Post on 13-Jul-2020
Phys 210: May 19, 2014
● Modern Physics– Structural Biology
Class Comments
● Quiz 11 will open today– Will have questions based on todays lecture
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LENGTH SCALES(wikipedia)
Structural Biology(from wikipedia)
Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of biological macromolecules, especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures affect their function. This subject is of great interest to biologists because macromolecules carry out most of the functions of cells, and because it is only by coiling into specific three-dimensional shapes that they are able to perform these functions. This architecture, the "tertiary structure" of molecules, depends in a complicated way on the molecules' basic composition, or "primary structures."
Cells● The cell is the basic structural, functional and
biological unit of all known living organisms. Cells are the smallest unit of life that can replicate independently, and are often called the "building blocks of life".
SCALE Micrometers10E-6 meters
Biomolecules are cellular building blocks
● Molecule: collection of atoms covalently bound together.
● Four classes of biomolecules
Atoms
Atoms and Moleculesscale atomic radius:
Quantum mechanics can tell us about the interactions between nuclei and electrons
Classical mechanics can tell us about the interactions between atoms
Water
Molecular Interactions
Scales: 1 nm = 10 E-9 meters
Atomic Radius ~ Angstrom = 10E-10 meters
Size of Cell ~ micro meters = 10E-6
Sugars: Store Energy
Fatty Acids: Make membranes
Fatty Acids and Membranes
Amino Acids and Proteins
● The 20 amino acids and a peptide bond
The 20 Amino Acids
Protein Structure
Protein Structure
● Primary●
● Secondary●
● Tertiary●
● Quartenary
Nucleic Acids and DNA/RNA
● DNA = deoxyribonucleic acid● RNA = ribonucleic acid● Both have a phosphodiester backbone● hydrogen bonding make two strands into
dsDNA.
Structure of DNA
DeoxyriboNucleicAcid
DNA : The Genetic Stuff
DeoxyriboNucleicAcid
DNA : The Genetic Stuff
Chem. & Eng. News; July 17, 2006
The Human Genome is 3,000,000,000 basepairs long.That's one meter long.
It is stored as 23 pairs of chromosomes... so there is actually 2m of DNA in every cell of your body!
Felsenfeld, Nat. 2003Luger Nat. 1997
DNA Folding
Zlatanova and LeubaJMB 2003
Luger, 1997Schalch Nature 2005
Bednar, PNAS 1998
Biology 101Nucleosomes and Chromatin
Energy Landscape
Molecular Biology Dogma
● Sequence → Structure → Function
● Applies to nucleic acids as well as amino acids.
●
Experimental Methods
● X-ray crystallography– Diffraction of x-rays from crystals of protein and/or DNA
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– See the Protein Data Bank
● Separation Techniques– Gel mobility:
● Depends on “holes” in gel and on shape + charge of molecule
● Single Molecule Force Spectroscopy– Can't see it but can feel it.
X-ray Crystallography
X-ray CrystallographyMyoglobin first protein Structure to be determined by X-ray crystallography. 1950
Electrophoresis
Atomic Force Spectroscopy
Modeling Methods
● Quantum Mechanics– Solves the Schrodinger Equation and thus gives information
about the electronic structure
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● Molecular Mechanics– Solves Newtons equations using approximate models for the
ineractions between molecules. This is classical mechanics.● Each atom is a ball with radius (occupies space)● Atoms connected by springs● Atoms have “partial charge” even for neutral atom