3.8.2.3 Gene Expression and Cancer

What do we need to know from the specification? 

1. Distinguish between benign and malignant tumours
2. Explain the role of oncogenes and tumour suppressor genes in the development of tumours
3. Explain the effects of abnormal methylation of tumour suppressor genes and oncogenes
4. Explain how increased oestrogen levels can cause breast cancer

Distinguish between benign and malignant tumours

What is a tumour? A tumour is a group of abnormal cells which experience unrestrained mistosis and as a result constantly grow and develop.

There are two main types of tumour; benign and malignant.

There are 10 characteristics of benign and malignant tumours which need to be known.

Size

Benign: Benign tumours can grow to a large size.

Malignant: Malignant tumours can grow to a large size.

Rate of Growth

Benign: Benign tumours grow at a very slow rate

Malignant: Malignant tumours grow at a very rapid rate

Differentiation of Cells

Benign: The cells in benign tumour are often highly differentiated (specialised)

Malignant: The cells in malignant tumours are often undifferentiated (unspecialised)

Metastasis?

Benign: Benign tumours produce molecules called adhesion molecules. These adhesion molecules make the tumour cells stick together and so they stay within the tissue they arise from. These are known as primary tumours.

Malignant: Malignant tumours do not produce adhesion molucules, therefore do not stick together. Therefore the tumour cells tend to spread to other regions of the body, through a process known as metastasis. These are known as secondary tumours.

Capsule?

Benign: Benign tumours are surrounded by a capsule of dense tissue, and so remain as a compact structure.

Malignant: Malignant tumours do not have any kind of capsule surrounding them. They grow finger like projections into other tissues.

Damage Level

Benign: Benign tumours are much less likely to be life threatening than malignant tumours, however they can disrupt the functioning of vital organs.

Malignant: Malignant tumours are much more likely to be life threatening than benign tumours.

Locality of effects

Benign: Benign tumours tend to have much more localised effects on the body.

Malignant:  Malignant tumours often have systemic (whole body) effects, e.g. weight loss & fatigue.

Removal

Benign: Benign tumours can usually be removed by surgery alone.

Malignant: Malignant tumour's removal usually involves surgery, radiotherapy and chemotherapy.

Rate of recurrence

Benign: Benign tumours very rarely recur after removal.

Malignant: Malignant tumours have a high rate of recurrence after removal.

The process of metastasis is illustrated below:

2. Explain the role of oncogenes and tumour suppressor genes in the development of tumours

In most cases, cancers are developed from a single mutant cell. The initial mutation will cause uncontrollable mitosis in a cell, and later on a second mutation of one of the resultant cells leads to another change where all subsequent cells are abnormal in growth and appearance. There are two main genes which are involved in the development of tumours:

• Oncogenes
• Tumour Suppressor Genes

Oncogenes

Oncogenes are mutations of a different type of gene called a proto-oncogene, Ordinarily, a proto-oncogene will stimuate a cell to divide by mitosis when a growth receptor is detected by a protein on the cell surface membrane. This attachment then activates the genes (proto-oncogenes) which cause DNA to replicate and cell division to occur. If a proto-oncogene mutates into a oncogene, it can become permenantly activated. This can occur for two reasons:

1. The receptor protein which detects growth factors on the cell surface membrane is permanently activated, so that cell division is  always switched on even in the absence of growth factors.
2. The oncogene may itself code for a growth factor which is then produced in excessive amounts, causing excessive cell division.

Either way, the result is that the cells divide too rapidly and out of control, and as a consequence, a tumour develops.  There are a few cancers which are caused by inherited proto-oncogene mutations, however most are acquired.

Tumour Suppressor Genes

Ordinarily, a tumour suppressor gene is active, and its roles include; slowing down cell mitosis, repairing mutated DNA, and apoptosis (programmed cell death) of cells it cannot repair. Therefore the function of the tumour suppressor gene is largely the opposite of that of the oncogenes. If  mutation occurs to a tumour suppressor gene,  it becomes inactive, and therefore stops inhibition of cell division, and thus cells can grow out of control. The mutated cells which are formed from these divisions are usually structurally and  functionally different from normal cells. While most die, those which survive can make cones of themselves and form tumours. There are a number of forms of the tumour supressor genes inculding TP53, BRCA1 and BRCA2l.

Some cancers are caused by inherited mutations of tumour suppressor genes, however most are acquired. For example, ore than half of human cancers display abnormalities of the TP53 gene, which codes for the protein p53, which is involved in causing cell apoptosis. Apoptosis is the programmed death of a cell, when its mutated DNA cannot be fixed. If  the protein p53 is not functioning properly due to a mutation in the TP53 gene, then it won't be able to suppress a tumour and the cells can divide in an unrestrained manner.

The key difference between oncogenes, and tumour suppressor genes is that oncogenes is that it is the activation of the oncogene which causes cancer, whereas it is the silencing off the tumour suppressor gene which causes cancer.

3. Explain the effects of abnormal methylation of tumour suppressor genes and oncogenes

It was learnt in the previous topic that the methylation of DNA induces the silencing of the localised gene (due to more coiling). 

It is now known that in the early stages of tumour development, there are abnormal levels of methylation in tAfthe tissue.

Two abnormalities known as hypermethylation and hypomethylation both have consequences which can bring about cancer.

Hypermethylation occurs at the promoter region of tumour suppressor genes. This leads to the silencing of the tumour suppressor gene by two metiods:

1. the methyl group attaches to a cytosine base, so that no transcription factors can bind to it. Therefore the transcription cannot begin.
2. the methyl group attracts proteins which make the chromatin more coiled (into homochromatin) by carrying out deacetylation of the associated histones, which makes the DNA more tightly coiled around the histones, thus making the base sequence inaccessible for the transcription factor.

The result of both of these is that the process of transcription, and therefore the production of mRNA cannot occur, and so the gene is silenced. Therefore, the proteins which inhibit cell division are not produced, allowing cells to divide by mitosis freely to form a tumour.

Hypomethylation also occurs at the promoter region, but this time on an oncogene. This is where there is reduced methylation, which leads to the expression of the oncogenes, thus stimulating the cell to divide, and a tumour to be formed.

4. Explain how increased oestrogen levels can cause breast cancer

After menopause, a woman's likelihood of developing breast cancer is reduced. At the point of menopause, the steroid hormone oestrogen ceases to be produced in the ovaries, and in the breasts the fat cells begin to produce increasing amounts. If a tumour were to develop in the breasts, the high levels of oestrogen would cause it grow, and in turn produce even more oestrogen.  In addition white blood cells are drawn to the tumour and increase oestrogen production, which leads to even greater tumour growth. 

But how does the oestrogen cause a tumour to grow?

The oestrogen is a steroid hormone, which means it's role is to activate transcription factors. In turn these transcription factors bind to a specific gene. If this gene is involved in cell mitosis, then it will stimulate increased cell division and lead to a tumour.  It is known that oestrogen in  the breasts causes proto-oncogenes to develop into oncogenes, which leads to the development of breast cancer.

Summary Questions

1. Describe a process by which oestrogen might cause breast cancer in post-menopausal women

Post-menopause, the ovaries produce less oestrogen and the fat cells of the breast produce more oestrogen. These locally produced oestrogen release an inhibitor molecule which prevents transcription, and causing proto-oncogenes of the breast tissue to develop into oncogenes. Thee oncogenes increase the rate at which cell division happens, hence the rate at which the tumour grows.

2. Explain why the activation of an proto-oncogene can cause cancer, while it requires the deactivation of a tumour suppressor gene. 

Proto-oncogenes increase the rate of cell division, and so their activation produces a mass of cells (i.e. a tumour). Contrastingly, a tumour suppressor decreases the rate of growth of tumours, so the deactivation of them will allow the cells in the tumour to divide freely

.

 3. Suggest two reasons why the surgical removal of a benign tumour is usually sufficient to prevent the tumour growing again. 

1. The benign tumour doesn't undergo metastasis due to the production of adhesive molecules. Therefore the tumour remains within the tissue of the cell in which it arises, so surgery will remove 100% of the tumour.
2. The benign tumour is enclosed in a dense tissue capsule, so that none of the tumour cells can escape into other tissues. Therefore, as long as the contents of the capsule are all removed, the tumour will totally removed.

4. Suggest why the surgical removal of a malignant tumour requires follow-up treatments such as chemotherapy and radiotherapy

The malignant tumour doesn't produce any adhesion molecules so the cells don't stay together and undergo the process of metastasis, which means secondary tumours can form around the body. Therefore surgical removal of the primary tumour means there's a chance not all of the tumour was removed and so some of it remains, which needs to be killed by chemotherapy/radiotherapy.

5. The enzyme histone deacetylase (HDAC) removes acetyl groups from the histones. Phenylbutyric acid is an inhibitor of the enzyme HDAC. Suggest how phenybutyric acid might be used to treat cancer. Explain your answer.

The removal of acetyl groups is a process which acts to silence certain genes. The act of removing an acetyl group from a histone results in an increase in charge on the histone, and so a greater attraction between the DNA and the histones, causing greater coiling, and meaning the gene is inaccessible for the transcription factor, therefore the transcription cannot occur. If phenylbutyric acid inhibits this process, then it prevents the process of silencing genes, and so will keep them active. A possible treatment using this is if the cancer is caused by the silencing of tumour suppressor genes, the phenylbutyric acid could be added to prevent their silencing and therefore stop the tumour growing. Tumour suppressor genes are used to slow down mitosis, repairing mutated DNA, and the apoptosis of irreparable cells. The reactivation of these genes would allow tumour growth to be stopped and thus cancer to be combated.

Students should be able to evaluate evidence showing correlations between environmental and genetic factors and various forms of cancer.

Students should be able to interpret information relating to the way in which an understanding of the roles of oncogenes and tumour suppressor genes could be used in the prevention, treatment and cure of cancer.

3.8.2.1 Most of a cell's DNA is not tranlated

     3.8.2.1 Most of a cell's DNA is not translated

What do we need to know from the specification?

         What is a stem cell?

         1. Explain what totipotent cells are

         2. Explain how cells lose their totipotency and become specialised

         3. Describe the origins and types of stem cells

         4. Describe and explain induced pleuripotent stem cells and their significance in medical ethics

         5. Explain how pleuripotent stem cells can be used to treat human disorders

         

1. Explain what totipotent cells are

When an organism is developing from a signle fertilised egg, the resulting zygote has the potential to give rise to all of the types of body cell found in the organism.  A cell which can mature into any body cell is called a totipotent cell.

2. Explain how cells lose their totipotency and become specialised

The initial embryonic cells are totipotent, however as they mature, divide and develop, they lose this totipotency. Earlier cells which are derived form the initial embryonic cells are called pleuripotent, and again as these become more and more specialised, the cells lose their totipotency. The specialisation of cells allows it to be more suited to a specific function. For example mesophyll cells are more specialised for photosynthesis, and muscle cells are specialised for contraction. The process of specialisation is simultaneous with the loss of totipotency, and occurs through the selective expression of genes. This means only some of the cells DNA is translated into proteins. This DNA includes those for vital processes like respiration and membrane synthesis, and also those which are needed for the cell to carry out its specific function (e.g. the genes which allow B-cells of the pancreas to secrete insulin). The cell exclusively makes these proteins, and the production of unnecessary proteins would be a waste of energy and resources. The inhibition of such genes is carried out by 

• preventing transcription and thus the production of mRNA
• preventing translation and thus the productions of the protein.

In animal cells, while all body cells contain the entire genome for the body's proteome, once a cell has become specialised, they cannot develop into any cell. The act of specialisation in an animal cell is usually irreversible, due to the fact that genes outside of what it needs are switched off.

Few cells retain the ability to develop into other types of cell; these are called stem cells.

3. Describe the origins and types of stem cells

Stem cells are classed as stem cells because of their ability to differentiate into other cell types. However the extent of this ability can vary depending on the stem cell. Therefore stem cells can be classified according to their ability to differentiate;

• Totipotent stem cells- can differentiate into all types of body cell, the zygote is the first totipotent cell, and as it divided and matures, the resulting cells become slightly more specialised and become pleuripotent stem cells.
• Pleuripotent stem cells - can differentiate into almost any type of body cell, these are found in later stage embryos, and the fetus.
• Multipotent stem cells - can differentiate into a limited number of specialised cells. They usually develop into cells of a particular type, e.g. stem cells in bone marrow can differentiate into any type of blood cell. Adult stem cells, and umbilical blood stem cells are both multipotent.
• Unipotent stem cells- can differentiate into only one type of cell. They're a more specialised form of multipotent stem cells and are formed in adult tissue.

In mature mammals, on a few cells retain the ability to differentiate into other cells. These are called stem cells. Stem cells have various points of origination in mammals;

• Early embryonic stem cells. come from embryos in the early stages of development. These can differentiate into any type of cell in the initial stages of development, and so are totipotent.
• Umbilical cord blood stem cells,  found in umbilical cord blood and can differentiate into a limited range of cells, therefore are multipotent.
• Placental stem cells, come from the placenta and are multipotent.
• Adult stem cells (e.g. bone marrow cells) and found in body tissues of fetus through to adult and are specific to an organ or tissue. These are multipotent.

 4. Describe and explain induced pleuripotent stem cells and their significance in medical ethics

Induced pleuripotent stem cells (iPS) are a type of stem cell derived from unipotent stem cells. They are produced in a laboratory, in a process where they are genetically altered to make them acquire the characteristics of a later embyronic cell (which is pleuripotent). In order to do this, certain genes and transcription factors are induced, i.e. certain genes are reactivated.

Although they are not exact copies of embryonic cells, they are very similar in form and function.

One significant feature of them is that they are capable of self renewal. This mean they can potentially divide to form a limitless supply, the medical research profession would no longer require the use of real embryos which would solve some of the ethical issues surrounding embryonic use in labs.

5. Explain how pleuripotent stem cells can be used to treat human disorders

There are many possible uses of pleuripotent stem cells in treating disorders. The cells can be used to regrow tissues which have been damaged either by disease (e.g. parkinsons) or by accident (e.g. burns / wounds). 

Summary Questions

1. Explain what is meant by a totipotent cell.

Totipotent cells are cells with the ability to develop into any other cell of the organism.

2. Distinguish between totipotent, pleuripotent, multipotent and unipotent cells

Totipotent- can differentiate into any type of cell in the body and comprise the first few cells that form from the zygote.

Pleuripotent - can differentiate into almost any type of cell  and are found in the embryo and young fetus. 

Multipotent - can differentiate into a limited number of cells and are found in the umbilical cord, and some adult tissues (e.g. bone marrow)

Unipotent - can only differentiate into one type of cell and are found in adult tissues such as skin.

3. All cells possess the same genes and yet a skin cell can produce the protein keratin but not the protein myosin, while a muscle cell can produce myosin but not keratin. Explain why.

This is due to the inhibition (switching off) of certain genes. For example, in skin cells, the gene for keratin is switched on, but the gene for myosin is switched off. This means the keratin will be transcribed and translated into a protein, while myosin will not.

The inverse is true for the muscle cells.

4. Suggest a reason why skin cells retain an ability to divide by being unipotent when the cells of some other organs do not.

Skin cells, being on the outside of the body are much more prone to damage and so need replacing more frequently. Many other organs are less prone to damage and need little cell replacement.

Students should be able to evaluate the use of stem cells in treating human disorders

For the specification, it's necessary to know some arguments surrounding the ethical issue of the use of embryos in treating human disorder. Below are some reasons for and against.

For

• They have huge potential to cure debilitating diseases
• It is wrong to not cure suffering when it can be relieved
• If embryos are allowed to be created for other reasons (IVF), why can't they be produced for stem cells. 
• Embryos younger than 14 days are not recognisably human and so don't command the same respect as adults or fetuses.
• There is no risk of research escalating to include fetuses and current legislation prevents this.
• adult stem cells are not as suitable as embryonic stem cells and it may be years before they are, in the meantime many people suffer unnecessarily.

Against

• It is wrong to use humans (inc. potential humans) as a means to an end.
• Embryos are human as they have human genes and deserve same respect as an adult.
• Is a 'slippery slope' to the use of older embryos and fetuses.
• Could lead to research and development of human cloning.
• Undermines respect for human life.
• Adult stem cells are available and energies should be used developing these.

3.8.2.2 Regulation of Transcription and Translation

     3.8.2.2 Regulation of Transcription and                              Translation

What do we need to know from the specification?

         1. Explain how transcription factors stimulate / inhibit transcription

         2. Explain how oestrogen affects gene transcription

         3.i  State what is meant by epigenetics
         3.ii Describe the nature of the epigenome

         4. Describe and explain the link between heredity and epigenetics

         5.1 Explain how environmental factors are detected by the epigenome

         5.2 Explain the effects of decreased acetylation of histones

         5.3 Explain the effects of increased methylation of DNA

         6. Explain the relevance of epigenetics on the development, diagnosis and treatment of diseases              such as cancer

         7.i  State what small interfering RNA (siRNA) is

         7.ii Explain how siRNA affects gene expression

1. Explain how transcription factors stimulate / inhibit transcription

In multi-cellular organisms, each cell is specialised to perform a certain type of role. For example, Beta cells in the pancreas are specialised to produce the hormone insulin. Insulin is a protein and therefore, the production of insulin requires the transcription of the gene coding for the polypeptides which make up insulin into mRNA. All cells are genetically identical, which means that (e.g.) a muscle cell also contains the gene for insulin in its DNA. However as insulin is produced only in the Beta cells, not the muscle cells, there must be some process by which the expression of a gene is controlled. This process is the Regulation of transcription and translation and involves the use of molecules such called transcription factors.

A transcription factor is a molecule  which stimulates the transcription of a gene.

The transcription factor is shown to the left and is comrpised of two many parts The part in left is responsible for binding to DNA ans the part on the right is responsible for activating the transcription factor.. It is found in the cytoplasm of a cell, and needs to be activated before it can induce transcription. The transcription factor has a receptor site (on the blue part) to which another specific molecule e.g. oestrogen can bind to. Once this binding occurs, a change in the tertiary structure is caused in the part responsible for DNA binding (LHS). This change makes the DNA binding site complementary to a specific sequence of base pairs in the DNA and so the transcription factor moves into the nucleus through a nuclear pore to bind with a specific section of DNA and from there induces the process of transcription.

• The transcription factor is described as active only if it has bound to the molecule on the RHS in the image. If this binding doesn't occur, the transcription factor is inactive and the DNA binding site will not change shape to be complementary to the requires section of DNA. Therefore when inactive, the transcription factor will not cause transcription and protein synthesis.

2. Explain how oestrogen affects gene transcription

Oestrogen itself is not a transcription factor, however is the molecule which binds to a transcription factor in order to activate it. Therefore oestrogen can be described as an activator molecule. It is a lipid hormone. Oestrogen is produced in women in the ovaries, however it has effects all over the body. Oestrogen is therefore carried in the blood to its target cells. As it's a lipid molecule, it therefore is lipid soluble so can move across the cell's surface membrane. Oestrogen then binds with the transcription factor as shows in image above. This activates the transcriptions factor and it is now able to enter the nucleus via a nuclear pore. Inside the nucleus, the transcription factor binds to specific DNA base pair sequences on the DNA molecule. The binding of the transcription factor to the DNA stimulates transcription of the gene. The process is demonstrated below.

3.i  State what is meant by epigenetics

The definition for epigenetics is
 "the study of changes in organisms caused by modification of gene expression by environmental factors rather than alteration of the genetic code itself.", however if asked to state the definition in an exam, make sure to incorporate some of the following:
 Epigenetics is a relatively new field in biology, which explores how environmental factors such as toxins, diet, exercise cans subtly alter the genetic inheritance of the organisms offspring. It is also the exploration as to how these influences can cause diseases such as autism and cancer.

3.ii Describe the nature of the epigenome

We know from GCSE that DNA is wrapped around proteins called histones, which together form the DNA-histone complex, called a chromatin. Relatively recent scientific research has discovered that both the DNA and the histones are covered in chemical 'tags'. These tags form a second layer to genetic coding, and together they are called the epigenome. It is the genome which determines the shape of the chromatin. Through its determination of the shape of the chromatin, the epigenome has the ability to determine which genes can and cannot be expressed. The shape of the epigenome is determined by all the chemical signals it has received in its lifetime, therefore acts as a cellular memory.
We learnt above that in order for a gene to be transcribed, it needs to have a transcription factor attached to it, however sometimes the epigenome will make the gene inaccessible for the transcription factor. It does this by coiling the gene tightly around the histones so that it is very compact and the transcription factor cannot reach it.In this way, the gene can be described as being 'switched off'. By contrast, genes which are 'switched on' are not coiled tightly around the histones and so are accessible for the transcription factors.
   

The chromatin has two states it can be in;

• Heterochromatin; which is shown on the left of the above image. This is when the DNA is wrapped tightly around the histones, creating a very condense chromatin. In this state, a gene is inaccessible for a transcription factor.
• Euchromatin; which is shown on the right of the above image. This is when the DNA is wrapped loosely around the histones, creating a not very condense chromatin. In this state, a gene is accessible for a transcription  factor. 

4. Describe and explain the link between heredity and epigenetics

It used to be believed that a new born embryo had has all of its epigenome erased through a process of reprogramming, which happens in the sperm and eggs in order to create a 'clean' genome. However recent discoveries show this process of reprogramming doesn't erase all of the tags that make up the epigenome. In fact about 1% of genes escape the process of genetic reprogramming by a process called imprinting (beyond spec.)
An example of epigenetic inheritance is the inheritance of the condition gestational diabeties. If a pregnant mother has the condition, the fetus is exposed to very high levels of glucose, which cause epigenetic changes in the offsprings DNA, and increase the likelihood of the offspring developing gestational diabetes.

 5.1 Explain how environmental factors are detected by the epigenome

Every kind of environmental factor (signal) which can influence the epigenome will have a specific 'message'. The signal will stimulate proteins to transport its message across the cell membrane into the cell, where it is passed via a series of other proteins through the cell's cytoplasm into the nucleus where it binds to a specific protein. This specific protein attaches to a specific sequence of bases in the DNA. Once attached the protein can have two effects:

• It can affect the levels of acetylation of the associated histones
• It can affect the levels of methylation of the DNA

 5.2 Explain the effects of decreased acetylation of histones

Acetylation is the process by which an acetyl group is added to a molecule. When the histones are receiving acetyl groups, it is from the donor molecule Acetylcoenzyme A. Deacetylation is the reverse of the process. Acetyl groups have a negative charge, therefore there is natural repulsion between the acetyl groups and the DNA's phosphate groups (which also have a negative charge). If the levels of acetylation on the associated histones were to be decreased, then the charges on the histones would increase which would lead to greater attraction between the histones and the DNA and so more, tighter coiling. Therefore, in the region in which decreased acetylation occurs, the genes would be switched off, as transcription factors would be unable to access the gene. Therefroe decreasing acetylation is an inhibitory action.
 If acetylation were to be increased, then there would be a decrease in charge on the histones, and so greater repulsion between the histones and the DNA, and so looser, less condense coiling. This would allow any genes in this region to be accessible to the transcription factors. Therefore the gene would be switched on. Increasing acetylation is an exhibitory action.

5.3 Explain the effects of increased methylation of DNA


Methylation is the process of adding a CH3 group to a molecule. In this context, the molecule receiving the CH3 group is the DNA base cytosine. The methylation of DNA in this way, inhibits the transcription of DNA in two different ways:

• With the CH3 group bound to the cytosine, no transcriptional factors are able to access the cytosine and therefore no transcription can occur.
• The methyl group attracts proteins which condense the chromatin by inducing the deacetylation of histones

Therefore, increasing the methylation acts to inhibit gene transcription, whereas decreasing the methylation levels will increase gene expression.

6. Explain the relevance of epigenetics on the development, diagnosis and treatment of diseases  such as cancer

While some epigenetic changes are normal for healthy development, some are responsible for diseases, such as cancer. Any alteration of the genetic processes can cause the unwanted expression / silencing of certain genes.
In 1983, researchers discovered that tissue taken from patients suffering from colorectal cancer had a lower level of methylation in their diseased tissue than their normal tissue. As increased methylation of DNA causes gene inhibition, those with lower levels of DNA inhibition therefore exhibited higher levels of gene activity than normal.
Cancer- in DNA, there is a region near the promoter region which has no methylation, in order to ensure gene expression. In cancer cells however, this region becomes methylated and so switches genes which should be active to off. This happens early on in the development of cancer. Epigenetic changes don't cause changes in base sequence, but can cause changes in the frequency of mutation. There exists certain genes which should remain on, which produce proteins whose purpose is to repair DNA which has mutated. It has been discovered that very early on in the development of cancer, there is increased methylation of these genes, meaning they are not expressed and so these protective genes are switched off, and mutated genes are free to develop into cancer.
   Diseases such as cancer are caused by epigenetic changed which activate or silence a gene. Therefore treatments have been developed to try and counteract the initial epigenetic changes. These treatments use drugs which inhibit certain enzymes involved in either histone acetylation or DNA methylation.
   E.g. A drug which inhibits enzymes which cause DNA methylation would act to reactivate a silenced gene.
 It is important that epigenetic treatments only affect the affected cells, otherwise they could activate or silence genes unnecessarily, which could actually cause cancer.
  Epigenetics can also be used in the diagnosis of diseases such as autism, arthiritis and cancer, by testing levels of methylation/acetylation in the potentially diseased tissue. Early diagnosis will allow a better chance of cure.

7.i  State what small interfering RNA (siRNA) is

Small interfering RNA (siRNA) is a small double stranded molecule of RNA responsible for breaking up strands of mRNA before they can be translated into a polypeptide.

 7.ii Explain how siRNA affects gene expression

• An enzyme cuts down large double stranded molecules of RNA into smaller sections called small interfering RNA.
• One of the two siRNA strands combines with an enzyme.
• The siRNA molecule guides the enzyme to a messenger RNA molecule by pairing up its bases with the complementary ones on a section of the mRNA molecule.
• Once in position, the enzyme cuts the mRNA molecule into smaller sections.
• The mRNA is no longer capable of being translated into a polypeptide
• Therefore the gene hasn't been expressed, i.e. it is blocked.

Summary Questions

1. Explain what is meant by epigenetics
Epigenetics is the process by which environmental factors can cause heritable changes in gene function without changing the base sequence of DNA.

2. Name two mechanisms by which changes in the environment can inhibit transcription

• Decreased histone acetylation
• Increased DNA methylation

3. One of the two strands of siRNA combines with an enzyme and guides it to a mRNA molecule which it then cuts. Explain why the mRNA is unlikely to be cut if the other strand of siRNA combines with the enzyme

The other strand would have complementary bases (i.e. GCUA instead of CGUA respectively). It is unlikely that these opposite base pairings would complement a sequence on the mRNA. The siRNA, with enzyme attached, would therefore not bind to the mRNA and so would be unaffected.

4. Suggest how siRNA could be used to:

   a) identify the role of genes in a biological pathway

   b) to prevent certain diseases

a) Some siRNA that blocks a particular gene could be added to cells. By observing the effects (or lack of) we could determine what the role of the blocked gene is.

b) siRNA could be used to prevent the disease by blocking the gene that causes it.

5. The enzyme histone deacetylase (HDAC) removes acetyl groups from histones. Suggest what the effect of this enzyme would be on:

   a) the arrangement of chromatin (DNA-histone complex)

   b) transcription

a) The chromatin would be more closely condesnsed, it would be heterochromatin.

b) Transcription would cease

Students should be able to interpret data provided from investigations into gene expression

1. The advantage of fetal haemoglobin having a greater affinity for oxygen is that it can load oxygen efficiently from the mother at the placenta where the two supplies come close together.

2. At birth, there is 20% beta globulin, 30% gamma globulin and 50% alpha globulin

3. At 30 weeks, the expression of alpha globulin remains constant, however gene for gamma globulin is expressed less, and the gene for beta globulin is expressed more.

4. After 30 weeks, there is a decrease in the expression of the gene for gamma globulin. This could be due to the gene being blocked due to the mRNA being broken down by siRNA, or the prevention of transcription due to increased methylation of DNA or decreased acetylation of histones.

5. A possible therapy would be to express the gene for gamma globulin and to inhibit the gene for beta globulin. This would result in the haemoglobin produced being similar to that of fetal, and so reduced symptoms of sickle cell disease.

Students should be able to evaluate the appropriate data for the relative influences of genetic and environmental factors on phenotype.

1. Environmental
2. If the influence were totally genetic, then the plants which were genetically identical would show the same phenotype regardless of where they were grown. The greater the environmental influence, the greater the differences in phenotype between the genetically identical plants. As there are major differences in phenotype for the genetically identical plants, the main factor must be environmental.
3.Environmental conditions at higher altitudes are more extreme than those at lower altitudes, and less suited for photosynthesis (colder, windier, less soil). Plants from high altitudes have adapted to survive in these extremes, therefore the conditions at lower altitudes prevent fewer problems and they thrive. Plants that have evolved at low altitude, by contrast, find harsher conditions at higher altitudes and struggle to grow.