Happy new year, my friends! I hope you are having a great new year so far! With the new year, comes a new series on Biochemistry for Life! I am planning to start a series called: The enzyme of the month. Every month, I will write a blog describing various enzymes and their contribution to the normal functioning of a biological system. Just as an introduction blog, I will like to describe what enzymes are.
For starters, enzyme names end with the suffix “-ase.” For example, lipase, an enzyme that breaks down lipids (fats), DNA Polymerase, which has a major role in DNA replication, and topoisomerase, enzymes that bring about the winding and unwinding of the DNA. The enzymes mentioned here end with the suffix “ase.” Biologists are very serious about naming their beloved macromolecule. Why are these enzymes so important? The answer lies in the fact that enzymes are biological catalysts. Without these enzymes, carrying out the metabolic processes in the body would become difficult because of the high activation energy. Enzymes, thus, lower the activation energy of a particular chemical reaction. There are various methods that enzymes apply for lowering the activation energy. One of these methods is changing the conformation of the reactants. Because structure defines function in biology, a small conformational change in the reactants can help with initiating the chemical reaction. You must be wondering, why on Earth we require enzymes for lowering the activation energy in the biological systems? Without the ability to lower the activation energy, the chemical reactions in living organisms would be a problem. In biological systems, high activation energy can be unsuitable, especially, because the energy is in the form of heat. High temperature can lead to a change in structure, and as mentioned earlier, structure defines function in biology. A slight structural change can lead to damage to the function.
Let us now explore the structure of the enzyme. Enzymes are proteins which means their structure comprises amino acids. The site where the enzymes bind to their substrates (reactants) is referred to as an active site. These active sites are very particular about what substrates they bind to. Therefore, an enzyme has a specific role in a biological system. Two models describe the enzyme-substrate binding:
A. Lock and Key model: The enzyme and substrate binding is perfect. There is no conformational change observed in the enzyme for the substrate to bind to the active site.
B. Induced Fit model: The enzyme has to undergo a slight structural change for the substrate to bind to the active site1. (Please refer to the image below)
There are many natural factors that regulate the activity of the enzymes including pH, temperature, substrate saturation, and enzyme concentration. All the enzymes have a typical pH and temperature range where they optimally perform their tasks. If the enzyme experiences changes in the pH or temperature, the structure of the enzyme, and its function can be compromised. Moreover, if there are more substrates than the enzymes, the rate of the reactions lower than normal. The body, therefore, has a system that “communicates” the imbalance in the ratio between substrates and enzymes to the nucleus to induce gene expression. Cellular communication is a rather complex topic that is a discussion for the other day! These are natural factors that can affect the reaction rates carried out by the enzymes.
There can be competitive and noncompetitive inhibition that can affect the rate of the enzymes. Competitive inhibitors2 bind to the active site of the enzymes and “compete” with the substrates of the enzymes. The binding of the inhibitors can cause a conformational change in the active sites which has the ability to permanently block the enzyme activity. Whereas non-competitive substrates bind to the allosteric site 3 of the enzymes that temporarily blocks the enzyme activity. This allows for saving the energy of the cells when the enzyme activity is not needed.
On an ending note on this introductory blog, I would like to mention that I absolutely respect the value of enzymes. With this new year series, I hope to cultivate this respect for the enzymes within my readers. Please stay tuned for more enzyme-related blogs!
Footnotes:
1 Even though structure defines function in biology, this slight conformational change is needed for the enzymes to carry out their tasks.
2. An example of competitive inhibitors is cyanide which blocks the enzymes participating in cellular respiration. Hence, the cells cannot produce energy leading to dangerous consequences.
3. A binding site that is different than an active site on an enzyme. A substrate that induces or inhibits the enzyme activity binds to this site to regulate the activity of the enzyme.
Works Cited:
Enzymes - an overview | ScienceDirect Topics. (2011). Sciencedirect.com. https://www.sciencedirect.com/topics/neuroscience/enzymes
6.2D: Activation Energy. (2018, July 10). Biology LibreTexts. https://bio.libretexts.org/Bookshelves/Introductory_and_General_Biology/Book%3A_General_Biology_(Boundless)/6%3A_Metabolism/6.2%3A_Potential_Kinetic_Free_and_Activation_Energy/6.2D%3A_Activation_Energy
Enzyme of the month January edition - Alanine Aminotransferase (ALT)
The enzyme I would like to introduce you to in January is a liver enzyme called Alanine Aminotransferase. It is a very crucial enzyme in cellular respiration. The purpose of cellular respiration is to produce energy in the form of a chemical molecule known as ATP. Many biochemical pathways are involved in cellular respiration. Examples of animal cellular energy pathways include Glycolysis1 and Tricarboxylic Acid Cycle (TCA)2.
Cellular respiration is a very neat and detailed process that breaks down the food molecules we ingest. The chemical reaction for cellular respiration is:
C6 + H12 → 6 CO2 + 6 H2O
Where does the enzyme ALT fall into this complex process? ALT contributes towards the functioning of the TCA cycle. We will now discuss how ALT carries out its important function in cellular respiration.
A very important thing to remember is that the goal of cellular respiration is to create chemical energy to be utilized by the body. Cellular respiration produces intermediates of the molecule that ultimately produce ATP3. Specifically, the production of the chemical molecules NADH4, Hydrogen and GTP5 take place in the TCA cycle of cellular respiration. These molecules later engage in the synthesis of ATP when needed by the body. There is an intermediary process that follows glycolysis and takes place before the TCA cycle. In this process, the pyruvate molecule produced in glycolysis is converted to Acetyl-CoA. The complete oxidation of Acetyl-CoA7 in the TCA cycle leads to the production of NADH, H, and GTP.
It is now time to discuss where the enzyme ALT falls into cellular metabolism. ALT is involved in the metabolism of amino acids (proteins). Through this process, the protein sources are broken down for the body to convert them into forms of energy. ALT, specifically, converts the amino acid Alanine to Pyruvate. Then as discussed earlier, the pyruvate6 molecule is essential for producing the energy molecule, ATP.
As I mentioned earlier, ALT is a liver enzyme that participates in protein digestion. Because it is a liver enzyme, ALT is considered to be an indicator of liver health. ALT enzymes are stored in the liver itself. A very little amount of this enzyme is found in the other parts of the body like muscles, kidney, brain, and heart (Patrick, 2020). In a healthy body, ALT enzyme levels in the bloodstream are quite low. According to Medicine Net, the normal ALT level in units per liter of serum is 7 to 56 (Patrick, 2020). Therefore, liver disease can be evident if there is an abnormally high level of ALT in the bloodstream. However, high levels of ALT do not immediately suggest liver disease. There can be numerous factors that lead to elevated ALT levels. Hence, consulting with a doctor when the ALT levels are abnormally high is advised.
I hope this blog helps you understand the role of the enzyme ALT! Stay tuned for the enzyme of the month in February
2. Follows the process of glycolysis where the glucose molecules are oxidized to produce water and carbon dioxide which serve as waste products of the metabolic pathways
3. An adenosine molecule packed with three phosphate molecules that repel each other. When the phosphate molecules are released, a lot of energy is produced to be used by the body for various functions.
4. A coenzyme that helps in producing energy from the food molecules. Plays a crucial role in oxidation-reduction reactions of cellular metabolism by donating or accepting Hydrogen.
Alanine Aminotransferase - an overview | ScienceDirect Topics. (2017). Sciencedirect.com. https://www.sciencedirect.com/topics/pharmacology-toxicology-and-pharmaceutical-science/alanine-aminotransferase
A Glimpse at The function of NADH and FADH2 in Cellular Respiration. (2015, April 4). Biology Wise. https://biologywise.com/function-of-nadh-fadh2
BD Editors. (2017, January 27). Pyruvate. Biology Dictionary. https://biologydictionary.net/pyruvate/
5 Major Metabolic Pathways in Organisms| Microbiology. (2016, November 28). Biology Discussion. https://www.biologydiscussion.com/metabolism/microbial-metabolism/5-major-metabolic-pathways-in-organisms-microbiology/65509
Guanosine Triphosphate - an overview | ScienceDirect Topics. (2013). Sciencedirect.com. https://www.sciencedirect.com/topics/medicine-and-dentistry/guanosine-triphosphate
Knapp, S. (2020, December 6). Alanine Aminotransferase. Biology Dictionary. https://biologydictionary.net/alanine-aminotransferase/
Enzyme of the Month February edition - DNA Polymerase
We all know that little kids grow with time, we also know that a skin injury is healed when healthy skin is replaced. Do we know how little children grow up physically? Or do we know how new skin grows? The simple answer is that the cell replicates. In order to replicate, the genetic material needs to be copied. It is a complex process that involves various enzymes. The star of this process is the enzyme DNA polymerase. Before we dive into DNA polymerase, we will describe the process of DNA replication.
DNA replication in eukaryotes (eukaryotes are described as organisms with cells consisting of a nuclear envelope) begins with an origin of replication where the DNA strand is unwounded. Now the DNA replication has a peculiar fact, it can only be synthesized in one direction which is the 3’hydroxl end to the 5’ phosphate end of the DNA. This enables the DNA strands to form a bond with other DNA strands. DNA is very particular about this rule and that is why the enzymes are designed in a way that suits the fancy of the unbending attitude of DNA. Enzymes, therefore, produce an RNA primer that provides a 3’hydroxyl end to the growing template strand of the DNA. The template or the old strand is used to synthesize a new strand by adding new bases in a complementary manner. Adenine is paired with Thymine, Guanine is paired with Cytosine. After the genetic material is copied, the DNA molecule is wounded. This process is very similar in the prokaryotes; however, the DNA polymerase enzymes used are different.
DNA polymerase is divided into families of polymerase enzymes that carry out different functions. This blog focuses on A, B, and C families. The A family of the polymerase is involved with the repair and elongation of the DNA strands. Whereas the B family of the polymerase is important for checking base (Adenine is paired with Thymine and Guanine is paired with Cytosine) mismatch in the DNA strands. Finally, the C family is reserved for the bacterial DNA elongation. Blocking the function of the C family enzymes can produce an antibacterial effect as the DNA elongation is halted and the bacteria cannot grow anymore. Hence, preventing bacterial growth.
With the process of DNA replication discussed, we can now begin looking at the enzyme DNA polymerase and its magnificent role in this super important process. We will first focus on the types of DNA polymerase in the prokaryotes. DNA polymerase I belong to the A family of the polymerase enzyme. Like the other A-family enzymes, this type of polymerase helps in strand elongation of the bacterial DNA. This enzyme adds bases on the 3’OH end of the new strand. DNA polymerase II is useful for checking the base mismatch in the newly elongating strand. As this enzyme is involved in the base mismatch check, it belongs to family B of the polymerase enzymes. DNA polymerase III is a busy enzyme! It can add bases and can also check base mismatches! It is a part of the C family of enzymes.
Now we can move on with the DNA polymerases in the eukaryotes. The biologists are very particular with the naming process as you can tell. The DNA polymerases in the prokaryotes are identified with the Roman numerals whereas the eukaryotic DNA polymerases are identified with the Greek alphabets. The DNA Polymerase alpha initiates the DNA replication process by synthesizing an RNA primer. After the primer is synthesized, the DNA polymerase beta and epsilon, take over the show by synthesizing the lagging and the leading strand. As the DNA is anti-parallel (meaning the DNA is organized with one strand running from 5’ to 3’ end and the other 3’ to 5’ end), the template strand is elongated in a lagging and leading manner because of the fact that DNA bases are added in the 3’ end. Please refer to the image below)
Works Cited:
News-Medical. (2019, May). Eukaryotic DNA Polymerase Enzymes. News-Medical.net. https://www.news-medical.net/life-sciences/Eukaryotic-DNA-Polymerase-Enzymes.aspx
Knapp, S. (2020, May 24). DNA Polymerase. Biology Dictionary. https://biologydictionary.net/dna-polymerase/
Enzyme of the Month March edition - RuBisCo
I hope you enjoyed reading about DNA polymerase last month! This month we are discussing an essential enzyme also known as Rubisco. We have to respect this mighty enzyme which happens to be the most abundant enzyme on this planet. Without this plant enzyme, planet Earth would have no life. Hence, dedicating a blog to this ultra-important enzyme makes sense, right?
RuBisCo or Ribulose biphosphate carboxylase/oxygenase is found in the plants and is a major enzyme in the process of photosynthesis. We will first briefly go over the process of photosynthesis. Ideally, photosynthesis is the reverse pathway to cellular respiration (refer to the January edition of the blog to understand cellular respiration). Unlike cellular respiration which is a catabolic (breaking down the energy source) pathway, photosynthesis is an anabolic pathway (synthesizing an energy source) that synthesizes glucose from water and carbon dioxide. The reaction formula of photosynthesis is as follows:
6 CO2 + 6 H2O → C6 + H12
This chemical formula makes it appear that photosynthesis is a reverse reaction of cellular respiration reaction which is as follows: C6 + H12 → 6 CO2 + 6 H2O. But, this is biology; nothing that appears simple is simple. It is complicated. Nevertheless, just for our basic understanding, we can assume that photosynthesis makes the sugar to store energy, and cellular respiration breaks down the sugar to release the energy. Photosynthesis occurs in 2 stages:
1. The light-dependent reaction that features light and chlorophyll1
2. The light-independent reaction that occurs with the help of the products formed in the light-dependent reaction
In this section of the blog, we will talk about the Light-dependent reaction. The chlorophyll pigment absorbs a certain wavelength of light (aka photon). This absorption of photon excites electrons in the reaction center that functions to convert light energy into chemical energy (please refer to January blog to read more about chemical energy in the form of ATP). The main purpose of this reaction is to produce ATP and NADPH2.
Now we move to the Light-independent reactions, also regarded as the Calvin Cycle, which is broken down into three stages: Carbon Fixation, Reduction, and Regeneration. The products of the Light-dependent reactions are used in this process. The carbon atoms which are taken in from the atmosphere by the stomata of the leaves are fixed into three-carbon compounds called 3-phosphoglyceric acid (3-PGA). In the reduction phase, 3-PGA is reduced to a sugar molecule, glyceraldehyde-3 phosphate (G3P). This phase utilizes the NADPH and ATP produced in the Light-dependent reactions as the NADPH donates hydrogen atoms to reduce 3-GPA. After the glucose molecule in the form of G3P is produced, some molecules are transported out of the photosynthesis site to produce glucose while other glucose molecules are regenerated to make a 5-C RuBP compound which is required to carry out the Calvin Cycle again. Hence, this stage is referred to as the Regeneration step.
Where does the enzyme RuBisCo fall into this complex process? The role of RuBisCo is evident in the Carbon Fixation step of Calvin Cycle (Please refer to the image below). RuBisCo fixes the atmospheric CO2 molecule with a carbon acceptor molecule Ribulose-1, 5-biphosphate (RuBP). After this step, the reactive 6-carbon compound is broken down into PGA. This whole reaction is catalyzed by RuBisCo. Without this reaction, photosynthesis would have been impossible. That is why this enzyme is crucial for the existence of life on Earth. As through this enzyme, plants produce food that powers life on Earth! So I am not lying when I say that respect this enzyme!
Footnotes:
1. A pigment found in the leaves of the leaves that produces a green color and absorbs a certain wavelength of light to initiate photosynthesis.
2. Similar to NADH, however, NADPH is found in the anabolic pathways that donate Hydrogens to other molecules and therefore acts as a reducing agent, unlike NADH which is an oxidizing agent.
Works Cited:
Aparna Vidyasagar. (2018, October 15). What Is Photosynthesis? Livescience.com; Live Science. https://www.livescience.com/51720-photosynthesis.html
BD Editors. (2016, November 10). Calvin Cycle. Biology Dictionary. https://biologydictionary.net/calvin-cycle/
BD Editors. (2017, February 14). NADPH. Biology Dictionary. https://biologydictionary.net/nadph/
Cellular respiration | Process & Products | Britannica. (2021). In Encyclopædia Britannica. https://www.britannica.com/science/cellular-respiration
RuBisCO - an overview | ScienceDirect Topics. (2017). Sciencedirect.com. https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/rubisco
Enzyme of the month April edition - Ribonuclease
Thank you so much for joining me in my one more blog about enzymes! This month we are going to explore Ribonuclease. In my February edition of this series, I briefly mentioned DNA replication. DNA replication is a part of the process of protein production. After DNA replication, the cell engages in a process known as Transcription where the DNA is converted to RNA. The RNA is then transported out of the nucleus of the cell to be synthesized into proteins. This process is commonly referred to as Translation.
Cells produce messenger RNA which acts as a messenger that transports the genetic information
to the cytoplasm of the cell. Now cells do not produce protein continuously. I mean cells are busy creatures. They would not waste their time and energy on something they do not have to do continuously. That is why it becomes crucial for the cells to regulate the mRNA levels in the cells. There are numerous regulatory mechanisms that are employed by the cells to ensure that the cells
are not overly producing proteins. One of the most important mechanisms is mRNA modifications and degradation. When the DNA is transcribed into mRNA, the mRNA is regarded as a pre-mRNA. This pre-mRNA has to undergo many modifications that make it into a proper genetic information carrier that can translate into proteins. A few of these modifications include an addition of a 5’cap and a 3’tail to protect the mRNA from degradation. Once the job of the mRNA is done, it is degraded by RNase or ribonuclease enzyme. There are many types of RNase, but the most common type used in laboratory research is RNase A. This enzyme cleaves a single-stranded RNA molecule from its 3’ end
to a 5’ end of the mRNA. Therefore, RNase are important enzymes that regulate
the gene expression in the cells.
Enzyme of the month May edition-Acetylcholinesterase
An important aspect of
muscle contraction is the generation of the action potential. How is this
action potential generated? The answer is the neurotransmitter Acetylcholine.
When this neurotransmitter binds to the receptor, the process of muscle contraction
begins. If you want to explore the complexity of the muscle contraction, please
refer to the image below:
As seen in the picture above,
for contraction to take place, the step of the ACh binding to the receptor is
super important. However, I am sure you do not want to keep running forever and
you do not want to digest food when you have not eaten in a while. So what
causes the muscle contraction to stop? This is where our enzyme of the month-
Acetylcholinesterase comes into the picture. As a typical enzyme, it catalyzes
the breakdown of the neurotransmitter into acetic acid and choline. And as
structure defines the function, the neurotransmitter cannot bind to the
receptor anymore and the contraction stops. This allows you to stop running
when you are tired.
Have you wondered what
might happen if this awesome enzyme stops working? The inhibitors of this
enzyme are referred to as organophosphates and are commonly used in
agricultural pesticides2.In
fact, many researchers have raised their concerns about over-exposure to the
organophosphates to humans through the food consumed. A common condition caused
by the organophosphates is muscle fasciculations or involuntary muscular
contractions2. Another condition that might result from
organophosphates is bradycardia (a condition associated with a slower heart
rate). Hence through the pathologies described above, we can really evaluate
the importance of our enzyme of the month.
I hope that this month’s
edition of the Enzyme of the Month series has helped you to really understand
the importance of enzymes. As always please remember to respect the amazing
complexities of biochemistry.
References:
1. Purves D, Augustine GJ, Fitzpatrick D, et al., editors.
Neuroscience. 2nd edition. Sunderland (MA): Sinauer Associates; 2001.
Acetylcholine. Available from: https://www.ncbi.nlm.nih.gov/books/NBK11143/
2. Trang A, Khandhar PB. Physiology, Acetylcholinesterase.
[Updated 2020 Jul 10]. In: StatPearls [Internet]. Treasure Island (FL):
StatPearls Publishing; 2021 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK539735/
Enzyme of the month June edition-Pepsin
I bet you have indulged in a favorite food item that contains lots of proteins. Do you know that your body needs proteins for basically everything? Proteins are so crucial for your body that there are special enzymes present to break down the food you eat to make protein. Now, isn’t that incredible? In this month’s edition of the Enzyme of the month series, we are going to discuss pepsin- a protein-digesting enzyme found in the stomach.
We require this amazing enzyme for absorbing
essential amino acids that is they are obtained only from our diet1. I am sure that most of you are aware that our stomach contains
hydrochloric acid that helps in the digestion of food. This acid also functions
to activate the inactive version of pepsin (pepsinogen) when we eat protein.
This is because a low pH environment produced by HCl activates the enzyme.
Synthesizing inactive pepsinogen prevents the digestion of the proteins
contained in the stomach lining. In other words, it is a “just-in-case” defense
mechanism.
So when we eat food containing protein, HCl is
secreted from the parietal cells located in the stomach lining which in turn
activates pepsinogen2. This allows for the pepsin to catalyze the
breaking of the peptide bonds in the consumed protein. The broken-down protein
is transported to regions where the body requires it for synthesizing hormones,
neurotransmitters, and other functions. Please refer to the image below for
learning how exactly pepsin works.
Image Citation link: https://healthjade.net/pepsin/
Now, we have to consider one more important
thing. As you have guessed, it is important for the body to ensure that pepsin
does not digest proteins that constitute the inner linings. Hence, a sphincter3 that acts as a gate between the stomach and the esophagus remains
closed when there is no food to be transported into the stomach. However, due
to various reasons, the opening of the sphincter becomes a chronic condition.
And when the activated enzymes get into the esophagus they can possibly begin
digesting the body’s inner linings. This is truly dangerous as it can lead to
the involuntary contraction of the vocal cords, destroy the laryngeal mucosa
and perhaps cause laryngeal cancer (1). This syndrome is known as
gastroesophageal reflux disease and also causes the symptoms of heartburn due
to the stomach acid entering the esophagus.
Nevertheless, we should appreciate pepsin as it
enables our bodies to gain an important macronutrient group, amino acids4. Without these enzymes, building muscles, inter-body communication
through hormones and neurotransmitters, and many other functions would have
been challenging. So take a moment and say thank you to pepsin! I hope you
liked this blog. Hoping to see you next month for a new enzyme! Bye!
Notes:
1. If you want the list of amino acids that our
bodies require from the diet please visit the website: https://www.ncbi.nlm.nih.gov/books/NBK557845/
2. Pepsinogen is secreted by the gastric chief
cells
3. Refer to the image above
4. Amino acids are monomers of proteins
Works Cited:
- “Pepsin | Description,
Production, & Function | Britannica.” Encyclopædia Britannica,
2021, www.britannica.com/science/pepsin.
Accessed 1 June 2021.
Introduction:
Our DNA is a tightly packed structure that is wrapped by the proteins known as “histones.” There are numerous reasons why the DNA is wounded by histones and the major reason is DNA regulation. This is where the study of epigenetics becomes relevant. Epigenetics refers to the ability of the genome to inherit phenotypic reversible changes. In other words, instead of changing the DNA sequence, how the sequence is read is altered. In this edition of the Enzyme of the month series, we are going to look at one of the epigenetics mechanisms that deal with the access of the transcription factors1 to DNA.
Histone and DNA Structure:
As mentioned earlier, DNA is wrapped tightly around the histone proteins to prevent transcription factors to access it. Hence, any unnecessary gene expression and cell division is prevented. Please refer to the image below to understand the structure of the DNA and histones.
Process of histone acetylation and deacetylation:
The acetylation (addition of the acetyl group2 ) of histones allows the transcription factors to access the DNA as the compact structure is unwounded. This happens only when the body signals the need for gene expression. There are robust communication pathways that allow for the acetylation of histones. When the body no longer needs the gene to be transcribed, the histones are deacetylated. Meaning the acetyl group is removed from the histones by the Histone Deacetylase enzyme.
Histone Deacetylase (HDACs):
The role of an enzyme is to catalyze the breaking down process. Similarly, HDACs catalyze the removal of acetyl groups from the histone. The important theme of this series is that structure defines function in biology. Hence, HDACs bind to the particular structure of the histone to carry out the process of deacetylation. We will look at the general mechanism of how HDACs work and carry out their function. To explore the processes of histone acetylation and deacetylation, we need to understand that DNA is a negatively charged molecule and histone is a positively charged protein. As the charge model of physics explains to us that opposite charges attract, histone and DNA stay tightly wound due to the charge interactions. However, when the acetyl group is added to the histones, the positive charge of the histone is neutralized and hence the charge interaction reduces. This allows gene expression to occur. However, when the body signals the halt of gene expression, HDACs removes the acetyl group and restricts the access of transcription factor (1).
Cancer and HDACs:
Current research suggests that anomalous patterns of HDACs are seen in certain cancers. Cancer is the uncontrolled growth of cells in a certain region of the body. In our body, there are many mechanisms that regulate cell division. One such mechanism is the gene p21 that is a widely recognized tumor-suppressor protein as it functions in the regulation of cell division. However, certain cancers show the hyperactivity of HDACs in the p21 gene. This means that the transcription factors are unable to access this tumor-suppressor gene. Without the expression of this gene, cell division is unregulated.
Conclusion:
HDAC enzyme is very important to our body as it regulates gene expression. Without this enzyme, there would be no check on gene expression. However, certain anomalies associated with this enzyme are observed in cancer. Hence, research related to this enzyme and its relevance to cancer treatment is crucial.
Works Cited
Histone Deacetylase - an overview | ScienceDirect Topics. (2014). Sciencedirect.com. https://www.sciencedirect.com/topics/neuroscience/histone-deacetylase
Parbin, S., Kar, S., Shilpi, A., Sengupta, D., Deb, M., Rath, S. K., & Patra, S. K. (2013). Histone Deacetylases. Journal of Histochemistry & Cytochemistry, 62(1), 11–33. https://doi.org/10.1369/0022155413506582
Notes:
Transcription factors: Factors that aid the process of converting DNA to RNA. This process is known as “DNA Transcription”
Acetyl group: a chemical compound comprising of carbonyl and methyl group
Introduction:
The food we eat contains a lot of sugar. How do our bodies convert this ingested sugar into energy for everyday use? There is an extensive process known as “cellular respiration” dedicated to converting the consumed sugar to energy. And as always, there are multiple enzymes that are involved in this process. In this edition of enzyme of the month, we are going to explore lactase dehydrogenase that is involved in this process.
Lactate Dehydrogenase:
The enzyme that we are exploring this month is an intracellular enzyme (1) which means that it is found everywhere in our bodies. This enzyme functions in the synthesis of lactase and pyruvate. The conversion of pyruvate to lactase is a reversible process. And this conversion is a part of glycolysis. Glycolysis is a process that is a part of cellular respiration. Therefore to understand this enzyme, I will give a brief introduction to glycolysis.
In a one-sentence summary, glycolysis can be described as the conversion of glucose to form two molecules of pyruvate. When there is enough oxygen present in the cellular environment, the newly formed pyruvate is transported to mitochondria aka “powerhouse of the cell” for the further processes of cellular respiration. Nevertheless, when there is less oxygen present in the cells1, pyruvate is converted to lactate through the enzyme lactate dehydrogenase. In the instances where the body requires more energy rapidly and oxygen is less, only glycolysis is carried out. This type of respiration is referred to as anaerobic respiration. Although the full process of cellular respiration produces more ATP than glycolysis alone, glycolysis is faster.
Pathologies associated with lactate dehydrogenase:
There are numerous pathologies associated with this enzyme. A lower concentration of this enzyme is associated with a condition commonly known as fibromyalgia where the levels of pyruvate and lactate production are elevated as compared to healthy individuals and the ATP levels are decreased.
Another pathology associated with this enzyme is the Warburg effect observed in cancer. Cancer is the rapid proliferation of cells in the body. These cells rely on anaerobic respiration which occurs with the help of lactate dehydrogenase. Many observations have led to the fact that lactate dehydrogenase is overexpressed in cancers. Hence, this is a valuable piece of information that can help scientists in research related to cancer treatment.
Notes:
this is common in skeletal muscles cells because they demand more energy when performing activities like high-intensity exercise
Citation:
Lactate Dehydrogenase - an overview | ScienceDirect Topics. (2014). Sciencedirect.com. https://www.sciencedirect.com/topics/neuroscience/lactate-dehydrogenase
Melkonian, E. A., & Schury, M. P. (2020, October). Biochemistry, Anaerobic Glycolysis. Nih.gov; StatPearls Publishing. https://www.ncbi.nlm.nih.gov/books/NBK546695/
Mishra, D., & Banerjee, D. (2019). Lactate Dehydrogenases as Metabolic Links between Tumor and Stroma in the Tumor Microenvironment. Cancers, 11(6), 750. https://doi.org/10.3390/cancers11060750
Introduction:
There are four basic building blocks or monomers in biology and they are monosaccharides, nucleotides, fatty acids, and amino acids. However, many complex carbohydrates found in our food are available in a polysaccharide form. This simply means that our food contains a chain of monosaccharides known as polysaccharides. To digest these chains of sugar, we need our enzymes to break the bond that holds the sugar chain together. The special enzyme that has the duty to break the sugar chain is known as glycosidase.
Glycosidic linkage:
A glycosidic linkage (aka glycosidic bond) is a covalent bond formed between a carbohydrate and another carbohydrate. This type of bond is also found between a carbohydrate and a functional group1. A glycosidic bond is formed when a hydroxide from an alcohol molecule attacks the anomeric carbon2 of a sugar. This reaction regarded as the condensation reaction results in the formation of a water molecule. The reverse of this reaction breaks the glycosidic linkage by adding a water molecule to the bond. Breaking of the bond is referred to as hydrolysis. This reaction is carried out by the enzyme glycosidase.
Glycosidase:
The main task of this enzyme is to bind to substrate3 and catalyze the hydrolysis of glycosidic linkages. Through structural research of these enzymes, it has been discovered that by binding the substrate to its active site, glycosidase can cause conformational changes that allow for the catalysis of the reaction. When required, these enzymes can also form a glycosidic bond through the condensation reaction.
Therefore we can comment that glycosidases are important for carbohydrate digestion. Nevertheless, recent research articles have explored the role of glycosidases in plant cell wall structure and modeling. As described in this paper authored by Chandrashekar et. al, “Glycosidases with these substrate-hydrolyzing activities process the major cell wall polysaccharides, including glucan, xylan, arabinoxylan, galactan, and arabinan, during cell wall assembly and reorganization (2).”
Researching this enzyme is important as it can suggest possible ant-viral treatments like described in the paper penned by Cerqueira et. al, where glycosidic inhibitors can be utilized for preventing the development of the viral envelopes, a process crucial for infection development (1).
Conclusion:
As always, we should appreciate the amazing work pioneered by the research scientists who study this biochemical molecule. Enzymes are so essential that researching them can allow us to understand life in a better way.
Notes:
A functional group is a variable in a particular molecule that influences its characteristic behavior
A chiral center formed in a ring-structured sugar that was previously in a chain orientation
The reactant of an enzymatic reaction
Citation:
Cerqueira, N., Brs, N., Joo, M., & Alexandrino, P. (2012). Glycosidases – A Mechanistic Overview. Carbohydrates - Comprehensive Studies on Glycobiology and Glycotechnology. https://doi.org/10.5772/52019
Chandrasekar, B., Colby, T., Emran Khan Emon, A., Jiang, J., Hong, T. N., Villamor, J. G., Harzen, A., Overkleeft, H. S., & van der Hoorn, R. A. L. (2014). Broad-range Glycosidase Activity Profiling. Molecular & Cellular Proteomics, 13(10), 2787–2800. https://doi.org/10.1074/mcp.o114.041616
Introduction:
Our bodies are constantly engaged in intracellular communication for initiating an immune response, digesting food, synthesizing neurotransmitters, and various other tasks. For these intracellular communications to occur, it is important for the body to oxidize the consumed polyunsaturated fats to create oxygenated lipids. These oxygenated lipids prove to be useful for downstream reactions like intracellular communication. Lipoxygenase enzyme is involved in numerous oxygenation reactions occuring in our bodies. For instance, lipoxygenase is involved in off-flavor development observed in legumes (4). In general, this enzyme is responsible for major oxygenation reactions occurring within living organisms.
Oxidation reactions:
In chemistry, an oxidation reaction is defined as the addition of oxygen to a substance. These types of reactions are involved in the cellular respiration of living organisms. Typically, oxidation reactions are carried out with the help of enzymes like catalase and dehydrogenases (3). Oxidation reactions result in something known as “free-radicals” known for their bad effects on the human body. Hence, lipoxygenase malfunction has been associated with various pathologies.
Pathologies:
The “Oxidative LDL theory”, as mentioned in the article titled “The role of lipoxygenases in pathophysiology; new insights and future perspectives”, suggests that the oxidation of LDL or low-density lipids can result in the onset of atherosclerosis (2). The researchers have also pointed that this condition can be treated by the addition of anti-oxidants. The condition of atherosclerosis is worsened by the oxidation of polyunsaturated fats as they produce free radicals (ROS).
Conclusion:
Although this enzyme is involved in various pathologies, it is an important enzyme for fruit ripening and essential oxidation reactions (1). Research on this enzyme is crucial for understanding how to treat pathologies associated with it.
Citation:
Lipoxygenase - an overview | ScienceDirect Topics. (2013). Sciencedirect.com. https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/lipoxygenase
Mashima, R., & Okuyama, T. (2015). The role of lipoxygenases in pathophysiology; new insights and future perspectives. Redox Biology, 6, 297–310. https://doi.org/10.1016/j.redox.2015.08.006
Oxidation Reaction - an overview | ScienceDirect Topics. (2013). Sciencedirect.com. https://www.sciencedirect.com/topics/engineering/oxidation-reaction
Stephany, M., Bader-Mittermaier, S., Schweiggert-Weisz, U., & Carle, R. (2015). Lipoxygenase activity in different species of sweet lupin (Lupinus L.) seeds and flakes. Food Chemistry, 174, 400–406. https://doi.org/10.1016/j.foodchem.2014.11.029
Introduction:
During COVID, we all have heard the test referred to as “RT-PCR” or Reverse-Transcriptase- Polymerase Chain Reaction. In this edition of the enzyme of the month series, we are going to explore the enzyme known as Reverse Transcriptase. This enzyme is commonly found in retroviruses that synthesize DNA strands by reading the RNA template. Reverse transcriptase catalyzes the formation of DNA from RNA.
Transcription:
The process of transcription is responsible for the conversion of DNA strands to RNA. This is an important step while expressing genes as proteins are synthesized from RNA templates. Protein synthesis from RNA is regarded as translation.
Reverse transcriptase:
Reverse transcriptase catalyzes the formation of DNA from RNA, hence, the name of reverse transcriptase. This is a reverse of the transcription process of gene expression. When the viral genome enters the host, the retrovirus needs to inject its DNA for causing an infection. This is seen in HIV infections.
Reverse transcriptase applications:
In research, reverse transcriptase is an important tool to study gene expression. Through reverse transcription, complementary DNA(cDNA) can be synthesized when the reverse transcriptase binds to the DNA. later, the cDNA is amplified through a technique known as “Polymerase Chain Reaction.” Reverse transcriptase is also used to detect whether a subject has contracted COVID. Since the COVID virus is an RNA-based virus, reverse transcriptase can be utilized to first synthesize the DNA strand. If the virus is present in a patient, a PCR machine will detect the sequence through fluorescent dyes. If not, the lack of fluorescent dye will ensure that the person tests negative. Details about PCR will be published in the final blog of the series. Stay tuned!
Citation:
Home. (2021, February 21). Retrieved August 11, 2021, from Iaea.org website: https://www.iaea.org/newscenter/multimedia/videos/how-do-covid-19-tests-work-rt-pcr-explained
Reverse Transcriptase - an overview | ScienceDirect Topics. (2015). Sciencedirect.com. https://www.sciencedirect.com/topics/neuroscience/reverse-transcriptase
Reverse Transcriptase - an overview | ScienceDirect Topics. (2017). Sciencedirect.com. https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/reverse-transcriptase
Welcome to the final blog of the enzyme of the month series. I cannot believe that it is the end of 2021 already. I hope this series was informative and inspired you to appreciate these amazing biochemical molecules- enzymes. We all owe a lot to these enzymes as the daily functioning of life is possible through the jobs they execute. In this finale, we are going to explore the enzyme known as polymerase. In the November edition’s blog, we explored part 1 of the “RT-PCR” story. In this blog, we will complete the next part. Thank you so much for waiting and I promise to tell you the whole story now. As a recap, we learned that reverse transcriptase helps us to synthesize new DNA strands from RNA. Now how does polymerase helps the lab technicians decide whether a person is tested positive or negative for COVID?
Polymerase:
The basic function of the enzyme polymerase is to make long strands of polymer or nucleic acids (DNA and RNA). Hence the name, polymerase. This enzyme is essential for gene expression as it synthesizes a complementary strand based on the parent strand. Through the Watson-Crick base pairing rule, if the polymerase is synthesizing a DNA strand, A-T and G-C base pairing is observed. If it is an RNA strand, A-U and G-C base pairing occur. With these rules, the polymerase is able to synthesize polymer chains. Now how does it help in the COVID detection tests? With the help of Reverse Transcriptase, a cDNA strand is synthesized. Through polymerase, the cDNA strands are amplified. With numerous strands, the PCR machine can detect the COVID virus strains through fluorescent dyes. The PCR machine is complex scientific equipment that allows for the polymerase to create multiple strands by annealing and re-annealing the strands whenever required.
Conclusion:
Polymerase is an essential enzyme that allows for the gene expression is living organisms. Through these enzymes, cDNA strands can be synthesized for expressing a particular gene.
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