Chemical Bonding and
Non-Covalent Interactions
for Biochemistry
Student Edition
8/27/13
Dr. Brad Chazotte
213 Maddox Hall
chazotte@campbell.edu
Web Site:
http://www.campbell.edu/faculty/chazotte
Original material only ©2004-14 B. Chazotte
Pharm. 304
Biochemistry
Fall 2014
GOALS
•Review and be able to identify different chemical functional groups.
•Understand the significance of and remember the electronegativities
of atoms that are biologically important.
•Review the nature of covalent bonds and the importance of bond,
strengths, angles and lengths.
•To review the nature and importance of dipole moments.
•Review the types of noncovalent interactions and there biological
importance.
•Review the classes of chemical reactions in cells.
•Develop an understanding of the chemical logic of biochemistry
from the molecular forces and chemical principles that determine
chemical properties.
Elements Essential for Animal Life
and Health
Lehninger 2000 Fig 31
Covalent Bonding and Carbon Atoms
•H, O, N, & C are
the most abundant
biological elements.
•Above are the
lightest elements
capable of forming
1, 2, 3, & 4 covalent
bonds, respectively.
•Generally true that
lightest elements
form the strongest
bonds.
Lehninger 2000 Fig 3.2
An Element’s Chemical Reactivity
and It’s Outermost Electron Shell
Alberts et al , 2004 Figure 2.5
Bonding & Stability
Valance: the number of electrons an atom must gain or lose to have a filled
outer shell.
Alberts et al , 2004 Figure 2.6
Biomolecules are Carbon Compounds
•Chemistry of living organisms is organized around the
element carbon (“carbon-based life forms”)
•Molecules with covalently bonded carbon backbones are
termed organic compounds.
•Carbon accounts for 50% of the dry weight of cells
•Carbon can form:
single bonds with hydrogen
double bonds with oxygen
bonds with other carbon atoms (important!)
Carbon Versatility in Bonding
•Carbon can form single, double or
triple bonds.
•Covalently linked carbon atoms in
biomolecules can form linear chains,
branched chains, or cyclic structures.
•These chains or skeletons can have
other groups of atoms, called functional
groups, added to them which give rise
specific chemical properties.
Lehninger 2000 Fig 3.3
Red dot=unpaired electron
Carbon-Bonding Geometry
tetrahedral arrangement
freedom of rotation about the single bond
The geometry of the bonds and the
extent of free or hindered rotation
affects the properties of the molecules.
Double bonds are shorter and DO NOT allow
for free rotation
Lehninger 2000 Fig 3.4
Van der Waals Radii and Bond length
Van der Waals Radii
Note: OTHER, ADJACENT ATOMS EFFECT
BOND LENGTHS.
Lehninger 2000 Table 3.1
Matthews et al , 1999 Table 2.2
Van der Waals Radii, Bond
Lengths & Angles, and the Water
Molecule: Diagram
1Å = 1 x 10-10 cm = 0.1 nm
Voet. Voet & Pratt, 2013 Fig 2.1
Biomolecule Chemical
Functional Groups
•Most biomolecules can be considered derivatives of
hydrocarbons. Compounds with covalently linked carbon
backbone to which only hydrogens are bonded.
•Backbones of hydrocarbons are very stable.
•Substitution of the hydrogens by various chemical
functional groups
a)
determines molecule’s chemical properties
b)
yield different families of organic compounds
Hydroxyl, Carboxyl, & Carbonyl
Functional Groups
R
is used to represent a substituent group
(R can be a simple hydrogen atom to complex carbon-containing moieties.)
Lehninger 2000 Fig 3.5
Methyl, Ethyl & Phenyl
Functional Groups
Lehninger 2000 Fig 3.5a
Amino, Amido, Imidazole, and
Guanidino Functional Groups
(In Histidine)
Lehninger 2000 Fig 3.5b
Sulfhydral & Disulfide
Functional Groups
Lehninger 2000 Fig 3.5c
Phosphoryl Functional Group
Lehninger 2000 Fig 3.5d
Ester & Ether Functional Groups
Lehninger 2000 Fig 3.5e
Anhydride Functional Groups
Lehninger 2000 Fig 3.5f
Common Functional Groups in a
Biomolecule
Lehninger 2000 Fig 3.6
Chemical Reactivity
Biochemical Reactions may be understood and predicted
from the nature of the reactant’s functional groups similar
to regular chemical reactions.
Key concept: Functional groups alter the electron
distribution and the geometry of neighboring atoms,
thus affecting the chemical reactivity of the entire
molecule
Matthews et al , 1999 Figure 2.X
Covalent Bond Strength
Strength of a chemical bond depends on:
•
Relative electronegativities of the bonding atoms
•
The distance of the bonding electrons from each nucleus
•
Nuclear charge on each atom
•
The number of electrons shared
triple > double > single
(Bond strength is expressed in terms of bond energy in joules)
Matthews et al , 1999 Figure 2.X
Selected Elements’
Electronegativities
The higher the number the
higher the affinity for
electron and the more
strongly electrons will be
pulled toward the nucleus.
Increasing
electronegativity
Lehninger 2000 Table 3.2
Common Biomolecule Bond
Strengths
Bond energy (one
definition): the amount
of energy to break a
bond
Bonds with lower
energies can be made to
break before other
stronger bonds.
When bonds are broken and formed in a chemical reaction the energy can be
approximated as the enthalpy change, H = the difference between the energy
extracted from the surroundings to break the bonds and the energy released to the
Lehninger 2000 Table 3.3
surroundings by the formation of a new bond.
Conformation and Bond Energy
The conformation of a molecule can also affect its bond strength.
Lehninger 2000 Fig 3.11
Dipole Moments of Some Molecules
Molecules that have NO net
charge may have an
asymmetric distribution of
the internal charge.
that is, a polar molecule, or it
is said to have a permanent
dipole moment.
Note: a dipole moment affects
the properties of a molecule.
red arrow =dipole vectors
blue arrow = vector sum dipole moment
Matthews et al , 1999 table 2.1
Noncovalent Interactions of
Molecules
•Much weaker than covalent bond.
(10 to 100-fold weaker than, e.g. C-C and C-H bonds)
•Weakness actually makes them essential - allows them to
be continually be broken and reformed –essential to
dynamic biological processes.
•Depends on the rapid interchange of partners.
(would be impossible with strong interactions.)
•Fundamentally electrostatically-based.
Matthews et al , 1999 Chapter 2
Dipole Moments can Interact
Permanent dipole-dipole interaction are
weaker than ionic bonds.
Dipole-induced dipole interaction are
weaker than permanent dipole
interactions.
Even though very weak the dispersion
forces can have a very significant effect on
the structure of biological molecules that
have many closely packed chemical groups
in their interior.
Voet. Voet & Pratt, 2013 Fig 2.5
Types of Noncovalent Interactions
a. Charge-Charge
b. Charge-Dipole
c. Dipole-Dipole
d. Charge-induced
dipole
e. Dipole-induced
Dipole
f. (London) Dispersion
g. van der Waals
h. Hydrogen bond
Matthews et al , 1999 Figure 2.2
Noncovalent Interaction Energy of
Two Approaching Particles
Matthews et al , 1999 Figure 2.6
Hydrogen Bonding
Matthews et al , 1999 Figure 2.7
H-Bonds in Biologically Important
Molecules
Matthews et al , 1999 Table 2.3
The Classes of Reactions in Cells
•Oxidation-Reduction (all involve electron transfer)
•Cleavage & Formation of Carbon-Carbon Bonds
•Internal Rearrangements
•Group Transfers
•Condensation Reactions (monomeric subunits joined & water eliminated)
Oxidation-Reductions
& Oxidation State of Carbon in Biomolecules
Reduction gain
of electrons.
Oxidation
loss of
electrons.
Lehninger 2000 Figure 3.15
C-C Bond Cleavage
Homolytic vs Heterolytic
C-C Bond Heterolytic Cleavage:
Nucleophilic Substitution Reactions: SN1 & SN2
Occurs when a second electronrich group replace the departing
anion
Nucleophile: functional groups rich in electrons that can donate them.
Lehninger 2000 Figure 3.19a,b
Internal Rearrangements
Lehninger 2000 Figure 3.20
Group Transfer
General metabolic theme: attachment of a good leaving group,
e.g. phosphoryl group, to a metabolic intermediate to “activate”
the intermediate for subsequent reactions
Condensation and Hydrolysis
Hydrolysis
Condensation
Important concept: monomeric subunits that make up proteins,
nucleic acids, and polysaccharides are joined by nucleophilic
displacement reactions that replace a good leaving group.
END OF LECTURES