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3 December 20243 December 2024

Organic Chemistry: The Fascinating World of Functional Groups 🌿

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Organic chemistry is the key to understanding the molecular building blocks of life. Functional groups are the fundamental elements that organise this complex world. Ranging from carboxylic acids to alkanes, these groups determine the properties of organic compounds and determine the direction of chemical reactions. Carboxylic acids in particular play a critical role in vital processes such as esterification and acid-base reactions. Understanding functional groups is essential for understanding chemical reaction mechanisms and biochemical pathways.

Functional groups and the hierarchy between them provide guidance in understanding the basic rules of organic chemistry. This hierarchy is organised based on the chemical reactivity and priority of the groups. For example, carboxylic acids are ranked high because they have both high polarity and reactivity, while alkanes are generally simple hydrocarbons that are less chemically active. The order of these groups determines how compounds are named in the IUPAC nomenclature rules and is an important concept to learn for chemistry students.

This table categorises functional groups in detail for organic chemistry enthusiasts and provides information on their structures, nomenclature rules and example compounds. Organised under headings such as “Functional Group Class,” “Structure,” “Suffix-name,” “Prefix-name,” and “Example,” this table covers a wide range from carboxylic acid to alkane. For those who want to understand the properties and naming logic of functional groups, this table is both a visual and theoretical guide. You can examine this table to discover the cornerstones of organic chemistry and enrich your learning process!

Priority Order of Functional Groups

Functional Group Class	-suffix name	prefix- name	Example
Carboxylic acids	-oic acid / -carboxylic acid	carboxy-	hexanoic acid
Sulphonic acids	-sulphonic acid	sulpho-	benzenesulfonic acid
Carboxylic anhydrides	-oic anhydride / -carboxylic anhydride	-	ethanoic anhydride
Esters	-oate / -carboxylate	alkoxycarbonyl-	methyl ethanoate
Acid halides	-oyl halide	halocarbonyl-	ethanoyl chloride
Amides	-amide / -carboxamide	carbamoyl- / aminocarbonyl- / amido-	ethanamide
Nitriles	-nitrile / -carbonitrile	cyano-	butanenitrile
Aldehydes	-al / -carbaldehyde	formyl- / oxo-	4-bromo-pentanal
Ketones	-one	oxo-	acetone
Alcohols	-ol	hydroxy-	ethanol
Phenols (Benzenole)	-ol	hydroxy-	2-hydroxyphenol
Thiols	-thiol	mercatpo-	ethanthiol
Amines	-amine	amino-	methylamine
Alkenes	-ene	alkenyl-	2-pentene
Alkynes	-yne	alkynyl-	1-hexyne
Alkanes	-ane	alkyl-	octane

Subordinate Groups

Functional Group Class	-suffix name	prefix- name	Example
Ether	ether	alkoxy-	methoxyethane
Sulfides (Thioethers)	sulfide	alkylthio-	methylthio-methane
Halides	-	halo-	1-bromo-butane
Nitro	-	nitro-	nitropropane
Azides	-	azido-	azidopropane
Diazo	-	diazo-	diazomethane
Benzene	-benzene	phenyl-	ethylbenzene

Footnotes

Sub-functional groups do not have a set priority. The functional group at the top of the list (carboxylic acid) has the highest priority for nomenclature, while the functional group at the bottom of the list (alkane) has the lowest priority for nomenclature.
In organic chemistry, the symbol “R” is used as a general placeholder or abbreviation for any group to which a carbon or hydrogen atom is attached to the rest of the molecule.

18 October 202418 October 2024

Differences and Usage Areas of Wet and Dry System Biochemistry Analysers

Wet and dry system biochemistry analysers are different technological devices used in laboratories to perform various biochemical tests.

Wet and dry system biochemistry analysers have significant differences in terms of sample preparation, reaction environment and result accuracy.

Sample Preparation

Wet System Analysers: In wet system analysers, the biochemical reactions to be tested are provided with liquid reagents. Liquid reagents are mixed with the sample and the reaction takes place. Such analysers work especially with liquid samples such as blood sera, plasma and urine. For each individual analysis, the instrument automatically measures the amount of reagent required and combines it with the sample. This increases the reaction sensitivity required for detailed analyses.
Dry System Analysers: Dry system analysers do not use liquid reagents. Instead, the reagents are placed in solid or dried form on test strips or slides. In this system, the sample is applied directly to the surface containing the reagent and the reaction takes place there. As the reagents are in dry form, there is no mixing with the liquid, making the process faster and more practical.

Precision and Accuracy

Wet System Analysers: Generally offer higher precision and accuracy. The homogeneous mixing of liquid reagents with the sample ensures that measurements provide more detailed and reliable results. It is therefore preferred for tests that require more comprehensive and precise analyses.
Dry System Analysers: Can provide adequate accuracy in some biochemical tests, but are generally more limited than wet systems. The dry form of the reagents can make it difficult to achieve the desired accuracy, especially in some tests where high sensitivity is required. Nevertheless, it provides sufficient accuracy for some clinical applications and gives fast results.

Ease of Maintenance and Operation

Wet System Analysers: These systems require more maintenance. The use of liquid reagents can lead to problems such as clogging or reagent build-up inside the instrument over time. Therefore, regular cleaning and maintenance is important. In addition, wet systems are often more complex to install and operate.
Dry System Analysers: It is very easy to maintain and operate. Since liquid reagents are not used, there are no problems such as accumulation or clogging inside the device. This makes cleaning and maintenance of the instrument simpler. It is especially preferred in laboratories that are not busy or in environments that require practical use.

Areas of Use

Wet System Analysers: Generally preferred in large-scale hospitals, research laboratories and specialised clinics requiring extensive testing. It is ideal for critical biochemical measurements where high-precision results are required, for example in disease diagnosis and treatment. It is also used in complex analyses that require multiple combinations of reagents and assays.
Dry System Analysers: It is widely preferred especially in outpatient clinics, emergency situations, field work or small laboratories when practical and fast results are required. Due to their easy portability and low maintenance requirements, these analysers are also frequently used in areas where rapid diagnosis is required in emergency situations.

Speed and Cost

Wet System Analysers: They are generally more expensive devices and maintenance costs are high. However, the wide range of tests they offer and their high accuracy is the reason why many laboratories prefer this system. Also, the processing time can be longer because the liquid reagents for each test need to be prepared, added and the reaction completed.
Dry System Analysers: Provides lower cost and fast results. It is especially preferred when performing low-cost tests. Since the cost per test is lower, it is advantageous to use in routine analyses in hospitals or in emergency situations requiring rapid diagnosis.

These differences are of great importance for the selection and use of biochemistry analysers. Considering factors such as the analysis sensitivity, test volume and budget required by laboratories, the choice of wet or dry system analyser is decided.

9 October 20249 October 2024

2024 Nobel Prize in Chemistry: Major Breakthroughs in Protein Design and Artificial Intelligence

The 2024 Nobel Prize in Chemistry has been awarded to three scientists who have made revolutionary discoveries in understanding the structure of proteins, the building blocks of life. David Baker, Demis Hassabis and John Jumper won this prestigious prize for their work to design and predict the structure of proteins.

The Power of Protein Design: David Baker
US scientist David Baker has taken groundbreaking steps in the field of biotechnology with his new protein designs. The methods developed by Baker enable the design of special proteins in the field of medicine and bioengineering, enabling the development of new drugs, vaccines and nanomaterials.

Artificial Intelligence Predicting Protein Structure: AlphaFold
Demis Hassabis and John Jumper from Google DeepMind have developed an artificial intelligence model called AlphaFold that answers a problem that has been waiting to be solved for 50 years: predicting the three-dimensional structure of proteins from their amino acid sequences. This system enabled scientists to accurately model the structure of millions of proteins, ushering in a new era in biological research.

Conclusion: Innovations Leading Science
The work of Baker, Hassabis and Jumper not only offers unique opportunities for protein science and biotechnology, but will also play an important role in combating disease in the future. These discoveries show how far humanity can go in unravelling the complex secrets of biology.

Source: Nobel Prize

7 October 20247 October 2024

2024 Nobel Prize in Medicine: A Milestone in Genetic Research with the Discovery of microRNA

The 2024 Nobel Prize in Physiology or Medicine has been awarded to Victor Ambros and Gary Ruvkun for their groundbreaking discovery of microRNA and its regulatory role in gene expression.

This small RNA molecule controls various cellular functions by modulating gene expression, marking a major advance in our understanding of genetic regulation.

Ambros and Ruvkun’s findings have opened new avenues in genetic and medical research, shedding light on the molecular mechanisms behind diseases such as cancer, neurological disorders, and metabolic conditions. The discovery of microRNA offers significant potential for developing new therapies, allowing for more targeted treatments by influencing gene expression pathways.

Recognized by the Nobel Committee as a “revolutionary breakthrough” in gene expression, this discovery has profoundly impacted biomedical sciences, providing critical insights into cellular processes and enhancing genetic research.

Source: The Nobel Prize

2 October 20242 October 2024

Promising Developments for Cats in the Fight Against FIP

Feline Infectious Peritonitis (FIP) has been known for years as a fatal disease for cats. However, thanks to new treatments with antiviral drugs such as GS-441524 and remdesivir, this disease can now be managed more effectively.

Feline Infectious Peritonitis (FIP) is caused by mutation of the enteric coronavirus (FCoV), which is common in cats. FCoV causes mild intestinal infections in most cats, but in some cases the virus can mutate into FIP virus, which attacks immune system cells

FIP is caused by a coronavirus that attacks the immune system of cats and is particularly common in kittens. Research in 2019 has shown that these antiviral drugs have great success in treating various forms of FIP (wet, dry, neurological, eye).

Laboratory findings play a very important role in the diagnosis of FIP (Feline Infectious Peritonitis).

In addition to clinical signs, the following laboratory tests can help diagnose FIP

Blood Tests: Cats with FIP usually have high globulin, low albumin, and increased protein levels. In addition, anaemia and increased white blood cells are common.
X-ray and Ultrasound: Used to detect fluid accumulation in the abdominal and chest cavities.
PCR Test: RNA of the coronavirus (CoV) can be detected.
Serology: Measures antibody levels to feline coronavirus (FCoV), but does not provide a definitive diagnosis on its own.

Clinical evaluation in combination with these findings is critical to confirm the diagnosis of FIP.

Treatment Options

Originally used by veterinarians in Australia and the UK, these treatments are now available in many countries. GS-441524 can be prescribed as a compound for special feline patients in accordance with FDA guidance issued in 2024.

Ball-and-stick model of a remdesivir molecule, FIP — Ball and stick model of Remdesivir molecule

GS-441524, FIP — Ball and stick model of Remdesivir molecule

Challenges and Future

The black market of uncontrolled and unlicensed FIP drugs has led cat owners to unsafe treatment options. Inconsistencies in dosage and poor quality control of these drugs pose serious risks and jeopardise the health of cats.

Diagnosing FIP is still challenging because there is no test that can accurately detect the disease. However, thanks to new treatment methods, veterinarians can now follow a clearer path in the treatment of FIP and prevent the disease with early diagnosis. It is of great importance to be careful against viral resistance and to avoid overtreatment.

The Power to Revolutionize Healing: The Power of Platelets in PRP Therapy

In the dynamic world of veterinary medicine, a remarkable treatment method stands out: platelet-rich plasma (PRP) therapy. Using the body’s own healing mechanisms, this innovative approach opens new doors in regenerative medicine for our animal friends.

What is PRP?

PRP therapy involves concentrating platelets from the patient’s blood. Platelets, small blood cells that play a role in clotting and are rich in growth factors, are isolated and concentrated and used to accelerate the healing of injured tissues such as tendons and ligaments.

The Effect of PRP: Healing Our Four-Legged Friends

Veterinarians are now using PRP therapy for a variety of conditions, especially on dogs and horses. Muscle tears, ligament strains, and even more complex conditions such as major wounds or burns are showing significant improvements with PRP. It is also noted for its effectiveness in treating eye conditions such as corneal ulcers.

Today, veterinary medicine effectively uses platelet-rich plasma (PRP) therapy in many areas such as skeletal-muscular system disorders (osteoarthritis, tendon and ligament injuries, muscle damage), wound healing, post-operative healing processes, dental and oral surgery interventions, and eye diseases. This method plays an important role in the development of modern veterinary medicine, contributing to the health of animals and accelerating their healing processes.

PRP, platelet zengin plazma, köpek

Adobe FireFly ile yaratılmıştır.

The Science of PRP

The secret behind the success of PRP lies in the high concentration of platelets. These platelets release growth factors that help tissue repair and reduce inflammation, attracting stem cells to the site of injury. This process activates the body’s natural healing mechanisms, leading to a faster and more effective recovery.

Recent advances in PRP therapy have expanded its applications. Veterinarians can now use it not only for musculoskeletal injuries, but also in new treatment areas such as laminitis, a painful hoof disease of horses, and even traumatic brain injuries.

The effectiveness of PRP therapy depends on several factors: the concentration of platelets, the method of activation, and their correct delivery to the site of injury. Veterinary scientists are constantly improving these parameters to maximize the therapeutic benefits of PRP.

A Bright Future Ahead

As we delve deeper into the potential of PRP therapy, it is clear that this technique has great promise in veterinary medicine. By harnessing the body’s innate healing power, PRP therapy is not just a treatment, it is a revolution in the way we care for our animal companions.

PRP therapy is an example of the extraordinary advances being made in veterinary medicine. As research develops, this therapy offers a beacon of hope for pet owners and their companions, poised to transform our approach to healing and recovery in animals.

Understanding Myocardial Metabolism: An Introductory Overview

Author: Doğa İsmailoğlu

Myocardial metabolism refers to the complex biochemical processes that occur within the heart muscle, or myocardium, to provide the energy needed for its continuous and vigorous contraction.

The heart has the highest metabolic demand of all our organs. Thus, myocardial metabolism is an area of interest for biochemists. The heart requires a sufficient supply of ATP to facilitate muscle contraction, sarcomere relaxation, and the active transport of ions across the cell membrane, as seen in processes like Na⁺/K⁺-ATPase. This demand for energy is contingent on the availability of oxygen. When an adequate supply of oxygen is present, glycolysis occurs aerobically, proceeding to the tricarboxylic acid (TCA) cycle and electron transport. In cases where oxygen is limited or absent, anaerobic glycolysis ensues, stopping at the pyruvate stage, which is then converted to lactate. This lactate is subsequently transported to the liver, where it is transformed into glucose through gluconeogenesis. In the cardiac muscle, the Cori cycle can become active in situations of heightened energy demand or stress, such as during exercise or in specific disease conditions.

Cori Cycle plays a vital role in mycocardial metabolism

The Cori cycle plays a vital role in upholding energy production and glucose balance within cardiac muscle and other tissues, particularly when energy demand surges or oxygen availability is limited. In cardiac muscle, the Cori cycle comprises the subsequent stages.

Glycolysis: Glucose undergoes glycolysis, which consists of a sequence of chemical reactions within the cytoplasm of cardiac muscle cells. This process yields pyruvate and a modest quantity of ATP.

Lactate generation: In specific scenarios, such as when oxygen is scarce or during periods of elevated energy requirements, pyruvate is transformed into lactate via anaerobic glycolysis. Subsequently, lactate is released into the bloodstream.

Lactate Uptake: Lactate generated within the cardiac muscle has the capacity to be absorbed by various tissues, including the liver, skeletal muscles, or even other cardiac muscle cells. In these tissues, it can serve as an energy source or be reconverted into glucose.

Glucose Regeneration: Within the tissues that receive lactate, such as the liver, there exists a process called gluconeogenesis, which can convert lactate back into glucose. This glucose is subsequently released into the bloodstream and taken up by cardiac muscle cells, where it is utilized as an energy source, effectively concluding the Cori cycle.

Cori cycle, metabolism — Cori Cyle (For more click and look into Carbohydrate Metabolism-III)

The heart’s energy requirements are also influenced by the availability of substrates beyond just oxygen. About 70% of the cardiac ATP is generated through the beta-oxidation of fatty acids, which serve as the primary energy source for an adult heart. These fatty acids originate from chylomicrons and result from the hydrolysis of triglycerides by lipoprotein lipase. Carbohydrates, on the other hand, serve as the energy source for the fetal heart and for an adult heart under stressful conditions, such as during ischemia.

In unusual situations like starvation, amino acids, and ketone bodies can also be utilized to produce ATP in metabolism. Apart from substrates, there is an additional requirement for nutrients to support ATP synthesis, which includes fat-soluble vitamins such as A, D, E, and K. These vitamins are present in chylomicrons and circulating lipoproteins and are released through the action of lipoprotein lipase. Vitamin D plays a crucial role in calcium absorption from the intestines. Coenzymes like TPP (thiamine), NAD (niacin), and FAD (riboflavin), as well as electrolytes such as calcium, sodium, potassium, and chloride, are essential for ATP production as well.

the three main substrates for ATP synthesis, metabolism — Figure 1. The three main substrates for ATP synthesis—lactate, ketone bodies, amino acids, or even acetate can be oxidized under certain circumstances.

Within a myocardial cell, myocardial metabolism, glucose from the bloodstream, and glycogen stored in the myocardium go through glycolysis with the assistance of the pyruvate kinase enzyme, leading to the production of pyruvate. During this process, substrate-level phosphorylation takes place, yielding a small quantity of ATP. This pyruvate is then transported into the mitochondria, where it is converted into acetyl-CoA by the pyruvate dehydrogenase enzyme complex. Additionally, acetyl-CoA can also be produced from ketone bodies, synthesized by the liver but not utilized, and the ketothiolase enzyme plays a role in this process.

metabolism, nutrients — Figure 2. The nutrients needed for ATP synthesis.

Fatty acids are activated into Acyl-CoA in the cytoplasm and are then transported to the mitochondria, where they are transformed into acetyl-CoA through beta-oxidation. This acetyl-CoA enters the TCA cycle, combining with oxaloacetate. Within the TCA cycle, substrate-level phosphorylation occurs once more, generating a small amount of ATP. Besides ATP production, the TCA cycle also produces NADH+H⁺ and FADH₂, which act as carriers of electrons. As these electrons move from one complex to another, protons enter the intramembranous space. These protons subsequently pass through ATP synthase, causing it to rotate at a high speed, which facilitates the combination of ADP and Pi to form ATP.

This newly formed ATP combines with creatine, a compound synthesized by the liver from three amino acids (glycine, arginine, and methionine). This combination results in the formation of creatine phosphate, which is synthesized in the cytoplasm of myocardial cells from creatine and ATP. Importantly, it can be rapidly converted back into ATP during periods of elevated energy demand, such as during myocardial contraction. The enzyme creatine kinase, found in the myocardium, catalyzes the transfer of a high-energy phosphate group from creatine phosphate to ADP, effectively regenerating ATP. This process offers a swift source of ATP to support myocardial contractile function during times of increased heart rate or heightened stress.

myocardial metobolism — Figure 3. A summary of myocardial metabolism pathways

Several animal species are known to be susceptible to cardiac diseases.

Dogs: Certain dog breeds, including Boxers, Doberman Pinschers, Great Danes, and Cavalier King Charles Spaniels, are predisposed to specific cardiac conditions like dilated cardiomyopathy (DCM) and mitral valve disease. DCM is characterized by the weakening and enlargement of the heart, making it less efficient at pumping blood, resulting in symptoms like fatigue, breathing difficulties, and fluid retention. Mitral valve disease involves a faulty closure of the valve between the left atrium and left ventricle, leading to blood leakage, which can cause heart chamber enlargement and symptoms such as coughing, breathing problems, and heart murmurs.

Cats: Hypertrophic cardiomyopathy (HCM) is a prevalent feline cardiac ailment, particularly affecting breeds like Maine Coon, Ragdoll, and Sphynx. HCM involves thickening of the heart’s walls, reducing its pumping efficiency, and resulting in symptoms like lethargy, breathing difficulties, and irregular heartbeats.

Horses: Horses can also suffer from cardiac diseases, including atrial fibrillation, valvular heart disease, and myocarditis. Atrial fibrillation refers to an abnormal heart rhythm affecting the atria.

Birds: Certain bird species, notably parrots and pigeons, can be vulnerable to cardiovascular diseases such as heart failure and atherosclerosis.

This article has been prepared from the presentation of our student, Doğa İsmailoğlu.

References

Heinrich Taegtmeyer (2012). Chapter 15 – Cardiomyocyte Metabolism: All Is in Flux, Editor(s): Joseph A. Hill, Eric N. Olson, Muscle, Academic Press, Pages 187-202, ISBN 9780123815101 https://doi.org/10.1016/B978-0-12-381510-1.00015-6.

Kodde IF, van der Stok J, Smolenski RT, de Jong JW (2007). Metabolic and genetic regulation of cardiac energy substrate preference. Comp Biochem Physiol A Mol Integr Physiol., 146(1):26-39. https://doi.org/10.1016/j.cbpa.2006.09.014

Kalp hastalıklarına Yatkın Irklar (2023). Veteriner Kardiyoloji. Available at:
http://kardiyoloji.veterinary.ankara.edu.tr/hangi-irk-hangi-kalp-hastaligina-yatkindir/
(Accessed: 27 October 2023).