Chris Rhodes Week 10

DO THE SHARED JOURNAL! M. smeg DNA Arrays

3D Structure Changes

• Using the alignment of Kwong gp120 and Subject 13 amino acid sequences from the previous lab the regions of conservation between Kwong and the Subject 13 proteins were identified.
• The two conserved changes that occur in the Visit 4 clones of Subject 13 occur within the established conserved regions. The positions of the two residue changes are highlighted on the 3D structure of the Kwong gp120 protein shown below:

Both residues are located on the surface of the final gp120 protein and could therefore play a key role in protein interactions and function. As discussed in the previous lab the conserved changes that we see in these regions, G->R and R->G, would have fairly drastic effects on the protein folding in this region since there is a large shift in size, hydrophobicity and charge between the two residues. The drastic differences between the properties of the two amino acids along with their positioning in the gp120 protein provide strong evidence that the residue changes will have some effect on function.

Discovery Questions

Number 5

The graphical representation of gene expression versus time for DMCI and SPS100 of Fig 4.6 are shown below:

Number 6b

1. Gene X
   • Hour 1: Black
   • Hour 3: Red
   • Hour 5: Black
   • Hour 9: Green
2. Gene Y
   • Hour 1: Black
   • Hour 3: Red
   • Hour 5: Green
   • Hour 9: Green
3. Gene Z
   • Hour 1: Black
   • Hour 3: Red
   • Hour 5: Red
   • Hour 9: Red

Number 7

All of the genes show an initial increase in gene expression as oxygen decreased up to hour 3. After hour 5 both Gene X and Gene Y show decreasing gene expression with decreasing oxygen though Gene Y shows a much sharper drop in gene activity over time than does Gene X. On the other hand, at hour 5 the gene expression of Gene Z showed further increase and remained constant up till hour 9. This indicates that Gene Z is most likely responsible for some sort of cell function that is needed in an anaerobic environment while Gene X and Y are more likely responsible for aerobic cell function.

Number 9

Assuming that the genes being studied are a part of the process of regulating the metabolism of glucose, since the color yellow indicates that the expression of the gene is neither induced or repressed it makes sense that we would see all yellow at the first time point where glucose is in ample supply and doesn't need more regulation than normal. As time goes on, the culture grows, and glucose becomes more sparse the regulation genes would need to be activated in order to better use or conserve the glucose available.

Number 10

Over the course of the experiment TEF4 expression was held fairly steady across the first three time points then became more and more repressed in the last three time points. Knowing that the experiment is studying cell growth and glucose intake it can be concluded that TEF4 most likely plays a role in cell growth and multiplication. As the amount of glucose decreases, cells must also decrease the expression of their growth factors as a means of conserving the available food supply.

Number 11

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