1.4 PROTEINS
Learning outcomes:
a) Describe the basic structure of amino acids.
b) State how amino acids are grouped.
c) Describe the primary, secondary, tertiary and
quaternary levels of proteins and the types of
bonds involved.
d) Describe the effects of pH and temperature on
the structure of proteins.
e) Explain the formation and breakdown of
dipeptide.
f) Classify proteins according to structure and
compositions.
❖ Biological macromolecules built from
polymers of amino acids
PROTEIN
❖ Main chemical constituents are carbon
(C), hydrogen (H), oxygen (O) and
nitrogen (N).
❖ Some also have sulphur (S) and
phosphorus (P).
The side chain / residual group
R
✓varies in different amino acids.
✓determines the amino acid
characteristics & proteins
properties.
AMINO ACID
H2 N
Amino group (NH2)
C
H
COOH
Carboxyl group
AMINO ACID
• Amino acids are amphoteric -consist both acidic
carboxyl group & basic amino group
• At cellular pH ( ~ 7.4 ) amino acids exist as
bipolar ionic molecule
i.e have positive and negative charge on same
molecule ; known as zwitterions
GROUPS OF AMINO ACID
i. Non-polar side chain (hydrophobic)
ii. Polar side chain (hydrophilic)
iii. Acidic side chain (hydrophilic)
iv. Basic side chain (hydrophilic)
• Non-polar side chains
✓
✓
✓
usually the hydrocarbon.
insoluble and unreactive (hydrophobic characteristics)
usually forms structural proteins (such as collagen)
• Polar side chains
 have electronegative atoms (such as oxygen and nitrogen) in
their R groups
 produce partial charges (hydrophilic characteristics)
(but do not receive or donate electrons)
 increases the solubility of proteins
 enables hydrogen bonding between polypeptide chains
• Electrically charged side chains
 Acidic amino acids have second carboxyl group on the
side chain (negatively charged)
 Basic amino acids have second amino group on the
side chain (positively charged)
•
Amino acids are
✓ joined together by
peptide bonds
✓ bonded together to form
polypeptide chain
•
A protein is a
biologically
functional molecule
made up of one or
more polypeptides,
each folded and
coiled into a specific
3D structure
LEVELS OF PROTEIN
1. Primary Structure
•Specific linear sequence of amino acids in
a polypeptide chain ; linked by peptide bond
2. Secondary Structure
• Coiling/ folding of polypeptide chains due to
formation of hydrogen bonds between the
repeating constituents of the polypeptide
backbone
 – helix
TYPES
 – pleated sheet
 – helix
• coiled polypeptide chain held together
by hydrogen bond
e.g. keratin found in hairs, nails, horn
and feathers
 – pleated sheet
• two or more segments of a polypeptide
chain lie parallel to each other
• hydrogen bonds hold the structure
together
e.g. silk protein
3. Tertiary Structure
•Coiling / folding of the secondary structure
to form a globular shape (3D shape)
• resulting by interactions between R groups
(side chains) of amino acids
i) Hydrophobic & van der Waals interactions
ii) Hydrogen bonds
iii) Ionic bonds
iv) Disulfide bridge
i) Hydrophobic and van der Waals interactions
• involving non polar side chains
ii) Hydrogen bonds
• between polar side chains
iii) Ionic bonds
• between positive and negative
charged side chains
iv)Disulfide bridge
• between two cysteine amino acids ;
amino acids with sulfhydryl groups ( -SH )
• Sulfur of one cysteine bonds to sulfur
of other cysteine forming disulfide bridge
e.g. myoglobin
One polypeptide chain containing ironbearing heme group
Function: oxygen
storing pigment
in muscle
4. Quaternary Structure
•Combination of two or more polypeptide
chains into one functional macromolecule
e.g. Collagen, Haemoglobin
Review: the four levels of protein structure
EFFECT OF PH AND TEMPERATURE
ON PROTEIN STRUCTURE
 Temperature ( extreme)
• cause the breakage of :
- hydrogen and ionic bonds
- disulphide bridges
- hydrophobic and van der Waals interactions
• change in conformation of protein (denatured)
 pH ( extremely acidic or basic )
• cause the breakage of ionic bonds
• change in conformation of protein (denatured)
❖ Most of denaturation are
irreversible. Why?
✓ Denatured protein
loses its threedimensional structure
& functions.
e.g.
Albumin turns into
insoluble egg white
when proteins are
denatured by high
temperature.
❖ If the denatured protein remains dissolved, it may
renature when the chemical and physical
aspects of the environment are restored to normal
How denaturation occurs at levels of protein
structure
Primary structure
• not disrupted by denaturation.
• Remain as sequence of amino acids held together by
covalent peptide bonds
Secondary structure
• proteins lose all regular patterns (alpha-helixes & betapleated sheets) because of the disruption of hydrogen
bonds.
Tertiary structure
Disruption of:
◦ Covalent bonds such as disulfide bridges
◦ Hydrogen bonds
◦ van der Waals & hydrophobic interactions
◦ Ionic bonds
Quaternary structure
•Dissociation of protein sub-units.
•Disruption of the arrangement of the subunits.
FORMATION AND BREAKDOWN OF DIPEPTIDE
• Two amino acids are positioned so that the carboxyl
group of one is adjacent to the amino group of the
other
• They are joined by condensation reaction, with the
removal of a water molecule forming a dipeptide
• The resulting covalent bond is called a peptide bond
• Breakdown of the peptide bond can be done by
hydrolysis reaction
FORMATION AND BREAKDOWN OF DIPEPTIDE
Condensation
Amino
end
Hydrolysis
Carboxyl
end
POLYPEPTIDE
•Polypeptide is a polymer of
many amino acids linked by
peptide bonds
•Repeated sequence of
(-N-C-C-N-C-C-) is the
polypeptide backbone
•Polypeptide has a free amino
group (amino end) at one end
and a free carboxyl group
(carboxyl end) at the other end
CLASSIFICATION OF PROTEIN
BASED ON STRUCTURE AND COMPOSITION
• conjugated
• fibrous
• globular
1. Fibrous protein
• Most have secondary structure
•
Long, coiled strand/ threads
• Static molecule
• Insoluble in water
• For support/ structure
e.g. Keratin, collagen
2. Globular protein
• Most have tertiary and some quaternary structure
• Compact/ spherical form
• Dynamic/ non-static molecule
• Generally water soluble
• Biological agent/ catalyst/ metabolic function
e.g. immunoglobulin ( antibody ),
enzyme, hemoglobin, peptide hormone
3. Conjugated protein
• Consist of amino acids & non-protein materials/
prosthetic group
Conjugated Protein
Prosthetic Group
Location
myoglobin
haem (with iron)
muscle
haemoglobin
haem (with iron)
erythrocyte
nucleoprotein
nucleic acid
chromosomes
cytochrome
oxidase
copper
electron carrier
1.5 DNA and RNA
molecules
Learning outcomes:
a) State the structures of nucleotide as the basic
composition of nucleic acids
b) Illustrate the structure of DNA based on the
Watson and Crick Model
c) State the types of RNA
d) Compare DNA and RNA
NUCLEIC ACID
▪ Nucleic acids are macromolecules that exist as
polymers called polynucleotides
▪ Nucleic acids are composed of hydrogen, oxygen,
carbon, phosphorus and nitrogen.
▪ Two types of nucleic acids: DNA and RNA
TYPES OF NUCLEIC ACIDS
DNA
Deoxyribonucleic acid
RNA
Ribonucleic acid
NUCLEOTIDES
▪ Each polynucleotide made up of basic units called
nucleotides
✓ Individual
nucleotide
comprises of 3
parts :
o Phosphate
group
o Pentose sugar
o Organic base /
Nitrogenous
base
NUCLEOTIDE
A nucleotide
Phosphate group
• Derived from phosphoric acid
• Give acidic property to nucleic acids
Pentose sugar
A nucleotide
Nitrogenous base
A nucleotide
NUCLEOTIDE
Phosphoester linkage
Glycosidic linkage
❖
Phosphoester linkage links pentose sugar and
phosphate group (sugar-phosphate backbone).
❖
The bond between nitrogenous base and pentose
sugar is glycosidic linkage.
DINUCLEOTIDE
•
Combination of two nucleotides through
condensation.
Phosphoester
linkage
POLYNUCLEOTIDE
• Continued condensation forms polynucleotide.
• Phosphate group
3rd
is linked to the
carbon of one
pentose sugar &
to the 5th carbon
of the next
pentose sugar
• Nitrogenous base is
linked to the 1st carbon
of the pentose
DNA
•
Consists of two
polynucleotide strands
(coiled together to form
double helix)
•
Contains 4 bases:
i. Adenine (A)
ii. Guanine (G)
iii. Cytosine(C)
iv. Thymine (T)
✓ A always pair with T
✓ C always pair with G
✓ The amount between
A&T and C&G is equal
•
2 strands run in
opposite directions
i.e anti-parallel:
5’ → 3’
and
3’ → 5’
• Both strands are held together
by hydrogen bond between
complementary base pairs
• A&T
( linked by 2 hydrogen bonds )
• C&G
( linked by 3 hydrogen bonds )
• Each full turn of the helix has 10 base pairs
•
Sugar & phosphate molecules are linked by
phosphodiester bond to form sugar-phosphate
backbones
One complete turn :
(3.4 nm long)
contains 10 bases pairs
Sugar-phosphate
backbone
RNA
• Single stranded polymer of
nucleotide.
• Pentose sugar : ribose
• Organic bases : Guanine,
Cytosine, Adenine and
Uracil (replacing thymine)
• 3 types of RNA :
i. Ribosomal RNA (rRNA)
ii. Transfer RNA (tRNA)
iii. Messenger RNA (mRNA)
COMPARISON BETWEEN DNA AND RNA
The similarities between DNA and RNA
1. Both are made of monomers called nucleotides
2. Both contain pentose sugars
3. Both have the three nitrogenous bases:
Adenine, Cytosine & Guanine
4. Both have phosphate groups in their nucleotides
5. Both are necessary for the cell to synthesise
proteins.
The differences between DNA and RNA
DNA
• Consists of two
polynucleotide strands
• Forms double helix
• Larger molecular mass
• Deoxyribose as pentose
sugar
• Nitrogenous bases:
A,T,C,G
RNA
• Consists of one
polynucleotide strands
• No double helix is formed
• Smaller molecular mass
• Ribose as pentose sugar
•
Nitrogenous bases:
A,U,C,G
The differences between DNA and RNA
•
•
•
•
•
DNA
Manufactured in nucleus
Chemically very stable
Permanent
Only one basic form
Ratio of A and T to C and
G is one
•
•
•
•
•
RNA
Manufactured in nucleus
but found throughout the
cell
Chemically unstable
Temporary existing
3 basic forms
Ratio of A and U to C and
G varies