CHEMICAL NATURE OF THE
CELL 1
EL: To begin investigating what cells
are and the molecules they are made
of
CELL THEORY
•
All living things are made cells – they are the building blocks from
which living things are made.
•
New cells are produced from existing cells.
Where do cells fit in to the bigger
picture?
Where do cells fit in to the whole
organism?
ATOM
MOLECULE
ORGANELLE
CELL
TISSUE
ORGAN
ORGANISM
Did you know?

Some organisms are one cell (uni cellular)

Other organisms have more than one cell
(multi cellular)

Organisms have adapted to serve the
needs of their cell or cells
CELLS ARE
REALLY SMALL!
Types of cells

Prokaryotic
◦ Very small: less than
2mm in diameter
◦ Lack internal
compartments
◦ Bacteria and
archaeans

Eukaryotic
◦ Much larger: 10100mm in diameter
◦ More complex
structure –
compartments called
organelles
◦ Animals, plants, fungi
and protists
What is a cell?
A fluid filled compartment containing atoms and
molecules
INTRACELLULAR
AQUEOUS
ENVIRONMENT – CYTOSOL
or CYTOPLASM
EXTRACELLULAR
AQUEOUS
ENVIRONMENT
CELL BOUNDARY
(PLASMA MEMBRANE)
WHAT IS A CELL?
A chemical factory
Inputs
(small molecules)
Outputs:reactions
useful
Chemical
Outputs:
useful
products
for
products
for
export
between
inputs
driven
by
export
(biomacromolecules)
(biomacromolecules)
energy
in response to
Output: waste products
external/internal
signals
Signals
WHAT IS A CELL?
A chemical factory
Inputs
(small molecules)
Outputs: useful
products for export
(biomacromolecules)
Chemical reactions
Outputs: useful products for
between
inputs
export driven by
(biomacromolecules)
energy
in response to
external/internal signals
Signals
Output: waste products
What are cells made of?
Six
atoms make up most of the matter in
living organisms
 Carbon, hydrogen, nitrogen, oxygen, sulfur and
phosphorus
These
atoms can combine to form large
molecules
 Many important concepts in Unit 3 Biology can
be explained by the interaction between these
molecules
Molecular representations

http://www.concord.org/~btinker/workbe
nch_web/unitIV_revised/molecular_repre
sentations.html
Molecules
Non-polar molecules
 Molecules that have no overall charge
are called non-polar.
 They are not attracted to water
molecules and are described as
hydrophobic (water fearing)
Polar molecules
 Molecules that have regions of positive
and/or negative charge are called polar.
 They are attracted to other polar
molecules, like water, and are described
as hydrophillic (water loving)
Water molecules
Cells contain the molecule water – H2O
 Water is called a polar molecule

 The oxygen atom attracts the electrons it shares with
the hydrogen atoms more strongly
 This makes the oxygen atom slightly negative (d-)
and the hydrogen atoms slightly positive (d+)
d+
d-
d+
water molecules
The d-
oxygen atom of one water molecule
attracts the d+ hydrogen atom of another
water molecule - this is called hydrogen
bonding
Carbon molecules

Many molecules contain carbon due to its
ability to form strong stable covalent bonds
with carbon and other atoms

Each carbon atom can form four covalent
bonds – these bonds can be single
(saturated), double or triple (unsaturated)
Hydrocarbon molecules

Hydrocarbons are made of carbon and
hydrogen atoms (eg methane – CH4)

Hydrocarbons are non-polar
Hydrocarbon molecules

Other groups can be substituted for a H,
giving it a new chemical character (eg
methanol – CH3OH)

These functional groups can make a
hydrocarbon polar and explain many of the
molecular interactions in a cell

Common functional groups are OH,
COOH, NH2 and HS
BIOMACROMOLECULES
Large molecules that are integral to the structure and function of cells are
called biomacromolecules. There are four types:
Carbohydrates
Lipids
Proteins
Nucleic acids
BIOMACROMOLECULES
Cells
make biomacromolecules from
smaller subunits
Each
kind of biomacromolecule has
characteristics or properties that
make it effective for carrying out its
particular function
ACTIVITY/HOMEWORK
 Use
pages 9-26 from your text book and/or the
Biomacromolecule MP3 G-Casts at
http://www.gtac.edu.au/site/gcasts/g_casts.html
to fill in the table below.
Type of
biomacromolecule
 Start
Atoms in
molecule
Sub-units/
monomers
Chapter 1 questions
Structure
(picture)
Polar/
Non
Polar
Cellular
functions
Reflection

How well did you remember the content
of the lesson today from Unit 1

OR

How well did you understand the new
content today?
CHEMICAL NATURE OF THE
CELL 2
EL: To review our biomacromolecule table from last
class and learn how biomacromolecules are
synthesised
HOMEWORK
Type of
biomacromolecule
Atoms in
molecule
Sub-units/
monomers
Structure
(picture)
Polar/
Non
Polar
Cellular
functions
lipids

Made of C, H and O atoms

Subunits are fatty acids or glycerol

Insoluble in water due to non-polar HC
regions

Three important cellular functions
◦ Chemical energy storage (store two times as much
energy as carbohydrates)
◦ Structural
◦ Chemical signal
lipids
Type
Function
Fatty acids (eg stearic acid,
oleic acid)
Energy source
Subunit of other lipids
Triglycerides
Energy storage
Phospholipids
Structural component of plasma
membranes
Glycolipids
Recognition sites on plasma membranes
Steroids (eg cholesterol, sex
hormones)
Component of plasma membranes
(regulates fluidity)
Signaling molecule
Terpenes (eg Vitamin A)
Antioxidant
lipids

Saturated
◦ single covalent bonds
between atoms
◦ Straight molecule
◦ Solid at room
temperature

Unsaturated
◦ Double or triple
covalent bonds
between molecules
◦ Bent molecule
◦ Liquid at room
temperature
Glycerol – a fatty alcohol

Glycerol has three OH groups that bond
with three fatty acids
◦ When the fatty acid group reacts with the
alcohol group, water is formed and is
therefore a condensation reaction
◦ However, there are no repetative linkages: so
lipid not a polymer
phospholipids

Phospholipids have:
◦ a hydrophopic tail of two fatty acids
attached to a glycerol
◦ A hydrophillic phosphate head with
another small groups attached to the
phosphate
carbohydrates

Also made of C, H & O atoms in a 1:2:1 ratio

Subunits are simple sugars called
monosaccharides and disaccharides

Solubility in water – depends on size and polarity

Three important cellular functions
◦ Chemical energy storage
◦ Component of other important molecules (eg DNA)
◦ Structural (esp. in plants)
carbohydrates
Type
Simple
carbohydrates
Complex
carbohydrates
Example
Function
Monosaccharides (single
sugar unit)
General formula:
(CH2O)n
Glucose
Energy source
Fructose
Energy source
Ribose
Component of DNA
Disaccharides
(two sugar units)
Sucrose
Transport sugar in
vascular plants
Lactose
Component of milk
Maltose
Obtained in breakdown
of starch
Starch
Storage molecule in
plants
Glycogen
Storage molecule in
animals
Cellulose
Component of plant cell
wall
Chitin
Component of insect
and crustacean
exoskeleton
Polysaccharides
(many sugar units)
Nucleic acids – DNA & RNA

Subunits are called nucleotides and are
composed of:
◦ A five carbon (pentose) sugar
 Ribose in RNA
 Deoxyribose in DNA
◦ A negatively charged phosphate group
◦ An organic nitrogen containing compound called a
base
 Purines: Adenine (A) and Guanine (G)
 Pyrimidines: Thymine (T) and Cytosine in DNA or Uracil in
RNA
Nucleic acids
Double
ring
Single
ring
PURINES
Adenine
Guanine
PYRAMIDINES
Thymine
Cytosine
Uracil (in RNA)
Nucleic acids

5’-Sugar molecule of one
nucleotide binds to the
phosphate group of the next
in a condensation
polymerisation reaction
(http://www.gtac.edu.au/
site/gcasts/UNIT3/biomacromolecules/index.html)

A phosphodiester bond is
formed between the
nucleotides creating a
polynucleotide strand

Polynucleotide strand extends
in a 5’-> 3’ direction – said to
have directionality
Nucleic acids
5’-carbon
3’-carbon
 DNA
is made of two
polynucleotide strands
that are held together
by hydrogen bonding
between the
complementary base
pairs
 The
two strands are
anti-parallel
3’-carbon
5’-carbon
Nucleic acids – DNA & RNA

Found within nucleus

Store information in a chemical code called
a gene that directs cells to make proteins

Differences between DNA & RNA
DNA
RNA
Double stranded
Single stranded
Deoxyribose sugar (one less
O atom)
Ribose sugar
Thymine base
Uracil base
Proteins

Subunits are amino acids composed of:
◦ Central carbon atom attached to:





Hydrogen atom
Carboxyl (COOH) group
Amine group (NH2)
R group
Type of R group:
◦ Distinguishes an amino acid and gives it
particular properties
◦ Gives protein molecule polar and non-polar
regions
Protein structure

Each protein molecule has a
characteristic 3D shape

The function of the protein depends on
the shape of the molecule

Protein structure can be explained by
four levels
Protein structure

Primary:
◦ Sequence of amino acids peptide
bonded through condensation
polymerisation reaction into
polypeptide chain

Secondary:
◦ Parts of the chain undergo coiling
(a-helices) and folding (b-sheets)
due to hydrogen bonding
between amino acids.
◦ Other parts form random loops
Protein structure

Tertiary:
◦ Hydrophilic and hydrophobic R groups of one
amino acid attract like groups of another amino
acid, making the chain more folded, coiled or
twisted into the protein’s functional shape
◦ Determines biological functionality

Quarternary:
◦ Many large protein molecules have two or more
polypeptide chains
Protein function
Function of protein
Example
Structural
Collegen, keratin, fibrin
transport
Haemoglobin, protein carrier,
serum albumin
Hormone, enzyme
regulatory
Making a BIOMACROMOLECULE
 Biomacromolecules
are synthesised inside cells.
This involves linking smaller sub-units to form
large chains.
 Carbohydrates, proteins
and nucleic acids are
formed when sub-units called monomers link to
form a polymer in a condensation
polymerisation reaction
 Lipids
are not polymers as they are composed
of distinct chemical groups of atoms that don’t
undergo a condensation reaction
Condensation polymerisation
reaction

The OH groups on adjacent monomers
can react, eliminating a water molecule.
Nucleic acids
Phosphate
group (-ve)
5’-carbon
Nitrogen
base
O
C 5’
4’
1’
3’
2’
H
OH
Phosphate
group (-ve)
Nitrogen
base
O
C 5’
4’
1’
2’
H
3’
OH
3’-carbon
SYNTHESIS OF
BIOMACROMOLECULES
 Autotrophs: organisms
that are able to synthesise their
own biomacromolecules from inorganic compounds
Plants and algae  photosynthesis
Certain species of chemosynthetic bacteria use
the energy released from areas of geothermal activity
 Heterotrophs: synthesise
their own biomacromolecules
from organic molecules they have ingested
animals
fungi
majority of bacteria
many protists
Activities

Use the molecular model kits to make some
carbohydrate and lipid molecules

Use pipe cleaners to demonstrate different levels of
protein organisation

Build a model of DNA using pipe cleaners and
papererclips

For both, write a short script explaining DNA and
proteins to a year 7 or 8 science class
Reflection

Did the hands on activities help you to
better understand biomacromolecules or
do you think the table helped you more?
CHEMICAL NATURE OF THE
CELL 3
EL: To investigate where
biomacromolecules fit in to the
“tree of life”
Activity

In groups of 3 – 4 (4 groups in total), go to
http://www.concord.org/~btinker/workbench_web/unitIV_revised/tree_life
_wrkst.html

Investigate the biomacromolecule that has been assigned to you – you will
zoom into organs and tissues of plants and animals in order to discover
life's essential building blocks. The exercise includes just a few of the many
possible "zooms" into the structures of living organisms.

Answer the following questions:
◦ What can you find out about macromolecules building blocks of our
organs and tissues ?
◦ How different are these building blocks from one another? Are there
similarities between them?

Also answer the relevant questions to your molecule on the bottom of the
main zoom page

Report back to the rest of the class what your group learnt
Activity/Homework

Finish Chapter 1 Questions, including
concept map (due next lesson)

Study for test (next lesson)
Reflection

Did the tree of life activity help you to
better understand biomacromolecules?

Why or why not?