aspark's blog

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.

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. 

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. 

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? 

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. 

When you think about the replication of DNA, it is actually quite complex. There are many components necessary to duplicate the genome, including proteins and the correct environment. Considering the number of base pairs in the genome, the duplication of it is quite astounding, especially while trying to duplicate it with minimal errors. This is why there are checkpoints during which the cell checks for DNA damage, the preparation of the correct proteins, and whatever else is necessary to continue with the replication process. There is also a proofreading function built into the DNA polymerase that is extending new strands of DNA, and this helps minimize the number of mutations. Still, mutations are not uncommon when DNA is being synthesized. Point mutations are when a base pair is entered wrongly. This can be harmless and result in a silent mutation, meaning the resulting amino acid is still the same as the original sequence would have coded for. Still, there are worse effects that can result. A nonsense mutation is when the change causes a stop codon to be coded for too early. There are also other missense mutations where a different amino acid than was meant to be is entered due to the mutation. This can alter the entire protein that is being coded for in the DNA. Of course, all of these mutations are assuming that the mutation occured in the coding region of the DNA. Other mutations can go unnoticed because it is within an intron region. 

Proteins are made up of amino acids, which are molecules with a carbon center bound to a hydrogen, amino group, carboxyl group, and a "R" group. The R group vareis between amino acids. The chemistry of the functional groups is what determines the properties of ionization. Some R groups are ionizable, while others are not. Some R groups are polar and uncharged, nonpolar, or charged. In a high pH environment, the common functional groups are usually deprotonated, which means the amino group is neutral and the carboxyl group has a negative charge. On the other hand, in a low pH environment, the common functional groups are usually protonated, meaning the amino group has a positive charge and the carboxyl group is neutral. However, at the neutral physiological pH, the amino group is usually protonated while the carboxyl group is deprotonated. This is how pH affects the surface charge of a protein. In low pH or acidic environments, the surface charge is more positive since the functional groups are protonated. In high pH or basic environments, the surface charge is more negative since since the functional groups of the amino acid are deprotonated. Some R groups ionize, meaning they have a conjugate acid and base form. This means that some amino acids have three ionizable groups instead of just two. This can be determined through titration, which is when a strong base is added to an acid. At a low pH, all the groups are protonated. As base is added and the pH increases, groups begin to deprotonate. Inflection points are visible, which are when enough base is added to react with half of the acid. Then at the equivalence point, enough base has been added to completely deprotonate the acid. Based on how many inflection and equivalence points there are, one can determine the number of ionizable groups present and determine the identity of the amino acid present in solution. 

Figure 1: Dumbo octopus. Dumbo octopuses have large fins that resemble the ears of famed cartoon elephant Dumbo. The fins protrude from the mantle just above the eyes and are used for motility. Photo by NOAA Ocean Exploration & Research available at https://www.flickr.com/photos/oceanexplorergov/14142089822/in/photolist-... uunder CC BY-SA 2.0 license. 

There are four main types of biomolecules: carbohydrates, proteins, lipids, and nucleic acids. These biomolecules make up the cells that make up organisms and are responsible for the mechanisms within the body. Carbohydrates are composed of carbons, hydrogens, and oxygens. Monosaccharides bond to form oligosaccharides that can be bound to cell surface proteins to aid in cell signaling. Proteins are made up of amino acids, which are composed of a central carbon bound to an amino group, a carboxyl group, and a variable "R" group. The R group can be nonpolar, polar without charge, negatively charged, or positively charged, and the polarity of the R group will influence how different amino acids interact intramolecularly or intermolecularly with other molecules. On the other hand, lipids are made up of mainly hydrocarbons and are therefore insoluble in water. The saturation of different lipids vary, affecting the solidity of the lipid at room temperature. Fully saturated lipids have carbons saturated with hydrogens, while unsaturated lipids have double bonds between carbons, resulting in less surrounding hydrogens. Lastly, nucleic acids are composed of nucleotides that consist of a sugar ring, a phosphate group, and a nitrogenous base. The most recognized nucleic acid is DNA, and in DNA, nucleotide phosphate groups and sugars form phosphodiester bonds that make up the sugar-phosphate backbone. The nitrogenous bases form hydrogen bonds across the two strands of DNA to form the DNA ladder.

There are four main types of biomolecules: carbohydrates, proteins, lipids, and nucleic acids. These biomolecules make up cells, which make up organisms, and are responsible for the mechanisms within the body. Carbohydrates are made up of carbon, hydrogen, and oxygen. They form oligosacharrides that can be bound to cell surface proteins to aid in cell signaling and other functions. Proteins are made up of amino acids, which are composed of a central carbon bound to an amino group, a carboxyl group, and a variable "R" group that determines the nature of the amino acid's interactions. The R group can be nonpolar, polar without charge, negatively charged, or positively charged. The polarity of the R group will influence how different amino acids interact intramolecularly or intermolecularly with other molecules. Lipids are made up of mainly hydrocarbons and are therefore insoluble in water. Lipids can be saturated or unsaturated to different levels, which will affect their solidity at room temperature. A saturated lipid is saturated with hydrogens, while unsaturated lipids have double bonds which cause there to be less hydrogens bonded to the carbons. Lastly, nucleic acids are mostly know for making up the DNA in cells. Nucleic acids are made up of nucleotides that consist of a sugar ring, a phosphate group, and a nitrogenous base. In DNA, phosphate groups and sugars form phosphodiester bonds, which make up the sugar-phosphate backbone. The nitrogenous bases form hydrogen bonds across two strands of DNA to form the DNA ladder.