Biochemistry

QUESTION: The Managing Director of a well-known company on Wall Street thrives on a diet of fruit jam, bread, pasta, and coffee. She exercises intermittently. One day she decides to go to her primary healthcare provider for a routine checkup. The healthcare provider recommends that she take the Benedict's test. Assume that the glucose levels of the patient are high. 1. State the results that the test would indicate (specify the color of the solution). 2. State the composition and the properties of the ketohexose derived from fruit jam. 3. Describe the manner in which ketohexose acts as a reducing sugar in the test.

ANSWER: 1. Benedict's test detects reducing sugars (such as glucose). Benedict's reagent contains blue copper ions (Cu2+) which are reduced to copper (Cu+) in the presence of reducing sugars. These are precipitated as red copper(I) oxide which is insoluble in water.Therefore the color of the solution would be Red.

2.Ketohexoses is a ketone containing hexose i.e. it consists of six carbon monosaccharides with a keto group ( R-CO_R ) and other carbon atoms consists an OH group and remaining hydrogens. Ketohexoses are soluble in , doesnt have sharp melting points, can char and sweetin taste because of which are added in the jam. 

3. When the hemi-acetal or ketal hydroxyl group is not engaged or locked or linked to another sugar molecule but  free then the aldehyde (or keto-) form (i.e. the chain-form) is available for reducing copper (II) ions. When a sugar is oxidized, its carbonyl group (i.e. aldehyde or ketone group) is converted to a carboxyl group.
 

Ecogenomics and Its main Objectives

The study of structure and function of a genome in order to understand its relationship between the organism and biotic and abiotic factors of the environment is called ecogenomics. The main objectives of ecogenomics are as follows:

1. To investigate the evolution pattern of an organism with the help of DNA sequences.

2. To discover and explore uncultivable microorganisms with the help of metagenomic techniques.

3. To study the relationship between a species and effect of environmental factors on the species at a molecular level utilizing DNA microarray.

4. To study the effect of genetic and epigenetic variation on evolutionary change due to stress.

5. To study the relationship between different species and gene-environment-function with the help of comparative genomics.

6.  Assessment of region specific biodiversity with the help of DNA microarrays and find the difference between impacted and control regions.

There are several projects going on in order to get more insight into the composition and working of microbes and other soil organisms at a genetic level. For example, a new species of thermophilic bacteria was discovered in order to understand the life sustainable system in the soil by ecogenomics. Samples at a depth of about 8,000 ft below the surface from a gold mine were collected for genome analysis in in South Africa, Witwatersrand Basin. The DNA was extracted from fracture water. Analysis of 16s rDNA in the sample showed that a sulfate reducer and a methylotroph with some thermophilic microbes were present in high quantity. In the thermophiles obtained, there was a dominant Desulfotomaculum like organism discovered which supposedly represented a new species and new family of thermophiles. This organism has several differences from other thermophiles and sulfate reducers in terms of biosustainability in deep subsurface environments so are considered to be a completely new species.

Ecogenomics not only has application in general and pure science but it is also used to understand the function of microbial communities in disease processes which cannot be understood by traditional culture based methods like metagenomics.

While researching the in situ communities like the host system, ecogenomics allows studying the interaction of a pathogen with other microorganisms. This may help to keep a check on the pathogen if the interaction is antagonistic.

With the help of ecogenomics, extensive amounts of genetic information can be analyzed and generated. It can used to explore several factors such as ecological systems which enable the scientists to analyze thoroughly and make more reliable and specific decisions for ecosystem viability.

Ecogenomics can be utilized to determine several aspects altogether as compared to other techniques such as metagenomics. Ecogenomics may investigate factors such as interactions of food web in aquatic environments, spraying effects of fertilizer, ecological effects of different pesticide and land management and functioning in terms of sediment and soil biodiversity. Whereas traditional techniques can analyze limited factors at a time, for example metagenomics studies only the genetics of environmental samples. 

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Genome Sequencing Strategy

Here we have discussed a genome sequencing strategy which is commonly adapted in labs.

The steps in the complete genome sequencing will generate the cDNA sequences that can be used to develop BACs and cDNA microarrays. But since there limited genome data of the organism available, the sequencing will be carried out in two distinct stages.

 

Stage I:

In this stage, the cDNA library of the organism will be generated. The database of novel EST’s from the most diverse EST library would be prepared that can be used for gene annotation, cloning and development of microarray’s etc. The EST’s will expand the understanding of types of genes expressed in the organism . The genome size of the organism will be estimated by comparing the reassociation rate. The genome size will provide a significant information by which we aim to generate BAC genomic DNA library that will inform about GC content of the genome, repetitive sequences and level of polymorphism in the genome.

Stage II:

In this stage, whole genome random shotgun sequencing is proposed for the complete genome sequencing of the organism. This method utilizes comparative genomics protein coding and regulatory regions on the genome. The sequence-tagged BAC clones are mapped to the polytene chromosomes so as assembled scaffolds are directly localized in the genome of the organism  with specific orientations. We aim to produce a draft genome with the knowledge of genomic organization, to carry out the comparative genome analysis and the complete finishing of the genome is done. The finished genome is released to a public domain after getting approval by several committees.

 

Nature and Limits of Science

Science is a public domain and is free from any social or political situation.

The scientific advances made by a country have global impact. For instance: polio vaccine. Scientific research also helps in the betterment of one country through research project grants that can be granted to the needy from various research institutions across the globe. For example, BCPB (British Counsel for Prevention of Blindness) has granted a Trachoma Research Funding Project to Tumaini University, Tanzania, Africa .Also along with the advantages, it has certain limitations as well. All research is funded, and any situation that affects a country’s financial situation as a whole will have its effect on research. Scientific findings are reported back to the community and will be subject to discussion, which may also result in a change in research policies.

GLOBAL WARMING: Fact or Myth?

 

INTRODUCTION:

In the year 2009, more than 200 countries participated in a climate control conference held in Copenhagen for discussing the threats posed to the environment by global warming. The representatives of the countries along with more than 2,500 scientists from several countries were of the opinion that global warming is a major threat to the environment and the future of human population because of pollution and greenhouse gases in particular. Despite of that many scientists were debating that whether this climate change was caused due to human activities or the natural process in the universe and is affecting earth’s climate. There are several natural factors that determine earth’s environment, such as the orbit and degree of tilt determine the warming and cooling of earth. Moreover volcanic eruptions were a cause of global warming in the prehistoric era but due to reduction in these eruptions lately life forms produced on earth. The fact cannot be ignored that after the industrial revolution, the warming of the earth has increased by 35% due to greenhouse gas emission (Edwards 2010).

Greenhouse gases are those gases which trap the heat in the atmosphere and emit radiation which affects the temperature of the surroundings. Greenhouse gases involves several gases produced naturally or by human activities such as carbon dioxide (CO²), Methane (CH⁴), Nitrous oxide (N²O), and other fluorinated gases etc (USEPA 2011).   Although scientists believe that natural process have also caused a variable change in earth’s atmosphere but it has been caused mainly due to human activities emitting greenhouse gases, deforestation, emission of aerosols etc (Mohr 2005 & Mitchell 2010).

The scientists had predicted about the changes in temperature in the coming decade as the atmosphere of earth is continuously changing naturally but studies showed that the climate and temperature of the earth has increases at a much higher rate than the scientists predicted and is still accelerating which can have disastrous consequences such as floods, extreme weather and mass extinction of species, skin diseases and other epidemics etc. (Meinshausen et al, 2009).  

Human activities have emitted a lot of carbon dioxide in the earth’s atmosphere. A study showed that the natural carbon sinks of the nature, where carbon was absorbed and diminished, have been disrupted by human activities. According to a report by US National Oceanic and Atmospheric Administration (NOAA), the concentration of carbon dioxide alone in the environment has elevated up to 19 billion tones since past four years. And after carbon dioxide, it is methane whose concentration has been increased considerable in the past few years (Greenhouse Gas, 2011).

The graph below shows an increment in the amount and concentration of greenhouse gases such as methane, carbon dioxide, nitrous oxide etc. over a decade.

MAJOR THREATS POSED BY GLOBAL WARMING:

Even a small rise in the global temperature can give rise to extreme situations because the entire environment is interconnected with each other. Several factors such as, water currents, rainfall, wind, intensity of sunlight, atmospheric pressure, presence of debris in the atmosphere etc  are connected with each other and together form the weather of the earth. If any of these factors in misbalanced it can pose major threats to environment. According to various researches and studies it has been concluded that if the atmospheric temperature increases, it can lead to increase in the sea level by 0.09 - 0.88 m (Stanford Solar Center 2008) because of the melting of glaciers and polar ice caps, increase in storms, floods, drought and other such abrupt changes in the climate and if it is nor brought under control, then by the end of this century we can expect to see a raise of 7 °F in earth’s climate. Global warming is a serious threat posed to the earth’s environment and can have severe effects which can ultimately lead to the extinction of several wildlife and other species including human being from the face of earth (Edwards, 2010). It also poses a major threat to human health because it can result in the spreading of diseases such as malaria and other epidemic due to poor air quality and living conditions. Greenhouse gases are also a major cause of atmospheric pollution causing breathing problems and asthma. The depletion of ozone layer can allow the UV lights to enter into earth’s atmosphere and can give rise to visual and skin related diseases such as skin cancer. There have been several cases of skin cancer reported in the United States due to radiation of the sun   (Stanford Solar Center 2008).

CONTRIBUTION OF GREENHOUSE GASES IN GLOBAL WARMING:

Greenhouse gases play a major role in global warming. Green house gases such as methane, nitrous oxide and chlorofluorocarbons even if found in low concentrations, can give rise to major issues because even though they are lower in concentration but their each molecule can absorb high amount of infrared radiation as compared to molecules of other gases. According to a study, it was observed that greenhouse gases have caused about 43% of elevation in radiative forces and therefore pose a major threat to environment. (Lashof & Ahuja, 1990)

We know that our atmosphere is made up of 78% nitrogen and 21% oxygen along with water vapor and several other gases contributing the rest. These other gases which include argon, carbon dioxide, neon, helium, methane, hydrogen, nitrous oxide and ozone are the cause of global warming and greenhouse gas issues.  Natural and various human activities lead to the emission of greenhouse gases (carbon dioxide, methane, nitrous oxide and fluorinated gases which includes fluorine, chlorine and bromine). These gases trap the atmospheric heat and emit radiation and their increased concentration in the atmosphere which can lead to global warming. (Greenhouse Gas, 2011)   

Why are they called “greenhouse” and how do they cause global warming:

The earth absorbs the heat in the daytime and radiated it in the space during the night except some amount which is used to maintain earth’s atmosphere. These specific gases do not allow the earth to radiate the heat back in the space and trap it in the earth’s atmosphere making the atmosphere of the earth warmer than required and converting the earth into something which can be compared to a green house. That is why these gases are called ‘greenhouse gases”.  (Greenhouse Gas, 2011)

The emission of greenhouse gases has resulted into a variable depletion of ozone layer found in the atmosphere which protects the atmosphere from harmful ultraviolet radiation. With the depletion of atmospheric ozone, the UV rays can easily penetrate into earth's atmosphere causing elevation in earth's atmosphere. The green house gases are one of the primary reasons for ozone depletion because when they move above to the stratosphere, they do not get washed away by rainfall but instead they react with atmospheric ozone and react with it to destroy it. The scientists have estimated that with a decrease on one percent atmospheric ozone, there will be an increase of about two percent in the penetration of UV light in the earth’s atmosphere. (Greenhouse Gas, 2011)

Although, certain scientists debate that these changes in earth’s atmosphere are not caused by human activities, but are seen due to natural changes such as cloud cover. They also suggest that increased level of carbon dioxide and other greenhouse gases are the result of warming of earth, changes in the solar system and radiation of the sun and human activities are not the potential cause of global warming because earth’s atmosphere is continuously changing over the years (Edwards, 2010).

CONCLUSION:

There are certain reports by the workers who claim the temperature of the earth is not increasing but dropping eventually, the increase in the level of carbon dioxide is due to natural changes in earth’s environment, activity of the sun and global warming is a myth. But the reports from Intergovernmental Panel on Climate Change (IPCC) support the fact that global warming is a result of human activities which produce factors such as greenhouse gases, aerosols, debris etc. which continue to deplete the earth’s covering and this theory is the result of a research conducted on the CO₂ trapped in the ice. Although there is not much reports of the opinion that global warming is not driven by human activities and most of the studies support the human driven theory of climate change. It is evident that human activities have increased the level of atmospheric pollution and given rise to environmental problems such as deforestation, pollution of water reservoirs such as rivers and increase in the carbon dioxide level by burning of fossil fuels etc. In the end, no matter what factors are responsible for global warming, it is our duty to keep our planet pollution free and reduce the emission of harmful gases and byproducts which whether or not harm the environment, do harm human health.

Model of E.coli replication fork

A replication fork is formed during the replication of the DNA and is initiated by the enzyme helicase which breaks the hydrogen bond formed between the nucleotides thus separating the strands. The two strands will act as a template for leading and lagging strand, during replication. In the leading strand, replication is carried out in 3’ to 5’ direction allowing the new strand to be synthesized 5’ to 3’. The DNA polymerase continuously reads and adds nucleotides to the growing strand. In the lagging strand, the replication fork moves in 5’ to 3’ direction and the growing strand is synthesized 3’ to 5’. Since DNA polymerase catalyzes the polymerization of dNTPs only in the 5′ to 3′ direction, therefore the enzyme primase reads the DNA and adds short segments of RNA to it. DNA polymerase lengthens the segments and Okazaki fragments are formed which are joined by DNA ligase. Thus with the help of leading and lagging strand the replication form moves forward till the total DNA is replicated.

Biology Fact-Sheet on ‘Fragile X Syndrome’

CHARECTERISTICS

Fragile X syndrome is an X-linked dominant disorder causing mental and emotional disabilities. This disorder is heritable and can be passed from one generation to another. The persons suffering from this disorder show phenotypes like prominent ears, long face, autism and behavioral problems (Fragile X Syndrome). It is called “fragile X syndrome” because the affected X chromosomes are narrowed at the end when observed under high resolution microscope. (Fragile X Syndrome, 2007)

 Since the gene causing is present on the X chromosome, the number of affected males is higher than the number of affected females. It is so because, males have only one X chromosome present (XY chromosome) while females have two X chromosomes (XX chromosomes). Most of the females with fragile X syndrome have one normal X chromosome and one defective X chromosome but they have only one functional copy of X chromosome. During protein formation cell randomly chooses only one X chromosome for translation, therefore sometimes females with a defective X chromosome also have normal phenotype. Where as in males the X chromosome is always utilized in protein formation and the disorder is expressed. (Fragile X Syndrome)

CAUSES

It is caused by the mutation in a gene that encodes for the Fragile X Mental Retardation Protein (FMRP) required for the brain to carry out normal functions. Due to the transcriptional silencing of the Fragile X Mental Retardation 1 (FMR1) gene the expression is inhibited. (Garber 2008)

The promoter region of the FMR1 gene consists of a repeated CGG sequence. A normal FMR1 gene has about 6 to 40 CGG repeats where a mutated FMR1 may have more than 200 repeats. The number of repeats vary from person to person.  A mutation ranging from 55 to 200 repeats is called “Premutation” where as a mutation with more than 200 repeats in a gene is known as “Full Mutation” and the phenomenon is called as methylation. (Fragile X Syndrome)

 Due to extended CGG repeats in the untranslated 5′- region the gene is inactivated and production of FMRP is halted. FMRP is a protein which selectively binds to RNA and carries out the negative regulation of protein synthesis in neuronal dendrites (Hagerman 2005). When FMRP is not present, the transcripts regulated by FMRP are over translated resulting in the abundance of proteins. The protein abundance reduces the synaptic strength due to trafficking of AMPA receptor (α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor). Because AMPA receptors get inhibited, the synaptic transmission to the Central Nervous System is reduced leading to synaptic plasticity and mental abnormalities. Because synaptic plasticity is responsible for learning and memory, its alteration results into fragile X syndrome. (Garber 2008)

TREATMENT

There are several ongoing research projects funded by National Institute of Child Health and Human Development (NICHD), which aim to find a suitable cure for this disorder. NICHD has established three research centers across the country for the treatment of Fragile X Disorder.  The disorder can be determined by carryings genetic testing. In order to find the treatment, the research is carried out on several model analogous to human brain the possible outcomes are discussed as follows: (Fragile X Syndrome)

1.    Production of certain chemical in the brain that repairs the mutated, extended FMR1 gene.
2.    A drug that initiates reverse methylation.
3.    Replacing the mutated FMR1 gene with a normal gene.
4.    To introduce FMRP artificially into brain via pills or injections.
5.    To find a substitute for FMRP that carries out similar function.