Weak Chemical Interactions

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Weak Chemical Interactions
Weak chemical interactions or non-covalent bonds
are key to life They can form and break with
minimal energy costs They allow for very dynamic
systems as observed in living organisms
- nearly all of the interactions
between macromolecules in the cell are highly
dynamic
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Covalent Bonds
The most stable bond type involves electron
sharing H C N P O S outer shell
electrons Each type of atom forms a
characteristic number of covalent bonds with
other atoms shortest bond lengths Covalent
bonds are strong and require a lot of energy to
break thermal energy at 25o (i.e. in cell) is 1
kcal/mol C-C bond requires 83 kcal/mol to
break
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Figure 2.1 bond energies
most biologically relevant covalent bonds
all biologically relevant noncovalent bonds
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Non-covalent Bonds
Much weaker than covalent bonds - these bonds
break and reform at Room Temperature
(RT) Transient Bonds - however, cumulatively
they are very effective e.g. ? helix for proteins
and double helix for DNA
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Figure 2.2 non-covalent interactions
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Non-covalent Bonds forces involved

• Charge Charge Interactions
• - electrostatic interactions between a pair of
  charges
• - in a vacuum (or in a crystal ) very strong
  interactions
• as strong as some covalent bonds.

Force between a pair of charges (q1 and q2,
separated by distance r)
Coulombs law
If F is , corresponds to repulsion (qs have same
charge)
If F is -, corresponds to attraction (qs have
different charge)
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Charge-charge interactions within a cell
-In a cell, charges are surrounded by dielectric
medium- screens charges from one another. -much
weaker interaction than that seen in vacuum
Dielectric Constant
- higher ? weaker force between particles
Dielectric constants H2O 80 organic
solvents 1-10
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Charge-charge interactions energy of interaction
Energy of Interaction (U) -energy required to
separate two charged particles from distance r to
infinite distance
Interaction/repulsion between charges is
nondirectional varies linearly with distance (as
opposed to some of the other interactions)
(as r becomes very large, U approaches zero)
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Dipole interactions-permanent and induced

• Molecules with no net charge but with asymmetric
  distribution of charge (eg. CO)
• Polar (permanent dipole)
• Dipole moment m
• expresses a molecules polarity
• A vector always directed towards the positive
  charge q
• Molecules with large dipole moments are highly
  polar

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Dipole moments
? qx
?, dipole moment q, charge (or fractional
charges) x, distance between charges
Dipole moment
glycine
O
C
0.12
q-
q
0
O
O
C
q
q-
q-
Equal in magnitude but opposite direction, cancel
each other out
Because the distance between charges is so great
q-
O
1.83
H
H
q
q
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Dipole interactions

• Charge-dipole sometimes
• Dipole-dipole called
  
• Charge-induced dipole van der Waals
• Dipole-induced dipole attractions
  

Interactions involving permanent dipoles depend
on the orientation of the dipole and they are
shorter range than charge-charge
interactions. Some dipoles are induced in
polarizable molecules
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Induced Dipoles
- electric fields can induce a dipole in a
molecule which does not have a dipole - a
molecule in which a dipole can be induced is said
to be polarizable - Interactions of polarizable
molecules are called induced dipole interactions.
They are even shorter range than permanent
dipole interactions
Molecules with neither a net charge or permanent
dipole moment can attract one another if close
enough. This is due to the fluctuations in the
electronic charge distribution - When two
molecules approach to a very close distance, they
synchronize their charge fluctuations so as to
give a net attractive force Such mutual dipole
induction is called Dispersion Forces. Also
known as van der Waals attractions
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van der Waals repulsion
When molecules or atoms come so close together
their outer electron orbitals begin to overlap,
there is a mutual repulsion This repulsion
increases very rapidly as the distance between
centers (r) decreases. This repulsive force
increases so drastically at small distances it
acts as a wall, effectively barring approach
closer than distance rv - defines the so-called
van der Waals radius. The balance between these
forces is important in biology- mediate binding
of enzymes with substrates and antibody-antigen
interactions and base stacking in DNA.
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Figure 2.6 van der Waals forces
Table 2.2
van der Waals radii
rv
Note Covalently and H-bonded atoms are closer
than the van der Waals distance
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Hydrogen Bonds
VERY important in biochemistry. An interaction
between a covalently bonded hydrogen atom on a
donor group and a pair of non-bonded electrons on
an acceptor group.
Shares features with covalent and non-covalent
interactions
N-H . . . OC, predict H-O distance of 0.26 nm
actually 0.19 nm
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Hydrogen bonds in protein structure
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Water
water is actually a rather remarkable
chemical! Comparing water with chemicals of
similar Molecular Weight, reveals several obvious
differences
Why is water unique?
-Strong Hydrogen Bonding
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Structure of Water
ice
Flickering cluster
water
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Sphere of hydration
Sphere of Hydration
- Sphere of hydration surrounding proteins is
important high concentrations of certain salts
(e.g., ammonium sulfate) make the proteins become
less soluble and precipitate
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Water can also dissolve a wide variety of polar
molecules, via dipole-dipole interactions and/or
Hydrogen bonding.
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Hydrogen Bond Exchange
Figure 2.11
Probably helps to dissolve macromolecules
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Hydrophobic Interaction
Hydrophobic, water-fearing Hydrophilic, water-lovi
ng
Amphipathic, both H-philic and H-phobic, e.g.,
lipids

• NOT a true force.
• The consequence of the energy needed to insert a
  non-polar molecule into water.
• water clatherate structure formed
• hydrogen bonds broken
• non-polar molecules form van der Waals
  interactions between each other

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Hydrophobic molecules in aqueous solution
-molecules that cannot form hydrogen bonds
have limited solubility in water ie. non-polar,
non-ionic substances that cannot form H bonds
(eg. hydrocarbons)
When hydrophobic molecules dissolve in water,
ice-like Clathrate structures cage the
molecules highly ordered, so not energetically
favoured Less energy is required to encage 2
molecules than each alone-so they tend to cluster
and form aggregates
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Amphipathic molecules simultaneously exhibit
hydrophilic and hydrophobic properties.

• Includes phospholipids, fatty acids and
  detergents
• Form monolayers, micelles or bilayer vesicles
• Basis of cellular membrane bilayers
• Polar or ionic head groups become hydrated

Hydrophilic head groups
Hydrophobic tail groups
fatty acid detergent
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Review ionic equilibria equations and terms- be
able to solve simple problems (Matthews et al. pp
41-47)
pH -log H Ka H A-/HA pKa -log Ka
pH pKa log (A-/HA) (Henderson-Hasselbalch
equation) pI isoelectric point

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Practice Problems ( not to be handed in) Most of
these questions should be chemistry
review! Matthews 3rd edition- p. 51, problems
2, 3, 8, 11 p. 80, problems 5a, 7a, 7b The
answers are in the back of the text.