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School Biology Notes: The HUMAN GENOME - what is it? what is its importance?

Introduction to the GENOME of an organism & gene expression

The importance of knowing the human genome - the 'project'

Considering chromosomes, alleles, genotypes, phenotypes, variations

 Doc Brown's school biology revision notes: GCSE biology, IGCSE  biology, O level biology,  ~US grades 8, 9 and 10 school science courses or equivalent for ~14-16 year old students of biology

 This page will help you answer questions such as ...  What is a gene?  What is a chromosome?  What is the human genome?   What are alleles?   What is the difference between genotype and phenotype? Give examples of medical applications of data from the human genome project. Why is genetic testing controversial?

Sub-index for this page

(a) The connection between DNA, genes, alleles, chromosomes and the genome

(b) Genetic instructions and the characteristics of an organism

(c) The importance of genome knowledge - the human genome project

(d) Genetic screening - using data from the human genome project - potential medical treatments - issues



(a) The connection between DNA, genes, alleles, chromosomes and the genome

The genome is the whole of the genetic material of an organism - all of the DNA - coding and non-coding!

In animal and plant cells the genetic material (DNA) is contained in the cell nucleus and arranged in 'packages' called chromosomes.

Chromosomes often occur in pairs e.g. human cells have 23 pairs of chromosomes, 46 chromosomes in all.

Every chromosome is a very long strand of DNA that is coiled up to give it a characteristic shape.

Reminders: DNA is a very long natural polymer in which the monomer is a nucleotide that makes up the repeating unit in the molecular chain. The DNA molecule consists of two strands wound and bound together to form the double helix molecule.

For more on structure of DNA see DNA and Protein Synthesis  gcse biology revision notes

A gene is a relatively short strand of DNA that forms a section of a chromosome that codes for a specific protein.

Each gene has the coded instructions to tell a cell to combine a particular sequence of amino acids to form a specific protein. In this case the monomer unit is an amino acid and the resulting polymer is called a protein.

Proteins control the development of an organism's characteristics and all its functions.

As if this wasn't complicated enough, there is an extra layer of complexity due to the existence of alleles!

Genes can exist in different versions called alleles - subtle differences in the genetic DNA code.

Each allele produces a different form of the same characteristic of an organism.

e.g. brown or blue eyes is a good example.

Each chromosome in a pair carries the same genes, BUT, they may carry different alleles.

The diagram below sums up the relationship between all the terms described and explained above.

Note: Genetic variants

Genetic variants (mutations) are caused by alterations in the common nucleotide sequences in the DNA of genes.

The term variant can be used to describe an alteration that may be benign (harmless), pathogenic (harmful), or of unknown significance.

The term variant is increasingly being used in place of the term mutation.

Variants are key to successful evolution because genotype changes (usually of the smaller type) can lead to changes in phenotype. 

Human genetic variation is the genetic differences both within and among populations. There may be multiple variants of any given gene in the human population.

A mutation may defined as any change in a DNA compared to normal that results in a rare and abnormal variant.

For more on structure of DNA see DNA and Protein Synthesis  gcse biology revision notes

For much more on mutations and variants see Genetic variation and mutations

and section on variation in Evolution - theories and evidence, variation, speciation - new/old species & extinctions


(b) Genetic instructions and the characteristics of an organism

The combination of all alleles for each gene of an organism are called genotypes.

It is the genotypes of each organism that makes it unique.

However, the characteristics shown by an organism are called their phenotypes.

The phenotype of an organism is primarily determined by the genotype, but the phenotype can be influenced by the environment the organism is interacting with.

e.g. under what conditions does an organism grow and develop?

The diet of an animal can affect how well it grows and how healthy it is. A well nourished child grows strong and healthy. A malnourished child short of protein, vitamins etc. may have stunted growth, be too thin, physically weak and the immune system weakened so the individual is more susceptible to infectious diseases.

A flower exposed to lots of sunlight, rich soil and adequate water may grow a healthily rich green and have attractively coloured flowers. If a plant is deprived of enough sunlight, nutrients or water, it grows somewhat thinly and becomes limp, it tends to be yellowish rather than green and petal colours may fade.

In both of the above cases, the genotype determines the maximum healthy growth of organism, but this may be reduced by environmental factors.

Therefore the variation of the phenotype is determined by a combination of the genotype (genetic factors) and the conditions of growth and development (environmental factors).

For more see An introduction to genetic variation and the formation and consequence of mutations  gcse biology notes

also Introduction to the inheritance of characteristics and genetic diagrams  gcse biology revision notes

and section on variation in Evolution - theories and evidence, variation, speciation - new/old species & extinctions


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(c) The importance of genome knowledge - the human genome project

The genome is the term that describes the total genetic material of an organism - all the DNA.

The human genome projects has mapped and identified all the genes found in human DNA.

Every organism has its own unique genome and scientists can now completely work it out - clever stuff!

Genome data is used to characterise species and help research plant and animal evolution patterns.

See note 3. below on the human genome.

The human genome has around 3 billion base pairs in the DNA sequences of the genes-chromosomes!

Apparently quite a lot of your DNA is 'junk', but don't worry, and we won't go into that, just study hard, play hard and enjoy life!

Thousands of scientists around the world have collaborated on the human genome project.

We now know the complete human genome and over 20,000 to 25,000 genes have been located on it, but although we know what many do (code for), there is much more to find out.

Around 1800 genes have been identified that relate to human diseases - and this data is the target of medical research to benefit medicine.

PLEASE NOTE that all humans share 99.9% of their genomes, which makes you think!

 

How is our understanding of the human genome helping science e.g. evolution theory or medicine?

Any new drug must be targeted at some specific medical condition where there is a need.

The target might be blocking the action of an enzyme or a gene with a chemical agent (drug) you can interfere with the development of a disease e.g. the anti-cancer drugs used in chemotherapy treatments to reduce the growth of tumour cells or kill them.

Studies of the genomes and resulting proteins in both plants and animals are proving useful to identify 'targets'.

You then have to find a chemical that will have an effect on the target, fortunately there are databases of chemicals that have been previously screened for likely effectiveness.

The screening might not initially indicate the best molecule to 'hit the target' in a biochemical sense, but, it may provide a starter molecule - which you can then modify to make different derivative molecules, one of which might provide a more effective treatment.

Medical applications

e.g. prediction and prevention of disease, testing for and treating inherited diseases, more effective medicines, BUT, there are ethical issues to deal with too.

1. It has been possible for genetic scientists to identify particular genes (genetic variants) in the genome that are linked to certain types of non-inherited diseases.

Hopefully it will lead to predicting predisposition to certain diseases, leading to early intervention with medical treatment and perhaps a preventing disease actually developing.

If you know what genes predispose people to certain diseases, medical advice can be more accurately given e.g. choice of diet and other lifestyle factors based on the results of genetic screening tests.

Many common diseases like cancer and heart conditions are caused by the interaction of different genes, as well as lifestyle factors.

See also Introduction to genetic variation - formation and consequence of mutations 

and Stem cells and uses - leukaemia treatment

 

2. From the human genome project, by knowing the genes associated with an inherited disease (genetic disorder), we can understand it more clearly and then develop more effective treatments - which may involve genetic engineering itself.

We know inheriting certain genes greatly increase your risk of developing certain cancers, this can help with making lifestyle choices to minimise the risk of suffering from the disease - as with 1. above, its a sort of risk management situation.

In the UK newborn babies are routinely tested for particular genetic variants known to cause genetic disorders e.g. the double recessive allele that causes cystic fibrosis.

The results from genetic screening enables the medical treatment-management to begin promptly while the baby is still very young.

Children with leukaemia can have a genetic test to help decide which is the most effective treatment in terms of medication and its dose.

See further notes on genetic screening of an embryos or fetus (much more controversial)

and Introduction to the inheritance of characteristics and inherited disorders

It is hoped that all this new genetic science will lead to the development of better, and more personal, treatments for a wide range of medical conditions.

We are now developing drugs and other techniques that work at the molecular level in combating disease and tailored to suit the individual's body chemistry.

The variations in patients genetic variants (alleles) mean that one drug isn't necessarily as effective with all patients suffering from the same condition - so new drugs can be designed to suit these 'varying' patient situations.

3. We know certain alleles affect how our body responds to certain diseases and their treatment.

Scientists hope to use this knowledge to develop more effective drugs that can be specifically suited to patients with certain alleles in their genome.

Different drugs can be tested, and their effectiveness compared with the patient's alleles, and you can compare existing drugs with new ones.

It has been found that some breast cancer drugs are only effective in women if they have certain alleles in their genome.

4. To help in these medical quests, scientists are analysing the genomes of human pathogens to help us understand and control certain infectious diseases.

The complete genome of bacteria such as the deadly MRSA, which is resistant to antibiotics.

It is hoped that pathogen genome knowledge will allow swifter decisions as to the best treatment administered to patients i.e. determined by the genomics of the specific bacterial strain.

 

The science of human evolution and migration

The human genome project can be tackled by various genetic strategies.

(i) Analysis of data from people's Y chromosome inherited down the male line.

(ii) Analysing mitochondrial DNA inherited through mothers.

Our knowledge of the human genome is being used to trace the migration of certain populations across the continents of the world.

The latest research suggests that all modern humans have descended from a common ancestor who lived in Africa, and their descendents have spread over all over the Earth - moving by both land and sea.

This is known as the 'Out of Africa' theory and seems to have begun around 60 000 years ago.

Why did this happen?

Maybe change in climate, so seeking more food for hunter-gathering tribes?

It is known the climate in Africa at this time became much dryer - less rain, less plant life, less food for animals, less plants and animals for humans to eat.

All humans have a very similar genome.

In terms of ancestors - genetically, who you were and where you have been is 'hidden' in your genome! until, that is, modern DNA analysis reveals all !!!

However, as different populations of people migrated to different areas of the planet, small differences in DNA 'evolved' (incorporated) into their genome e.g. producing different skin or hair colour or facial features.

The genetic variation is as little as 0.001%, but even so, genetic scientists can work out when these new populations split off in a different 'genetic' and geographical direction.

People who are related will have an even more similar genome.

The human genome is being compared to some of closest relative in the world e.g. primates.

Ever since researchers sequenced the chimp genome in 2005, they have known that humans share about 99% of our DNA with chimpanzees, making them our closest living relatives - that should make you think!


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(d) Genetic screening - using data from the human genome project - potential medical treatments - issues

Introduction

When you know that a particular allele causes an inherited genetic disorder you can take action e.g.

if an allele that causes an inherited disorder is identified, we could have regular medical checks for these specific diseases and get early diagnosis and subsequent treatment.

Genetic treatment might be able to cure the disease.

From the human genome project scientists can identify the genes and alleles that may be responsible for causing inherited disorders, and much faster prior to the mapping of the complete human genome.

Common diseases like cancer and heart conditions are caused by the interaction of our genes and our lifestyle factors.

If we know which genes predispose an individual to certain types of disease we could be given personal advice on diet and lifestyle (in general) to minimise the risk of suffering from particular diseases.

However, there are many issues to with genetic testing results e.g.

(i) From the point of view of potential parents, there maybe crucial choices regarding whether children may be born with a genetically inherited disorder - especially if both parents carried the same faulty allele.

(ii) Would insurance companies be allowed to see your 'genetic profile', are they entitled to know it e.g. as regards health or life insurance?

More on these points below in section (d)

 

Examples of using genetic testing

Example 1.  A couple wishing to start a family might wish to know whether there is a risk of the baby developing a genetic disorder. This another aspect of family planning at the discretion of parents.

This can involve genetic testing at various point e.g.

1. Prior to conception, parents can be tested to see if they are carriers of a defective gene known to cause a genetic disorder.

It may be known that one of the parents comes from a family line where a genetic disorder has occurred.

The parents may not suffer from the genetic disorder, but they may be a carrier of the defective gene.

The genetic tests would show if any parent was a carrier and the probability of the baby inheriting the disorder - the parents can then make an 'informed decision' as to whether to have a child.

see Introduction to the inheritance of characteristics and inherited disorders

2. After conception or laboratory fertilisation, the embryo or fetus (embryo >8 weeks old) can be tested - see section (ii) below on embryonic genetic testing.

A pregnant woman can be tested by extracting a sample of DNA from the amniotic fluid which surrounds the fetus in the womb - there is a very small risk of causing a miscarriage.

The tests will show whether the foetus's DNA is carrying any of the genetic variants linked with a disorder.

If a positive test for such a variant is found, the couple can then make an 'informed decision' as to whether to terminate or continue with the pregnancy - a very personal and agonising family planning decision.

3. The newborn baby can be genetically tested to show whether a genetic disorder has been inherited allowing early intervention of medical treatment and subsequent long-term management of the disorder.

Example 2. Using in vitro fertilisation (IVF) embryos are fertilised in a laboratory and then implanted into the mother's womb.

Prior to implantation it is possible to remove a cell from an embryo and analyse the DNA i.e, the genes and likely genotypes/phenotypes.

This allows the detection of genetic disorders e.g. cystic fibrosis (described above) which is caused by the presence of one or more faulty genes.

You can choose to allow a genetic disorder free embryo to fully develop into a baby in the mother's womb - this minimises the baby inheriting the genetic variants linked with the disorder.

However, this ability to analyse genes in this way leads to ethical, social and economic concerns and questions about embryonic testing i.e. embryo screening for abnormal-undesired genetic traits, on which crucial decisions can be made e.g. termination of pregnancy.

e.g. after screening, embryos produced by IVF, containing abnormal alleles can be destroyed.

Example 3. Other points on genetic testing

Genome research data shows scientists the common genetic variations between people, most of which are benign and no danger to our health.

However, as I've already pointed out:

Some genetic variations are linked to our predisposition to certain disease - so this will help to design new drugs specifically tailored to suit people of a particular genetic trait.

In the UK newborn babies are routinely tested for particular genetic variants known to cause genetic disorders e.g. the double recessive allele that causes cystic fibrosis.

The results from genetic screening enables the medical treatment-management to begin promptly while the baby is still very young.

 

Arguments for embryonic/fetal screening and other genetic testing

(i) It stops newborn babies suffering as they grow up into adults.

(ii) Reducing the number of people suffering with a genetic disorder that is costly for healthcare systems to deal with.

(iii) Procedures like IVF, accompanied by genetic testing, are strictly regulated and parents are not allowed to choose desirable traits.

Parents are not allowed to choose the sex of their child, unless it is for good medical health reasons.

(iv) Other 'positive' points on genetic testing:

Early intervention for potentially serious diseases has already been mentioned.

Drugs for chemotherapy in cancer treatment are continually being developed and tested - you match a drugs performance against a person's specific genetic profile - this increases a 'working' database of treatment for future patients - another positive outcome from such treatment research is the minimising of side-effects which can quite drastic from ant-cancer drugs.

 

Arguments against embryonic/fetal screening and other genetic testing

Many objections centre around the ethical issues of IVF.

(i) IVF procedures often result in unused embryos being destroyed and some people consider this unethical - immoral, because you have destroyed a potential human life.

Even using embryos in research projects is considered to be unethical.

(ii) Terminations of IVF pregnancies on the grounds the baby may be born with a genetic disorder implies that the resulting children are undesirable and prejudice increased towards them.

Would potential parents feel under pressure NOT to have children with a potentially inherited genetic disorder.

(iii) The genetics and genetic testing of embryos before implantation in the mother's womb raises the ethical issue of preferential choice of characteristics of the baby e.g. choice of gender, eye colour irrespective of whether you allow a child to be born with disabilities.

(iv) Genetic screening is expensive and the costs of gene technology treatments are high.

The cost increases, the more personal the treatment, because the more specialised the drugs must be.

Surely this risks unfair access to these expensive treatments?

In the UK NHS treatment is free - BUT, is it locally available? Can you jump the queue by using private medicine?

In other countries, or UK private medicine - what does your insurance premium cover?

(v) The accuracy of genetic testing

Unfortunately, due to the complexity of DNA structure, genetic testing is not 100% accurate.

A positive test for a faulty gene, that is incorrect, will causing stress to the couple, and possibly the wrong decision to terminate a pregnancy because of fear of the baby inheriting a genetic disorder when there is actually no need to be concerned.

A negative test for a faulty gene, that is incorrect, means the couple are completely unprepared for the birth of a child with a genetically inherited disorder, causing considerable stress in their lives when the baby is born.

(vi) Other 'negative' points on genetic testing:

Is the use of gene technology good in the long term, since we don't actually know what the effects will be on future generations?

What might you think if you know from an early age you are more susceptible (more predisposed) to a particular disease? Won't this lead to stress thinking about it, especially if there isn't cure for it? Might you feel uneasy and worried if you 'seem' to exhibit symptoms?

Would you be discriminated against by insurance companies (e.g. insurance refusal or increased premiums) or employers (e.g. refused long-term job contract) if they knew you were likely to suffer from a genetically inherited disorder.

Society must decide on a code of conduct relating to potential discrimination AND privacy of your medical details.

Just imagine the problems caused if you genetic profile had to be submitted with a job application!


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