Biochemistry Lecture 1 (Week 1) PDF

Biochemistry Prof. Lali Shanshiashvili  “I’ve learned that I still have a lot to learn.” Maya Angelou - an American memoirist, poet, and civil rights activist. “Never regard study as a duty, but as the enviable opportunity to learn.” - Albert Einstein - a German-born theoretical physicist,...

Biochemistry Prof. Lali Shanshiashvili  “I’ve learned that I still have a lot to learn.” Maya Angelou - an American memoirist, poet, and civil rights activist. “Never regard study as a duty, but as the enviable opportunity to learn.” - Albert Einstein - a German-born theoretical physicist, widely held to be one of the greatest and most influential scientists of all time. “Live as if you were to die tomorrow. Learn as if you were to live forever.” - Mahatma Gandhi - an Indian lawyer, anti-colonial nationalist and political ethicist. “Success is the maximum utilization of the ability that you have.” — Zig Ziglar - an American author, salesman, and motivational speaker.  Biochemistry Is a Modern Science Friedrich Wohler (1800-1882). Wohler was one of the founders of biochemistry. By synthesizing urea, Wohler showed that compounds found in living organisms could be made in the laboratory from inorganic substances; that compounds found exclusively in living organisms could be synthesized from common inorganic substances.  Louis Pasteur (1822–1895) is best known as the founder of microbiology and an active promoter of germ theory. But Pasteur also made many contributions to biochemistry including the discovery of stereoisomers.  Two major breakthroughs in the history of biochemistry are especially notable— 1). The discovery of the roles of enzymes as catalysts ; 2) The role of nucleic acids as information-carrying molecules.  The last half of the 20th century saw tremendous advances in the area of structural biology, especially the structure of proteins. The first protein structures were solved in the 1950s and 1960s by scientists at Cambridge University (United Kingdom) led by John C. Kendrew and Max Perutz. The Nobel Prize in Chemistry 1962 was awarded jointly to Max Ferdinand Perutz and John Cowdery Kendrew "for their studies of the structures of globular proteins." Since then, the three-dimensional structures of several thousand different proteins have been determined and our understanding of the complex biochemistry of proteins has increased enormously.  What Is Medical Biochemistry? Chemistry is a science of matter. Biochemistry focuses on the studies of biological matter. Previously, biochemistry was referred to as ‘biological chemistry’ or ‘physiological chemistry’ (a term that is still occasionally used for the sake of tradition). Nowadays Medical biochemistry is regarded as biochemistry (and molecular biology) applied to human organisms in health and disease. Medical biochemistry seeks to advance the understanding of chemical structures and processes that constitute health and disease and underlie transformations between these two states.  Clinical biochemistry is an important applied sub-discipline of medical biochemistry, also known under the names of clinical chemistry, pathological biochemistry or chemical pathology. Clinical biochemistry is concerned with the methodology and interpretation of biochemical tests performed on body fluids and tissues, to support diagnosis, treatment and monitoring of disease.  The Chemical Elements of Life Six nonmetallic elements— carbon C, hydrogen H , nitrogen N, oxygen O, phosphorus P , sulfur S — account for more than 97% of the weight of most organisms. All these elements can form stable covalent bonds. Covalent bond formation by e pair sharing. Defines its properties  Many Important Macromolecules Are Polymers In some cases, such as certain carbohydrates, a single monomer is repeated many times; in other cases, such as proteins and nucleic acids, a variety of different monomers is connected in a particular order. Train and carriages  Macromolecules have properties that are very different from those of their constituent monomers. For example, starch is a polymer of the sugar glucose but it is not soluble in water and does not taste sweet. The levels of complexity, in increasing order, are: Atoms molecules macromolecules organelles cells tissues organs organe systems whole organisms. Note that many species lack one or more of these levels of complexity: Single-celled organisms, for example, do not have tissues and organs.  Macromolecules A. Proteins B. Polysaccharides C. Nucleic Acids D. Lipids and Membranes  The Energetics of Life Life also requires the input of energy. Living organisms are constantly transforming energy into useful work to sustain themselves, to grow, and to reproduce. Almost all this energy is ultimately supplied by the sun. Water  Life on Earth is often described as a carbon-based phenomenon but it would be equally correct to refer to it as a water-based phenomenon. Water is the most abundant molecule in most cells accounting for 60% to 90% of the mass of the cell.  There is nothing softer and weaker than water, And yet there is nothing better for attacking hard and strong things. For this reason there is no substitute for it. —Lao-Tzu - philosopher and poet of ancient China. Some important properties of water arise from its angled shape and the intermolecular bonds that it can form.  Hydrogen bonding by a water molecule. A water molecule can form up to four hydrogen bonds: the oxygen atom of a water molecule is the hydrogen acceptor for two hydrogen atoms, and each O group serves as a hydrogen donor.  The Water Molecule Is Polar Oxygen atoms are more electronegative than hydrogen atoms because an oxygen nucleus attracts electrons more strongly than the single proton in the hydrogen nucleus. As a result, an uneven distribution of charge occurs within each O—H bond of the water molecule with oxygen bearing a partial negative charge (δ ) and hydrogen bearing a partial positive charge (δ). This uneven distribution of charge within a bond is known as a dipole and the bond is said to be polar.  Hydrogen Bonding in Water One of the important consequences of the polarity of the water molecule is that water molecules attract one another. The attraction between one of the slightly positive hydrogen atoms of one water molecule and the slightly negative electron pairs in one of the sp3 hybrid orbitals produces a hydrogen bond. Hydrogen Bonding in Water In a hydrogen bond between two water molecules the hydrogen atom remains covalently bonded to its oxygen atom, the hydrogen donor. At the same time, it is attracted to another oxygen atom,called the hydrogen acceptor. In effect, the hydrogen atom is being shared between the two oxygen atoms. The distance from the hydrogen atom to the acceptor oxygen atom is about twice the length of the covalent bond.  A water molecule can form up to four hydrogen bonds: the oxygen atom of a water molecule is the hydrogen acceptor for two hydrogen atoms, and each O---H group serves as hydrogen donor. Water Play of Glass Beads  Water Is an Excellent Solvent The physical properties of water combine to make it an excellent solvent. The small size of water molecules means that many of them can associate with solute particles to make them more soluble. wyali NaCl https://www.google.com/search?sca_esv=567963742&rlz=1 C1CHBD_enGE987GE987&q=sodium+chloride+solving+in+w ater&tbm=vid&source=lnms&sa=X&ved=2ahUKEwj35KKJ78 KBAxUTS_EDHQL2CPoQ0pQJegQIVhAB&biw=1534&bih=751 &dpr=1.25#fpstate=ive&vld=cid:b37f7a5b,vid:9aYLonML69 w,st:0 Molecules that can dissociate to form ions are called electrolytes. Substances that readily dissolve in water are said to be hydrophilic, or water loving. Substances that does not dissolve in water are said to be hydrophobic, or water fearing, substances.  DISTRIBUTION OF BODY WATER Total body water in an adult of 70 kg varies from 60 to 70 % (36-49 litres) of total body weight, when expressed as percentage of lean body mass, i.e., sum of the “fat-free tissue.”  The body water can be visualised to be distributed mainly in two “compartments”: (a) Intracellular fluid (ICF): The fluid present in the cells which is approx. 50 % (35 L), and (b) Extracellular fluid ECF: The fluid present outside the cells which constitutes approx. 20 % (14 L).  The extracellular fluid (ECF) is considered to be present in the two compartments as follows: 1. Plasma: The fluid present in heart and blood vessels, approx, 5 % (3 L) and 2. Interstitial tissue fluid (ITF): 15 % (11 L).  The extracellular compartment must be recognised as more “heterogenous” and should be subdivided into four main subdivisions: 1. Plasma 2. Interstitial and lymph fluid 3. Fluid of dense connective tissue, cartilage and bones 4. Transcellular fluid  1. Plasma volume: This comprises in general the fluid within the heart and blood vessels. 2. Interstitial and lymph fluid: This is considered to represent an approximation of actual fluid environment outside the cells.  3. Fluid of dense connective tissue, cartilage and bones: Due to differences in structure and relative avascularity, the fluid present in these tissues does not exchange fluid and electrolytes readily with remainder of body water. This includes approx. 4.0 L (7.5 % of total body water) and should be considered a “distinct subdivision of ECF”. 4. “Transcellular” fluid: A variety of extracellular fluid collections are formed by the “transport” or “secretory activity” of cells. Examples are: Fluids found in salivary glands, pancreas, liver and biliary tract, skin, mucous membrane of respiratory and GI tracts; The fluids present in “spaces” within the eyes (aqueous humour), cerebrospinal fluid (CSF) in the spinal canal and ventricles of the brain, and that within the lumen of the GI tract (mostly reabsorbed and not lost).  Ionization of Water One of the important properties of water is its slight tendency to ionize. Pure water contains a low concentration of hydronium ions (H3O) and an equal concentration of hydroxide ions (OH ). The hydronium and hydroxide ions are formed by a nucleophilic attack of oxygen on one of the protons in an adjacent water molecule.  The pH Scale Many biochemical processes—including the transport of oxygen in the blood, the catalysis of reactions by enzymes, and the generation of metabolic energy during respiration or photosynthesis—are strongly affected by the concentration of protons. It is convenient to use a logarithmic quantity called pH as a measure of the concentration of H iones. pH is defined as the negative logarithm of the concentration of H.  In pure water [H] [OH ] = 1.0 × 10-7 Pure water is said to be “neutral” with respect to total ionic charge since the concentrations of the positively charged hydrogen ions and the negatively charged hydroxide ions are equal. Neutral solutions have a pH value of 7.0 (the negative value of log 10-7 is 7.0).  Acetic acid is the weak acid present in vinegar. The equilibrium reaction for the ionization of acetic acid is The equilibrium constant for the dissociation of a proton from an acid in water is called the When the reaction reaches equilibrium, which happens very rapidly, the acid dissociation constant is equal to the concentration of the products divided by the concentration of the reactants. For this reaction the acid dissociation constant is The Ka value for acetic acid at 25°C is 1.76 × Because K values are numerically small and inconvenient in calculations it is useful to place them on a logarithmic scale. The parameter pKa defined by analogy with pH. A pH value is a measure of the acidity of a solution and a pKa value is a measure of the acid strength of a particular compound. The pKa of acetic acid is 4.8.  Buffered Solutions Resist Changes pH If the pH of a solution remains nearly constant when small amounts of strong acid or strong base are added the solution is said to be buffered. The ability of a solution to resist changes in pH is known as its buffer capacity.  Mixtures of acetic acid and sodium acetate can be used for the pH range from 4 to 6 ; and mixtures of KH2PO4 and K 2HPO4 can be used in the range from 6 to 8. The amino acid glycine is often used in the range from 9 to 11. https://www.youtube.com/watch?v=_X7mEmT7JWs