lect 3 biomolecule.ppt

8/13/2019 Lect 3 Biomolecule.ppt

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BIOMOLECULESBiochemistry - 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

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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

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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

CarbonCarbon bonds

Methane, Ethane, Ethene, Ethyne.

Bonding versatility choice for carbon

Makes least contamination

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Biomolecules

Atomic Radii: Typical distance from the nucleusto 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

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http://en.wikipedia.org/wiki/Atomic_nucleushttp://en.wikipedia.org/wiki/Electronhttp://en.wikipedia.org/wiki/Electronhttp://en.wikipedia.org/wiki/Atomic_nucleus


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Cis trans Isomers: Fumaric / Maleic acid

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http://en.wikipedia.org/wiki/File:Fumaric-acid-2D-skeletal.pnghttp://upload.wikimedia.org/wikipedia/commons/a/a8/Maleic-acid-2D-skeletal-A.pnghttp://upload.wikimedia.org/wikipedia/commons/6/69/Fumaric-acid-3D-balls.png


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Enantiomers

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If a pair of stereoisomers are non-superimposable

mirror images of each other, then they are enantiomers.
http://upload.wikimedia.org/wikipedia/commons/1/12/Milchs%C3%A4ure_Enantiomerenpaar.svg


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Diastereomers

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Spearmint

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Caraway

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Rule for R/S

Attach the pole to the back of the clock, so that whenyou 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 acrossthe face of a clock. If it is going clockwise, then it is an R-

enantiomer; If it is going counterclockwise, it is an S-

enantiomer.

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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-thehighest 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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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

CC (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

CC 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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Absorbance at 340nm

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http://upload.wikimedia.org/wikipedia/commons/8/89/NADNADH.svg


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FAD

Flavin Adenine Dinucleotide

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FAD FADH2

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CC bond Formation/Cleavage

Homolytic cleavage

Heterolytic cleavage

SN1reaction: Carbocation intermediate

SN2reaction: Pentavalent intermediate

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http://upload.wikimedia.org/wikipedia/commons/b/bb/SN1_reaction_mechanism.png


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SN2Pentavalent Intermediate

Configuration inverted

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CC Bond Cleavage

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http://upload.wikimedia.org/wikipedia/commons/9/97/ALDO_reaction.png


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Mechanism

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http://upload.wikimedia.org/wikipedia/commons/9/97/ALDO_reaction.pnghttp://upload.wikimedia.org/wikipedia/commons/9/97/ALDO_reaction.png


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Internal Arrangement

Isomerization

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High Energy Compound Adenosine triphosphate

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Energy Transfer

Glucose + ATP Glucose-6-Pi

ATP ADP + Pi

ATP AMP + PPi

PPi + H2O 2 Pi

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Phosphorylation

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Condensation

Amino acylCOtRNA + HN - R

O H

H

Amino acylCN - R

O 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 P1position) is a tyrosine, tryptophan, or phenylalanine.

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Decomposition

Lipase

Fat Fatty acid + Glycerol

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Common Functional Groups

Amino Glycine

Carboxyl Fatty acid

Carbonyl (Ald) Glucose

Carbonyl (Keto) Fructose

Methyl Alanine

Hydroxyl Serine

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Ethyl Isoleucine

Phenyl Phenylalanine

Ester Fat

Thioester Acetyl CoA

Sulfhydryl Cysteine

Disulfide Cystine

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Amido Gln

Imidazole His

Guanidino 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 hormonesand toxins.

Adenine

ATP, cAMP, NAD, FAD

Fatty Acids, Glycerol, Choline

Lipid Bilayer membrane, Eicosanoids

lect 3 biomolecule.ppt

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