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Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

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Page 1: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

• Cell Chemistry and Biosynthesis

Page 2: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Overview

• Major Atoms• Covalent bonds, Ionic bonds• Water, non-covalent force in water• Four major families of small molecules• Sugar, fatty acids, amino acids, nucleotides• Three macromolecule families: polysaccharide,

protein, nucleic acid • Non covalent bonds determine molecular shape

and interactions

Page 3: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

The Chemical Components of A Cell

• Basic Element: Atom, protons, Neutrons, Electrons

• Atomic Weight, Molecular Weight

• Avgadro’s number (6x1023 molecules), Mole (1 mole= 6x1023 molecules), Molar solution (1M=1mole/liter)

• Electron shells (2,8,8,18,18)

Page 4: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Carbon and Hydrogen

Page 5: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Chemical Elements for Live Organisms

H, C, O, and N make up 96.5% weight of a living organism

Page 6: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 7: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

The Chemical Bonds

• Ionic Bonds, Covalent Bonds

• Bond length and bond strength

• Covalent bonds: Single bond, double bond, polar bond

• Van der waals force

Page 8: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Covalent Bond and Ionic BondIonic bond: electron transfer

Covalent bond: electron sharing

Page 9: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Sodium Chloride: ionic bond formation

Page 10: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

The geometry of covalent bonds

Page 11: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 12: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 13: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 14: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 15: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Important Energy Levels

Page 16: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

The Van der Waals forces

Page 17: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

The Water Environment

• 70% of cell is water• Hydrogen bond• Hydrophilic and hydrophobic• Acid and base• Proton and hydroxyl• Non-covalent interactions in water: Ionic

bonds, hydrogen bonds, van der waals attractions, hydrophobic force

Page 18: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 19: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 20: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 21: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 22: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

AcidDonate a proton

BaseAbsorb a proton or donate OH-

NH3+H2O->NH4++OH-

NaOH->Na++OH-

Page 23: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 24: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Ionic bonds in Water

Page 25: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 26: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 27: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 28: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Hydrogen bondPolar interaction: a

elecgtropositive hydrogen is shared by two neighboring

electornegative atoms

Page 29: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 30: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 31: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 32: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Molecular Interaction in solution1. H-bond (hydrogen bond), 2. Ionic bond, 3. Van der Waals

4. Hydrophobic “force”

Page 33: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Four Major Families of Small Organic Molecules

• Sugars-> polysaccharides

• Fatty acids -> fats, lipids, membranes

• Amino acids -> proteins

• Nucleotides -> nucleic acids

Page 34: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Four Major Small Organic Molecules

Page 35: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Sugar [(CH2O)n, carbohydrates]Glucose

Page 36: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Disaccharide Condensation and hydrolysis

Page 37: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 38: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 39: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 40: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 41: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Fatty Acids

Page 42: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Phospholipid (amphipathic)

Page 43: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 44: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 45: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 46: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 47: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Amino Acid

Page 48: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Amino Acid and pH values

Page 49: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Peptides and proteins

Page 50: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

ATP (ribonucleotide adenosine triphosphate)

Nucleotides

Page 51: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Nucleotides and DNA, RNADNA: deoxyribonucleic acids

A(adenine) G(guanine) T(thymine) C (cytosine)

RNA: ribonucleic acidsA G U(Uracil) C

Page 52: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 53: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 54: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 55: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 56: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Macromolecules

Page 57: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules
Page 58: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

Three families of macromolecules

Page 59: Cell Chemistry and Biosynthesis. Overview Major Atoms Covalent bonds, Ionic bonds Water, non-covalent force in water Four major families of small molecules

The assembly of macromolecules


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