macromolecules i the importance of weak interactions

MACROMOLECULES IMACROMOLECULES I

THE IMPORTANCE OF WEAK THE IMPORTANCE OF WEAK INTERACTIONSINTERACTIONS

BONDS OF INTERESTBONDS OF INTEREST

Covalent bonds—NOT a weak Covalent bonds—NOT a weak interaction. interaction. G= -50 to -110 kcal/molG= -50 to -110 kcal/mol

Weak interactions in biological Weak interactions in biological systemssystems Hydrogen bondsHydrogen bonds Ionic bondsIonic bonds Van der waals bondsVan der waals bonds Hydrophobic interactionsHydrophobic interactions

Formed between a covalently bound H and a covalently bound acceptor

The H is bound to an electronegative atom and interacts non-covalently with another electronegative atom (usually O or N)

Much weaker than covalent bonds.

Very important in protein and nucleic acid structure.

HYDROGEN BONDSHYDROGEN BONDSPower in NumbersPower in Numbers

H-bonding between water molecules

Generalized H-bonding

Hydrogen bonding of water molecules

H-bonding of hydroxyl groupsHOR

H

O R

H

O H

H

O H

H

O HH

O H

Keto groups

OR H O RH-bonds will form with various combinationsof hydroxyl, amino and keto groups thatmeet the H-bonding criteria.

H-bonding of amino groups

HN

R

N

R

R

R

R —

Hydrogen bonding between amino acids in a protein

| H-C-R1 | C=O | N-H | H-C-R2 | C=O | N-H | H-C-R3 |

| R4-C-H | H –N | O=C | R5-C-H | H –N | O=C | Rc- C-H |

Secondary Structure in ProteinSecondary Structure in Protein

DNA Double HelixDNA Double Helix

Hydrogen bonding between bases in DNA

Three H-bonds between G and C

N

NNH

NN-H

H

H

Oguanine cytosine

NN

H-N-H

O H

IONIC BONDSIONIC BONDS

Interaction between opposite chargesInteraction between opposite charges Many biologically significant molecules Many biologically significant molecules

are charged at physiological pH.are charged at physiological pH. Proteins EX:Proteins EX: Glutamic acid : negativeGlutamic acid : negative Lysine: positive Lysine: positive

PROTEINSPROTEINS

GlutamateGlutamate

LysineLysine

Van der WaalsVan der Waals

Result of a temporary dipole moment Result of a temporary dipole moment in atoms close to one another.in atoms close to one another.

Non-specificNon-specific Very weakVery weak Requires close proximityRequires close proximity

Hydrophobic InteractionsHydrophobic Interactions

Why do non-polar substances not Why do non-polar substances not dissolve in water? dissolve in water? EX.EX.

Are not bonds. What are they?Are not bonds. What are they? Valuable inValuable in

Protein 3Protein 3ºº structure structure Base stacking in DNABase stacking in DNA

Selective Advantage of Weak Selective Advantage of Weak Interactions in Biological Interactions in Biological

SystemsSystems Allows specificity—small differences Allows specificity—small differences

are easily distinguished (Ex. Allows are easily distinguished (Ex. Allows recognition).recognition).

Dynamic—Interior of cell remains Dynamic—Interior of cell remains fluid, allows responsiveness.fluid, allows responsiveness.

Summary of Chemical InteractionsSummary of Chemical Interactions

Bond::

Energy Energy needed needed

to break:to break:

CommentsComments::

Strength Strength class-class-

ification:ification:

Covalent

~100kcal/mole

Electrons shared

strong

Hydrogen

~3

Water-water;Organic-water;Organic-organic

weak

Ionic

~5

Full charge transfer;Can attract H-bond;Strong in crystal

weak

Van der Waals

~1

Fluctuating induced dipole;Close range only

weak

Hydro-phobic forces~3

Not a bond per se;Entropy driven;Only works in water

weak

Water cages around methane: CH4

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