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BIOMOLECULES

Biochemistry - I

Dr. Muhammad Kalim Tahir


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Biomolecules
What kinds of molecules in living organisms In what proportion

Structure of these molecules


Monomeric subunits What forces stabilize their structure

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

Carbon Carbon bonds


Methane, Ethane, Ethene, Ethyne. Bonding versatility choice for carbon Makes least contamination
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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

Cis trans Isomers: Fumaric / Maleic acid

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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Rule for R/S


First look at the atoms that are directly attached to the stereocenter of the compound. A substituent that has a higher atomic number takes precedence over a substituent that has a lower atomic number. Hydrogen is the lowest possible priority substituent, because it has the lowest atomic number. When you are dealing with isotopes, the atom with the higher atomic mass receives higher priority. When visualizing the molecule, the lowest priority substituents should always go away from the viewer (dashed line indicates going away from the viewer). To understand how this works or looks, imagine that you have a clock and a pole.

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Rule for R/S


Attach the pole to the back of the clock, so that when you look at the face of the clock the pole points away from you. That is the same way the lowest priority substituent should point away from you.

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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Rule for R/S


When you have two substituent with equal rank, you must proceed along the two substituent chains until you find a point of difference. First, you determine which of the chains has the first connection to an atom with the highest priority-the highest atomic number. That chain will have the higher priority. If the chains are similar keep going down the chain, until you can find a point of difference. For example: an ethyl substituent will take priority over a methyl substituent.

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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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Types of Chemical Transformations


Oxidation reduction involving Electron transfer C C bonds cleavage /Formation by Nucleophilic substitution Internal rearrangement Group transfer Condensation

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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

Heterolytic cleavage: Cabocation and Carbanion

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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SN2 Pentavalent Intermediate


Configuration inverted

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C C Bond Cleavage

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Mechanism

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Internal Arrangement
Isomerization

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High Energy Compound


Adenosine triphosphate

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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

Polypeptide Elongation Hydrolysis of Polypeptide: Water serves as a nucleophile

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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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Common Functional Groups


Amino Carboxyl Carbonyl (Ald) Glycine Fatty acid Glucose Fructose Alanine Serine

Carbonyl (Keto) Methyl Hydroxyl

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Common Functional Groups


Ethyl Phenyl Ester Thioester Sulfhydryl Isoleucine Phenylalanine Fat Acetyl CoA Cysteine

Disulfide

Cystine

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Common Functional Groups


Ether Sucrose

Phosphoryl Anhydride Mixed anhydride

AMP

COO -Pi

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Common Functional Groups


Amido Imidazole Guanidino Gln His

Arg

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Biomolecules in Cell
Water Protein: amino acids

Carbohydrates Monosaccharides, Disaccharides, Oligosaccharides, Polysaccharides


Lipids Fats, Fatty acids, Glycerol, Oils and Waxes

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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.

Adenine ATP, cAMP, NAD, FAD


Fatty Acids, Glycerol, Choline Lipid Bilayer membrane, Eicosanoids

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