Download Week 2 - Chemical Nature of Cells

2.1
Week 2
Chemical Nature of Cells
Area of Study 1
Molecules of Life
This week you will study some of the biologically important organic
molecules.
Key knowledge
 Properties of biologically important organic molecules
 Synthesis of biomacromolecules
Key skills
 Investigate and inquire scientifically
 Apply biological understandings
 Communicate biological information and understanding
Tasks this week relate to outcome 1
 Analyse and evaluate evidence from practical investigation related to
biochemical processes.
Relevant websites – see online biology course environment. Go to the
Links section.
Glossary terms for Week 2 can be found here:
http://quizlet.com/_c46j
2.2
Chemical Nature of Cells
Introduction
Read carefully through this week’s work before completing the tasks. Check
for any practical exercises that may require you to obtain materials and
equipment.
This is Week 2 – your second week of work. You do not need a text book
to complete it. Make sure that you have ordered the required text book for
future weeks of work.
The Objectives
By the end of this week you should be able to:


Describe the basic structures of carbohydrates, proteins, nucleic acids
and lipids
Make a model of a protein
Read through the following text and complete the tasks or questions that
follow. Use your own A4 paper or send work as MSWord documents
attached to an email.
The following text is courtesy of Nelson Biology VCE Units 3 and 4, second edition.
Synthesis of Biomacromolecules
Autotroph
An organism that makes its
own food from light energy
or chemical energy without
eating; most green plants,
many protists (one-celled
organisms such as slime
moulds) and most bacteria
are autotrophs.
Chemotroph
An organism that obtains
its energy from the oxidation
of chemical compounds.
Heterotrophs
Organisms that consume
other organisms as food;
organisms that are not able to
make organic molecules from
simple inorganic compounds.
Some organisms are able to synthesise their own biological
macromolecules, whereas others synthesise them from organic
compounds that they have ingested. Organisms that can synthesise their
own organic compounds from the inorganic materials that they take in
from their surroundings are called autotrophs (self-feeders). For example,
seaweeds, eucalypts, grass and microscopic algae all produce the basic
building unit – simple sugars – through the process of photosynthesis.
From the products, autotrophs then synthesise the other kinds of organic
compounds that they need.
Some autotrophic organisms, such as certain kinds of bacteria, are able to
synthesise their organic requirements through chemical processes other
than photosynthesis. These organisms are described as chemosynthetic
autotrophs or chemotrophs, and are typically found in extreme
conditions, such as in the depths of the ocean near hydrothermal vents, in
thermal springs or in places deprived of oxygen or light.
Heterotrophs, such as humans, have to synthesise their own
biomacromolecules from existing organic compounds. Heterotrophs have
to take in a range of organic compounds in their food, which they then
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breakdown into simpler substances. These are then synthesised, or built
up, into the kinds or organic compounds that are required by the
organism.
Making a Polymer
Large biomacromolecules are synthesised on site inside the cell. Proteins
nucleic acids and complex carbohydrates are built up by linking smaller
repeating molecules, each called a monomer (mono – one, mer – unit), to
form long chains called polymers (poly – many). This process is known as
polymerisation. Even though lipids are large biomolecules, they are not
polymers; they are composed of distinct chemical groups of atoms.
Monomers link together when the hydroxyl (-OH) group of one monomer
reacts with a hydrogen atom of another monomer, forming a water
molecule. Thus, the reaction is called condensation polymerisation.
Polymerisation
Single units (monomers) → many linked units (polymer)
(small units)
(macromolecules)
Successive monomers are added in the same way to produce a long
polymer chain (see Figure 2.1 above).
SEND…
Question 1
Which macromolecules are polymers?
Question 2
Distinguish between autotrophs and heterotrophs in sourcing nutrients to
build their macromolecules.
Read through the following text and complete the tasks or questions that
follow. Use your own A4 paper or send work as MSWord documents
attached to an email.
The following text is courtesy of Heinemann Biology Two 4 th Edition.
2.4
Carbohydrates
Carbohydrates are the most abundant organic compounds in nature. They
 Are an important source of chemical energy for living organisms;
 Are used as energy reserves in plants and animals;
 Form structural components such as cell walls;
 Form part of both DNA and RNA;
 Combine with proteins and lipids to form glycoproteins and
glycolipids as in cell membranes.
Carbohydrates are found on the surface of every cell in our bodies and are
involved in a wide variety of interactions. Cell surface glycoproteins
identify a cell as being of a particular type and are important in cell-cell
communication and adherence.
Carbohydrates are compounds made of carbon, hydrogen and oxygen. In
simple carbohydrates (such as glucose) the hydrogen and oxygen are
present in the same proportions as in water: there are two hydrogens for
each oxygen atom. The general formula is Cn(H2O)n (for example,
glucose is C6H12O6).
There are three main groups of carbohydrates – monosaccharides,
disaccharides and polysaccharides (Figure 2.1). The basic subunits of
carbohydrates are the simple sugars, called monosaccharides, meaning
‘single sugars’. For example, glucose is a simple sugar that is formed
during photosynthesis. Common 6-carbon sugars include glucose,
galactose and fructose. When two sugars are joined together they form a
disaccharide (meaning ‘two sugars’) and a molecule of water is removed.
Milk sugar (lactose) is made from glucose and galactose whereas can
sugar (sucrose) is made from glucose and fructose.
When many sugars are joined together they form long chains or polymers
called polysaccharides (‘many sugars’). Cellulose, the major component
of plant cell walls, is the most abundant organic molecule on Earth. Starch
is the polysaccharide used for energy storage in plants. In animals, the
polysaccharide glycogen is used or energy storage. These three
polysaccharides are each composed of glucose subunits, but they differ in
a number of ways (Figure 2.1). Starch is a long chain molecule, glycogen
has a branching structure and cellulose has additional bonds cross-linking
between the subunits of the chain.
2.5
Table 2.1 Classes of Carbohydrates
Carbohydrate
Example
Monosaccharides Triose
(mono=one,
saccharide=sugar)
Pentose
eg. Ribose
Hexose
eg.
Glucose
Disaccharides
Maltose
(di=two)
Sucrose
Lactose
Polysaccharides
Cellulose
Starch
Glycogen
Chitin
Description
Location and function
Single chain of carbon atoms to Glyceraldehyde
which hydroxyl groups are
attached. Soluble in water.
Five carbon atoms in backbone Found in RNA molecules
Six carbon atoms in backbone
Makes jelly beans sweet; It
is an ideal quick energy fix.
Two glucose molecules bonded Found in high
concentrations in some
grains
Glucose and fructose bonded
Table sugar, sugar cane,
sugar beet
Glucose and galactose bond
In milk
together
Complex carbohydrates
Energy storage and
composed of several hundred
structural support
to several thousand monomers
in chains
Straight chains that lie next to
Form tough, insoluble fibres
each other, promoting
giving structural support to
hydrogen bonding between
plant cells
them and producing tight
bundles called microfibrils.
Mixture of two different
Energy storage in plants
polysaccharides linked in
(e.g. starch grains in seeds
branched and sometimes
eg of wheat, corn)
twisted chains
Storage compounds in animals Energy storage in muscles
and liver of animals
Cellulose-like polymer; each
Present in the hard
monomer glucose molecule has exoskeleton of insects and of
an N-containing group
crustaceans, such as crabs;
attached.
cell walls of fungi, such as
mushrooms.
The above table is courtesy of Nelson Biology VCE, Units 3 and 4, second edition.
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Question 4
Describe the chemical composition of a carbohydrate.
Question 5
What distinguishes the three classes of carbohydrates from each other?
2.6
Question 6
Glycogen and starch are called storage polysaccharides. In what
organisms would you find?
a) glycogen
b) starch
Read through the following text and complete the tasks or questions that
follow. Use your own A4 paper or send work as MSWord documents
attached to an email.
The following text is courtesy of Heinemann Biology Two, 4 th Edition and Nelson
Biology VCE Units 3 and 4, 2nd Edition.
Proteins – The Work Horses of the Cell
Virtually everything a cell is or does depends on the proteins it contains.
What does your hair have in common with the feathers of birds, the rattle
of a rattlesnake and the spines of an echidna? They are all composed of a
strong fibrous protein known as keratin. Keratin is just one of an amazing
variety of proteins produced by the activities of cells.
The whole set of proteins produced by a cell is called its proteome and
the study of proteomes is proteomics – a term first used in 1994 by Marc
Wilkins of Macquarie University, Sydney. Functional proteomics refers
particularly to what proteins do in different cells and tissues.
Proteins are more complex molecules than carbohydrates and make up
more than 50% of the dry weight of cells. All proteins contain carbon,
hydrogen, oxygen and nitrogen. Many also contain sulphur, and often
phosphorus and other elements. There are thousands of different kinds of
proteins and their functions vary widely (see Table 2.3). Enzymes
catalyse cellular reactions, hormones communicate information
throughout the body of an organism, while other proteins form structural
components of cells. Some proteins act as carrier molecules, such as
haemoglobin which transports oxygen. Proteins may also form channels
in membranes, which is important for the transport of certain molecules
across membranes.
Proteins are composed of chains of smaller subunits called amino acids.
Because amino acids in proteins are linked by a certain kind of bond
called a peptide bond, proteins are called polypeptides (polypeptide
meaning ‘many peptide bonds’). There are 20 different amino acids
commonly found in proteins. While carbohydrates and lipids are similar
in most plants and animals, each kind of organism has its own unique
proteins.
Amino acids are small molecules that have the same basic structure – a
central carbon atom to which are attached a hydrogen atom, a carboxyl
acid group (COOH), an amino group (NH2) and what is called an R
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group. It is the difference in the R group that distinguishes one amino acid
from another and gives each amino acid its particular chemical properties.
The 20 different R groups mean that there are 20 different amino acids.
Some R groups make the protein molecule polar and other kinds of R
groups make regions of the protein molecule non-polar. These
hydrophobic regions are generally tucked away within the protein
molecule, away from the water molecules in the aqueous environment.
Eleven amino acids are hydrophilic. They tend to be on the surface of
protein molecules because of their affinity (attraction) for the polar water
molecules in their environment.
Table 2.3 The functional diversity of proteins. (Try to remember the ones in bold).
Protein type
Motility
Structural
Enzymes
Transport
Hormones
Cell-surface
receptors
Neurotransmitters
Immunoglobulins
Poisons or toxins
Function (job)
Examples
Allow movement of
cells and their
organelles.
Provides support,
strength and
protection
Catalyse biochemical
reactions
Tubulin forms microtubules to move flagella, cilia,
chromosomes and organelles. Actin and myosin work
together to move muscles.
Collagen (a fibrous protein) supports body tissues.
Fibroin makes a spider web stronger, weight for weight,
than steel. Keratin forms nails and hair.
Catalase removes toxic hydrogen peroxide from cells by
breaking it down into water and oxygen. All organisms
have DNA polymerase, an enzyme that duplicates genetic
information (DNA).
Lysozyme is an enzyme found in egg white, tears, and
other secretions. It is responsible for breaking down the
polysaccharide walls of many kinds of bacteria and thus it
provides some protection against infection.
Haemoglobin carries oxygen to body cells.
Porin forms a hydrophilic pore in the outer membrane of
mitochondria for the passage of molecules.
Carry molecules from
one location to
another or across cell
membranes
Signalling between
different cell types;
stimulation or
inhibition
Label cells as targets
for hormones, viruses,
growth factors,
recognition of ‘self’,
transmission of nerve
impulse
Signalling between
neurons
Insulin travels in the blood and binds to cell receptors to
trigger the uptake of glucose. Follicle-stimulating hormone
(FSH) stimulates the maturation and release of ova (female
gametes).
Insulin receptors blind insulin to trigger the uptake of
glucose by the cell. Rhodopsin in the retina membrane
allows us to see dim light. Major histocompatibility
complex (MHC) markers allow the immune system to
recognise ‘self’ so the body does not destroy its own cells.
Endorphins activate nerve receptors to alleviate pain or
stress.
Enkephalins act as analgesics (pain relievers) and sedatives
affecting mood and motivation.
Recognition of foreign Antibodies cause foreign material to clump so it can be
substances (antigens)
ingested by large white cells (macrophages).
Chemicals for defence Red means danger. The castor oil plant produces the
and to aid in the
deadly toxin, ricin. Snake venom contains many proteins
capture of food
that can paralyse and digest prey.
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The properties of many proteins are determined by their shape, which is
determined by their amino acid sequence. There are four levels of proteinstructure – primary, secondary, tertiary and quaternary. Primary structure
is the actual sequence of amino acids in a polypeptide. The particular
sequence causes arrangements of the polypeptide into secondary
structures, such as pleating or coiling, held by hydrogen bonds between
the amino acids. The protein then folds into its distinctive threedimensional shape, which is its tertiary structure, usually fibrous or
globular. When two or more polypeptides are joined together, such as in
the haemoglobin molecule it is called a Quaternary structure.
Primary structure
DNA determines the sequence of amino acids in the polypeptide. Amino
acids bond together in the process of condensation polymerisation and
each bond between two adjacent amino acids is called a peptide bond.
Secondary structure
Once the polypeptide chain is formed, various parts undergo coiling and
folding due to hydrogen bonding between the various amino acids that are
present. Tight coils are known as ά-helices and the folding forms are
known as β-sheets. Other parts of the polypeptide chain remain
unchanged and are called random loops. β-sheets and random loops form
the basis of the active site in enzymes, being less rigid than ά-helices.
Figure 2.2
(a) The order of amino
acids in the polypeptide
is called the primary
structure.
(b) Coiling (ά-helices)
and folding (β-sheets)
Results in the secondary
structure of a protein.
Coils and sheets are
connected by random
loops.
Tertiary structure
Hydrophilic R groups attract other hydrophilic R groups and
hydrophobic R groups attract other hydrophobic R groups according to
the ‘like attracts like’ rule. These interactions between the R groups of the
amino acids cause the polypeptide chains to become folded, coiled or
twisted into the protein’s functional shape or conformation. The
interactions between the R groups of amino acids result in hydrogen
bonds, ionic bonds or disulfide bridges between adjacent cysteine amino
acids. Protein molecules with the same sequence of amino acids will fold
into the same shape. A change to just one amino acid will alter the shape
of the protein molecule and it may not function properly.
2.9
Figure 2.3
The secondary structure shown above, changes shape according to the interactions between the R groups. The
specific function of a protein is determined by its tertiary structure. The tertiary structure arises from interactions
between R groups of amino acids in the polypeptide chain. The interactions between the R groups will pull the
protein chain into a ‘ball’ shape which is the tertiary structure. See Figure 2.4 below.
Figure 2.4 A protein in its tertiary structure as a spherical globular shaped molecule.
It is the tertiary structure that usually determines the function of the
protein – its biological functionality, however the secondary structure
may also determine function (see the past exam question at the end of this
Week’s work). Some proteins form long, closely packed fibres that are
structural components of cells as in silk. Most proteins form spherical or
globular-shaped molecules that are soluble in water and perform a
variety of functional tasks.
Quaternary structure
Many large, complex protein molecules consist of two or more
polypeptide chains. Haemoglobin, for example, which carries oxygen in
the blood, consists of four polypeptide chains (also referred to as amino
acid chains). A variety of hydrogen bonds, ionic bond and covalent bonds
hold the polypeptide chains together and gives the overall shape to the
molecule.
Changing the nature of proteins
The function of protein molecules may change as a result of a number of
factors, apart from misreading the DNA code for proteins. Proteins may
lose their functional shape if they are exposed to high temperatures,
strong salty solutions or very acidic or alkaline conditions. These
2.10
conditions can denature or change the shape of the protein molecules. If
the change is minor, the protein molecule can return to its original shape,
but if it is major, then it cannot.
Summarising Protein Structure
2.11
How Do Balls of Protein Form Structures?
Read through the following text and complete the tasks or questions that
follow. Use your own A4 paper or send work as MSWord documents
attached to an email.
The following text is courtesy of Times Mirror, Mosby college
Publishing, Biology 2nd Edition.
The Cytoskeleton Proteins
Figure 2.5
In this diagrammatic cross section of a cukaryotic cell, the mitochondria, ribosomes, and
endoplasmic reticulum are all supported by a fine network of filaments, through which
pass microtubules linking various portions of the cell.
The cytoplasm of all eukaryotic cells is crisscrossed by a network of
protein fibres, which support the shape of the cell and anchor organelles
such as the nucleus to fixed locations (Figure 2.5). This network, called
the cytoskeleton, cannot be seen with an ordinary microscope because the
fibres are single chains of protein, much too fine for microscopes to
resolve. The fibres of the cytoskeleton are a dynamic system, constantly
being formed and disassembled. Individual fibres form by polymerization,
a process in which identical proteins are attracted to one another
chemically and spontaneously assemble into long chains. Fibres are
disassembled in the same way, but the removal of first one subunit, then
another from one end of the chain.
Cells from plants and animals contain the following three different types
of cytoskeleton fibres, each formed from a different kind of subunit
(see Figure 2.6):
1. Actin filaments. Actin filaments (also called microfilaments) are long
protein fibres about 7 nanometers in diameter, each fibre composed of
two chains of protein loosely twined around one another like two
strands of pearls (Figure 2.6, A). Each “pearl” of a filament is a ball-
2.12
shaped molecule of a protein called actin, the size of a small enzyme.
Actin molecules left alone will spontaneously form these filaments,
even in a test tube; a cell regulates the rate of their formation by
means of other proteins that act as switches, turning on polymerization
only when appropriate.
Tubulin is an
example of a
fibrous protein.
2. Microtubules. Microtubules are hollow tubes about 25 nanometers in
diameter, each a chain of proteins wrapped round and round in a tight
spiral (Figure 2.6, B). The basic protein subunit of a microtubule is a
molecule a little larger than actin, called tubulin. Like actin filaments,
microtubules form spontaneously, but in a cell microtubules form only
around specialized structures called organizing centers, which
provide a base from which they can grow.
3. Intermediate filaments. The most durable element of the
cytoskeleton is a system of tough protein fibres, each a rope of
threadlike protein molecules wrapped around one another like the
strands of a cable (Figure 2.6, C). These fibres are characteristically 8
to 10 nanometers in diameter, intermediate in size between actin
filaments and microtubules; this is why they are called intermediate
filaments. Once formed, intermediate filaments are very stable and do
not usually break down. The most common basic protein subunit of an
intermediate filament is called vimentin, although some cells employ
other fibrous proteins instead. Skin cells, for example, form
intermediate filaments from a protein called keratin. When skin cells
die, the intermediate filaments of their cytoskeleton persist – hair and
nails are formed in this way.
Figure 2.6
A comparison of the molecules that make up
the cytoskeleton.
Actin filaments: In the micrograph, actin
filaments parallel the cell-surface membrane
in bundles known as stress fibres, which may
have a contractile function.
Microtubules: Each microtubule is
composed of a spiral array of tubulin
subunits. The microtubules visible in this
micrograph radiate from an area near the
nucleus (most heavily stained region).
Microtubules act to organize metabolism and
intracellular transport in the nondividing
cell.
Intermediate filaments: It is not known how the individual subunits are arranged in an
intermediate filament, but the best evidence suggests that three subunits are wound
together in a coil, interrupted by uncoiled regions. Intermediate filaments, like
microtubules, extend throughout the cytoplasm. In a skin cell, such as the one shown,
intermediate filaments form thick, wavy bundles that probably provide structural
reinforcement.
2.13
SEND…
Question 7
Explain why there are so many different kinds of protein.
Question 8
Where in a protein molecule would you find a hydrophilic amino acid?
Explain why some amino acids are hydrophilic.
Helicase is the name of the protein that unzips DNA so the coded
information on it may be read. A zipper is a good model of this. The
zipper runner represents helicase. Notice that it has a very specific shape
(structure) that makes it work (function) as a zipper runner.
Question 9
What level of protein structure determines its function?
Below is a collection of some proteins (plant and human) that have been identified and
named. Courtesy of PDB Protein Data Bank www.pdb.org
The cholesterol and phospholipid molecules have been included to show the
phospholipid bilayer which some proteins are embedded in or attached to.
2.14
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Practical Activity 2A – Making A Model of A Protein
Now you will do a short practical exercise. You don’t have to present it as
a standard prac report – simply complete the tasks.
Equipment
You will need at least fifteen pipe cleaners, each 30 cm long, available
from craft shops and some newsagents.
Procedure
Interesting fact
Spider silks are proteins and are
the strongest natural fibre known.
The golden orb weaver spider
uses a silk ‘dragline’ to escape its
web in case of danger. The
dragline is a mixture of two types
of proteins that are dry and
essentially indestructible. They
are also elastic and exceptionally
strong, features that are directly
attributable to the protein
structure.
Hint: to make the coils
you could wind the pipe
cleaner around a pencil as
shown below.
1. Connect the three pipe cleaners as shown at left, so that you
have a long pipe cleaner. This represents the primary structure
of your protein (polypeptide). You may like to put texta
markings along the pipe cleaners to represent the amino acids
that make up the polypeptide. About every 2 cm.
2. Use the diagrams in Figures 2.2, 2.3 and 2.4 and the information
given earlier to construct four different models. Each model
will show one of the four levels of structure (primary,
secondary, tertiary and quaternary) of a protein.
3. Squeeze the tertiary structured (ball) protein in your hand. Can
you feel the prickly ends of the wire? Yes! These represent the
“sticky” reactive hydrophilic parts of the protein. The
hydrophobic (scared of water) parts are “hiding” on the inside
of the protein.
4. Send your four models naming the structure they represent, to
me. Or send in photos of your made models (including their
name).
Secondary structure
Question 10
What have you learnt from doing this activity?
2.15
Question 11
Explain how your model of a protein is different from the real thing.
Question 12
How could you improve your models?
Read through the following text and complete the tasks or questions that
follow. Use your own A4 paper or send work as MSWord documents
attached to an email.
Nucleic Acids – Information Molecules
Nucleic acids store information in a chemical code that directs the
machinery of the cell to produce proteins. Nucleic acids are every
organism’s genetic material; they are the means by which the story of life
extends through time and across all life forms.
Commonly recognised by the letters DNA (deoxyribonucleic acid) and
RNA (ribonucleic acid), nucleic acids are large, linear polymers that form
when monomers bond together. A molecule of DNA is composed of two
long strands of subunits called nucleotides, wound around each other to
form the familiar double helix. RNA is usually composed of a single
chain of nucleotides and forms a single strand.
Analysing DNA: the stuff genes are made of
Genes are made up of a chemical called DNA (deoxyribonucleic acid).
The DNA of our genes contains all the instructions which control our
inherited characteristics.
Nucleotides
Nucleotides are the monomers that make up these amazing nucleic acid
molecules. A nucleotide has three distinct chemical components:
1. a five carbon sugar (ribose in RNA and deoxyribose in DNA)
2. a negatively charged phosphate group
3. an organic nitrogen-containing compound called a base (Figure 2.7).
There are four kinds of nitrogenous (nitrogen-containing) bases in DNA:
 Adenine (A)
 Thymine (T)
 Guanine (G)
 Cytosine (C)
Figure 4.1 The four nucleotides found in DNA (with cytosine labelled fully)
2.16
In each nucleotide strand, the sugar molecule of one molecule binds to the
phosphate groups of the next nucleotide, leaving the nitrogenous base
sticking out from each sugar and opposite the nitrogenous base of the
second strand. Hydrogen bonds between the opposing pairs of
nitrogenous bases hold the double helix together, much like the rungs of a
twisted ladder or a spiral staircase. The bonding of the nitrogen bases does
not happen by chance: A bonds with T and C bonds with G, giving rise to
the base-pairing rule.
When nucleotides link to form a strand, a bond forms between the sugar
on one nucleotide with the phosphate group on the next nucleotide.
The phosphate end is called the head and is known as the 5/ end. The
sugar end is known as the tail and is the 3/ end (see cytosine labels above).
Experiments on the DNA of various organisms show that the amounts of
the nucleotide Adenine (A) equal those of Thymine (T).
The amount of Guanine (G) equals those of Cytosine (C).
The levels of A and T were different from those of G and C.
The difference between DNA and RNA
The difference between DNA and RNA is that DNA has deoxyribose
sugar and RNA has ribose sugar. The nitrogenous base thymine in DNA is
replaced by the base uracil (U) in RNA. RNA is usually single stranded
and DNA is usually a double stranded chain forming a double helix.
Nucleotides link together in what is called a 51 to 31 direction to form long
polymers. See Figure 2.7 & 2.8 (two different visual representations of DNA and
RNA). Translated this means that the phosphate group attached to the 51
carbon of one ribose monomer bonds to the hydroxyl group attached to
the 31 carbon of another ribose monomer, forming a particular bond called
a phosphodiester bond. In the process of polymerisation, the hydrogen
from the sugar and the hydroxyl from the phosphate ‘condense’ out as a
water molecule.
2.17
Figure 2.7 Above image courtesy of Nature of Biology Book 2 by Jacaranda
DNA consists of two complimentary polynucleotide strands held together
by hydrogen bonds. If we know the nucleotide sequence on one strand,
we also know the nucleotide sequence on the other strand because we
know which nucleotide bonds with which. One strand is a template
(strand) for the other strand called the complementary strand.
DNA is the master code that determines the very nature of cells and
therefore of life forms. Owing to its unique ability to replicate, DNA is a
semi-conservative molecule that passes on this information form one
generation of cells to the next and from one generation of organisms to
the next. Thus, it is an incredibly significant biomacromolecule.
The DNA of a cell is largely contained within the nucleus of cells so the
coded ‘message’ has to be carried out of the nucleus into the cytoplasm of
the cell where the proteins are actually synthesised in organelles (‘little
organs’) called ribosomes. RNA molecules carry out this function.
The Function of DNA
The particular sequence of nucleotides in the DNA molecule forms a code
which, until 1966, had not been cracked. The code carried by the DNA is
organised in triplets (three nucleotides) that determine the order in which
the amino acids are sequenced and, in turn, this sequence determines
which protein is formed.
It sounds simple but when we consider that each cell of our body carries
well over a metre in length of DNA, twisted and coiled into 46
chromosomes that have more than three billion base pairs (bp), it is not
surprising that there is such diversity of proteins. However, not all the
length of the DNA molecule codes for proteins. The parts that code are the
genes and the total set of genes that each cell of an organism has is called
its genome. The study of these sets of genes and the way they interact
with each other is called genomics
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Figure 2.8 (a) DNA is made up of deoxyribose sugars and RNA
of ribose sugars. (b) Nucleotides link together to form a singlestranded DNA molecule. (c) The DNA helix is a double-stranded
molecule. The two strands are held together by hydrogen bonding
between complementary nitrogenous bases.
Image below courtesy of Biology VCE Units 3 & 4 by Nelson
Thomson.
1
2
4
A=adenine, T=thymine, C=cytosine,
G=guanine, P=phosphate group,
S=sugar, B=base.
The Quizlet for week 2 might help with the following
Questions
http://quizlet.com/_c46j
2.19
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Question 13
a) Describe, by means of a simple annotated (labels and notes) diagram,
the structure of a nucleotide.
b) What distinguishes one nucleotide from another?
Question 14
Where is DNA located in a cell? Describe its function and explain its
significance.
Read through the following text and complete the tasks or questions that
follow. Use your own A4 paper or send work as MSWord documents
attached to an email.
DNA forms a double helix




Figure 2.9
5/
Each DNA molecule consists of two nucleotide strands, twisted in a
double helix structure (like a spiral staircase) in a regular manner.
The strands are ‘antiparallel’ – they run in opposite directions.
The ‘rungs’ of the DNA ladder, or the bonds between the two strands,
are formed by weak hydrogen bonds between the base pairs - cytosine
always pairs with guanine while thymine always pairs with adenine
and vice versa. These are called complimentary base pairs.
Bonding of these bases results in specific sequences of nucleotides on
a chromosome, which accounts for differences in genes. A single
gene may contain thousands of these base pairs.
3/
Model of a
small part of
a DNA
molecule.
3/
5/
Courtesy: Nature of Biology-book 2-Judith Kinnear and Marjory Martin
2.20
Figure 2.9 above gives you an idea of the structure of the DNA molecule.
Only a small part of the whole DNA molecule is shown here. It is quite a
large molecule.
This complementary structure gives DNA the following properties:
 It can be a template for its own replication (make sure you understand
what template means before going on)
 It contains genetic instructions (e.g. the code for protein production)
 It can undergo change or mutation.
DNA as a template
Due to the pairing of bases from one strand to the other it is possible to
tell what the bases in one strand are from the base sequence (order of
bases) in the other strand. Remember that A pairs with T and C pairs
with G.
If part of one DNA strand is:
GGTACCATA
Then the other DNA strand must be: C C A T G G T A T.
Relating DNA to genes and chromosomes
A chromosome is made of a single, double-stranded DNA molecule.
The length varies depending on the size of the chromosome and within its
length are all the genes on that chromosome.
Gene structure
Genes are made of DNA and are a part of a DNA molecule. One of the
two strands contains the information in a particular gene. This is called
the template strand. The complementary strand is often called the nontemplate strand.
Example of a small part of DNA represented by its bases:
The base sequence of the template strand of DNA is represented as
follows:
3/ A A T C C G T G A T T C
5/
Its non-template or complementary strand could be written below from
5/ to 3/
3/ A A T C C G T G A T T C 5/
5/ T T A G G C A C T A A G 3/
While this does not show the actual shape of the molecule it reveals the
base pairing rule and base sequence or genetic code. It is a simpler and
more informative way of presenting a piece of DNA.
2.21
5/ & 3/ What the …?
5/ is said as “five prime” and 3/ is said as “three prime”.
Nucleotides link together in what is called a 5′ to 3′ direction to form long
polymers. Translated this means that the phosphate group attached to the
5′ carbon of one ribose sugar bonds to the hydroxyl group attached to the
3′ carbon of another ribose monomer, forming a particular bond called a
phosphodiester bond. See page 33 of your text book for more detail.
Gene sequencing
As nucleotides only differ from one another by their different bases A, T,
C, G, if you know the base sequence you know the nucleotide sequence.
Gene sequencing is the process of identifying the order of nucleotides
along a gene. The sequences of nucleotides are different for different
species of organisms. This seems very logical when you consider that the
DNA of an organism contains the instructions for making that organism.
Nature of the genetic code
The DNA of genes carries all the genetic information of an organism. It is
in the form of a code made up of different combinations of just four
nucleotides: A, T, G and C.
The genetic code contains information for joining amino acids into
proteins. Proteins in turn control the biochemistry, structure and
physiology of an organism. In other words the genes have all the
instructions to make a particular organism.
Organisation of the genetic code
The code is a triplet code as three bases make one genetic instruction.
See below for some examples.
A mnemonic for remembering that a triplet (three) code is made up of
three nucleotides (letters) such as TTA, CCG, GGG, etc. is to remember
that the word DNA is made up of three letters.
Example
Consider a piece of DNA (template strand) with the following base
sequence (broken up into four triplets):
TACAAACAAACT
It then gets transcribed (copied) into mRNA. Notice that U replaces T in
mRNA:
TACAAACAAACT
TRANSCRIPTION
(copying)
Base sequence in
mRNA
AUGUUUGUUUGA
TRANSLATION
Amino acid sequence
in polypeptide chain.
met
phe
val
Stop
translation
2.22
This DNA has four triplets, four coded instructions. Below is a list of what the above codes
(codons) mean to the cell:
The DNA triplet
code (codon) on the
template strand
TAC
What it is
transcribed to on
mRNA
AUG
AAA
CAA
ACT
UUU
GUU
UGA
What it means to the cell.
What it instructs the cell to do.
start building a protein, commencing with the amino
acid methionine abbreviated as met …then …
add the amino acid phenylalanine abbreviated as phe…
add the amino acid valine abbreviated as val…
now stop.
See Figure 4.3 below for the genetic code used in the example above:
Figure 4.3 The genetic code. The mRNA codons correspond to the 20
amino acids made by translation on the ribosomes found in the cytosol.
Ribosomes “make proteins” by reading the mRNA codons. Three codons
act as stop codons and under certain conditions the codon AUG initiates
protein synthesis.
Image courtesy of Biology VCE Units 3 & 4, 2nd edition by Nelson Thomson.
SEND…
Question 14
Describe using an example what is meant by the ‘base-pairing’ rule.
2.23
Question 15
Have a go at the following animation
http://learn.genetics.utah.edu/content/begin/dna/transcribe/
(a) Write down the RNA strand you created
(b) Name the amino acids you created.
Question 16
Draw a table comparing DNA to RNA.
So … why should we care about proteins?
Below is an article taken off the internet. It presents a real life example of
how we use knowledge about bacteria and the proteins they produce. It is
also an example of biomimcry – looking to nature for solutions to our
questions and problems. I don’t expect you to understand the whole article
as it is written for industrial scientists. I do want you to understand that
what you are learning has very real applications to your life now and in
the future.
You do not have to answer any questions related to this. It is for your interest only.
The following edited article is from:
http://www.istc.ru/istc/sc.nsf/html/projects.htm?open&id=3060
Full Title
Producers of the protein - Bacteriorhodopsin (BR)
Leading Institute
Institute of Genetics and Selection of Industrial Microorganisms
Collaborators
University of Amsterdam
Sogang University / Department of Chemical and Biomolecular
Engineering
Project Summary
Project Objective:
Construction of Halobacterium salinarum strains as a promising source for
the industrial production of bacteriorhodopsin. Halophilic bacteria
Halobacterium possess a unique biosystem, converting solar energy into
electrochemical energy. Bacteriorhodopsin (BR) is a key element of this
natural system. BR is a retinal-containing protein of the purple membranes
of halobacteria.
$US 43 – 61 billion for a protein!! Hey lets start making it!! NOW!
Experts in advanced applied biotech research, in particular,
nanotechnology, emphasize a dramatic growth in the amount of funding
allocated to such studies [Research Review, 2002, 15(2)]. In the estimate
published by the Journal Nanotechnology the cost of such research
activities, performed in the U.S. since 2000, has exceeded $US 2 billion.
And the increment rate of venture capital investments in
nanobiotechnology in the last two or three years has achieved 313%. This
2.24
area of science is also considered as the most promising for long-term
capital investments [Nanotechnology, The Nanotech Report, 2003].
German experts, referring to the US Int. Trade Commission, state that the
international market of BR comprises about $US 43-61 billion
[www.archiv.ub.uni-marburg.de]. Germany is known for the most active
studies of bacteriorhodopsin application areas, in particular, in the
protection of securities against counterfeiting.
In the last years some evidence has been obtained that halobacteria could
be put on the list of industrial microorganisms as bacteriorhodopsin
producers. Based on our data, the world practice has no industrial
technology of continuous cultivation of halobacteria for bacteriorhodopsin
production, while the available laboratory techniques for the production of
this protein are capable to generate this product only in a gram scale.
Strong arguments have been generated to demonstrate that the
introduction of purple membrane preparations of halobacteria (containing
bacteriorhodopsin in high concentration and in the condition, applicable
for bioelectronic devices) to the world market will facilitate completion of
the relevant studies and development of commercially available
instruments. Thus, a successful project implementation would advance
bacteriorhodopsin production that will undoubtedly attract consumers in
the world market.
Future applications:
The potential areas of BR application are impressively diverse. They
include a double-side holographic memory, ultra-fast random access
memory (RAM), spatial light modulation, non-linear optic filters,
recognition systems, high-contrast displays, optic switches, and
picosecond detectors. Bacteriorhodopsin is also used in the production of
materials, protecting securities against counterfeit and as antioxidants in
medicine, pharmacy, and cosmetology.
Currently, halobacterium strains, capable to produce BR, are primarily
used in the laboratory conditions mainly for research purposes. It is known
from the literature that individual attempts were made to launch semiindustrial production of BR. However, no strains have been developed
which meet all the requirements for the industrial strains-producers. In our
opinion, the industrial strains of halophilic bacteria should be
characterized by the enhanced efficiency of nutrition, high growth rate,
and the maximal level of accumulation of the key target product –
bacteriorhodopsin.
The following tasks should be solved to meet the stated objective:
1. To review factors, restricting growth and accumulation of the biomass
of H. salinarum in the course of their massive cultivation.
2. To select H. salinarum strains, characterized by the highest production
rates. As source strains, promising for practical applications, it will be
possible to use wild H. salinarum strains and several strains with
mutations of the structural gene of bacteriorhodopsin (bop).
3. To clone structural bacteriorhodopsin gene of H. salinarum in Bacillus
cells, ensuring the highest level of production and secretion of the target
protein.
2.25
Key Summary Points
Courtesy of Heinemann Biology Two, 4th Edition








Macromolecules (polymers) are large organic molecules formed by
joining together many smaller molecules.
The four main types of organic molecules are carbohydrates, lipids,
proteins and nucleic acids.
Carbohydrates are the most abundant organic compounds in nature.
Their general formula is Cn(H2O)n. They are grouped into
monosaccharides, disaccharides and polysaccharides and have many
different properties.
Proteins are more complex molecules than carbohydrates or lipids,
and make up more than 50% of the dry weight of cells. All proteins
contain carbon, hydrogen, oxygen and nitrogen; many also contain
sulphur, phosphorus and other elements.
Proteins are chains of amino acids known as polypeptides. The
properties of proteins are determined by their shape, which is
determined by their amino acid sequence.
The nucleic acids DNA and RNA are the genetic materials of
organisms and they determine inherited features.
Lipids are non-polar hydrophobic molecules and can form an effective
barrier between two watery environments. They have a much smaller
proportion of oxygen than carbohydrates, and often contain other
elements, such as phosphorus and nitrogen.
Lipids include fats and oils (important as energy-storing molecules),
phospholipids (the important component of cell membranes) and
steroids (hormones and vitamins).
Key Terms
Carbohydrate, protein, nucleic acid, lipid, phospholipid, macromolecules,
autotroph, heterotroph, chemotroph, polymer, monosaccharide,
disaccharide, polysaccharide, glucose, glycogen, amino acids,
polypeptide, hydrophilic, hydrophobic, DNA, RNA, nucleotide genes,
genome
Challenging Activity: Mnemonic Activity
Choose one or more of the terms encountered during this week from the Key
terms above and create a memory aid to help you remember the definition of
that term.
You may use drawings, poetry, song, sound, whatever works for you!
Share your ‘mnemonic’ (memory aid) with the other students of your class via
the chat room. Look at the examples I’ve given throughout this weeks notes for
help and guidance. Feel free to discuss your ideas with me.
2.26
Here’s an example for this week:
Hydrophobic: Think of water when you see the word “hydro” as in
hydroelectricity – electricity generated by water from dams. With the “phobic’
part, think of ‘phobia’ as in ‘fear of’. So, hydrophobic is ‘fear of water’. This
helps you to work out ‘hydrophilic’ which is the opposite that is, ‘love of
water’. So when something is hydrophobic it repels water, moves away from it,
is “scared” of it. So the hydrophobic parts of a protein will hide themselves
inside the ‘protein ball’ because proteins are made in the watery environment
of the cell, whereas the hydrophilic parts will be found around the outside of
the protein ball in contact with the surrounding water.
Log on to the www.decvonline.vic.edu.au check out the back of your DECV
book for your login details if you have forgotten.
Click on the link to the Unit 3 Biology course.
Click on the button “Discussion Room”
Place your Mnemonic as a comment to the Discussion post titled
Mnemonics Week 2.
Make sure you check out the other Mnemonics left by your classmates and
leave them a comment.
Challenging Activity: Personal Reflection
Log on to the VCE Biology Course. Place your Personal Reflection in the Biology
Blog as outlined on 0.7 in the introduction of this book.
Checklist
This week you should have submitted the following work to me.
Please tick the items you have sent, and keep this as your record.





Responses to Questions 1-16
Practical Activity 2A Making A Model of A Protein
At least one mnemonic of a biological term placed online
Your Personal Reflection for week 2 placed online
The signed Student Declaration from page 0.15
(if you didn’t do so in Week 1)
Don’t forget to drink plenty of water!
Most of us do not drink enough water. Generally, adults need to drink at least 2.5 litres of water
per day! Simple dehydration is a common cause of tiredness and fatigue. We need water to
transport nutrients, chew and digest food, create blood, move muscles, breathe and think! Using
thirst as the reason for drinking water is not a good indicator for when you need to drink. Water
should be drunk at regular intervals whether you desire it or not.
2.27
Exam Practice Exercise
Past Exam Questions
Each week you will get at least one question that relates to the weeks
work, that comes from a past VCE exam paper.
The purpose of this task is to familiarize yourself with the type of
questions you will encounter during the exam and the timing you should
devote to each.
Timing
You should allow 1 minute and 10 seconds per mark assigned to the
question.
Here are your practice exam questions:
Question 1 taken from the 2006 VCE Biology Unit 3 exam paper.
Question 3 taken from the 2003 VCE Biology Unit 3 exam paper.
Question 8 taken from the 2003 VCE Biology Unit 4 exam paper.
Question 1
Scientists are now turning to the study of the proteome (all of the proteins)
of an organism rather than the study of single proteins.
a. Briefly outline one reason why the emphasis is now on the study of all
the proteins of an organism rather than on one protein at a time.
1 mark
Protein molecules come in many shapes and forms that can be classified
into primary, secondary, tertiary and quaternary. The secondary, tertiary
and quaternary shapes arise as a result of different kinds of folding of a
primary structure.
One kind of secondary structure is a pleated sheet where the primary
molecule extends along the folded sheet. The primary structures in the
layers are held together by hydrogen bonding.
2.28
b. Explain why such a structure may be important in the function of a
particular protein.
1 mark
Proteins can also be classified on the basis of their general function. Three of
these functions are shown in the table below.
c. Complete the table by giving an example of a protein for each of the
functions listed.
Function of protein
Example
Structural
Transport
Regulatory
3 marks
Total 5 marks
The following are multiple choice questions each worth one mark. You should
allow yourself 1 minute and 10 seconds to complete each question.
Choose the correct response for each question.
Question 3
Many biological compounds are large molecules made of many smaller units
joined together. Each of the units has the same basic structure. Such molecules
are called polymers.
Biological polymers include
A. cellulose composed of glucose.
B. glycogen composed of glycerol.
C. starch composed of amino acids.
D. proteins composed of fatty acids.
Question 8
In DNA, the number of
A. phosphate groups equals the number of nitrogen bases.
B. adenine nucleotides equals the number of cytosine nucleotides.
C. phosphate groups equals twice the number of sugar molecules.
D. guanine nucleotides equals the number of uracil nucleotides.
Feedback
If anything needs to be improved, corrected, cleared up or presented better from
the material presented in this week please let us know. Your honesty is
appreciated. Write your comments on the back of the cover sheet.
END OF WEEK 2
2.29
Answers to Past Exam Questions
Question 1a.
The emphasis is on the study of all proteins because of the interaction between proteins, and the
reliance that some have on others. Although this question was well answered by many students,
others failed to identify either of the points above.
Question 1 b.
Structures may be important because: • of the ability of the protein to stretch or contract
(elongate or shorten) in particular situations • pleating may strengthen the molecule and that may
be important for its function • particular structures may provide an active or binding site for an
enzyme or other molecule. Few students appeared to understand that secondary-structure
proteins may have a particular function in that state, with many writing only about them being
part of a tertiary-structure protein. Answers that gave general comments, such as ‘the protein
could be an enzyme’, without explaining the relevance of structure received no credit.
Question 1c.
Function of protein
Structural
Transport
Regulatory
Example
collagen, keratin, silk, cytoskeleton, cilia, fibrin, fingernails
haemoglobin, protein carrier, serum albumin
hormone (or specific example), enzyme (or specific example), major
histocompatibility complex (MHC)
This question was generally well answered. Incorrect answers generally referred to compounds
such as carbohydrates and other non-protein compounds.
Question 3: A - cellulose composed of glucose (glycogen and starch are composed of glucose
and proteins are composed of amino acids.)
Question 8: A – Phosphate groups equal the number of nitrogen bases.
2.30
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STUDENT NUMBER ___________________
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STUDENT NAME ______________________
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WEEK
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SEND
Please check that you have attached:

Responses to Questions 1-16

Practical Activity 2A – Making A Model of A Protein

At least one mnemonic of a biological term placed online

Your Personal Reflection for week 2 placed online

The signed Student Declaration from page 0.11 (if you didn’t do so in Week 1)
If you have not included any of these items, please explain why not.
_____________________________________________________________________________
_____________________________________________________________________________
Use the space on the back of this sheet if you have any questions you would
like to ask, or problems with your work that you would like to share with
your teacher.
2.31
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Please provide the following information:
Were you able to complete the tasks in the time frame allocated? ____________________
Roughly how long did it take for you to complete this week of work? _____________
Use this space for any queries or comments you have, (or maybe errors you’ve found).
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