Tagged: gene

Cell division video: a revision video for DNA structure and chromosomes

This is a summary video that might help those of you still struggling to get to grips with chromosomes and genes.  I apologise for the terribly amateur production values on the video but hope the biological content at least might be useful….

GFP fly

en_GFP_fly3[1]

Just doing the pGLO practical this morning with my Y12 group and came across a great photo of a fly that has been genetically modified to express a gene from a species of Arctic jellyfish.  The fly now makes a protein called GFP that causes it to flouresce green.

Three great Biology books to read over the Christmas holidays

It is one of the really good things about the extended curriculum at my school that students are not set work to do in the holidays.  This allows time at home to be spent resting, recuperating and preparing for the term ahead.  But can I make a suggestion as to what some of you might like to do before the start of next term?  Find a really good book to read and read a chapter a day.  Here are some personal suggestions as to some of my favourite Biology books.

genome

“Genome” by Matt Ridley is a really interesting read.  I have read it over and over again since it was first published in 2000.  The chapters are short but the ideas contained within are important and challenging.  The 23 chapters are each devoted to a single gene on a different human chromosome but Ridley is able to draw out some deep ideas with entertaining stories, anecdotes and superb detail.  I would say this is ideal for either Y11 (D block) or Y12 (C Block) students.

power sex suicide

Nick Lane came to Eton last year to speak to the Scientific and Banks Societies and he was about the best speaker we have had for a long time.  This book is more suitable for Y12/13 students than GCSE readers as it has direct links to the pre-U course and contains some complex ideas.   He is interested in the role mitochondria have played in the history of life and for me, Nick Lane is the best contemporary writer.  If you like this, I can also recommend his later book “Life Ascending” which is also a super read.

The Ancestors Tale

This is my favourite Dawkins book.  If you are interested in understanding the grand sweep of the tree of life and the history of life on our planet, there are a lot worse ways to start than reading this.  Dawkins has a superb writing style and is able to make a complex chronology of species entertaining and easy to follow.  If you do read any of these books and would like to tell me your thoughts, or indeed if you have other recommendations, please add a comment to this post so that others can see.

Happy Christmas!

3.19 Understanding Pedigrees: A* Genetics for iGCSE

Sometimes genetics problems are based around a pedigree diagram.  These diagrams show the phenotypes of individuals over several generations and allow deductions to be made about certain individuals phenotypes.  Often pedigrees are used to show the inheritance of a particular disease in a family.

566Pu

You can see that circles in the pedigree represent females, squares represent males.  If the symbol is filled in, then the person suffers from the disease.  Empty symbols represent people who do not have the disease.

Have a look at the pedigree above?  What does this tell you about the disease?

Well the first and most obvious thing is that this disease is caused by a recessive allele, h.

If you see two people who don’t have the disease producing one or more children who do, then this must be a genetic disease caused by a recessive allele.  In the top generation, parents 1 and 2 do not have the disease, but they have three children 2,3,4 one of whom has the disease.

What does this tell us about the genotype of parents 1 and 2 in generation I?  Well if neither have the disease and they have a child who does, both 1 and 2 in the top generation must be heterozygous – Hh

Anyone with the disease must be homozygous recessive hh.

Have a look at generation II in the diagram above?

The man, number 2, who is a sufferer and so genotype hh marries woman 1 who does not have the disease.  They produce 4 children, three with the disease and one without.  What must the genotype of the woman 1 be?  Well she must be heterozygous Hh.  How do we know?  What children would she produce if she were a homozygous HH woman?

AutosomalDominant

A pedigree caused by a dominant allele would look very different.  Every sufferer would have at least one parent who also suffers from the disease.  Two sufferers producing some children who do not have the disease is indicative of a disease caused by a dominant allele.  If we use the symbol P for the dominant allele that causes the disease, and p for the recessive allele that is “normal”, can you work out the genotypes of all 12 people on the diagram above?

  1. Pp
  2. Pp
  3. pp
  4. Pp
  5. PP or Pp
  6. PP or Pp
  7. pp
  8. pp
  9. Pp
  10. pp
  11. pp
  12. pp

A* Genetics: avoid a common error in understanding at iGCSE 3.16 3.17 3.18 3.20

There are one or two things which make a biology teacher’s (and indeed an exam marker’s) blood pressure rise.  Well in fact in my case there are many dozens of things, as some of you know, but let’s keep it to the things candidates write in genetics answers in exams.  This post is an attempt to encourage you to avoid the commonest “howler”.

The dominant allele does not have to be the more common one in a population.

Just because an allele is dominant, it does not mean it will be the most common in a population.  I often hear answers in which people think that in a population 3/4 of the population will have the dominant phenotype, 1/4 will be recessive.  This is utter nonsense of course.  The ratio of 3:1 only applies to the probabilities of offspring produced by mating two heterozygous individuals.

There is a gene in humans in which a mutation can cause polydactyly:  this rare condition results in babies born with an extra digit on each hand.  Anne Boleyn was a famous sufferer in the past.  But the allele of the gene that causes polydactyly is dominant – it is a P allele.  I would imagine everyone reading this post, (all 12 of you…..), will probably have the genotype pp.  The p allele that causes a normal hand to form is very very common in our population whereas the P allele is very very rare.

Don’t ever believe that just because an allele is common, it must be dominant.

How to score full marks on a genetics question in iGCSE Biology? 3.16 3.17 3.18 3.20

Few things in life are certain, famously just death and taxes.  Northampton Town flirting with relegation can perhaps be added to this list.  But you can be pretty certain that tucked away somewhere in your iGCSE Biology exam there will be a genetics question that asks you to draw a genetic diagram.  There are usually four or even five marks available and so learning how to ensure you get all these marks is vital in your quest for an A* grade.

GCSE candidates are terrible at doing genetic diagrams: they fill the space with messy scribbles, doodles, strange tables and lines and then confidently write 3:1 at the bottom… Not a recipe for success.  So learn how to do it, be neat, take your time and you can guarantee full marks.

If the question doesn’t do it for you, you should start by defining what the letters you will use for the alleles.  If one allele is dominant over the other, it is conventional to use the upper case letter for the dominant allele, the lower case letter for the recessive one.  It will tell you in the question which allele is dominant.

Start your genetic diagram by writing the phenotype of the parents in the cross.

e.g.          Parental Phenotype:             Tall                         Tall

Underneath the phenotype, write the genotype of the parents.

Parental Genotype:                Tt                            Tt

Then you need to think about which alleles are present in the gametes.  Gametes are haploid and so will contain one of each pair of homologous chromosomes – in this example there can only be one allele in each gamete (as we are only looking at one gene)

Gametes:           T               t                       T                   t

Next show random fertilisation.  I think it is much better to draw a Punnett square that has the male gametes down one side, the female gametes down the other and then carefully pair them up.  This is a stage where mistakes can be made if you rush so however simple you think this process is, take your time…..

Random Fertilisation

9.02.PunnetSquare

Finally you need to copy out the offspring genotypes from your Punnet square, like so

Offspring Genotypes:        TT            Tt              Tt             tt

And underneath each one, write the offspring phenotype

Offspring Phenotypes:       Tall           Tall            Tall           Dwarf

Finally, answer the question.  If it asks for a probability, express your answer as either a percentage or a decimal or a fraction.  So if I were asked what is the probability of a homozygous pea being produced, the answer is 50% or 0.5 or 1/2

Follow these rules and you will always score full marks – happy days……..

Genetics jargon: A* understanding for iGCSE 3.16 3.17

The science of genetics looks at how inherited characteristics are passed from one generation to the next.  The father of genetics was the Moravian monk, Gregor Mendel, who showed with his breeding experiments in peas that individual, discrete “particles” are passed from one generation to the next.  We now know that these “particles” are actually small sections of a DNA molecule called genes.

Mendel worked out that there were always two such “particles” in any cell which acted together to determine the feature described.  But he knew that gametes (sex cells such as pollen grains and egg cells) only contained one “particle” for each feature.  You should understand why this is.

The discrete particles that are passed from generation to generation are genes:  these are sections of a DNA molecule and are located on chromosomes.  Chromosomes in most organisms are found in pairs within the nucleus of a cell.  The word for a cell that contains pairs of homologous chromosomes is a diploid.  The gametes do not have pairs of chromosomes:  they are haploid cells that contain one member of each pair.  This ensures that at fertilisation when two gametes fuse, a diploid zygote is produced.

iGCSE candidates can find genetics a difficult topic and one reason is that there is lots of jargon.  Have a look at my definitions for these jargon words and ensure that you understand what they mean.  Genetics is not a topic in which rote learning and memorisation are helpful – the very top candidates at iGCSE will understand what is going on, and can then answer all possible questions with ease.

Gene: ” a section of a DNA molecule that codes for a single protein”

Allele: “an alternative version of a gene found at the same gene locus”

Gene locus: “the place on a chromosome where a particular gene is found”

Phenotype: “the appearance of an organism, e.g tall, short, blue eyes etc.”

Genotype: “the combination of alleles at a single gene locus that an organism possesses – e.g TT, Tt”

Homozygous: “a gene locus where the two alleles are identical is said to be homozygous – e.g. TT, tt”

Heterozygous: “a gene locus where the two alleles are different is heterozygous – e.g. Tt”

Dominant allele: “a dominant allele is the one that determines the phenotype in a heterozygous individual”

Recessive allele: ” a recessive allele can only determine the phenotype in a homozygous individual”

Codominance: “two alleles are codominant if they both contribute to the phenotype in a heterozygous individual”

Genetically Modified Plants: A* understanding for iGCSE 5.15 5.16

You should understand how bacteria can be genetically modified to produce useful proteins (e.g.human insulin, human growth hormone, vaccine antigens etc.) – see previous post if you are unsure.  In this post, I will try to explain how transgenic plants can be made and indeed what kind of genes might be added to plants to benefit humans.  Genetically modifying a plant will be a more complex process since plants are multicellular and so many millions of cells need to be genetically altered.

Luckily a vector exists that can transfer genes into many varieties of plant.  Agrobacterium tumefaciens is a species of bacterium that contains a plasmid that can be transferred into plant cells.  This plasmid (called the Ti plasmid) can be cut open with a restriction enzyme and a new gene inserted with DNA ligase.

agrobacterium

The Agrobacterium that have been genetically modified will then infect the plant tissue and then when this plant tissue is cultivated using the micropropagation techniques you learned about with cauliflower, a whole GM plant can be produced.

Agrobacterium Image tomato

Genes can also be inserted into plants by a gene gun.  A gene gun literally fires “bullets” made of tiny particles of gold that have been coated with the required DNA and while Agrobacterium does not infect all species of plant, the gene gun can work to get foreign DNA into any plant species.

What are the potential advantages of GM crops?

Time-mag

Resistance to Herbicide:  some crop plants have been altered so they contain a gene that makes them resistant to a particular herbicide.  This means a farmer can spray the herbicide on his crop without risk of harming the crop plant.

Resistance to Frost: some GM plants have a gene from a species of Arctic fish that codes for an “antifreeze” chemical in the fish blood.  Plants that contain this gene will be frost-resistant and so produce can be transported in refrigerated containers without damaging the plant cells.

Golden Rice:  rice plants have been altered so they contain genes that make the molecule beta-carotene.   This is the orange pigment found in carrots and is a precursor for making vitamin A.   So in populations who rely on rice as a staple component of their diet, the rice will be more nutritious and so prevent the night-blindness associated with vitamin A deficiency.

Antibody production:  plants may also be genetically modified to produce antibodies for treatment of human disease.

cropcircle1504_468x348 ISAAA-Major-GMO-Crops

Recombinant DNA: A* understanding for iGCSE Biology 5.12 5.13 5.14 5.8

In the last post on this topic, I explained about the two types of enzymes needed for the genetic modification of organisms:

Restriction enzymes that can cut up DNA molecules at specific target sequences, often resulting in fragments with sticky ends

DNA ligase that joins together fragments to form a single DNA molecule

The EdExcel iGCSE syllabus uses the example of the genetic modification of bacteria to produce human insulin.  Human insulin is a hormone that helps regulate the concentration of glucose in the blood.  It is made in the pancreas when the blood glucose concentration gets too high and causes liver cells to take up glucose from the blood and convert it to the storage molecule glycogen.  Patients with type I diabetes cannot make their own insulin and so need to inject it several times a day after meals to ensure they maintain a constant healthy concentration of glucose in their blood.

Bacteria can be genetically modified so that they produce human insulin.  These transgenic bacteria can be cultured in a fermenter and the insulin produced can be extracted, purified and sold.

How do you get hold of the human insulin gene?

Well the honest answer is that there are a variety of ways of achieving this.  It can now be synthesised artificially as we know the exact base sequence of the gene but it can also be cut out of a human DNA library using a restriction enzyme.  There are other ways too but for the sake of brevity (and sanity) I am not going to go into them here.  [If you are really interested in this, find out how reverse transcription of messenger RNA from cells in the pancreas can allow you to build the insulin gene.]

How do you get the human insulin gene into a bacterium?

Remember that bacterial cells are fundamentally different to animal and plant cells.  One difference is that bacterial cells have no nucleus and their DNA is in the form of a ring that floats in the cytoplasm.  Many bacteria also have plasmids which are small additional rings of DNA and these provide a way for getting a new gene into a bacterium.

2000px-Plasmid_(english)

Bacteria exchange plasmids in a process called conjugation and so it is fairly easy to get the plasmid out of the bacterium.  If the plasmid is cut open using the same restriction enzyme as was used to cut out the human insulin gene, the sticky ends will match up and so DNA ligase will join the two pieces of DNA together to make a recombinant plasmid.  The diagram below shows the process for human growth hormone but it would be exactly the same for the example we are looking at.

32 Recombinant DNA

If the recombinant plasmids are inserted into bacteria, the bacteria will read the human insulin gene and so produce the protein insulin.

recombinant dna

How do you grow the transgenic bacteria on an industrial scale?

The bacteria that have taken up the recombinant plasmid are grown in a fermenter.  This is a large stainless steel vat (easy to clean and sterilise) that often has several design features conserved between different varieties:

2000px-Agitated_vessel

The fermenter  usually has a cooling jacket to carry away excess heat.  The jacket often has a cold water input pipe and the warmer water is carried away.  There has to be some mechanism for mixing the contents of the fermenter so the diagram above shows paddles attached to a motor.  Fermenters also need a sterile input system for getting air, water and nutrients into the fermenter but without introducing foreign bacteria and fungi.  Air is needed as the bacteria are aerobic and need oxygen for respiration.

500px-UCL-BIOREACTSRS

If the bacteria in the fermenter contain the human insulin gene, then they will be able to produce human insulin. This can be extracted, purified and sold to the NHS for treating type I diabetics.