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Introduction to Biochemistry. Connie Giroux BME 602 SDSMT/USD Spring 2007. Overview of Topics. History of Biochemistry Formation of Biomolecules Dynamic Functions of Biomolecules: amino acids peptides proteins enzymes carbohydrates lipids Cellular Metabolism.

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introduction to biochemistry

Introduction to Biochemistry

Connie Giroux

BME 602

SDSMT/USD

Spring 2007

overview of topics
Overview of Topics
  • History of Biochemistry
  • Formation of Biomolecules
  • Dynamic Functions of Biomolecules: amino acids peptides proteins enzymes carbohydrates lipids
  • Cellular Metabolism
biochemistry
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.
why study biochemistry
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.
history of biochemistry
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.
history of biochemistry6
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.
modern biochemistry
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.
elements in biomolecules
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.
elements in biomolecules10
Elements in Biomolecules
  • Biomolecules vary in their chemical structure and reactivity based on the chemical elements that are combined with them.
biological macromolecules
Biological Macromolecules
  • Three major classes of natural macromolecules found in biological cells: nucleic acids, proteins, and polysaccharides.
  • All macromolecules are polymers.
biological macromolecules12
Biological Macromolecules
  • Nucleic acids – heteropolymers composed of nucleotides.
  • Proteins – heteropolymers produced by joining together amino acids.
  • Polysaccharides – composed of many saccharide molecules.
supramolecular assemblies
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.
cells
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)
flow of biological information
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.
dna and rna
DNA and RNA
  • Structural and functional elements.
  • Biosynthesis of DNA and RNA.
  • Translation of RNA.
  • Recombinant DNA technology and their applications.
biomolecules in water
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.
amino acids
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.
peptides
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.
proteins
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).
four levels of protein structure
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.
enzymes
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.
enzymes28
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.
carbohydrates
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.
lipids
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.
cellular metabolism
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.
cellular metabolism32
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.
metabolism of carbohydrates
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.
metabolism of carbohydrates36
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.
metabolism of carbohydrates38
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).
metabolism of carbohydrates39
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.
slide40

Lactate Fermentation

Boyer, 1999

Ethanol Fermentation

Boyer, 1999

biosynthesis of carbohydrates
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.
atp formation by electron transport chains
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.
metabolism of fatty acids and lipids
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.
metabolism of amino acids and other nitrogenous compounds
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.
biochemistry at sdsm t
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
references
References
  • Boyer, R., 1999. Concepts in Biochemistry, Pacific Grove, CA: Brooks/Cole.
  • Fox, S.I., 2006. Human Physiology, New York, NY: McGraw-Hill.
additional resources
Additional Resources
  • http://web.indstate.edu/thcme/mwking/subjects.html
  • http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html