terms of natural selection and evolution. The mitochondrion can be used as an example. If
mitochondrial structure varied, those organisms
with the mitochondria that produced ATP most
efficiently would have an advantage. They would have an increased chance of survival and
would tend to produce more offspring. These
offspring would inherit the type of mitochondria
that produce ATP more efficiently. If this trend
continued, the structure of mitochondria would
gradually evolve to become more and more
efficient. This is called adaptation - a change in
structure so that something carries out its function more efficiently.

The mitochondrion is a semi-autonomous organelle in that it can grow and reproduce itself but it still depends on the rest of the cell for resources and is otherwise part of the cellular system. 70S
ribosomes and a naked loop of DNA are found
within the mitochondrial matrix.

The mitochondrion is the site of aerobic respiration. The outer mitochondrial membrane separates the contents of the mitochondrion from the rest of the cell creating a compartment specialized for the
biochemical reactions of aerobic respiration.

The inner mitochondrial membrane is the site of
oxidative phosphorylation. It contains electron
transport chains and ATP synthase, which carry
out oxidative phosphorylation. Cristae are tubular projections of the inner membrane which increase the
surface area available for oxidative
phosphorylation.

The intermembrane space is the location where protons build up as a consequence of the electron transport chain. The proton build-up is used to produce ATP via the ATP synthase. The volume of the space is small, so a concentration gradient across the inner membrane can be built up rapidly.

The matrix is the site of the Krebs cycle and the link reaction. The matrix fluid contains the enzymes necessary to support these reaction systems.
Absorption of light by photosystems generates
excited electrons.

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
electron acceptor.

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.
Excited electrons from Photosystem I are used to reduce NADP.

The remaining parts of the light-dependent reactions involve
Photosystem I. The useful product of these reactions is reduced NADP, which is needed in the light-independent reactions of photosynthesis. Reduced NADP has a similar role to reduced NAD in cell respiration: it carries a pair of electrons that can be used to carry out reduction reactions.

Chlorophyll molecules within Photosystem I absorb light energy and
pass it to the special two chlorophyll molecules in the reaction centre. This raises an electron in one of the chlorophylls to a high energy level. As with Photosystem II, this is called photoactivation. The excited electron passes along a chain of carriers in Photosystem I, at the end of which it is passed to ferredoxin, a protein in the fluid outside the thylakoid. Two molecules of reduced ferredoxin are then used to reduce
NADP, to form reduced NADP.

The electron that Photosystem I donated to the chain of electron carriers is replaced by an electron carried by plastocyanin. Photosystems I and
II are therefore linked: electrons excited in Photosystem II are passed along the chain of carriers to plastocyanin, which transfers them to
Photosystem I. The electrons are re-excited with light energy and are
eventually used to reduce NADP.

The supply of NADP sometimes runs out. When this happens the
electrons return to the electron transport chain that links the two
photosystems, rather than being passed to NADP. As the electrons flow back along the electron transport chain to Photosystem I, they cause pumping of protons, which allows ATP production. This process is cyclic
photophosphorylation.
Active uptake of mineral ions in the roots causes absorption of water by osmosis.

Water is absorbed into root cells by osmosis. This happens because the solute concentration inside the root cells is greater than that in the
water in the soil. Most of the solutes in both the root cells and the soil
are mineral ions. The concentrations of mineral ions in the root can be 100 or more times higher than those in the soil. These concentration
gradients are established by active transport, using protein pumps in the plasma membranes of root cells. There are separate pumps for each type of ion that the plant requires. Mineral ions can only be absorbed by active transport if they make contact with an appropriate pump protein. This can occur by diffusion, or by mass flow when water carrying the ions drains through the soil.

Some ions move through the soil very slowly because the ions bind to
the surface of soil particles. To overcome this problem, certain plants have developed a relationship with a fungus. The fungus grows on the surface
of the roots and sometimes even into the cells of the root. The thread-like hyphae of the fungus grow out into the soil and absorb mineral ions such as phosphate from the surface of soil particles. These ions are supplied to the roots, allowing the plant to grow successfully in mineral-deficient soils. This relationship is found in many trees, in members of the heather family and in orchids. Most, but not all, of these plants supply sugars and other nutrients to the fungus, so both the fungus and the plant benefit. This is an example of a mutualistic relationship.
Xerophytes are plants adapted to growing in
deserts and other dry habitats. There are various
strategies that plants can use to survive in these
habitats, including increasing the rate of water

uptake from the soil and reducing the rate of
water loss by transpiration. Some xerophytes
are ephemeral, with a very short life cycle that
is completed in the brief period when water is

409

9.1 Transpor T in The x y l em of pl anTs

available after rainfall. They then remain dormant
as embryos inside seeds until the next rains,
sometimes years later. Other plants are perennial
and rely on storage of water in specialized leaves,
stems or roots.
Most cacti are xerophytes, with leaves that are so
reduced in size that they usually only consist of
spines. The stems contain water storage tissue and
become swollen after rainfall. Pleats allow the stem
to expand and contract in volume rapidly. The
epidermis of cactus stems has a thick waxy cuticle
and unlike most plant stems there are stomata,
though they are spaced more widely than in leaves.
The stomata usually open at night rather than in
the day, when it is much cooler and transpiration
occurs more slowly. Carbon dioxide is absorbed
at night and stored in the form of a four-carbon
compound, malic acid. Carbon dioxide is released
from the malic acid during the day, allowing
photosynthesis even with the stomata closed. This
is called Crassulacean acid metabolism. Plants such
as cacti that use this system are called CAM plants.
C4
physiology also helps to reduce transpiration.
Use of micropropagation for rapid bulking up of new varieties, production of virus-free strains of existing varieties and propagation of orchids and other rare species.

The international exchange of plant materials carries with
it the risk of transmission of pathogens. Micropropagation
techniques can be used to produce virus-free strains of plants. Viruses are transported within a plant from cell to
cell through vascular tissue and via plasmodesmata. The
apical meristem is therefore often free of viruses.

Micropropagation can be used in the production of plants with
desirable characteristics, producing many identical copies of an individual. The process is also much faster and takes up less
space than traditional methods of production. For example, it is being used in the preservation of species such as orchids. Often the target of collection in the wild, the bulk production of endangered varieties of orchids allows for wild replanting as well as a method for commercial production. Further, the seeds of orchids are difficult to germinate. Asexual reproduction is
often more successful. Micropropagated plantlets can be stored
in liquid nitrogen - a technique known as cryopreservation.
This is equivalent in function to a seed bank.

The loss of habitat for the orchid species Ophrys
lutea in Malta, combined with their normally low seed production and low rates of successful germination identified them as a target for conservation. The material needed to start the cultures was collected from open fields. Once the process of plantlet production is complete, the intent is to both replant the orchid back into the wild habitat as well as to maintain a stock of the
threatened species.
Flowering involves a change in gene expression in the
shoot apex.

When a seed germinates, a young plant is formed that grows roots, stems and leaves. These are called vegetative structures and the plant
is in the vegetative phase. This can last for weeks, months or years, until a trigger causes the plant to change into the reproductive phase and
produce flowers. The change from the vegetative to the reproductive phase happens when meristems in the shoot start to produce parts of
flowers instead of leaves.

Flowers are structures that allow for sexual reproduction, thereby
increasing variety. They are produced by the shoot apical meristem and are therefore a reproductive shoot.

Temperature can play a role in transforming a leaf-producing shoot
into a flower-producing shoot, but day length is the main trigger, or more precisely the length of the dark period. Some plants such as the poinsettia (Euphorbia pulcherrima) are categorized as short-day plants because they flower when the dark period becomes longer than a critical length, for example in the autumn. Other plants such as red clover (Trifolium pratense) are long-day plants because they flower during the
long days of early summer when nights are short.

Light plays a role in the production of either inhibitors or activators
of genes that control flowering. For example in long-day plants, the
active form of the pigment phytochrome leads to the transcription of a flowering time (FT gene). The FT mRNA is then transported in the
phloem to the shoot apical meristem where it is translated into FT
protein. The FT protein binds to a transcription factor. This interaction
leads to the activation of many flowering genes which transform the
leaf-producing apical meristem into a reproductive meristem.
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
enough.

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
and PFR

● 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
binds.

● 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
plant flowers.
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.

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