lpotter's blog

Today I learned a lot about the ebola virus. The virus has many different ways that it can evade the host’s immune system. For example, one way that the virus can “hide” is by taking lipids from the host’s cells and making a membrane out of those lipids. This lipid membrane tells the host’s immune system that the virus is self and to not attack it. If the virus can evade the immune system it can successfully replicate in the cells of the host. Ebola has been a documented virus for quite some time with the earliest observations dating back to the 1970s. It has only recently made headlines. This is because the virus kills the host so fast that anyone who comes in contact with it dies before the virus can find a new host. So the majority of ebola cases were very limited because infected people couldn't travel to spread it. In 2014 there was an outbreak which ended up killing more than 10,000 people. This was a new strain of ebola, the Zaire strain. This strain is just as deadly as previous ebola strains however it is unique in the fact that it has an extended incubation period, meaning that it kills the host at a slightly reduced rate. This now means that sick people are able to come in contact with more people than with previous cases. This strain is the cause of the current outbreak in which almost 1000 cases have been confirmed.

I was asked to do an extra credit survey for my recent biochem exam. One of the questions asked was what we would do differently studying. I said that I would watch a lot more of the lecture videos before the  exam to clear up any confusion that I couldn’t on my own or from just looking at the slides. I think that re-watching something that you don’t understand is very helpful in figuring out what it really means. It also helps to just confirm what you already know. For example if you don’t understand protein folding you should google it and find some resources that might help explain it a little bit better, but after reading those and learning what it means re-watching the lecture so that you can understand it in the words of the instructor. Because after all they are going to be the ones writing the exam, so it is imperative that you understand what they are trying to say. One other thing that I will try and do for preparation for my next exam is write everything out. Write everything in words as well as in drawings. This will help me personally connect more abstract topics to something that is more tangible.

I have a biochem exam this week so I have been using my thirty minutes of writing each day to go further in depth with topics that I don’t fully understand and want to get a better grasp on. I went to a review session for it to try and help me with some of the topics and one of the questions that the SI asked us really confused me. She asked if the pKa of an amino acid could change and then said the answer to the question was no. She started to explain why it was no then said the question didn’t make sense and scrapped it all together. I made a note of it and tried to figure it out when I got back home. It turns out that in fact the pKa of amino acids can be altered. That is the pKa of the R-group. The pKa’s get altered when a neighboring R-group, which is ionizable, has a similar pKa. This means that the R-groups will be similarly protonated at similar pH levels which means that they will have similar charges. This will cause the R-groups to repel each other and can alter the folding of a protein which will alter the structure. So if an amino acid like glutamic acid (pKa of 4.25) is located close to aspartic acid (pKa of 3.86) they will have the same negative charge at around the same pH. If they are in a cell at physiological pH of 7 they will both be fully deprotonated and have negative charges, this will cause the two groups to repel. Since aspartic acid has a lower pKa it will become deprotonated first and in an effort to prevent repulsion the pKa of glutamic acid will be raised so it doesn’t acquire a negative charge from deprotonation. This helps maintain protein structure.

Observations

1. The figure on the left has uniform sized images but the figure on the right has one different sized image.

2. The angles at which the photos were taken are different in both figures.

3. The figure on the left had bold text labeling, the figure on the right did not.

4. The figure on the left placed letters slightly away from the edge of the photo, the figure on the right had had the letters lined with the side of the image.

5. The images on the right were brought to the outer edge of the black background whereas on the left they were not.

6. The backgrounds of the images aren’t corresponding.

There are multiple differences between both the left and right figures. However, the most apparent difference is the size of images within the figure. For example, the photos on the left figure are all uniform in size, all photos on the right figure are uniform in size except for the photo labeled D. The angle at which every photo was taken is different in both figures, none of which correspond. Additionally the background of the image was different in every instance and again did not correspond with the other figure. The figures are lettered in the same order, A, B, C, D. The font size and placement of the lettering is different between the two separate figures, but remains consistent within the figure itself. Another difference in the lettering is the alignment with the side of the image, on the left figure the letters are left a small distance away from the edge of the photos while in the right figure the letters are lined up with the side of the images. Another difference is that the spacing between the photos and between the edges of the figure on different.

Inferences

1. The last image (D) may have been cropped different on the right figure, or the camera was held at a different orientation.

2. The camera was most likely held at different heights, possibly because the person taking the pictures were different heights or maybe one used a tripod and the other did not.

3. The font choice was slightly different between authors, also resulting in a different bolding of the images.

4. The function to align the letters used by both authors may have been in a different software of different function within the same software.

5. The separate authors may have set margins to different widths causing the images to be differently set.

6. It might be a picture of a similar but tree, the angle at which they were photographed may also be different.

The difference in size of images between figures may be due to the orientation at which the photographer held the camera for that image, the image may have also been cropped differently. The angle of the photos may be be different because the the height of the photographer may be different, additionally they could have been standing in different places, at or on different things, or using different equipment. These same factors could also contribute to why the background would be different. The font size and placement of letters on the figure could have been caused by a different software used by both authors, or different setting applied to different figures. Similarly the alignment of images to the background within the separate figures may have been due to different software used or different setting applied by the author.

Titration curves have always confused me. I was introduced to them as a freshman in college. I didn’t really understand the whole concept of conjugate base and an acid and how they related. I didn’t understand what pKa or Ka meant but now I think after taking upper level courses the relationship between pKa, pH, acids, and conjugate bases all finally makes sense. On a titration curve there are inflection points, this point represents the amount of base required to react one half of the desired acid. At this point the acid becomes half deprotonated and half protonated. Next is the equivalence point, the point that represents the amount of base to react with all of the desired acid. This now makes sense to me why the acid is noted as HA and the conjugate base is noted as A-. The acid (HA) is neutral and when it becomes deprotonated taking on its conjugate base form (A-) it loses a proton and now has a net negative charge. This is how I started to understand the relationship between pKa and pH. Again, at the inflection point the amount of conjugate base is equal to the amount of acid. When you plug this ratio into the Henderson-Hasselbalch equation you get pH=pKa+log(1), log(1)=0. So that means that pH=pKa. Which now makes sense why stronger acids have a lower pKa. It essentially means that they are more will to give up a proton at a lower pH.

Change in pH can have serious effects on the structure of a protein which ultimately changes the function of the protein. Changing pH can affect the charge of ionizable groups of amino acids. Amino acids make up polypeptide chains via peptide bonds. These peptide bonds are not affect by a change in pH, however the alpha amino group at the N-terminus of a polypeptide chain (the subunits of proteins), the alpha carboxyl group at the C-terminus of a polypeptide chain, and the ionizable R groups of acidic and basic amino acids, as well as the ionizable R groups of tyrosine and cysteine. pH is directly related to pKa, this is the amount of base require to react with half of the acid present. Which in this case means at which point the ionizable group will start to become primarily deprotonated. The alpha carboxyl group at the C-terminus has a pKa of 2.2, so whenever the pH is above around 3 every alpha carboxyl group will be deprotonated. The pH of a cell is 7 so most of the times the group has a negative charge. The alpha amino group at the N-terminus has a pKa of 9.5, so unless the pH goes above 9.5 this group will remain protonated with a positive charge which it almost always is in the cell. A lot of ionizable R groups have a pKa of around 6-10 so if the pH of a cell is significantly raised or lowered the R groups will become deprotonated or protonated. This will in turn affect the charges of these groups and disrupt the electrostatic interactions they are taking part in causing the protein to fold differently which alters the function of the protein.

The differences between polypeptides and proteins are incredibly significant. Polypeptides are covalently bound amino acids via a phosphate bond. This phosphate bond is always the same between amino acids regardless of the amino acid. The bond is the same because all amino acids have an identical alpha amino group and an alpha carboxyl group. The peptide bond forms via dehydration, you can break the bond with the use of hydrolysis. The peptide bond forms between the alpha carboxyl group of the “old” amino acid and the alpha amino group of the “new” amino acid. When multiple amino acids are bound together in this fashion they form a polypeptide chain. Proteins are made up of one or more of these polypeptide chains which are referred to as subunits. Proteins employ different types of bonding, they use noncovalent bonding. Noncovalent bonds don’t share electrons rather they are electrostatic interactions. This means that atoms interact based off of charge differences. Proteins fold based off of the charge of certain R groups of amino acids and the noncovalent interactions that they form. Proteins can even make disulfide bonds if two cysteine amino acid R groups interact in the polypeptide chain. So the main difference between proteins and polypeptides is that proteins are made up of polypeptides, not vice versa.

The hydrophobic effect is something that I did not understand until recently. Essentially what the hydrophobic effect states, is that hydrophobic molecules will clump together in an aqueous (water) environment. This is because by nature water prefers to be in a state of high entropy, meaning a highly disordered system. When hydrophobic molecules in water the water can not interact with them and the water molecules start to form ordered cages around the hydrophobic molecules. Water does not want to do this because that means that the system is more ordered. In response to this, water forces the hydrophobic molecules to clump together so that in total there is less surface area created by the hydrophobic molecules. This means that less water molecules will be taking part in making the ordered cage around the clump of hydrophobic molecules and since less water molecules are ordered the overall disorder (entropy) of the system is significantly higher. The hydrophobic molecules themselves are not what cause the clumping, rather it is the nature of the water molecules.

The hydrophobic effect is something that is very interesting and that I didn’t understand until recently. Essentially what the hydrophobic effect states is that hydrophobic molecules will clump together in an aqueous environment. This is because water like high entropy, or high disorder, something that nature favors. When there are hydrophobic molecules in water the water can’t interact with them and start to form ordered cages around the molecules. Water doesn’t want to do this because that means that it is more ordered. In response to this water clumps the hydrophobic molecules so that there is less surface area. This means that less water molecules will be taking part in making the ordered cage around the molecule and since less water molecules are ordered the overall disorder (entropy) of the system is significantly higher. So the hydrophobic molecules themselves aren’t what cause the clumping it is the nature of the water molecules. It is the opposite with hydrophilic molecules. Most hydrophilic molecules have an ionic nature to them. Water can interact with this bond and break it apart. Water then forms a shell around the free atom. This allows water to stay disordered. You can see this in instances when you put salt or sugar into water, the molecules dissolve and appear to become part of the liquid.

Today I went to the emergency room with my friend. They have been sick for quite some time, throwing up and nausea at random times throughout the day. Over the past few days they stomach has physically started hurting and their vomiting has gotten way worse. So here I am in the emergency room and hospitals just seem so dirty. I feel like hospitals are supposed to be clean and sterile but hospitals are just the breeding grounds for the worst kinds of viruses and bacteria. Everyone who is comes here and leaves and micro organism on them here in the hospital after they leave. Superbugs have been something that have started appearing in recent years. Bacteria that have many drug resistant properties. Hospitals are responsible for inadvertently creating many of these superbugs. The doctors over prescribe antibiotics and then the bacteria continue to live and now have a gene that makes them resistant. Now that sick person comes back to the hospital or has yet to leave and leaves behind the bacteria that is now resistant to drugs. I just really don’t like being in hospitals as they seem like these bacteria and antibiotic resistant bacteria are lingering around each and every corner.