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Biochemistry - I
Biomolecules
What kinds of molecules in living organisms In what proportion
Biomolecules
Covalent bonding of C with itself and with other elements The functional groups Three dimensional structure
Stereochemistry
The common classes of chemical reactions
Evolution
Biomolecules
Four most abundant elements: C,H,N,O Ca, P, S, K, Mg, Na, Cl, Fe Trace elements: I, Co, Zn, F, Cu, Se
Biomolecules
Atomic Radii: Typical distance from the nucleus to the boundary of the surrounding cloud of electrons. Vander Waals radii: Half the minimum distance between the nuclei of two atoms of the element that are not bound to the same molecule. Configuration: Fixed spatial arrangement of atoms in an organic molecule Double bond Chiral center Geometric or Cis trans isomerism
Retinal
Fatty acids
Enantiomers
If a pair of stereoisomers are non-superimposable mirror images of each other, then they are enantiomers.
Diastereomers
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Isomerism
D-isomer L-Isomer Racemic mixture RS system of nomenclature View from the side with the lowest priority away from the viewer R: Priority decrease clockwise S: Priority decrease anti clockwise Carvone forms two mirror image forms or enantiomers: R-()-carvone smells like spearmint. Its mirror image, S-(+)-carvone, smells like caraway
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Spearmint
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Caraway
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Then, draw an arrow from the highest priority atom to the 2nd highest priority atom to the 3rd highest priority atom. Since you have placed the 4th highest priority atom in the back, you arrow should seem like it is going across the face of a clock. If it is going clockwise, then it is an Renantiomer; If it is going counterclockwise, it is an Senantiomer.
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R S Nomenclature
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Problems
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Solution
(1) S I > Br > F > H. The lowest priority substituent, H, is already going towards the back. It turns left going from I to Br to F, so it's a S. (2) R Br > Cl > CH3 > H. You have to switch the H and Br in order to place the H, the lowest priority, in the back. Then, going from Br to Cl, CH3is turning to the right, giving you a R.
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Solution
(3) Neither R or S This molecule is achiral. Only chiral molecules can be named R or S. (4) R OH > CN > CH2NH2 > H. The H, the lowest priority, has to be switched to the back. Then, going from OH to CN to CH2NH2, you are turning right, giving you a R. (5) S COOH > C triple bond CH > HOH2C > H. You have to switch H with COOH so that H is going towards the back. Then, going from COOH to C triple bond CH to HOH2C, you are turning left, giving you a S.
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Conformation
Rotation around a single bond Eclipsed Staggered
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Projections
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Bond Strength
Depends on electronegativities Number of electrons sharing also influence bond strength Strength of a bond :bond Energy Bond Dissociation Energy C C (Single bond) : 348 kJ/mol C = C (Double bond) : 611 C C (Triple bond): 816
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Bond Strength
Enthalpy change H The energy extracted from the surroundings to break the bond or the energy released to the surrounding during the formation of bond
Exothermic reaction Endothermic reaction
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Oxidation Reduction
Oxidation: Loss of Electrons Fe2+ Fe3+ Oxidation Oxidase Oxygenase Dehydrogenase Hydrogenase Reductase Oxidation Reduction Oxidant is reduced while the Reductant is oxidized
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NAD+ NADH
Nicotinamide Adenine Dinucleotide
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NAD Oxidation-Reduction
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Absorbance at 340nm
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FAD
Flavin Adenine Dinucleotide
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FAD
FADH2
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Bond Cleavage
Homolytic cleavage: Carbon radicals
CC
Co + Co
CC
C+ +
C:
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C C bond Formation/Cleavage
Homolytic cleavage Heterolytic cleavage SN1 reaction: Carbocation intermediate SN2 reaction: Pentavalent intermediate
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C C Bond Cleavage
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Mechanism
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Internal Arrangement
Isomerization
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Energy Transfer
Glucose + ATP ATP ADP + Pi Glucose-6-Pi
ATP
PPi + H2O
AMP + PPi
2 Pi
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Phosphorylation
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Condensation
Amino acyl C O tRNA O H Amino acyl C N - R O + H N - R H
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Decomposition
Trypsin
Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine
Chymotrypsin
Chymotrypsin preferentially cleaves peptide amide bonds where the carboxyl side of the amide bond (the P1 position) is a tyrosine, tryptophan, or phenylalanine.
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Decomposition
Lipase Fat Fatty acid + Glycerol
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Disulfide
Cystine
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AMP
COO -Pi
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Arg
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Biomolecules in Cell
Water Protein: amino acids
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Biomolecules in Cell
Nucleic Acids DNA RNA
Nucleotides, Nucleosides
Base, Sugar (Ribose, Deoxyribose), Phosphate
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Functional Role
D-glucose Sucrose, Lactose, Starch, Glycogen, Cellulose, Amino Acids Proteins, Neurotransmitters, Precursors of hormones and toxins.
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