Biol 1362 End Game


First and for most, I have to say, ” I Survived Biochemistry.” I have approached the end of my BIOL 1362 blog. To say this was was best course so far in the University of the West Indies is an understatement. I have grown to appreciate and understand the science of biochemistry. although it was a tough road, the journey was well spent and exciting. Though the “biggest” obstacle is approaching i.e. Finally, I am confident that I will deliver a passing grade and more. Mr Mathew, hats off to you. At first I had the impression of being overwhelmed will all his assignments but I now see the strategy behind it and I must say it works fantastically. I have earned many skill with all his assignments such as researching, documenting, paraphrasing and summarizing as well as group work just to name a few. I look forward in entering Mr. Mathews second year class though it seems that it is going to be even more challenging. So Mr. Mathew I say bring it on.


Thank you all for taking the time to read my posts and giving exclusive feedback.



Nucleosides, Nucleotides and Nucleic Acids

1) A nucleoside (with an s) consists of a nitrogenous base covalently attached to a (ribose or deoxyribose) sugar but without the phosphate group.


2) A nucleotide (with a t) consists of a nitrogenous base, a sugar, and a phosphate group. So, a nucleotide is a “nucleoside mono-phosphate.”


3) A nucleic acid contains a chain of nucleotides covalently linked together to form a sugar-phosphate backbone with protruding nitrogenous bases. In RNA (ribonucleic acid), the sugar groups are ribose, whereas in DNA (deoxyribonucleic acid), deoxyribose sugars are present instead of ribose.



“Nucleic Acid VS Nucleotide,” Newton; accessed on april13,2013.

Who say Slice I mean Splice


Gene splicing is just what it sounds like: cutting the DNA of a gene to add base pairs. Contrary to the immediate image, however, no sharp instruments are involved; rather, everything is done chemically.


Chemicals called restriction enzymes act as the scissors to cut the DNA. Thousands of varieties of restriction enzymes exist, each recognizing only a single nucleotide sequence. Once it finds that sequence in a strand of DNA, it attacks it and splits the base pairs apart, leaving single helix strands at the end of two double helixes. Scientists are then free to add any genetic sequences they wish into the broken chain and, afterwards, the chain is repaired (as a longer chain with the added DNA) with another enzyme called ligase. Hence, any form of genetic material can be spliced together; bacteria and chicken DNA can, and have been, combined. More often, though, splicing is used for important efforts such as the production of insulin and growth hormone to cure human maladies.With modern splicing techniques, enough insulin can be produced for all diabetics. The insulin-producing genes from human DNA are spliced into plasmid DNA; the plasmids are then allowed to infect bacteria, and, as the bacteria multiply, large amounts of harvestable insulin are produced. Splicing has other practical medicinal uses, too. In July of 1996, a 68-year-old woman became the first patient to be treated for arthritis (a disease which affects an estimated 2.1 million Americans) via gene therapy. At the University of Pittsburgh, therapeutic DNA that blocks the production of a specific protein (IL-1) that causes arthritis pain was injected into two of her knuckles.


“The Gene School,” Think Quest; accessed on April 13, 2013.

Nucleotides and Nucleic Acids WTH are they

What Are Organic Molecules?
Organic molecules contain carbon-hydrogen bonds, are found in living things and can be very large molecules. The major classes of organic macromolecules are  carbohydrates, proteins, lipids and nucleic acids.
 What Are Nucleotides really?
Nucleotides are monomers (small molecules) that are the building blocks of nucleic acids. Each nucleotide, and consists of 3 portions:
-a pentose sugar called ribose
-one or more phosphate groups
-one of five cyclic nitrogenous bases
Some nucleotides are put together to form nucleic acid (DNA & RNA) macromolecules, whereas others function on their own. ​
Nucleic Acid Structure
Nucleotides can be linked together by covalent bonds between the phosphate of one nucleotide and the sugar of next. These linked monomers become the phosphate-sugar backbone of nucleic acids. The nitrogenous bases extend out from this phosphate-sugar backbone like teeth of a comb.
Deoxyribonucleic Acid (DNA)
DNA (deoxyribonucleic acid) is the genetic material, the original blueprint, inside each biological cell. The molecule is double-stranded and twisted, like a spiral staircase, with the two sugar-phosphate chains as the side rails, and the nitrogenous base pairs, linked by hydrogen bonds, forming the rungs. In addition to linking the bases together, hydrogen bonding twists the phosphate-sugar backbones into a helix, thus DNA is a double helix.There are four different types of nitrogenous bases that can be found in a DNA molecule: adenine (A), guanine (G), cytosine (C) and thymine (T). Adenine and guanine are larger, double ring nitrogenous bases called purines. Cytosine and thymine are smaller, single ring nitrogenous bases called pyrimidines. When bases pair up between the two DNA strands, a purine always pairs with a pyrimidine. Specifically adenine (A) and thymine (T) pair up, and cytosine (C) and guanine (G) pair up. These bases are attracted to each other through hydrogen bonding.When the DNA molecule is inactive, the bases are linked by these hydrogen bonds and the molecule is in its spiral-shaped state. When DNA is being used—either being copied (a process called replication) or being employed to build proteins (involving the processes of transcription and translation)—the DNA molecule must be opened up, essentially “unzipped” between the bases.
Ribonucleic Acids (RNA)
In living organisms, RNA is a single stranded nucleic acid molecule. In viruses, non-living infectious particles, RNA can be single or double stranded.There are four different types of nitrogenous bases found in an RNA molecule: adenine (A), guanine (G), cytosine (C) and uracil (U). In RNA, uracil takes the place of the thymine found in DNA.
When RNA bases are laid down to build an RNA molecule, DNA is unzipped, and the new RNA molecule made is compliment of the DNA template. For example, if the DNA strand has the following bases, in this order, ATTGCACT, the new RNA molecule being made will have the base sequence UAACGTGA. After the RNA segment is made, the DNA zips back up and the RNA floats off to carry out its function in the cell.Genetic information copied from DNA is used to build three types of RNA:
1) Ribosomal RNA – The Protein Factories: Most of the RNA in cells is part of the structure of small cellular organelles known as ribosomes, the protein factories of the cells.
2) Messenger RNA – The Genetic Blueprint: Messenger RNA is a copy of the genetic information that was transcribed from the cell’s original blueprint, DNA. This copy of the genetic information is brought to the ribosome and used as instructions for building proteins.
3) Transfer RNA – The Amino Acid Suppliers: Transfer RNA is also part of the process of building proteins. Like a little truck, tRNA brings the amino acid to the ribosome. Which amino acid it brings depends on which was coded for in the mRNA instructions. At the ribosome, these amino acids are joined together to form proteins.
ATP: The Energy Transfer Molecule
Adenosine 5′-triphosphate (ATP) is a multifunctional nucleotide, most important as the “molecular currency” of intracellular energy transfer. Like tiny rechargeable batteries, ATP molecules transport chemical energy within a biological cell. These molecules can move energy around because the phosphate bonds contain a lot of potential energy, which is released when they are broken.During photosynthesis and cellular respiration, ATP is produced from ADP (adenosine diphosphate), an inorganic phosphate and added energy. ATP energy is consumed by a multitude of cellular processes.
 Chemical Structure of ATP (Adenosine Triphosphate
So how was my presentation:url-3
“What are Nucleotides and Nucleic Acids,” Science Prof Online; accessed on April 13, 2013.


Relatively large biological molecule that mostly does not dissolve in water.Lipids include fats, oils, cholesterol, a number of steroid hormones, the major constituents of cell membranes, etc.Lipids are predominantly hydrophobic substances, though can have hydrophilic portions as well. An example of the latter are lipids associated with membranes, that is, lipid bilayers, include phospholipids and the molecule, cholesterol.Unlike proteins, carbohydrates, and nucleic acids, lipids are less homogenous in terms of their structures. In particular, lipids do not have a consistent subunit from which they are polymerized but instead are categorized together as a group based upon their relative inability to dissolve in aqueous solutions. That is, they are oil-like in the generic sense of that term. The video placed a whole new spin on the age of rap and showed that is just not for young persons.Furthermore, while being enjoyable it also teaches one about lipids in a fun interactive session.


“Michael Eskin Lipids Rap,” Youtube Video, 2:52,posted by”Lipids Get a Real Bad Rap: It’s Just Not Fair,” May 17,2012,

My two reflective pieces for my published papers


Topic 1 Reflection: “Neurological Effects of Caffeine”


“Neurological Effects of Caffeine,” Medscape, accessed on March 29, 2013, overview#aw2aab6b4


Thought to be a drug addiction, caffeine got the “award” for being the most consumed psychoactive essence. Caffeine lead to various neurological effects on the body. Related to uric acid in design, 1, 3, 7-trimethylxnthine (caffeine) undergoes “oxidation and demethylation” when metabolized. Derivatives such as acetylated uracil, 1-methyluric acid and 1-methylxanthine are urinary metabolites which occurred from 1, 7-dimethylxanthine. However the conversion of methyl xanthine to uric acid has not been evidentially supported. Genetic and the environment played a role in the determination of the rate at which methyl xanthine was eliminated. Metabolism of methyl xanthine followed “first order kinetics” but at higher concentrations, obeyed “zero-order kinetics” due to metabolic enzymes being saturated. The presence of other disease in the body also played a role in the breakdown of methyl xanthine. With a half-life of 3-7 hrs in plasma, methyl xanthine’s life increased through late pregnancy and ‘long term use” of “contraceptive steroids.” Methyl xanthine, “Translocated intracellular calcium,” “increased the build-up of cyclic nucleotides” and “Blocked adenosine receptors.” Caffeine interfered with the uptake and cache of calcium through the ‘sarcoplasmic reticulum” in striated muscles whilst it caused relaxation in smooth muscles. Caffeine also acted as a competitive ‘antagonist’ by receptors of adenosine within the therapeutic concentration range. Some other inferior effects of caffeine included inhibiting “prostaglandin synthesis” and the reduction of the breakdown of catecholamine’s. Low concentrations of caffeine suppressed the outbreaks of adenosine in the brain. Adenosine decreased the rate of neuronal transmission and inhibited synaptic transmission as well as neurotransmitters. The turnover number of a batch of neurotransmitters also increased. Furthermore, caffeine also lead to the inhibition and blockage of adenosine receptors which lead to “potentiation of dopaminergic neurotransmission.” Various clinical tests have been carried out and revealed that caffeine stimulated the ‘autonomic nervous system and increased alertness.” Caffeine also showed the relief of sleepiness. One the other hand, trials revealed that caffeine had no effect on the ‘arousal of memory.” Further studies are required to understand the long and short term effects of caffeine as it applies to the nervous system and so the human system as a whole.


I choose this topic because I love caffeinated drinks and I wanted to learn exactly how it affects my body. This article revealed some interesting facts about coffee. I am a frequent coffee consumer and I always thought it had an effect on memory. It showed me a wider understanding of caffeine with respect to the benefits but it did not reveal any disadvantages with consuming too much caffeinated drinks. Presume away but caffeinated drinks have kept me up in times of need and so i dedicated my first review to understanding how it really works. That said, the relevance of choosing the topic at hand was to portray my urge to understand how certain “necessities” work in the body. Thank you for reading and have a productive day.


Topic 2 Reflection: “Bacteria can Morph Host cells into Stem cells”


“Bacteria can Morph Host Cells into Stem Cells,” Medical News Today, accessed on March 24,2013,


Upon studying what happened to mice infected with “leprosy bacterium,” scientists have discovered that at early stages prior to infection, the leprosy bacterium protected itself from the immune responses from the host by be cloistered away in Schwann cells. Upon infection, the leprosy bacterium then went ahead to reprogramme the host cell into stem cells, leaving the host (mice) unprotected. This then prevented (Schwann cell) the nervous transmissions to the brain. The new stem cells had the ability to now transform into any cell which helped the leprosy bacterium to go from the nervous system to other systems. Astonishingly, they also discovered that the leprosy bacteria was able to trick the immune system and thus helped the bacteria in spreading. This was done through the secretion of proteins called “chemokines” which gathered immunity cells to obtain the bacteria and disperse it to other parts of the body system. This was the first discover in terms of a bacteria transforming mature cells into stem cells. Researchers were interested in this new mechanism because this process did not have the potential risks of developing tumors which was always a result otherwise when scientists tried to develop stem cells in the lab. Scientist revealed that they would get stem cells through means of the leprosy bacterium and then get rid of the bacterium using antibodies so the new stem cells could be inserted to tissues that have underwent degeneration through diseases. Furthermore they planned to use this knowledge, in order to improve synthetic stem cell creation in the lab as well as applying the knowledge to other diseases.


I choose to reflect upon this topic because I saw substantial relevance as it pertains to my field of interest. Many breakthroughs have been discovered and this is no exception. I have definitely learned something interesting however I would have liked to know how exactly the bacteria works as in converting the host cells to stem cells. I understand that it is a new discovery (article posted on 19 January 2013) and such more research is needed to understand how it works at the biochemical basis. The significance of this topic, well could be found in my first ever post. As I stated at the beginning, I would like to study microbiology in various aspects and for this, i see it fascinating and paramount to keep up with the “micro-trends” in the world. Some people prefer the “newest and latest” materials in the world today but i prefer to keep up with the new developing trends of the micro-world. Thank you for reading and have a blessed day.



Identification of Lactose positive and Lactose negative Bacteria using MacConkey agar


MacConkey agar contains bile salts and crystal violet to inhibit most gram + organisms.Lactose is a carbohydrate that may be used as a nutrient. The utilization of lactose is important in identifying gram negative rods. Lactose + means that the organism can use lactose as an energy source whilst lactose – means they cannot. Differential media is used to distinguish organisms from each other based on a reaction that occurs as they grow. Lactose + organisms ferment the lactose and produce acid whilst lactose – organisms do not produce any acid as they grow. MacConkey agar contains a pH indicator called neutral red that detects the acid production in lactose + organisms. As lactose + bacteria produce acid, it causes the pH to drop and where neutral red is absorbed and the colony turns red.


Lactose – bacteria remains colorless and translucent as they do not produce any acid.



“Identification of Lactose Positive and Lactose Negative Bacteria using MacConkey Agar,” Wisc-online, accessed on April 10, 2013,

BioTork develops xylose-fermenting yeast for ethanol facilities


After nearly two years of collaborative research, biotechnology company BioTork LLC and the National Corn-to-Ethanol Research Center have developed a yeast strain capable of fermenting the xylose found in ligno-cellulosic biomass in a commercial-scale environment.Xylose is the second most abundant sugar in ligno-cellulosic biomass but cannot be fermented by Saccharomyces cerevisiae, the predominant yeast used in ethanol production. The USDA had previously engineered a strain of S. cerevisiae capable of fermenting xylose, but the genetic engineering negatively impacted the strain’s growth rate, making it inapplicable for use in an industrial environment.  BioTork utilized proprietary continuous culture technology developed by Florida-based Evolugate LLC as part of an adaptive evolution method to essentially teach that strain to grow under industrialized settings. Xylose was placed in a medium with the yeast strain and the fittest yeast cells were then selected and re-introduced to increasing proportions of xylose over the course of several months until they eventually learned to grow on xylose alone.“While improvements to the growth rate and initial scale-up of its performance in an industrial setting are underway, this strain has the potential to be one of the first economically viable xylose-fermenting strains, and represent a fruitful combination of genetic engineering and adaptive evolution,” Tom Lyons, BioTork chief scientific officer said in a news release.Because D-xylose comprises up to 30 percent of cellulosic biomass, BioTork’s yeast strain could be applied to various types of biomass for cellulosic ethanol production but one of the first applications envisioned for the yeast strain, currently known only as SC48-EVG51, is to produce ethanol from distillers dried grains (DDGs) at existing corn ethanol facilities. According to BioTork, if the glucose and xylose in distillers grains were converted to ethanol, producers could increase their ethanol output by 10 percent without increasing their capital expenditures. “The sugar xylose represents close to 18 percent of the dry weight of distillers grains, and our partnership with NCERC has mostly solved the way to ferment it,” said Ziad Ghanimi, public relations manager at BioTork. While the U.S. ethanol industry is currently facing a domestic blendwall, Ghanimi noted that there continues to be demand internationally for increasing amounts of ethanol, which could provide the market for additional U.S. capacity.BioTork does not plan to make the newly developed yeast commercially available in one standard strain for distillers grains-to-ethanol production, simply because the chemical composition of distillers grains varies from plant to plant, Ghanimi said. Instead, the company will optimize the strain for use with each specific product. Licensing fees will likewise vary, he said.

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“BioTork develops xylose-fermenting yeast for ethanol facilities,” Ethanol producer magazine,   accessed on April 10 2013,