Biochem Lecture (1st Semester) PDF

BIOCHEM Lecture (1st semester) BIOCHEMISTRY BIO INORGANIC SUBSTANCES: Is sometimes called as “Biological Chemistry” May be defined as the investigation of molecular Substanc...

BIOCHEM Lecture (1st semester) BIOCHEMISTRY BIO INORGANIC SUBSTANCES: Is sometimes called as “Biological Chemistry” May be defined as the investigation of molecular Substances that do not contain carbon basis of life includes water and inorganic salts Is the study of Chemistry in living organisms. It The bioinorganic substance water constitutes over deals with biomolecules and biochemical reactions two-thirds of the mass of the human body viewed in context of biological structures Another 4%–5% of body mass comes from inorganic salt 3 BRANCHES: 45% BIO ORGANIC SUBSTANCES: 1. Structural [BIOMOLECULES] 2. Metabolism 3. Genetics Substances that contain carbon include carbohydrates, lipids, proteins, and nucleic ROOTS OF BIOCHEMISTRY acids ➔ Carl Scheele – Swedish founder of biochemistry. bioorganic molecules make up only about ¼ of body Studied the chemical composition of matter in mid mass 1700. oxygen & hydrogen -present in all living organisms ➔ Friedrich Wohler (1828) – prove the fallacy that biochemicals can only be produced by living organisms by producing urea by heating ammonium cyanate. urea ➔ Schleiden & Schwann – formulated the cell theory in 1840. ➔ Walther Flemming – discovered chromosomes in 1875. father of biochemistry ➔ Carl Neuberg – German scientist who coined the word “biochemistry” glycolysis ➔ Eduard & Hans Buchner – found that extracts from yeasts could bring about fermentation of sugar into alcohol in 1897. BIOMOLECULES ➔ Embden & Meyerhof – describe the glycolytic Present in plant and animal cells pathway in 1925. Composition of the cell: ➔ Hans Krebs – Proposed the Krebs cycle of the 50-95% - H2O TCA in 1937. 1% - Ions ➔ Avery, MacLeod & McCarty (1944) – identified others: organic molecules carbohydrates, lipids DNA as information molecules Organic molecules ? ➔ James Watson & Francis Crick (1953) – propose - Carbon based molecules that are covalently bonded the double helical structure of DNA. to itself or other elements like H, O, N, S, P. ➔ Francis Crick (1958) – proposed the central - One important organic molecule is the Hydrocarbon. dogma of biology ➔ Paul Boyer & John Walker – discovered the BIOMOLECULES: HYDROCARBON “rotary engine” that generated ATP in 1997. from DNA ➔ Jens Christian Skou – Danish biochemist who studied the “pump” that drives sodium and Biomolecules are derived from HC potassium across membranes Is non-polar, therefore, they are insoluble in H2O (Sodium-potassium-ATPase) Hydrophobic - Biomolecules with HC group – has ➔ Stanley Prusiner – discovered the organism that hydrophobic character (Cell membranes) caused “mad cow disease” prions two broad types: small biomolecules and ➔ Ernst Ruska– discovered the electron microscope macromolecules and provided a whole new level of insight into Importance of Macromolecules: cellular structure. a) Essential structures for the basis of life BIOCHEMICAL SUBSTANCE b) Control and regulate this processes c) Responsible for energy exchanges, irritability, a chemical substance found within a living organism metabolism, mobility and reproduction divided into 2 groups: Bioinorganic substances and Bioorganic substances 1 BIOCHEM Lecture (1st semester) Functions as: 4 MAJOR CLASSES OF SMALL BIOMOLECULES 1. Energy source 4 families of small molecules are found inside the cell 2. Structural components 1. Amino acids protteins 3. Intercellular communication 2. Sugars carbohydrate 3. Fatty acids lipids macromolecules Basic Unit of Sugar is Monosaccharides. It is also 4. Nucleotides nucleic acid known as simple sugar. What are their functions? 3-20 polygosaccharides A. They are used to synthesize large molecules like Monosaccharides can be described in terms of polymers (proteins, nucleic acids) functional group: B. Some have special biological functions (ATP – a a. Polyhydroxyl Aldehyde nucleotide) b. Polyhydroxyl Ketone C. Involve in complex reaction pathways Sugar containing an Aldehyde is called Aldose Sugar containing a ketone group is called Ketose AMINO ACIDS (AA) There are 20 common α-amino acids (usually in EXAMPLES: protein) 1. Glucose glucose + glucose (maltose) 2. Fructose fructose + glucose (sucrose) 3. Ribose RNA 4. Deoxyribose DNA SUGARS: POLYSACCHARIDES The chemical properties of the AA are determined a polymer containing large amount of largely by the R group monosaccharides are being used as to synthesize long chain polymer Examples: called Polymerization. 1. Glycogen – energy storage molecule human/ animals Short polypeptide – AA is less than 50 (and are 2. Starch – energy storage molecule plants called peptide) 3. Cellulose – structural material plants Longer polypeptides – are called Proteins FATTY ACIDS (FA) EX OF POLYPEPTIDES: - Monocarboxylic acid - usually contains an even number of carbon atoms - 1. Transport proteins hemoglobin, iron FAs are components of Lipids 2. Structural proteins collagen and keratin 3. Enzymes 2 TYPES OF FA AMINO ACIDS: PEPTIDE BONDS I. Saturated FA – are single bonded II. Unsaturated FA – contain one or more double bonds is the bond connecting the amino acids in the polypeptide Ex. of Saturated FA 1. Palmitic acid – hexadecenoic acid Ex. of Unsaturated FA 2. Oleic Acid (18:1) TRIACYLGLYCEROLS (FATS & OILS) NOTE: the R groups of the polypeptide determines its final 3-D shape and therefore its biological are ester containing glycerol and 3 FAs Glycerol functions. SUGARS are called as carbohydrates the most abundant organic molecules in nature 2 BIOCHEM Lecture (1st semester) a three carbon-alcohol with 3 hydroxyl group NUCLEIC ACIDS 1. Deoxyribonucleic Acid (DNA) - Contains/Stores -Genetic Information 2. Ribonucleic Acid (RNA) - Involves in expressing the information primarily in protein synthesis OTHER ROLE OF NUCLEOTIDES ADENOSINE TRIPHOSPHATE PHOSPHOLIPIDS involves in biosynthetic and energy generating reactions major component of cell membrane or the Ex: Formation of Phosphate bonds to form ATP plasma membrane -have hydrophilic head and tail OTHER EXAMPLES OF LIPIDS 1. Steroids EX: Cholesterol - a sex hormone - important part of animal cell membrane 2. Fat-soluble Vitamins - Vitamin E and Vitamin A 3. Carotenoids - a plant pigment molecule that plays a BIOCHEMICAL REACTIONS role in photosynthesis [ORANGE, BRIGHT RED, The sum of all the enzyme-catalyzed reactions in a YELLOW] living organism is called “Metabolism” Anabolism- small to larger molecules using ATP NUCLEOTIDES Catabolism- larger to small molecules the primary component of Nucleic Acids (GLYCOLYSIS) 3 COMPONENTS/ PARTS 4 FUNCTIONS OF METABOLISM 1. 5-C sugar 1. Acquisition and utilization of energy 2. Synthesis of molecules needed to cell structure and 2. Phosphate group function 3. Nitrogenous Base 3. Growth and development 4. Removal of waste products 2 CLASSES OF BASES: BIOCHEMICAL PROCESS there are 5 frequent chemical reactions: 1. Purine – A and G [ADENINE] and GUANINE 1. Nucleophilic substitution 2. Pyrimidine – T, C and U Electrophile - Electron-loving specie; usually a THYMINE, CYTOSINE AND URACIL cation, radical or lewis acid Nucleophile- Nucleus-loving specie; usually an NITROGENOUS BASES: anion or atom with a lone-pair electron-rich Leaving group - leaves with the bonding pair of electrons, and is replaced by the nucleophile; can be negatively charged or neutral HAVE 2 RINGS! -URACIL - CAN ONLY FOUND IN RNA 3 BIOCHEM Lecture (1st semester) HYDROLYSIS REACTION Methods of Determining Biomolecular Structures is the cleavage of covalent bonds by WATER Elemental Analysis a kind of SN reaction and can be catalyzed by an UV, visible, infrared, and NMR spectroscopy acid, base and enzymes Mass Spectroscopy (MS) X-ray Crystallography Specific sequencing methods (e.g., for proteins and nucleic acids) Use of battery of enzymes of known specificity to degrade biomolecule of study Use of acid or alkaline hydrolysis to degrade the biomolecule of study Importance: digestion of food involves Hydrolysis Hydrolysis of ATP – involves breaking of phosphate bonds 2. Elimination A double (=) bond forms when atoms are removed from the molecule. Dehydration of 2-phosphoglycerate 3. Addition Two molecules combine to form a single product From double bond to single bond 4. Isomerization (isomers- rearrangement of atoms) It involves intra-molecular shift of atoms Example of biochemical isomerization 1. Aldose-ketose pair 5. Redox involves transfer of electron from a donor (RA) to an electron acceptor (OA). Oxidation – Gain of Oxygen, Loss of Hydrogen Reduction – Loss of Oxygen, Gain of Hydrogen Ex. 4 BIOCHEM Lecture (1st semester) 5