Transcript hydrogen bonds

CELL CHEMISTRY – CHPT 2
• Chemical composition of living things is unique
• Four most abundant elements in life:
– Hydrogen, oxygen, carbon, nitrogen
• Life systems depend upon/evolved in water
• Biomolecules have characteristic bonds
(linkages between atoms/elements):
– Covalent: strong bonds holding monomers in
macromolecular polymers
– Noncovalent: weaker bonds – hydrogen, ionic,
van der Waals interactions, hydrophobic
interactions
50-60%
3-4%
8-10%
25-30%
Carbon, hydrogen, nitrogen and oxygen together constitute >99%
(dry weight) of life molecules (mostly macromolecules) ; these are
>1% in the earth’s crust
Differences in
chemical
abundance
comparing living
organisms and
the earth’s crust
What are the
consequences for
living
organisms?
30 SMALL MOLECULE PRECURSORS
OF MACROMOLECULES
• 20 amino acids – monomers of proteins
• 5 aromatic bases make nucleotides- the monomers
of nucleic acids:
– 2 purines – adenine and guanine
– 3 pyrimidines – cytosine, uracil, thymine
• 2 sugars:
– D-glucose (photosynthesis product and glycolysis
substrate)
– ribose/deoxyribose (nucleotide sugars)
• 3 membrane phospholipids:
– fatty acid - palmitate,
– the tri-alcohol – glycerol,
– the amine - choline
Water is typically ~70% of cells
~30 precursor molecules but ~3000 kinds of molecules total in a
cell
CARBON
• Over 50% of organism’s dry weight –
primary element upon which life is based.
• Very diverse forms & quite stable
molecules.
– Long chains, rings, combinations of these
– Bonds a variety of other elements
• i.e.: oxygen, hydrogen, nitrogen, sulfur
• Forms covalent bonds sharing pairs of
electrons:
– Single, double, triple
Covalent
bonds have
shared pairs of
electrons
Free radicals (highly
reactive) may form
when a covalent bond
is broken such that
each atom retains one
of the two shared
electrons comprising
the bond. They may
also form when an
atom or molecule
accepts a single
electron transferred
during an oxidation reduction reaction.
Normally complete rotation around C-C single bonds (unless
large/charged side groups attached to both)
Double bonds are more rigid – do not allow complete rotation
Rigidity has enormous structural/functional significance
Bond Strength:
amount of
energy required
to break 1 mole
(6 x 1023
molecules)
One calorie =
amount of
energy to raise
the temperature
of 1 gm (1 cm3)
of water 1
degree C
One kilocalorie
= 1000 calories
Know approximate strengths!
Bonds are oriented at precise angles as a result of repulsions of
the outer electron orbitals
Ball-and-stick
models show
bond angles but
not lengths well
Space-filling
models show
outer contours
and are
proportional in
dimensions to
the radius of
different atoms
dipolar
symmetrical
WATER
• Most abundant component of cells – 70%
• Organisms evolved in water and all aspects of cell
structure/function adapted to physical/chemical
properties of water
– Modeling of molecule structure depends on
interactions with water
– Solvent of cells (hydrophilic substances dissolve,
hydrophobic substances avoid water)
• Polar, electrophilic oxygen more attracts shared
electrons, producing electrical asymmetry.
– Forms important hydrogen bonding with other
molecules
• Liquid at most environmental temperatures in spite of
low MW
Water as an electrical dipole. Delta represents a partial weak
charge. Size and direction of the charge separation is the dipole
moment
Hydrophilic substances readily dissolve in water (ions, salts,
nonionic molecules with hydroxyl, aldehyde, or ketone groups.
Hydrophobic substances do not dissolve in water (nonpolar
substances which associate with each other, avoiding interactions
with water).
Dotted lines
represent the
transient
hydrogen bonds
between water
molecules that
provide a
cohesiveness
Hydrogen bonds
are weaker than
covalent bonds
and in this case are
formed between
the negative
oxygen atoms and
positive hydrogens
The bonding in ice
crystals indicates
tighter packing, more
ordered interactions
= high for water, due to the hydrogen bonding providing cohesiveness;
high specific heat (amt heat input to change temp) buffers against rapid
temperature changes
4 KINDS OF NON-COVALENT BONDS
1.
2.
3.
4.
Hydrogen bond
Ionic bond
van der Waals interaction
Hydrophobic bond
These are transient because they are weaker
than covalent bonds (~1-5 kcal/mol)
Important in stabilizing 3D structure of large
molecules because large numbers of these
bonds work together
RELATIONSHIP
BETWEEN ENERGY AND
WAVELENGTH
140
Covalent
double/triple
bonds
140
Energy
120
120
(kcal/
Einstein);
Einstein = 100
a mole of
photons
Covalent single
bonds
100
Ionic bonds
60
60
Hydrogen
bonds
40
20
(kcal/mole)
80
80
Ultraviolet
200
Visible
400
600
Wavelength (nm)
Infrared
800
40
20
1000
Bond
Energy
Hydrogen bond: a weak
associations between an
electronegative atom and a
hydrogen atom covalently
bound to another atom.
There is a characteristic length
to the bond, depending on the
specific atoms.
Atoms which
attract electrons
more have a
greater
electronegativity
Differences in
electronegativity
determine bond
polarities
H2O
NaCl
An ionic bond
forms when a
dipolar bond
breaks and
electrons stay
with the more
electronegative
atom. Here the
chlorine atom
is much more
electronegative
than the sodium
atom.
Sodium atom, Na (0.9)
Chlorine atom, Cl (3.0)
11+
11n
17+
17n
11+
11n
17+
17n
Chlorine
anion, ClSodium cation, Na+
HYDROPHOBIC INTERACTIONS
• Occur between nonpolar molecules or
parts of molecules
• Based on avoidance of water and
charged molecules
• Since energy is required to force
hydrophobic-hydrophilic interactions,
association of two hydrophobic
molecules is less costly.
Hydrophobic molecules associate with each other and avoid
interaction with water or charged molecules
A van der Waal bond is a non-specific attraction due to transient dipoles
between 2 atoms 3-4o apart (here 2 oxygen molecules). It is a weak force (~1
kcal/mol). Because atoms repel each other if close, it is a measure of the size of
the electron cloud surrounding an atom.
Where are the covalent bonds?
REVIEW QUESTIONS:
•1. Which is more flexible/variable in shape - a small or large
organic molecule? Why is size a factor?
•2. Why are the atomic spheres depressed at their intersections in
spacing-filling models?
•3. What force is a measure of the electron cloud?
•4. What is the importance of double/triple bonding to the
determination of the three-dimensional shape?
•5. Why is the three-dimensional shape of a molecule critical to
its function?
•6. What is the significance to the cell of differing internal and
external chemicals & proportions?
•7. Generally, how do molecules within cells differ in size from
those outside?