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Unformatted text preview: UC Davis, BME BIM 162 Quantitative Concepts in Biomolecular Engineering Lecture 02
Structure of bi
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 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
(thermal agitation) bio molecule basic building block for living organisms
g g integrity / stability strength flexibility function variability evolution Structure of Biomolecules: Strength Flexibility
“backbone” held together by
covalent bonds Flexibility
rotation about axis of
single covalent bonds limited lifetime of ”weak” bonds
(“physical bonds”, e.g.,
van der Waals forces
hydrophobic interactions, …) “decorations”
(Alberts) Structure of Biomolecules: Strength Flexibility Strength Flexibility Covalent bonds: OO
CC HW Bond
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
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
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 )
#displays (if Internet Explorer doesn’t work, use Firefox)
a. Load “An Introduction to DNA Structure (Jmol)” and inspect the whole sequence of
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.
- Spring '11