The chemistry of cells: an overview Restricted to a subset of known elements, dominated by the chemistry of carbon… Reactions occur over a narrow range of temperatures ( o C)… Dominated by macromolecules and polymers (-X-X-X-X-)… Many reactions facilitated by protein catalysts: “enzymes”… Chemical reactions are often localized to a specific cell surface or compartment…

“Strong” and “weak” chemical bonds contribute to the structure of biomolecules… Covalent bonds are strong bonds ( kcal/mol)… –Covalent bonds are formed when atoms share pairs of electrons… –-C-C- bonds ~85 kcal/mol… Weak “bonds” (<5 kcal/mol)… –Ionic bonds (~3 kcal/mol)… –Hydrogen bonds (~1 kcal/mol)… –van der Waals interactions (~0.1 kcal/mol atom)… –Hydrophobic interactions (NA)…

Atoms joined by “covalent” bonds share electron pairs… Distance at which attraction and repulsion are equal is bond length

Opposites attract: ions and ionic bonds…

Weak chemical “bonds” play a significant role in biomolecules: Hydrophobic interactions… Summation of many weak bonds makes a significant contribution to structure, stability, and binding specificity of biological macromolecules… Van der Waals interactions… ECB Fig. 2-32

Three elements comprise >95% of the atoms in living cells… ECB 2-4 #P Atomic number #e - #NMass% H1101~48% C66612~24% N77714~1% ~24% Na <0.5 Mg 12 24<0.5 P <0.5 S 16 32<0.5 Cl <0.5 K <0.5 Ca 20 40<0.5 ECB Fig. 2-4

Valences and bond configurations for some “biological” elements… ECB Fig. 2-10

Functional groups common in biomolecules: carbon atoms form the backbone of many biomolecules… ECB Panel 2-1

Functional groups common in biomolecules: compounds of carbon and oxygen or nitrogen… (hydroxyl group…) (carbonyl group…) ECB Panel 2-1

Electronegativity and bonding Number of electrons in outer shell H He 3 Li C N O F Ne 11 Na Si P S Cl Ar

Electronegativity and bonding Number of electrons in outer shell H He 3 Li C N O F Ne 11 Na Si P S Cl Ar Electronegativity decreases as move down a column; ex. O vs S

Electronegativity and bonding Number of electrons in outer shell H He 3 Li C N O F Ne 11 Na Si P S Cl Ar Atomic nuclei vary in their “electronegativity” (the strength of their attachment to electrons)… ECB Fig. 2-8

Electronegativity and bonding Numer of electrons in outer shell H He 3 Li C N O F Ne 11 Na Si P S Cl Ar Atomic nuclei vary in their “electronegativity” (the strength of their attachment to electrons)… O and N cannot steal electrons… but “borrow” them from their partners (C and H)… Polar covalent bond “partial” negative charge (  - ) on O and N…  + on H… allows H-bonding…      NH CO  H C O

Water molecules are extensively H-bonded… Adapted from ECB panel 2-2 Water molecules interact via “Hydrogen bonds”…     Covalent bond ~110 kcal/mol ~ 0.1 nm Hydrogen (H)-bond 3-4 kcal/mol nm (O to O) Raises B.P.… Ice floats… Solubility… e - ECB Panel 2-2

H-bonding affects the solubility of molecules in water… “Amphipathic” molecules… contain both hydrophilic and hydrophobic domains… “Hydrophilic (water loving)” They are considered “hydrophilic (water loving)”… Hydrophobic = water fearing ECB panel 2-2

Review: Chemical bonds in cell biology… Bond typeLength (nm) Bond strength (kcal/mol in water) Covalent Non-covalent (weak) Ionic Hydrogen van der Waals Hydrophobic effectNA

Acids and bases… Liquid H 2 O is heavily H-bonded… In pure water [H+] = M -log[H + ] = pH Carboxylic acids donate a proton… Amino groups accept a proton… Acids increase [H+] and lower pH… Bases lower [H+] and increase pH…

The stuff cells are made of: the approximate chemical composition of a mammalian cell… Protein 18% Phospholipids 3% Misc. small metabolites 3% General lipids 2% Polysaccharides 2% DNA 0.25% RNA 1.1% Inorganic ions 1% Water 70% Chemicals 30% Plant cells - much more polysaccharide due to cell wall

Small organic molecules are the building blocks of biological macromolecules… Building blocksLarger units Fatty acids Fats/lipids/Membranes SugarsPolysaccharides Amino acids Proteins NucleotidesNucleic acids Adapted from ECB 2-15 Condensation reactions = monomer to polymer Hydrolysis reactions = polymer to monomer

Location of the 4 major groups of macromolecules: Polysaccharide = carbohydrate

Small organic molecules are the building blocks of biological macromolecules… Building blocksLarger units SugarsPolysaccharides Adapted from ECB figure 2-15

Monosaccharides: Aldehyde (“aldose”)… or ketone (“ketose”)… Invert C4 = galactose… Invert C2 = mannose… ECB panel 2-3

Glucose Sugar molecules react with themselves to form rings…… (see ECB Panel 2-3)

Rings open and close rapidly in solution

Monosaccharides are linked by “glycosidic bonds” to form polysaccharides… Adapted from ECB Fig and Panel 2-3

Polysaccharides are used for energy storage and structural support… Starch: Amylose:  (1>4) glucose (unbranched) Cellulose:  (1>4) glucose (straight chain, unbranched) (Dietary fiber… most animals cannot digest cellulose) Glycogen:  (1>4) glucose with  (1>6) branches ECB Panel 2-3

Next two lectures Lipids and membranes… Amino acids and proteins… Protein structure and function…