MUTATIONS AND GENE EXPRESSION

MUTATIONS

MUTATION - any chnage to the base sequence of DNA. Rates are increased by mutagenic agents. Types can include;

SUBSTITUTION - one or more bases are swapped for another

DELETION - one or more bases are removed

ADDITION - one or more bases are added

DUPLICATION - one or more bases are repeated

INVERSION - a sequence of bases is reversed 

TRANSLOCATION - a sequence of bases is moved from one location in the genome to another, could be within the same chromosome or movement to a different chromosome. . 

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MUTATIONS

If a mutation occurs in a gene the sequence of amino acids in the ppt it codes for could be changed. A change in the amino acid seqeunce of a ppt may change the final 3D shape of the protein - could mean its non-functionalSome mutations can cause genetic disorders - inherited diosrders caused by abnormal genes or chromosomes e.g. CF Some can increase the likelihood of developing certain cancers e.g. BRCA1 mutations increase chance of breast cancer.If a gamete contains a mutation for a genetic disorder or a type of cancer and is fertilised this will be present in the new fetus formed - these are hereditary mutations as theyre passed onto offspring. 

Not all mutations affect the order of AA - degenrate nature of genetic code means some AA are coded for by more than one DNA triplet. Not all mutations will result in a change to the AA sequence. e.g. substitutions will still code for the same amino acid. Additions, deletions and duplications within a gene will almost always change the AA sequence of a ppt, as they change the number of bases in the DNA code. This causes a frameshift in the bases that follow so the triplet code is read in a different way. 

Mutagenic agents increase the rate of mutation, e.g. UV radiation, ionising radiation, chemicals and some viruses. They can act as a base -chemicals (base analogs) can sub for a base during DNA replication, changing the base sequence of the new DNA. They can also alter bases - some chemicals can delete or alter bases. They can also change the structure of DNA - some types of radiation can change the structure of DNA causing problems during replication.

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CANCER

Mutations in genes can cause uncontrolled cell growth. Mutations that occur after fertilisation = acquired mutations. When these occur in cell that control cell divison = uncontrolled cell division. Uncontrollable cell division = tumour (a mass of abnormal cells) Tumours that invade and destory surrounding tissue = cancers. Tumour suppressor genes and proto-oncogenes (mutations in these can cause cancer)

Tumour suppressor genes can be inactivated if a mutation occurs in the DNA sequence. Tumour suppressor genes slow cell division by producing proteins that stop cells dividing or cause them to self-destruct. If a mutation occurs the protein isnt produced, the cells divide uncontrollably resulting in a tumour.

The effect of a proto-oncogene can be increased if a mutation occurs in the DNA sequence. A mutated proto-oncogene is known as an oncogene. Proto-oncogenes stimulate cell division by producing proteins that make cells divide. In an oncogene the gene becomes overactive, stimulating uncontrollable cell division resulting in a tumour.  

Malignant - cancers. They usually grow rapidly and invade and destory surrounding tissues. Cells can break off the tunours and spread to other parts of the body in the blood or lymphatic system

Benign - not cancerous. Usually grow slower and are often covered in fibrous tissue that stops cells invading other tissues. Theyre often harmless but can cause blockages and put pressure on organs. They can become malignant. 

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CANCER

Tumour cells differ from normal cells;

  • they have an irregular shape
  • the nucleus is larger and darker, sometimes they may have more than one
  • they dont produce all the proteins needed to function normally
  • have different antigens on their surface
  • dont respond to growth regulating processes
  • divide by mitosis more frequently 

Abnormal methylation of cancer related genes can cause tumour growth. Methylation = adding a methyl (CH3) group. Methylation of DNA is an important part of regulating gene expression - can control whether or not a gene is transcribed and translated. Too much or too little methylation can cause a problem. When TSG are hypermethylated, genes are not transribed - proteins they produce to slow cell division are not made, therfore cells are able to divide uncontrollably by mitosis and tumours can develop. Hypomethylation of POG causes them to act as oncogenes - increasing production of proteins that encourage cell division, stimulating uncontrollable cell division causing tumours to form.

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CANCER

Increased oestrogen may contribute to some breast cancers. Increased exposure to oestrogen over an extended period of time is thought to increase the chance of developing breast cancer. There are a few theories as to why this is; oestrogen can stimulate certain breast cells to divide and replicate, as their are more cell divisions occuring naturally chance of mutations increases & chance increases of them becoming cancerous. 

DATA ON CANCER 

Genetic and environmental factors affect the risk of cancer

Genetic - some cancers are linked with specific inherited alleles. If you inherit that allele your more likely to get that type of cancer.

Environmental - exposure to radiation, lifestyle choices e.g. smoking, increased alcohol consumption have been linked to an increased chance of developing some cancers. 

Its difficult to interpret relative contributions of genes and the environment, some characteristics can be affected by many different genes and many environmental factors. Its difficult to know which factors are having the greatest effect, making it hard to draw conculsions about the causes of variation. 

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STEM CELLS

Stem cells are unspecialised cells that can develop into any other type of cell, they divide to become new cells which then become specialised. Theyre found in the embryo and in some adult tissues. 

Totipootent stem cells = stem cells that can develop into any type of body cell in an organism. Theyre only present in mammals in the first few cell divisions of an embryo.After this they become pluripotent.

Pluripotent stem cells = stem cells that can specialise into any cell in the body, but loose the ability to become cells that make up the placenta.

Multipotent stem cells = these are able to differentiate into a few different types of cell. e.g both red and white blood cells can be formed from multipotent stem cells in bone marrow. 

Uinpotent stem cells = can only differentiate into one type of cell. e.g. theres one type that can only divide into empidermal skin cells.

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STEM CELLS

Stem cells become specialised during their development, they only transcribe and translate part of their DNA;

  • they all contain the same genes - not all are transcribed and translated (expressed) 
  • under the right conditions some genes are expressed and other are switched off
  • mRNA is only transcribed from specific genes
  • this is then translated into proteins
  • these proteins modify the cell - determine cell structure and control the cell processes 
  • changes to the cell produced by these proteins cause the cell to become specialised, these changes are difficult to reverse. 

Cardiomyocytes (heart muscle cells) can be made from unipotent stem cells. Old or damaged cardiomyocytes can be replaced by new ones derived from a small suply of unipotent stem cells in the heart. Some researchers think this process is constantly occuring but differ on how quickly it happens. Some believe its quite slow and that its possible some are never replaced thoughout a lifetime. Others think it soccuring quicker, every cardiomyocyte is replaced several times in a lifetime. 

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STEM CELLS

Stem cells can be used to treat human disorders. Some therapies already exsist for some diseases affecting the blood and immune system. 

Bone marrow contains stem cells that can become specialised to form any type of blood cell. Bone marrow transplants can be used to replace faulty bone marrow that produces abnormal blood cells. Stem cells in the transplanted marrow divide and specialise to produce healthy blood cells. This has been used to treat lukemia and lymphoma.

They can also be used to treat other diseases e.g. spinal cord injuries - can be used to replace damage tissue or respiratory diseases - donated windpipes can be stripped down to their simple collagen structure and then covered in tissue generated by stem cells, this is then transplanted into patients. 

There are huge benefits to  using stem cells in medicine. They could save many lives - many waiting for organ transplants may die before a donor becomes available, stem cells could be used to grow organs for those awaiting transplants. They can also improve quality of life for many people - can be used to replace damaged cells in the eyes of the blind. 

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STEM CELLS

Human stem cells can come from adult tissue or embryos, there are three main sources of human stem cells;

  • ADULT STEM CELLS - obtained from body tissues of an adult e.g. bone marrow. Csn be obtained in a simple operation with little risk. They arent as flexible as embryotic stem cells as they can only specialise into a limited range of cells theyre multipotent.
  • EMBRYOTIC STEM CELLS - obtained from embryos at an early stage of development. Embryos are created via IVF, once theyre 4-5 days old, stem cells are removed and the rest of the embryo is destroyed. These stem cells are pluripotent and can specialise into any type of body cell.
  • iPS STEM CELLS - created in the lab, involves 'reporgamming' specialised adult body cells so they become pluripotent. They are made to express a range of transcriptional factors associated with pluripotent stem cells, this causes genes to be expressed associated with pluripotency.One way the transcription factors are introduced can be through infection with a specially modified virus which contains gene coding for the transcription factors in its DNA. When the virus infects the cell the genes are passed into the cells DNA meaning the cell can produce the transcription factors.
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STEM CELLS

There are ethical issues surrounding the use of embryotic stem cells;

  • some believe at the moment of fertilisation an individual has the right to life - wrong to destroy embryos.
  • some think that scientists should only use adult stem cells because their production doesnt destroy an embryo. However, adult stem cells cant develop into the specialised cells that embryotic cells can.
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REGULATION OF TRANSCRIPTION AND TRANSLATION

Transcription factors control the transcription of target genes. Transcription is when a gene is copied from DNA into mRNA. Enzyme responsible = RNA polymerase;

  • in eukaryotes, transcription factors move from the cytoplasm to the nucleus where they bind to specific DNA sites near the start of their target genes.
  • they control expression by controlling rate of transcription.
  • some factors - activators stimulate or increase rate of transcription (help RNA polymerase bind to the start of the target gene and activate transcription)
  • other factors - repressors inhibit or decrease rate of transcription (bind to start of target gene preventing RNA polymerase binding, stopping transcription) 

Oestrogen can also initiate the transcription of target genes. Oestorgen is a steroid hormone that affects transcription by binding to a transcription factor (oestrogen receptor) = an oestrogen-oestrogen complex. This complex moves from the cytoplasm into the nucleus where it binds to specific DNA sites near the start of the target gene. This complex acts as an activator of transcription (helping RNA polymerase bind to the start of the target gene).

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REGULATION OF TRANSCRIPTION AND TRANSLATION

In eukaryotes, gene expression is also affected by RNA interference (RNAi). RNAi is where small, double stranded RNA molecules stop mRNA from target genes being translated into proteins. A similar process occurs in prokaryotes. RNAi = siRNA & miRNA.

siRNA (and miRNA in plants)

  • once mRNA has been trancribed it leaves the nucleus for the cytoplasm.
  • in the cytoplasm, double stranded siRNA associates with several proteins and unwinds, a single strand then binds to the target mRNA.
  • the base sequence of siRNA is complimentary to the base sequences in sections of the target mRNA.
  • proteins associated with siRNA cut the mRNA into fragments - cant be translated. The fragments then move into a processing body which contains 'tools' to degrade them.
  • a similar process happens with miRNA in plants.
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REGULATION OF TRANSCRIPTION AND TRANSLATION

miRNA in mammals

  • in mammals, miRNA isnt usually fully complimentary to the target mRNA - less specific than siRNA & may target more than one mRNA molecule.
  • like siRNA it associates with proteins and binds to target mRNA in the cytoplasm.
  • miRNA - protein complex blocks the translation of the target mRNA.
  • mRNA then moves into a processing body, can be either stored or degraded. When stored it can be returned and translated at another time. 

Gene expression system in bacteria - example and experiment; ECOLI & the lac repressor;

  • ecoli is a bacterium that respires glucose, uses lactose if glucose isnt available.
  • when lactose is present, ecoli makes an eznyme to digest it - if theres no lactose the enzyme isnt made, the gene is only expressed when lactose is present
  • production of the enzyme is controlled by the lac repressor (transcription factor) 
  • when theres no lactose, lac repressor binds to the DNA at the start of the gene, stopping transcription. 
  • when lactose is present, it binds to the lac repressor, stopping it binding to the DNA & gene is transcribed. 
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EPIGENETIC CONTROL OF GENE EXPRESSION

epigenetic changes are another way of controlling gene expression.

epigenetic control can determine whether or not a gene is expressed. In eukaryotes, epigenetic control can determine whether a gene is switched on or off - whether the gene is expressed or not. Works through attachment or removal of chemical groups (epigenetic marks) to or from DNA or histone proteins - these dont alter the base sequence of DNA. They alter how easy it is for the enzymes and other proteins needed for transcription to interact with and trancribe the DNA. Epigenetic changes to gene expression can occur in response to changes in the environment - pollution and availability of food. 

epigenetic changes can be inherited by offspring - some epigenetic marks on DNA are removed, some escape the removal process and are passed on to offspring. Expression of some genes in the offspring can be affected by environmental changes that affected their parents and grandparents. e.g. epigenetic changes in some plants in response to drought have been passed on to later generations. 

increased methylation of DNA switches a gene off. When a methyl group (e.g of epigenetic mark) us attached to the DNA coding for a gene. The group always attches at the CpG site (cytosine and guanine base are next to each other in the DNA). Increased methylation changes the DNA structure - transcriptional machinery (enzymes, proteins) cant interact with the gene = gene is not expressed (its switched off)

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EPIGENETIC CONTROL OF GENE EXPRESSION

Decreased acetylation of histones can also switch genes off.

Histones are proteins DNA wraps around to form chromatin - makes up chromosomes. How condensed the chromatin is can affect the accesibility of the DNA & whether or not it can be trancribed;

  • histones are epigenetically modified by the addition or removal of acetyl groups (e..g of a epigenetic mark)
  • when histones are acetylated the chromatin is less condensed - transcriptional machinery can access the DNA, allowing genes to be transcribed.
  • when acetyl groups are removed from the histones, the chromatin becomes highly condensed & genes in the DNA cant be transcribed because the transcriptional machinery cant physically access them.
  • histones deacetylase (HDAC) enzymes are responsible for removing the acetyl groups.

Epigenetics can lead to the development of diseases - abnormal methylation of tumour suppressor genes and oncogenes can cause cancer. Another example is fragile X syndrome (genetic disorder with symptoms such as learning and behavioural difficulties & characteristic physical features). Caused by a heritable duplication mutation in a gene on the X chromosome - FMR1 - CGG is repeated more times than usual. This repeat means there are more CpG sites in the gene that usual = increased methylation = genes are switched off. Because the gene is switched off, proteins it codes for arent produced, this lack of protein causes the symptoms of the disease. 

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EPIGENETIC CONTROL OF GENE EXPRESSION

Drugs may be able to treat diseases caused by epigenetic changes. Epigenetic changes are reversible. Drugs are designed to counteract the epigenetic changes that cause the diseases. e.g. increased methylation can lead to genes being switched off, drugs that stop DNA methylation can sometimes be used to treat diseases caused this way. e.g. azacitidine is used in chemo for types of cancer caused by increased methylation of tumour suppressor genes. 

Decreased acetylation of histones can also lead to genes being switched off. HDAC inhibitor drugs (romidepsin) can be used to treat diseases caused in this way - including some types of cancer. They work by inhibiting the activity of histone deacetylase (HDAC) enzymes which remove acetyl groups from histones. Without the action of HDAC, genes remain acetylated and the proteins they code for can be transcribed. 

The problems include the fact that these epigenetic changes take place normally in a lot of cells, so its important to make sure the drugs are as specific as possible. e.g. drugs used in cancer therapies can be designed to only target dividing cells to avoid damagine normal body cells. 

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EVALUATING DATA ON PHENOTYPES

The phenotype of an organism is the result of the organisms genotype and the interaction of its genotype with the environment. Its not always clear how much a phenotype is influenced by genes and how much by the environment 

OVEREATING - was thought to be caused by environmental factors (increased availability of food) in 1st world countries. It was later discovered that food consumption increases brain dopamine levels in animals, once enough dopamine is produced animals would stop eating. People with one particular allele had 30% fewer dopamine receptors (they wouldnt stop eating when dopamine levels increased). Based on the evidence, scientists think that overeating has both genetic and environmental causes.

ANTIOXIDANTS - many foods contain antioxidants - thought to play a role in preventing chronic diseases e.g. berries have high antioxidant levels. Berries produced by different species of plant contained different levels of antioxidants because of genetic factors. Experiments found out that environmental factors caused variation. Scientists now believe that antioxidant levels in berries is due to both genetic and environmental factors. 

Twin studies help to determine influences on phenotype - twins are genetically identical (monozygotic) so any difference in phenotype must be due to environmental factors. If a characteristic is very similar in identical twins genetics probs play a more important role. If its different between the two twins the environment must have a larger influence.

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Comments

12s_r

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Great Card!

Just to clarify what doe ppt, CF, AA mean on the mutations card 

POG and TSG on the second cancer card

Thanks!! :D

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