Cell Compounds

2/25/09

Cell Biology 1 Cell Compounds
A. Bonding
- When substances react together, the tendency is
always for their atoms to gain, lose or share electrons
so that they each acquire a full outershell. The
attractive force that holds atoms together is a
chemical bond

Compounds
- consist of atoms of two or more elements that are
joined by chemical bonds e.g., Water (H
2
O)

1. Ionic bond (= ionic compound)
- two ionic, and oppositely charged atoms (ions)
are attracted to one another
- one donating electron(s) and the other accepting
the electron(s)

- e.g., Na
+
+ Cl
-
= NaCl


- This a biologically weak bond, as ionic
compounds will readily solvate in water (diagram
solute/solvent, solvation)

- An ionic compound is not a molecule



2. Covalent bond (= molecule)
- forms when two or more atoms share one or more
pairs of electrons (to form a stable outer energy
shell)
-
e.g., Polar, H
2
O
;
Nonpolar, N
2

- Non-Polar covalent bond
- is formed where the electrons are pulled exactly
equally by the atoms involved, e.g., N
2
, O
2
,
CO
2
, CH
4
.


Notes
s
o
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r
c
e
:

h
t
t
p
:
/
/
w
w
w
.
a
c
c
e
s
s
e
x
c
e
l
l
e
n
c
e
.
o
r
g
/
A
B
/
G
G
/


Cell Compounds


Cell Biology 2 Cell Compounds


Source: LifeThe Science of Biology, 7
th
ed.


b. Polar covalent bond
- is formed
when atoms of two different elements
share e
-
, such that the charge between them is
asymmetrically distributed, e.g., H
2
O, NH
3
(Ammonia) (diagram)


- (*) lone e- pair which are not part of the
bond - found in outermost shell

- Forms biologically strong bonds
- Covalent compounds are usually gases or liquids at
room temperature
- Carbon (organic compounds) bond covalently

- a molecule is a group of atoms held together by
covalent bonds

3. Two Other Important Bonds
- Hydrogen Bond
- Are formed when a single hydrogen atom
(H
+
) is shared between two electronegative
atoms, (usually N or O).



Cell Compounds


Cell Biology 3 Cell Compounds

- Hydrophobic Interactions
- Occur between groups that are insoluble in
water. These groups, which are non-polar,
tend to clump together in the presence of
water.

- Some sticky terminology:
- Adhesion - requires an adhesive/glue to
join different things, e.g., wood to paper
- Cohesion - to join the same things, e.g.,
water to water

Chemical Bonds and Interactions
Name
Basis Of
Interaction
Structure
Bond
Energy
a

(Kcal/Mol)
Covalent Bond Sharing of electron
pairs

50110

Hydrogen
Bond
Sharing of H atom

37

Ionic Bond Attraction of
opposite charges

37

Hydrophobic
interaction
Interaction of
nonpolar substances
12 in the presence
of polar substances

12

van der Waals
interaction
Interaction of
electrons of
nonpolar 1
substances

1
a
Bond energy is the amount of energy needed to separate two bonded or
interacting atoms under physiological conditions.
Source: LifeThe Science of Biology, 7
th
ed.

B. Acids and Bases
- Each organism lives within a narrow acceptable range
of acidity and alkalinity.

Hydrophilic substances are:
water-loving
soluble in water
polar

Hydrophobic substances are:
water-fearing
soluble in lipids
o insoluble in water
non-polar


Cell Compounds


Cell Biology 4 Cell Compounds

1. pH
- is a measure of the relative amounts of
hydronium (oxonium) [H
3
O
+
] and hydroxide
(hydroxyl) [OH
-
] dissolved in solution
- [H
3
O
+
] > [OH
-
] is an acid
- [H
3
O
+
] < [OH
-
] is a base/alkali

- the scale is logarithmic, a difference of one
pH unit represents a tenfold change
- a pH of 5 is ten times greater than that
of a sample with a pH of 6, and 100x
greater than 7

- Hydrogen ion concentration and pH are
inversely related, i.e.,
- the higher the [H
+
]ion concentration, the
lower the pH
- the lower the [H
+
] ion concentration, the
higher the pH

2. Acid
- if hydrogen chloride (HCl) is dissolved in water,
some of its molecules dissociate to form
hydrogen ions (H
+
) and chloride ions (Cl
-
). The
hydrogen combines with water molecules to
form hydronium ions (H
3
O
+
). Such a solution
contains many more [H
3
O
+
] than [OH
-
] and is
therefore defined as an acid.
- sour taste; tingling or burning sensation on
skin; can be corrosive, e.g., citric acid in
citrus fruits, like oranges; detergents
3. Base / Alkaline
- NaOH (sodium hydroxide) dissolved in water
dissociates to form Na
+
and adds more OH
-
,
shifting the concentration in favour of OH
-
,
([H
3
O
+
] < [OH
-
]) a base
- bitter taste; slippery to the touch, e.g., baking
soda; soap

Note:
If pH is increasing, it is more
alkaline/basic !
If pH is decreasing, it is more
acidic "

Reminder:
H
3
O
+
! H
2
O + H
+


Abbreviation:
In chemistry concentration is
indicated by use of square
brackets [ ].
Cell Compounds


Cell Biology 5 Cell Compounds

4. Buffer
- biological buffers stabilize fluctuating pH
levels, by donating or accepting excess H+ ions.
(diagram)

Primary Biological Buffers
1. Bicarbonate (HC0
3
-
)
HC0
3
-
+ H
+
! H
2
C0
3
! CO
2
+ H
2
O [these
substances can easily be excreted by the kidneys
and lungs]
2. Phosphates H
2
PO
4
-
/ HPO
4

3. Protein Buffers
a. Amino acid residues of proteins take up H+
NH
2
(Amine) !NH
3
-
Ammonia ion
NH
3
-
+ H
+
! NH
4
[Ammonium, is relatively
non-toxic]
b. Red Blood Cells (hemoglobin)
Hb + H
+
! HHb [reduced hemoglobin]

Relative Buffering Power
- HC0
3
-
1
- Phosphate 0.3
- Plasma proteins 1.4
- Hemoglobin 6.5

- Most important buffer is protein. 75% of all
buffering power of the body is within cells as
protein. Hemoglobin is important due to high
concentration and its increased buffering capacity
when deoxygenated.

- Lung and Kidney respond with excretion & de
novo synthesis.
- buffers DO NOT neutralize pH, buffers help
keep the pH constant by compensating for
changes

Homeostasis:
- Respiratory acidosis cause - hypoventilation
- Retention of CO
2

- Respiratory alkalosis cause - hyperventilation
To first understand how amino acids and
proteins function as buffers in the body, you
need to understand a little about the structure of
an amino acid (you might want to jump ahead in
your notes to our section on Biomolecules:
Proteins, or re-read this after we have discussed
proteins). If we look at the general structure of
an amino acid, you can see that it has an amine
(NH
3
) group on one end and a carboxyl (COOH)
group on the other end.

Example: glycine 3HN-CH
2
-COOH

If the amino acid is in solution, as the pH
changes the amino and carboxyl
hydrogens (protons) will be affected.

Using glycine as an example again:

LOW pH [pH 2.3]
+
3HN-CH
2
-COOH
(+1 net charge)
|
NEUTRAL pH [pH 7]
+
3HN-CH
2
-COO
-

|
HIGH pH [pH 9.7]
2HN-CH
2
-COO
(-1 net charge)

As the pH changes an hydrogen can be lost or
gained affecting the charge (see above).

Glycine is a simple example since it doesn't have
any R groups attached to the carbon. Many R
groups can also gain or lose hydrogens, such as
arginine, glutamic acid, etc. This means that at
any particular pH an amino acid may have a net
(+ ) or (-) charge.

To complicate this a little bit more, proteins are
made up of many amino acids each of which
contributes to the proteins overall charge.
Remember that there will be only 1 terminal
amine and carboxyl group, BUT there will be
many R groups affecting the charge.

We now consider a basic definition of a buffer as
a solution that consists of a mixture of a weak
acid and its conjugate base. A good buffer will
tend to resist changes in pH upon addition of
moderate amounts of strong acid or base.

Amino acids that have this capability are glycine
and histidine. For proteins to act as buffers, you
must take into account all of the R groups and
the pH that they will gain or lose protons.

Source: Jeffrey Stiefel, http://www.madsci.org
Cell Compounds


Cell Biology 6 Cell Compounds

- Blow off CO
2

Defence against addition of acid.
1. First line of defence: buffering
H
+
+ HCO
3
-
! H
2
CO
3

2. Respiratory component H
2
CO
3
! CO
2
&
H
2
O and the CO
2
excreted by the lungs.
- Advantage: in min pH can be restored
towards normal.
-
Disadvantage: One of the primary
extracellular buffers has been
depleted. i.e. # [HCO
3
-
]

3, Renal - kidney excretes H
+
and replenishes
[HCO
3
-
]

- But, this is a slow process taking hours to
days.


C. Water
- it provided a medium in which other molecules could
move and interact without being bound by strong
covalent or ionic bonds

- life evolved as a result; and as such all life
requires it, and the greater the availability the
greater the array of life (oceans ! tropical forest
! desert)

- all reproduction requires a water medium

- Key to this, water has the ability to form weak
chemical associations with only 5-10% the strength
of covalent bonds
- This property derived from waters structure is
directly responsible for the shape of life

a. Water Molecules
- Water is a polar molecule
- it has positively and negatively charged
ends; one portion of the molecule attracts
electrons more strongly then
Body is
~70% water

~30% other chemicals
- ions, small molecules ~4%
- phospholipids ~2%
- DNA ~1%
- RNA ~6%
- Proteins ~15%
- Polysaccharides ~2%
Cell Compounds


Cell Biology 7 Cell Compounds

- because of their polarity they tend to form
hydrogen bonds with each other.

- The high degree of
cohesiveness between
water molecules due to
H bonding results in
waters unusually high
surface tension,
melting pt., boiling pt,
heat of vaporization,
and heat capacity.
-
b. Water as Solvent
- since water molecules
are polar, they are able
to dissolve ionic
compound readily,
e.g., NaCl

- i.e., 4 or 5 water
molecules can fit
around one Na
+
ion
or Cl
-
ion and the
sum of their
collective weak
charges is enough
to attract the ion
away from other
ions in the crystal
(cf. hydration, solvation)

- NB. Electrically neutral (e.g., fats) and non-
polar substances (e.g., O
2
) are not soluble in
water.
Source: LifeThe Science of Biology, 7
th
ed.

Cell Compounds


Cell Biology 8 Cell Compounds

c. Water as a Regulator
- Water is also important in regulating
environmental temperatures, because it is able
to absorb much heat energy without a very large
increase in temp. (conversely it may also release
much heat energy without a great loss in temp.)

- It acts like a highly cost efficient rechargeable
heat/energy battery
- dampens fluctuations in temperature
- the amount of water vapour in the atmosphere
exerts a strong greenhouse effect



Property of Water Explanation Example for life
High polarity
(universal solvent)
- polar water molecules
are attracted to ions
and polar compounds,
making them soluble
- many kinds of molecules
can move freely in cells,
permitting a very diverse
array of chemical reactions

High specific heat - hydrogen bonds absorb
heat when they break,
and release heat when
they form, minimizing
temp. change
- water stabilizes body temp.,
as well as that of the
environment

High heat of
vaporization*
- many hydrogen bonds
must be broken for
water to evaporate

- evaporation of water cools
body surfaces

Lower density of ice - water molecules in an
ice crystal are spaced
relatively far apart
because of hydrogen
bonding

- because ice is less dense
than water, lakes do not
freeze solid, and they
overturn in spring to enrich
the lakes food/nutrient chain

Cohesion
(surface tension)
- hydrogen bonds hold
molecules of water
together
- leaves pull water upward
from roots; seeds swell and
germinate
* Ammonia (NH
3
) with a molecular weight of 17 (water is 18) has a
freezing pt. of ~ -78C and a boiling pt. of ~ -33C Why? H-bonds in
water mean water has a much higher freezing pt and boiling pt. (recall
our simile of a loan, principle and interest, you need to pay off the
interest first, a lot of E has to go into the H-bonds to break them before
Lubricant
Water is also an excellent lubricant,
blame those H-bonds (and surface
tension) for forming a sheet of water
between two bodies, thus reducing
friction.
Cell Compounds


Cell Biology 9 Cell Compounds

the water will boil). Household ammonia is a solution of NH
3
in water
(ammonium hydroxide).

D. Biomolecules: A Quick Introduction

Water
function - universal solvent
composition - H O

Carbohydrates
function - energy source
composition - H O C

Lipids (Fats)
function - energy storage
composition - H O C

Proteins
function - structural & catalytic
composition - H O C N (sometimes P, S)

Nucleic Acids (DNA & RNA)
function - genetic code
composition - H O C N P