Reverse Transcription-Polymerase Chain Reaction... ¿Qué es?

The abstract of this article talks about RT-PCR. Well what exactly is RT-PCR? RT-PCR stands for Reverse Transcription-Polymerase Chain Reaction. It is a technique used in genetic studies that allows the detection and quantification of mRNA , particularly in samples with limited quantities of extracted RNA. It is a very sensitive method that shows whether or not a specific gene is being expressed in a given sample. RT-PCR is a very important test in the field of Genetically-Modified Organisms (GMO's) because it gives researchers a mechanism to test whether any specific gene is turned on (active) or turned off (inactive). This allows researchers to identify the benefits of genetically-modified organisms with respect to their "natural" counterparts and search for any significant differences in which genes are expressed in the two types of organisms.

Article:

Real-time reverse-transcription polymerase chain reaction: technical considerations for gene expression analysis.

Has it all been a lie???

According to the latest findings from researchers of the Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch of the Helmholtz Association, Germany, control mainly occurs in the cytoplasm of the cell and not in the 'high-security tract' of the cell nucleus. Their results also highlight where gene expression (the activation of a gene for protein production) can get out of control. This study was researched by a team of scientists led by biologists Björn Schwanhäusser and Matthias Selbach, biomathematician Jana Wolf (all from MDC) and the biotechnologist Wei Chen of the Berlin Institute for Medical Systems Biology (BIMSB) of the MDC.

As described in my previous post, transcription is the process of creating a complementary RNA copy of a sequence of DNA. Translation is the process that converts an mRNA sequence into a string of amino acids that form a protein. Both of these processes work in cohesion with one another to go through the journey from DNA sequence to a functional protein. The researchers questioned which of the two processes (transcription or translation) plays the dominant role in regulating cellular protein levels.

To answer this question the MDC researchers measured the turnover of cellular mRNAs and proteins and mRNA and protein levels as their starting point. They used high-throughput technologies such as quantitative mass spectrometry and the latest sequencing techniques. In total, they evaluated proteins and mRNAs for more than 5,000 genes. The researchers drew conclusions from the collected data about the control of protein levels by using mathematical modeling. They observed that cellular protein levels mainly depend on translation of mRNAs in the protein factories of the cytoplasm.

The researchers found that cells use their resources very efficiently. Most mRNAs and proteins of abundantly expressed housekeeping genes (these genes maintain the normal operations of the body) are very stable. This is good because the cells will save worthy energy for future needs. However, the proteins responsible for rapid signaling processes are usually unstable. Therefore, cells can quickly adapt to changes in their surroundings. This may also explain why the decisive control step takes place in the cytoplasm and not in the nucleus.

According to Matthias Selbach, "so far, this is purely basic research. But we also know that the production of proteins is disturbed in many diseases, for example cancer." There is not much information about where the process gets out of control. Until now, researchers focused mainly on the nucleus to find answers to this question. However, the new findings show that the protein factories in the cytoplasm have great significance.

Article:

From Gene to Protein: Control Is Mainly in the Cytoplasm, Not Cell Nucleus

Chapter 12: Useful Materials

These animations for both transcription (CLICK HERE: TRANSCRIPTION) and translation (CLICK HERE: TRANSLATION) are from the Institute of Agriculture and Natural Resources at the University of Nebraska. I think these animations are interesting because they go into detail about the process of transcription and translation.

Now I shall somewhat explain both these processes...yay!

Transcription is the process of creating a complementary RNA copy of a sequence of DNA. During transcription, a DNA sequence is read by RNA polymerase, which produces a complementary, antiparallel RNA strand. Transcription is initiated when the RNA polymerase complex assembles at the promoter. RNA polymerase catalyzes the elongation of the RNA while the DNA template is unwound and rewound.

Translation is the process that converts an mRNA sequence into a string of amino acids that form a protein. This fundamental process is responsible for creating the proteins that make up most cells. It also marks the final step in the journey from DNA sequence to a functional protein; the last piece of the central dogma to molecular biology.

DNA Polymerase and its Conformational Transitions

The abstract of this article explains the conformation transitions in DNA polymerase. DNA polymerase is an enzyme that catalyzes the polymerization of deoxyribonucleotides into a DNA strand. DNA polymerases are best-known for their role in DNA replication, in which the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand. DNA polymerases depend on a series of early steps in the reaction pathway. This allows the selection of the correct nucleotide substrate before the enzyme carries out the chemical step of nucleotide incorporation. The conformational transitions that are involved in these early steps are easily detectable with a variety of fluorescence analysis, which include the fingers-closing transition that has been characterized in structural studies. Scientists have developed a FRET-based assay for the fingers-closing conformational transition that occurs when a binary complex of DNA polymerase I (Klenow fragment) with a primer-template binds a complementary dNTP; they have used this and other fluorescence assays to place the fingers-closing step within the reaction pathway.

Article:

Conformational transitions in DNA polymerase I revealed by single-molecule FRET

Breakdown of DNA in Cancer Cells

This article talks about researchers at the Hebrew University of Jerusalem and how they discovered why cells suffer from insufficient building blocks to support normal DNA replication, during the early stages of cancer development. DNA replication is the process of making an identical copy of a section of duplex (double-stranded) DNA, using existing DNA as a template for the synthesis of new DNA strands.

There is a possibility that cancer development can be ceased by externally supplying the building blocks of DNA. Thus, resulting in reduced DNA damage and significant lower potential of the cells to develop cancerous features. Researchers at the Hebrew University of Jerusalem demonstrated that insufficient levels of the DNA building blocks (nucleotides) required to support normal DNA replication is caused by abnormal activation of cellular generation, which drives many different cancer types. By using laboratory cultures in which cancerous cells were introduced, the researchers were able to show that it is possible to reactivate normal DNA synthesis through external supply of those DNA building block. Thus, opposing the damage caused by the cancerous cells and the cancerous potential it may of caused.

Article:

Researchers Demonstrate Why DNA Breaks Down in Cancer Cells

Chapter 11: Useful Materials

This video describes the structure of DNA and everything involved with it. Nucleotides are the building blocks of DNA (and RNA). Each nucleotide consists of a 5-carbon sugar (deoxyribose), a nitrogen containing base attached to the sugar, and a phosphate group. There are four different types of nucleotides found in DNA, differing only in the nitrogenous base; adenine, guanine, thymine, and cytosine. Adenine and guanine are purines, which are the larger of the two types of bases found in DNA. Cytosine and thymine are pyrimidines; like purines, all pyrimidine ring atoms lie in the same plane. This is just an overview on the structure of DNA. But I thought this video was helpful in knowing the basic components of DNA.

This website (CLICK HERE) provides an animation about DNA replication. I thought this website was quite interesting because it breaks down DNA replication into eight sections to better help you learn. You can also pause, rewind, and fast forward the animation. There are also review questions after each section to check if you retained the knowledge that you just learned. I advise you check out this website!

Cell Adhesion

Cellular adhesion is the binding of a cell to a surface, extracellular matrix or another cell using cell adhesion molecules such as integrins, cadherins, and selectins. Cell adhesion is critical for the genesis and maintenance of both three-dimensional structure and normal function in tissues. Cell adhesion receptors are typically transmembrane glycoproteins that mediate binding to extracellular matrix molecules (ECM) or to counter-receptors on other cells; these molecules determine the specificity of cell-to-cell or cell-to-ECM interaction.

The integrins are cell-surface glycoproteins that act as receptors for ECM proteins, or for membrane-bound counter-receptors on other cells. They also play a role in cell signaling and therefore regulate cellular shape, motility, and the cell cycle. Each integrin is a heterodimer that contains an α and a β subunit with each subunit having a large extracellular domain, a single membrane-spanning region, and in most cases, a short cytoplasmic domain.

The cadherins are a class of type-1, transmembrane proteins. They share an extracellular domain consisting of multiple repeats of a cadherin-specific motif. They play important roles in cell adhesion, ensuring that cells within tissues are bound together. Their name is derived from the fact that they are dependent on calcium (Ca2+) ions to function. This subfamily includes the N-, P-, R-, B-, and E-cadherins, also including 10 other members. These molecules localize in specialized sites of cell-to-cell adhesion that are termed adherence junctions; at these sites cadherins can establish linkages with the actin-containing cytoskeleton.

The selectins are lectin-like adhesion receptors composed of three members, L-, E-, and P-selectin. P-selectin is present in latent form in endothelial cells and platelets; it is rapidly translocated from secretory granules to the cell surface upon cell activation by thrombin or other agonists. E-selectin is synthesized and expressed on endothelial cells in response to inflammatory cytokines such as tumor necrosis factor (TNF) or IL-1. L-selectin is expressed constitutively on leukocytes, but its presentation at the cell surface may be regulated. All selectins are single-chain transmembrane glycoproteins that share similar properties to C-type lectins due to a related amino terminus and calcium-dependent binding.

Article:

Signal Transduction and Signal Modulation by Cell Adhesion Receptors: The Role of Integrins, Cadherins, Immunoglobulin-Cell Adhesion Molecules, and Selectins

Why Does Apoptosis Occur?

This article basically summarizes apoptosis and why it occurs with cells. Apoptosis, or programmed cell death, is a normal component of the development and health of multicellular organisms. Cells die in response to a variety of stimuli and during apoptosis they do so in a controlled, regulated way. In this article, two researchers give their explanations on this topic.

Why are cells that die by programmed cell death generated?

According to Michael Hengartner, senior staff investigator at Cold Spring Harbor Laboratory, "there are several reasons, such as that it gets rid of cells that are not needed, in the way or potentially dangerous to the rest of the organism. Cells that are not needed may never have had a function. In other cases, they may have lost their function, or they may have competed and lost out to other cells. One of the most fascinating reasons for cell death is to get rid of dangerous cells, those that could be harmful to the rest of the organism. Cells could be mutants that would become cancerous; therefore, apoptosis is very important in the formation of cancer. "

H. Robert Horvitz, an expert on apoptosis at the Massachusetts Institute of Technology explains that "the mechanism that generates cells that are needed generates unneeded ones as well (which happens in the immune system); and some cells that die are needed, but only briefly. Cells die either because they are harmful or because it takes less energy to kill them than to maintain them."

Article:

Why does programmed cell death, or apoptosis, occur? Does it take place among bacteria and fungi or only in the cells of higher organisms?

Chapter 9: Useful Materials

This video is an overview of the pathway of signal transduction. Signal transduction pathway is a group of proteins that convert an initial signal to a different signal inside a cell. He explains how signal transduction pathways are used by cells to convert chemical messages to cellular action. Epinephrine is used as a sample messenger to trigger the release of glucose from cells in the liver. The G-Protein, adenylyl cyclase, cAMP, and protein kinases are all used as illustrative examples of signal transduction. He also gives several examples that help you better understand these concepts. Overall, I thought this video was very helpful and was a quick and easy way to help me study!

As I have shared before, Quizlet is a website where you can make flashcards to help you study. I love this website because it really helps when it comes to knowing important terms or definitions. Another thing I like about Quizlet is that you can print out these flashcards to study on the go! You can also quiz yourself and create your own useful flashcards.

Phosphorylation: New and Improved Ways

This article talks about new ways to detect phosphorylation. First off, what is phosphorylation? It is the addition of a phosphate (PO43-) group to a protein or other organic molecule. Phosphorylation plays a significant role in a wide range of cellular processes. After years of research, scientists now know that the presence of a phosphate molecule (usually attached to threonine, serine, and tyrosine residues) can show the difference between health and disease. Protein kinases transfer phosphate groups from ATP to the serine, threonine, or tyrosine residues on protein peptide substrates, which directly affects the activity and function of the target. Through time, research has revealed how cells respond to insulin, and how cancer can develop when there is a mishap in phosphorylation. Other discoveries are showing that phosphorylation could be involved in mood disorders, diabetes, and Alzheimer’s disease.

Studying phosphorylated proteins is always a challenge. Nowadays, a popular method in viewing these proteins is the use of antibodies that specifically bind phosphorylated proteins. The availability of phospho-specific antibodies has opened the door for the improvement of traditional methods as well as the development of new immunoassay techniques. These antibodies can be used as investigation to detect phosphorylated proteins on a Western blot (adaptation of the Southern blot procedure, used to identify specific amino-acid sequences in proteins). The Western blot is the most common method used for assessing the phosphorylation state of a protein.

Assessing protein phosphorylation is often an essential component of the biologist's collection for understanding intracellular factors underlying cellular activities. Given the important role kinases play, it is critical for researchers to have quality tools for measuring protein phosphorylation. Each technique excels in different contexts, and scientists should have the knowledge to choose the method that best fits the experimental design.

Article:

Improved Ways to Detect Phosphorylation

DNP: Weight Loss Drug Caused Deaths

This article explains the pros and cons of DNP (2,4-Dinitrophenol). DNP is a potent chemical promoted as a weight loss drug because it speeds up fat metabolism. While DNP significantly enhances your weight loss efforts, this drug can be toxic to humans, and its use has already resulted in death.

DNP was first used as a weight loss drug in the 1920s. As a result, DNP became a popular weight loss drug and was used until 1938, when it was banned by the Food and Drug Administration (FDA) due to the number of toxic effects and deaths associated with its use.

How exactly does DNP help aid in weight loss? The way that this drug works is that it greatly increases the rate your metabolism. This is because it interferes with your body's ability to produce ATP (adenosine triphosphate), which provides energy for your body. When this deficiency occurs, your body must increase its metabolic rate and burn more fat to meet energy demands. This results in excessive weight and fat loss over a short time.

However, the side effects included increased heart and breathing rates, along with increase of body temperature. This is due to the large amount of heat that is produced during the DNP's interference with the body's ATP production. In severe cases, DNP can cause rapid heart and respiration rate, kidney failure, and may also lead to death.

(The image above shows the chemical structure of 2,4-Dinitrophenol)

Article:

DNP and Weight Loss

Chapter 7: Useful Materials

This video gives a complete overview of glycolysis. He breaks down the process of glycolysis and explains the steps involved in this process. Glycolysis is part of cellular respiration, which also consists of two other parts called the Krebs Cycle (Citric Acid Cycle) and the electron transport chain. This video mainly focuses on glycolysis, which is the break down of glucose. He explains how there are two main stages of glycolysis; which can be called the investment phase (which uses 2 ATPs to break down glucose into two 3-carbon compounds with a phosphate attached) and the pay-off phase (when each of the phosphate attached to the carbon turns into pyruvate, which is essentially the end product of glycolysis - for every one molecule of glucose there are 2 molecules of pyruvate). I thought this video was very helpful in reviewing the process of glycolysis.

I found an animation of the Krebs Cycle (Click Here) online. It explains the Krebs Cycle and each individual step involved in this process. The Krebs Cycle begins after the two molecules of the three carbon sugar produced in glycolysis are converted to a compound called acetyl CoA. At the end of the animation there is a review, where you have to place each step of the Krebs Cycle in the correct order.

What Are Ribozymes?

First off, what is a ribozyme? Well ribozymes are RNA molecules that are able to catalyze chemical reactions. Up until the 1980s, scientists thought all biological catalysts were proteins. But then it was discovered that some RNA molecules can act as enzymes; meaning that they can catalyze covalent changes in the structure of substrates. However, since their discovery there has been intense research in learning about the structure and activity of ribozymes.

(The image above is the crystal structure of a full-length hammerhead ribozyme. Image A is a schematic diagram, while image B is a ribbon diagram.)

Among RNA molecules, the large ribozymes, mainly groups I and II introns (nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene) and RNase P (ribonuclease P, which is a catalyst found in bacterium), are of special importance. Why? Well these three groups of ribozymes show a significant requirement for metal ions in order to establish the active tertiary structure that enables catalysis. The primary role of metal ions to screen the negative charge associated with the phosphate sugar backbone.

Article:

Multiple roles of metal ions in large ribozymes.

Drug Improving Metabolism!

A new asthma drug, formoterol, showed significant ways to improve fat and protein metabolism. Formoterol is a synthetic catecholamine (hormone that regulates heart rate, metabolism and breathing), the metabolic effects have not previously been studied in people. However, therapy doses given to animals have shown that it stimulates metabolism without affecting the heart.

This was proved by a team of Australian researchers, including team leader, endocrinologist Dr Paul Lee. According to Lee, "formoterol is a new generation of this class of medication. It is highly selective for the kind of catecholamine receptors found in the lungs, and not those in the heart. The new drug is also more selective for a similar receptor found in muscle and fat. In theory at least, it should have beneficial metabolic effects -- like the older class of medication -- without affecting the heart." In an experimental test, formoterol was given to eight healthy men over the span of one week. Within that week their energy metabolism increased over 10%, fat burning increased over 25%, and protein burning decreased by 15%. Therefore, these men burned fat while reducing the burning of protein. These results are beneficial because over a period of time, such effects can lead to a loss in fat mass but an increase in muscle.

Article:

New Generation Asthma Drug Could Improve Metabolism, Research Suggests

A Violation in the 2nd Law of Thermodynamics?

This article basically explains how the second law of thermodynamics does not make sense when systems get sufficiently small. The second law of thermodynamics states that the transfer of energy or transformation of energy form one form to another increases the entropy (degree of disorder). A perfect example of the second law of thermodynamics: a hot frying pan cools down when it is taken off the kitchen stove. Its thermal energy ("heat") flows out to the cooler room air; the frying pan cannot heat up again without adding energy. Scientists prediction about how the second law of thermodynamics may not always be accurate occurred nearly a decade ago; their prediction stated that small assemblages of molecules inside larger systems may not always tolerate this law.

From the Australian National University, Genmiao M. Wang and his colleagues discovered the inconsistency of such law when they dragged a micron-sized bead through a container of water using optical tweezers. They found that, sometimes the water molecules interacted with the bead in a way that energy was transferred from the liquid to the bead. This occurred by using the random thermal motion of the water to do the work of moving the bead. According to these researchers, if such movement lasted less than two seconds, the bead would most likely be able to gain energy from the water as it was to add energy to the reservoir. These findings suggest that the function of machines may have basic limitations.

Article:

Second Law of Thermodynamics Violated

Nobel Prize: Chemistry

The Nobel Peace Prize in Chemistry was awarded to Israeli scientist, Dan Shechtman on October 5, 2011. Daniel Shechtman won for the discovery of quasicrystals. Most crystals are composed of a three-dimensional arrangement of atoms that repeat in an orderly pattern. Depending on their chemical composition, they have different symmetries. But quasicrystals behave differently than other crystals. They have an orderly pattern that includes pentagons, fivefold shapes, but unlike other crystals, the pattern never repeats itself exactly.

(This picture displays Israeli scientist, Daniel Shechtman, sits next to a transmission electron microscope at the Haifa Technion Institute of Technology in Israel on Wednesday.)

The existence of quasicrystals, though controversial, was anticipated much earlier, but Shechtman was the first to see them in nature. Shechtman first saw the startling image on April 8, 1982, while studying a rapidly chilled molten mixture of aluminum and manganese under an electron microscope. What he saw appeared to counter the laws of nature.

The finding was more than just theoretical. Quasicrystals have been used in surgical instruments, LED lights and non stick frying pans. They have poor heat conductivity, which makes them good insulators.

(The image above is an atomic model of a silver aluminum (AgAl) quasicrystal)

Article:

What are Quasicrystals, and What Makes Them Nobel-Worthy?

Hold Your Wee for a Wii!

In 2007, Jennifer Strange died after competing in a radio station contest. The contest was held to see how much water you could drink without going to the bathroom; the prize was a Nintendo Wii video game system. Jennifer supposedly drank 2 gallons (7.5 liters) of water over approximately two hours.

What caused Jennifer Strange's death? Well she died due to water intoxication, which is caused by drinking too much water and can also cause hyponatremia (dilution of sodium in the body). When too much water enters the body's cells, the tissues swell with the excess fluid. The cells in our body maintain a specific concentration gradient, so excess water outside the cells (the serum) draws sodium from within the cells out into the serum in an attempt to re-establish the necessary concentration. As more water accumulates, the serum sodium concentration drops (hyponatremia). The other way cells try to regain the electrolyte balance is for water outside the cells to rush into the cells via osmosis. Osmosis is the movement of water across a semipermeable membrane from higher to lower concentration. Both electrolytes and water move across the cell membrane in an effort to balance concentration.

Therefore, Jennifer Strange died not specifically from the amount of water she drank but how fast she drank that water. You are unlikely to suffer from water intoxication, even if you drink a lot of water. As long as you drink over time as opposed to intaking an enormous volume all at once.

Article:

Woman dies after water-drinking contest

Glycosylation!

You might be asking yourself, what exactly is glycosylation? Glycosylation is the adding of a glycoside (sugar) to a protein. This process occurs in the endoplasmic reticulum (ER), while the polypeptide is still being biosynthesized and is partially unfolded. This suggests that glycosylation plays a role in protein folding and stability. Glycosylation is one of the most common and important protein modifications.

(The image above shows O-linked glycosylation)

This article basically talks about the process of glycosylation and its glycoproteins. A glycoprotein is formed when a membrane associated carbohydrate is exclusively in the form of oliogsaccharides covalently attached to proteins. Glycoproteins consist of proteins covalently linked to a carbohydrate.

(The image above shows N-linked glycosylation)

Article:

Research Highlights

Chapter 4 Article: Enzymes Cutting HIV

This article explains how scientists have designed a special enzyme that rids the process of human immunodeficiency virus (HIV), which inserts its genetic material into host DNA. When testing the mutated enzyme (Tre recombinase) on cultured human tissue, it snipped HIV DNA out of chromosomes. Scientists suggest that treatment with similar enzymes could potentially remove infected cells of the virus.

(This picture shows the modified a bacterial enzyme, which is shown as red scissors, that will remove HIV DNA, gray double helix, from infected cells)

First off, why is HIV harmful? Well the articles states that HIV infects the immune system's disease-killing T cells; it does this by converting its genome into double-stranded DNA and using the enzyme integrase to embed that DNA into a T cell's genome. Scientists have adapted bacterial DNA-cutting enzymes for adding and subtracting genes from mice and other multicelled organisms. From this creation, they speculate that they could reverse the process of HIV.

Article:

Designer Enzyme Cuts HIV Out of Infected Cells

Protein Diseases: Cataracts!

This article basically talks about what type of diseases can occur if proteins are folded defectively or if the cell’s quality control apparatus fails. In order for proteins to properly function, all of its necessary components must be correctly compartmentalized. This article also presents ways for therapeutic intervention.

One type of disease that can occur from conformational errors is cataracts. Conformational diseases are disorders in which the structure of the fundamental protein mutates, leading to the aggregation and deposition of abnormal proteins. Cataracts is when there is clouding in the lens of your eye.

The major structural protein in the lens is crystallins, which form complex protein-protein interactions with each other. There are several types of crystallins, such as α-Crystallins, which act as molecular chaperones to prevent the aggregation and precipitation of the crystallins. β-Crystallins contain aggregates that range in size from dimers to octomers. A major lens protein is αB-Crystallin because it has a structural role in maintaining the transparency of the lens and confers protection to cells against thermal, osmotic, and oxidative damages.

αB-Crystallin's non-lenticular function is to bind irreversibly to denaturing proteins, thus preventing the formation of large light-scattering aggregates. This function is significantly important in the lens because it prevents cataracts from occurring. Proteins are prone to denaturation and aggregation and are subjected to osmotic and oxidative stresses over the lifetime of the organism.

Article:

Beyond the signal sequence: protein routing in health and disease.

What is Tay-Sachs disease???

(The image above shows two neurons; one is a healthy neuron and the other a neuron affected by TSD. In the healthy neuron (top) lysosomes act as the waste processing center of the cell. In Tay-Sachs disease, genetic deficiencies hamper with lysosome enzymes that break down fatty cell products, which build up and destroy the cell.)

You might be asking yourself what exactly is Tay-Sachs disease? Well Tay-Sachs disease (TSD) is a fatal genetic (runs through the family) lipid storage disorder in which harmful quantities of a fatty substance called ganglioside GM2 build up in tissues and nerve cells in the brain. This condition is caused by the absence of a vital enzyme, beta-hexosaminidase A.

Tay-Sachs disease occurs in infants and progressively damages the central nervous system as they age. A baby with TSD appears to develop normally for the first few months, but then there is a relentless deterioration of mental and physical abilities. The child gradually becomes blind, is unable to swallow, and has inefficient pulmonary function. Unfortunately, there is no cure or treatment for TSD and the average life expectancy is 3-5 years of age.

This condition is particularly high among people from Eastern European and Jewish descent. Patients and carriers of TSD can be identified by a receiving a blood test to measure beta-hexosaminidase A activity. In order to have an affected child, both parents must carry the mutated gene. In such instances, there is a 25% chance with each pregnancy that the child will be affected with Tay-Sachs disease.

Chapter 3: The Chemical Basis of Life II

I. Summary:

In this blog post I will only be discussing proteins and nucleic acids. But don't fret! I will explain the structure of protein, nucleotides, and the difference between DNA and RNA.

First off....what is a protein? Well proteins are polymers that are found in ALL cells and play crucial roles in most processes of life. Proteins have various functions throughout the body. However, the function of a certain protein is determined by its structure. Some of these proteins include (not all are listed below):

• Antibodies: involved in defending the body from antigens (foreign invaders); destroy antigens by immobilizing them so that they can be destroyed by white blood cells
• Enzymes: speed up biochemical reactions (often referred to as catalysts)
• Structural: fibrous, stringy proteins that provide support
• Hormones: messenger proteins which help to coordinate certain bodily activities by sending signals between cells
• Storage: store amino acids

The structure of proteins is viewed through four levels: primary, secondary, tertiary, quaternary. These levels basically break down the folding of a protein into a 3-Dimensional structure. The protein structures are very important because they DETERMINE the FUNCTION of the protein!

• Primary Structure is referred to as the sequence of amino acids. Proteins are large polypeptides of defined amino acid sequence. The sequence of amino acids in each protein is determined by the gene that encodes it. The gene is transcribed into a messenger RNA (mRNA) and the mRNA is translated into a protein by the ribosome.
• Secondary Structure is a local regularly occuring structure that is mainly formed through hydrogen bonds between backbone atoms. There are two types of basic secondary structures: alpha helix and beta-pleated sheets. Alpha helix and beta-pleated sheets determine the protein's characteristics and are preferably located at the core of the protein.
• Tertiary Structure is the 3-D shape of a single polypeptide. It includes all secondary structures and any interactions involving amino acid side chains. For single polypeptide chains, this is the final level of structure.
• Quaternary Structure involves the association of two or more polypeptide chains into a multi-subunit structure. These types of proteins are called multimeric proteins, while individual polypeptides are called protein subunits.

Nucleic acids are biological molecules essential for life because they are responsible for the storage, expression, and transmission of genetic information. Nucleic acids are broken down into two classes: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA molecules store genetic information coded in the sequence of their monomer building blocks. Molecules of RNA are involved in decoding the info from DNA. They decode this information into instructions for linking together a specific sequence of amino acids to form a polypeptide chain.

Both DNA and RNA are polymers that consist of linear sequences of repeating monomers. A single monomer is a nucleotide, and is made up of a phosphate group, five-carbon sugar (ribose or deoxyribose), and a single/double ring of carbon and nitrogen atoms (known as a base).

DNA forms a double helix, consisting of two strands of nucleotides coiled around each other. The nucleotides in DNA have deoxyribose and are presented in four different ways. It is composed of the purine bases, adenine (A) and guanine (G), and the pyrimidine bases, cytosine (C) and thymine (T). The purine bases have double rings of carbon and nitrogen, while the pyridine bases have a single ring.

RNA differs slightly from DNA because it has a single strand of nucleotide rather than a double. Unlike DNA the sugar in RNA has ribose and the pyrimidine base of thymine is replaced. In RNA this base is the pyrimidine base of uracil (U); the other bases remain the same in both nucleic acids. There are different forms of RNA, including messenger RNA (mRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). But these types of RNA shall be discussed in a later chapter (so you will just have to wait and see what they really are)!

II. Useful Materials:

This video is a song about functional groups. It differentiates between the different types of functional groups. I think the song is super catchy and fun, meaning you should listen too it! Trust me, you will not regret it!

In my previous blog post, I posted a video from this guy, who explained the chemical basis of life. Well now I found another video from the same person. In this video he is basically giving a brief overview of chapter three. He talks about isomers, functional groups, proteins, and a lot more! I enjoy watching his videos because they are very useful and also helps me study as well.

III. Article: Surgical Approach to l-Dopa-Induced Dyskinesias

This article from Pubmed talks about how to treat dyskinesias, which is caused from levodopa. Levodopa (L-Dopa) is an amino acid that is the metabolic precursor of dopamine, and is converted in the brain to dopamine to treat Parkinson's disease. A side effect of L-Dopa is dyskinesia (the inability to control muscles). Dyskinesia can occur in several forms; most often uncontrolled flailing of the arms and legs or chorea, rapid motions that can affect the limbs, face, tongue, mouth, and neck. Anyways, this article basically explains the common surgical targets used to treat LID and the appropriate selection of patients with LID for surgery.

Thalidomide Causing Birth Defects!

In 1961 a drug called thalidomide was discontinued for several reasons. Thalidomide was a drug prescribed for pregnant women who had morning sickness. It was discovered that this drug causing severe deformities in developing fetuses. About 10,000 children, worldwide were affected from thalidomide!

This article is basically about the reasons why thalidomide caused those

problems for the fetus. The primary cause for thalidomide's effect to cause fetal malformations is due to a protein called cereblon. Researchers from the Tokyo Institute of Technology proved this reason by using zebra fish and chick embryos. They presented that thalidomide binds to cereblon, causing pectoral fin mutations in the zebra fish and complete absence of forelimbs in the chicks. The researchers concluded that thalidomide exerts these effects by inhibiting cereblon function, because overproduction of cereblon prevented the malformations. However, the normal function of cereblon is still unknown.

(The picture above is the chemical structure of thalidomide: 2-(2,6-Dioxo-3-piperidinyl)-

1H-isoindole-1,3(2H)-dione)

Article:

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