Biochemistry

Assignment 2

1.   Animals that live in polar environments spend much of their time with their lower limbs buried in snow. What differences in lipid composition might you expect to see if you compared cell membranes of lower limbs with those of the upper body?  (5 marks)  

All lipids in cell membrane is usually phospholipid, which two layers sandwiched together to form a ‘phospholipid bilayer. Phospholipid is composed of polar hydrophilic phosphate head, which is electrically charged to associate with water and non-polar hydrophobic fatty acid tail from which water is repelled. The phospholipid is arranged so that polar groups face outward and the non-polar groups are interiorized within the bilayer structure. The non-polar groups act to prevent the free passage of the water across the cell membrane. (Chambers, Huang & Matthews, 2015). The fatty acids of the phospholipids make the membrane somewhat fluid, which permits some molecules to move literally within the plane of the membrane  (Hillis, Sadava, Heller & Price, 2012). At low temperature, the fatty acid of the phospholipids will become more rigid that influence the fluidity, permeability and also the ability for a cell to survive (Los & Murata, 2014). The cold environment tends to compress the membrane to compose of largely amount of saturated fatty acids and the membrane become less fluid, which vital molecules cannot pass through the membrane easily. For the polar animals, the fatty acids are mainly unsaturated with shorter chain in the cells to ensure the fluidity of the membrane. This is because the unsaturated fatty acid has much lower transition temperature between liquid and solid than saturated fatty acids (Campbell, 2015). Thus, polar animals have adaptations to cold conditions by replacing saturated fatty acids to unsaturated and shorter tailed fatty acids to maintain fluidity in response to the lowering of the temperature.

1.   DNA polymerases have proof-reading ability, but RNA polymerase does not. Does the use  of RNA as a primer affect the accuracy of DNA replication in E.coli? Explain (5 marks)  

A primer is oligunonucleotide that serve as a starting point for DNA synthesis, as DNA polymerase can only add new nucleotide to 3’ OH free and of an existing strand of DNA. Enzymes responsible for making RNA from DNA are called RNA polymerase. Like DNA synthesis, transcription proceeds in the 5’ to 3’ direction. RNA polymerase differs from DNA polymerase in a couple of important aspects.  RNA polymerase can initiate the synthesis of new strands in the absence of a primer. Secondly, RNA polymerase has no proof-reading ability because it lacks of 3’ to 5’ exonuclease activity (Lieberman & Marks, 2013). The first primase was discovered in a E.coli cell that catalyzes the synthesis of RNA primer (Campbell & Farrell, 2015). DNA polymerase I is used to repair DNA and also involve in the synthesis of DNA strands during replication while DNA polymerase II plays a role in repairing (Lodish, Berk & Zipursky, 2000). DNA polymerase III is the major replication enzyme, which function in the synthesis both the leading strand of DNA and of Okazaki fragments by the extension of RNA primers.  The accuracy of DNA replication is critical to cell reproduction, as the proof reading of DNA polymerase is the major responsible for DNA replication. Polymerase I plays an important role in E.coli DNA replication, which acts as exonuclease that can hydrolyze DNA or RNA in either 3’ to 5’ or 5’ to 3’ direction. A short fragment of RNA serves as a primers in DNA replication for the initiation of the synthesis of Okazaki fragments. 5’ to 3’ exonuclease activity of Polymerase I is then used to remove the RNA primers and fills the gaps between the Okazaki fragments with DNA (Cooper, 2004). Lastly, DNA ligases will seals the remaining nicks. Exonuclease also related to E.coli polymerase III, which will cut the mismatched bases that have been included at the end of growing DNA chain. RNA primer is subsequently removed and hence, will not affect the accuracy of DNA replication.