BCH 3033: Biochemistry 1 Fall 2024 Lecture Notes PDF

BCH 3033: Biochemistry 1 08.23.2024 – Ch. 1 DONELLA BECKWITH, Ph.D. [email protected] 1  [email protected] What is Biochemistry? “Chemistry of the living cell” GOAL: Explain in mole...

BCH 3033: Biochemistry 1 08.23.2024 – Ch. 1 DONELLA BECKWITH, Ph.D. [email protected] 1  [email protected] What is Biochemistry? “Chemistry of the living cell” GOAL: Explain in molecular terms the structures, mechanisms, and chemical BIOCHEMISTRY processes shared by all organisms and provide the organizing principles that underlie life in all its diverse forms Uses basic laws of chemistry, biology, and physics to explain processes of living cells Has aspects of many different disciplines: cell biology, genetics, immunology, microbiology, pharmacology, and physiology… Asks how the remarkable properties of living organisms arise from thousands of different biomolecules 2 Life Arose on Earth Around 4 Billion Years Ago Simple microorganisms: Extracted energy from chemical compounds and sunlight Used energy to make biomolecules from the simple elements and compounds on the Earth’s surface Nearly all the elements in the human body were made in a star We Are Stardust 3  [email protected] Organisms Smallest organisms (microorganisms): consist of single cells Multicellular organisms: larger and contain many different types of cells Vary in shape, size, and function Share fundamental properties: Cytoplasm: aq. solution of cytosol ~20 nm Plasma membrane: 0.020 µm hydrophobic barrier of lipids and proteins Ribosomes: site of protein synthesis Nucleus: complete set of genes is replicated and stored (has “Prokaryote” “Eukaryote” membrane) 4  [email protected] Organisms Belong to Three Distinct Domains of Life Diverged early in evolution: Bacteria: inhabit soils, surface waters, and the tissues of other living or decaying organisms Archaea: inhabits extreme environments (hot springs, acid bogs, and ocean depths) Eukarya: all eukaryotic organisms; are more closely related to archaea than bacteria It is important to think about how these organisms get their energy…. 5  [email protected] Organisms: Their Source of Energy Classified according to how they obtain the energy and carbon they need for synthesizing cellular material: Phototrophs: trap and use sunlight Chemotrophs: derive energy from oxidation of a chemical fuel Fe2+ to Fe3+ Autotrophs: can synthesize all their biomolecules directly from CO2 Heterotrophs: require some preformed organic nutrients made by other organisms 6  [email protected] Organisms: Their Source of Energy 7  [email protected] Organisms: Their Source of Energy Classified according to how they obtain the energy and carbon they need for synthesizing cellular material: Question Phototrophs: trap and use sunlight Humans are which of the following: Chemotrophs: derive energy from oxidation of a chemical fuel A. photoautotrophs B. chemoautotrophs Fe2+ to Fe3+ C. photoheterotrophs Autotrophs: can synthesize D. chemoheterotrophs all their biomolecules directly from CO2 Heterotrophs: require some preformed organic nutrients made by other organisms 8  [email protected] Organisms: Their Source of Energy Classified according to how they obtain the energy and carbon they need for synthesizing cellular material: Question Phototrophs: trap and use sunlight Cyanobacteria are: Chemotrophs: derive energy from oxidation of a chemical fuel A. photoautotrophs B. chemoautotrophs Fe2+ to Fe3+ C. photoheterotrophs Autotrophs: can synthesize D. chemoheterotrophs all their biomolecules directly from CO2 Heterotrophs: require some preformed organic nutrients made by other organisms 9  [email protected] Bacterial and Archaeal Cells Common features: Cell envelope: a single or double membrane with a thick, rigid layer of peptidoglycan or lipopolysaccharide (LPS) on its outside surface Pili: provide adhesion points Flagella: propel cell through its surroundings Ribosomes: site of protein synthesis from an RNA messenger Nucleoid: contains 1 or several long, circular DNA molecules Escherichia coli (E. coli): Plasmids: circular 2 µm long and 1 µm in diameter segments of DNA in cytoplasm Protective outer membrane and inner plasma membrane Between the membranes are a thin layer of peptidoglycan (responsible for shape) Gram-negative 10  Gram-Negative/Positive [email protected] Parameter Gram-Positive Bacteria Gram-Negative Bacteria Cell wall Single-layer, smooth cell wall Double-layered, wavy Cell wall thickness 20-80 nm 8-10 nm Peptidoglycan layer Thick layer (can be multilayered) Thin layer (often single-layered) Toxins Present and released Present but cell wall must be disturbed Lipopolysaccharide Not present Present Outer membrane Not present Mostly present Lipid content Very low 20-30% Resistance to antibiotics Very susceptible Very resistant Shape Spherical, rod, or branching Spherical, rod, or spiral 11  [email protected] Archaea and Bacteria Subgroups by Habitats Aerobic: plentiful supply of O2; organisms transfer electrons from Question fuel to O2 for energy You discover a new single-celled organism in a salt lake. Subsequent laboratory experiments Anaerobic: devoid of O2; reveal that the organism can live in the presence organisms transfer electrons to or absence of oxygen. This organism would nitrate, sulfate, or CO2 for energy most likely be classified as: Obligate anaerobes: die when A. an obligate anaerobe in the Bacterial domain exposed to O2 B. an obligate anaerobe in the Archaeal domain Facultative (fac-ul-tative) C. a facultative anaerobe in the Archaeal domain anaerobes: can live with or D. a facultative anaerobe in the Bacterial domain without O2 12  [email protected] Eukaryotic Cells Present in the cytoplasm: 5-100 µm (not membrane-bound) Mitochondria: site of most of the energy- extracting reactions of the cell, oxidative phosphorylation which generates ATP by utilizing the energy released during the oxidation of the food we eat, membrane bound Endoplasmic reticulum and Golgi complexes: play central roles in the synthesis and processing of lipids and membrane proteins, membrane bound Peroxisomes: site of the oxidation of very- long-chain fatty acids and detoxification of reactive oxygen species, membrane bound Lysosomes: filled with digestive enzymes that degrade intracellular debris, membrane bound Granules or droplets: containing stored nutrients such as starch and fat 13  [email protected] Subcellular Fractionation of Tissue Method for separating organelles from the cytosol and from each other: 1st : gently disrupt cells or tissues by physical shear to rupture the plasma membrane (homogenize), internal contents spill out and mix together 2nd : centrifuge the homogenate at a high rate of speed (differential Nuclei and centrifugation) cellular debris 3rd : depending on the speed you use; different parts of the cell will accumulate at the bottom of the tube (organelles differ in size and density and sediment at different rates) Review Example and Speeds... 14  [email protected] Question Which organelle is found in both plant and animal cells? A. starch granule B. chloroplast C. mitochondria D. glyoxysome 15  [email protected] Question Differential centrifugation is based on the differences in sedimentation rate of biological particles of different __________. A. Density B. Size and density C. Size D. Structure 16  [email protected] The Cytoplasm Is Organized by the Cytoskeleton and Is Highly Dynamic cytoskeleton = three-dimensional network of protein filaments in eukaryotic cells and it provides many functions -Internal transportation system: shuttling material throughout the cell Three types of fibers within the cytoskeleton: -actin filaments (microfilaments) -microtubules -intermediate filaments https://directorsblog.nih.gov/2020/01/09/seeing-the-cytoskeleton-in-a-whole-new-light/ Microtubules Actin Intermediate filaments (outside) 17  [email protected] Cytoskeletal Filaments actin filaments microtubules microtubules chromosomes chromosomes centrosomes intermediate filaments Fluorescence Microscopy: Super resolution: allows us to see only specific tiny structures by adding 18 fluorescent molecules to only those components (link)  [email protected] The Structural Organization of the Cytoplasm endomembrane system = segregates specific metabolic processes and provides surfaces on which certain enzyme-catalyzed reactions occur exocytosis and endocytosis = mechanisms of transport (out of and into cells, respectively) – involve membrane fusion and fission – provide paths between the cytoplasm and the surrounding medium 19  [email protected] Endocytosis –vs- Exocytosis Extracellular fluid Cell takes in substances from Cell releases intracellular the outside of the cell by substances by merging vesicular engulfing them in a vesicle membrane into the cell membrane Examples: Cholesterol Proteins, neurotransmitters 20  [email protected] Cells Build Supramolecular Structures Cells use a relatively small set of carbon-based metabolites to create polymeric machines, supramolecular structures, and information repositories held together by Non-covalent Covalently linked noncovalent interactions (hydrogen bonds, nucleus ionic interactions, van der Waals interactions, and the hydrophobic effect) Plant cell 21  [email protected] In Vitro Studies May Overlook Important Interactions among Molecules One approach to understanding a biological process is to study purified molecules in vitro = “in glass” -without interference from other molecules present in the intact cell -example: enzymes in vivo = “in the living” molecules may behave differently in vivo and in vitro 22  [email protected] Question Supramolecular complexes, such as chromatin, are held together by: A. covalent bonds between monomeric units. B. noncovalent interactions, such as hydrogen bonds. C. covalent bonds between macromolecules. D. interactions between the cytoskeleton and organelles. 23  [email protected] Elements Essential to Animal Life and Health Fewer than 30 of the more than 90 naturally occurring elements are essential Four most abundant elements in living organisms: H, O, N, and C The elements shaded in red: Are structural components of cells and tissues 24 Required in the diet in gram quantities daily  [email protected] Biomolecules Are Compounds of Carbon with a Variety of Functional Groups carbon can form covalent single, double, and triple bonds 25  [email protected] Geometry of Carbon Bonding carbon atoms have a characteristic tetrahedral arrangement of their four single bonds free rotation around each single bond limited rotation about the axis of a double bond 26  [email protected] Common Functional Groups of Biomolecules H atoms replaced by a Derivatives of variety of functional hydrocarbons groups that confer specific chemical properties 27  [email protected] Additional Functional Groups of Biomolecules 28  [email protected] Question Important functional groups in biomolecules include: A. lipids. B. thioesters. C. nucleic acids. D. carbons. 29  [email protected] Many Biomolecules Are Polyfunctional Polyfunctional: contain two or more types of functional groups Acetyl-coenzyme A (Acetyl-CoA): metabolite derived from glucose, fatty acid, and amino acid catabolism (glucose pyruvate Acetyl-CoA) Important take away: the chemical “personality” of a compound is determined by the chemistry of its functional groups and their disposition in 3D space 30  [email protected] Cells Contain a Universal Set of Small Molecules central metabolites: occur in nearly every cell and are trapped in the cell because the plasma membrane is impermeable to them – common amino acids – nucleotides – sugars and their phosphorylated derivatives – mono-, di-, and tricarboxylic acids secondary metabolites = specific to the organism - give plants their scent and color metabolome = entire collection of small molecules in a given cell under a specific set of conditions – metabolomics = the systematic characterization of the metabolome under very specific conditions 31  [email protected] Macromolecules Are the Major Constituents of Cells macromolecules = polymers with molecular weights above ~5,000 Da that are assembled from relatively simple precursors – proteins – nucleic acids – polysaccharides oligomers = shorter polymers (a few monomer units) informational macromolecules = name for proteins, nucleic acids, and some oligosaccharides, given their information-rich subunit sequences (many times these carry genetic information) 32  [email protected] Biomolecules Carbohydrates Lipids Proteins Nucleic Acids High Energy Compounds 33  [email protected] Protein Macromolecules proteins = long polymers of amino acids – can function as enzymes, structural elements, signal receptors, transporters 34  [email protected] Question Proteins are classified as macromolecules because they: A. can associate noncovalently into very large structures. B. are polymers with molecular weights above ~5,000 Da. C. can function as enzymes, structural elements, signal receptors, or transporters. D. are composed of multiple oligomers. 35  [email protected] Nucleic Acid Macromolecules nucleic acids = DNA and RNA = polymers of nucleotides – store and transmit genetic information – some RNA molecules have structural and catalytic roles in supramolecular complexes genome = entire sequence of a cell’s DNA or RNA genomics = the characterization of the structure, function, evolution, and mapping of genomes 36  [email protected] Biomolecules Carbohydrates Lipids Proteins Nucleic Acids High Energy Compounds 37  [email protected] Polysaccharide Macromolecules Polysaccharides: polymers of simple sugars – energy-rich fuel stores – rigid structural components of cell walls (in plants and bacteria) – extracellular recognition elements that bind to proteins on other cells oligosaccharides: shorter polymers of sugars glycome: entire complement of carbohydrate-containing molecules 38  [email protected] Lipid Molecules lipids = water-insoluble hydrocarbon derivatives – structural components of membranes – energy-rich fuel stores – pigments – intracellular signals lipidome = the lipid containing molecules in a cell 39  [email protected] Building Blocks of Biochemistry 40  [email protected] Question What nucleobase is not present in DNA? A. Cytosine B. Adenine C. Guanine D. Uracil 41  [email protected] Interactions between Biomolecules Are Stereospecific 42  [email protected] Biological Systems Can Distinguish Stereoisomers stereospecificity = the ability to distinguish between stereoisomers 43 Physical Foundations 44  [email protected] Living Organisms Exist in a Dynamic Steady State, Never at Equilibrium with Their Surroundings small molecules, macromolecules, and supramolecular complexes are continuously synthesized and broken down living cells maintain themselves in a dynamic steady state distant from equilibrium - a system at equilibrium cannot perform work - a system in a steady state has a higher level of energy than its surroundings maintaining steady state requires the constant investment of energy 45  [email protected] Organisms Transform Energy and Matter from Their Surroundings system = all the constituent reactants and products, the solvent that contains them, and the immediate atmosphere universe = system and its surroundings types of systems: – isolated = system exchanges neither matter nor energy with its surroundings (bomb calorimeter, closed thermos bottle) – closed system = system exchanges energy but not matter with its surroundings (earth, baggie of ice on an injury) – open system = system exchanges both energy and matter with its surroundings (human, automobile engine) 46  Question A living organism is a(n): A. isolated system. B. closed system. C. open system. D. universe. 47  [email protected] Energy Transformation in Living Organisms First law of thermodynamics: in any physical or chemical change, the total amount of energy in the universe remains constant, although the form of the energy may change Energy is used by a system, but IT IS NOT USED UP 48 It is converted from one form to another  [email protected] Extracting Energy from the Surroundings photoautotrophs: during photosynthesis the light-driven splitting of water releases its electrons for the reduction of CO2 and the release of O2 into the atmosphere chemotrophs: oxidize energy rich products of photosynthesis stored in plants, then passing the electron acquired to atmosphere O2 to form water, CO2, …. 49  [email protected] Oxidation-Reduction Reactions autotrophs and heterotrophs participate in global cycles of O2 and CO2, driven by sunlight, making these two groups interdependent All of these reaction involved in electron flow ARE oxidation-reduction reactions = one reactant is oxidized (loses electrons) as another is reduced (gains electrons) – describes reactions involved in electron flow – OIL (oxidation is loss) – RIG (reduction is gain) 50  [email protected] Creating and Maintaining Order Requires Work and Energy second law of thermodynamics: randomness in the universe is constantly increasing (ever greater disorder) entropy, S = represents the randomness or disorder of the components of a chemical system To bring about the synthesis of macromolecules from their monomeric units, free energy must be supplied to the system (cell) 51  [email protected] Free Energy, G enthalpy, H = heat content, roughly reflecting the number and kinds of bonds free energy, G, of a closed system = H – TS, where H represents enthalpy, T represents absolute temperature, and S represents entropy 52  [email protected] Three-Dimensional Structure Is Described by Configuration and Conformation configuration = the fixed spatial arrangement of atoms stereoisomers = molecules with the same chemical bonds and same chemical formula stereospecific = requiring specific conformations in the interacting molecules – describes typical interactions between biomolecules 53  [email protected] Illustrating Stereochemistry 54  [email protected] Configurations of Geometric Isomers geometric isomers, or cis-trans isomers = differ in the arrangement of substituent groups with respect to the double bond 55  [email protected] Chiral and Achiral Molecules chiral centers = asymmetric carbons a molecule can have 2n stereoisomers, where n is the number of chiral carbons 56  [email protected] Question Molecules that differ in configuration cannot be: A. stereoisomers. B. cis-trans isomers. C. chiral centers that are mirror images of each other. D. chiral centers that can be interchanged by rotation of a single bond. 57  [email protected] Enantiomers and Diastereomers enantiomers = stereoisomers that are mirror images of each other diastereomers = stereoisomers that are not mirror images of each other 58  [email protected] Optical Activity of Enantiomers enantiomers have nearly identical chemical reactivities, but differ in optical activity a racemic mixture (equimolar solution of two enantiomers) shows no optical rotation 59  [email protected] Naming Stereoisomers Using the RS System each group attached to a chiral carbon is assigned a priority, where: —OCH3 > —OH > —NH2 > —COOH > —CHO > —CH2OH > —CH3 > —H 60  [email protected] Question Enantiomers: A. are only associated with amino acids. B. can be specific types of diastereomers. C. are always designated either D or L. D. can exist for molecules with more than one chiral carbon. 61  [email protected] Molecular Conformation conformation = the spatial arrangement of substituent groups that are free to assume different positions in space 62