Chapter 1 - Intro Biochemistry Lecture Notes PDF

CHEM 311 Biochemistry I (3 Lectures, 3 Laboratories – 4 Credits) Prof. Syed Salman Ashraf Department of Chemistry, CoAS CHAPTER 1: BIOCHEMISTRY FUNDAMENTALS Lecture Outline  Basic Themes: functional groups, biomolecules and macromolecules  Origins of Life: RNA early molecule  Prokaryotes vs. Euka...

CHEM 311 Biochemistry I (3 Lectures, 3 Laboratories – 4 Credits) Prof. Syed Salman Ashraf Department of Chemistry, CoAS CHAPTER 1: BIOCHEMISTRY FUNDAMENTALS Lecture Outline  Basic Themes: functional groups, biomolecules and macromolecules  Origins of Life: RNA early molecule  Prokaryotes vs. Eukaryotes  Kingdoms and Domains  Biochemical Energetics Levels of Structural Organization in the Human Body Chemical Foundations of Biochemistry Organic chemistry: the study of the compounds of carbon the cellular apparatus of living organisms is made up of carbon compounds biomolecules - molecules produced in living organisms the reactions of biomolecules can be described by the methods of organic chemistry The experiment of Friedrich Wöhler in 1828 Biomolecules – Functional groups Functional group: an atom or group of atoms that show characteristic physical and chemical properties Biomolecules – Functional groups ATP – the energy currency of the cell ATP – the energy currency of the cell Phosphoester Phosphoanhydride Origins of Life The “big bang” theory all matter was originally confined in a very small space as the result of an explosion, it started to expand with great force; temperature approx. 15 x 109 K the average temperature of the universe has been decreasing ever since in the earliest stages of the universe, the only elements present were H, He, and Li other elements formed by thermonuclear reactions in stars explosions of stars the action of cosmic rays outside the stars Relative Abundance of Important Elements Biomolecules Gases present in the atmosphere of the early earth included NH3, H2S, CO, CO2, CH4, N2, H2, and H2O Experiments have demonstrated that important biomolecules, such as proteins and nucleic acids, could have arisen under abiotic (nonliving) conditions from reactions of these simple compounds in the earth’s oceans on the surface of clay particles Biomolecules (Cont’d) Living cells include very large molecules, such as proteins, nucleic acids, polysaccharides, and lipids these biomolecules are polymers (Greek: poly + meros, many + parts) they are derived from monomers (Greek: mono + meros, single + part) --amino acids → proteins --nucleotides → nucleic acids --monosaccharides → polysaccharides --glycerol and 3 fatty acids → lipids → Lipid membranes Proteins and Nucleic Acids play a role in life processes. Biological macromolecules (biopolymers) Directionality in Macromolecules Directionality in macromolecules. Biological macromolecules and their building blocks have a “sense” or directionality. N-terminus C-terminus Directionality in Macromolecules H2N-Serine – Valine – Tyrosine – Cysteine-COOH Note: Ser-Val-Tyr-Cys is NOT the same as Cys-Tyr-Val-Ser! Directionality in Macromolecules Example of polysaccharides are starch and cellulose; both are C1 to C4 linkages, but the linkage is α-C1toC4 in starch and βC1toC4 in cellulose Directionality in Macromolecules The 3' hydroxyl group forms a bond to the phosphorus atom of the free nucleotide closest to the 5' oxygen atom. Meanwhile, the bond between the first phosphorus atom and the oxygen atom linking it to the next phosphate group breaks The 5' group of a nucleotide triphosphate is held close to the free 3' hydroxyl group of a nucleotide chain. In nucleic acids the 3'-OH of the ribose ring of one nucleotide forms a bond to the 5'-OH of the ribose ring of a neighboring nucleotide. Source: https://www.chem.wisc.edu/deptfiles/genchem/netorial/modules/ biomolecules/modules/dna1/dna13.htm A new phosphodiester bond now joins the two nucleotides. Biomolecules (Cont’d) Enzymes: a class of proteins (and RNA) that display catalytic activity. the catalytic effectiveness of a given enzyme depends on its amino acid sequence Genetic code: the relationship between the nucleotide sequence in nucleic acids and the amino acid sequence in proteins 3 D structure of Human salivary amylase http://www.rcsb.org/pdb/explore.do?structureId=1smd Molecules to Cells: Biomolecules (Cont’d) catalytic activity normally associated with proteins coding associated with nucleic acids It has been discovered recently that certain types of RNA have catalytic activity (ribozymes) and are capable of catalyzing their own further processing. RNA is now considered by many scientists to have been the original coding material it still serves this function in some viruses In 1989, American Scientists Thomas R Chech and Sidney Altman shared Nobel Prize in chemistry for their discovery of catalytic properties of RNA Hairpin ribozyme Catalyzes self-cleavage and joining (ligation) The Biggest Biological Distinction-Prokaryotes and Eukaryotes Prokaryote: Greek derivation meaning “before the nucleus” single-celled organisms include bacteria (cyanobacteria are bacteria) and archae (e.g. methanogens; extremophiles) Eukaryote: Greek derivation meaning “true nucleus” contain a well-defined nucleus surrounded by a nuclear membrane can be single celled, such as yeasts (which are fungi), or multicellular, such as animals and plants Comparison of Prokaryotes and Eukaryotes Summary of Organelles and their Function(s) Biochemical Energetics All cells require energy to functions Light from the sun is the ultimate source of energy for all life on earth photosynthetic organisms use light energy to drive the energy-requiring synthesis of carbohydrates non-photosynthetic organisms consume these carbohydrates and use them as energy sources The energetics of a chemical reaction (free energy: ΔG) if ΔG < 0 (free energy decreases), the reaction is spontaneous; exothermic or exergonic ΔG > 0 (free energy increases), the reaction will not occur unless energy is supplied from an external source ; endothermic or endorgonic Biochemical Energetics Exergonic vs Endergonic Reactions Exothermic/Exergonic reactions are favored Endothermic/Endergonic reactions are NOT favored Exergonic vs Endergonic Reactions Exergonic vs Endergonic Reactions Activation Energy… EA