You are here

aspark's blog

Draft: Methods Discussion

Submitted by aspark on Fri, 02/22/2019 - 12:13

The photographic differences between figures 1A and 2A and figures 1B and 2B are because the photos in figure 2 were taken at a further distance. This is because the location of the top of the steps were misinterpreted for photo A, and the distance at which photo B was taken was not specified in a detailed manner. The differences in tree exposure in figures 1C and 2C were also due to the photos in figure 2 being taken at a further distance. The description for where photo C was taken was relative to the distance at which photo B was taken, which was already taken further than in the original. The lichen in figure 2C was also not centered because that was not specified in the Methods, and the angle at which the photo was taken was also not discussed. The car in the background of figure 2C, which was not present in figure 1C, is because the tree is on a busy street with constantly changing conditions, and the blue tint in the photo was probably due to the sunlight being shaded at the moment the photo was taken.

Lastly, the difference in font for the boxed letters was because the Methods specified for the default font settings, which may be different on different computers. The instructions for the figure layout must have been relatively clearer than the instructions for the photography because the layouts between the figures were nearly identical.

Draft: Methods Results

Submitted by aspark on Fri, 02/22/2019 - 05:04

There were some photographic differences between the two figures. Figure 2A showed more of the tree and foreground than shown in figure 1A. Figure 2B also showed more bark than in figure 1B, and the lichen in figure 1B occupied half of the photographed space, while the lichen in figure 2B occupied only one tenth of the space. Figure 2C also showed the full width and more length of the tree trunk compared to figure 1C. Additionally, in figure 1C the lichen is centered horizontally and vertically, while in figure 2C the lichen is located in the lower right region of the photograph. Figure 2C also has a red car in the background, along with an overall blue tint throughout the whole photo.

 

In terms of the figure layout, the dimensions and relative locations of the photos are identical. The white boxes in the upper left corners of each photo are also identical, except for a difference in font between the letters.

 

PP: Activation Energy

Submitted by aspark on Fri, 02/22/2019 - 04:46

Exergonic reactions are spontaneous, while endergonic reactions are not; however, it is not the free energy change that determines the rate of a reaction. The rate of a reaction is determined by the activation energy, which is the energy needed to reach the transition state between reactants and products. Reactions with higher activation energies have slower rates because fewer molecules have enough energy to reach the transition state. When the activation energy is lower, more molecules can easily reach the transition state, accelerating the reaction. Enzymes speed up reactions by lowering activation energies. They do so by stabilizing the structure of the transition state, which then requires less energy to be reached. Enzymes do not affect the free energies of the substrates or products, and they do not alter the equilibrium of a reaction. They simply allow equilibrium to be reached faster. Enzymes can enhance the rate of a reaction in many ways: forming favorable interactions in its active site, orienting two substrates to react, directly participating in the reaction, or strain the substrate bonds. Enzymes usually use more than one of these strategies to stabilize the transition state, lower the activation energy, and speed up a mechanism.

 

Draft: Methods Introduction

Submitted by aspark on Fri, 02/22/2019 - 04:36

The Methods Project has three goals: to practice writing the Methods section of a research paper, which is used by scientists to replicate the research described, to differentiate observations from inferences by writing the Results and Discussion sections, and to identify controls needed for an experiment. For my figure, I will depict the interspecific interaction between a tree and a lichen, an example of commensalism that is often overlooked in everyday life. The specific tree and lichen I will portray are on a busy street in Amherst Center, one that is walked past by students frequently.

 

In order to maintain strict consistency between the photos in both the original and replicated figures, I will have to set several controls described in the methods. I will control the time at which the photos are taken, in order to keep the lighting uniform, and the relative distance at which the photos are taken. I will also control the instructions for combining and labeling the photos to create the final multi-panel figure, specifying dimensions and coordinates.

 

Draft: Activation Energy

Submitted by aspark on Thu, 02/21/2019 - 00:13

Exergonic reactions are spontaneous, while endergonic reactions are not. However, it is not the free energy change that determines the rate of a reaction. The rate of a reaction is determined by the activation energy instead. An exergonic reaction can be slow, while an endergonic reaction is fast. The activation energy is the energy needed to reach the transition state between reactants and products, and all reactions require activation energy, even exergonic reactions. Reactions with smaller activation energies have faster rates than those with larger activation energies. With a high activation energy, fewer moleules have enough energy to reach the transition state, causing the reaction to proceed slower. When the activation energy is lower, more molecules can easily reach the transition state, accelerating the reaction. This is precisely how enzymes work to speed up a reaction: They lower the activation energy of the reaction. They do so by stabilizing the structure of the transition state, which then requires less energy to be reached. Enzymes do not affect the free energies of the substrates or products, and they do not alter the equilibrium of a reaction. They simply allow equilibrium to be reached quicker. Enzymes can enhance the rate of a reaction in many ways. They can form favorable interactions with the transition state in its active site. It can also orient two subtrates to react easier. An enzyme can also directly participate in the reaction, or it can strain the bonds in the reactant(s). Enzymes usually use more than one of these strategies to stabilize the transition state, lower the activation energy, and speed up a mechanism. 

PP: Protein Structure

Submitted by aspark on Thu, 02/14/2019 - 00:59

Proteins have complex structures that determine the many functions proteins will perform in the body, and these structures are a result of the endless combinations of the 20 biological amino acids. There are four levels of protein structure. The primary structure of a protein is simply its amino acid sequence. Covalent peptide bonds between the amino and carboxyl groups of amino acids form, building a polypeptide chain. The secondary structure is the structure of the polypeptide backbone, excluding the R groups of the amino acids. It involves hydrogen bonds that stabilize alpha-helices and beta-sheets formed. The tertiary structure factors in the chemistry of the R groups, finalizing the overall structure of the protein, which can be globular or fibrous in form. R groups can be nonpolar, polar and uncharged, positively charged, or negatively charged. Depending on the proximity of these groups, different structures can result from the non-covalent electrostatic interactions. Finally, the quaternary structure is only relevant to proteins that are composed of multiple polypeptides. It involves the various electrostatic interactions between the different subunits within the overall protein.

Draft: Cell Signaling

Submitted by aspark on Thu, 02/14/2019 - 00:47

Cells receive an array of signals that tell them what to do. Cells receive signals to survive, grow, divide, or differentiate, and if a cell receives no signals, it will undergo apoptosis and die. Cancer cells dont need survival signals, and this is why they continue to survive even when no signals are being received. Signals are typically small molecules or proteins. Hydrophobic signals, such as hormones, will enter the cell across the membrane and attach to receptors in the cell. On the other hand, hydrophilic signals cannot get inside of the cell and will bind to receptors on the cell surface. The same signal can be received by the same receptor, but depending on the cell type, the signal may cause different outcomes in the cell. For example, acetylcholine is a common signal, but when it binds to the same receptor on a different cell, different downstream proteins result. Signals usually set off signal cascades in which the message is amplified. Any time there are enzymes and multiple steps incolced in the transduction cascade, the signal can be amplified. This amplification of signals makes crosstalk more plausible. Crosstalk is when pathways intersect, affecting one another. The more steps in the pathway, the more opportunities for crosstalk. And the only way to completely stop the communication of a signal is to eliminate the last step of the pathway. 

Draft: Nuclear Import

Submitted by aspark on Wed, 02/13/2019 - 22:49

Different proteins need to be in different areas on the cell, and the different areas of the cell are sectioned off as organelles with walls and membranes that block the way. This is why protein trafficking is a very important area of regulation in a cell. Proteins start from genes contained within the DNA of a cell, and this DNA is strictly kept inside of the nucleus. This DNA is transcribed inside of the nucleus into mRNA, which is what is able to leave the nucleus and give rise to proteins that need to circulate to the rest of the cell. This mRNA codes for signal sequences within its transcript that indicate where the coded protein needs to be transported, where it needs to be translated into a protein. These signal sequences can signal for the resulting protein to be imported into the endoplasmic reticulum, to be retained in the endoplasmic reticulum, to be imported into the mitochondria, and so on. The signal sequence is usually an area where a transport protein can bind and move the mRNA to an organelle while being translated. The protein that is translated usually remains unfolded until iside its organelle, except for proteins going to the nucleus. Fully folded proteins are able to go inside of the nucleus through a regulated pore. The signal sequence for nuclear import is called the Nuclear Localization Sequence (NLS). A protein called Importin binds to the NLS and binds to the Nuclear Pore Complex (NPC) of the nuclear membrane. This allows the Importin and protein to enter. Once inside, the protein Ran bound to GTP binds to Importin, causing a change in conformation that releases the protein into the nucleus. This GTP-Ran-Importin complex exits the nucleus. 

Draft: Nervous System

Submitted by aspark on Wed, 02/13/2019 - 20:44

I've always been interested in the nervous system becasue it is such a unique system within the body. Nerves span the entire human body, receiving and sending out signals that allow us to move, feel, think, see, etc. The neurons of the nervous system communicate with one another across synapses, which are the spaces between the neurons. Neurotransmitters travel across these synapses and bind to receptors on the next neuron, effectively passing on the message. The central nervous system is especially important. It includes the spine and brain, which integrate signals from all of our senses. The brain sends incoming signals to different areas of the brain to be interpreted and sent back out to the body. Multiple signals are interpreted at once for all of the things we do. There is also a lot of internal communication we are unaware of. It's amazing how we are able to live our lives, moving, eating, seeing, experiencing, feeling, thinking, and so much more, because our nervous system is able to integrate all the signals that intake and output. The simple ability to think about moving my hand and actually being able to move it however I want is amazing. The speed at which our body communicates internally is impossibly fast. One thing that I have yet to know about is how emotions play into the central nervous system. When someone is sad or in love or mad, how does that show in our brains, and why? I've always been curious if there is a clearcut explanation for emotional feelings. Is there a reason some people are more sensitive than others or more empathetic? Is there an explanation within the nervous system for why some people have anger management issues or an inclination to cry? 

Draft: Protein Structure

Submitted by aspark on Tue, 02/12/2019 - 22:55

Protein's have complex structures because a protein's structure determines its function, and there are many functions for proteins within the body. There are 20 biological amino acids, and there are endless combinations of these amino acids that will result in different proteins. A protein's structure has four levels. The primary structure of a protein is the linear sequence of amino acids. This involves peptide bonds between the amino and carboxyl groups of amino acids, building a polypeptide chain. The secondary structure is the structure of the backbone that is created. It involves hydrogen bonds that stabilize alpha-helices and beta-sheets, which are different secondary forms a polypeptide can take. The secondary structure does not include the R groups of the amino acids; however, the tertiary structure does. The tertiary structure involves all the electrostatic interactions that can occur between amino acids in the protein, including the chemistry of the R groups. This will finalize the final structure of the overall protein, which can be globular or fibrous in form. R groups can be nonpolar, polar and uncharged, positively charged, or negatively charged. Depending on the proximity of these groups, different structures can result. Finally, the quaternary structure is only relevant to proteins that are made up multiple polypeptides, or subunits. It is the interaction between the different subunits within the overall protein. This level of protein structure also involves all types of electrostatic interactions. 

Pages

Subscribe to RSS - aspark's blog