eChapters

Introduction

Protein metabolism is a complex and multifaceted process that plays a crucial role in the overall health and function of living organisms. At the most fundamental level, protein metabolism involves the synthesis, breakdown, and utilization of proteins, which are essential macromolecules that serve a wide range of structural, functional, and regulatory roles within the body.

The process of protein synthesis, or translation, begins with the transcription of genetic information stored in DNA into messenger RNA (mRNA) molecules. These mRNA molecules then serve as templates for the assembly of specific sequences of amino acids into polypeptide chains, which ultimately fold into the three-dimensional structures of functional proteins. This highly regulated process is essential for the production of the diverse array of proteins required for cellular processes, tissue repair, immune function, and numerous other physiological activities. In contrast, protein degradation, or catabolism, refers to the breakdown of proteins into their constituent amino acids. This process is mediated by various proteolytic enzymes, such as endopeptidases, exopeptidases, and dipeptidases, which cleave the peptide bonds that hold the amino acid residues together Protein degradation serves important functions, such as the recycling of amino acids for energy production or the synthesis of new proteins, the removal of damaged or misfolded proteins, and the regulation of cellular signaling pathways.

Introduction

Carbohydrates, the aldehyde/ ketone derivatives of the higher polyhydric alcohols, or compounds that yield these derivatives on hydrolysis, constitute of mainly four groups viz. monosaccharides, disaccharides, oligosaccharides and polysaccharides. Energy comes mostly from carbohydrates, and products of their degradation are also used for the synthesis of other substances including fatty acids, cholesterol, amino acids etc They are also components of compound lipids, conjugated proteins, and some of their derivatives can even function as medications (e.g., cardiac glycosides, etc). Disorders such as glycogen storage disorders (GSDs) and galactosemia can be brought on by an inherited lack of certain enzymes in the metabolic pathways of various carbohydrates. Diabetes mellitus is characterized by disruption of the metabolism of glucose.

In ruminants, the end products of digestion are largely volatile fatty acids viz. acetic acid, propionic acid and butyric acid and some monosaccharides. As they pass through the ruminal epithelium, they undergo different degrees of metabolism. The fate of volatile fatty acids are as follows: Acetate as precursor to Acetyl CoA (TCA cycle; fat synthesis); Propionate as precursor to glucose (glycolysis; milk lactose) and Butyrate as precursor to Acetyl CoA (TCA cycle). All the digested and absorbed monosaccharides and volatile fatty acids enter into the liver, where two mechanisms operate such as withdrawal of carbohydrates from blood (e.g. glycogenesis; glycolysis etc) and release of glucose by liver to blood (e.g. glycogenolysis; gluconeogenesis etc). In case of monogastrics, the processes of digestion/ fermentation of carbohydrates especially occur in the small intestine. The fate of absorbed glucose and metabolic conversions in the animal body mainly comprise of storage as glycogen in liver and muscle (small amount); oxidation of glucose for providing energy (via Glycolysis pathway; other alternative pathways such as Hexose Monophosphate Pathway (HMP)/ HMP Shunt and Uronic acid pathway etc) and fat synthesis as well as storage in the form of fat in adipose tissue.

Introduction

Energy is the major source required to maintain the structure and function of all living cells. This energy is derived from oxidation of carbohydrates, lipids and proteins that is taken in the form of diet. The energy liberated from the process of oxidation is generally captured in the form of ATP, which is known as energy currency of the living cells. Each gram of carbohydrate and protein gives about 4 Kcal on oxidation, while each gram of fat gives about 9 Kcal. Oxidation means addition of oxygen or removal of hydrogen from a compound or removal of electron from an ion or atom increasing its positive charge. Reduction means removal of oxygen or addition of hydrogen to a compound or addition of electron to an ion or atom decreasing its positive charge. Commonly the oxidation reactions are conjugated with reduction reactions and known as redox reactions. Redox reactions are often associated with release of energy. The redox chain constitutes chain of different compounds of increasing redox potentials between hydrogen and oxygen. The living cells depend on redox reactions for their energy requirements. The reactions start by removal of H2 from the substrate, which is then transferred to different components of redox chain, then finally to oxygen to form water. Components of redox chains have a redox potential higher than hydrogen and lower than oxygen.

Introduction

All enzymes are proteins, except a tiny subset of catalytic RNA molecules. Most of the classical metabolic enzymes are named by adding the suffix -ase to the name of their substrates or to a descriptive term for the reactions they catalyze. For example, urease has urea as a substrate. Alcohol dehydrogenase catalyzes the removal of hydrogen from alcohols (i.e., the oxidation of alcohols). A committee of the International Union of Biochemistry and Molecular Biology (IUBMB maintains a classification scheme that categorizes enzymes according to the general class of organic chemical reaction that is catalyzed The six classes are Oxidoreductases, Transferases, Hydrolases, Lyases, Isomerases, and Ligases.

The integrity of their natural protein structure is necessary for their catalytic activity. Catalytic activity is typically lost when an enzyme denatures or dissociates into its constituent subunits. An enzyme’s catalytic activity is always eliminated when it is disassembled into its constituent amino acids. Thus, the catalytic activity of protein enzymes depends on their primary, secondary, tertiary, and quaternary structures. Aside from their amino acid residues, certain enzymes don’t need any other chemical groups to function. Others need a cofactor, which is an extra chemical element. Cofactors can be complex organic or metalloorganic molecules called coenzymes, or they can be one or more inorganic ions like Fe2+, Mg2+, Mn2+, or Zn2+.

Introduction

A pentose sugar, one or more phosphate groups, and a nitrogenous base (purine or pyrimidine) make up a nucleotide. Phosphodiester bonds, which connect the 5’-hydroxyl group of one pentose to the 3’-hydroxyl group of the next, bind nucleic acids together as polymers of nucleotides. RNA and DNA are the two different forms of nucleic acids. RNA nucleotides contain ribose, while uracil and cytosine are typical pyrimidine bases. Thymine and cytosine are common pyrimidine bases, and DNA contains 2’-deoxyribose in its nucleotides. In both RNA and DNA, adenine and guanine are the main purines. There is ample evidence to suggest that genetic information is encoded in DNA The Avery MacLeod-McCarty experiment, in particular, demonstrated how DNA obtained from one bacterial strain may infiltrate and change the cells of another strain, giving it some of the genes from the donor. The Hershey-Chase experiment demonstrated that a bacterial virus’s DNA contains the genetic instructions needed for the virus to replicate in a host cell, but not its protein coat. Watson and Crick proposed that native DNA is made up of two antiparallel chains arranged in a right-handed double helical configuration based on a compilation of numerous published data points. A-T and G-C, two complementary base pairs, are created by hydrogen bonds inside the helix. 10.5 base pairs are stacked per turn, perpendicular to the double helix’s long axis, at a distance of 3.4 Å. There are various structural configurations for DNA A- and Z-DNA are two variants of the Watson-Crick form or B-DNA The DNA molecule bends as a result of certain sequence-dependent structural differences.

Introduction

Proteins are complex biomolecules composed of amino acids, playing crucial roles in virtually all biological processes. They serve as enzymes, hormones, structural components, signaling molecules etc.

Structure/ Levels of Organization of Proteins

Generally, Proteins are polymers of L-alpha amino acids, linked by peptide bonds. The sequence and structure of these amino acids determine the protein’s function. Protein structure is hierarchically organized into four levels:

1. Primary Structure

• The linear sequence of amino acids in a polypeptide chain, determined by the genetic code.

2. Secondary Structure

• Local folding of the polypeptide chain into structures such as α-helices and β-pleated sheets, stabilized by hydrogen bonds.

Introduction

Lipids may be regarded as organic substances relatively insoluble in water, soluble in organic solvents (chloroform, ether, benzene, ethanol and other non-polar solvents, etc.), actually or potentially related to fatty acids and utilized by living cells. Lipids are a diverse group of hydrophobic or amphipathic biomolecules that play crucial roles in energy storage, cell membrane structure, and signaling. Unlike carbohydrates and proteins, lipids are not defined by a specific polymer structure but rather by their solubility in non-polar solvents. Broadly lipids are classified based on their function as ‘Storage lipids’ and ‘Structural lipids’. Some of them are co-factors, hormones, electron carriers, light-absorbing pigments and hydrophobic anchors of proteins.

Fatty Acids: Fatty acids are straight aliphatic chains with a methyl group at one end and a carboxyl group (-COOH) at the other end. They are the simplest form of lipids.

• Saturated Fatty Acids have no double bonds between carbon atoms, leading to straight chains (e.g., palmitic acid).

• Unsaturated Fatty Acids contain one or more double bonds, causing kinks in the chain (e.g., oleic acid). Fatty acids containing more than one double bond (polyunsaturated fatty acids/PUFA) are found in relatively minor amounts.

Introduction

Carbohydrates are essential organic biomolecules/macromolecules composed of carbon c., hydrogen (H), and oxygen (O) atoms, typically in a 1:2:1 ratio. They are one of the four major classes of biomolecules, alongside proteins, lipids, and nucleic acids. Carbohydrates play critical roles in energy storage, structural integrity and cell signaling. Carbohydrates with an aldehyde as their functional group are called Aldoses. Those with keto as a functional group are called Ketoses.

Classification of Carbohydrates: They are broadly classified into three major groups:

1. Monosaccharides: The simplest form of carbohydrates, consisting of a single sugar unit. They cannot be hydrolyzed to yield simpler forms of sugar. They can be subdivided into trioses, tetroses, pentoses, hexoses, heptoses and octoses etc., depending upon the number of carbon atoms they possess. Important monosaccharides are:

• Glycerose / Glyceraldehyde (Aldotriose): Glyceraldehyde 6-phosphate is an intermediate in Glycolysis.

• Ribose (Aldopentose): found in Nucleic acids.

• Glucose (Aldohexose): The primary energy source for cells, known as blood sugar.

• Fructose (Ketohexose): Found in fruits (fruit sugar), a major component of sucrose.

• Galactose (Aldohexose): Known as brain sugar. It is a part of lactose sugar.

Introduction

The smallest, most basic, most primitive organisms are known as prokaryotic (Greek: pro= primitive or prior, and karyon = nucleus). Likely, they originated around 3.5 billion years ago. Bacteria, such as Mycoplasma and Cyanobacteria, are known to contain these cells. A prokaryotic cell is a deeply organized single-enveloped system. Its constituent nuclear parts are encased in a plasma membrane, with the cytoplasmic ground substance encircling the center. Prokaryotic cells’ cytoplasm lacks distinct cytoplasmic organelles, the nuclear envelope, and any other cytoplasmic membrane.

Despite being incredibly thin and delicate structures, in Eukaryotes plasma membranes are essential to many of a cell’s most vital processes. Membranes are lipid-protein assemblages where non-covalent linkages hold the constituents in place in a thin sheet. Both integral protein and phospholipid lateral mobility are significantly impacted by the physical condition of the lipid bilayer. The plasma membrane is a selectively permeable barrier that permits solute passage via assisted diffusion, active transport, and simple diffusion via membrane channels or the lipid bilayer. A system of membrane organelles, such as the endoplasmic reticulum, Golgi complex, and lysosomes, is found in the cytoplasm of eukaryotic cells. These organelles are physically and functionally connected to the plasma membrane and one another. The cytoplasm is separated into a luminal region inside the ER membranes and a cytosolic space outside the membranes by the endoplasmic reticulum (ER), a network of tubules, cisternae, and vesicles. Additionally, the ER is where the majority of a cell’s membrane lipids are generated and transported to different locations. Proteins’ asparagine residues are added with sugars (a process known as glycosylation), which starts in the rough ER and continues in the Golgi complex.

Introduction

pH is a quantitative measure of the concentration of hydrogen ions in a solution. The pH scale ranges from 0 to 14, with 7 being neutral. Lower pH indicates acidity, while higher pH indicated alkalinity. Pure water at 25°C has a pH of 7.0 as the concentrations of H3 O+ and OH-. pH is defined as potential of hydrogen and is a measure of how acidic or basic a substance or solution is. The concentration of Hydrogen (H+) in a solution determines its pH. Higher concentrations of H+ ions correspond to lower pH values (more acidic), and lower concentrations of H+ ions correspond to higher pH values (More alkaline/basic). pH is an important measurement concept in many fields, including chemistry, biology, and environmental science. pH of blood and other fluids of the body, secretions etc?, determine the health status of an individual. Likewise, pH determines the quality of soil for plant growth. In medical sciences, pH plays a crucial role in maintaining a healthy internal environment for various bodily functions. Internal environment of an animal or human is tightly regulated more so the pH of different body fluids like blood, saliva and stomach acid.

pH balance is a very prime aspect to maintain homeostasis inside a biological system. Speaking of which the first thing that comes to mind is the enzyme function. Many enzymes have a specific pH range for optimal activity. Any deviation from this specific pH range not only significantly disrupt their function but also hinder biochemical processes involved. Most vital operations of a cell are nutrition transport and waste disposal i?e?, excretion. pH of the fluids surrounding cells impacts these activities; hence, maintaining a proper pH is vital for healthy cell function. Different organs of the body need to maintain different pH ranges for functioning accordingly. Stomach operates at acidic pH to digest the food material ingested whereas, blood need alkaline pH for optimal oxygen transport by RBC.

Introduction

“Bio” means pertaining to life and “Chemistry” is the Study of chemicals and chemical reactions. So Biochemistry may be defined as the study of chemical processes within and relating to, living organisms. It is a field of science that explores the chemical processes and substances within living beings. Biochemistry bridges the gap between biology and chemistry, aiming to understand how biological molecules give rise to the complex processes of life. In other words “Biochemistry is the science dealing with various molecules that are present in living cells and organisms and their chemical reactions.”

Scope of Biochemistry

As a life itself, the scope of biochemistry is vast and ever changing. It has its influence on vide range of fields playing a major role in understanding and influencing living organisms. Here some of the fields were put forth that have applications of biochemistry.

Human and Medical Healthcare

Nutrition and metabolism: As they say, we are what we eat; nutrition is a prime aspect of the being and knowing how the body process what it eats is a necessary knowledge that comes from biochemical aspect of nutrition. The dietary component of the beings converting into energy, protein and other essential bodily macro and micro molecules is a great knowledge imparted by biochemistry aspect of nutrition. Metabolism which broadly includes anabolism and catabolism deals with various activities of the physiological systems with in the body. Knowledge of biochemistry is very essential these days as the metabolic diseases are very much prevailing. Biochemistry imparts basic to complex know-hows about various metabolic processes and their derailments.

Q1. Fill in the blanks with appropriate answers.

1. India ranks …first…. position in cattle population in the world.

2. India ranks … first …. position in buffalo population in the world.

3. India ranks … first ……. position in total milk production in the world.

4. …Buffalo…….. species produce the highest amount of milk in India.

5. Frieswal cattle is a cross of …Holstein Friesian….and ……Sahiwal…

6. Mehsana buffalo is a cross of …Murrah….and ……Surti……

7. India ranks … first …. position in goat population in the world.

20th Livestock Census of India

India has highest cattle population (192.49 million), buffalo population (109.85), in the world producing 24% is the highest milk yield (221.1 million tons in the year 2021-2022, and per capita availability was 444 gm/day) in the world (Source NDDB). India produces 43% of world buffalo meat production. Unfortunately, 80% cattle and 70% buffaloes are non-descriptive and yield very low amount of milk.

After independence Indian Council of Agricultural Research (ICAR) has developed serval projects and plans for research and characterization of livestock species all over the country. Our country holds enormous genetic biodiversity in our domestic animals, result in increasing number of registered breeds in every decade. Breed registration Committee on its online meeting held on 5th December, 2023 approved registration of eight new breeds of livestock. This includes Aravali Chicken (Gujarat) Andamani Duck (Andaman and Nicobar Islands), Anjori Goat (Chhattisgarh), Andamani Goat (Andaman and Nicobar Islands), Bhimthadi Horse (Maharashtra), Andamani Pig (Andaman and Nicobar Islands), Macherla Sheep (Andhra Pradesh), Frieswal Cattle (Uttar Pradesh and Uttarakhand). Endangered, critical and vulnerable breeds of livestock also have been identified by ICAR which need more scientific research and multiplication breed.

Using the FAO criteria, Bargur and Siri cattle breeds and Attapadi goat breeds were categorized under vulnerable status of risk; Krishna Valley, Mewati, Pullikulam and Punganur cattle breeds, Chilika and Toda buffalo breeds and Karnah and Poonchi sheep breeds under endangered status of under risk and Vechur cattle under critical status of risk. All these breeds need immediate steps for rescue by using suitable conservation methodology. Breed-wise census should be continued in future so that trends in breed populations may also be estimated for fine tuning of risk assessment of breeds.

Rate of inbreeding in Indian livestock breeds: The rate of inbreeding estimated for different breeds of cattle was well below 0.5% (needed for a breed ‘not at risk’) except for Mewati (1.193%), Pullikulam (0.72%) and Vechur (17.893%). The rate of inbreeding in buffalo breeds was also well below 0.5% except in Chilika buffalo, where it was 0.731%. The rate of inbreeding of these breeds may be reduced by increasing the number of breeding males and in Vechur also the breeding females. The rate of inbreeding in all the breeds of sheep (Indian or exotic), goat and pig were estimated to be less than 0.5%. In these species, a good balance of breeding males and females is always expected.

Some have described Mithun as domesticated Gaur others as a hybrid descent from the crossing of gaur bulls and common cows. Considered to have originated along the Assam and Myanmar border. • Mithun, also known as ‘Cattle of Mountain” is an important bovine species of north-eastern hill region of India and also of China, Myanmar, Bhutan and Bangladesh. This magnificent massive bovine is presently reared under free-range condition in the hill forests at an altitude of 1000 to 3000 m above mean sea level.

• Mithun plays an important role in the socio-economic and cultural life of the local tribal population.

• Presently, this animal is mainly reared for meat, which is considered to be more tender and superior over the meat of any other species.

• Mithun milk, though produced less in quantity, is of high quality and can be used for preparation of various milk products.

• Leather obtained from this species has been found to be superior to cattle.

The yak is a bovine species that provides livelihoods for people in high altitude conditions of extreme harshness and deprivation. Yaks live predominantly on the “roof of the world”, as the Qinghai-Tibetan Plateau is often called, and provide milk, meat, hair and down fibre, hides, draught power and dung (principally used as fuel). The yak has physical and physiological characteristics that allow it to thrive at high altitudes (low oxygen) and in extreme cold (at temperatures as low as -40 °C) and to survive feed shortages in the winter (FAO).

The milk yield of the yak cow is often no more than the amount suckled by the calf and is not comparable to the milk yield of dairy cattle. However, although milk offtake for human consumption may be at the expense of the calf, yak milk is important for households. In economic terms, milk is often the most important yak product. Yak milk is generally produced by small-scale farmers in traditional systems where management is highly influenced by climate and seasons. Lactation is seasonal and yak cows produce between 150 and 500 litres; yields vary by breed and location. Lactation can generally continue into a second year without another calving. During the winter, yak cows do not go dry and continue to produce a small amount of milk, with milk yields as low as 2 to 4 litres/month. During the second year of lactation, milk yields are between half and two-thirds of those in the first year. Currently, there are no specialized dairy yak breeds (FAO).

The full name of an organism technically has eight terms. For the dog it is: Eukarya, Animalia, Chordata, Mammalia, Carnivora, Canidae, Canis, and lupus. Notice that each name is capitalized except for species, and the genus and species names are italicized. Scientists generally refer to an organism only by its genus and species, which is its two-word scientific name, or binomial nomenclature. Therefore, the scientific name of the dog is Canis lupus. The name at each level is also a taxonomy Carnivora is the name of the taxon at the order level; Canidae is the taxon at the family level, and so forth. Organisms also have a common name that people typically use, in this case, dog. Note that the dog is additionally a subspecies: the “familiaris” in Canis lupus familiaris. Subspecies are members of the same species that are capable of mating and reproducing viable offspring, but they are separate subspecies due to geographic or behavioural isolation or other factors. Dogs, which are under the species Canis lupus familiaris, are known to have a total of 78 chromosomes (2n). The diploid genes can be classified into 38 pairs with two sex chromosomes.

Donkeys can also be termed as ass (Equus africanus asinus) and is a domesticated member of the horse family, Equidae with chromosome number 62. The Wild ass of Africa, E. africanus is the wild ancestor of the donkey. For approximately 5000-7000 years, the donkey has been used as a working animal.

An adult male donkey is a jack or jackass, an adult female is a jenny or jennet, and an immature donkey of either sex is a foal. Jacks are often mated with female horses (mares) to produce mules, the less common hybrid of a male horse (stallion) and jenny is called hinny. NBAGR-ICAR has registered three breeds of donkey till date.

1. Kachchhi

• These donkeys are found in Kachchh district of Gujarat.

• Coat colour is mainly grey (dorsal surface grey and ventral surface white) followed by white, brown and black.

• Forehead is convex. Nasal bone is straight.

• Height at wither ranges from 77 to 115 cm.

• Docile in temperament.

• Only donkeys are used for agricultural purposes like inter cultivation for weed removing.

• Also utilized for transportation as donkey cart, as pack animal during pastoralist migration, etc.

In some developing countries, milk from horses (Equus caballus) and donkeys (Equus asinus) is an essential food for poor farmers. Generally, horses are more commonly used for dairy purposes in cool areas and donkeys in dry semi-arid regions. Milking equines is time-consuming and has to be repeated five or six times a day. In addition, an equine will not release milk unless it is stimulated by the presence of its foal. Mare’s milk is commonly consumed in the steppe areas of Central Asia, where a traditional lactic-alcoholic beverage called koumiss is produced through fermentation. Horse milk is also an important source of animal protein for pastoralists in Mongolia. The consumption of donkey milk has become very marginal. In some African communities, donkey milk is consumed for medical purposes.

Equus is a genus of mammals in the family Equidae, which includes horses, asses, and zebras. Within the Equidae, Equus is the only recognized existing genus, comprising seven living species. Like Equidae more broadly, Equus has numerous extinct species recognized only from fossils. Equines are odd-toed ungulates with slender legs, long heads, relatively long necks, manes (erect in most subspecies), and long tails. All species are herbivorous, and mostly grazers, with simpler digestive systems than ruminants but able to subsist on lower-quality vegetation. The chromosome number of a horse is 64 (2n).

Camels could be exploited for augmenting the country’s milk production capacity as a supplementary milk resource in India for the benefit of increasing human population. Since milk production potential of camels in India have remained unexploited and considering its therapeutic utility it can fetch good prices. Camels are raised for milk, meat, fibre (wool and hair), transport and other work; their dung is used as fuel. Milk is often the most important camel product and is the staple food of nomads.

The camel is an important species of the Indian fragile desert ecosystem, a proven icon of adaptation with its unique bio-physiological characteristics and has formidable ways of living in harsh situations of arid and semi-arid regions. The proverbial Ship of Desert earned its epithet on account of its indispensability as a mode of transportation and draught ability in desert. However, its utilities are subject to continuous social and economic changes. The camel has also played a significant role in civil law and order, defence and battles from the ancient times till date. Camels formed an important component of the Mauryan Army (C.322-232 BC) and continued through the Mughal period (1200-1700 AD) to the present times.