Transcription and Translation

This video provides a brief overview about transcription and translation. It explains the difference between the two. This has always been a hard concept for me to grasp because I always used to get the two processes confused. This video is clear and explains these two processes in great detail. Included in the powerpoint that he goes over, are some fun animated videos that help explain these two processes.

Identical Twins: Not as Identical as You Think

This article talks about how identical twins show differences in their gene expressions. In many aspects, identical twins seem, well, identical! However, there are dissimilarities and it is unclear how they have come about. A new report suggests that epigenetic differences, differences in how the genome is expressed, could be responsible. Mario F. Fraga, of the Spanish National Cancer Center, studied 160 identical twins, ranging in all different ages. Two external factors through the entire genome were analyzed for each set of twins. Both DNA methylation and histone acetylation govern gene expression and can magnify or reduce the effects of certain genes. The team's research showed that twins tended to be indistinguishable in their gene expression, earlier in life. As the twins got older, more differences in gene expression became evident. Also, twins who had spent more time apart and had more varying medical histories showed the greatest epigenetic differences.

This is a picture of methylation patterns of three-year-old twins (left) and 50-year-old twins (right). The differences have been highlighted in red.

Environmental factors, physical activity levels, and diet can influence epigenetic patterns and may help in understanding how the same genotype can be translated in different ways. Scientists suggest that specific mechanisms that cause this so-called epigenetic drift in identical twins should be studied in the future.

Tetrahymena Telomerase

This article talks about the structural basis for Tetrahymena telomerase processivity factor Teb1 to single-stranded telomeric-repeat DNA. Telomerase is an enzyme that adds nucleotides to telomeres, especially in cancer cells. When DNA is synthesized, it loses a part of it's telomere each time. These are protective compound structures located at the ends of chromosomes. Telomerase duplicates its own internal RNA template to synthesize telomeric DNA repeats. Unlike other polymerases, telomerase can retain its single-stranded product through many rounds of template dissociation and repositioning to accomplish repeat addition processivity (RAP). Tetrahymena telomerase holoenzyme RAP is dependent on a subunit, Teb1, with independent DNA-binding activity. Sequence homology and domain modeling tell us that Teb1 is a paralog of RPA70C, the largest subunit of the single-stranded DNA-binding factor replication protein (RPA), but unlike RPA, Teb1 binds DNA with high specificity for telomeric repeats.

This is an animated picture of a Tetrahymena Telomerase molecule.

To begin to understand the structural basis and significance of telomeric-repeat DNA recognition by Teb1, researchers had to solve crystal structures of three proposed Teb1 DNA-binding domains and defined amino acids of each domain that had contributed to DNA interaction. Their studies indicate that two central Teb1 DNA-binding oligonucleotide/oligosaccharide-binding-fold domains, Teb1A and Teb1B, achieve high affinity and selectivity of telomeric-repeat recognition by principles similar to the telomere end-capping protein POT1 (protection of telomeres 1). An additional C-terminal Teb1 oligonucleotide/oligosaccharide-binding-fold domain, Teb1C, has similar characteristics as the RPA70 C-terminal domain including a presumed direct DNA-binding surface that is very important for high-RAP activity of reconstituted holoenzyme (which is a biochemically active compound formed by the combination of an enzyme with a coenzyme). The Teb1C zinc ribbon motif does not contribute to DNA binding but is nonetheless required for high-RAP activity, perhaps contributing to Teb1 physical association with the remainder of the holoenzyme. This research team's results suggest the biological model that high-affinity DNA binding by Teb1AB raises holoenzymes to telomeres and subsequent Teb1C-DNA association traps the product in a sliding-clamp-like manner that does not require high-affinity DNA binding in order to achieve high stability of enzyme-product association.

Leading vs. Lagging Strands

This is an excellent video to watch if you are having trouble understanding leading and lagging strands. It gives a basic explanation of leading vs. lagging strand replication during DNA synthesis. He goes through all of the basic steps from template orientation to the rNA primer to which enzymes were used where. He also explains Okazaki fragments which were a hard concept for me to grasp. Overall, this video was very helpful in clarifying each of the basic steps in DNA synthesis.

My, What Long Telomeres You Have

This article talks about telomeres and what they say about you. For example, smokers and couch potatoes are common offenders of damaging their chromosomes. Two groups of well known researchers have started companies solely to come up with a test that can measure the length of someone's telomeres. Telomeres are caps on the ends of chromosomes meant to protect. A good analogy is to think of them as plastic tips on the ends of shoelaces that keep the laces from fraying.

These are chromosomes capped with telomeres.

The telomeres appear bright, on the ends.

Whenever chromosomes—the store­houses of our genes—are replicated for cell division, their telomeres shorten. Many scientists have been led to believe that this shortening has led  to view telomere length as a marker of biological aging. Similar to a “molecular” clock telling the cell’s life span, as well as an indicator of overall health. Studies have compared telomere length of white blood cells among groups of volunteers; they have found that there were many distinct correlations between telomere length and lifestyle. Those who were exercising regularly had longer telomeres than those who did not. Folks who perceived themselves as the most stressed had shorter telomeres than those who saw themselves as the least. Certain diseases also seemed to correlate with shorter telomeres, including cardiovascular, obesity and Alzheimer’s.
In the future, telomere research can tell us more about our health. Knowing whether our telomeres are of normal length or not for a given chronological age will tell us about the status of our health status and our physiological "age". Telomere length is probably the best single measure of our integrated genetics, previous lifestyle and environmental exposures.
Although research has gotten very far, telomere experts still haven’t defined what they consider to be a norm and what they consider to be abnormal, either long or short. Regardless, the data, would be  sufficient to help people make personal lifestyle decisions regarding diet, exercise, and stress.

Understanding DNA Replication Control

This article talks about understanding how DNA replication is controlled. Completion of genome duplication during the S-phase of the cell cycle is crucial for the maintenance of genomic cohesion. The S-phase is where DNA replication takes place in the cell cycle. The cell also forms a second centrosome during this phase. The synthesis phase occurs after the first growth (G₁) phase, and therefore about midway through interphase. At the start of the S phase, each chromosome has only one DNA molecule, but by the end of the S phase each has two, which, barring copying errors, are genetically identical, i.e. they have identical base sequences.

This is a picture of the cell cycle. In purple is the synthesis phase where DNA is replicated.

In eukaryotes, chromosomal DNA replication is accomplished by the activity of multiple origins of DNA replication throughout the genome. Origin specification, selection and activity, and the availability of replication factors and the regulation of DNA replication licensing have unique and frequent features that can be found amongst eukaryotes. Although the studies on the semiconservative nature of chromosome duplication were carried out in the mid 1950s in Vicia faba; plant DNA replication studies have been scarce. They have received a drive in the last decade, after the completion of sequencing the Arabidopsis thaliana genome, that hasn't been seen before, and more recently of other plant genomes. This past year, for example, has seen major advances with the use of genomic approaches to study chromosomal replication timing, DNA replication origins and licensing control mechanisms. In this minireview article is a discussion of the recent discoveries in plants in the context of what is known at the genomic level in other eukaryotes. These studies make up the basis for addressing, in the future, key questions about replication origin specification and function that will be of great importance for plants and for the rest of multicellular organisms.

A Different Perspective: Apoptosis

A fun little skit on apoptosis on the cellular level. 

This video starts off with giving various reasons why a cell might die. It then goes further into explaining what steps the cell takes, what enzymes bind where, and ultimately how the cell is destroyed. It also explains how the cell death affects it's environment. Overall, I found this to be very helpful and easy to understand.

Where and Why: Apoptosis

This article addresses two main questions:
Why are cells that die by programmed cell death generated?

Obviously, the answer would be different depending on different cell types but for the most part some cells are generated in excess and only those that become properly functional survive (as happens in parts of the nervous system). This is kind of like survival of the fittest because only the competent cells will survive. In some cases, the mechanism that generates cells that are needed also generates unneeded ones as well (as happens in the immune system). And some cells that die may be needed, but only temporarily.

 Cells die because they are harmful or because it takes less energy to destroy them than to keep them alive and healthy. As of now, programmed cell death has been known to occur only in animals, although it remains possible that bacteria, fungi and plants may also use similar processes to eliminate unwanted cells.

Why do these cells die instead of surviving?

One of the main reasons for cell death is to get rid of dangerous cells, the one's whose existence can harm the organism. Cells literally "kill themselves for the greater good". They could be mutants that can lead to cancer--apoptosis is therefore very important in the formation (or nonformation) of cancer. Also, positive and negative selection occur among the cells of the immune system. Cells that recognize "self" (ones that would attack the organism's own cells) are instructed to die during this process. Also, cells that are infected by a virus, can sometimes recognize the infection and kill themselves as to not allow the virus to be spread further.

Cell Apoptosis

Pulmonary emphysema is a chronic lung condition in which the alveoli are destroyed, narrowed, collapsed, stretched, or over-inflated. Over-inflation of the air-sacs is a result of a breakdown of the walls of the alveoli, and causes a decrease in respiratory function and breathlessness. Damage to the air sacs is irreversible and results in permanent "holes" in the tissues of the lower lungs.

This picture shows the difference between normal alveoli and alveoli with pulmonary emphysema.

This article talks apoptosis and it's role in pulmonary emphysema. Pulmonary emphysema is a powerful phenomenon that involves the gradual destruction of extracellular matrix by presence of an extra amount of proteases, but also apoptosis, cellproliferation, and senescence (process of deterioration with age). Cellular proliferation makes up for enhanced alveolar cell death, whereas cell aging caused by cigarette smoking and increased cell turnover slows/stops cell proliferation, leading to apoptosis. As a result, alveolar cells gradually disappear and emphysematous lesions advance. At the same time, cellular senescence causes long-term inflammation through enhanced production of proinflammatory cytokines. Recent research suggests that DNA damage (double strand breaks) underlies the molecular mechanisms of these factors in the gradual destruction of extracellular matrix; apoptosis, cell senescence, and chronic inflammation.

Cell Respiration Song

 

This is actually a very helpful video. It's based on a really catchy Black Eyed Peas song and has already helped me remember the steps of cell respiration. You'll have to watch/listen to understand. The song explains the 3 steps of cell respiration. It explains what the products of each step are. It also goes over the energy intermediates. It explains aerobic and anaerobic respiration. Overall, I thought this was a very clever and helpful video.

Lactic Acid ≠ Soreness

After a long day benching at the gym, I sometimes wonder why my arms are so sore... this article explains why. This article talks about why lactic acid builds up in muscles and why it causes soreness. As we start to perform more strenuous exercises, we breathe faster to attain more oxygen to keep our muscles working. Although the body prefers to generate energy using oxygen, sometimes our bodies require energy production faster than we can adequately deliver oxygen. Our bodies have to produce energy without the presence of oxygen. Through glycolysis, glucose is broken down or metabolized into a substance called pyruvate through a series of steps. When oxygen is limited, the body temporarily converts pyruvate into a substance called lactate, which allows glucose breakdown--and thus energy production--to continue. Sometimes the lactate levels get high because we cannot get enough oxygen over an extended period of time. This increases the acidity of the muscle cells. The same metabolic pathways that permit the breakdown of glucose to energy perform poorly in this acidic environment. This is a natural defense mechanism from the body. Eventually the body slows down, oxygen becomes available and lactate reverts back to pyruvate, allowing continued aerobic metabolism and energy for the body to recover.

 This is a diagram showing how lactate forms.

Lactic acid is not the cause of the soreness in the days to follow. Researchers who have examined lactate levels right after exercise found little correlation with the level of muscle soreness felt a few days later. Though the exact cause of delayed-onset muscle soreness is still unknown, most research suggests actual muscle cell damage and an elevated release of various metabolites into the tissue surrounding the muscle cells. These responses to extreme exercise result in an inflammatory-repair response, and are probably the  leading cause of the swelling and soreness that peaks a day or two after the event and resolves a few days later, depending on the severity of the damage.

Reduced Respiration Rates in the Periwinkle Littorina littorea

This article talks about how exposure to elevated temperatures and Pco(2) (partial pressure of carbon dioxide; is a blood gas test that checks for the amount of carbon dioxide gas that is in the blood) reduces the respiration rate and energy status in the periwinkle Littorina littorea. Scientists investigated the effects of elevated Pco(2) and temperature on the whole-organism and cellular physiology of the periwinkle Littorina littorea.
 

 This is a picture of  the periwinkle Littorina littorea

They chose to study this organism because in the future marine organisms will have to cope with multiple environmental changes associated with increased levels of atmospheric Pco(2), such as ocean warming and acidification. They wanted to find out how organisms will adapt to these changes and if they will survive. To understand this they would need an in-depth understanding of the physiological and biochemical mechanisms that are the basis of  organismal responses to climate change. Respiration rates, adenylate energy nucleotide concentrations and indexes, and end-product metabolite concentrations were measured. The final results were compared to the controls'. We saw that the snails decreased their respiration rate by 31% in response to elevated Pco(2) and by 15% in response to a combination of increased Pco(2) and temperature. We saw that the decreased respiration rates were associated with metabolic reduction and there was an increase in end-product metabolites in acidified treatments, indicating an increased reliance on anaerobic metabolism. They concluded that marine organisms will probably adapt in complex ways to future environmental drivers, which will likely have negative effects on growth, population dynamics, and, ultimately, ecosystem processes.

Chemical Equilibrium

This video goes in depth about the reactions in chemical equilibrium. Chemical equilibrium is a state in a chemical reaction in which the rate of formation of products is equal to the rate of formation of reactants. Vmax, activation energy, and Km are all explained thoroughly. Sal from KhanAcademy also explains the graph of the energy of a chemical reaction. You can fully understand what each curve represents and how they can be changed (how activation energy might be lowered). He explains how and what a cell might do to reach that chemical equilibrium. The potential energy that may allow an object to move is also described. He gives similar analogies as a ball at the bottom and top of a hill, that will help you remember and understand the concepts of exergonic/endergonic reactions. I found this video very helpful in understanding exergonic and endergonic reactions! 

Hammerhead Ribozymes

In my previous blog, I briefly mentioned the hammerhead ribozyme. This article talks about them in more depth. Hammerhead ribozymes are tiny, self-cleaving RNAs that boost strand scission by internal phosphoester transfer. They have two types; type I and type II. They also have two major properties which are cleavage site specificity and catalytic activity.
To identify numerous additional representatives of this ribozyme class (including the first representatives in fungi and archaea), comparative sequence analysis was used. The first natural samples of “type II” hammerheads have been uncovered. These results show that this altered form occurs in bacteria as frequently as type I and III architectures. A commonly occurring pseudoknot that forms a tertiary interaction that is very important for high-speed ribozyme activity has also been discovered. Genomic factors of many hammerhead ribozymes can tell what biological functions they perform that are different from their known role in generating unit-length RNA transcripts of multimeric viroid and satellite virus genomes. In rare occurrences, nucleotide variation occurs at places within the catalytic core that are otherwise strictly conserved. Thus suggesting that core mutations are occasionally tolerated or even preferred.

Hammerhead Ribozymes have three helical stem regions and unpaired loops at the ends of two helices. Helices radiate out from central unpaired core of nucleotides. The cleavage site is next to a small, unpaired "U-turn" loop. 

This picture shows the secondary and tertiary structure of a hammerhead ribozyme.

Metal Ions that Bind and Function in RNA Enzymes

This article was about metal ions that bind and function in natural and artificial RNA enzymes. Ribozymes are catalysts that are present in RNA molecules. Recent research has shown that many new catalytic RNA concepts seem to be deviations off of common themes. This has led researchers to believe that ribozymes have evolved. They probably evolved to satisfy specific RNA-essential biological niches. Due to its small structure, many people are led to believe that ribozymes may not carry out many functions; however, analyses at the lab have proven that RNA has the ability to function in carbon-carbon reactions and even tRNA aminoacylation. 
Four naturally occurring enzymes are the hammerhead, hairpin, hepatitis delta virus, and glmS metabolite sensing ribozyme. The full article, which is not available to RVCC, would have explained these four enzymes in detail regarding their fundamental structure, metal binding properties, and the fold and ion coordination of three artificial ribozymes developed to study the boundaries of RNA catalysis (the acceleration of a chemical reaction by a catalyst). The three ribozymes under study were the leadzyme, the flexizyme, and the Diels-Alder ribozyme. The experiment compared STRUCTURE TO FUNCTION (which is uber-important in biology) but, kept in mind the idea of ideal metal-ion coordination geometry that was obtained from surveys of high-resolution small molecular structures. A newly developing theme is that natural and artificial ribozymes which catalyze single-step reactions also usually possess a pre-formed active site. Multivalent ions aid in the active site formation for RNA, but can also provide Lewis acid functionality which is required for catalysis. When this metal ion bonding is not possible, ribozymes survive/adapt by ionizing their bases, or by recruiting cofactors that increase their chemical functionality.

And the Winner is... Uh-Oh!

This article talks about a precedent in Nobel Prize history. Dr. Ralph Steinman, a biologist at Rockefeller University, was named winner of the 2011 Nobel Prize in Physiology, this Monday. Unfortunately, Steinman died of pancreatic cancer this Friday. Ironically, he had actually extended his own life using therapy that he had designed himself! The Nobel Prize Rules state that the prize cannot be awarded to someone after their death. In this situation, the Nobel committee was not aware of his death and had already declared him to be the winner. He would have received the prize of almost $1.5 million!

Steinman discovered the immune system's sentinel dendritic cells. He also demonstrated that science can productively harness the power of these cells and other components of the immune system to curb infections and other communicable diseases. Brilliantly enough, when Steinman was diagnosed with cancer, he prolonged his life using exactly this; his own dendritic cell-based immunotherapy. The Nobel Committee recognized Steinman for his discovery of the dendritic cell and its role in adaptive immunity.

In further detail, Dr. Steinman discovered dendritic cells in 1973. He found that these new class of cells are very important in activating the body's adaptive immune system. He later, found out how they function. Overall, his reasearch set a foundation for more studies in immunology and has led to advanced, new approaches to treating cancer, infectious diseases, and disorders of the immune system. Dr. Steinman applied his research on his own life. He deployed his own dendritic cells to mount an assault on his own cancer! Truly an inspiration for all.

Wee for a Wii

This article talks about Jennifer Strange, a 28 year-old woman who died due to water intoxication. Water intoxication results when the normal balance of electrolytes are disturbed and pushed out of safe limits from drinking excessive amounts of water. As we talked about in class today, cells prefer to stay in an isotonic solution. With the excess water coming in, the fluid outside the cells would get more water, becoming diluted. This would cause the fluid outside the cell to become hypotonic. Cells in hypotonic solutions start to swell up. Because, in comparison, the cells would have a higher concentration of salts and the water would rush into the cells. Eventually the cells would burst due to all the pressure. In the brain, this swelling increases intracranial pressure. This may cause headaches, confusion, and drowsiness; symptoms that Strange went through just hours before her death. Eventually, vital signs will be effected; including bradycardia which is an abnormally slow heart rate. Cerebral edema can occur; an excess accumulation of water in the intracellular and extracellular spaces of the brain. This can cause cerebral infarctions because blood vessels may collapse due to all the pressure, resulting in paralysis. In sum, the body will slowly stop working causing brain damage, coma, or even death.
Water intoxication can be prevented if your water intake does not exceed your losses. Healthy kidneys can micturate about a quarter of a gallon an hour; stress may reduce this number. Water intoxication, before it goes too far, can be treated with diuretics to help you urinate :) Another treatment is vasopressin receptor antagonists which are one of the cell surface receptors that play an important role in your body's retention of water.

Glycosylation

This article goes into depth about the process of glycosylation. Glycosylation is the attachment of carbohydrates to a lipid or protein, referred to as a glycolipid or glycoprotein respectively. Formation of the sugar-amino acid linkage is very important in the biosynthesis of the carbohydrate units of glycoproteins. the modification of proteins through enzymatic glycosylation is an event that goes beyond the genome and is controlled by factors that are very different amongst various types of cells and species. Many different glycosylation routes have been found in organisms that lead to the mature carbohydrate units on glycoproteins that are secreted by cells or become components of its membrane, cytoplasm, or nucleus. One major event in the biogenesis of peptide-linked oligosaccharides is the formation of the sugar–amino acid bond; this determines the nature of the carbohydrate units that will subsequently be formed by the cellular enzymatic machinery, which in turn influences the protein’s biological activity. This is a perfect example of structure fits function. 
This article talks about two types of glysoylation. N-glycosylation and O-glycosylation. I'm not going to go in depth about those because it is wayyyy too confusing but feel free to read the article if you're interested! It also talks about phosphoglycosylation. Phosphoglycosylation is the enzymatic attachment of a sugar to the polypeptide chain, through a phosphodiester bridge. 
Defects in the attachment of a carbohydrate to protein have lead to some human diseases. The disorders that have been present at birth are most often neurological and developmental deficiencies. 
Appreciation of the major role that oligosaccharides play in the framework of proteins with many different amino acid sequences make glycopeptide bond multiplicity more understandable. After all, it is the formation of these linkages that determines to a large extent the nature of the final carbohydrate units (where they are going to go and what role they will play in the cell) that are subsequently formed by the the many processing enzymes.

EndoSIMBAyosis

This article gives a brief history/overview of what endosymbiosis is. So, there is this preconceived notion that the first photosynthetic organisms were single-celled bacteria. About 1.5 million years ago, something phenomenal occurred. Non-photosynthetic plants (way back in the day), took in tiny green bacteria. They maintained a mutual relationship. The host cell provided a healthy/safe environment for the bacteria; and the bacteria provided energy for the cell that was harvested from sunlight. Eventually these two became so dependent on each other that they pretty much got to a point where one couldn't live without the other. Plastids are remnants of organisms inside a cell. Chloroplasts are the green plastids inside plant cells.
More recently amoebas also decided to take advantage of the sunlight. Now, amoebas are usually not photosynthetic but, there is a species that has plastids that are closely related to cyanobacteria. This leads scientists to suggest that this new species must be relatively new.
Endosymbiosis can actually happen again and again with the same organism. For example, Hatena arenicola (a unicellular organism) hosts algae; which itself is a product of endosymbiotic events. There are also some red and green algae that have been used by other cells to become plastids.
This article also mentions a couple other organisms that have been trying to "go green" such as the: green sea slug and the photosynthetic salamander!

Alzheimer's and Parkinson's

This article is about how protein synthesis accounts for many components necessary to the cell. But along with protein synthesis compartmentalization is necessary. This article talks about how proteins know where to go in a cell, how they get to their specific destinations, how there is a chance for errors, and what diseases those errors might cause. The article mentions a couple of diseases that arise from defective protein folding, and failures of the cell's quality control center.
One disease that may result from conformational errors is Alzheimer's Disease. Conformational diseases arise when a protein changes size or shape and tissue disposition occurs as amyloid fibrils. Alzheimer's specifically results when a specific protein undergoes a conformational rearrangement that results in aggregation and deposition within tissues. Alzheimer's has occasional patterns such as appearing later in life and causing neuronal loss and synaptic abnormalities.
Alzheimer's itself is the most common form of dementia. You gradually lose your memory, and your brain functions and behavior start to deteriorate. 
Relating to trafficking, what causes Alzheimer's is extracellular plaques and intracellular neurofibrillary tangles. Extracellular plaques are primarily made up of amyloid-β-peptide and tangles are made of cytoskeleton proteins. 
Another disease and second most common neurodegenerative disorder is Parkinson's Disease. Parkinson's is the degeneration of dopaminergic neurons in the substantia nigra. Parkinson's will give you muscular rigidity, postural instability, and a resting tremor. It is caused by deposition in brain cells of intracytoplasmic inclusion bodies, Lewy bodies.

Tay-Sachs Babies Make Me Sad :(

This article is about Tay-Sachs Disease. Tay-Sachs is a genetic disorder that usually occurs in children. It is caused by the absence of hexosaminidase-A (hex A). Without this enzyme, a lipid accumulates abnormally in cells, specifically in nerve cells of the brain. The excessive accumulation will eventually start to damage cells. This is why/how Tay-Sachs progressively destructs the nervous system.
Babies with Tay-Sachs appear normal until about 6 months, which is when their development slows. By the time they turn 2 years old they may experience seizures and their mental state starts to degress. They will forget how to crawl, reach, sit... and death usually results by the age of 5, if not earlier.   :'(
Tay-Sachs babies develop a "cherry-red" macula (spot) in the back of their eyes (retina). Eventually they lose their ability to see altogether. This is a picture of their retina, seen through an opthalmoscope:

Tay-Sachs results from a defect on chromosome 15 and can be identified through a simple blood test.
A common misconception is that this disease is limited to people of jewish decent. This is not true, although it is most common amongst people of Eastern (Ashkenazi) Jewish decent, anyone can be a carrier. There is no cure or treatment for Tay-Sachs. Researchers are in the process of finding a cure but, none so far. Scientists have looked at enzyme replacement therapy to provide for the Hex-A that Tay-Sachs' babies are lacking. Bone marrow transplants have been attempted, but did not slow down or reverse the symptoms of Tay-Sachs. Scientists still have hope on gene therapy. Hopefully the cure will show up in the near future!!!
On a brighter note, and mildly off-topic, but nonetheless interesting, this article talks about how there may be a Jewish gene for intelligence! Like Tay-Sachs and Gaucher's, there are certain things that are common, if not limited to, Jews. In my opinion, it sounds a bit ludicrous, but Gregory Coch-ran has teamed up with anthropologists and they have proposed that Ashkenazi Jews are more intelligent because of genetic mutation. After much assessment these researches concluded that genetic diseases are linked to a tendency to having greater intelligence. I don't know how accurate these researchers are but, I think we should keep in mind that Coch-ran was also the one who proposed that homo-sexuality is caused by an infectious disease... yeah!

The Chemical Basis of Life: Organic Molecules

I. Summary
Proteins
Proteins are what allow a cell to carry out most of it's functions. Proteins play a structural role, they maintain cell shape and provide support. They are catalytic and this is why some proteins (enzymes) speed up reactions. Cells communicate with their environments by regulation through membrane proteins. Proteins also allow cells mobility. For example, sperm cells have flagellum (protein) that helps them move. Cells respond to their environment through regulatory and receptor proteins. They allow cells to respond to stimulus. Hormone proteins carry regulatory signals between cells. Antibody proteins defend against invading molecules and organisms. Storage proteins store substances for later use.
Proteins have four different levels of structure. Primary Structure is the sequence of amino acids that characterize a specific protein. The amino acids are joined together by peptide bonds (formed through dehydration synthesis). Proteins differ based on their primary structure, the sequence of their amino acids. Not all amino acids are hydrophilic. To protect the hydrophobic ones, the linear chain may fold, which leads us to the secondary structure. Secondary Structure is where amino acids interact with other amino acids around them. They might twist or bend, forming hydrogen bonds. It can form an alpha-helix or a beta-strand, which are essentially zig-zags in a flat plane. Beta-strands continue to form beta-sheets. Hydrogen bonds are what help stabilize secondary structures. Tertiary Structure is the overall conformation or three-dimensional shape of a protien. As the structures progress, they become more globular and compact. Now that the structure is more spherical and compact, we see that the hydrophobic regions can easily be protected from any aqueous solution because they can hide on the inside of the structure. Tertiary structures are stabilized by their R-groups. Of all the interactions (hydrogen, ionic, hydrophobic, and disulfide linkages) disulfide linkages are the strongest because they are covalent. Denaturation is the loss of protein structure and function. Folded proteins are functional and unfolded proteins are inactive. In this sense, primary and secondary structured proteins are not functional, only tertiary and quaternary are. Denaturation occurs at high heat, change in pH, and addition of salt. Quaternary Structure represents the interaction between two or more protein chains.
In sum, these structures are important because they determine the function and it is the sequence of the linear chains of amino acids that determine that function. Primary structures are stabilized by peptide bonds, secondary are stabilized by hydrogen bonds, tertiary are stabilized by ionic, hydrogen, hydrophobic interactions, and disulfide linkages. Of these, disulfide linkages are the most stable.
Nucleic Acids
Nucleic acids are long polymers of nucleotide building blocks. DNA (deoxyribose nucleic acid) stores all the information for proper cell function. DNA information is what determines the primary structures of proteins. RNA (ribose nucleic acids) is used in various forms to help assemble proteins. Nucleotides are made of a five-carbon sugar, nitrogenous base, and three phosphate groups. The general structure is numbered. One way to differentiate between DNA and RNA is that DNA has H on its 2' (that's why it's called deoxy... without oxygen). Meanwhile, RNA would have OH on its 2'. Nucleoside is the term used when referring to the sugar and nitrogenous base only. Nucleoside monophosphate is the sugar, nitrogenous base, and one phosphate. Diphosphate and triphosphate would have two or three phosphates respectively.
There are 20 amino acids used to make a protein. Of those, there are 4 nucleotides used to construct DNA and 4 to construct RNA. DNA uses A, T, C, G and RNA uses A, U, C, G. Nucleotides vary in sugar and nitrogenous bases. Two categories of nitrogenous bases are pyrimidines (one ring) and purines (two rings). DNA has a double helical structure because the partially negatively charged oxygen molecules form hydrogen bonds with the partially positively charged hydrogen molecules.
DNA and RNA polynucleotide chains are formed by linking the phosphate group of one nucleotide to the sugar of the next one. These are linked together by phosphodiester bonds which are covalent bonds specifically found in nucleic acids. Dehydration reactions link nucleotides. Just like how proteins have N and C termini, DNA has opposite ends, 5' and 3'. DNA is anti-parallel because one strand runs 5' to 3' and the other runs 3' to 5'. Two strands of DNA are joined by hydrogen bonds between the nitrogenous bases following base-pairing rules: A-T and C-G. A-T forms two hydrogen bonds and C-G forms three hydrogen bonds. Bonding of these purines-pyrimidines gives ideal spacing for hydrogen bonding.
RNA usually exists as a single strand. It uses a ribose sugar, instead of deoxyribose and Uracil instead of Thymine. The difference is just the Thymine has a methyl group and Uracil doesn't. It also follows same base-pairing rules as DNA.
II. Useful Materials
This website provides interactive flashcards and can help you memorize the 20 amino acids. It keeps track of how many you get correct and incorrect. Then, when you're ready you can take a test and the website will generate different kinds of questions to test your knowledge on the topic!

This video shows DNA and RNA bonding. It explains the components of nucleotides, base pairing specificity, and the main differences between DNA and RNA.

III. Article
This article is about thalidomide. Kevadon, which is known today by it's generic name thalidomide was meant to be a sedative. When William S. Merrell Co. applied for this drug to be approved by the FDA, they declined. Dr. Frances Kelsey was the one who was assigned to this drug, and she automatically declined it. She had always been very cautious about taking drugs while pregnant.
When articles began to pop up about women who took thalidomide during their pregnancy giving birth to severely deformed babies, America had Dr. Kelsey to thank. The only Americans who were exposed to the drug were travellers taking it while travelling the seas, and people who took part in experimental studies. This close encounter with thalidomide caused congress to pass the Kefauver Act, which required more in-depth documentation and careful review of drug safety.

Thalidomide Approved by the FDA

Researchers Gain New Insights into the Mystery of Thalidomide-Caused Birth Defects

In 1957 a drug, thalidomide, was introduced to help relieve pregnant women of morning sickness. It turns out, this drug had some major side-effects that caused sever malformations in developing fetuses. These "thalidomide babies" had many defects including shortened upper limbs; as shown below:

The drug was finally discontinued in 1961.

In the 1990s, the FDA approved the use of thalidomide for multiple myeloma and some complications of leprosy. The drugs powerful anti-inflammatory and anti-angiogenic effects actually will help you feel better, but they have horrible side-effects. There is still study going on about whether it can be used for arthritis, breast cancer, and more than 30 other diseases.

Recently Tokyo Institute of Technology have been conducting experiments on zebra fish and chick embryos to see why exactly thalidomide causes birth defects. Previous studies suggest that the side-effects are caused by thalidomide's therapeutic effects on inflammation, blood vessel formation, and cell stress.

Despite the past with thalidomide, and with ongoing research, it is surprising to see that the FDA actually has approved supervised, modicum use of the drug.

The Chemical Basis of Life: Atoms, Molecules, and Water

I. Summary


Atoms
Biology is the study of life, and to understand it, we have to know a little bit about chemistry and physics; as they help us understand how atoms and molecules interact. All living organisms are composed of matter, anything that takes up space and has mass. Matter is made up of atoms, which are the smallest functional units of all living things. Atoms are made up of tiny little particles. Atoms can also bond together to create molecules. Examples of some atoms are Hydrogen, Carbon, Nitrogen, and Oxygen. These specific types of atoms are called elements, pure substances of only one kind of atom. Protons, neutrons, and electrons can be found within an atom. The protons and neutrons can be found within the atomic nucleus and the electrons occupy orbitals around an atom's nucleus. Orbitals are the regions around the nucleus where the electrons are most likely to be found. They are almost like rings around the nucleus. Orbitals occupy energy shells, or energy levels.  The electrons in the outermost shell are called valence electrons. These are the most important electrons that we need to know for this chapter. They determine whether an atom can bond with other atoms.
The atomic number is the number of protons an atom contains. The atomic mass is an atom's mass relative to other atoms. This is usually confused with weight, which is the the gravitational pull on a given mass. The atomic mass is measured in daltons. A Dalton, also known as atomic mass unit, is equivalent to 1/12 the mass of a carbon atom. A mole of any substance contains the same number of particles as there are atoms in exactly 12g of carbon. <------ this is something that I'm still a little iffy about!
Traditionally, the number of neutrons are the same as the number of protons, in any given atom. However, variations of an element in their numbers of neutrons, can exist; these are called isotopes. An isotope found in nature that is inherently unstable and usually does not exist for long periods of time is called a radioisotope. They decay and emit energy in the form of radiation.
Oxygen, Nitrogen, Carbon, and Hydrogen make up the majority of atoms in all living organisms. Hydrogen and oxygen we know form water, carbon is the building block of all living matter, and nitrogen is vital in proteins. Trace elements are also necessary for normal function in all living organisms, but is only needed in small quantities. Iron and copper are examples of trace elements.
Chemical Bonds and Molecules

A molecular formula is a representation of a molecule that consists of the chemical symbols for all of the atoms present and and subscripts that indicate how many of those atoms are present. A molecule that is composed of two or more different elements is called a compound. Water is a compound as it contains two hydrogen molecules and one oxygen molecule. Chemical bonds are what hold atoms in molecules together.

Covalent bonds are where atoms share electrons. This is the strongest type of chemical bond.

For most atoms, 8 electrons are needed to fill their outer most shells. The octet rule states that atoms are stable when they have 8 electrons in their outermost shell. Keep in mind, this rule doesn't always apply (hydrogen only needs 2 electrons to fill its valence shell).
A double bond is when the atoms of a molecule share two pairs of electrons, rather than one. An atom's ability to attract electrons, electronegativity, is not the same for each atom. In a covalent bond, although the two atoms are sharing electrons, they don't always necessarily share electrons evenly. Sometimes one atom's electronegativity is greater than the other and the shared electrons spend more time around one atom than the other. This phenomenon is called a polar covalent bond. Water is a great example of a polar covalent bond. Although hydrogen is sharing its electrons with oxygen, oxygen has a greater electronegativity and therefore hydrogen's two electrons spend more time orbiting oxygen's nucleus than they do their own. Nonpolar covalent bonds are where the electrons shared in a covalent bond, are shared equally because the electronegativity of the two atoms are similar. A single molecule can have areas with nonpolar bonds and areas with polar bonds. When the bonds in a molecule are predominantly nonpolar, it is called a nonpolar molecule. Vice versa is referred to as a polar molecule.
Hydrogen bonds are the weakest bonds and form when a hydrogen atom from one polar molecule is electrically attracted to an electronegative atom in another polar molecule. The strength of hydrogen bonds increases relative directly as the number of bonds increase. AKA 3 hydrogen bonds are stronger than 2 hydrogen bonds. A good example is DNA; it takes considerable amount of energy to pry the two strands apart because of the amount of hydrogen bonds. Enzymes are proteins that either facilitate or catalyze chemical reaction in a cell. Van der Waals forces are attractive forces between molecules in close proximity of each other, caused by the variations in the distribution of electron density around individual atoms. <------ another unclear topic!
An ion is when an atom or molecule gains or loses electrons, giving it a net electric charge. Cations are ions that have a net positive charge and anions are ions that have a net negative charge. What helps me remember that cations are the positive ones and anions the negative is that cations has a t which kind of looks like a +, for positive. Yes, every time I read cation I read it like ca+tion! Ionic bonds occur when a cation bonds to an anion. Essentially one atom is giving electrons and the other is recieving. This exchange of electrons will change it's charge.
A free radical is an atom that only has one valence electron. Free radicals steal electrons from other atoms until their valence shell is full.
A chemical reaction is the formation and breaking of chemical bonds, resulting in a change in the composition of substances. This can be when two elements combine to form a compound, or when a compound is broken down into elements. Chemical reactions require energy, which is partly provided through heat. Heat energy allows atoms and molecules to move and vibrate; this is known as Brownian motion. Chemical reactions also need to be catalyzed. Chemical reactions proceed in a particular direction and will eventually reach a state of equilibrium unless something happens to prevent equilibrium. A reactant is something that participates in a chemical reaction and becomes changed by that reaction and a product is the end result of the reaction. Chemical equilibrium is a state in the chemical reaction where the rate of formation of products equals the rate of formation of reactants.
Properties of Water
A substance dissolved in a liquid is a solute and a solvent is the liquid in which a solute is dissolved. A solution is a liquid that contains one or more dissolved solutes. Aqueous solutions are solutions made with water. Ions and molecules that contain polar covalent bonds and WILL dissolve in water are known as hydrophilic. Molecules that don't have partial charges and are not attracted to water molecules are hydrophobic. They are composed of carbon and hydrogen and are relatively insoluble in water. Cohesion is when water molecules are attracted to each other and adhesion is when water adheres to a surface that is not electrically charged. Water also has a very high specific heat which is the amount of heat energy needed to raise the temperature of 1g by one degree Celsius. DON'T GET THIS CONFUSED WITH heat capacity which is the amount of heat energy needed to raise the temperature of an entire object or substance.
The colligative properties of water are dependent on the number of dissolved solutes and allow water to function as an anti-freeze in certain organisms. Water's high heat of vaporization and high heat of fusion help it be very stable while in liquid form. Hydrolysis is the breaking down of large molecules into smaller units and a dehydration reaction combines smaller molecules into a larger one.
The pH of a solution refers to it's concentration of hydrogen ions. The pH scale is from 0-14. 0 is acidic and contains the most H+ ions, whereas 14 is basic, or alkaline, and has more OH- ions. PH balance can be regulated by using a buffer. A buffer is a compound that minimizes pH fluctuations in fluids of living organisms; they can raise or lower pH, as needed.

II. Useful Materials


Above, I mentioned how the concept of a mole was still a little unclear to me. This song demonstrates how to find a mole, gives the definition, and helps remember everything. Its super catchy, LISTEN TO IT!!!

*     *     *     *     *

I also mentioned how I didn't quite understand the van der Waals force. Here's a video that actually explains and clarifies it. He digresses a little but, in the end he actually helped! He pretty much said that the van der Waals force is a weak attractive force between atoms of nonpolar molecules caused by a temporary change in dipole moment from a brief shift of orbital electrons to one side of an atom or molecule, creating a similar shift in adjacent atoms/molecules.

III. Article


This article is about physicists that came about creating the heaviest isotope of magnesium. While experimenting, however, an isotope of aluminum also showed up. How exciting! This could help us come closer to understanding occasional X-ray emissions from neutron stars that are growing in mass.
On the 5th day of a 7-day-long experiment in Michigan State University, an isotope of aluminum appeared unexpectedly. Most theories predicted that aluminum-42 wouldn't exist; this is why it's appearance was so shocking. In sum, the discovery of aluminum-42 suggested that even heavier aluminum isotopes could exist and maybe even other elements, that are higher in the periodic table, would be able to accommodate more neutrons than expected.

The Moon Isn't Watery After All :(

Moon Not So Watery After All, Lunar-Rock Study Says

In the past, scientists believed that the moon was bone dry; but, during recent missions, some rocks were brought back, and showed considerable traces of hydroxyl which is a compound formed by the breakdown of water. Thus, scientists believed that the Moon contained significant amounts of water. A new study, however,  by geochemist Zachary Sharp, measured chlorine isotopes and found that the chlorine isotope values were almost 25 times more than Earth's. Since chlorine is strongly attracted to hydrogen, and when they are both present in molten rock, they tend to form hydrogen chloride gas. Sharp concluded that when the rocks cooled 4.5 billion years ago, they were low in hydrogen because instead of becoming mostly hydrogen chloride gas, the chlorine bonded with other elements (leading to more chlorine isotopes). Basically, if moon rocks lack hydrogen, they must lack water.
In essence, this article shows how much isotopes can prove and how important they are in research. A prior notion was that the Moon contained a lot of water but recent study on chlorine isotopes showed how the Moon is actually very dry and contains very little water. Study is still going on about water existing on the Moon but, perhaps this means living on the Moon could actually be possible in the future?

Techno Temporary Tattoo?? WHAT?

Skinlike Electronic Patch Takes Pulse, Promises New Human-Machine Integration

This article talks about an invention that a team at Stanford is researching about. It is a flexible silicon film that will act as a temporary tattoo. The team is hoping that this tattoo will be able to collect and transmit information about your heart rate, temperature, muscle contractions and brain waves. The team has already demonstrated how the patch can be used to measure vitals. In the future, it may even be able to help stimulate muscles, speed wound healing, improve prosthetics and maybe even communicate with video games!

Many people believe that medical innovations like this are unnecessary and dangerous. But the benefits are amazing. In retrospect, monitoring equipment has always been bulky and burdensome. This new device will be "almost mechanically invisible to the wearer". I found this article interesting because it is talking about an invention that may be attainable in our near future. It also has many interesting advantages that will affect and hopefully better many peoples' lives.

Intro

Hi! I'm Urma. My favorite color is blue. I like food, traveling, music, art, and YOU! Dermatology, Ophthalmology, Interventional Radiology, and Musculoskeletal Radiology interest me!