SBP3411 Cell Chemistry PDF

SBP3411 Cell chemistry/ Chemical basis of life Dr. Hanis H. Harith Dept. of Biomedical Science, UPM [email protected] Learning Outcomes At the end of this lecture the student is able to: Describe the chemical and molecular composition of cells Describe how cell chemistry influence...

SBP3411 Cell chemistry/ Chemical basis of life Dr. Hanis H. Harith Dept. of Biomedical Science, UPM [email protected] Learning Outcomes At the end of this lecture the student is able to: Describe the chemical and molecular composition of cells Describe how cell chemistry influences the properties of chemical components in cells Explain the roles of essential cellular components in cell biology Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM Lecture Outline Composition of an eukaryotic cell Types of chemical bonds Noncovalent interactions Water & Macromolecules Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Cell composition: H20, organic molecules, inorganic ions Water is an important component in cells A cell is composed of 70% H20 Intracellular reactions occur in an aqueous environment Most macromolecules are hydrophilic Each component is made up of a combination of elements Alberts et al. (2015). The Molecular Biology of the Cell (6th Ed) Each element consists of an atom Atoms interact by electron exchange (chemical bonds) The chemical components of a cell Fig 2.7: Alberts et al. (2018). Essential Cell Biology (5th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM Covalent bond(s) between atoms make up a molecule Bond strength influences the 3D shape of most Double bonds are macromolecules; single vs double bond shorter/stronger but less flexible e.g. ethene Polar bond Covalent bonds with unequal electron distribution form polar molecules e.g. water Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Ionic bonds generally make up salts Atoms donate/accept electrons (not shared) → electrically charged ions A noncovalent bond = electrostatic attraction e.g. NaCl Na atom donated an e- to Cl Na becomes positively charged (cation) = Na + Cl becomes negatively charged (anion) = Cl- Ionic bond forms between the oppositely charged ions Bond strength Ionic bonds are weaker than covalent bonds in aqueous environment due to the polarity of H20 → high solubility in water NaCl Fig 2.7: Alberts et al. (2018). Essential Cell Biology (5th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Molecules mainly interact via noncovalent interactions H bond & H2O Polar molecules (e.g. water) interact with each other via weak electrostatic attractions called hydrogen bonds. Hydrophilic molecules (e.g. salts) interact well with water because of their polarity Individually weak but Specific but transient strength increases with interactions between number molecules Noncovalent attractions Ionic bonds, hydrogen Easily broken by bonds, hydrophobic Hydrophobic molecules contain nonpolar random thermal force, van der Walls bonds and tend to interact with each other motions attractions due to repulsion from water molecules Hydrophobic molecules are uncharged and do not readily form H bonds in aqueous environment Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  The chemical properties of water facilitates intracellular pH regulation Some polar molecules form acids & bases in aqueous environment Alberts et al. (2014 ). Essen tial Cell Biology (4th Ed) Water dissociates into hydronium and hydroxyl ions Continuous, rapid and reversible reaction between water Strong acid/base (irreversible reaction) molecules vs Pure water = pH 7; [H3O+] = [OH-] Weak acid/base (reversible reaction) Increased [OH-] forces a decrease in [H3O+] Intracellular pH is regulated by the presence of weak acid/bases pH is maintained at around 7 by releasing or accepting protons Molecules with highly polar covalent bonds involving a H + e.g. molecules containing a carboxyl group (-COOH) vs an amino Modified from Alberts et al. (2014). Essential Cell Biology (4th Ed) group (-NH2) Weak acids/bases are more sensitive to pH changes Weak acid/bases release or accept protons less readily than strong acid/bases (partially ionize) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Small molecules are the building blocks in cells Organic molecules: carbon compounds synthesized by cells This is attributed to C’s ability to form up to four covalent bonds readily Each C atom can form highly stable covalent bonds with other C atoms to produce rings and chains; important for the backbone structure of complex molecules in cells Monomers refer Macromolecules: Polymers formed by covalently linked monomers to the small organic building Synthesis and breakdown involve specific sequential chemical reactions blocks Alberts et al. (2014). Essential Cell Biology (4th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Polysaccharides are composed of C, H and O Biological roles of polysaccharides in cells Glucose Glycogen Alberts et al. (2014). Essential Cell Biology (4th Edition) Glycolipids on the cell Glycoprotein membrane of RBC 1 Energy source/storage Cell adhesion e.g. 2 glycoprotein Cell recognition 3 e.g. blood typing Protein transport e.g. 4 N-linked glycoproteins are usually membrane- bound or secreted Modified from Lucila & von Andrian (2005) Encyclopedia of Life Sciences. Wiley Online Library. http://www.els.net/WileyCDA/ElsArticle/refId-a0000925.html https://www.chemistryviews.org/details/ezine/85221 Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM 31/Blood_Types_and_Carbohydrate_Chemistry.html  DNA structure is more Biological roles of nucleic acids/nucleotides in cells stable than RNA Nucleotide subunits are linked by phosphodiester bonds RNA DNA Storage of hereditary 1 information Breakdown of phosphoanhydride bonds Transient carriers release large amount of energy 2 of molecular instructions Source of 3 chemical energy e.g. ATP Karp (2013) Cell and Molecular Intracellular Biology: Concepts & Experiments 4 signaling e.g. (7th Ed) GDP/GTP DNA bases: A, T, C, G; RNA bases: A, U, C, G Alberts et al. (2014). Essential Cell Biology (4th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Biological roles of proteins in cells Proteins have diverse functions in various cellular processes Monomers of proteins: amino acids (aa) 20 types; each consists of a central ⍺-C atom, a carboxyl group, an amino group & a specific side chain A polypeptide has a structural polarity; N-terminus vs C-terminus Monomers of aa are linked A polypeptide folds into together by peptide bonds a unique 3D structure (involving noncovalent interactions) 1 Enzymes 2 Cell structure 3 Cell signaling 4 Cell metabolism 5 Cell motility 6 Cell cycle 7 Immune system e.g. Abs Karp (2013) Cell and Molecular Biology: Concepts & Experiments (7th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Protein function is determined by its 3D shape Protein folding is influenced by: Chemical properties of amino acids (side chains) – determine the noncovalent interactions involved Chaperone proteins – prevent formation of protein aggregates in crowded conditions of cytoplasm Temporarily bind to exposed hydrophobic regions in partly folded proteins or act as isolation chambers Alberts et al. (2014). Essential Cell Biology (4th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM A protein may be composed of separate functional domains Protein domains Segments of a polypeptide chain that fold independently into a compact stable structure Contain 40-350 aa Different domains in a protein usually have distinct functions E.g. Src protein kinase An enzyme involved in cell signalling Contains 2 domains which play a regulatory role: SH2, SH3 Contains a C-terminal domain that has a catalytic activity Alberts et al. (2015). The Molecular Biology of the Cell (6th Ed) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM Protein function depends on physical interaction with other molecules Selective binding of ligands: Ligands e.g. ions, small molecules or macromolecules bind to specific binding sites the binding site may be lost if protein is incorrectly folded or a change in aa sequence Some protein function can be enhanced by binding of small molecules e.g. heme groups in hemoglobin 1 hemoglobin = 4 heme groups (noncovalently bound) Ring-shaped molecule containing a single central iron atom Enables hemoglobin to transport oxygen from the lungs to other tissues Gives hemoglobin its red color Heme group Hemoglobin Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM Alberts et al. (2014). Essential Cell Biology (4th Ed) Strength of protein interaction depends on specificity Movie 2.4 Alberts et al. (2014). Essential Cell Biology (4th Ed) Specific interaction between molecules regulates protein function Mismatched molecules interact via few noncovalent interactions and easily separated by thermal motion A perfect fit maximizes the noncovalent interactions between molecules – bound to each other longer Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  Biological roles of lipids in cells Lipids/fat are made up of fatty acids (FA) Hydrophilic FA has both hydrophobic and hydrophilic regions (Amphipathic) carboxylic Its carboxyl group (-COOH) can form covalent bonds with other acid head molecules or acts as an acid in aqueous environment saturated vs unsaturated FA Some types of lipid are not amphipathic e.g. fat Triacylglycerol (Fat) Hydrophobic HC tail Modified from Alberts et al. (2014). Essential Cell Biology (4th Ed) Karp (2013) Cell and Molecular Biology: Concepts & Glycolipids Experiments (7th Ed) on the cell Ester bond links the membrane 1 Energy source/storage FA to glycerol of RBC Cell structure e.g. 2 cell membrane Cholesterol Cell recognition e.g. 3 glycolipids Cell signalling e.g. 4 steroid hormones Steroid hormones Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM Alberts et al. (2015). The Molecular Biology of the Cell (6th Ed) Summary: Cell chemistry significantly influences cell biology Cell biology: structure, size, function of living cells Macromolecules are important for cellular structure and function (polymer synthesis) Chemical properties of individual molecules determine the interaction Cell biology with other molecules and function non-covalent attractions 3D structure of larger & complex Chemical molecules Macromolecules elements Chemical bonds determine the chemical properties and structure of individual molecules polar vs non-polar molecules Small molecules Molecules/ Salts hydrophilic vs hydrophobic molecules (in aqueous environment) Hanis Harith SBP3411 (2023) Dept of Biomedical Science UPM  References Alberts, B., Bray, D., Hopkin, K., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P. (2014). Essential Cell Biology (4th Edition). New York: Garland Science, Taylor & Francis Group. Alberts, B., Johnson, A., Lewis, J., Morgan, D., Raff, M., Roberts, K. & Walter, P. (2015). Molecular Biology of The Cell (6th Edition). New York: Garland Science, Taylor & Francis Group Cooper, G.M. & Hausman, R.E. (2016). The Cell: A Molecular Approach (7th Edition). Massachusetts: Sinauer Associates, Inc. Karp, G. (2013). Cell and Molecular Biology: Concepts and Experiments (7th Edition). New Jersey: John Wiley & Sons, Inc. Lodish, H., Berk, A., Kaiser, C.A., Krieger, M., Bretscher, A., Ploegh, H., Amon, A. & Scott, M.P. (2013). Molecular Cell Biology (7th Edition). New York: WH Freeman and Company.