Biochemistry Unit - I PDF

BIOCHEMISTRY Unit -I Element of Life Of the approximately 115 elements known, only the 19 highlighted in purple are absolutely required in the human diet. These elements—called essential elements—are restricted to the first four rows of the periodic table, Essential elements? An essential element...

BIOCHEMISTRY Unit -I Element of Life Of the approximately 115 elements known, only the 19 highlighted in purple are absolutely required in the human diet. These elements—called essential elements—are restricted to the first four rows of the periodic table, Essential elements? An essential element is one that is required for life and whose absence results in death. An element is considered to be essential if a deficiency consistently causes abnormal development or functioning and if dietary supplementation of that element—and only that element—prevents this adverse effect. Classification of the Essential Elements Macronutrients Micronutrients Required in large amounts Required in trace amounts carbon, phosphorus, nitrogen, copper, iron, zinc, boron, hydrogen, potassium, magnesium, manganese, molybdenum, nickel, oxygen, calcium, sulfur chlorine Four elements are common to all living things: carbon (C), hydrogen (H), oxygen (O), and nitrogen (N). These four elements alone make up approximately 96% of all living matter. Sulfur (S), phosphorus (P), calcium (Ca), potassium (K), and a few other elements constitute the other 4% of an organism’s mass. In addition to water which constitutes about 70% of a cell's mass, cells are composed of carbon- based compounds that may contain up to 30 or so carbon atoms. Macronutrients Carbon (C): Carbon is the key element in organic chemistry and is fundamental to life. It forms the backbone of organic molecules, including proteins, carbohydrates, lipids, and nucleic acids. Carbon's ability to form stable bonds with other elements, including itself, allows for the complexity and diversity of life. Hydrogen (H): Hydrogen is the most abundant element in the universe. It is a crucial component of water (H2O), which is essential for life as a solvent and for various metabolic processes. Hydrogen ions (protons) also play a vital role in cellular respiration and energy production. Oxygen (O): Oxygen is necessary for cellular respiration, where it acts as an electron acceptor during the breakdown of organic molecules to release energy. Oxygen is also a major component of water and plays a role in many biological processes. Nitrogen (N): Nitrogen is a key element in proteins and nucleic acids, such as DNA and RNA. It is essential for the structure and function of these biomolecules. Nitrogen is often obtained by living organisms through the uptake of nitrogen-containing compounds from the environment. Phosphorus (P): Phosphorus is a critical component of nucleic acids, such as DNA and RNA, as well as ATP (adenosine triphosphate), which is the primary energy currency in cells. Phosphorus is also present in phospholipids, which are important for the structure of cell membranes. Sulfur (S): Sulfur is found in certain amino acids, such as cysteine and methionine, which are building blocks of proteins. It also plays a role in enzyme activity and is involved in the formation of disulfide bonds, which contribute to protein structure and stability. Micronutrients Micronutrients are vitamins and minerals needed by the body in very small amounts. However, their impact on a body's health are critical, and deficiency in any of them can cause severe and even life-threatening conditions. Trace elements While organisms require some elements in giant quantities (for instance, we have mentioned earlier that plants require macronutrients like carbon and phosphorus in huge amounts), they require other elements in minute quantities. The latter are called trace elements. Some trace elements–like iron (Fe)–are required by all living organisms, while other trace elements are needed only by certain organisms. For instance, vertebrates require iodine (I), an essential component of a hormone produced by the thyroid gland. In humans, 0.15 milligrams (mg) of iodine is required daily for the thyroid to function properly. A person deficient in iodine will suffer from a condition called goiter, wherein the thyroid gland grows to an abnormal size. This is why table salt is typically "iodized", meaning a small amount of iodine is added to it.  Chemical bonds to stabiles life Attraction forces between atoms ,strong enough to permit the combination of atoms to function as a single unit. It originate due to the attraction of electrons and atomic nuclei(Coulombic interactions). Major stabilizing forces are two types covalent and non covalent  A. Covalent bonds In this bond electrons are shared by two atomic nuclei. These electron pairs are known as shared pairs or bonding pairs. The bonding electrons are relatively localized in the region of the two nuclei. Single covalent bond includes sharing of two electrons ,double bond has 4shared electrons ,and triple bond has 6 electrons. Ester bond in nucleic acids ,peptide bond and disulphide bond in proteins,and Glycosidic bond in carbohydrates are examples of covalent bonds Covalent bond: A. Non polar:This type of covalent bond is formed whenever there is an equal share of electrons between atoms Example:gas molecules like Hydrogen gas, Nitrogen gas A. polar: This type of covalent bond exists where the unequal sharing of electrons occurs due to the difference in the electronegativity of combining atoms. More electronegative atom will have a stronger pull for electrons. Example: water Non- Covalent Interactions They are weak and non- specific in nature. They are significant in producing macromolecular structures ,stabilizing transition states of biochemical reactions ,folding proteins to 3D structures etc. They can be Intra molecular ( within the same molecules) and inter molecular (Between different molecules) It include: 1. Electrostatic or Ionic bonds 2. Hydrogen Bonds 3. Hydrophobic interactions 4. Van –der Wall’s interactions Electrostatic or Ionic Bonds Ionic bonding is the complete transfer of valence electron(s) between atoms. Ionic bonds require an electron donor, often a metal, and an electron acceptor, a non-metal. In ionic bonds, the metal loses electrons to become a positively charged cation, whereas the non-metal accepts those electrons to become a negatively charged anion. Salt bridges special type of ionic bond formed between positively charged amino acids (e.g. Arginine, Lysine) and negatively charged amino acids (Aspartic acid ,Glutamic acid )in proteins. Helps to stabilize proteins. Hydrogen Bonds Hydrogen bonding is a special type of dipole-dipole attraction between molecules. It results from the attractive force between a hydrogen atom covalently bonded to a very electronegative atom such as a N, O, or F atom and another very electronegative atom. Inter and Intra molecular H bonding Hydrogen bonding between the different molecules of same substance or different substances. Intermolecular H bonding causes the association of molecules Eg). Hydrogen Bonding in HF Hydrogen bonding in Water molecule Hydrogen bonding within the molecule. Eg). H bonding in Salicylic acid and o-nitrophenol.  Hydrophobic Interactions Hydrophobic molecules are nonpolar molecules and usually have a long chain of carbons that do not interact with water molecules. Hydrophobic interactions are those interactions either between nonpolar molecules or between non- polar parts of amphipathic molecules, which have no affinity for water and hence would be repelled by water. Many biomolecules such as proteins ,sterols etc shows hydrophobicinteractions Van der Wall’s interactions Van der Waals Forces are intermolecular forces The forces are due to the attractions between the partial positive and partial negative electrical charges between molecules These forces are affected by the distance between the molecules (like how when you bring magnets closer together, the attraction is greater) Types of Van der Waals Forces: 1) London Dispersion Forces : The weakest force of the three Van der Waals and occurs between any two atoms in a molecule (note: this is a temporary force!) 2) Dipole-Dipole Interactions : Occurs between the positive end of one polar molecule and the negative end of another polar molecule 3) Hydrogen Bonding : The strongest of the three Van der Waals forces and occurs between hydrogen atoms and highly electronegative atoms 5 Main Forces that Stabilise Protein Structures Salt Linkages: Hydrogen Bonding: Disulfide Linkages Hydrophobic Interactions Van der Waals’ Forces:  Salt Linkages Salt linkages (ionic bonds) result from interactions between positively and negatively charged groups on the side chains of the basic and acidic amino acids. For the mutual attraction between an aspartic acid carboxylate ion and a lysine ammonium ion helps to maintain a particular folded area of the protein: Hydrogen Bonding Hydrogen bond definition: Hydrogen bond is an electrostatic attraction between a hydrogen atom, which is covalently bound to a high electronegative atom (such as Oxygen and Nitrogen), to another electronegative atom of same or different molecules of their close neighborhood. Hydrogen present in the-OH group of –NH2 of amino acids become slightly electropositive. This is due to the high electronegativity of O and N when compared to hydrogen.Due to the high electronegativity, Oxygen and Nitrogen attract the shared electron of hydrogen more towards them.  Thus hydrogen attached to these high electronegative atoms will get a partial positive charge called 𝛅 positive whereas the electronegative atoms will get a partial negative charge called 𝛅 negative. Consequently, the slightly positive H is then attracted towards the neighboring electronegative oxygen of –C=O or nitrogen atom –NH2 group. These –C=O and NH2 groups occur along the length of the polypeptide chain in regular sequence. Thus the formation of hydrogen bonds gives a regular shape to the polypeptide chain such as alpha helix and beta plates. Hydrogen bonds are very weak bonds. Occurrence of hydrogen bonds in high frequency makes a considerable contribution towards the molecular stability of proteins. Hydrogen bonds are involved in stabilizing the secondary, tertiary and quarternary structure of proteins.  Disulfide Linkages Two cysteine residues may come in proximity as the protein molecule folds. The disulfide linkage results from the subsequent oxidation of the highly reactive sulfhydryl (—SH) groups to form cysteine: This disulfide bridge is the second-most important covalent interaction involved in protein structure. Disulfide linkages are frequently found in proteins as a general aid to the stabilization of the tertiary structure. Note, that one or more of these bonds may join one portion of a polypeptide chain covalently to another, thus interfering with the helical structure. Hydrophobic Interactions Many investigators now believe that the non-covalent hydrophobic forces are the most signi- ficant in stabilising the conformation of a polypeptide chain. It is not because they are so strong, but rather because there are so many of them. The majority of the nonpolar amino acid groups, cluster together at the interior of the chain and the strength of all their hydrophobic interactions is considerable: Van der Waals’ Forces: These are extremely weak forces and act only over extremely short distances; include both an attractive and a repulsive component. The attractive force involves interaction between induced dipoles formed by momentary fluctuations in the electron distribution in nearby atoms. The repulsive force comes into play when two atoms come so close that their electron orbitals overlap. The distance at which the attractive force is maximal and the repulsive force is minimal is termed the Van der Waals’ contact distance.  STRUCTURE AND PROPERTIES OF WATER when a large amount of water is observed, as in a lake or the ocean, it is actually light blue in color. The blue hue of water is caused by selective absorption and scattering of white light. Transparency allows sunlight to pass through it. Sunlight is needed by water plants and other water organisms for photosynthesis. These properties of water are caused by its unique chemical structure. Polarity Water is a polar molecule, with an unequal distribution of charge throughout the molecule Solvency Water is one of the most common ingredients in solutions. A solution is a homogeneous mixture composed of two or more substances. In a solution, one substance is dissolved in another substance, forming a mixture that has the same proportion of substances throughout. The dissolved substance in a solution is called the solute. The substance in which it is dissolved is called the solvent. An example of a solution in which water is the solvent is salt water. In fact, so many substances are soluble in water that water is called the universal solvent. Water is a strongly polar solvent, and polar solvents are better at dissolving polar solutes. Many organic compounds and other important biochemicals are polar, so they dissolve well in water. On the other hand, strongly polar solvents like water cannot dissolve strongly nonpolar solutes like oil  Cohesion Cohesion refers to the attraction of molecules for other molecules of the same kind, and water molecules have strong cohesive forces thanks to their ability to form hydrogen bonds with one another. Hydrogen bonds between water molecules explain some of water’s other properties. For example, hydrogen bonds explain why water molecules tend to stick together. Surface Tension Cohesive forces are responsible for surface tension, the tendency of a liquid’s surface to resist rupture when placed under tension or stress. Water molecules at the surface (at the water-air interface) will form hydrogen bonds with their neighbors, just like water molecules deeper within the liquid However, because they are exposed to air on one side, they will have fewer neighboring water molecules to bond with, and will form stronger bonds with the neighbors they do have This results in a “skin” of water at the surface in which the molecules are held together very tightly. Surface tension is a measurement of the amount of force required to break this skin on the surface of water. Other liquids have a surface tension as well, but the surface tension in water is quite strong due to the hydrogen bonds. Adhesion When water form hydrogen bonds with other substance, the attraction is called adhesion. Due to cohesion and adhesion, seeds swell and germinate; ascent of sap and capillary movement of water takes place. Capillary Action The grip-like characteristic that results from the water molecules property of adhesion helps to form capillary action. Capillary action is the ability of a liquid to flow against gravity in a narrow space. Capillary action occurs when water climbs upward through a small space, defying gravity due to the forces of adhesion and surface tension. Capillary action is important in moving water upwards through small spaces. Plants depend on capillary action to move water upward from the roots to the leaves. In the soil, capillary action also tends to move water upward between the soil particles. Water is moved through small blood vessels in animals through capillary action also TEMPERATURE MODERATION In addition to the properties already discussed in this chapter, water also has a high heat capacity. What this means is that water can absorb or release large amounts of energy in the form of heat while only slightly changing its temperature. Energy must be absorbed to break hydrogen bonds, and energy is released as heat when hydrogen bonds form. Furthermore, water has a high specific heat, meaning it takes a lot of energy to raise or lower the temperature of water. Specific heat is a measure of how much energy it takes to raise the temperature of a substance. Specific heat (measured in cal/(g°C)) is a property that is unique to a given type of matter. That’s why it’s called specific. Every substance has its own specific heat capacity, with the specific heat capacity of water being 1 cal/(g°C). As a result, water plays a very important role in temperature regulation. Since cells are made up of water, this property helps to maintain homeostasis. Water Supports Cellular Structure Water also has an important structural role in biology. Visually, water fills cells to help maintain shape and structure Water also contributes to the formation of membranes surrounding cells.