Topic 8 Flashcards

1
Q

what are gene mutations?

A
  • an alteration of a base in the sequence of bases for one gene.
  • Likley to occur during DNA replication, which is in interphase of cell cycle
  • occur spontaneously but frequency of them occurring can be increased by mutagenic agents
  • can result in different amino acid sequence in the encoded polypeptide, as they alter the gene
  • if amino acid sequence changes when protein modified into tertiary structure, it will form hydrogen and ionic bonds in different places and fold differently, resulting in a different 3d shape and so a non functioning protein e.g. active site changes shape so no longer works as enzyme
  • alterations to genes can result in a mutation that causes cancer
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2
Q

What are mutagenic agents?

A
  • high energy and ionising radiation include alpha and beta particles and x ray, gamma rays and ultraviolet light (UV)
  • Carcinogens are chemicals that can alter the structure of DNA and interfere with transcription. Include chemicals in tobacco smoke, mustard gas and peroxides.
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3
Q

What are addition mutations?

A

one or more extra bases added to the base sequence
* causes a frame shift (all subsequent codons altered) to the right
* mutation can be harmful as all altered codons may code for a different amino acid and result in a different amino acid sequence resulting in a non functioning protein

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4
Q

What is a deletion mutation?

A

one or more bases are removed from the base sequence
* causes a frame shift to the left which may result in a different polypeptide chain and a non functioning protein

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5
Q

What are substitution mutations?

A

one or more bases are swapped for another

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6
Q

What are inversion mutations?

A

A sequence of bases is reversed e.g. ATGCCT becomes ATCCGT (GCC reversed to CCG)

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7
Q

What is a duplication mutation?

A

one or more base sequences are repeated e.g. ATGCCT becomes ATGCCCCT (CC repeated)

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8
Q

What is a Translocation Mutation?

A

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

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9
Q

What effect do Mutations have?

A
  • order of DNA bases in a gene determines the amino acid sequence of a particular polypeptide
  • if mutation occurs in a gene, the sequence of amino acids in the polypeptide that it codes for could be changed.
  • polypeptides make up proteins and a change in amino acid sequence of polypeptide may change the tertiary structure of the protein, resulting in a non functioning protein e.g. mutation in a polypeptide that makes up an enzyme may change the shape of an enzyme’s active site. This may stop substrates from being able to bind to active site, meaning enzyme cannot catalyse reaction as it is denatured.
  • some mutations can increase likelihood of developing certain acncers
  • some mutations can cause genetic disorders (inherited disorders caused by abnormal genes/chromosomes e.g. cystic fibrosis)
  • if a gamete containing a mutation for a type of cancer/genetic disorder fertilised, mutation will be present in new fetus formed- hereditary mutations as passed to offspring.
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10
Q

Why do not all types of mutation always result in a change to the encoded amino acid sequence of the polypeptide?

A
  • not all mutations affect the order of amino acids in a protein, as some mutations change only one triplet code
  • genetic code is degenerate so some amino acids are coded for by more than one DNA triplet e.g. tyrosine can be coded for by TAT or TAC in DNA)
  • some substitutions will still code for the same amino acid, as DNA triplet may still code for same amino acid even after substitution
  • sometimes inversion mutations do not cause a change in the amino acid sequence, as DNA triplet may still code for same amino acid even after base sequence inverted.
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11
Q

What are Frameshifts?

A
  • Some gene mutations change the nature of all base triplets downstream from the
    mutation, ie result in a frameshift
  • addition, duplication and deletion mutations almost always change amino acid sequence of a polypeptide because they change the number of bases in the DNA code
  • causes a frameshift in the base triplets that follow, so the triplet code is read in a different way.
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12
Q

What are Mutagenic Agents?

A
  • mutations occur spontaneously e.g. when DNA is misread during replication
  • BUT mutagenic agents can increase the rate of mutations e.g. ultraviolet radiation, ionising radiation, some chemicals and viruses increase rate of mutations in many ways.
    1. Acting as a base- base analogs (chemicals) can substitute for a base during DNA replication, changing the base sequence in the new DNA
    2. Altering bases- some chemicals can delete or alter bases e.g. Alkylating agents can add an alkyl group to guanine, which changes the structure so it pairs with thymine, instead of cytosine
    3. changing the structure of DNA- some types of radiation can change the structure of DNA, which causes problems during DNA replication e.g. UV radiation can cause adjacent thymine bases to pair up together.
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13
Q

What are Stem cells?

A
  • undifferentiated cells that can continually divide and become specialised. Differentiation is the process by which stem cells become specialised
  • multicelluar organisms have a diverse range of specialised cells that all originate as undifferentiated stem cells.
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14
Q

What are Totipotent Stem cells?

A
  • stem cells that can divide and produce any type of body cell in an organism (including cells that make up placenta in mammals)
  • during development, totipotent stem cells translate only part of their DNA, resulting in cell specialisation
  • only present in mammals in first few cell divisions of an embryo, and after this point become pluripotent.
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15
Q

What are Pluripotent stem cells?

A
  • found in embryos and can differentiate into almost any cell in body (all except cells that make up placenta)
  • used in research with the prospect of using them to treat human disorders. These cells could be used to regrow damaged cells in humans, such as replace burnt skin cells. These treatments are potential as there are issues.
  • this can cause issues as sometimes the treatment does not work or the stem cells continually divide to create tumours
  • there is an debate on whether it is ethical to make therapeutic clones of people to make an embryo to get the stem cells to cure a disease and then destroy the embryo.
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16
Q

What are Multipotent Stem cells?

A
  • present in adult mammals
  • able to differentiate into a limited number of different cell types
  • e.g. both red and white blood cells can be formed from multipotent stem cells found in bone marrow
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17
Q

What are Unipotent stem cells?

A
  • present in adult mammals
  • can only differentiate into one type of cell
  • e.g. a type of unipotent stem cell that can only divide to produce epidermal skin cells, which make up outer layer of skin
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18
Q

How do Stem cells become specialised?

A
  • stem cells become specialised because during their development they only transcribe and translate part of their DNA. stem cells all contain same genes but during development not all of them get trasncribed and translated (expressed)
  • under one set of conditions, certain genes are expressed and others are switched off. Under different conditions different genes are expressed and others are switched off
  • expressed genes get transcribed into mRNA, which is then translated into proteins. These proteins modify the cell (determine cell structure and control cell processes, including the expression of more genes, which produces more proteins
  • changes to the cell produced by these proteins cause the cell to become specialised. Changes are diffcult to reverse, so once a cell has specialised, it stays specialised.
  • summary: genes expressed, mRNA transcribed and translated into proteins, proteins modify cell, cell becomes specialised
  • genes switched off, mRNA not transcribed or translated, proteins not produced.
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19
Q

What are Cardiomyocytes and how are they formed?

A
  • cardiomyocytes are heart muscle cells that make up much of heart tissue
  • In mature mammals, it’s though they cannot divide to replicate themselves, so for ages people thought it wasn’t possible to regenerate an individual’s own heart cells at all, which is a problem if the heart becomes damaged e.g. by heart attack or the cells became worn out through age
  • recent research suggests heart has some regenerative capability. Some scientists believe old/damaged cardiomyocytes can be replaced by new cardiomyocytes derived from a small supply of unipotent stem cells in heart
  • some researchers believe this process may be constantly occurring, but haven’t agreed how fast. Some believe it’s a very slow process and some cardiomyocytes are never replaced throughout a person’s lifetime. Others believe it occurs faster, so every cardiomyocyte in heart replaced several times in a lifetime.
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20
Q

How are stem cells used in bone marrow transplants?

A
  • 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 in patients that produce abnormal blood cells
  • the stem cells in transplanted bone marrow divide and specialise to produce healthy blood cells
  • technique has been used successfully to treat leukaemia and lymphoma and has also been used to treat some genetic disorders, such as sickle cell anaemia and severe combined immunodeficiency (SCID)
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21
Q

What stem cell therapies could be in place to treat many conditions in the future?

A
  • spinal cord injuries: stem cells could be used to replace damaged nerve tissue
  • heart disease and damage caused by heart attack: stem cells could be used to replace damaged heart tissue
  • organ transplants: organs could be grown from stem cells to provide new organs for people on the donor waiting lists.
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22
Q

What are the 3 main potential sources of stem cells?

A
  1. adult stem cells- obtained from body tissues of adult in an operation with little risk involved but a lot of discomfort. They are multipotent, so can only differentiate into a limited number of cell types, not all body cell types (like embryonic)
  2. embryonic stem cells- obtained from embryos that are created in a laboratory using in vitro fertilisation (IVF)- egg cells are fertilised by sperm outside the womb. Once embryos are 4-5 days old, stem cells removed and rest of embryo destroyed. Embryonic stem cells can divide an unlimited number of times and develop into all types of body cells (pluripotent)
  3. Induced pluripotent stem cells (iPS cells)
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23
Q

How are Induced Pluripotent Stem Cells (iPS) produced from adult somatic cells using appropriate transcription factors?

usied to treat human disorders and used to overcome some of the ethical issues with using embryonic stem cells

A
  • adult somatic unipotent cells are altered in a lab to return them to a state of pluripotency
  • to do so, genes that were switched off to make the cell specialised must be switched back on, which is done using transcription factors
  • adult cells made to express a series of transcription factors that are normally associated with pluripotent stem cells. Transcription factors cause adult body cells to express genes that are associated with pluripotency
  • transcription factors can be introduced to adult cells by infecting them with specially modified virus, with genes coding for the transcription factors in its DNA. When virus infects adult cell, these genes passed into adult cell’s DNA, so cell able to produce the transcription factors
  • iPS cells could become useful in research and medicine in the future, but more research into how similar they are to true pluripotent emryonic stem cells needed before they can be properly used.
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24
Q

What are the ethical considerations surrounding obtaining stem cells from embryos created by in vitro fertilisation (IVF)?

A
  • raises ethical issues as the procedure destroys the embryo, which could become a fetus if placed in the womb
  • some people believe an individual is formed at the moment of fertilisation and so has the right to life, so believe it is wrong to destroy embyos
  • some have fewer objections to stem cells being obtained from eggs cells that have not been fertlised by sperm, but have been artificially activated to start dividing. This is because the cells cannot survive more than a few days and would not produce a fetus if placed in a womb
  • some people believe scientists should only use adult stem cells as no embryos are destroyed in their production. BUT adult stem cells cannot develop into all specialised cell types but embryonic stem cells can
  • iPS cells can differentiate into any cell type BUT are obtained from adult tissue so have less ethical issues than obtaining stem cells from embyos
  • possible that iPS cells could be made from own patient cells. They would be genetically identical to patient cells and could be used to create new tissue or an organ that wont be rejected by patient body
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25
What are the benefits of stem cell therapy?
* could save many lives e.g. many people waiting for organ transplants die before a donor organ becomes available, so stem cells could be used to grow organs for those awaiting transplants * may be possible to make stem cells genetically identical to a patient's own cells, which could be used to grow some new tissue or an organ that wont be rejected by patient's body * could improve the quality of life for many people e.g. they could be used to replace damaged cells in the eyes of blind people
26
What controls transcription?
* in eukaryotes, transcription of target genes can be stimulated or inhibited when specific transcriptional factors move from the cytoplasm into the nucleus * this can turn on/off genes (only certain genes can go through protein synthesis to make a particular protein), so only certain proteins are produced in a particular cell * turning on/off particular genes in a cell is what enables them to become specialised
27
What are Transcription factors?
* Genes are regulated by transcription factors * Transcription will only occur when a transcription factor from the cytoplasm enters the nucleus and binds to the DNA in the nucleus * transcription factors are proteins and each one can bind to different base sequences on DNA, which they are complementary in shape to, which enables RNA ploymerase to bind, and so transcription factors initiate transcription of genes * Transcription factors are three dimensional proteins. One part binds to DNA and another part of protein often a receptor for another molecule to attach to before it can then attach to DNA * once bound, transcription begins, creating mRNA molecule for that gene which can then be translated in the cytoplasm to create the polypeptide chain/protein * without the binding of a transcription factor, the gene is inactive and the protein will not be made
28
How does Oestrogen initiate transcription?
* oestrogen is a **steroid hormone** that can initiate transcription. * lipid soluble as is a steroid hormone so can enter cell through cell surface membrane via simple diffusion * it binds to the transcription factor (called an oestrogen receptor) by the receptor site, as oestrogen is complementary in shape to the receptor site. This forms an oestrogen-oestrogen receptor complex * when it binds to transcription factor it causes the DNA binding site of the protein to change shape slightly, so it is complementary in shape to DNA. * The transcription factor is now activated * The transcription factor/ oestrogen-oestrogen receptor complex can move through nuclear pores into the nucleus and bind to specific DNA sites near start of target gene. Complex acts as an activator of transcription by helping RNA polymerase bind to start of target gene. * RNA polymerase can then bind to DNA/start of target gene to create mRNA (transcription factor binding to DNA initiates transcription, as RNA polymerase can only bind to DNA once transcription factor is bound as RNA polymerase is only complementary in shape to DNA and transcription factor together)
29
What regulates genes?
* genes are regulated by transcription factors * all cells in an organism carry the same DNA but the structure and function of different cells varies because not all the genes in a cell are expressed (transcribed and used to make a protein) * as different genes are expressed, different proteins are made and these proteins modify the cell, so determine the cell structure and control cell processes such as the expression of more genes, which produce more proteins
30
How do transcription factors control gene regulation?
* in eukaryotes transcription factors move from the cytoplasm to the nucleus * they bind to specific DNA sites called **promoters** which are found near the start of their target genes (the genes the transcription factors control the expression of). Transcription factors control gene expression by controlling rate of transcription * transcription factors called **activators** stimulate/increase rate of transcription e.g. help RNA polymerase bind to the start of the target gene and activate transcription * transcription factors called **repressors** inhibit/decrease rate of transcription e.g. they bind to the start of the target gene, preventing RNA polymerase from binding, stopping transcription
31
What is one way in which gene expression is controlled in eukaryotic organisms?
epigenetics * epigenetics is the heritable change in gene function without changing the DNA base sequence * changes caused by changes in the environment and can inhibit transcription * factors such as diet, stress and toxins can add epigenetic marks (chemical tags) to the DNA and this can control gene expression in eukaryotes. * epigenetic marks do not alter base sequence of DNA. They alter how easy it is for the enzymes and other proteins needed for transcription to interact with and transcribe DNA * epigenome= single layer of epigenetic marks on DNA, which impacts the shape of the DNA-histone complex and whether the DNA is tightly woud so wont be expressed or unwound wo will be expressed * if DNA tightly wound, transcription factors cannot bind, SO the epigenome, which is due to changes to the environment, can inhibit transcription
32
How does increased Methylation of DNA inhibit transcription? | one method of epigenetic control
* when methyl groups (e.g. of an epigenetic mark) are added to DNA they attach to the cytosine base * this prevents transcriptional factors from binding and attracts proteins that condense the DNA-histone complex, so methylation prevents a section of DNA from being transcribed. * Methylation of DNA and histones causes changes to the DNA structure and causes DNA to coil tightly so transcriptional factors cannot bind the DNA and genes are not expressed (switched off)
33
How does Acetylation of Histone proteins inhibit transcription? | one method of epigenetic control
* histones are proteins that DNA wraps around to form chromatin that makes up chromosomes. How condensed chromatin is affects the accessibility of DNA and whether or not it can be transcribed. * acetyl groups are e.g. of epigenetic marks * decreased acetylation of associated histones proteins on DNA inhibits transcription * if acetyl groups removed from DNA the histones become more positive and are attracted more to the phosphate group on DNA * this makes DNA and histones more strongly associated and hard for transcription factors to bind. * when acetyl groups removed from the histones, the chromatin becomes highly condensed and genes in DNA cannot be transcribed because transcription factors cannot access them * when histones are acetylated, the chromatin is less condensed so transcription factors can access DNA so genes are transcribed * Histone deacetylase enzymes (HDAC) remove acetyl groups
34
What is Heterochromatin?
* transcription cannot occur * caused by increased methylation of DNA that inhibits transcription * caused by decreased acetylation of associated histones proteins on DNA that inhibits transcription
35
What is Euchromatin?
* transcription can occur * caused by decreased methylation * caused by increased acetylation of associated histones proteins
36
How can all tumours cause harm to the body?
* damaging the organ in which the tumour is located * causing blockages or obstructions * damaging other organs by exerting pressure
37
What are Malignant tumours?
cancerous tumours
38
How do Malignant tumours cause cancer?
* by growing rapidly, then invading and destroying surrounding tissues * cells within malignant tumours secret chemicals that cause the formation of blood vessels to supply the tumour with nutrients, growth factors and oxygen * cells can break off tumours and spread to other parts of body through bloodstream or lymphatic system **(Metastasis)** * Metastasis causes the spread of tumours to other places in the body, affecting multiplt organs * when removed with surgery, malignant tumours can still grow back * **carcinogens** can initiate the formation of malignant tumours * carcinogens may include UV or X ray exposure, Tobacco, asbestos, processed meat
39
What is a Carcinogen?
an agent with the capacity to cause cancer in humans. If the agent causes cancer, it is carcinogenic
40
What are Benign tumours?
* non cancerous tumours * grow slowly * do not invade other tissues and no not metastasise, unlike malignant tumours * often covered in fibrous tissue that stops cells invading other tissues
41
How can Bignign tumours damage the body?
* can cause blockages or obstructions * can exert pressure on the organ it is growing in or those surrounding it * when removed they do not usually grow back * formation of benign tumours initiated by inflammation or infection, injury, diet, genetics, toxins and radiation * some benign tumours can become malignant * examples of benign tumours include non cancerous brain tumours and warts, caused by a viral infection
42
How are Tumours formed due to mutation or silencing of Tumour Suppressor genes?
* Tumour Suppressor genes are genes that produce proteins that slow down cell division, repair DNA, signal Apoptosis (cell death) when the cells are faulty * the proteins ensure that cells do not replicate if they contain mutated DNA or are faulty as that can lead to tumour formation * tumours occur if tumour suppressor genes are mutated or silenced * if mutations result in the tumour suppressor genes not producing these proteins that slow down cell division then cell division could continue and mutated cells would not be identified and destroyed. BRCA1 and BRCA2 are two known mutated tumour suppressor genes linked to breast cancer
43
How does Abnormal Methylation of DNA lead to tumour development?
* Methylation of DNA is important method of regulating gene expression as it can control whether or not a gene is transcribed and translated * when occurring normally it plays a key role in many bodily processes * growth of tumours can be caused by abnormal methylation of certain cancer-related genes * Tumour suppressor genes could become hypermethylated (too many methyl groups are attached to it), so the genes are not trancribed. The gene is inactivated and becomes turned off * the necessary regulatory proteins produced by the tumour suppressor gene (for slowing cell division, DNA repair and apoptosis) are not produced, so this could result in a tumour, as cells can divide uncontrollably by mitosis. * proto-oncogenes may be hypomethylated (reduction in number of methyl groups attached to cytosine base), which causes them to act as oncogenes, increasing the production of proteins that encourage cell division. * This stimulates cells to divide uncontrollably, which causes the formation of tumours. * hypomethylation of proto-oncogenes causing them to act as oncogenes results in the gene being permanently switched on.
44
What are Oncogenes?
* Proto-oncogenes are normal genes that stimulate cell division by coding for proteins that make cells divide * Proto-oncogenes can mutate to become oncogenes * mutation occurs because of carcinogens such as smoking etc * Oncogenes are mutated genes that can cause cancer through deregulation of cell growth * mutations to proto-oncogene can cause the gene to become overactive which stimulates cells to divide uncontrollably, resulting in a tumour
45
How can increased Oestrogen increase the risk of developing some breast cancers?
* oestrogen is a steroid hormone that can initiate transcription of certain genes * increased exposure to oestrogen over an extended period of time is thought to increase the risk of developing breast cancer (can be the result of starting menstruation earlier than usual or the menopause later thsn usual or taking oestrogen containing drugs such as HRT) * different theories as to how oestrogen can contribute to the development of some breast cancers: 1. oestrogen can stimulate certain breast cells to divide and replicate, so increased cell division increases chance of mutations occurring so increases chance of cells becoming cancerous 2. ability to stimulate cell division could mean that if cells become cancerous then oestrogen could cause them to rapidly divide further so tumours form faster 3. other research suggests oestrogen is able to introduce mutations directly into the DNA of certain breast cells, increasing the chance of these cells becoming cancerous
46
What is RNA Interference (RNAi)?
* RNAi can inhibit the translation of the mRNA produced from target genes in eukaryotes and some prokaryotes * RNAi is where small double stranded RNA molecules stop mRNA from target genes being translated into proteins * molecules involved in RNAi are siRNA (small interfering RNA) and miRNA (micro RNA) * RNAi molecules are small lengths of non coding RNA
47
How does RNAi work in plants?
1.Transcribed mRNA leaves the nucleus of the cell to go to cytoplasm 2. in cytoplasm, double stranded siRNA associates with several proteins and unwinds. A single strand then binds to the target mRNA. Base sequence of siRNA is complementary to the base sequence in sections of target mRNA 3. proteins associated with siRNA cut mRNA into fragments, so it can no longer be translated. Fragments then move into a processing body, where they are degraded 4. similar process happens with miRNA in plants
48
How does RNAi work in mammals?
1. in mammals, miRNA is not usually fully complementary to target mRNA, which makes it less specific than siRNA, so it may target more than one mRNA molecule 2. miRNA associates with proteins and binds to target mRNA in cytoplasm 3. mRNA then moves into a processing body where it is either stored or degraded. When it's stored, it can be returned and translated at another time.
49
What is the genome?
The genome is the entire genetic material of an organism in the nucleus of a cell (in eukaryotes)
50
What does genome sequencing refer to?
sequencing a genome means working out the DNA base sequence for all the DNA in a cell. All the cells have the same DNA (except gametes as they are haploid and red blood cells because they do not have a nucleus). Many organisms genomes have been sequenced, including the human genome which took 13 years and was completed in 2003.
51
Methods of sequencing genomes
* the methods being ued to sequence genomes are continuously being improved and updated and has now become automated * methods have included the Sanger method
52
What can the sequenced genome of simpler organisms be used for?
* simpler organisms, like prokaryotic cells (bacteria) do not contain introns in their DNA * this means the genome can be used directly to sequence the proteins that derive from the genetic code (the proteome) of the organism * this is very useful for many reasons, including identifying potential antigens to use in a vaccine
53
Why can the genome not be easily translated into the proteome in complex organisms?
* complex organisms (eukaryotes) have introns (non coding DNA) and regulatory genes in their DNA * this means that knowledge of the genome cannot easily be translated into the proteome.
54
What does Recombinant DNA technology involve?
* The combining of different organisms' DNA, which could enable scientists to mnipulate and alter genes to improve indstrial processes and medical treatment * recombinant DNA technology involved transferring a fragment of DNA from one organism to another * as the genetic code is universal, (the same DNA base triplets code for the same amino acids in all living things, and because the mechanisms of transcription and translation are universal, the transferred DNA can be translated to produce a protein in the cells of the recipient organism. * the first step in this technology is to produce or isolate the fragments of DNA to be recombined with another piece of DNA * There are 3 methods to create fragments of DNA: reverse transcriptase, restriction endonuclease enzymes and using a 'gene machine'
55
Outline the process of Reverse Transcription to create DNA fragments in Recombinant DNA Technology
1. Reverse Transcription enzyme makes DNA copies from mRNA, (as most cells only contain 2 copies of each gene so it's difficult to obtain a DNA fragments with the target gene BUT they contain many mRNA molecules complementary to the target gene, so mRNA can be used as a template to produce DNA). Reverse Transcription naturally occurs in viruses such as HIV 2. A cell that naturally produces the protein of interest is selected 3. These cells should have large amounts of mRNA that are complementary to the target gene, so the protein can be made. The mRNA molecules can be used as templates to make lots of DNA 4. The reverse transcriptase enzyme joins the free DNA nucleotides that has complementary bases to the mRNA sequence 5. single stranded DNA is made (cDNA) 6. to make this DNA fragment double stranded, the enzyme DNA polymerase is used
56
Provide an example of reverse transcription to produce DNA fragments
* pancreatic cells produce the protein insulin * have many mRNA molecules complementary to insulin gene but only 2 copies of the gene itself * reverse transcriptase could be used to to make cDNA from the insulin mRNA * mRNA is first isolated from cells * mRNA is mixed with free DNA nucleiotides (that have complentary bases to the mRNA sequence) and reverse transcriptase * reverse transcriptase uses mRNA as a template to synthesise a new strand of cDNA
57
What are the advantages of reverse transcription?
* the cDNA is intron free because it is based on the mRNA template * This is important if carrying out genetic engineering on prokaryotic cells as they cannot remove introns through splicing * secondly, mRNA present in cell is from actively transcribed genes, so lots of the mRNA of interest available to make cDNA
58
Outline the process of using restriction endonucleases to obtain DNA fragments in Recombinant DNA Technology
1. some sections of DNA have palindromic sequences of nucleotides, which consist of antiparallel base pairs (read the same in opposite directions) 2. restriction endonucleases recognise specific palindromic sequences (known as recognition sequences) and cut the DNA at these places 3. different restriction endonucleases cut at different specific reognition sequences because the shape of the recognition sequence is complementary to enzyme active site 4. if recognition sequences present at either side of the DNA fragment you want, restriction endonucleases can be used to separate it from the rest of the DNA 5. The DNA sample is incubated with specific restriction endonuclease which cuts the DNA fragment out via a hydrolysis reaction 6. some endonucleases cut the DNA to leave sticky ends (small sections of unpaired bases at each end of the DNA fragment). Sticky ends can be used to bind (anneal) the DNA fragment to another piece of DNA that has sticky ends with complementary sequences.
59
What are restriction endonucleases?
* enzymes that cut up DNA * naturally occur in bateria as a defence mechanism * many restriction enzymes that have an active site complementary in shape to a range of different DNA base sequences, decsribed as recognition sequences (the specific location each enzyme cuts the DNA from) * some enzymes cut at the same location in the double strand and create a blunt end * other enzymes cut to create staggered ends and exposed DNA bases. * exposed staggered ends are palindromic and referred to as 'sticky ends' because they have the ability to join to DNA with complementary base pairs. This is why these enzymes are the most useful * enzymes cutting DNA to create staggered ends and exposed DNA bases is an advantage as sticky ends provide larger SA
60
Outline the process of Gene Machine, to obtain DNA fragments in Recombinant DNA Technology
* most modern technology * DNA fragments can be created in a lab using a computerised machine * scientists first examine the protein of interest to identify the amino acid sequence (primary structure of protein) and from that work out what the mRNA sequences that coded for the amino acids and, from that, DNA sequence can be worked out * The DNA sequence is entered into the computer which checks for biosafety and biosecurity that the DNA being created is safe and ethical to produce * The computer can create small sections of overlapping single strands of nucleotides that make up the genes (called **oligonucleotides**) (oligo=small sections) * oligonucleotides can then be joined to create the DNA for the entire gene * PCR can be used to amplify the quantity and to make the double strand * This process is very quick, accurate (as exact desired sequence is designed and entered, so can be designed to be intron free and to have sticky ends) and makes intron free DNA so can be transcribed in prokaryotic cells
61
What are the disadvantages of reverse transcriptase to obtain DNA fragments in recombinant DNA technology?
more steps, so more time consuming and technically more difficult
62
What are the advantages of using restriction endonucleases to obtain DNA fragments in recombinant DNA technology?
sticky ends on DNA fragment which make it easier to insert to make recombinant DNA
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What are the disadvantages of using restriction endonucleases to obtain DNA fragments in Recombinant DNA technology
still contains introns, as cutting the original DNA - would be an issue if inserting DNA into a prokaryotic cell, as prokaryotic cells cannot remove introns through splicing, so an extra step would need to take place to remove introns before the DNA is inserted into prokaryotic cells
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What are the advantages of using gene machines to obtain DNA fragments in recombinant DNA technology?
can design exact DNA fragment you want, with sticky ends, labels and preffered codons
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What are the disadvantages of using gene machines to obtain DNA fragments in recombinant DNA technology?
need to know the exact sequence of amino acids or bases
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How are DNA fragments cloned to amplify them, via **in vivo** cloning (copies of the DNA fragment are made inside a living organism)
1. DNA fragment isolated via one of 3 methods: Extraction using restriction endonucleases, the conversion of mRNA to cDNA using reverse transcriptase or artificial synthesis in a "gene machine". 2. **Promoter region** added at start of DNA fragment (sequence of DNA that is the binding site for RNA polymerase to enable transcription to occur). **Terminator region** added at end of gene, which causes RNA polymerase to detach and stop transcription so only one gene at a time is copied into mRNA * DNA fragment inserted into a vector (carries isolated DNA fragment into host cell). Most common vectors are plasmids (circular DNA, separate from main bacterial genome which only contains a few genes) * Vector DNA cut open using same restriction endonuclease used to isolate DNA fragment containing the target gene. Sticky ends of vector complementary to sticky ends of DNA fragment containing the gene * vector DNA and DNA fragment combined together with DNA ligase enzyme, which joins sticky ends of DNA fragment to sticky ends of vector DNA (anneals them). Process called**ligation**. Ligase catalyses the condensation reaction to form phosphodiester bonds between nucleotides * This forms **recombinant DNA** 3. vector with recombinant DNA used to transfer gene into host cell, where gene is expressed to create protein required * to do this, cell membrane of host cell must be more permeable. * Host cells mixed with ice cold calcium chloride solution to make cell walls more permeable, splamids added and mixture is heat shocked (sudden increase in temp) * enables vector to enter host cell cytoplasm * host cell has now been **transformed** by vector containing the gene, as host cell has taken it up. 4.
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How are Transformed Host cells identified?
* not all host cells will take up a recombinant vector, so important to be able to identify which cells have been transformed. This can be due to the recombinant plasmid does not get inside the host cell, the plasmid re joins before the DNA fragment entered, or the DNA fragment sticks to itself, rather than inserting into the plasmid * marker genes can be used to identify transformed cells 1. marker genes can be inserted into vectors at the same time as the gene to be clones, meaning any transformed host cells will contain the gene to be clones and the marker gene 2. host cells grown on agar plates. Each plate divides and replicates DNA, creating a colony of clones cells. Transformed cells produce colonies where all cells contain clones gene and marker gene 3. marker gene can code for antibiotic resistance, so host cells grown on agar plates containing the specific antibiotic so only transformed cells with the marker gene will survive and grow 4. marker gene can code for fluorescence, where agar plate placed under UV light and only transformed cells will fluoresce 5. markers can be enzymes. The enzyme lactase can turn a certain substance blue from colourless. Gene for this enzyme inserted into plasmid. The DNA fragment inserted in the middle of this gene to disrupt it. The bacteria are then grown on an agar plate with the colourless substance. The colonies which cannot turn the colourless substance blue contain the recombinant plasmid. 5. identified transformed cells are allowed to grow more, producing many copies of the cloned gene
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How is the host cell grown after it has been amplified using in vivo amplification, transforming host cells
* a fermenter is used to grow multiple copies of the host cell which have been identified as containing the recombinant plasmid (transformed host cell) * large clones population of host cell can then produce the protein coded for by the inserted DNA fragment (e.g. bacteria producing insulin from an inserted insulin gene)
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How are DNA fragments cloned to amplify the sample, using in vitro amplification?
* ONce DNA fragments isolated, they are cloned to create large quantities. This is done either in vivo or in vitro * DNA fragments amplified using **in vitro** cloning, where copies of the DNA fragments made **outside**of a living organism using the polymerase chain reaction (PCR) 1. Reaction mixture set up containing DNA fragment, free nucleotides, primers and DNA polymerase. Primers are short pieces of DNA that are complementary to the bases at the start of the DNA fragment. DNA polymerase creates new DNA strands 2. DNA mixture heated to 95*C to break the hydrogen bonds between the two DNA strands. **(DNA is denatured)** 3. mixture then decreased to 55*C so that primers can bind **(anneal)** to the strands 4. reaction mixture heated to 72*C which is the optimum for DNA polymerase to work 5. DNA polymerase lines up free DNA nucleotides alongside each template strand and joins nucleotides together. Specific base pairing means new complementary strands formed. **(synthesis)** 6. two new copies of the DNA fragment formed and one cycle of PCR complete. Cycle starts again and all 4 strands (two original and two new) used as templates 7. each PCR cycle doubles the amount of DNA e.g. 1st cycle = 2 x 2= 4 fragments, 2nd cycle = 4 x 2= 8 fragments
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What are the Advantages of PCR?
* automated- more efficient * rapid- 100 billion copies of DNA can be made within hours * does not require living cells- quicker and less complex techniques needed compared to in vivo cloning
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How are Transformed organisms made usinf Recombinant DNA Technology?
* microorganisms, plants and animals can all be transformed using recombinant DNA technology (this is called genetic engineering) * transformed microorganisms (aka genetically engineered/genetically modified (GM) organisms) can be made using same technology as in vivo cloning. DNA fragment isolated and is inserted into plasmid vector. Plasmid containing recombinant DNA tranferred into a bacterium. Tranformed bacteria identified and grown. The insulin (protein) produced from cloned gene is extracted and purified. * transformed plants can be produced. A gene that codes for a desirable protein inserted into a plasmid. Plasmid added to bacterium and bacterium used as a vector to get the gene into the plant cells. If correct promoter region has been added along with the gene, the transformed cells will be able to produce the protein * transformed animals can be produced. Gene that codes for desired protein inserted into early animal embryo/ egg cells of female. If gene inserted into a very early embryo, all the body cells of the resulting transformed animal will contain the gene. Inserting it into egg cells means when female reproduces, all the cells of offspring will contain gene * promoter regions that are only activated in specific cell types can be used to control exactly which of an animal's body cells the protein is produced in. If the protein is only produced in certain cells, it can be harvested more easily. Producing the protein in the wrong cells could damage the organism.
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How can Recombinant DNA Technology be used in Agriculture to benefit humans?
* algricultural crops can be transformed so they give higher yields or are more nutritious SO these plants can be used to reduce the risk of famine and malnutrition. * crops can be transformed to have pest resistance so fewer pesticides needed, which reduces costs and reduces any environmental problems associated with using pesticides * for examples, golden rice is a variety of transformed rice containing one gene from a maize plant and one gene from a soil bacterium, which together, enable the rice to produce **beta carotene**. This is used by our bodies to produce **vitamin A** * golden rice being developed to reduce vitamin A deficiency in areas where there is a shortage of dietary Vitamin A, which can cause problems such as blindness
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How can Recombinant DNA Technology be used in Industry to benefit humans?
* industrial processes often use biological catalysts. These enzymes can be produced from transformed organisms, so they can be produced in large quantities for less money, reducing costs * e.g. Chymosin (or rennin) is an enzyme used in cheese-making, which used to be made from rennet (sybstance produced in the stomach of cows), but it can now be produced by trasnformed organisms * this means it can be made in large quantities, relatively cheaply and without killing any cows, making some cheese suitable for vegetarians
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How can Recombinant DNA Technology be used in Medicine to benefit humans?
* many drugs and vaccines produced by transformed organisms * they can be made quickly, cheaply and in large quantities using recombinant DNA technology * e.g. insulin used to treat Type I diabetes and used to come from animals (cow, horse or pig pancreases). * This was not human insulin so it did not work quite as well * human insulin now made from transformed microorganisms, using a cloned insulin gene
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Outline the ethical, financial and social issues associated with **Agricultural** use of Recombinant DNA Technology
1. * farmers may plant only one type of transformed crop **(monoculture)** * this may make the whole crop vulnerable to the same disease because the plants are **genetically identical** . Environmentalists also concerned about monocultures reducing biodiversity, as this could damage the environment 2. * some people are concerned about the possibility of **'superweeds'**(weeds that are resistant to herbicides. * These could occur if transformed crops interbreed with wild plants * There could then be an uncontrolled spread of Recombinant DNA, with unknown consequences 3. Organic farmers can have their crops **contaminated** by wind-blown seeds from nearby genetically modified crops. This means they cannot sell their crop as organic and may lose their income
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Outline the ethical, financial and social issues associated with **Industrial** use of Recombinant DNA Technology
* antiglobalisation activists oppose globalisation (e.g. the growth of large multinational companies at the expense of smaller ones). A few, large biotechnology companies control some forms of genetic engineering. As the use of this technology increases, these companies get bigger and more powerful. This may force smaller companies out of business e.g. by making it harder for them to compete * without proper labelling, some pople think they will not have a choice about whether to consume food made using genetically engineered organisms, which is an ethical issue * some consumer markets, such as the EU, wont import GM foods and products, which can cause an economic loss to producers who have traditionally sold to those markets.
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Outline the ethical, financial and social issues associated with **Medicinal ** use of Recombinant DNA Technology
* companies who own genetic engineering technologies may limit the use of technologies that could be life saving * some people worry this technology could be used unethically e.g. to make designer babies (babies that have characteristics chosen by their parents). This is currently illegal though.
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Outline **ownership issues**, created by Recombinant DNA Technology
* some debate about who owns genetic material from humans once it has been removed from the body (the donor or the researcher). Some argue the individual donor holds the right to their own genetic information, but others argue that value is created by the researcher who uses it to develop a medicine or in diagnosis * a small number of corporations own patents to particular seeds. They can charge high prices, sometimes including a 'technology fee', and can require farmers to repurchase seeds each year. If non-GM crops are contaminated by GM crops, farmers can be sued for breaching the patent law.
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Outline the Potential Humanitarian benefist of Recombinant DNA technology | benefits to people
1. Agricultural crops could be produced that help reduce the risk of famine and malnutrition e.g. droight resistant crops for drought prone areas 2. Transformed crops could be used to produce useful pharmaceutical products e.g. vaccines, which could make drugs availabke to more people, e.g. in areas where refrigeration (usually needed for storing vaccines) is not available 3. medicines could be produced more cheaply, so more people can afford them 4. recombinant DNA technology has the potential to be used in gene therapy to treat human diseases
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Recombinant DNA Technology could be used to treat human diseases (known as **gene therapy**). How does gene therapy work?
1. gene therapy involves altering the defective genes (mutated alleles) inside cells to treat medical disorders and cancer. The way this is done depends on whether the disorder is caused by a mutated **dominant allele** or **two mutated recessive alleles** 2. if caused by 2 mutated recessive alleles then a working dominant allele can be added to make up for them ('supplemet' the faulty alleles) 3. if caused by a mutated dominant allele, the dominant allele can be **silenced** (e.g. by inserting a DNA fragment in the middle of the allele so it does not work anymore) 4. Both these processes involve inserting a DNA fragment into the orginal DNA
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How is the DNA fragment inserted inside the cell, in gene therapy? (recombinant DNA technology used to treat human diseases)
1. The allele is inserted into cells using vectors just like in recombinant DNA technology 2. different vectors can be used e.g. altered viruses, plasmids or liposomes (spheres made of lipid)
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What are the 2 types of gene therapy (recombinant DNA technology used to treat human diseases)
1. **Somatic therapy:** involves altering the alleles in body cells, particularly cells most affected by the disorder. E.g. Cystic Fibrosis (CF) is a genetic disorder that is very damaging to the respiratory system, so somatic therapy for CF targets the epithelial cells lining the lungs. Somatic therapy does not affect the individual's sex cells/gametes (sperm or eggs), so any offspring may still inherit disease 2. **Germ line therapy:** involves altering the alleles in the sex cells. This means that every cell of any offspring produced from these cells will be affected by the gene therapy and they won't suffer from the disease. Germ line therapy in humans is currently illegal.
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What ethical issues are associtaed with gene therapy?
* some people are worried the technology could be used in ways other than for medical treatment, such as for treating the cosmetic effects of aging * other people worry there is the potential to do more harm than good by using the technology (e.g. risk of overexpression of genes- gene produces too much of the missing protein)
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