Lecture2 - UC Davis, BME BIM 162 Quantitative Concepts in...

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Unformatted text preview: UC Davis, BME BIM 162 Quantitative Concepts in Biomolecular Engineering Lecture 02 Structure of bi St t f biomolecules l l Follow-up M a t h C o n c e p t s Derivation of bond angle of carbon atom Taylor expansion Energy versus force; Equilibrium “Zero temperature” versus “finite temperature” Summary: Energy and Boltzmann distribution A system (e.g., a molecule, or two interacting molecules) always tends towards its lowest energy state. Therefore: equilibrium minimum energy. Minimizing energy is the same as balancing forces. At finite temperature, thermal agitation causes random excursions of the system from the state of minimum energy. However the higher the energy However, energy of some state, the less likely is the system observed in this state. The Boltzmann distribution gives the likelihood (probability pi) of finding the system in a state i that has the energy Ei : pi e Ei kBT kBT is often used as energy unit Biomolecules as part of the bigger picture Biomolecules as part of the bigger picture Recall: Central dogma of molecular biology Structure of Biomolecules: Design considerations H 2O (aqueous environment) size (<< visible) Tbio (temperature) kBTbio (thermal agitation) bio molecule basic building block for living organisms g g g integrity / stability strength flexibility function variability evolution Structure of Biomolecules: Strength Flexibility Strength “backbone”: “backbone” held together by g y covalent bonds Flexibility rotation about axis of single covalent bonds limited lifetime of ”weak” bonds weak (“physical bonds”, e.g., hydrogen bonds, van der Waals forces forces, hydrophobic interactions, …) “decorations” “d ti ” and their interactions: Example: E l (Alberts) Structure of Biomolecules: Strength Flexibility Strength Flexibility Covalent bonds: OO CC CO OH CH HH CC CC HW Bond Energy distance di t nm kJ/mol kBT* Bond energy ”weak” interactions between biomolecules: ~ 5 – 35 kBT most frequently: ~ 15 kBT *at T=300K Structure of Biomolecules: DNA Purins: Pyrimidins: Structure of Biomolecules: ssDNA in 3D Structure of Biomolecules: dsDNA in 3D Structure of Biomolecules: Proteins Hierarchy of structures: primary secondary tertiary quaternary primary, secondary, tertiary, Genetic code: (Alberts) HW Structure of Biomolecules: Proteins Peptide bonds link amino acids biopolymer (Alberts) Structure of Biomolecules: Proteins Many sequences within the linear polymer of amino acids fold into one of two common 3D structures: the -helix and the -sheet. (Alberts) Structure of Biomolecules: Proteins Example: Immunoglobulin (= Antibody) [IgG1] Structure of Biomolecules: Proteins Typical sizes: (Alberts) Structure of Biomolecules: Lipids Example: Phospholipid [SOPC] 18:0-18:1 18:0 18:1 PC 1-Stearoyl-2-Oleoyl-sn-Glycero-3-Phosphocholine BIM 162 Homework 01 Due date: Thursday, 01/13/11 Please note: Include sufficient detail about your approach to solving homework problems. Explain the important steps in all derivations and calculations and arrange them in a logical and reproducible order Consider a write-up using a computer calculations, order. computer, especially if your handwriting is hard to decipher. It is okay to work in teams on the solution of homework problems; however, you must prepare the write-up yourself using your own words and figures. 1. 1 2. 3. 4. 4 Look up bond energies and distances (you may want to compare values from at least two different sources if you use the WEB) to fill in the table given on the slide on covalent bonds. p y, y, y, q yp What is primary, secondary, tertiary, and quaternary protein structure? What distinguishes a protein domain? (Brief answers.) (Reference: http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.section.388 ) Go to http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/exhibits.htm #displays (if Internet Explorer doesn’t work, use Firefox) a. Load “An Introduction to DNA Structure (Jmol)” and inspect the whole sequence of individual renderings. b. Find the dsDNA width and the distance between base pairs of the dsDNA. c. Measure the distance between nucleotides of the ssDNA. Find at least one scientific publication (give reference) that lists a value for the spacing of bases in ssDNA. How does the value compare to your measurement in 4c? ...
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This note was uploaded on 07/12/2011 for the course BIM 162 taught by Professor Heinrich during the Spring '11 term at UC Davis.

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