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Biophysics II Life: based on materials By A/Prof. Xiang Yang Liu Biophysics & Micro/nanostructures Lab Department of Physics, NUS Organelle, formed by a variety of molecules: protein, DNA, RNA, polysaccharides… Even elephants are molecules… Molecule and chemical bonding Molecules: clusters that consist of a chemical combination (of one, two or more atoms are called molecules. Key points to be covered C molecules-basic units display the chemical and physical properties of a compound. ica h em nd s l bo Molecule and chemical bonding Bio Molecules and structures-bio functions: determined by Chemical bonds-covalent bonds (primary structure) Non-bond interactions (secondary, tertiary structures). Primary structure Strong Bond Covalent bond Weak interactions Weak interactions 3D structure 2nd , tertiary structures 1 Molecule and chemical bonding What is the Bond force to bind different atoms together to form a molecule? Chemical bond: an attractive force linking two or more atoms is called a chemical bond. Molecule and chemical bonding: chemical bonding More electrons will go to the next shelllike a “party” shell. They like a party in a group of “8”. If there are less than 8 electron, the atom will find another atom to bond to. Molecule and chemical bonding: chemical bonding …or it finds a relationship with O by sharing its election with O, creating a covalent bond. Molecule and chemical bonding: chemical bonding Electrons follow a certain rule of behavior: The first two always hand out on the orbit close to the nucleus. And only 2 electrons (↑↓) on the first shell because they like have their privacy. Molecule and chemical bonding: chemical bonding H atom has only one e – it really feels “lonely”, likes company… … find a relationship with another atom. Example H → H2 Molecule and chemical bonding: chemical bonding O has 8 electrons-6 in the outer shell. To keep the O happy, “he” needs 8 electrons in the outer shell… 2 Molecule and chemical bonding: chemical bonding … the O atom finds another H. He has 8 in his outer shell. Two covalent bonds have been formed. A molecule of water H2O. Molecule and chemical bonding: chemical bonding A rule: 2 electrons in the inner and 8 in the outer. To achieve the most stable electronic structure of atom, the outer shell should be completely empty or filled. Sharing electrons forms covalent bonds, then forms molecules, like H2O H shares 1, O → 2, N→ 3, C → 4. Molecule and chemical bonding: chemical bonding Molecule and chemical bonding: chemical bonding A covalent bond is a pare of electrons shared by two atoms Molecule and chemical bonding: chemical bonding Why do you need covalent bond? 1. Strength Covalent bonds are strong… Strength = togetherness 2. Energy… Molecule and chemical bonding: chemical bonding Some key points about covalent bond: … 3 Life: based on materials (cont’d) Biologically important molecules: DNA- RNA-Protein DNA (deoxyribonucleic acid) – to control Carbohydrate, lipids, proteins and nucleic acids –utmost important organic molecules in the structure and function of living things. the way a organism looks and performs Biologically important molecules: DNA- RNA-Protein RNA (ribonucleic acid)massager single-stranded enables information in DNA to be expressed double-stranded helix held together by hydrogen bonds is the genetic material Biologically important molecules: DNA-RNA-Protein Cells synthesize proteins; proteins to perform cellular functions, maintain inner stability, grow, and reproduce. Genes control life activities by controlling protein synthesis. The genetic codes in DNA are copied to RNA molecules, and the codes in the RNA molecules are translated by ribosomes to certain sequences of amino acids. Copy Biologically important molecules: DNA-RNA-Protein Protein: contain C, H, O, N, (S) Amino Acid: Protein build Blocks (~20 found) Protein: polypeptide Biologically important molecules: Carbohydrates nC+mH2O 4 Biologically important molecules: Carbohydrates- storage of energy, building materials Biologically important molecules: Lipids (1)Storage of energy (2) Building materials Biologically important molecules: Lipids Biologically important molecules: Lipids H C Oils: unsaturated fatty acids. Triglycerides: fat and oils Fat: straight-chain fatty acids with no double bonds. These fatty acids are saturated with hydrogen. At some positions in these fatty acid molecules, adjacent carbon atoms are joined by two covalent bonds (a double bond). A diet high in saturated fats appears to contribute to diseases of the heart and blood vessels. H C Biologically important molecules: Bio-macromolecule - 4 level Lipids structure H 2N KAA folding HD P Phospholipids as Waterproof barriers in living Organisms. CWL H WY Phospholipids KLM CTH DEW WN … Primary structure Secondary structure CO OH folding Assembly Aggregation quaternary structure Tertiary structure 5 Bio-macromolecule - 4 level Bio-macromolecule – structure & functionality structure Biological functions of biological molecules are not only determined by the primary structure, but also to a large extent by the secondary, tertiary, quaternary structures • Myoglobin-monomer- responsible for oxygen storage in muscle cell • Hemoglobin-tetramer: 4 polypeptide assembly α2β2: a transport protein to carry oxygen from thelung to the various tissues. • The geometric shape (3D structure) will determine the functionalities Molecular Interactions & Macromolecular Structures Bio-macromoleculeConfigurations and conformations Covalent Bond – the formation of molecules (the primary structure of molecules) H The arrangement of atoms or groups of atoms in a molecule is described by configuration and conformation. Molecular configuration, and molecular steric configuration H H H H H C C C C C H H H H H H H H H H C C C C H H H C H H H H n-Pentane H iso-Pentane Bio-macromolecule- Bio-macromolecule- Configurations and conformations Configurations and conformations H COOH CH3 Conformations: describing the spatial arrangement of groups about one or more freely rotating bonds. (Torsional angle) H COOH H CH3 H 6 Bio-macromolecule- Molecular Interactions & Macromolecular Structures Configurations and conformations The secondary, tertiary, and quaternary structures of macromolecules correspond to different conformations. Non-bonding interactions stabilize the conformation of macro molecules, and lead to the aggregation/assembly of molecules Why does different biomacromolecules appear as different three-dimensional structures? How do macromolecules fold into secondary, tertiary, and quaternary structures? Hemoglobin Cytochrome C Key Message The properties of life are based on atoms and molecules. Atoms are bounded together by chemical bonds to form more stable clusters-molecules. Covalent Bond-sharing electrons. Strength, energy storage. Bio-molecules: DNA-RNA-Proteins, carbohydrate, lipid, … Conformation and configuration. And 3D (4o) structure of biomolecules 7