Introduction to Biochemistry PDF

CHEM 104: BIOCHEMISTRY Prepared by: M. K. Salazar-Pascua BIOCHEMISTRY Biochemistry is a special branch of organic chemistry that deals with matter inside the living cell. It deals with the reactions, processes, and metabolism of molecules found in the body....

CHEM 104: BIOCHEMISTRY Prepared by: M. K. Salazar-Pascua BIOCHEMISTRY Biochemistry is a special branch of organic chemistry that deals with matter inside the living cell. It deals with the reactions, processes, and metabolism of molecules found in the body. D making of molecules It shows the delicate balance of anabolism and catabolism. - breakdown of molecules It provides fundamental understanding of the molecular basis for the function (and malfunction) of living things. How did life begin? Theories on the Origin of Life BIG BANG THEORY Cataclysmic eruption of hot, energy-rich subatomic particles Formation of simple elements (hydrogen and helium) Formation of stars Explosion of supernovae and release of energy needed to fuse simpler atomic nuclei into more complex elements Formation of life Source: Nelson, D. and Cox, M. Lehninger Principles of Biochemistry, 4th Edition CREATION THEORY Theistic evolution It states that life was created by the divine being or by the transcendental being or the creator The belief in the account of the creation of the universe as presented in Genesis. PANSPERMIA THEORY Life developed elsewhere in the universe and then arrived on earth. ○ Microbial spores from space were supposedly brought to earth by asteroids or meteors; which jump-started life on earth. This theory states how life spread, not how life began. PRIMORDIAL SOUP THEORY Oparin-Haldane Hypothesis Proposes that life originated from simple organic compounds that formed in the atmosphere and oceans of the early Earth. ○ Life could have arisen from non-living matter through a process of “gradual chemical evolution.” Basis of the Miller-Urey Experiment RNA WORLD HYPOTHESIS It suggests that life on Earth began with a simple RNA molecule that could copy itself without help from other molecules. ○ RNA stored both genetic information and catalyzed the chemical reactions in primitive cells. RNA is the precursor to the every life form that exists today on the earth  The study of biochemistry shows how the collections of inanimate molecules that constitute living organisms interact to maintain and perpetuate life animated solely by the physical and chemical laws that govern the nonliving universe.  PRINCIPAL AREAS OF BIOCHEMISTRY 1. Molecular Biology – deals with the composition, structure and interactions of cellular molecules that carry out the biological processes essential for the cell's functions and maintenance. 2. Metabolism – the totality of chemical reactions that occur in living matter. 3. Molecular Genetics – the chemistry of processes and substances that store and transmit biological information  PRINCIPAL AREAS OF BIOCHEMISTRY 4. Structural Chemistry – deals with the relationship of the chemical structure and biological function. 5. Pharmacology – The study of drugs, their sources, their nature, and their properties. 6. Immunology – deals with physiological functioning of the immune system HISTORY OF BIOCHEMISTRY 1780s: Antoine Lavoisier proposed that the combustion of a candle is similar to the respiration of animals, as both need oxygen. 1810s –1830s : A major substance from animals and plants was identified. In 1938, it was called “Protein”. 1850s –1890s: Carbohydrates, lipids, and nucleic acids were recognized Source: https://www.researchgate.net/publication/296692559_Biochemistry_Chapter_1_A_Brief_History_of_Biochemistry HISTORY OF BIOCHEMISTRY 1893: Eduard Buchner demonstrated alcoholic fermentation in cell-free yeast extracts 1903: The term “Biochemistry” was coined Carl Neuberg. 1953: The Miller-Urey experiment showed that a variety of organic molecules, including the amino acids could form in an early, reducing atmosphere. Sources: Singh, P., Batra H., and Naithani M. History of biochemistry. 2004 Jan-Jun;34(1):75-86. https://www.researchgate.net/publication/296692559_Biochemistry_Chapter_1_A_Brief_History_of_Biochemistry MILLER-UREY EXPERIMENT Experiments recreating the atmosphere of primitive earth have led to the spontaneous formation of amino acids and other biological molecules. MAJOR BREAKTHROUGHS IN BIOCHEMISTRY 1. The discovery of the roles of enzymes as catalysts 2. The role of nucleic acids as information-carrying molecules BUCHNER’S EXPERIMENT A B Buchner showed that extracts of dead yeast cells could convert sugar to alcohol ○ Enzymes found in yeast are responsible for fermentation and not the cell itself  JAMES SUMNER Sumner isolated crystals from jack beans. Continued research showed that the crystals were composed of a pure form of urease and that urease is a protein.  GRIFFITH’S EXPERIMENT – TRANSFORMATION PRINCIPLE S strain R strain Heat-killed Heat-killed S strain S strain R strain Transformation allows a bacterium to take up genes from its surrounding environment, which could lead to acquisition of new genetic characteristics.  AVERY, MCCARTY AND MACLEOD 1. Lipids and carbohydrates were removed from a solution of heat-killed S cells 2. Subject the solution to enzyme treatments 3. Add a small portion of each sample to a culture containing R cells 4. Test for the presences of virulent S cells HERSHEY-CHASE EXPERIMENT Hershey-Chase experiment helped confirm that DNA is the genetic material FOUR MAJOR BIOMOLECULES 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acid  CARBOHYDRATES Carbohydrates are the most abundant organic molecules in nature. Pure carbohydrates contain C, H, and O atoms “Hydrates of carbon” Aldehyde or ketone compounds with multiple hydroxyl groups Monosaccharides LIPIDS ) Fats (for insulation Derived from the Greek word lipos which means “fat” Insoluble in water but soluble in nonpolar solvents NOT polymers Most contains fatty acids Carboxylic group Hydrocarbon chain  PROTEINS The most important of all biological compounds Derived from the Greek word proteios which means “of first importance” Composed of C, H, O, and N atoms Amino acids Amine Carboxylic acid NUCLEIC ACID Nucleic acids are molecules that store information for cellular growth and reproduction Contain C, H, O, N, and P atoms Two types of nucleic acid: DNA and RNA Nucleotides ↓ ↓ stores & decodes genesis Sugar bensmitt information Phosphate information in DNA to make porting Base Properties of Water Maria Kristina M. Salazar-Pascua Physical Science Department Centro Escolar University Manila Water ◎ The predominant chemical component of living organisms. ◎ Odorless, colorless, and tasteless ◎ Boiling point - 100°C (at sea level) ◎ Freezing point - 0°C Water ◎ Water is the only substance that occurs naturally as a solid, a liquid and a gas. ◎ Universal solvent ◎ Most of the major components of cells are dissolved in water ◉ Proteins ◉ DNA ◉ Polysaccharides  miles cusic 332,500,000 mi Approximately 70% of the earth is covered by water 3 97.5% is saltwater undrinkable 2.5% is freshwater 77% of freshwater is frozen 0.01% of freshwater Accessible surface freshwater Function of Water in Body Fluid Compartments ◎ Essential constituent of all living cells ◎ Medium ◉ chemical and enzymatic action ◉ physical processes i.e. diffusion, osmosis and filtration ◉ regulation of pH and osmotic pressure ◎ Vehicle for physiological processes ◎ Body temperature regulation ◎ Lubricant in potential spaces ◎ Refractive medium ◎ Mechanical buffer in CSF ◎ Essential for gaseous exchange in tissues and lungs  1 Polar Hydrogen bonds Polarity of Water A water molecule has two hydrogen atoms covalently bonded to an oxygen ◉ Water has positive and negative ends ◉ Water molecules are also attracted to other polar molecules and to ions. ￮ Hydrophilic Crater Lovind) - ￮ Hydrophobic waser-fearivep)  2 Cohesive and Adhesive Surface tension Capillary action Cohesion The attraction of molecules for other molecules of the same kind ◉ Water molecules have the ability to form hydrogen bonds with one another. ◉ Surface tension - the tendency of a liquid’s surface to resist rupture when placed under tension or stress. Surface Tension Adhesion The attraction of molecules of one kind for molecules of a different kind ◉ Water molecules have a strong attraction to other molecules bearing positive or negative charges. ◉ Capillary action - Enables water to “climb” upwards through thin glass tubes Capillary Action  3 Density Density of Water The maximum density of water occurs at 4°C. ◉ Between 4°C and freezing temperature, water becomes less dense as more of it becomes structured. water less dense from solid later liquid  4 High specific heat Thermal buffer Specific Heat The amount of energy required to change the temperature of a substance ◉ Water can absorb a lot of heat with little change in temperature  5 Neutral pH pH = 7 pH ◎ A measure of how acidic or basic a substance is. ◎ A measure of the relative amount of free hydrogen and hydroxyl ions in the water. ￮ Water dissociates into anions (OH-) and cations (H+) H3O+. CHEMICAL REACTIONS THAT MK Salazar-Pascua OCCUR IN THE CELL  easion REDOX (coupled Oxidation Example: Occurs when a molecule loses two hydrogen atoms and/or gains an oxygen. It involves the loss of electrons Reduction Occurs when a molecule gains two hydrogen atoms and/or loses an oxygen. It involves the gain of electrons.  Redox reactions are essential for cellular processes and cannot be avoided. However, the accumulation of free REDOX radicals, which are byproducts of these reactions, can lead to oxidative stress. This occurs when the balance between free radicals and antioxidants in the body is disrupted, potentially causing damage to cells, proteins, and DNA, and contributing to aging and diseases like cancer and cardiovascular disorders. Managing oxidative stress through antioxidants (from diet or Redox reactions are common in organic supplements) is crucial for maintaining cellular health. and biological chemistry, including the combustion of organic chemicals, respiration, and photosynthesis. Antioxidants are reducing agents. Ascorbic acid prevents damaging oxidation of living cells. Tocopherol scavenges harmful by-products of metabolism called free radicals.  water/H of , 0 HYDROLYSIS laddition The reverse reaction that splits larger molecules to monomers. A water molecule is used and a covalent bond is broken Smaller molecules are made, or split into monomers CONDENSATION A reaction that links biological molecules together. Water molecule (H2O) is released and a new covalent bond is formed It is also known as dehydration. A larger molecule, called polymer, is formed depending on the monomer: Amino acid = peptide Nucleotide = RNA/DNA Monosaccharide = polysaccharide  Alkame to alkamm HYDROGENATION Two hydrogen atoms are added across the double bond of an alkene, resulting in a saturated alkane. It is used in the food industry to make spreads and shortenings from liquid oils. Hydrogenation is also used in coal processing.  to Akene Alkame DEHYDROGENATION Dehydrogenation is the process by which hydrogen is removed from an organic compound to form a new chemical. Conversion of saturated into unsaturated compounds. It is used to produce aldehydes and ketones by the dehydrogenation of alcohols. Aldemssh  ketore TAUTOMERISM Aldelude - R C - - R Alcohol R- OH a phenomenon where a single chemical compound tends to exist in two or more interconvertible structures that are different in terms of the relative position of one atomic nucleus which is generally the hydrogen. -H-y - R It is the interconversion of aldehyde/ketone to alcohol. CARBOXYLATION = C - (OH) A chemical reaction in which carboxylic acid groups are produced by treating the substrate with carbon dioxide.  CO2 DECARBOXYLATION - C-COOH) - A chemical reaction that eliminates a carboxyl group and liberates carbon dioxide (CO2). A reaction of carboxylic acids removing a carbon atom from a chain of carbons. O PHOSPHORYLATION + (POs) - XTP - ADD The addition of a phosphoryl (PO3) group to a molecule. In biological systems, this reaction is vital for the cellular storage and transfer of free energy using energy carrier molecules. DEPHOSPHORYLATION - DADP Ap Dephosphorylation is the process by which phosphate groups are removed from a molecule by a phosphatase.