Introduction to Biochemistry

1. Introduction to Biochemistry Connie Giroux BME 602 SDSMT/USD Spring 2007

2. Overview of Topics • History of Biochemistry • Formation of Biomolecules • Dynamic Functions of Biomolecules: amino acids peptides proteins enzymes carbohydrates lipids • Cellular Metabolism

3. Biochemistry • “The chemistry of the living cell.” • Describes the processes of life at the level of molecules. • Has components of both biology and chemistry. • Need an understanding of the biological function of cellular molecules. • Need knowledge of chemical structures of the participating molecules.

4. Why Study Biochemistry? • Biochemistry provides a fundamental understanding of life. • Assists in our understanding of medicine, health, and nutrition. • Biochemical discoveries will advance biotechnology-the application of biological cells, cell components, and biological processes to technically useful operations.

5. History of Biochemistry • Early studies in biology had firm roots in philosophy and religion. • Studies concentrated on treatment of illness and attainment of good health. • Fourth century B.C.-Chinese believed humans contained five elements: water, fire, wood, metal, and earth. • Early Greeks-explained the body in terms of cosmological theories and used diet for the treatment of disease.

6. History of Biochemistry • Arabic biology - greatly influenced by early Greek scientific literature and advanced Greek pharmaceutical recipes by determining and classifying the strength and chemical nature of natural drugs. • Europe - Paracelsus (1493-1541 A.D.) had revolutionary ideas about medicine and biology. • 17th and 18th century biologists - had a more molecular approach to the study of biological material and processes. • 19th century – used vitalism to describe any biological process that could not be understood in chemical terms.

7. Modern Biochemistry • Two distinct paths led to current understanding: • 1st path - physical sciences used to emphasize the structural characteristics of biomolecules. • Basic laws of physics and chemistry are used to explain the processes of living cells. • 20th century – Linus Pauling used X-ray crystallography to study protein structures. • 2nd path – the study of cell organization and function by biologists, physiologists, and geneticists. • 1952 – two paths converged when double helix structure for DNA was proposed by James Watson and Francis Crick.

8. Boyer, 1999

9. Elements in Biomolecules • Over 100 chemical elements – only about 28 occur naturally in plants and animals. • Three categories for elements found in biological material: • 1: Elements found in bulk form and are essential for life: C, H, O, N, P, S (make up 92% of the dry weight of living things). • 2: Elements found in trace quantities and very likely essential for life: Ca, Mn, Fe, I. • 3: Trace elements that may be essential for life: As, Br, Mo.

10. Elements in Biomolecules • Biomolecules vary in their chemical structure and reactivity based on the chemical elements that are combined with them.

11. Biological Macromolecules • Three major classes of natural macromolecules found in biological cells: nucleic acids, proteins, and polysaccharides. • All macromolecules are polymers.

12. Biological Macromolecules • Nucleic acids – heteropolymers composed of nucleotides. • Proteins – heteropolymers produced by joining together amino acids. • Polysaccharides – composed of many saccharide molecules.

13. Supramolecular Assemblies • Organized clusters of macromolecules. • Cell membranes: complexes of proteins and lipids. • Chromatin: complexes of DNA and proteins. • Ribosomes: complexes of RNA and proteins. • Viruses: single DNA or RNA molecule contained in a protein package.

14. Cells • Fundamental unit of life. • Living cells contain compounds representing all three states of matter (gases, liquids, and solids). • Three basic classifications of organisms: • Eukaryotes (distinct membrane-enclosed nucleus and well-defined internal compartments) • Prokaryotes (simple, unicellular organisms with no distinct nucleus or internal cellular compartments) • Archaebacteria (thrive in extreme environments)

15. Flow of Biological Information • DNA • Signal transduction – the presence of a molecule outside of the cell which relays a command to an interior cell component.

16. Boyer, 1999

17. DNA and RNA • Structural and functional elements. • Biosynthesis of DNA and RNA. • Translation of RNA. • Recombinant DNA technology and their applications.

18. Biomolecules in Water • Typical cell contains 70 to 85% water. • Water can be used as a solvent or as a reactant molecule. • Hydrolysis – breaking of a chemical bond by water. • All biomolecules are not soluble in water. • Organisms create membranes from water insoluble molecules.

19. Amino Acids • Amino acid – any organic molecule with at least one carboxyl group (organic acid) and at least one amino group (organic base). • 20 amino acids are genetically coded for incorporation into proteins. • Comprised of carbon center (α-carbon) surrounded by a hydrogen, a carboxyl group, an amino group, and an R side chain. • Side chain determines the unique chemical and biological reactivity of each amino acid.

20. Boyer, 1999

21. Peptides • Peptide bond – carboxyl group on one amino acid bonds with the amino group of the other amino acid through condensation (loss of a water molecule). • Peptides – contain 2 to 10 amino acids. • Polypeptides – contain 10 to 100 amino acids. • Proteins – contain more than 100 amino acids.

22. Proteins • Provide mechanical support to cells and organisms. • Used as a biological catalyst (enzyme). • Used to transport smaller biomolecules and store nutrients. • Are functional components of the contractile system of skeletal muscle. • Used as a defense mechanism (antibodies). • Regulates cellular and physiological activity (hormones). • Mediates transmission of nerve impulses and hormone signals (receptor proteins).

23. Four Levels of Protein Structure • Primary Structure: the sequence (order) of amino acid residues in a protein held together by covalent peptide bonds. • Secondary Structure: localized regions of the primary sequence folded into regular, repeating structures (α-helix or β-sheet). • Tertiary Structure: secondary structural elements interact and pack into a compact globular unit. • Quarternary Structure: association of two or more polypeptide chains to form a multi-subunit protein molecule.

24. Boyer, 1999

25. Enzymes • Biological catalysts. • Michaelis-Menten Equation – mathematical relationship between the rate of an enzyme-catalyzed reaction and the concentration of an enzyme and substrate. • Lineweaver-Burk Equation – reciprocal of the Michaelis-Menten equation; Lineweaver-Burk plot used to determine constants for enzyme-catalyzed reactions and evaluates the inhibition of enzyme reactions.

26. ν0 = Vmax [S]/ {KM + [S]} Boyer, 1999

27. 1/ν0 = {KM/Vmax} {1/[S]} + 1/Vmax Boyer, 1999

28. Enzymes • Coenzymes – organic or organometallic molecule that assists an enzyme. • Allosteric enzymes – transmit messages, through conformational changes, between binding sites that are spatially distinct. • Isoenzymes – multiple forms of an enzyme that have similar but not identical amino acid sequences and reaction characteristics.

29. Carbohydrates • Used in energy metabolism (glucose). • Performs structural functions (plant cell walls and exoskeleton shells). • Ribose and deoxyribose (components of nucleic acids) serve a chemical structural role in RNA and DNA and are polar sites for catalytic processes (RNA). • Serves as a marker for molecular recognition by other biomolecules.

30. Lipids • Distinctive characteristic is their solubility behavior. • Hydrophobic nature so more soluble in non-polar solvents (diethyl ether, methanol, hexane) than in water. • Defined by their physical behavior rather than their chemical structure. • Lipid families: fatty acids, triacylglycerols, polar lipids, steriods. • Membranes – fluid–mosaic model, active and passive transport, Na+-K+ ATPase pump, and ion-selective channels.

31. Cellular Metabolism • Catabolism is divided into three major stages: • 1: Breakdown of macromolecules (proteins, fats, polysaccharides) – preparation stage for the next level of reactions. • 2: Amino acids, fatty acids, and monosaccharides are oxidized to a common metabolite, acetyl CoA. • 3: Acetyl CoA enters citric acid cycle and is oxidized to CO2, the end product of aerobic carbon metabolism.

32. Cellular Metabolism • Anabolism is divided into three stages: • 1: Monosaccharide and polysaccharide syntheses may begin with CO2, oxaloacetate, pyruvate, or lactate. • 2: Amino acids for protein synthesis are formed from acetyl CoA and by the amination of pyruvate and α-keto acids from the citric acid cycle. • 3: Triacylglycerols are constructed using fatty acids synthesized from acetyl CoA.

33. Boyer, 1999

34. Fox, 2006

35. Metabolism of Carbohydrates • Glycolysis – consists of ten enzyme-catalyzed reactions that begin with a hexose substrate and split into two molecules of pyruvate, an α-keto acid. • Two stages of glycolysis: • 1: Investment stage – glucose (a six-carbon substrate) is split into two molecules of a three-carbon metabolite; two ATP molecules are consumed for each glucose molecule that enters pathway.

36. Metabolism of Carbohydrates • 2: Dividend stage – each three-carbon metabolite is transformed into another three-carbon metabolite (pyruvate). • Four ATP molecules and two NADH molecules produced in stage 2. • Overall yield: two ATP and two NADH.

37. Figure 5.2 Glycolysis Fox, 2006

38. Metabolism of Carbohydrates • Lactate fermentation – most common fermentation process. • Transforms glucose to lactate. • Occurs in a variety of anaerobic microorganisms and in animal muscle during periods where low amounts of oxygen are available (strenuous activity).

39. Metabolism of Carbohydrates • Ethanol fermentation – production of ethanol by strains of yeast and other microorganisms. • Consists of a two reaction sequence: • 1: a nonhydrolytic cleavage step. • 2: reduction of the carbonyl in acetaldehyde to form ethanol.

40. Lactate Fermentation Boyer, 1999 Ethanol Fermentation Boyer, 1999

41. Biosynthesis of Carbohydrates • Synthesis of glucose – gluconeogenesis. • Formation of NDP-glucose (nucleotide diphosphate glucose). • Formation of UDP-galactose (uridine diphosphate-galactose). • Synthesis of glycogen, starch, lactose, sucrose, and cellulose.

42. ATP Formation by Electron-Transport Chains • Electron transport results in large amounts of free energy to be available for use. • Oxidative energy occurs in the form of electrons with high transfer potential located in the reduced cofactors, NADH and FADH2. • Energy in reduced cofactors is recovered by using molecular oxygen as a terminal electron acceptor (oxidizing agent). • More complete oxidation of substrate occurs with O2 than in anaerobic metabolism.

43. Fox, 2006

44. Metabolism of Fatty Acids and Lipids • Metabolism of dietary triacylglycerols. • Catabolism of fatty acids (β oxidation). • Metabolism of ketone bodies. • Biosynthesis of fatty acids. • Biosynthesis of cholesterol. • Metabolism of cholesterol.

45. Metabolism of Amino Acids and Other Nitrogenous Compounds • Nitrogen cycle – flow of nitrogen atoms between the atmosphere and biosphere. • Anabolism and Catabolism of Amino Acids. • Urea cycle – a mechanism to detoxify NH3; uses carbon in CO2, nitrogen in glutamate, and NH3 to synthesize urea.

46. Biochemistry at SDSM&T • Chem 460/560 Biochemistry • Prerequisites: Chem 112 General Chemistry I Chem 114 General Chemistry II Chem 326 Organic Chemistry I Chem 328 Organic Chemistry II • Recommended courses: Labs for Chemistry courses Biology courses: Biol 151 & 151L General Biology I and Lab Biol 153 & 153L General Biology II and Lab Biol 123 & 123L Basic Physiology and Lab

47. References • Boyer, R., 1999. Concepts in Biochemistry, Pacific Grove, CA: Brooks/Cole. • Fox, S.I., 2006. Human Physiology, New York, NY: McGraw-Hill.

48. Additional Resources • http://web.indstate.edu/thcme/mwking/subjects.html • http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html