BCH 101

STRUCTURE OF BIOMOLECULES
LECTURE Ia
General introduction & water

Course Outline
BCH 101: STRUCTURE OF BIOMOLECULES
Structure of biomolecules: Structure, chemistry, occurrence,
classification and function of biomolecules, water, pH and
buffers; carbohydrates, amino acids and proteins; Introduction to
enzymes: classification, properties, specificity, theories of binding
to substrates and the active site
concept; Lipids and
Eicosanoids:
functions,
properties,
classifications;
the
nucleosides; nucleotides and the nucleic acids structure, functions
and properties; Chemical and 3-D structures of DNA and RNA;
Qualitative and quantitative identification of lipids, carbohydrates,
nucleic acids and proteins; Analysis of biochemical components of
naturally occurring materials by separation methods.
2

Biochemistry

Function

Proteins

Genetics

Genes

Molecular Biology
Schematic relationship between biochemistry, genetics and molecular biology

 Biochemistry is the study of molecules (e.g. proteins).

Biochemists take an organism or cell and dissect it into its
molecular components, such as enzymes, lipids and DNA,
and reconstitute them in test tubes (in vitro).
Genetics is the study of the effect of genetic differences on
organisms. Often this can be inferred by the absence of a
normal component (e.g. one gene).

Molecular biology is the study of biology at a molecular

level. The field overlaps with other areas of biology,
particularly genetics and biochemistry. Molecular biology
concerns itself with understanding the interactions
between the various systems of a cell, including the
interrelationship of DNA, RNA and protein synthesis and
learning how these interactions are regulated.
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Macromolecules
Carbohydrates
.

Proteins

Lipids
.

Nucleic Acids

H2 O
6

H2O: The Molecule That Supports

All of Life
Water is the biological medium on Earth
All living organisms require water more than
any other substance
Most cells are surrounded by water, and cells
themselves are about 7095% water
The abundance of water is the main reason the
Earth is habitable

The Water Molecule

Water is a simple tri-atomic molecule, H 2O
Each O-H bond is highly polar, because of the high
electronegativity of the oxygen
bond angle of water = 105o
due to the bent shape, the O-H bond polarities do not
cancel. This means: water is a polar molecule.

10

The Water Molecule

is the lowercase Greek symbol delta
+ means a
partial positive
charge

- means a
partial negative
charge

O
Thus, water has a partial
negative end (0xygen) and
a partial positive end
(Hydrogen), and it is called
polar because of these
areas of difference

+
11

Waters bent
shape and ability
to hydrogen
bond gives it
many special
properties!

Hydrogen
bond

12

The propeties of Water Molecule

Four of waters properties that

facilitate an environment for life are:

Cohesive behavior
Ability to moderate temperature
Expansion upon freezing
Versatility as a solvent

13

Cohesion
Collectively, hydrogen bonds hold water
molecules together, a phenomenon called
cohesion
Cohesion helps the transport of water against
gravity in plants
Adhesion is an attraction between different
substances, for example, between water and
plant cell walls.

14

Adhesion

Water-conducting
cells

Direction
of water
movement

Cohesion
150 m

15

 Surface tension is a measure of how hard it is

to break the surface of a liquid
Surface tension is related to cohesion
One water molecule can hydrogen bond to
another because of this electrostatic attraction.
Also, hydrogen bonding occurs with many other
molecules surrounding them on all sides.

16

Surface Tension
A water molecule in the
middle of a solution is
pulled in all directions.

17

Surface Tension
Not true at the surface.
They are pulled down
and to each side, not
upward since the water
and air are not
attracted to each other.
This holds the
molecules at the
surface together tightly.
This causes surface
tension.

18

Surface Tension
Water drops are
rounded, because
all molecules on
the edge are pulled
to the middle, not
outward to the air!
A drop has the
least amount of
surface area for
any given volume.

19

Moderation of Temperature
Water absorbs heat from warmer air and
releases stored heat to cooler air
Water can absorb or release a large
amount of heat with only a slight change
in its own temperature

20

Waters High Specific Heat

The specific heat of a substance is the
amount of heat that must be absorbed or
lost for 1 g of that substance to change
its temperature by 1C
The specific heat of water is 1 cal/g/C
Water resists changing its temperature
because of its high specific heat

21

Waters High Specific Heat

Waters high specific heat can be traced
to hydrogen bonding
Heat is absorbed when hydrogen bonds break
Heat is released when hydrogen bonds form

The high specific heat of water minimizes

temperature fluctuations to within limits
that permit life

22

Evaporative Cooling
Evaporation is transformation of a substance
from liquid to gas
Heat of vaporization is the heat a liquid
must absorb for 1 g to be converted to gas
As a liquid evaporates, its remaining surface
cools, a process called evaporative cooling
Evaporative cooling of water helps stabilize
temperatures in organisms and bodies of
water

23

Expansion upon freezing

Ice floats in liquid water because hydrogen
bonds in ice are more ordered, making ice
less dense
Water reaches its greatest density at 4C
If ice sank, all bodies of water would
eventually freeze solid, making life
impossible on Earth

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Hydrogen
bond

Ice
Hydrogen bonds are stable

Liquid water
Hydrogen bonds break and re-form

25

Fig. 3-6a

Hydrogen
bond

Ice
Hydrogen bonds are stable

Liquid water
Hydrogen bonds break and re-form

26

The Solvent of Life

A solution is a liquid that is a homogeneous
mixture of substances
A solvent is the dissolving agent of a
solution
The solute is the substance that is dissolved
An aqueous solution is one in which water
is the solvent

27

 Water is a versatile solvent due to its polarity,

which allows it to form hydrogen bonds easily
When an ionic compound is dissolved in
water, each ion is surrounded by a sphere of
water molecules called a hydration shell

28

29

+
+

Cl

Cl

+
Na+

Na+

 Water can also dissolve compounds made

of nonionic polar molecules
Even large polar molecules such as
proteins can dissolve in water if they
have ionic and polar regions

30

(a) Lysozyme molecule in a

nonaqueous environment

(b) Lysozyme molecule (purple) in an aqueous

environment

(c) Ionic and polar regions

on the proteins surface
attract water molecules.

31

Hydrophilic and Hydrophobic

Substances
A hydrophilic substance is one that has
an affinity for water
A hydrophobic substance is one that
does not have an affinity for water
Oil molecules are hydrophobic because
they have relatively nonpolar bonds
A colloid is a stable suspension of fine
particles in a liquid
32

Solute Concentration in Aqueous

Solutions
Most biochemical reactions occur in water
Chemical reactions depend on collisions of
molecules and therefore on the concentration
of solutes in an aqueous solution

33

 Molecular mass is the sum of all masses

of all atoms in a molecule
Numbers of molecules are usually
measured in moles, where 1 mole (mol)
= 6.02 x 1023 molecules
Avogadros number and the unit dalton
were defined such that 6.02 x 1023 daltons
=1g
Molarity (M) is the number of moles of
solute per liter of solution
34

Solution Concentrations
Expressed as a ratio of the amount of
solute to the total amount of solution:
grams

Concentration =

(%, w/v)

Amount of solute
Total amount of solution

mL
35

Solution Concentrations
cont
Expressed as a ratio of the amount of
solute to the total amount of solution:
moles
Concentration =

( molarity, M)

Amount of solute
Total amount of solution

Liters
36

% Concentration has multiplier of 100 to

place ratio on parts per 100 basis:

%, w/v =

Grams of solute
mL of solution

X 100

37

Practice situation:
4.75 grams of NaCl is dissolved in sufficient water to
make 750 mL of solution.
What is the % (w/v) concentration of this solution?

%, w/v =
%=

Grams of solute
mL of solution

4.75 g
750 mL

X 100

X 100

= 0.633 %

The g/mL units are understood but not included.

38

4.75 grams of NaCl is dissolved in sufficient water to

make 750 mL of solution.
What is the % (w/v) concentration of this solution?

The concentration is
0.633 % (w/v).

0.633%
NaCl
750 mL
39

Another:
12.5 grams of H2SO4 is dissolved in sufficient water to make
0.500 liters of solution.
What is the % (w/v) concentration of this solution?

%, w/v =

Grams of solute
mL of solution

X 100

Solution volume units must be converted from liters to mL

12.5 g
before doing
calculations:
0.500
L = 500
mL.%
X 100
%=
= 2.50
500 mL
The g/mL units are understood but not included.

40

Once known, the solution concentration

work as a conversion factor.
Examples (all are wt/vol percents):
0.85 % NaCl
means
0.85 g NaCl = 100 mL solution
and the conversion factors are
0.85 g NaCl
100 mL solution
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Using the concentration as a conversion

factor:
Examples (all are wt/vol percents):
What mass of NaCl is present in 2000 mL of 0.85%
NaCl solution?

How much dissolved NaCl is in

this 2000 mL of saline solution?

0.85%
NaCl
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Using the concentration as a conversion

factor:
Examples (all are wt/vol percents):
What mass of NaCl is present in 2000 mL of 0.85%
NaCl solution?

2000 mL soln

0.85 g NaCl
100 mL solution

= 17.0 g NaCl

43

Using the concentration as a conversion

factor:
Examples (all are wt/vol percents):
What mass of NaCl is present in 2000 mL of 0.85%
NaCl solution?

17.0 grams of dissolved NaCl is

present in 2000 mL of this
solution

0.85%
NaCl
44

Using the concentration as a conversion

factor:
Examples (all are wt/vol percents):
What volume of 0.85% NaCl solution should contain 2.50
grams of dissolved NaCl?

What volume will contain

2.50 grams of dissolved
NaCl?

0.85%
NaCl
45

Using the concentration as a conversion

factor:
Examples (all are wt/vol percents):
What volume of 0.85% NaCl solution should contain
2.50 grams of dissolved NaCl?

2.50 g NaCl

100 mL solution
0.85 g NaCl

= 294 mL soln

46

Using the concentration as a conversion

factor:
Examples (all are wt/vol percents):
What volume of 0.85% NaCl solution should contain
2.50 grams of dissolved NaCl?

294 mL of this solution contains

2.50 grams of dissolved NaCl.

0.85%
NaCl
47

Molarity
M=

Moles of solute
Liters of solution

4.75 grams of NaCl is dissolved in sufficient water to make

750 mL of solution.
What is the molarity of NaCl in this solution?
We previously determined this solution to be 0.633%;
what is its molarity?
48

Molarity
M=

Moles of solute
Liters of solution

The 4.75 grams of NaCl will need to be converted to moles

before the calulations are done.
Similarly, to make units match, the 750 mL will be
converted to liters.
49

Molarity
Moles of solute

M=

Liters of solution

4.75 grams of NaCl is dissolved in sufficient water to make

750 mL of solution. M = ?
4.75 g NaCl
750 mL

X
X

1 mole NaCl
58.5 g NaCl
1 Liter
1000 mL

= 0.0812 mole NaCl

= 0.750 L
50

4.75 grams of NaCl is dissolved in sufficient water to make

750 mL of solution. M = ?
M=

M=

Moles of solute
Liters of solution
0.0812 moles NaCl
0.750 Liters of solution
0.0812 mole NaCl

= 0.108 M NaCl
= 0.108 moles NaCl/L
0.750 L
51

4.75 grams of NaCl is dissolved in sufficient water to

make 750 mL of solution.
What is the % (w/v) concentration of this solution and
what is its molarity?

The concentration is
0.633 % (w/v)
and
is 0.108 M

0.633%
0.108 M
NaCl
750 mL

52

.
.

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