Nature of Biology

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Chapter 1 The chemical nature of cells
Chapter 2 Membranes and cell organelles
Chapter 3 Biochemical processes in cells
Chapter 4 Molecular biology in medicine
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AREA OF STUDY 1
Molecules of life
2 NATURE OF BIOLOGY BOOK 1
1
The chemical nature
of cells
Figure 1.1 Laser confocal micrograph (x190) of cultured
human bronchial (from the lung) epithelial cells (grey) with
cilia (green) that are made of the globular protein, tubulin.
Red-orange indicates cystic brosis transmembrane conductance
regulator (CFTR). This protein acts as a chloride channel and also
controls the regulation of other transport pathways of a cell.
Note the absence of this protein on the bottle-shaped goblet cell
membrane near the centre of the image. Blue indicates DNA in
each cell nucleus.
In this chapter, we look at different kinds of molecules found
in living cells and consider their functions, particularly those of
carbohydrates, proteins, lipids and nucleic acids.
KEY KNOWLEDGE
This chapter is designed to enable students to:
enhance their knowledge and understanding
of the synthesis of biomacromolecules such as
polysaccharides, lipids, proteins and nucleic acids
enhance their knowledge and understanding of
the structure and function of nucleic acids
understand the structural diversity of proteins
and how this diversity relates to the variety
of functions that proteins carry out in living
organisms
develop an understanding of the concept of the
proteome of an individual or a cell.
THE CHEMICAL NATURE OF CELLS 3
ODD FACT
A fault in the
genetic material responsible
for the production of the CFTR
protein results in cystic brosis
(CF) and reduced development
of the vas deferens.
Examining molecules
Figure 1.1 is an example of the application of technology that makes it possible
to locate particular kinds of molecules in a cell. The image was obtained using
a confocal microscope (see Nature of Biology Book 1, Third Edition, page 12)
and multicolour uorescence techniques. The stain commonly used contains a
number of components that each bind to a particular kind of molecule. Each stain
uoresces with a different colour when exposed to laser light. In the example in
gure 1.1, two different kinds of protein and DNA molecules are located.
Information such as the location of particular molecules in a cell can be
important and gives valuable insights into the role of a molecule and how it
contributes to the function of a cell. In this chapter, we examine the various
kinds of molecules found in living cells and consider their various functions.
The molecules we consider in particular are carbohydrates, proteins, lipids
and nucleic acids. In addition, we consider water as it is the most abundant
molecule found in cells and the medium in which most cellular processes
occur.
First, read about the Australian Synchrotron. A synchrotron enables scientists
to examine high-resolution three-dimensional detail about molecules, particu-
larly proteins. In this book, you will read about ways in which biologists and
other scientists apply this technology and the valuable knowledge it provides.
The building in outer Melbourne that houses the
Australian Synchrotron (gure 1.2), due for completion
in 2007, has a diameter about the size of the playing
eld at the Melbourne Cricket Ground. A synchro-
tron produces light of greater intensity and brilliance
than that from any other source. It does this by using
magnetic elds to change the direction of movement of
very high-speed electron beams. The pinpoint beams
of light are directed to workstations where they can be
used for a range of research applications.
The Australian Synchrotron
BIOTECH
Figure 1.2 The Australian Synchrotron
building
Figure 1.3 The path that electrons follow
in the synchrotron: 1. electron source;
2. linear accelerator (linac) accelerates the
speed of the electrons generated;
3. booster ring; 4. storage ring;
5. beamline; 6. experimental station
(continued )
= oxygen
= hydrogen
(a)
(b)
We can think of a synchrotron as a super- microscope
that enables examination of molecules in very ne
detail. The brilliance and intensity of light from a syn-
chrotron allows examination of molecular structures
in much ner detail than is possible with electron
microscopes and X-ray machines (see gure 1.4).
It has many signicant applications, particularly in
biological and medical science, for example, knowled ge
of the detailed structure of the proteins that make up the
protein coat of the u virus made the design of a drug
against inuenza possible (see page 115).
To read more about the Australian Synchrotron,
access the website at www.synchrotron.vic.gov.au and
click on Information for teachers and students.
Figure 1.5 Each water molecule is made of a single oxygen atom
combined with two hydrogen atoms. (a) The hydrogen atoms are
joined to the oxygen with covalent bonds. (b) Water molecules are
attracted to each other and hydrogen bonds form between them.
Hydrogen bonds are shown as broken lines in the diagram.
Figure 1.4 Compare the range of the synchrotron with that of other optical tools.
Water: a unique compound
Water is the most abundant compound in our bodies and is the main solvent for
many of the organic molecules present. This makes water the ideal medium for
chemical reactions that take place in the body. The sum
total of these reactions is called metabolism.
Each water molecule consists of a combination of
a single oxygen atom with two hydrogen atoms (see
gure 1.5a). Each hydrogen atom is linked to the oxygen
atom by a strong covalent bond. Although a water molecule
overall has a neutral charge, the oxygen at the end of a
covalent bond is slightly negative and the hydrogen atoms
are slightly positive areas.
We discuss metabolic reactions in
greater detail in chapter 3.
Individual molecules of water are highly attracted to each other such that the
negative oxygen of one molecule of water is attracted to the positive hydrogen
of another water molecule. In fact, the oxygen of a water molecule attracts one
hydrogen in each of two other water molecules. Water molecules are said to be
highly cohesive. They tend to stick together, held by so-called hydrogen bonds,
which are weaker than covalent bonds (see gure 1.5b).
The attraction between water molecules and the presence of hydrogen bonds
give water unusual properties. It is a compound that exists in nature in three
different physical states ice, uid water and gas (see gure 1.6).
Figure 1.6 (a) Water in two of its physical states, as uid water and as ice. Note the
position of the ice in relation to the surface of the water. How would you account for its
position? (b) Water in its gaseous state, as steam
Although water molecules are attracted to each other, the hydrogen bonds that
hold them together are relatively weak and are continually breaking. At the same
time, hydrogen bonds are continually rejoining. The time between breaking and
rejoining is so short that, overall, water molecules retain their cohesive nature.
Most materials shrink as the temperature falls because movement of mol-
ecules within the material decreases. As the temperature of water falls, the rate of
molecule movement decreases but at 4C there is no longer sufcient movement
to break the hydrogen bonds. The water molecules form a lattice structure that is
less dense than liquid water because the hydrogen bonds keep the molecules at a
further distance apart than they may be when in liquid form. The lattice begins to
freeze and oats on the surface of the underlying water.
In a natural situation, such as a lake, the formation of a lattice of ice at the
surface provides protection for living organisms in the water. The water below
the ice remains above freezing point at about 4C, protected by the layer of ice
above at 0C. When temperatures rise again to 4C, molecules in the ice begin to
move and water returns to the uid state once more (as shown in gure 1.6a).
If the temperature of uid water increases signicantly to 100C, the move-
ment of water molecules increases to a point where hydrogen bonds no longer
hold them together. Water is converted to its gaseous state, steam (as shown in
gure 1.6b).
(b)
(a)
Cl
Cl
Na
+
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+
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Cl
Cl
Cl
Cl
Cl
Cl
Cl
Cl
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+
Water is a versatile solvent
Water is the predominant solvent in living organisms. Its versatility as a solvent
is due to the cohesive nature of the molecule that we examined in the previous
section.
Substances that dissolve readily in water are called hydrophilic or polar.
Substances that tend to be insoluble in water are called hydrophobic or
non-polar.
How would you classify fats?
How do substances dissolve in water? A substance such as sodium chloride
(salt, NaCl) dissociates into its parts positively charged sodium ions and nega-
tively charged chloride ions when it comes into contact with water molecules.
This occurs because the positive sodium ions are attracted by the negative oxygen
and the negative chloride ions are attracted by the positive hydrogen of water.
These attractions are sufcient to break the bonds between sodium and chloride.
A ring of water molecules surrounds each sodium and chloride atom and they
remain in solution (see gure 1.7).
Figure 1.7 A grain of salt contains
many sodium chloride molecules.
When salt is placed in water, salt
molecules dissociate because of the
attraction of sodium and chloride
to different parts of the water
molecules. A ring of water molecules
surrounds each sodium and chloride
atom and they remain in solution.
Acid or alkaline?
Pure water has a pH of 7.0 and is a neutral solution. What is pH? pH is a scale
that provides a measure of hydrogen ions in a solution and hence the state of the
acidity or alkalinity of a solution. The range of the pH scale is from 0 to 14 (see
gure 1.8).
Values of pH below 7 are acidic, indicating a higher concentration of hydrogen
ions than in neutral solution.
Values higher than pH 7 are alkaline, also called basic, and indicate a higher
concentration of hydroxide ions than is found at neutral pH.
High concentration
of hydrogen ions
High concentration
of hydroxide ions
INCREASING ACIDITY INCREASING ALKALINITY
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14
Hydrochloric
acid
Lemon
juice
Coffee Pure
water
Baking
soda
Soap
solution
Sodium
hydroxide
Gastric
juice
(1.03.0)
Acetic
acid
(vinegar)
Urine
(57)
ACID
H
+
H
+
H
+
H
+
H
+
H
+
H
+
OH
H
+
OH
OH
OH
OH
OH
OH
OH
H
+
OH
OH
OH
H
+
OH
OH
OH
H
+
OH
H
+
H
+
H
+
BASE
NEUTRAL SOLUTION
Blood
(7.37.5)
The pH of body uids is kept relatively constant because hydrogen ions are
continually being produced and used in cells. Note the value for blood in gure
1.8. The pH of urine is more variable because the kidneys assist in maintaining
the pH in the blood and body tissues by excreting more or less of the particular
ions as required to maintain the balance.
When the pH value of body uids, for example, blood or urine, is outside
the normal ranges expected in healthy persons, it may be an indication of some
metabolic problem or other defect. Cells contain buffer substances, that is, these
compounds combine with or release hydrogen ions in a cell as required to prevent
severe shifts in the pH of a cell or uid.
Figure 1.8 The pH scale. The
acidity or alkalinity of a solution is
indicated by a value between 0 and
14. Water at pH 7 is neutral, values
of less than 7 indicate acidity, values
above 7 alkalinity. Note other values
on the scale.
A synchrotron is a super microscope used to examine molecules in
ne detail.
All metabolic reactions occur in watery solutions.
Water can occur in three different states under natural conditions.
The pH scale is a measure of hydrogen ions in solution.
KEY IDEAS
1 What are the special characteristics of the light produced by a
synchrotron?
2 a Explain why ice is less dense than water.
b Explain how this difference in density is of vital importance to
organisms that live in water.
3 a What name is given to a solution that has equal numbers of
hydrogen and hydroxide ions?
b What general name is given to solutions that have many more
hydrogen ions than hydroxide ions?
QUICK-CHECK
Polysaccharides Sugars
larger units of the cell building blocks of the cell
POLYMERS: MONOMERS:
Proteins Amino acids
P
S
T
U
P
S
A
S
P
S
G
P
S
P
C
Nucleotides Nucleic acids
P
P
P
P
A
G
C
P
T
P
P
P
A T
G
C
5'
3'
3'
5'
Fats, lipids, membranes Fatty acids
Organic molecules
Organic molecules are often large molecules made of smaller sub-units that
are bonded together in various ways. Compounds formed in this way are called
polymers. The sub-units are called monomers. You will recall from your
previous studies that we classify polymers on the basis of the kind of sub-unit
they contain (refer to gure 1.9).
Figure 1.9 The four main groups of
organic molecules in cells. Note the
monomers that make up the polymers
of each group.
The kinds of organic molecules that we will consider are carbohydrates,
proteins, lipids and nucleic acids. For each of these, we will examine:
the basic unit of structure
how the units combine to form complex molecules
where each kind of molecule is found in a cell
the function for the molecules.
CARBOHYDRATES
Monosaccharides Disaccharides
contain a single sugar unit contain many sugar units contain two sugar units
Complex
Polysaccharides
Simple
Carbohydrates energy rich
Carbohydrates are organic compounds, composed of carbon (C), hydrogen (H)
and oxygen (O). The basic unit of carbohydrates is a sugar molecule, also called
a monosaccharide. A disaccharide contains two monosaccharides.
When two sugar molecules are joined together, a water molecule is released.
This is a typical situation when two monomers of any of the groups we are
dealing with join together. Carbohydrates containing one or two sugar units
are often referred to as simple carbohydrates; those containing many sugar
molecules are called complex carbohydrates (see gure 1.10).
Figure 1.10 Outline of the
classication of carbohydrates
Figure 1.11
Glucose is packaged
as a ne white powder
for sale and is called Glucodin.
Carbohydrates play an important role as a source of energy for plants and
animals, as food storage in the form of starch for plants and glycogen in animals,
and as structural elements in plants.
Simple carbohydrates
Simple carbohydrates have one or two sugar units in their molecule,
they are soluble in water, they have a sweet taste and are known as
sugars. Their general formula is (CH
2
O)
n
.
Monosaccharides
A monosaccharide is a molecule that comprises a single sugar unit
and usually has the formula C
6
H
12
O
6
. Although some monosaccharides
have the same molecular formula, their different properties arise from their
differences in structural formula the way in which their atoms are
arranged within the molecule. There are many monosaccharides
but the most important is glucose (see gure 1.11), also called grape
sugar.
Glucose is a product of photosynthesis. The simplied
summary for this complex process is:
light
6CO
2
+ 12H
2
O C
6
H
12
O
6
+ 6O
2
+ 6H
2
O
chlorophyll
Note the formula for glucose, C
6
H
12
O
6
. During the formation of
glucose in plants, energy of the sun is transformed into energy in glucose
molecules. Note also the structure of the glucose molecule as shown in
gure 1.12 (page 10). Simple sugars form such ring structures when in solution.
The ending -ose
indicates a sugar molecule.
Glucose is signicant in the formation of most other carbohydrates. Other
monosaccharides include galactose, mannose and fructose, also called fruit
sugar.
Figure 1.12 Different ways of representing a monosaccharide molecule such as glucose.
Note the numbering of the C atoms and that the letter C is often omitted from the
representation of ring structures.
O = C C C C C C OH
H H
H H H H
H OH OH
OH
OH
1 2 3 4 5 6
6
CH
2
OH
OH
OH
5
C
3
C
H
H
OH
O
H H
4
C
1
C
2
C
OH
H
6
CH
2
OH
HO
5
3
H
H
OH
O
H
4 1
2
OH
H
HO
H
H
H OH
glucose glucose glucose glucose glucose
Table 1.1 The structure and function of some simple sugars, monosaccharides and disaccharides
Example Function Formula Molecular structure
MONOSACCHARIDES
Glucose Energy source in plants and animals C
6
H
12
O
6
CH
2
OH
HO
H
H
OH
O
H
OH
H
HO
H
Fructose Derived from glucose and is called
fruit sugar; combines with glucose
to form sucrose
C
6
H
12
O
6
H
OH
OH
H
O
HOCH
2
CH
2
OH
H
OH
DISACCHARIDES
Sucrose Form in which carbohydrate is
transported through plants
C
12
H
22
O
11
OH
H
O
CH
2
OH H
CH
2
OH
H
OH
CH
2
OH
HO
H
H
OH
O
H
OH
glucose + fructose
H
H
O
Lactose Sugar present in milk
2 to 8 per cent of solids
C
12
H
22
O
11
OH
OH
O
OH
H
H
H
HOCH
2
HO
H
HOCH
2
H
H
OH
O
H
OH
H
H
H
O
galactose glucose +
Disaccharides
A disaccharide is formed when two monosaccharides combine (see gure 1.12).
The most familiar example is sucrose, the sugar you use in your tea or coffee
or the maple syrup you spread on pancakes. Sucrose is also the form in which
carbohydrate is transported in plants. It is formed from the combination of
glucose with fructose:
glucose + fructose sucrose + water
Note the water molecule released during the formation of a sucrose molecule.
If we include the formulae of the components in the equation, then the reaction
is written as follows:
glucose + fructose sucrose + water
C
6
H
12
O
6
C
6
H
12
O
6
C
12
H
22
O
11
H
2
O
In fact, glucose is a fundamental unit for the formation of both disaccharides
and polysaccharides.
Other disaccharides include lactose (see gure 1.12) and maltose.
Polysaccharides complex carbohydrates
Polysaccharides are polymers of sugar molecules. The most common sugar
component is glucose. Consider the structure of the polysaccharides starch,
glycogen and cellulose. They are all composed entirely of glucose and yet their
structures and properties are quite different from one another (see gure 1.13,
page 12). The differences in properties relate to the ways in which the glucose
molecules are linked together. These differences in bonding give each poly-
saccharide its characteristic shape and properties.
Unlike sugars, many polysaccharides are insoluble in water.
Glycogen
Glycogen is the form of energy storage in animals. When carbohydrates are
digested, glucose is absorbed into the bloodstream that carries it to the liver and
then to all cells of the body. If there is excess to body requirements, it is con-
verted into glycogen by the liver for storage (see gure 1.13a, which shows a
section through liver cells with the stored glycogen stained pink). The liver is
able to store about 100 gram of glycogen.
Another storage site of glycogen is muscle tissue. Muscle tissues can store
about 300 gram of glycogen. If the storage capacity of the liver and muscles is
reached, excess glucose is converted to fat storage.
The portion of the glycogen molecule shown in gure 1.13a indicates bonding
between molecules and branches of molecules but does not show the overall
nature of the molecule. It is a circular molecule (see gure 1.14, page 12) that
has a protein as its starting point and lots of branches each containing the same
number of sugar units. The protein that acts in this way for the formation of the
molecule is called a primer.
Starch
Glucose is distributed around a plant in the form of sucrose. Although some plants
do store excess requirements in this form, starch is the chief form of storage by
most plants. The storage can occur at a number of different sites (see gure 1.15,
page 13), for example:
potatoes and ginger store in modied stems
sweet potato stores in modied roots
onions store in modied leaves
seeds store in their endosperm and provide for the young plant until it becomes
established.
ODD FACT
Some sugars,
including glucose, can exist in
different structural forms, called
isomers, but this is not an
aspect that you need to cover
for your studies here.
Note in gure 1.13 that the way in which the glucose molecules bond together
results in a spiral-shaped starch molecule.
Starch is stored in the form of small grains, as shown in gure 1.15b. Different
species of plants generally have quite different shaped grains, and some have
striations as if the starch has been deposited in layers as the grain is formed.
Starch is an ideal compound for storage in plants. It is insoluble in water and
so its presence in a cell has little or no effect on osmotic action of the cell. Also,
because it has been formed from sugar, it can be readily converted back into
sugar and transported to where the plant needs it most. When extracted from
plants, starch is like a ne white powder.
Inulin is a storage polysaccharide present in some plants and belongs to the
general class of starches. It is rather like starch in appearance but its basic sugar
is fructose and, unlike starch, is soluble in water. Bananas, onions and asparagus
are some of the plants that store inulin. Inulin is not digested by animals and so
is not absorbed from the intestine.
Figure 1.13 The different structures of (a) glycogen, (b) starch and (c) cellulose.
Note the outline representation of the glucose molecules. Note also the three different
ways in which the glucose molecules link together.
2
Glycogen
1
Starch
2
Cellulose
3
Figure 1.14 Simplied diagram of
a glycogen molecule. In the complete
molecule there are 12 layers of
branching, and only ve are shown
here. All chains in molecules contain
the same number of sugar units.
The protein G is glycogenin.
(a)
(b)
(c)
B
A
B
B B
B
B
B
B
B
B
B
B
A
A
A
A
A
A
A
A
A
A
A
A
A
A
A
C 1
2
3
4
5
G
Cellulose
Cellulose is a structural polysaccharide with a general formula similar to that of
starch (C
6
H
10
O
5
)
n
. Every plant cell wall contains cellulose, making it the most
abundant of all the biological molecules. Note in gure 1.13 how the cellulose
molecules are very long and unbranched. Bundles of them together form very
tough bres, ideal for their structural role. Can you think of any plant parts that
you eat that have these tough bres?
Some animals also derive rm structural parts from cellulose. The plant in
gure 1.16 has cellulose cell walls in all its tissues. The y it has managed to
trap has a rm external covering of the polysaccharide chitin, a derivative of
cellulose.
Pectin, another polysaccharide, is a cementing material between the cell walls
of plant tissue cells.
Figure 1.15 (a) A photograph of carbohydrates. Almost all the cells of every potato are packed with starch
granules and every cell has a cellulose wall. (b) Scanning electron micrograph of starch grains from potato cell
Figure 1.16 Note the insect
caught by the sticky hairs of a
Drosera plant.
Small molecules called monomers join together to form large molecules
called polymers.
Organic polymers include carbohydrates, proteins, lipids and nucleic
acids.
Carbohydrate molecules are composed of carbon, hydrogen and oxygen.
Carbohydrates can also be classied into monosaccharides,
disaccharides and polysaccharides.
KEY IDEAS
4 Name the monomers of carbohydrates, proteins, lipids and nucleic
acids.
5 Where is the monosaccharide glucose found in its natural state? What
is its function?
6 Name two polysaccharides found (a) in plants, and (b) in animals.
QUICK-CHECK
(a) (b)
Proteins
Although water is the main compound in living cells, more than half of the
remainder, about 18 per cent, is protein. There are thousands of different proteins
in each cell and many of these control all metabolic processes within cells. All
proteins contain nitrogen (N), hydrogen (H), carbon (C) and oxygen (O). Some
also contain sulfur (S) and phosphorus (P). They are complex large compounds
as indicated by the following examples:
zian from Indian corn C
736
H
1161
N
184
O
208
S
3
gliadin from wheat C
685
H
1068
N
196
O
211
S
5
casein from milk C
708
H
1130
N
180
O
224
S
4
P
4
Some plants contain granules of solid protein that they store as reserve food.
Animals, as we will see in the next section, have most of their energy stores in fat.
The building blocks of proteins
Proteins are large molecules built of sub-units called amino acids. Note that all
amino acids and hence proteins contain nitrogen as well as carbon, hydrogen and
oxygen. Some proteins also contain sulfur and phosphorus.
There are 20 naturally occurring amino acids (refer to the Appendix). Humans
are unable to make all 20 amino acids and must rely on their food for the nine
they are unable to make (see the note at left). Not all plants can make all 20 amino
acids so a vegetarian diet should be well planned to ensure a balanced intake of
appropriate amino acids. Generally, animal proteins are a better source of amino
acids for humans because animal protein is more like that of humans. Different
proteins contain different numbers and proportions of each of the amino acids.
The general formula of an amino acid is:
R
amino group H
2
N C COOH carboxyl group
H
Each amino acid has one part of its molecule different from other amino acids.
The R group in the general formula is the part that varies.
Two amino acids join together as a dipeptide when a peptide bond forms
between the amino group of one amino acid and the carboxyl group of another
amino acid (see below and gure 1.17). When a number of amino acids join in
this way, a polypeptide is formed. Each type of protein has its own particular
sequence of amino acids. Polypeptide chains become folded in different ways
depending on their function.
threonine
methionine
lysine
valine
leucine
isoleucine
histidine
phenylalanine
tryptophan.
These nine amino acids cannot be
made by human cells but they are
essential and must be obtained in
food eaten:
Sulfur may be present in the
variable R group and makes
di-sulde bonds possible (see
gure 1.23, page 20).
H N N C C C C OH
O CH
3
O H
H
glycine peptide
bond
alanine
dipeptide + water glycine + alanine
H H H
E
H
H H
OH
O O
N
Amino
group
Peptide
bond
Carboxyl
group
N C N C
H H
Energy
Energy
Pool of amino
acids
C C
R R
Polypeptide
(amino acid
chain)
The structure and shape of proteins
Proteins are very large molecules; some contain thousands of amino acids. These
large molecules fold and organise into different shapes. Protein structure is
described at four different levels of organisation (see gure 1.18, page 16).
Primary structure
The primary structure of a protein is the specic linear sequence of amino acids
in the protein. Different proteins have different primary structures and hence have
different functions. The sequence of amino acids in a protein is determined by
the genetic material in the nucleus (this is discussed further in the next section).
Secondary structure
Amino acid chains fold in three different ways (gure 1.18b, page 16). Hydrogen
bonds form between segments of the folded chain that have come close together
and help stabilise the three-dimensional shape. The following are some examples
of secondary structure:
The major protein of wool is alpha-keratin, a spiral molecule. If the bre is
stretched and the hydrogen bonds are broken the bre becomes extended. If
the bre is then let go, the hydrogen bonds reform and the bre returns to its
original length.
The major protein of silk is broin that is fully extended and lacks the coiling
found in the structure of wool. The silk molecules form a beta-pleated sheet
(see gure 1.18b). The polypeptide chains of silk are already extended and
cannot be extended further.
Any major protein or portion is called random coiling if it does not t into
alpha- or beta-coiling. The oxygen-binding protein of muscle, myoglobin, has
random sharp turns in its coil. The place of the random coil is often the most
active site of a molecule.
Figure 1.17 Proteins are
assembled from amino acids that
are joined by peptide bonds. Each
peptide bond forms by the linkage
of an amino group from one amino
acid and a carboxyl group of another
amino acid. A number of amino
acids joined by peptide bonds form
a polypeptide chain. Note that the
different R groups are represented
by different colours. The remainder
of each amino acid molecule is
identical.
Figure 1.18 The four levels of
protein structure: (a) primary
order of amino acids in the molecule;
(b) secondary folding of some
portion of the amino acid chain
(note the three different modes;
(c) tertiary describes the shape
of the entire polypeptide chain;
(d) quaternary some proteins
comprise a number of polypeptide
chains.
(a) Primary structure
(b) Secondary structure
(3 configurations)
(c) Tertiary structure
Myoglobin Haemoglobin
(d) Quaternary structure
-Helix
Random coil
(or)
-pleated sheet
Amino acid sequence
(or)
Tertiary structure
The tertiary structure refers to the total irregular folding held together by ionic or
hydrogen bonds forming a complex shape such as that of myoglobin. The bonds
form between side chains of amino acids to form a complex internal structure.
Quaternary structure
Quaternary structure describes a structure in which two or more polypeptide
chains interact to form a protein. The resulting structure can be, for example,
globular as in haemoglobin (gure 1.18d and gure 1.19) or brous as in collagen,
the most common of animal proteins.
Table 1.2 lists a number of different types of protein and their functions. Some
examples of proteins are also shown in gure 1.20.
Red blood cell
Each red blood cell
contains 200300
million molecules
of haemoglobin.
Alpha
1
Beta
1
Beta
2
Alpha
2
Oxygen molecule
Molecule of adult haemoglobin
Haem group
Table 1.2 Examples of proteins and their functions
Type of protein Function Example
structural brous support tissue in skin, bone, tendons, cartilage,
blood vessels, heart valves and cornea of the eye
collagen, keratin
enzyme catalyse reactions ATP synthase
contractile muscle movement myosin, actin
immunoglobulin defence against disease antibodies
hormone regulate body activity insulin
receptor respond to stimuli insulin receptors
transport carry other molecules haemoglobin
Figure 1.19 The quaternary molecule of haemoglobin comprises
four chains, two alpha chains and two beta chains. Note how many
of these molecules are present in each red blood cell.
Figure 1.20 (a) A scanning electron micrograph (SEM) of collagen bundles from connective tissue that wraps around and supports
nerve bres (notice the characteristic banding of collagen bres). (b) A SEM of skeletal muscle bre showing the thick laments that
are made up of myosin (c) A transmission electron micrograph (TEM) showing Y-shaped structures (yellow) which are molecules of the
immunoglobulin G antibody, an important part of the immune system
(a) (b) (c)
Conjugated proteins
Many of the proteins we have described above are simple proteins the end
molecule contains amino acids only. With some proteins, the chains of amino
acids conjugate with other groups. This is particularly the case for those proteins
in the nucleus. They are mostly nucleoproteins they comprise a molecule con-
taining both protein and nucleic acid.
Another conjugated protein is haemoglobin. Each tertiary structure compo-
nent produced associates with a heme group. The quaternary molecule comprises
four chains, two alpha chains and two beta chains. The amino acid sequence in a
protein is important. If the order of amino acids in either chain is altered, a defec-
tive chain results. An individual inherits the ability to make a beta chain from
The popularity of television shows about forensics has
brought some knowledge about the detection of blood
into many homes. Turn off the light, spray a chemical
at the crime scene and examine the scene for signs of
luminescence. The luminescence produced is because
the chemical used reacts with any haemoglobin present
(gure 1.21).
Although the chemical Luminol has been the
star in many television shows, a new star has been
developed. BLUESTAR Forensic is an improved
product that gives a brighter luminescent result
visible in normal light. It is also non-toxic and
causes no change in the DNA so that minute
quantities that are present can also be used for
DNA-typing.
Although the presence of blood is indicated, further
testing is required to conrm that the substance lumi-
nescing is in fact blood because other compounds also
react with the chemical. The important factor is that
the position of minute blood remains are indicated even
though no blood was visible to the naked eye. Without
this, testing for blood would not be possible.
FORENSICS DETECTING HAEMOGLOBIN
Figure 1.21 Images from a crime scene investigation. Although no blood was visible to the naked eye, use of
BLUESTAR Forensic detected the presence of minute levels of haemoglobin. The luminescence indicates possible blood.
Additional tests can prove it to be so.
each parent. If the defect is inherited from each parent, an individual is unable
to produce any normal haemoglobin and they have the disease thalassaemia. If
the defect is inherited from one parent only, an individual is able to make normal
haemoglobin as well as affected haemoglobin and is able to live a normal life.
Read Marys story about a defective haemoglobin protein in her family.
I am a secondary school teacher of VCE Biology,
Mathematics and Science. When I was a university
student in the second year of my course studying
Genetics, we considered the disorder thalassaemia,
the gene responsible and its physical symptoms. I had
been experiencing lethargy, faintness and headaches
and, given my Greek-Cypriot background, my doctor
suggested a blood test. I was diagnosed as a carrier
of thalassaemia, that is, one of my two alleles for the
thalassaemia gene was defective and I had what is
called thalassaemia minor (thal-minor). People from
countries around the Mediterranean have a higher
chance of carrying a defective allele for thalassaemia
than those from other regions.
An individual who has inherited a defective thal-
assaemia allele from each parent has thal-major and,
although treatment is available, they generally have a
reduced quality of life and life expectancy. My blood
test results showed a low haemoglobin count and some
unusual-shaped red blood cells. The unusual-shaped
red blood cells have a lower oxygen-carrying capacity
than normal red blood cells. This would explain why I
had low oxygen levels and why I was always tired.
I was also diagnosed as having mild anaemia and was
prescribed iron tablets. I took these but later concen-
trated on eating a healthy diet that included high-iron
foods, such as red meat, which is generally sufcient
to prevent anaemia in a person with thal-minor. Much
more is known now about thalassaemia and its optimal
treatment.
Many members of my family have been tested and
diagnosed with thal-minor. A cousin and spouse each
tested positive with thal-minor. Knowing this meant
that they were aware of the chance of having a child
with thal-major and could consider all options and plan
accordingly rather than be faced with the unexpected.
Given that my parents were both carriers of a defec-
tive allele, each child of theirs had a 25 per cent chance
of having thalassaemia major. We consider ourselves
lucky that the odds were in our favour. Naturally I had
some concern about being thal-minor. My partner was
tested and luckily he was not a carrier. This made our
decision to have children easier as there was no chance
of having a thal-major baby. Each pregnancy had a fty
per cent risk of a thal-minor baby. This is really of little
concern because mild anaemia that may be present can
be readily controlled by careful diet.
I have two beautiful children, Stephen and Andrea,
who are both healthy. However, I had some concern
about their energy levels and therefore their iron and
haemoglobin levels, especially my daughter who had
a pale complexion and often tired easily. Some doctors
suggest that testing of children for thalassaemia status
can be delayed until they are thinking of starting a
family. We chose to have the children tested to see if
they had inherited the defective allele. We believed
that, if they did prove to be thal-minor, they would over
time come to a better understanding of what it meant,
I would have immediate information about whether
they needed a higher than average intake of iron and
we could discuss options that might arise. In the future,
the options could include testing of carrier status of a
partner before starting a family.
I am pleased to be able to share with students my
experiences and the knowledge that living with a genetic
disorder, or knowing that you can pass on a defective
allele to a child, does not have to control a persons life,
especially if they are informed and aware.
PERSONAL STORY
MARY THALASSAEMIA MINOR
Figure 1.22 Mary and her children, Andrea and Stephen
S
S
Gly
Gly
Gly
Gly
lle
Val
Val
Glu
Glu
Gln
Gln
Cys
Cys
Cys
Thr
Ser
lle
Cys
Cys
Ser
Ser
Leu
Val
Val
Leu
Tyr
Gln
Leu
Leu
Leu
Glu
Glu
Asn
Cys
Tyr
Tyr
Asn
Asn
Phe
His
His
Leu
Ala
Arg
Phe Phe Tyr
Thr
Pro
Lys
Thr
S
S
S
S
S
S
Gly
Gly
Gly
Gly
lle
Val
Val
Glu
Glu
Gln
Gln
Cys
Cys
Cys
Thr
Ser
lle
Cys
Cys
Ser
Ser
Leu
Val
Val
Leu
Tyr
Gln
Leu
Leu
Leu
Glu
Glu
Asn
Cys
Tyr
Tyr
Asn
Asn
Phe
His
His
Leu
Ala
Arg
Phe Phe Tyr
Thr
Pro
Lys
Thr
S
S
S
S
Arg
Gly
Gly
Gly
Gly
Gly Gly
Glu
Gln
Gln
Gly
Gln
Gln
Ser
Ser
Val
Val Leu
Leu
Leu
Ala
Pro
Pro
Lys
Leu
Glu
Leu
Leu
Ala
Asp
Glu
Glu
Arg
Arg
Ala
Non-active to active molecule
Insulin, produced by beta cells in the pancreas, is a protein hormone. It controls
the level of glucose in the blood by facilitating the uptake of glucose from the
blood into tissue cells. When this occurs the level of blood glucose declines. An
insulin molecule comprises two chains of amino acids held together by di-sulde
bonds (gure 1.23a). This is the active state of the hormone.
When initially produced, insulin is inactive as a hormone. It is produced as a
single chain of amino acids with folds that are held together by three di-sulde
bonds (gure 1.23b). A section of this molecule is removed by an activating
enzyme leaving the active enzyme as two chains of amino acids held together by
the three di-sulde bonds.
Hence, although a molecule may be made from a number of molecules linked
together by sulde or other bonds, they may derive from the same initial inactive
protein. Many enzyme proteins are produced in an inactive form and only become
active if the appropriate enzyme is present to convert them for active service. Can
you think of a situation that you considered in your previous studies that involved
an enzyme being converted from the inactive to the active state?
Figure 1.23 (a) A molecule
of insulin comprises two chains of
amino acids held together by three
di-sulde bonds. This is the active
state of the molecule. (b) Inactive
insulin is produced as a single chain
of amino acids folded on itself
and held together by the three
sulde bonds.
What is the proteome?
In living organisms, proteins are involved in one way or another in virtually every
chemical reaction. They may be the enzymes involved, they may be the reactants
or the products, or they may be all three. The complete array of proteins produced
by a single cell or organism in a particular environment is called the proteome of
the cell or organism. The study of the proteome is called proteomics.
Scientists are moving away from investigating single proteins because no
protein acts in isolation from other proteins. They are now exploring the total
ODD FACT
There has also
been a change in emphasis
regarding the genetic material.
The focus on single genes has
been replaced with a global
analysis of the genome, the
total genetic material. This
study is genomics.
(a)
(b)
pattern of proteins produced by a cell and analysing these patterns
to compare them with patterns from different kinds of cells. What
are the differences? What are the similarities? What is the proteome
prole of diseased tissue or even the uids surrounding the tissue?
In what ways do they differ from the healthy state?
There is also an emphasis on structural proteomics (see gure
1.24). Knowing that a protein exists is different from knowing
how it operates. Knowing how some operate and knowing about
their structures may enable testable predictions about the role of
other proteins on the bases of their structures.
O FACT
Glycerol has
the formula C
3
H
5
(OH)
3
.
Figure 1.24 Knowledge of
three-dimensional structures of
well-known proteins may give
insights into their function.
This three-dimensional atomic
model image is of tubulin, one
of the molecules identied in
the tissue in gure 1.1
(page 2).
Lipids
Lipid is the general term for fats, oils and waxes. They have little afnity for
water. Fats and waxes are generally solid at room temperature and oils are liquid.
Although lipids are composed of carbon (C), hydrogen (H) and oxygen (O), they
contain relatively little water. The lack of water in the molecule means they carry
much more energy per molecule than any other kind of compound found in either
plants or animals.
Fats
A fat molecule is made of two kinds of molecules, fatty acids and glycerol.
Triglycerides are a common form of fats. These fats have a single glycerol
molecule to which three fatty acid molecules are attached. The fatty acid
molecules may be the same or different and lack afnity for water. Hence, fats
also have little or no attraction for water and are insoluble in it. Fats and other
compounds insoluble in water are called hydrophobic.
Allproteinscontainnitrogen,carbon,hydrogenandoxygen.Somealso
contain sulfur and phosphorus.
Proteinsareverylargemoleculesandcanbeclassifedonthebasisof
the way in which their chains of amino acids, joined by peptide bonds,
are folded into different shapes.
Proteinscanalsobeclassifedonthebasisoftheirdifferentfunctions.
Theproteomeofanorganismisthecompletearrayofproteins
produced by that organism.
KEY IDEAs
7 What is the basic formula for an amino acid molecule?
8 How is a peptide bond formed?
9 List the four basic structures of protein molecules and draw an
exampleofeach.
10 Giveanexampleof(a)astructuralprotein,(b)acontractileprotein
and (c) a conjugated protein.
11 Why is proteomics considered important?
QUICK-CHECK
H
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
C=O
O
HC
H
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
C=O
O
CH
HCH
O
O-F O
R
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
HC
FhosphoIIpId
moIecuIe
H
2
O
Head
VarIabIe group
22 Nature of biology book 2
Figure 1.26 The phosphate head of a phospholipid
molecule is attracted to water (hydrophilic). The fatty acid
tails extend away from water (hydrophobic). Because of
these properties, the molecules align so that they develop
double-layered sheets which are the cell membranes found
in every living cell.
Some typical formulae of fats are:
stearinC
57
H
110
O
6
palmitinC
51
H
98
O
6
oleinC
57
H
104
O
6
linoleinC
57
H
98
O
6
.
Figure 1.25 (a) A fat molecule
consists of three long chain fatty
acids attached to a glycerol molecule.
The glycerol part is the lower end
of the molecule. (b) Fats are stored
in adipose tissue. In this coloured
transmission electron micrograph
(TEM), lipid droplets are shown in
yellow within a developing fat cell
(adipocyte). The cells nucleus is
coloured purple.
H
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
C=O
O
HC
H
H
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
HCH
C=O
O
C
H
HC
HCH
HCH
HCH
HCH
HCH
HCH
HCH
C=O
O
CH
H
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C
H
H
C

Howaremargarinesthataresolidataverageroomtemperaturesmadefrom
oilsthatareliquidatroomtemperatures?Noteinfgure1.25athebenttailin
oneofthethreechainsoffattyacids.Inthepreparationofmargarine,thistailis
straightenedsothatthemoleculesarepackedtogethermorecloselythantheycan
bewhenbent.Hence,benttails=liquid;straighttails=solid.
Phospholipids
Phospholipids,anotherkindoffat,havetwofattyacidsattachedtoaglycerol.
Theyalsohaveaphosphategroupattachedto
theglycerolandothersmallgroupsattached
tothephosphatetomakedifferentkinds
of phospholipids. Phospholipids are
a major component of cell mem-
branes(seefgure1.26).
o fat
Steroids are
another group of lipids
that includes vertebrate sex
hormones and cholesterol, a
common component of animal
cell membranes (see the
Biochallenge, page 28).
(a)
(b)
On a weight basis, fat stores twice as much energy as the same weight of
polysaccharide so fats are important energy stores in cells, particularly animal
cells because animals carry their energy store around with them. Plants are able
to rely more heavily on polysaccharide energy storage.
Lipid is the general term for fats, oils and waxes that are all made of
carbon, hydrogen and oxygen.
Lipids carry more energy per molecule than either carbohydrates or
proteins.
Triglycerides, common fat molecules, are each made of a glycerol
molecule with three fatty acids attached.
Phospholipid molecules each have two fatty acids and a phosphate
group attached to a glycerol molecule.
KEY IDEAS
12 Why are fats so energy dense?
13 Explain the meaning of the statement: Fats are hydrophobic.
14 What is a signicant function of phospholipids?
15 Olive oil is liquid at room temperatures and yet margarine made from
olive oil is solid. How is this difference achieved?
QUICK-CHECK
(a)
Figure 1.27 In celebration of the 50-year anniversary of
the discovery of the structure of DNA (a) Australian stamps
depicting, from top to bottom, a chromosome, a DNA molecule
and the base sequence of a DNA molecule (b) An English two-
pound sterling coin showing the double helix structure of DNA
Nucleic acids
There are two kinds of nucleic acid:
deoxyribonucleic acid (DNA) that is located in chromosomes in the nucleus
of eukaryotic cells (see gure 1.27). It is the genetic material that contains
hereditary information and is transmitted from generation to generation.
ribonucleic acid (RNA) that is formed against DNA which acts as the
template.
DNA an inuential molecule
The year 2003 marked a signicant celebration. It was the 50-year anniversary
of the discovery of the structure of DNA by James Watson and Francis Crick.
The discovery was a giant step forward in the eld of science and opened the
way to extensive research that has given us the molecular biology knowledge,
understanding and applications that we have today. Many coun-
tries around the world celebrated the anniversary through the
issue of special stamps. Australia was one of those coun-
tries (see gure 1.27a). The country in which Watson
and Crick did their work, England, also issued a coin
(gure 1.27b).
(a)
(b)
P
S
T
A
T
S
P
S
P
S
G
P
S
P
C
(a) (b) (c)
Nucleotide
Monomer
Polymer
Nucleotides
join to
form chain
P
P
P
P
A
G
C
P
T
P
P
P
A T
G
C
5'
3'
3'
5'
Complementary
pairing of
nucleotide bases
of two chains to
form a DNA double
helix (DNA molecule)
2 nm
3.4 nm
0.34 nm
DNA
double
helix
Each DNA
molecule
combines with
protein to form
a chromosome
Chromosome
700 nm
Chromosomes
in cell nucleus
Each
chromosome
contains one
DNA molecule
The genetic material deoxyribonucleic acid is a polymer of nucleotides. Each
nucleotide unit, or monomer, has:
a sugar (deoxyribose) part
a phosphate part
an N-containing base.
The sugar and phosphate parts are the same in each nucleotide.
There are four different kinds of nucleotides because four different kinds of
N-containing bases are involved: adenine (A), thymine (T), cytosine (C) and
guanine (G). Examine gure 1.28. The nucleotide sub-units (a) are assembled
together to form a chain (b) in which the sugar of one nucleotide is bonded with
the phosphate of the next nucleotide in the chain. Each DNA molecule contains
two chains (c) that bond with each other because the bases in one chain pair with
the bases in another. The base pairs between the two strands, namely A with T,
and C with G, are said to be complementary pairs. The two chains form a double-
helical molecule of DNA (see gure 1.29).
Figure 1.28 Deoxyribonucleic acid
is made from nucleotide sub-units.
Each DNA molecule is made of two
complementary chains of nucleotides.
Figure 1.29 The double helix
structure and dimensions of DNA.
The two chains are held together
by hydrogen bonds between
complementary bases.
Figure 1.30 In eukaryotic cells, each DNA molecule combines with proteins
to form a chromosome.
How does DNA control all functions within cells? As we discussed in the
section on proteins, many different kinds of proteins are produced in cells (refer
back to table 1.2, page 17). All metabolic reactions in cells are controlled by
enzymes. Proteins are formed from polypeptide chains chains of amino acids.
Hence, the DNA of a cell controls what occurs in a cell through the polypeptide
chains that the DNA causes to be produced.
The DNA double helix combines with certain proteins to form a chromo-
some (see gure 1.30). Chromosomes reside in the nucleus of a cell and the
DNA they contain carries genetic instructions that control all functions of
the cell.
How does a DNA molecule directly inuence the production of a polypeptide
chain? The sequence of nitrogen bases along one of the chains of nucleotides in
a DNA molecule carries a set of information. This set of information controls
the production of all the polypeptide chains for which that molecule of DNA is
responsible, and can be thought of as a code.
How does the DNA code work? The total process is quite complex and
involves action both in the nucleus of a cell and in the cytosol. We will discuss
this in greater detail later in this book but the following are simplied examples,
leaving out many of the steps involved:
The DNA code comprises the four bases in the four nucleotides that make
up the DNA structure, represented by the letters A (adenine), T (thymine), C
(cytosine) and G (guanine).
The code operates with three letters at a time.
A particular set of three letters together in a molecule of DNA codes for a
particular amino acid. For example:
the sequence AAA in a molecule of DNA results in the amino acid
phenylalanine being added into the polypeptide chain for which the
particular DNA molecule is responsible
the sequence GTA results in histidine being added and the sequence GCA
results in arginine and so on.
There is a virtually endless number of variations within DNA. This makes
possible a great number of different proteins. Each protein has a particular struc-
ture that enables it to perform its particular function within a cell.
If a mutation occurs in a DNA molecule and leads to a change in the order of
bases, there is likely to be a change in the amino acids in the polypeptide chain.
For example, if there is a change in a sequence from AAA AGA, the amino
acid added is serine and not phenylalanine; if a change is GCA CCA, glycine
is added and not arginine.
A change in amino acid sequence in a polypeptide chain may result in a non-
functional protein, or a protein that may act in a way that causes harm to a cell. It
is generally suggested that many cancers arise as a result of changes in the genetic
material. Proteins also exist in uids that surround cells. Current research into
cancer includes a study of these extracellular proteins, as well as those within cells,
as it is thought that they may play some role in directing the action of the DNA
within cells. Extracellular proteins and the organisation of tissues themselves, as
well as changes in the DNA, may be involved in the development of cancers.
The Appendix contains a table
showing the complete DNA code.
Figure 1.31 A transmission
electron micrograph (TEM) of a DNA
molecule (pink) in the bacterium
E. coli, a prokaryotic organism that
has a simple cell structure with
no organelles and no nucleus. The
image shows some uncoiling of the
molecule which occurs to allow
replication of the DNA and therefore
replication of the cell.
Ribonucleic acid
Ribonucleic acid (RNA) is also a polymer of nucleotides (see gure 1.32). It
differs from DNA in that it is an unpaired chain of nucleotide bases and exists
in three different forms. RNA is constructed from four different bases, three of
which adenine, guanine and cytosine are identical to those in DNA. The
fourth nucleotide is uracil that is
capable of pairing with A .
The three different forms
of RNA are all produced in
the nucleus against DNA as a
template:
messenger RNA (mRNA), that
carries the genetic message
to the ribosomes where the
message is translated into a
particular protein (see gure
1.33)
ribosomal RNA (rRNA)
which, together with particular
proteins, makes the ribosomes
found in cytosol
transfer RNA (tRNA),
molecules that carry amino
acids to ribosomes where they
are used to construct proteins.
The strand of nucleotides in
each of the RNAs is folded in a
different way.
There are two kinds of nucleic acid: DNA and RNA. Both are built from
nucleotide sub-units.
In DNA, each nucleotide consists of a deoxyribose sugar part, a
phosphate part and an N-containing base.
Each DNA molecule consists of two chains of nucleotides that are
complementary to each other and held together by hydrogen bonds.
In RNA, each nucleotide consists of a ribose sugar part, a phosphate
part and an N-containing base.
Each RNA molecule consists of a single strand of nucleotides.
KEY IDEAS
16 An acronym is a word formed from the initials or other parts of several
words, for example WHO from the initial letters of World Health
Organisation. What do the acronyms DNA and RNA stand for?
17 What are the four kinds of nucleotides (a) in DNA, and (b) in RNA?
18 Where in a cell would you nd DNA and what is its function?
19 There are three different kinds of RNA molecules. What are they and
where is each found in the cell?
20 In what ways do the kinds of RNA differ from each other?
QUICK-CHECK
Figure 1.32
The four nucleotide
sub-units, uracil,
adenine, guanine and
cytosine, from which
the three RNAs are
constructed
Figure 1.33 A transmission
electron micrograph (TEM) of a
fragment of an mRNA translation
unit from the salivary gland cell of a
midge (Chironomus sp.). Ribosomes
(blue) attach to the mRNA strand
(pink) and read its code. A tRNA
molecule carrying a corresponding
amino acid binds to the ribosome. As
the ribosome moves onto the next
bases along the mRNA, a protein
(green) grows from the ribosome.
A
U
S
P
S
P
S
G
P
S
P
C
I am a 3-D animator based at the Walter and Eliza
Hall Institute of Medical Research in Melbourne. The
goal of my animation is to visually explain scientic
dis coveries to the public on national news, science and
current affairs programs. I also create animations for
documentaries, museum exhibits and art gallery instal-
lations. A recent project involved creating visualisations
of the nasty bugs smallpox, ebola and anthrax for a
National Geographic documentary on bioterrorism.
I love what I do, yet when I nished school I intended
to follow a very different career path. I wanted to be
a marine biologist and study sharks. I was inspired
by the documentaries by Jacques Cousteau and David
Attenborough, and loved the lms by Australian couple
Ron and Valerie Taylor. The most memorable for me
was seeing Valerie Taylor put on a chain-mail diving
suit and shove her arm into the gaping mouth of a
hungry shark that looked like fun!
At the University of Melbourne, I studied all the
subjects for marine science. One subject was Cell
Biology, a topic that didnt interest me. However, the pro-
fessor who taught cell biology, Jeremy Pickett-Heaps,
gave the most amazing and entertaining lectures. His
specialty was filming living cells using time-lapse tech-
niques and his passion for cell biology and extra ordinary
footage hooked everyone in his classes. I decided to do a
BSc Honours year in Jeremys lab and went on to begin
a PhD on filming cells and conducting research into how
cells create their shapes (morphogenesis).
A couple of years into my PhD, I realised that I loved
science and found it fascinating but didnt want a career
doing experiments at a lab bench. I wrote up my thesis
and submitted it as a Masters degree instead. At the
same time, an opportunity came up to work in an adver-
tising company writing copy (text)
for magazine ads. I wasnt very
good at it and the company moved
me onto Photoshop work. This was
a time of high-pressure, relentless
work but I was also gaining many
new skills in design and visual
communication.
I joined the Walter and Eliza
Hall Institute as their Photoshop
guy, preparing scientic images
for publication. Because of my
skills from advertising, I was fast and efcient with
Photoshop and usually nished my work by morning
tea. I began playing around with 3-D software and
started to create animations for education videos.
Around that time, major discoveries were made at the
Institute about malaria and I created some animations
that explained how the parasite infects red blood cells
and causes disease. The malaria animation proved
pivotal in my career as it has been popular with many
TV programs and museum exhibitions. On the basis of
its success, I was able to transform my job into working
full time creating scientic animations.
For me it is the perfect job. I read journals and other
scientic literature, discuss ideas with scientists and
think about the concepts and discoveries at the cutting
edge of science. Once I have a clear understanding and
mental picture of the science, I access the raw data
wherever possible and import it into my animation
system. The next phase involves an enormous amount
of problem solving, creative design and visual story-
telling, which offers unlimited scope for exploring new
ideas and techniques.
The animation software, Maya, is the same type used
for blockbuster feature lms. The fact that it allows a
special-effects artist to create the amazing creatures in
Lord of the Rings and a scientist to build realistic and
accurate visualisations with the same set of tools is a
credit to the exibility and power of Maya.
Creating 3-D animation is not for everyone. You must
be condent with computers, able to troubleshoot the
frequent technical problems and have the patience and
perseverance to work through the design challenges.
If it does appeal to you, there is an endless amount of
science waiting to be explained to the public!
Drew Berry animator specialising in biomedical science
BIOLOGY IN THE WORKPLACE
Figure 1.34 Drew Berry at work on
some new animations
BIOCHALLENGE
1
Many spiders spin webs of silk to catch their
prey. Others, such as Calaenia excavata, the
bird-dropping spider (or bird-dung spider),
use silk as a support for the egg cases
they produce. They also wrap their prey in
silk. Spider silk is organised into a beta-folded
sheet. The photograph shows C. excavata with
two egg cases and two wrapped prey.
a What monomers combine to make spider
silk?
b What level of molecular organisation is a
beta-folded sheet?
c Of what importance is it for spiders to have
their silk molecules packed in a beta-folded
sheet?
2
a Note the structures of the three steroid lipid molecules. Compare their structure with the
general structures of fat and phospholipid molecules.
b What are two differences between the general structures of fat and phospholipid molecules and
the steroid molecules shown here?
3
Examine each of the molecules in the
diagram. For each one, answer the following.
a Decide whether it is a monomer or a polymer
and, if a polymer, name the monomers of
which it is made.
b Classify the molecule as comprehensively as
possible with regard to its organic molecule
category.
c Name where, in either a plant or an animal
cell, you could expect to nd such a
molecule.
HO HO
OH
OH
CH
3
Cholesterol
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
CH
3
O
(a) (b) (c)
Testosterone
male sex hormone
Oestrogen
female sex hormone
A
U
S
P
S
P
S
G
P
S
P
C
H N N C C C C OH
O
CH
3
O H
H H H H
A
C D
E
F
B
CHAPTER REVIEW
1 Making connections The key words listed above can be called concepts.
Concepts can be related to each other by the use of linking words or phrases
to form propositions (see the example at left). An arrow shows the sense of
the relationship.
When several concepts are related in a meaningful way, a concept map is
formed. Because concepts can be related in many ways, there is no single
correct concept map. Figure 1.35 shows one concept map containing some
of the key words from this chapter. Add to this map or prepare another by
using key words from the list above and other words of your choice.
Key words
Questions
acidic
alkaline
basic
bonds
carbohydrates
cellulose
chitin
cohesive
complex carbohydrates
conjugate
covalent bond
deoxyribonucleic acid
(DNA)
disaccharide
fatty acids
glucose
glycerol
glycogen
hydrogen bonds
hydrophilic
hydrophobic
inulin
lipids
metabolism
molecules
monomers
monosaccharide
neutral solution
non-polar
nucleic acids
nucleoproteins
nucleotides
pectin
pH
phospholipids
photosynthesis
polar
polymers
polypeptide
polysaccharides
primer
proteins
proteome
proteomics
ribonucleic acid
(RNA)
simple carbohydrates
starch
steam
steroids
sucrose
sugars
synchrotron
triglycerides
water
CROSSWORD
Figure 1.35 An example of a
concept map
Proteins
Polymers
Carbon
Amino
acids
Nitrogen
Lipids
Carbohydrates
Monosaccharides
contain
contain
contain
Oxygen
Glucose
Hydrogen
are monomers of
may be
are
may be
may be
contain
contain
is an example of
2 Applying your understanding You wish to carry out some research
on molecular structure. What advantage might it be to use a synchrotron
(see page 3), compared with the light and electron microscopes currently
in use?
3 Communicating your understanding Answer the following questions.
a Explain why water is solid by the time it reaches 0C.
b What is the chemical formula of glucose?
c What is the basic difference between a monosaccharide molecule and a
dis ac charide molecule?
d How many glycerols are there in a triglyceride fat molecule?
e Amino acids have the same basic structure and yet they are all different.
Explain which part of their structure confers this difference.
f If an amino acid is involved in the formation of a sulfur bond, what can
you conclude about the molecular formula of that amino acid?
g Explain what is meant by the tertiary structure of a protein.
h How many different nitrogenous bases are in DNA?
i How many chains of nucleotides are in a DNA molecule?
j How many chains of nucleotides are in a molecule of messenger RNA?
k In what form is glucose stored in the human body?
4 Applying your understanding What is a characteristic of fats that makes
them energy dense?
5 Applying understanding and drawing conclusions During an experi-
ment, you analyse a compound that has a chemical composition of carbon,
hydrogen and oxygen in the ratio of 1:2:1 and a six-sided molecular shape.
What predictions would you make with regard to classification of the
compound?
6 Applying your knowledge and understanding
a When two monomers such as amino acids join together, a molecule of
water is produced. Use two amino acid molecules to explain where this
water comes from.
b How many water molecules would be required to completely hydrolyse a
carbohydrate polymer that contained 100 monomers?
7 Applying understanding and drawing conclusions Before the introduction
of genetically engineered insulin for use by people with diabetes, the protein
hormone was extracted from beef or pig pancreas. Explain how you would
expect the sequence of amino acids in the beef and pig insulin to compare
with that of humans.
8 Analysing data and drawing conclusions A particular small poly peptide
contains nine amino acids. The polypeptide has been fragmented in various
experiments by breaking particular peptide bonds. The fragments obtained
were:
ser cys his pro arg cys
pro arg cys
X gly met cys
his pro arg cys
X gly met cys ser cys
X is known to be the first amino acid in the polypeptide. What is the primary
structure of the polypeptide?
9 Analysing data and drawing conclusions Assume that the nitrogen base
sequence in one of the strands in a DNA molecule is:
A-T-C-G-A-C-A-T-G-G-A-A-T-A-C-C-T-C.
a What is the base sequence in the complementary strand?
b How many amino acids does this piece of DNA code for?
10 Analysing data and drawing conclusions A piece of RNA has the base
sequence:
U-A-C-G-A-U-U-C-G-A-A-C-A-U-G
a Are you able to determine the kind of RNA this molecule is without any
further information?
b If you were told this piece of RNA carries the code for five amino acids,
would you change your answer to part a? If so, what would your expla-
nation be for change?
11 Applying your knowledge Match each statement on the left with the most
appropriate term on the right.
Statements Terms
1 Some organic molecules store and process
information at the molecular level.
hydrophilic
2 Some substances can dissolve other substances. proteins
3 Some molecules dissolve readily in water. nucleic acids
4 Our ngernails and hair are made of a particular
kind of molecule.
carbohydrates
5 One group of organic molecules contains
polysaccharides.
solvent
12 Using the web Go to www.jaconline.com.au/natureofbiology/natbiol2-3e
and click on the Protein weblink for this chapter.
a Click on Download to obtain a pdf file of the protein illustrations and
print a copy.
b Draw two columns, one at each side of the illustrations. Give one column
the heading Example and the other Function.
c Carry out web research or use the textbook to enter relevant information
in the columns for each protein structure.

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