1. UNIT 3 BIOLOGY
EARLY COMMENCEMENT
November 2010

2. EARLY
COMMENCEMENT
HANDBOOK
UNIT 3 BIOLOGY
2

3. 3

4. 4

5. Year 12 Biology Textbook
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6. 6

7. 7

8. 8

9. 9

10. 10

11. 11

12. 12

13. 13

14. 14

15. LOTUS ~
BIOMACROMOLECULES
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16. The Chemical Nature of Cells
Chapter 1
Unit 3 Biology

17. KEY KNOWLEDGE
The Chemical Nature of Cells
 By the end of this chapter, you should:
◦ Enhance your knowledge & understanding of the synthesis
of biomacromolecules such as polysaccharides, lipids,
proteins and nucleic acids.
◦ Enhance your knowledge & understanding of the structure
& function of nucleic acids.
◦ Understand the structural diversity of proteins & 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.
17

18. The Chemical Basis of Life
 All cells are
composed of
atoms and
molecules which
interact in
thousands of
simultaneous
chemical
reactions.
 Organisms are
composed of
chemicals that
react with each
other and with the
substances in the18

19. Biochemistry
 The study of the chemicals involved in living
organisms is called ‘biochemistry’.
 Investigations in biochemistry allow for the
development of pharmaceuticals, vaccines
and improvements in medical diagnoses.
 GENOMICS & PROTEOMICS are two recent
fields of science dealing with the study DNA
and proteins.
 All the data that is gathered needs to be
collated, analysed and stored in a systematic
way. Thus the field of BIOINFORMATICS has
been developed.
19

20. WATER ~ why is it so
important?
 ALL known life forms require water to
survive
 75% - 85% of a cell’s weight is water
 Almost all substances and chemical
reactions of biological significance
require water.
 Cells are constantly bathed by a watery
solution
 Water is essential for the cycling of
matter between the living & non-living
parts of ecosystems.
20

21. Chemical Properties of Water
 H2O
 Water can exist as a solid (ice), a gas (steam)
or as a liquid
 Water molecules are highly polar.
 The oxygen part of the molecule is negative so
it is attracted to the positive end of other water
molecules.
 Water molecules join together by HYDROGEN
BONDING
 Hydrogen bonds involve the bonding between
a hydrogen atom on one molecule and the
negative atom of another molecule or element21

22. Water: the versatile solvent
 The polarity of water molecules allows
substances to dissolve in it.
 This ability is due to the water molecules
interacting with other charged particles
 HYDROPHILIC: Polar molecules can
form hydrogen bonds with polar
molecules of water and so they dissolve
(water loving).
 HYDROPHOBIC: Non-polar substances
will not dissolve in water because they
cannot form hydrogen bonds with water
molecules.
22

23. BIOLOGICAL
MACROMOLECULES
 EVERY living cell is involved in
synthesising macromolecules for the
following:
◦ Building up body parts of the organism
◦ Maintain biochemical processes, including:
 Communication
 Transforming energy
 Relaying genetic information
 The four main classes of macromolecules
are:
◦ Proteins
◦ Nucleic Acids
23

24. Organic
Molecules
 Organic
molecules are
made up of
smaller subunits
 The subunits are
called monomers
 Polymers are
formed when the
monomers are
bonded together
24

25. Synthesis of
Biomacromolecules
 Some organisms can synthesise their own
biomacromolecules whereas others must rely
on the substances they have taken in.
 AUTOTROPH: an organism that is able to
synthesise organic molecules from
inorganic materials.
 CHEMOTROPH: an organism that is
able to synthesise organic molecules from
specific chemicals.
 HETEROTROPH: an organism that must
synthesise their organic molecules from
existing organic molecules that are taken in as
food. 25

26. Polymerisation
 Biomacromolecules are synthesised inside
the cell.
 Polymerisation is the process of smaller
repeating units (monomers) being linked
together to form long chains called polymers.
 Proteins, carbohydrates & nucleic acids are
synthesised in this way and are classed as
polymers.
 Lipids do not form polymers. They are
composed of distinct chemical groups of
atoms.
26

27. Condensation Polymerisation
 When monomers link together, a water
molecule is generated.
◦ The hydroxyl group of one monomer reacts
with the hydrogen atom of another monomer.
 This reaction is called Condensation
Polymerisation.
Monomers Polymers
single units/subunits many linked units/
macromolecules
polymerisation
27

28. CARBOHYDRATES
 Carbohydrates are the most common
compounds in living things.
 Organisms use carbohydrates as an energy
source and for structural components.
 Each molecule is composed of the following
atoms in the ratio of 1:2:1
◦ 1Carbon atom : 2 Hydrogen atoms : 1 Oxygen atom
◦ CH2O is the formula
 Carbohydrates are classified as:
◦ Monosaccharides
◦ Disaccharides
◦ Polysaccharides
28

29. Classification of
Carbohydrates
29

30. Monosaccharides
 Molecules contain a single sugar unit
 Usually has the formula C6H12O6
 Monosaccharides with the same molecular
formula have differing structural formula
(arrangement of atoms)
 Soluble in water
 Usually known as ‘sugars’
 Most important example is GLUCOSE
 Other examples:
◦ Fructose
◦ Galactose
30

31. Disaccharides
 Disaccharides form when two
monosaccharides combine.
 Examples include:
◦ Sucrose = glucose + fructose
◦ Lactose = glucose + galactose
◦ Maltose = glucose + glucose
31

32. Polysaccharides
 Between ten & several thousand
monosaccharides that have joined together
 The most common sugar component is
glucose
 The differences in properties relate to the
ways in which the glucose molecules are
linked together.
 Many polysaccharides are INSOLUBLE in
water
 Examples:
◦ Cellulose: structural component of every plant cell
wall
◦ Starch: main form of storage by most plants 32

33. 2009 VCAA Exam Question
An important structural carbohydrate in
plants is
A.
B.
C.
D.
cellulose
glucose.
chitin.
glycogen.
33

34. PROTEINS
 Almost everything a cell is made up of or
does depends on PROTEIN.
 Proteins contribute to building many
different structures and control the
thousands of chemical reactions that
maintain life processes.
34

35. Building Blocks of Proteins
 Proteins are made up of AMINO ACIDS.
 There are 20 different amino acids that
contribute to the proteins found in cells.
 The basic structure of proteins includes
up to thousands of amino acids bonded
together to form linear polymers that are
folded, twisted or coiled.
 Plants synthesise their own amino acids.
 Animals rely on their diet to obtain their
amino acids.
35

36. Amino Acids
 All amino acids have
the same basic
chemical structure:
◦ A central carbon atom
◦ A hydrogen atom
◦ A carboxyl acid group
(COOH)
◦ An amine group (NH2)
◦ An “R” group  this
group is different for
each type of amino
acid
Carbon
Atom
Amine
Acid
Carboxyl
group
R
Group
Hydrogen
Atom
36

37. Protein Structure
 Primary Structure:
◦ refers to the sequence of amino acids that
form the polypeptide chain.
 Secondary Structure:
◦ coiling (α-helices) &
◦ folding (β-sheets) of the polypeptide chain.
◦ Other parts remain unchanged (random
loops)
◦ Hydrogen bonds form between segments
of the folded chain that are close together
and help stabilise the 3-D shape 37

38. PRIMARY STRUCTURE
SECONDARY STRUCTURE
38

39. Protein Structure (cont…)
 Tertiary Structure:
◦ Interactions between R groups
◦ Results in hydrogen bonds, ionic bonds or disulfide
bridges between cysteine amino acids.
◦ Interactions follow the ‘like attracts like’ rule:
hydrophilic + hydrophilic
hydrophobic + hydrophobic.
◦ The polypeptide chain is folded, coiled or twisted
into the protein’s functional shape (conformation).
◦ Protein molecules with the same sequence of
amino acids will fold into the same shape.
◦ If an incorrect amino acid is present this will alter
the shape of the protein making it non-functional.
39

40. Tertiary Structure (cont…)
40

41. Protein Structure (cont…)
 Quaternary Structure:
◦ Many large complex
protein molecules consist
of two or more polypeptide
chains.
◦ Hydrogen bonds, ionic
bonds and/or covalent
bonds hold the
polypeptide chains
together and gives the
overall shape to the
molecule.
41

42. Protein
Structure
(cont…)
42

43. Functional Diversity of
Proteins
 Motility: movement of cells & organelles
 Structural: support, strength protection
 Enzymes: speed up reactions
 Transport: carry molecules around cell or
across membrane
 Hormones: chemical messengers
 Cell-Surface Receptors: act as a ‘label’ to
provide identification of the cell
 Neurotransmitters: chemical messengers
between neurons
 Immunoglobulins: antigens
 Poisons/toxins: chemicals for defence or
capturing food
43

44. 2009 VCAA Exam Question
The diagram below shows the structure
of a particular protein molecule.
44

45. 2009 VCAA Exam Question
(cont…)a. The protein contains two distinctive types of polypeptide chains
labelled X and Y. What are the names of these two types?
Chain X _____________________
Chain Y ______________________ (2 marks)
b. Name a polysaccharide found in animals and describe its
function.
Name: _________________________
Function: ______________________________________
(2 marks)
c. What is the function of cholesterol in cell membranes?
__________________________________________________
__________________________________________________
___________________________________________ (1 mark)
45

46. LIPIDS
 Lipids have three important functions:
◦ Energy storage
◦ Structural component of cell membranes
◦ Specific biological processes (eg:
transmission of chemical signals both within
and between cells).
 All lipid molecules contain carbon,
hydrogen & oxygen
 Lipids contain relatively little water
 Lipid molecules carry more energy per
molecule than any other kind of
compound found in plants or animals. 46

47. Fats
 Made up of two kinds
of molecules:
◦ Fatty acid
◦ Glycerol
 Triglycerides are a
common form of fats
47

48. Triglycerides
 Triglycerides: subunits of fats & oils
 Three fatty acids attach to the glycerol
backbone.
 SATURATED fats:
◦ Found in animals
◦ Solid
◦ Fatty acids are packed closely in a straight line
 UNSATURATED fats:
◦ Found in plants
◦ Liquid
◦ Fatty acids form double bonds and are not packed
closely together
48

49. Phospholipid
 HYDROPHOBIC TAIL:
◦ Two fatty acids chains
◦ Repel water
 HYDROPHILIC HEAD:
◦ Phosphate group attached to the glycerol head
◦ Attracted to water
 Phospholipids are the major component of
cell membranes
49

50. Phospholipids & Plasma Membrane
Structure
50

51. 2009 VCAA Exam Question
B. involved in active transport.
C. part of glycoprotein molecules.
D. transported by rough endoplasmic
reticulum
A. used as an energy source.
Lipids are
51

52. NUCLEIC ACIDS
 Nucleic acids are long
molecules made up of
three distinct chemical
parts.
 Nucleic acids store
information in a
chemical code for the
production of proteins.
 Nucleic acids are the
GENETIC MATERIAL
for every living
organism.
 DNA = deoxyribonucleic
acid 52

53. DNA vs RNA
DNA
 Linear molecule
 Double stranded
 The two strands wind
around each other to form
a double helix
 Made up of nucleotides
 Located in the nucleus
 Deoxyribose is the sugar
component
 Nitrogenous bases:
◦ Adenine
◦ Guanine
◦ Cytosine
◦ Thymine
RNA
 Linear molecule - shorter than
DNA
 Single stranded
 Made up of nucleotides
 Formed in the nucleus then
moves to the ribosomes in the
cytoplasm to function.
 Ribose is the sugar component
– ribose has one less oxygen
atom than deoxyribose
 Nitrogenous bases:
◦ Adenine
◦ Guanine
◦ Cytosine
◦ Uracil
53

54. Nucleotides
 Nucleotides are the monomers that bond
together to make the nucleic acid
polymers.
 Nucleotides have 3 distinct chemical
parts:
◦ A 5-carbon sugar (ribose or deoxyribose)
◦ A Negatively charged phosphate group
◦ An organic nitrogenous base
 Adenine - A
 Guanine - G
 Cytosine - C 54

55. Nucleotides (cont…)
 The sugar molecule of one nucleotide binds with
the phosphate group of the next nucleotide.
 The nitrogenous base is left sticking out and faces
the opposite nitrogenous base from the adjoining
DNA strand
 Hydrogen bonds hold the nitrogenous base pairs
together forming the ‘rungs’ of the helix.
 The bases pair according to the following rule:
◦ A pairs with T (T pairs with A)
◦ G pairs with C (C pairs with G)
 This is known as the COMPLIMENTARY BASE
PAIRING RULE
55

56. Chemical
structure
of DNA
56

57. DNA ~ function
 The sequence of nucleotides in DNA
codes for amino acids that will form a
particular protein.
 GENES: the segments of DNA that
code for protein formation
 GENOME: the total set of genes that
each cell of an organism carries.
 GENOMICS: the study of genes and
the way they interact with each other.
57

58. DNA ~ function (cont…)
 DNA passes on information from one
generation to the next.
 DNA, usually in the form of chromosomes, is
located in the nucleus of cells.
 One of the strands of DNA acts as a template
so that the complimentary strand of DNA can
be formed (following the base pairing rule).
 DNA is also used as a template for the
formation of RNA.
 Some DNA is located in mitochondria & in
chloroplasts.
 Biotechnology has allowed for the
manipulation & modification of DNA.
58

59. MAKING mRNA
 YouTube – Transcription
 YouTube - mRNA splicing 59

60. Transcription
 The mRNA used to make proteins is transcribed
from a particular region of DNA within the nucleus
of a cell.
 The DNA unwinds and the enzyme RNA
polymerase binds to a promoter site at the 5' end.
 The enzyme moves along the DNA and at each
nucleotide a complementary RNA nucleotide is
added to the growing mRNA strand.
 The transcribed mRNA (primary transcript or pre-
mRNA) will contain all the nucleotide sequences
within a given region of DNA.
 Some of the transcribed code contains introns,
which do not translate into proteins. These have to
be spliced out of the mRNA before it can move to
the ribosome.
 When introns are spliced out by enzymes in the 60

61. Animations on Transcription
 http://207.207.4.198/pub/flash/26/trans
menu_s.swf
 http://www-
class.unl.edu/biochem/gp2/m_biology/
animation/gene/gene_a2.html
 http://www.johnkyrk.com/DNAtranscrip
tion.html
 http://medlab.lzu.edu.cn/image/flash/8.
swf
 http://www.fed.cuhk.edu.hk/~johnson/t
eaching/genetics/animations/transcript61

62. Pre-mRNA to mature mRNA
 Non-coding regions (introns) are spliced
out
 Methylated cap is added on the 5’ end
 Poly-A tail is added on the 3’ end
62

63. RNA ~ function
 The major function of RNA is to produce proteins.
 GENE EXPRESSION: the information from the DNA
strand is taken by the RNA and the appropriate
proteins produced.
 mRNA: messenger RNA – the code from DNA is
transferred to mRNA in a process called
transcription. The mRNA strand moves out of the
nucleus into the cytoplasm and attaches to the
ribosomes.
 rRNA: ribosomal RNA – ribosomes are composed
of rRNA and other proteins.
 tRNA: transfer RNA – each tRNA molecule has an
amino acid attached at one end and an anti-codon
on the other end. The anti-codon pairs up with the
corresponding codon on the mRNA. This ensures
the correct sequence of amino acids for the 63

64. 2009 VCAA Exam Question
mRNA is
A. a double-stranded molecule.
B. found only in eukaryotic cells.
C. found exclusively in the nucleus.
D. formed during transcription of DNA
64

65. PROTEIN SYNTHESIS
 YouTube - Translation
65

66. Translation
 mRNA moves into the cytoplasm and is used as a
template to direct the assembly of amino acids at
the ribosome.
 The code on the mRNA is read as a triplet of
nucleotides, a codon.
 Given that there are 20 amino acids commonly
found in cells, four nucleotides alone cannot code
for this many different molecules. The nucleotides
cannot be read in pairs because this will produce
only 16 different combinations.
 The nucleotides must be read as groups of
three, which will be more than enough
combinations to make the 20 amino acids.
 Some amino acids have more than one codon
sequence.
66

67. Translation (cont…)
 To begin the translation of proteins, the
ribosomes attach to the codon sequence
AUG on the mRNA.
 As the ribosome passes each codon on the
mRNA, transfer RNA (tRNA) with a
complementary anticodon binds to the
exposed codon on the mRNA.
 At the top of the tRNA molecule is a specific
amino acid that attaches to the growing
polypeptide chain.
 Of the 64 codons, three of them (UAA, UAG,
UGA) are stop codons and will stop the
synthesis.
67

68. tRNA molecule
68

69. 69

70. 70

71. The codon sequences that code for all 20 amino
acids
71

72. TRANSLATION:
protein synthesis at the ribosome
1. New amino acid being
added ~ PHE corresponds
to the mRNA codon UUU
2. The amino acids join to
form the growing
polypeptide chain
3. The tRNA has detached
from the amino acid and
will leave the ribosome to
find another free-floating
amino acid in the
cytoplasm.
4. Three of the bases on the
mRNA form a base-triplet,
called a CODON.
72

73. 73

74. 74

75. 75

76. Animations on Translation
 http://www-
class.unl.edu/biochem/gp2/m_biology/a
nimation/gene/gene_a3.html
 http://www.biostudio.com/demo_freema
n_protein_synthesis.htm
 http://highered.mcgraw-
hill.com/sites/0072437316/student_view
0/chapter15/animations.html#
76

77. 2009 VCAA Exam Question
a. A section of one of the strands of a
DNA molecule has the sequence of
bases shown.
 DNA: C T T A C A T T A C T C
 In the spaces below, enter the sequence
of bases in the corresponding mRNA
which is complementary to this DNA.
(1 mark)
mRNA
77

78. 2009 VCAA Exam Question
(cont…)
b. The percentage of base T in a molecule of DNA is
30%. What is the percentage of G bases in the same
DNA molecule?
______________________________ (1 mark)
Another type of nucleic acid is tRNA.
c. i. Where is tRNA found in a cell?
___________________________
ii. Describe the role of tRNA.
____________________________
____________________________ (1 mark)
78

79. 2009 VCAA Exam Question
(cont…)d. The table shows the names of six amino acids
together with some of their DNA codes.
 Use the information in the table and write the order of
amino acid coded for by the DNA sequence given in
part a.
__________________________________ (1
mark)
AMINO ACIDS DNA TRIPLET(S)
cysteine ACA, ACG
glutamic acid CTT, CTC
aspartic acid CTA, CTG
asparagine TTA, TTG
leucine GAA, GAG, GAT, GAC
methionine TAC
79

80. 2009 VCAA Exam Question (cont…)
 Nucleic acids are made up of nucleotides. Each
nucleotide consists of three components, sugar
(S), phosphate (P) and nitrogen base (B), linked
together in a particular way.
e. In the empty box, draw a diagram to show the
way the three components are joined to make a
nucleotide. (1 mark)
Use the following symbols in
your diagram
80