BCH 463 Lecture Notes - Lecture 3: Nicotinamide, Heme, Tricine

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31 Oct 2016
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Most important diagram in the course!
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Fossils of Biochemistry evolution- still in DNA tree of life - in our DNA!
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---- End of Theory of Biochemistry Evolution!
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Remember the 5 Laws!
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Antropic vs. Cosmological Principle!
Anthropic Principle!
the world is so perfect for us that it could have not happened by chance!
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Cosmological Anthropic Principle!
all of the observable parameters of the universe must be consistent with the existence of the
observer !
you cannot open your eyes and notice you are on the surface of the sun!
you can only see Earth "green planet" because you would not have eyes if you would't exist!
NOTHING CAN BE PROVEN!!!
Problem?!
Prediction and observation!
Planet started with a dierent environment !
World was change by geological, cosmological and biological evolution!
(1988 Barrow and Tipler)!
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------- END of Foundation of Biochemistry -------!
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Proteins!
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Page 82 -85!
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Methods to analyze proteins!
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SKIPPING: Amino Acids as buers!
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General formula of an amino acid:!
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20 Functional groups !
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We can take 2 amino acids and we can polymerize them - peptide bond!
Where is that done?!
Ribosome!
Catalyst?!
RNA!
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What regulates the rotation?!
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The R groups!
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R groups:!
acid!
base!
hydrophilic!
hydrophobic!
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Range of dierent R group and rotation of peptide bond - gives specificity to protein!
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Binding and catalysis is enhanced by protein polymers then nucleic acid polymers!
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Polypeptides!
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Amino group to the left!
Carboxyl group to the right!
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Plot!
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Hydrophobic places!
interior of protein or membrane - away from the solvent!
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Hydrophilic regions!
in the solvent!
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Epitopes
pick most hydrophilic regions - peaks !
just get amino acid sequences for the peaks !
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Look at Tree of Life again:!
sequences!
folds?!
shapes?!
They are a primary sequence of nucleotides/nucleic acids is under selection!
"Good design space"!
Then, what is under selection is a primary sequence of amino acids!
How does a sequence of amino acids turn into a shape?!
If 1 amino acids sequence can fold into several shapes, then how can you put that amino acid
under selection?!
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How does this work?!
Molten Slobule!
-weak dipole-dipole interactions!
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Theory:!
Protein goes into all kinds of shapes, and it falls into energy trophs. The bottom shape is usually
the preferred and stable shape. !
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