7. Essential amino acids:
must be taken in with the
diet
the body cannot make them
(e.g. methionine)
Non-essential amino
acids:
can be synthesised by the
body (e.g. cysteine)
27. Why do amino acids differ in their
chemical and physical properties
(size, water solubility, electrical
charge)?
Because of their
different R groups
28. Table 3.2 (Part 1)
The side groups of
amino acids
determine folding of
polypeptide
29. Side chains of amino acids:
show a wide variety of chemical
properties
are important to determine the:
3D structure
of the protein
function
31. WHY?
hydrophilic
amino acids
hydrophobic
amino acids
Ions (black) can only pass through the pore of the ion
channel because this is the only part with hydrophilic
amino acids lining the pore (green = area of ion
channel with hydrophilic water-loving amino
acids). The rest of the ion channel mostly consists of
hydrophobic amino acids (purple).
32. ORDER of the side chains of
amino acids in a protein :
determines how it folds into a three
dimensional configuration
33. From amino acids to proteins
two amino acids
three amino acids
more than 50 amino
acids
6 000-1000 000
dipeptide
tripeptide
polypeptide
protein
34. All proteins can be hydrolysed into
amino acids
• Some:
need time &
a particular medium
• All proteins are broken when:
heated in 6M HCl at 115C for
several hours
36. Amino acids are joined together by a
condensation reaction
H
H2N
C
Carboxyl
group
O
Amino
group
H
+
C
OH
N
C
CH3
H2O
H2N C C
C
OH
H
H
O
H
H O
H H
O
N C C
H
CH3
OH
Peptide
bond
A peptide bond is a covalent C-N bond formed
by condensation between the -NH2 of one
amino acid and -COOH of another
37.
38. Many amino acids joined together =
Polypeptide chain
N-terminus
C-terminus
H H
H
O H H
O H
H
O H H
O H
N
C N
C
C
C
C
C
H
C
CH3
N
N C
CH2
CH2
OH
C OH
H
O H H
O H H
O
H H
O
N C
C N C
C N
C N C
C
CH2
CH
H3C
CH3
C
CH2
CH2
SH
O
OH
OH
39. Note R groups alternate in the
Polypeptide chain
Show the position of a peptide
bond
40. C-N atoms of the
peptide bonds:
lie in the same
plane to form the
backbone
Side chains of the individual
amino acids:
are arranged transversal
to each other across the
backbone – this confers
stability to the molecule
41. A protein molecule:
contains 100’s and 1000’s of amino acids joined
together by peptide links into one or more
chains
3 chains in collagen (in mouse tail)
44. Many different types of proteins
exist. How can this be?
MILLIONS of
Antibodies exist
A LARGE NUMBER
OF ENYZMES
45. Because any of 20 different amino
acids might appear at any position
• E.g. a protein containing 100 amino acids
could form any of 20100 different amino acid
sequences
• this is 10130, i.e. 1 followed by 130
zeros
46. Number and Sequence of amino acids
determine the protein
6 amino acids
5 amino acids
6 amino acids but in
a different
sequence
7 amino acids
48. Test for Protein: Biuret Test
Cheese is rich
in protein.
pestle
mortar
Add an equal amount of
NaOH to the solution
followed by 1-2 drops of
CuSO4 solution
49. When a protein reacts with copper(II) sulfate
(blue), the positive test is the formation of a
violet colored complex.
Purple / Lilac:
Positive test
50. Proteins have many functions:
hormones
enzymes
structural
proteins
What dictates the function of each protein?
The exact sequence of amino acids.
51. Where is the information stored in a cell
that determines the sequence of amino
acids?
52. Scrambled sequences of amino acids
are useless:
in some cases, just one wrong amino acid
can cause a protein to function incorrectly
What is the cause of
‘scrambled sequences
of amino acids’?
53. Is the amino acid sequence really important?
Let’s illustrate by an example: PKU
(phenylketonuria)
a genetic disorder
no enzyme is present to process
phenylalanine
phenylalanine
builds up – causes
mental retardation
54. A person with PKU must avoid foods that are
high in protein, such as milk, cheese, nuts or
meats
55. • Enzyme has about
452 amino acids
• One amino acid is
present instead of
another
57. Glycine is one of the 20 amino acids that
occur in proteins.
Proteins, in turn are useful organic
components of cells.
Proteins play various roles within a cell.
On the otherhand, glycine, is the simplest
amino acid, having hydrogen as the radical
and could have formed much more easily
than the other amino acids.
Complex machinery is required to convert
amino acids to functional proteins.
58. Structure of a Protein
• each protein has a characteristic three
dimensional shape called its conformation
• four levels of organisation exist:1) Primary structure
2) Secondary structure
3) Tertiary structure
4) Quaternary structure
60. Primary structure of a
protein:
the number and sequence of
amino acids held together
by peptide bonds in a
polypeptide chain
the primary structure of each
type of protein is
unique
62. Secondary structure:
• the way in which the polypeptide is arranged
in space
• secondary structure of many different
proteins may be the same
• bonds present:
1. Peptide
2. Hydrogen
63.
64. Hydrogen bonds between amino acids lead to the
secondary structure of a protein
Two common
secondary
structures are
the -helix and pleated sheet
66. helix
is in a right-handed coil, maintained by H-bonds
between:
CO of one amino acid and
NH group of the fifth amino acid
radical groups jut out in all directions
71. Side chains stick perpendicular to the plane of
the chains assuming a zig-zag pattern
-pleated sheet
72. Silk is an example of a pleated sheet
Silk Protein Structure
73. Elastin in elastic connective tissue consists of
many cross-linked polypeptides
74. It is common for a polypeptide to be partly:
an -helix
a - beta pleated sheet:
-helix
- beta pleated
sheet
75. Tertiary structure:
• is when the polypeptide
chain bends and folds
extensively to form a
precise compact
• is a complex, three-dimensional that
determines the final configuration of the
polypeptide
76. Tertiary structure is determined by
interactions of R-groups:
•
•
•
•
Disulfide bonds
Aggregation of hydrophobic side chains
Ionic bonds
Hydrogen bonds
77. Further folding of the polypeptide chain
contributes to the tertiary structure of a protein
Which amino
acid forms
disulfide bridges?
Cysteine
80. Myoglobin:
153 amino acids in a single polypeptide
chain
no disulfide bridges
molecule is unusual
as it consists almost
entirely of helices
Haem
81. Quaternary structure:
• the precise arrangement of the aggregation
of polypeptide chains held together by
hydrophobic interactions, H-bonds and ionic
bonds
• occurs in many highly complex proteins
• a huge variety of quaternary structures
82. Quaternary structure of various proteins
Antibodies comprise four
chains arranged in a Y-shape.
83. Quaternary structure of various proteins
Actin
- hundreds of globular chains
arranged in a long double helix
91. - haem is an iron-containing porphyrin, acting as
prosthetic group of several pigments
- prosthetic group is a non-protein group which
when firmly attached to a protein results in a
functional complex (a conjugated protein)
- porphyrin is a macromolecule
composed of four subunits
92. How is it possible for foetal
haemoglobin to obtain oxygen from
the maternal haemoglobin?
93. Foetal haemoglobin is structurally
different from that of an adult :
as it has gamma chains instead of beta
What does this difference in structure
result in?
94. Structural difference results in foetal haemoglobin
being able to obtain oxygen from the placenta as it has
a higher affinity for oxygen than the mother’s
haemoglobin
96. The final three-dimensional shape of a protein
can be classified as:
Fibrous
Tough
Insoluble in water
Globular
Soluble
Keratin
Silk
Collagen
Enzymes
Antibodies
97. A few proteins have both
structures e.g. the muscle protein :
myosin
long fibrous
tail
a globular
head
98. Proteins have tertiary and quaternary
structure.
The tertiary and quaternary structures of
proteins create a variety of molecules,
each able to carry out a particular
function.
99. Since proteins can twist and fold in
many ways, forming a variety of
active site shapes.
100. Two Types of Protein
SIMPLE :
only amino acids
e.g. albumins, histones
CONJUGATED :
globular proteins +
non-protein
material
(prosthetic group)
103. The loss of the specific three-dimensional
conformation (secondary structure) of a protein
A protein spontaneously refolds into its original
structure under suitable conditions
104. Why is denaturation of proteins
considered as harmful to an
organism?
The molecule unfolds and cannot
perform its normal biological
functions.
105. Denaturation agents can be:
i) Heat
ii) Strong acids & alkalis and high
concentrations of salts
iii) Heavy metals (e.g. mercury)
iv) Organic solvents and detergents
106. i) Heat
- weak hydrogen bonds and non
polar hydrophobic interactions
are disrupted
- Why?
107. Heat increases the
kinetic energy
Causes the molecules
to vibrate so rapidly
and violently that
bonds break
111. Breakage of peptide bonds may occur if the
protein remains in the reagent for a long time
112. iii) Heavy metals
cause the protein to precipitate out of the
solution
Cations (+) form strong bonds with carboxylate anions
(COOH-) and often disrupt ionic bonds
113. iv) Organic solvents & detergents
disrupt hydrophobic
interactions
form bonds with non-polar
groups
this in turn disrupts
intramolecular H-bonding
114. Why does the solution become purple when
beetroot discs are placed in detergent?
1. Proteins in cell membrane & tonoplast are
denatured.
2. Phospholipid bilayer is damaged.
115. Why is the skin wiped with alcohol before an
injection is given?
Alcohol is used as a disinfectant.
It denatures the protein of any
bacteria present on the skin.
116. What change has a protein undergone if it has been
denatured
When a protein is denatured it loses its three
dimensional shape in space. Its tertiary
structure is destroyed and cannot fold
properly. Hydrogen bonds, ionic bonds and
hydrophobic interactions that are useful to
determine the final shape of the molecule are
destroyed.
117. List TWO agents that may cause denaturation of a
protein. (2)
Extreme changes in pH
Heat
Heavy metals
Organic solvents
Detergents
123. Buffering capacity of amino acids
Zwitterion: a compound with both acidic and basic
groups
Isoelectric point is that pH at which a zwitterion
carries no net electrostatic charge
