Biochemistry

Short Answer Quest                                                  

1.      A 25 year old woman complains of severe pain in abdomen, photosensitivity, constipation, abnormal behavior and seizures. On examination Faster heart rate and higher blood pressure. Biochemical investigations showed high porphobilinogen (PBG).

     a.       What is the probable diagnosis?

    b.      Why did the patient have these symptoms?

    c.       What are the biochemical investigations required?

2.      Explain why von-gierke’s disease presents with hyperuricemia.

3.      What is lactic acidosis? Write a note on Cori’s Cycle.

4.      A 36 Years old woman was brought to emergency room complaining of dizziness. She had missed her dinner and breakfast. She had also started following a rigorous exercise regime to lose weight.  Plasma glucose = 43 mg/dL.

      a.       Give the probable Diagnosis

      b.      What measures must be taken for managing the condition?

     c.       Mention two other causes for the above condition?

    d.      What is the normal fasting plasma glucose concentration?

   e.       What advice should be given to the patient?

5.      TCA is an amphibolic pathway. Giving examples defend how this statement is true.                         

6.      Diet prescription for Diabetes mellitus and Atherosclerosis.                                                                      

7.      Describe the products of HMP shunt pathways and its significance.   

8.      Mucopolysachharides

9.      Dietary fibers and their clinical significance

 Long Answer Question (LAQ)                                                    

1.     Discuss the synthesis and breakdown of glycogen. Write a note on its regulation. Add a note on glycogen storage disorders

2.     Discuss how blood glucose is regulated.

4. Describe the process of gluconeogenesis      

Long Questions

1. Define mucopolysaccharides and discuss their role as structural elements in the human body with examples.
2. Define and classify carbohydrate with examples of each and their clinical/biological significance.

Short Answer Questions

1. Discuss properties and biological significance of disaccharides, with examples.
2. Define and discuss the importance of glycemic index giving examples of foods with high and low glycemic index.

Cell, in biology, the basic membrane-bound unit that contains the fundamental molecules of life and of which all living things are composed. A single cell is often a complete organism in itself, such as a bacterium or yeast. Other cells acquire specialized functions as they mature. These cells cooperate with other specialized cells and become the building blocks of large multicellular organisms, such as humans and other animals. Although cells are much larger than atoms, they are still very small. The smallest known cells are a group of tiny bacteria called mycoplasmas; some of these single-celled organisms are spheres as small as 0.2 μm in diameter (1μm = about 0.000039 inch), with a total mass of 10⁻¹⁴ gram—equal to that of 8,000,000,000 hydrogen atoms. Cells of humans typically have a mass 400,000 times larger than the mass of a single mycoplasma bacterium, but even human cells are only about 20 μm across. It would require a sheet of about 10,000 human cells to cover the head of a pin, and each human organism is composed of more than 30,000,000,000,000 cells.

Chemistry of Biomolecules focuses on the chemistry underpinning the biological roles of proteins, carbohydrates, nucleic and lipids. You will learn about the link between structure and function of these molecules at a chemical level within a biological context. Overview lectures will bring together this knowledge and apply it to key chemical process relevant to life: respiration, disorders treatment and signalling.

Carbohydrates are chemically defined as polyhydroxy aldehydes or ketones or compounds which produce them on hydrolysis. In layman’s terms, we acknowledge carbohydrates as sugars or substances that taste sweet. They are collectively called as saccharides (Greek: sakcharon = sugar). Depending on the number of constituting sugar units obtained upon hydrolysis, they are classified as monosaccharides (1 unit), oligosaccharides (2-10 units) and polysaccharides (more than 10 units). They have multiple functions’ viz. they’re the most abundant dietary source of energy; they are structurally very important for many living organisms as they form a major structural component, e.g. cellulose is an important structural fibre for plants.

Lipids are organic substances that are insoluble in water, soluble in organic solvents, are related to fatty acids and are utilized by the living cell. They include fats, waxes, sterols, fat-soluble vitamins, mono-, di- or triglycerides, phospholipids, etc. Unlike carbohydrates, proteins, and nucleic acids, lipids are not polymeric molecules. Lipids play a great role in the cellular structure and are the chief source of energy.

Proteins are another class of indispensable biomolecules, which make up around 50per cent of the cellular dry weight. Proteins are polymers of amino acids arranged in the form of polypeptide chains. The structure of proteins is classified as primary, secondary, tertiary and quaternary in some cases. These structures are based on the level of complexity of the folding of a polypeptide chain. Proteins play both structural and dynamic roles. Myosin is the protein that allows movement by contraction of muscles. Most enzymes are proteinaceous in nature.

Nucleic acids refer to the genetic material found in the cell that carries all the hereditary information from parents to progeny. There are two types of nucleic acids namely, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The main function of nucleic acid is the transfer of genetic information and synthesis of proteins by processes known as translation and transcription. The monomeric unit of nucleic acids is known as nucleotide and is composed of a nitrogenous base, pentose sugar, and phosphate. The nucleotides are linked by a 3’ and 5’ phosphodiester bond. The nitrogen base attached to the pentose sugar makes the nucleotide distinct. There are 4 major nitrogenous bases found in DNA: adenine, guanine, cytosine, and thymine. In RNA, thymine is replaced by uracil. The DNA structure is described as a double-helix or double-helical structure which is formed by hydrogen bonding between the bases of two antiparallel polynucleotide chains. Overall, the DNA structure looks similar to a twisted ladder.

The biological processes that occur within all living organisms are chemical reactions, and most are regulated by enzymes. Without enzymes, many of these reactions would not take place at a perceptible rate. Enzymes catalyze all aspects of cell metabolism. This includes the digestion of food, in which large nutrient molecules (such as proteins, carbohydrates, and fats) are broken down into smaller molecules; the conservation and transformation of chemical energy; and the construction of cellular macromolecules from smaller precursors. Many inherited human diseases, such as albinism and phenylketonuria, result from a deficiency of a particular enzyme. Enzymes also have valuable industrial and medical applications. The fermenting of wine, leavening of bread, curdling of cheese, and brewing of beer have been practiced from earliest times, but not until the 19th century were these reactions understood to be the result of the catalytic activity of enzymes. Since then, enzymes have assumed an increasing importance in industrial processes that involve organic chemical reactions. The uses of enzymes in medicine include killing disease-causing microorganisms, promoting wound healing, and diagnosing certain diseases

Before we study the details of metabolism, we must review the structure and functions(Chemistry) of the four major classes of biomolecules.

If you could peek inside of any cell in your body, you’d find that it was a remarkable hub of activity, more like a busy open-air market than a quiet room. Whether you are awake or sleeping, running or watching TV, energy is being transformed inside your cells, changing forms as molecules undergo the connected chemical reactions that keep you alive and functional.

Overview of metabolism

Cells are constantly carrying out thousands of chemical reactions needed to keep the cell, and your body as a whole, alive and healthy. These chemical reactions are often linked together in chains, or pathways. All of the chemical reactions that take place inside of a cell are collectively called the cell’s metabolism.

To get a sense of the complexity of metabolism, let's take a look at the metabolic diagram below. To me, this mess of lines looks like a map of a very large subway system, or possibly a fancy circuit board. In fact, it's a diagram of the core metabolic pathways in a eukaryotic cell, such as the cells that make up the human body. Each line is a reaction, and each circle is a reactant or product.

    Image credit: "Metabolism diagram," by Zlir'a (public domain)

Abstract diagram representing core eukaryotic metabolic networks. The main point of the diagram is to indicate that metabolism is complex and highly interconnected, with many different pathways that feed into one another. In the metabolic web of the cell, some of the chemical reactions release energy and can happen spontaneously (without energy input). However, others need added energy in order to take place. Just as you must continually eat food to replace what your body uses, so cells need a continual inflow of energy to power their energy-requiring chemical reactions. In fact, the food you eat is the source of the energy used by your cells!

To make the idea of metabolism more concrete, let's look at two metabolic processes that are crucial to life on earth: those that build sugars, and those that break them down.

Anabolic and catabolic pathways

The processes of making and breaking down glucose molecules are both examples of metabolic pathways. A metabolic pathway is a series of connected chemical reactions that feed one another. The pathway takes in one or more starting molecules and, through a series of intermediates, converts them into products.

Metabolic pathways can be broadly divided into two categories based on their effects. Photosynthesis, which builds sugars out of smaller molecules, is a "building up," or anabolic, pathway. In contrast, cellular respiration breaks sugar down into smaller molecules and is a "breaking down," or catabolic, pathway.

Anabolic pathway: small molecules are assembled into larger ones. Energy is typically required.

Catabolic pathway: large molecules are broken down into small ones. Energy is typically released.

Image credit: OpenStax Biology.

Anabolic pathways build complex molecules from simpler ones and typically need an input of energy. Building glucose from carbon dioxide is one example. Other examples include the synthesis of proteins from amino acids, or of DNA strands from nucleic acid building blocks (nucleotides). These biosynthetic processes are critical to the life of the cell, take place constantly, and use energy carried by ATP and other short-term energy storage molecules.

Catabolic pathways involve the breakdown of complex molecules into simpler ones and typically release energy. Energy stored in the bonds of complex molecules, such as glucose and fats, is released in catabolic pathways. It's then harvested in forms that can power the work of the cell (for instance, through the synthesis of ATP).

One final but important note: the chemical reactions in metabolic pathways don’t take place automatically, without guidance. Instead, each reaction step in a pathway is facilitated, or catalyzed, by a protein called an enzyme. You can learn more about enzymes and how they control biochemical reactions in the enzymes topic.

Nutrition is a science of food and its relationship to health. Nutrition refers to nourishment that sustains life. The study of nutrient requirements and the diet providing these requirements is also known as ‘nutrition’.  It includes the uptake of food, liberation of energy, elimination of wastes and all the processes of synthesis essential for maintenance, growth and reproduction.. It is a relatively new science with roots in physiology and biochemistry and is interrelated to various other subjects like Medicine, Agriculture, Food science & technology, Biochemistry, Biological sciences, Economics, Psychology, etc.

‘Balanced diet’ is defined as that ‘diet providing adequate nutritional needs as well as extra allowance for stress from different foods belonging to different food groups in specific quantities and proportions’. Since all foods don’t have similar nutritional quality, the nutrients provided and thus the health depends on the choice & quantity of foods selected. For a healthy & active life, diets should be planned on sound nutritional principals. Optimum nutrition /adequate nutrition or good nutrition is a diet “that provides all dietary nutrients in respect of kind and amount, and in proper state of combination or balance, so that the organism may always meet the varied exogenous and endogenous stresses in life, whether in health or disease, with a minimal demand or strain on the body’s natural homeostatic mechanisms”. Thus while planning the diet, in addition to the calorific value, the quantity and quality of food(Vitamins & Minerals) is taken into consideration. The three proximate principles of food are Protein, Carbohydrate and Fat. The main energy food sources are carbohydrate and fats; whereas for growth and development protein food sources are required. Deficiency, excess or imbalance of nutrients results in malnutrition, which could be either under nutrition or overnutrition. Proper nutrition is required for prevention of illness as well as for treatment of the illness.

Vitamins

 Vitamins are organic compounds. Although they are required in small amounts, but are essential for many important functions of the body. They can not be synthesized by the body. Due to shortage of specific vitamins various deficiency diseases could occur. The vitamins were designated by letters A, B and so on before their structures were determined. Foods contain small quantities of these vitamins.

Minerals 

Minerals are required for many purposes like forming the frame and rigid structure of the body, as part of the body/cell fluids and for number of cellular and sub cellular physiological functions.

Homeostasis, any self-regulating process by which biological systems tend to maintain stability while adjusting to conditions that are optimal for survival. If homeostasis is successful, life continues; if unsuccessful, disaster or death ensues. The stability attained is actually a dynamic equilibrium, in which continuous change occurs yet relatively uniform conditions prevail.

Water is made up of 2 hydrogen atoms and 1 oxygen atom (Figure 3.1 “The Water Molecule”). A human body is made up of mostly water. An adult consists of about 37 to 42 liters of water, or about eighty pounds. Fortunately, humans have compartmentalized tissues; otherwise we might just look like a water balloon! Newborns are approximately 70 percent water. Adult males typically are composed of about 60 percent water and females are about 55 percent water. (This gender difference reflects the differences in body-fat content, since body fat is practically water-free.

Fluid and Electrolyte Balance

Although water makes up the largest percentage of body volume, it is not actually pure water but rather a mixture of cells, proteins, glucose, lipoproteins, electrolytes, and other substances. Electrolytes are substances that, when dissolved in water, dissociate into charged ions. Positively charged electrolytes are called cations and negatively charged electrolytes are called anions. For example, in water sodium chloride (the chemical name for table salt) dissociates into sodium cations (Na+) and chloride anions (Cl−). Solutes refers to all dissolved substances in a fluid, which may be charged, such as sodium (Na+), or uncharged, such as glucose. In the human body, water and solutes are distributed into two compartments: inside cells, called intracellular, and outside cells, called extracellular. The extracellular water compartment is subdivided into the spaces between cells also known as interstitial, blood plasma, and other bodily fluids such as the cerebrospinal fluid which surrounds and protects the brain and spinal cord (Figure 3.2 “Distribution of Body Water”). The composition of solutes differs between the fluid compartments. For instance, more protein is inside cells than outside and more chloride anions exist outside of cells than inside.

ACID–BASE BALANCE

Maintenance of acid–base balance is fundamental for the normal functioning of biological processes, mainly due to the pH dependence of enzyme function. This article reviews definitions of acid–base balance and describes normal physiology of acid–base metabolism in the extracellular fluid and blood. The individual roles of the kidney, liver, bone, and lungs in maintenance of acid–base balance are outlined in detail in both health and disease. The pathogenesis of common conditions (diabetes, renal failure, drug intoxication) affecting acid–base balance are assessed as well as potential treatment strategies. The impact of dietary intake on acid–base status is also discussed.

The field of molecular biology has a profound impact in medical science investigation. Major advances in molecular biology over the last four decades have stimulated research and progress in almost all the disciplines of life science. 

This driving force involves:

 (1) the development of more and more sophisticated experimental techniques in molecular biology with a broad, interdisciplinary applicability; 

(2) the ever-expanding flow of information of technical novelties and scientific discoveries across the scientific community; and 

(3) the development of specific software and continuously updated databases for, respectively, analyzing and storing data on genotypes, gene expression levels, cytogenetic profiles and other molecular features.

 This has changed the rationale and approach of scientific experimentations allowing revolutionizing discoveries not only in molecular biology but also in biochemistry, biophysics, biotechnology, cell biology, and genetics. One major example is the innovation in high-throughput biology, next generation sequencing and recombinant DNA technology, which made possible to unveil the high complexity of the genome and elucidate the precise mechanisms for the transmission of the genetic information. So, it is now proven that gene expression, DNA replication, DNA repair, and sister chromatid segregation are processes much more complicated than previously thought. 

This complexity includes, but is not limited to:

 (1) the existence of interconnected regulatory pathways involving also previously unexpected actors, such as non-coding RNAs;

 (2) the relevance of epigenetic mechanisms and post-transcriptional modifications;

 (3) the importance of the correct execution, timing, sequentiality and coordination of all cell cycle events; 

(4) the pleiotropic functions of players operating in these processes; and 

(5) the influence of the energetic metabolisms and environmental signals. Moreover, it has become evident that the deregulation of these molecular processes is associated with, and in certain circumstances is the direct cause of, a wide range of pathological conditions. Although this module is focused on life sciences, it is, however, necessary to mention the biomedical relevance of molecular biology-related investigations for drug discovery and the development of a more personalized medicine.

Given the rapidly changing and continuously evolving nature of the molecular biology field, we can anticipate that the revolutionary impact of molecular biology in medical sciences is only at the beginning and is far from being finished.

This chapter provide a comprehensive view of vital organs with respect to their location, their importance and functions in the body; their respective disorders, diseases and various function tests.it provides basic knowledge on various routine function tests like Liver Function tests, Kidney Function tests, Thyroid Function tests, Adrenalin Function tests, Pancreas Function tests and Gastric Function tests. A few metabolic disorders have also been touched upon. 

less important but must known topics of biochemistry

This space will be a training "trial and error" playground for all faculty members to practise what they learn via the training videos. Any mistakes are reversible, so one need not worry about going ahead and exploring the software via this course.