Archive | February 2017

Drunken Monkey Hypothesis: some serious evolutionary and molecular biology

humanalcohol

This has to be a good read! Not just because it might be amusing but also because there is some serious evolutionary and molecular biology here. Our craving for alcohol seems to have a long, long evolutionary history, with a neat mutating gene, ADH4 (No! Not anti-diuretic hormone but alcohol dehydrogenase enzyme), which speeds up the digestion of alcohol, beginning in the mouth. Several primates are known to feast on fermented fruits and there is good evidence that this pursuit of alcohol has or had a significant calorific value for those animals.

From BBC, 23 February 2017

http://www.bbc.com/earth/story/20170222-our-ancestors-were-drinking-alcohol-before-they-were-human


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The evolutionary investigation done by Mathew Carrigan and his associates is so very interesting but of course way beyond what the IB might require. Nevertheless, if you are interested enough (Extended essay???) here is a link to the full text of Carrigan’s publication:  http://www.pnas.org/content/112/2/458.full. Early primate ancestors, about 50 million years ago, evidently possessed a gene to produce ADH in some form, and were able therefore to digest alcohol. Some 10 million years ago, primates began foraging on the ground and encountered fallen, fermenting fruit – an excellent source of sugar and thus calories. At about the same time the ADH4 gene underwent a significant, single mutation which enabled some primates to digest alcohol very much more efficiently and therefore be at a competitive and evolutionary advantage. In humans, this gene is one of a bunch of alcohol digesting genes on chromosome 4. The focus upon alcohol in different forms as a source of energy food, pre-dates the supposed time, maybe just 9,000 years ago, when humans apparently first began to enjoy alcohol as a drink and for its pleasurable effects of inebriation. Carrigan even argues that the pleasure ‘kick’ we modern humans get from alcohol can be explained by our ancient ancestors especially seeking out fermented fruits for their high energy value, and thus obtaining a cerebral ‘hit’ of satisfaction, even though they possibly did not obtain significant effects from inebriation.


I love this! it can go on and on and on ….!

What is the mutation? ADH is a zinc based enzyme. (See a molecular visualisation of it here:  http://www.proteopedia.org/wiki/index.php/3cos.) The mutation is one of the most frequent sorts of mutation – a ‘snip’ or SNP, SINGLE NUCLEOTIDE POLYMORPHISM, which occurs when just one nucleotide and its base is changed, resulting in a the synthesis of a modified protein. Research has shown that in humans there are two variants of the ADH1 SNP, with a resultant protein carrying either the amino acid histidine or arginine – effectively two different alleles. The first of these alleles, with the amino acid histidine, is much more effective at the breakdown of ethanol. People with this allele are consequently more tolerant to alcohol. A wonderful piece of research in China has shown how the less effective allele, containing arginine, was selected out of a population about 10,000 years ago. This time coincides with the early domestication of rice in Eastern Asia. Supposedly early humans commonly consumed alcohol derived from the fermented rice. Those with the arginine-coding allele were less tolerant to alcohol and were therefore less likely to have reproductive success, so the allele became uncommon.  (http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-15)

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Cytochrome c and cladistics – and much more!

cytochrome_c

I love the way the new syllabus can bring together different themes, concepts and understandings, through a focus upon one, seemingly small component. An understanding of cytochrome c might bring together and help a comprehension of this lot:

  • protein structure structure (2.4 Proteins & HL 7.3 Translation)
  • function in cell respiration as an electron carrier (8.2 Cell respiration HL)
  • coding gene, CYCS, on chromosome 7 (3.1 Genes & 3.2 Chromosomes)
  • mutations of DNA (1.6 Cell division, 3.1 Genes, 3.4 Inheritance)
  • synthesis of a protein through transcription and translation (2.7 DNA replication, transcription and translation & HL 7.2 Transcription and gene expression & 7.3 Translation)
  • comparing gene sequences in different species to provide support for cladistics and evolutionary arguments (5.1 Evidence for evolution & 5.3 Classification and biodiversity)

What is the specific context? Topic 3.1 – Genes. The IB syllabus suggests that students make a comparison between the amino acid sequences of cytochrome c in different species, using Genbank or some other database. Why cytochrome c? Because this electron carrier in mitochondrial membranes has been studied in depth as molecular evidence for the 3 Domain proposal for the classification of living organisms. Read on …. it is fascinating!

Now comparing amino acid sequences in different species. This is from Biology Second Edition, C.J. Clegg, 2014, Hodder Education and seems to work fine for cytochrome c oxidase, if you follow the instructions and use your head!p-137-gene-bankp-138

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3.1 Genes

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Chris Paine’s BioKnowledgy presentation – very complete: http://www.slideshare.net/diverzippy/bioknowledgy-31-genes


READING – from Biology in Context for Cambridge International A Level, Glenn and usan Toole, 2013, Nelson Thornes

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READING – from Biology for the IB Diploma Second Edition, C.J. Clegg, 2014, Hodder Education

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THE HUMAN GENOME PROJECT

The HGP was an international attempt to map the entire base sequence of the human genome, including the 1% which constitutes coding genes, the 8% regulatory sequences and the remainder, not all of which has clear functions . The project launched in 1990, funded by the US government and comprising an the international consortium of geneticists from the United Kingdom, France, Australia, China and several other collaborators. The HGP was officially completed in 2003 but not after some controversy caused by a privately funded attempt to unravel the genome, using different sequencing technology, with the intention of commercially capitalising on their results. This research was run by Craig Venter and his company Celera Genomics, but once President Clinton declared that the human genome and its information could not be patented, Venter collaborated with the HGP.

This powerpoint is some years old now and has a special focus upon ethical issues but the presentation is good; it is understandable; and it suffices! human-genome-project-ppt

The Nature of Science focus is upon gene sequencing and how the technology has so dramatically developed, and continues to develop, meaning that sequencing a genome can now be completed in as little as two days. In 1975 Sanger provided the first truly viable sequencing technique, from which were developed the automated techniques which assisted the HGP and Craig Venter. These techniques have now been well overtaken by the so-called ‘next-gen’ techniques which enable extremely rapid sequencing. 

Genomes of a staggering number of species have now been sequenced and analysed. Some interesting comparisons and insights have emerged:genomes-different-species


DNA MUTATIONS AND SICKLE CELLED ANAEMIA

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COMPARISON OF NUMBER OF GENES IN HUMANS WITH OTHER SPECIES

(Note – this is not a comparison of the genome size but is a comparison of the total number of genes which code for proteins. Remember that this coding DNA constitutes just 1% of the genome.)

bioknowledgy-presentation-on-31-genes-5-638ib-biology-31-slides-genes-4-638


COMPARING BASE SEQUENCES IN DIFFERENT SPECIES USING A DATABASE – and much, much more!

cytochrome_c

I love the way the new syllabus can bring together different themes, concepts and understandings, through a focus upon one, seemingly small component. An understanding of cytochrome c might bring together and help a comprehension of this lot:

  • protein structure structure (2.4 Proteins & HL 7.3 Translation)
  • function in cell respiration as an electron carrier (8.2 Cell respiration HL)
  • coding gene, CYCS, on chromosome 7 (3.1 Genes & 3.2 Chromosomes)
  • mutations of DNA (1.6 Cell division, 3.1 Genes, 3.4 Inheritance)
  • synthesis of a protein through transcription and translation (2.7 DNA replication, transcription and translation & HL 7.2 Transcription and gene expression & 7.3 Translation)
  • comparing gene sequences in different species to provide support for cladistics and evolutionary arguments (5.1 Evidence for evolution & 5.3 Classification and biodiversity)

What is the specific context? Topic 3.1 – Genes. The IB syllabus suggests that students make a comparison between the amino acid sequences of cytochrome c in different species, using Genbank or some other database. Why cytochrome c? Because this electron carrier in mitochondrial membranes has been studied in depth as molecular evidence for the 3 Domain proposal for the classification of living organisms. Read on …. it is fascinating!

Now comparing amino acid sequences in different species. This is from Biology Second Edition, C.J. Clegg, 2014, Hodder Education and seems to work fine for cytochrome c oxidase, if you follow the instructions and use your head!p-137-gene-bankp-138

eyyy-edited-tiny