Exercises for BIOL 3612 Biochemistry Lab
EXERCISE 1: SOME BASICS OF SECONDARY AND TERTIARY STRUCTURE
Exploring PDB files and secondary structure
The exercise was helpful in creating a picture for me to really understand the 3D structures of proteins. By navigating through different protein representations, I was able to recall several important concepts I learned from lecture. Also, by seeing those structures in relative to one another, I was able to putting the concepts together into a big pictures that allows me to fully understand the topic. Unlike figures in the book, Jmol clearly shows the position of the hydrogen bonds which is found between C=O and N-H residues on the backbone. Also, by seeing the R-chain pointing …show more content…
Different protein has different molecular weight, net charges, and functions partly because they contain different amino acid components. Hence, we would expect the pI value to vary from one protein to the other. Lysozyme is one example of proteins. Its molecular weight is of 16.23865 kD. It is composed of largely of alanine residues, which is a hydrophobic amino acid. Although alanine does not affect to the pI value of this protein, other amino acids component do, though not strongly, causing the pI of this protein to be 9.36. The pI Histone H3’s on the other hand can be determined by its functions. Since histone plays an important role in binding to the DNA, which contains highly negative charge through out the backbone, histone is positively charged in order to interact tightly with the DNA. These positively charge amino acid will become neutral at a very high pH acting as an acidic residue giving away protons only in a very basic environment resulting in the pI of 11.31. According to the two examples, the protein composition is not evenly distributed as the amino acids are represented in different frequency. Due to this variations, each protein acquires specific properties which allows them to effectively function in a wide range of relations and
EXERCISE 1: SOME BASICS OF SECONDARY AND TERTIARY STRUCTURE
Exploring PDB files and secondary structure
The exercise was helpful in creating a picture for me to really understand the 3D structures of proteins. By navigating through different protein representations, I was able to recall several important concepts I learned from lecture. Also, by seeing those structures in relative to one another, I was able to putting the concepts together into a big pictures that allows me to fully understand the topic. Unlike figures in the book, Jmol clearly shows the position of the hydrogen bonds which is found between C=O and N-H residues on the backbone. Also, by seeing the R-chain pointing …show more content…
Different protein has different molecular weight, net charges, and functions partly because they contain different amino acid components. Hence, we would expect the pI value to vary from one protein to the other. Lysozyme is one example of proteins. Its molecular weight is of 16.23865 kD. It is composed of largely of alanine residues, which is a hydrophobic amino acid. Although alanine does not affect to the pI value of this protein, other amino acids component do, though not strongly, causing the pI of this protein to be 9.36. The pI Histone H3’s on the other hand can be determined by its functions. Since histone plays an important role in binding to the DNA, which contains highly negative charge through out the backbone, histone is positively charged in order to interact tightly with the DNA. These positively charge amino acid will become neutral at a very high pH acting as an acidic residue giving away protons only in a very basic environment resulting in the pI of 11.31. According to the two examples, the protein composition is not evenly distributed as the amino acids are represented in different frequency. Due to this variations, each protein acquires specific properties which allows them to effectively function in a wide range of relations and