REVIEW PAPER 2- HIV Inhibitors





Davis,  Katharine. “ The shape of HIV drugs to come”,  Journal Reference- Chemistry and Biology,/ (accessed October 16th, 2004)



HIV Inhibitors- A Temporary Cure



HIV- Human Immunodeficiency Virus is a type of virus that destroys the body’s immune system, which in turn makes it harder to fight off infectious diseases. A class of HIV protease inhibitors that are used to fight the HIV enzyme have become useless because resistance against them have been acquired by the enzyme. An inhibitor is a compound that binds to an enzyme and stops its activity, hence products are not formed. The HIV enzyme is used in the last stage of viral replication and binds to the protein substrate and cuts it up, then making more pieces to build more virus.  The Proteins produced by the genetic material of HIV is much larger than the protein need to make viruses and must be cleavage.

The way the HIV protease inhibitor works is that, it is a transition state analogue. It is a chemical compound with a chemical structure that resembles the transition state of the substrate that the HIV enzyme binds to. The chemical reaction would not occur so the inhibitor ends up binding to the active site. Because the enzyme lowers the activation energy, when the transition state analogue aka inhibitor binds to its active site binds much stronger to the enzyme than a normal substrate because it doesn’t undergo a catalyzed reaction.

HIV is a very complex disease that it hard to resist. Because of its fast rate of mutation, scientists thought that they could use this to their advantage. They thought that sooner rather than later the virus would mutate in order to resist the inhibitor and hence the substrate to which it binds would also be resisted, they were wrong.

They were wrong because when Celia Schiffer of the university of Massachusetts Medical School crystallized the substrate and compared it to the enzymes structure she realized that the inhibitor contained protruding sides which were more important to the drug to carry out binding than to binding to the active site. Hence if the enzyme were to mutate its job would be unaffected by the drug. Schiffer explains that when the drug was being made its inhibiting properties were studies in more detail than how it actually binds. This was therefore a part time solution to a long-term virus. Inhibition can only work for so long until the virus mutates again.


Cyanide, A building Block For Earth

Review Paper


cyanide was a building block for earth.


What is life? How is life formed and where did it come from are the many questions asked by scientists of today. Life is a characteristic of processes that distinguishes animals and plants from inorganic matter. There are several theories as to how life was formed on earth.

One theory is organic matter formed on earth as a result of components coming together and forming one mass know as coalesced. This happened due to reactions such as lightning arching through the air. But these reactions could only happen in the early atmosphere full of methane.  The early atmosphere was a mixture of solids and gases and there was hardly any atmosphere. The surface of the earth was molten. But scientists later decided that was unlikely. The sun is a very powerful mechanism and limits the mounts of theories that can be made due to the high temperatures it projects. The sun is the star of the universe and is made up of hot plasma in magnetic fields. Molecules of gas and dust could have been the reason for formation but the suns heat would of destroyed it.

Comets are made up of an icy body and dust.  They exhibit a tail and a coma. An asteroid is a small body or minor planet of the inner solar system. These resemble comets but are different because of their volatile surfaces.  These two are made up of large amounts of carbon and when they enter the earth’s atmosphere, they condense. In order to make it into the earth’s atmosphere they would have to pass the very heated sun. Hence this theory was rejected because the sun’s heat would have destroyed the comets and asteroids before reaching to earth. 

Peter Schultz of Brown University however proved this theory wrong. He claimed that even if the comets and asteroids were destroyed by heat, the compounds could be revived.

Seiji Sugita of the University of Tokyo conducted an experiment by firing polycarbonate plastic at metal targets and the projectiles were vaporized in a flash of light when the contents were examined cyanide was found. It was formed from the polycarbonate’s plastic and the air’s nitrogen. Cyanide is a monovalent combining group with carbon triple bonded to nitrogen. Cyanide is highly reactive and takes part in further reactions. In the same way when comet and asteroids came to earth, is carbon combines with the earth’s nitrogen and formed cyanide.

The cyanide then took part in further reactions and made more complex compounds hence forming more complex carbon molecules and the nitrogen was used to make amino acids which makes proteins which makes up everything. This therefore led to the formation of the earth.


Shiga, David. “Was life founded on cyanide from space crashes?” Journal of Geophysical letters. / (accessed November,12th 2009)






Which of the following choice is TRUE


a)    For competitive inhibition, the Km value increases.

b)   For uncompetitive inhibition, the Km value increases and Vmax increases.

c)    For non competitive inhibition both Km and Vmax value increases.

d)   For competitive inhibition, the Km value decreases.

e)    For uncompetitive inhibition, both Km increases and Vmax decreases.






Select the correct multiple answers using one of the keys, A, B, C, D or E as follows.


a)    1, 2 and 3 are correct

b)   2 and 3 are correct

c)    2,4 and 5 are correct

d)   1 and 5 are correct

e)    2 and 5 are correct



Which of the following enzymes are used in the process of glycolysis


1- hexokinase

2- lipase

3- diastase

4- RNA polymerase

5- pyruvate kinase

Nucleic Acids, DNA and RNA

A nucleic acid is made up of nucleotides, which are the basic monomers. A pentose sugar, a phosphate and nitrogenous base make up a nucleotide. 

A polymer is made up of monomers that condense and joins by polydiester bonds. This bond is made between a phosphate group and a pentose (5Carbon) sugar.


DNA – diribonucleic acid


The pentose sugar is dioxyribose.


DNA has four types of bases hence four types of nucleotides can be formed.


  • There are adenine and guanine, which have a larger double ringed structure. These are classed as purines.
  • There are thymine and cytosine, which have a smaller single ringed structure. These are classes as pyrimidines.



The structure of DNA is made up of 2 polynucleotide chains. These chains are linked by hydrogen bonds.  Specific base paring is essential for DNA and RNA to carry out its functions.




Adenine and tymine bonds by 2 hydrogen bonds and cytosine and guanine bonds by 3 hydrogen bonds.


The DNA is tightly wound into a double helix and this helical structure is held together by hydrogen bonds. This tight conformation makes DNA very stable. This stability aids in the purpose of DNA, which is storing genetic information and protects against damage such as mutation.


Specific base pairing keeps the amount of adenine to thymine and cytosine to guanine constant.


RNA – ribonucleic acid.


For RNA the nucleotide purine bases are- adenine and guanine and the pyrimidine bases are – uracil and cytosine.

The pentose sugar is ribose.


There are 3 types of RNA-

  • Messanger RNA- mRNA – formed in the nucleus, single chain that wounds and is involved in protein synthesis.
  • Transfer RNA – tRNA – single chain folded into a cloverleaf shape. This contains 3 bases of anticodon that determines which amino acids attaches.
  • Ribosomal RNA – rRNA – found in the nucleolus and make up ribosome.


uses of lipids



Lipids contain a lot of energy meaning that 1g of lipid can yield twice as much energy as a carbohydrate. In humans they are stored as fats and in plants as oils and can easily be respired to release energy.




Because of their hydrophobic properties they can be used to prevent water loss. For example on leaves surface, a waxy cuticle is present to prevent evaporation on high temperature days. Humans produce an oily mixture, sebum, which prevents the skin from drying out.




Because of its arrangement of atoms it is a poor conductor of heat and hence is used to insulate. Humans store fat under the skin, which helps them to survive in colder temperatures. Also whales store blubber, which allows them to survive at deeper ocean depts, of very low temperatures.


It can be protective and act as shock absorbing layers. In the body certain organs such as the kidneys and the heart is covered by a layer of fat to prevent damage incase of harsh impact.



Lipids are made up of the atoms oxygen, hydrogen and carbon but its oxygen content is lower and hence the molecule is non polar and can only be dissolved in non-polar solvents.


The lipid grouping is quite diverse and includes- triglycerides, phospholipids, waxes and steroids.


Phospholipids are quite important because they contribute to the formation of cell membranes.

Steroids are quite famous for being used by body builders.

Waxes are used widely in the cosmetic industry.


A triglyceride is made up of the polar glycerol and 3 fatty acids, which are acidic because they contain a COOH group. It is acidic because its H dissociates in water. Glycerol is soluble because it has OH groups. Fatty acids vary according to the hydrogen carbon chain attached to the COOH group.



A saturated triglyceride is one in which there are no double bonds between the carbon atoms and an unsaturated triglyceride is one in which there are double bonds between the carbon atoms of the hydrogen carbon chain.


The glycerol is attached to the 3 fatty acids by ester bonds and are looses its polarity when this bond forms because the OH of the fatty acid and H of the glycerol is lost as water.


Fats are solid at room temperature and oils are liquids. Some of the fatty acids cannot be made by the body and must be obtained through food. These are therefore termed ESSENTIAL fatty acids.


WAXES are lipids whose molecules have a single hydrocarbon chain linked t an alcohol other than glycerol. Because of their insoluble properties, they are used as coverings for example chitin, which can be found on the exoskeleton of animals, are covered with a waxy layer to prevent water loss such as dehydrating.



STEROIDS make hormones and cholesterol, which actually has some use. This cholesterol includes high-density cholesterol, which is used in the making of cellular membranes.


PHOSPHOLIPIDS structure is unique, in that it has a phosphate atom that is attached to the glycerol and 2 fatty acids. This molecule is partly soluble because the phosphate group still has the OH group attached to it, making it hydrophilic and hence soluble in water.  The rest of the lipid is hydrophobic and therefore not soluble. This arrangement is specific for cell membranes.