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Lecture 2.pdf
Lecture_2.pdf
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Lecture 2.pdf-Part I – Lecture 2 &
Lecture_2.pdf-Part I – Lecture 2 &
Lecture 2.pdf-Part I – Lecture 2 &
Lecture_2.pdf-Part I – Lecture 2 &
Page 1
Part I –
Lecture 2 & 3, Chp
2 -
Chemical
Foundations
J.Rocheleau, P. Gilbert
Systems Biology BME205 (Winter 2013)
2
Chemical Foundations
•
Atomic bonds and molecular interactions
•
Chemical building blocks of cells
•
Chemical equilibrium
•
Biochemical energetics
Page 2
Systems Biology BME205 (Winter 2013)
3
Water and macromolecules
•
General classification of
macromolecules
can be based
on interaction with water
Water: H
2
O
Systems Biology BME205 (Winter 2013)
4
Water and macromolecules
–
Hydrophilic
–
water liking -
compounds that readily
dissolve in water (e.g. sugars)
–
Hydrophobic
–
water fearing –
compounds that
don’t dissolve in water (e.g. fat)
–
Amphipathic
–
compounds that are compose of
regions that are hydrophobic and hydrophilic (e.g.
lipids, proteins)
Page 3
Systems Biology BME205 (Winter 2013)
5
Linkages between atoms: covalent bonds
•
Covalent bonds
-
attractive forces that form when two atoms
share one electron pair (“single”
bond), 2 electron pairs
(“double”
bond), or 3 electron pairs (“triple”
bond)
•
Covalent bonds mediate interaction between atoms that make
up a molecule (strong = static)
•
Governed by the fundamental principle that an atom is most
stable when its outermost electron shell is filled
Systems Biology BME205 (Winter 2013)
6
Representations of covalent bonding
Page 4
Systems Biology BME205 (Winter 2013)
7
Electron sharing in a covalent bond
•
Bonds between atoms of the same element will share the
electrons equally
•
Between unlike atoms the positively charged nucleus of one
atom exerts greater attractive force (the more
electronegative
atom)
•
In biological macromolecules,
nitrogen
,
oxygen
and
sometimes
sulfur
are strongly electronegative
Nonpolar bonds
Polar bond (C=O)
-ve
+ve
How does this affect water interaction?
Systems Biology BME205 (Winter 2013)
8
Water has an asymmetric distribution of charge
(dipole)
Polar
–
Separation of electric charge resulting in a dipole
moment
Polar bonds make regions of macromolecules
hydrophilic
(dipole interaction)
Page 5
Systems Biology BME205 (Winter 2013)
9
Ionic interactions
•
Ionic interactions
–
attractive force between a positively
charged ion (
cation
) and negatively charged ion (
anion
)
Systems Biology BME205 (Winter 2013)
10
Ionic interactions
Energy of hydration
(ion-water bonding energy) is
greater than lattice energy that stabilizes the crystal.
Page 6
Systems Biology BME205 (Winter 2013)
11
Ionic interactions
Parts of this
hydration shell
must
be removed to directly
interact with
biomolecules.
Systems Biology BME205 (Winter 2013)
12
Noncovalent bonds
•
Covalent bonds mediate interaction between atoms that
make up a molecule (relatively static)
•
Noncovalent
bonds direct interactions between
molecules (or different parts of biomolecules) (relatively
dynamic)
Increasing Energy
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