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Proteins
Proteins / Polypeptides
The functional molecules of life
What are proteins?
Proteins are amino acid polymers folded
into specific three dimensional shapes.
A protein structure determines its
function.
Are proteins of different types?
Enzymes → biological catalysts
Immunoglobulins → protect against foreign
microbes & cancer cells
Proteins
Haemoglobin → oxygen carrier
Keratin → formation of hair & nails
Fibrin → essential for blood clotting
Collagen → formation of bones, ligaments
tendons
What are the building units of proteins?
These are called the amino acids.
What is a residue?
When two or more amino acids combine to
form a peptide, the elements of water are
removed, and what remains of each amino
acid is called a residue.
The general structural formula of amino
acids:
What are the two functional groups
that amino acids posses?
Amino acids posses both, the acidic
(carboxyl) and the basic (amino)
functional groups.
Amino acids
When dissolved in water the carboxyl
group donates an H+ ion to the amino
group, so both groups are ionized.
Acidic and basic amino acids
Acidic amino acids posses a carboxyl group on their
side chain (R), while basic amino acids have an
amino group on the side chain (R).
Polar (hydrophilic)
amino acids may be
Nonpolar (hydrophobic)
Charged (acidic or basic)
How many are the amino acids?
There are 20 important amino acids
used in protein synthesis, 8 of which
are “essential amino acids”, meaning
that the body can’t synthesize.
What is a proline kink?
Proline is the only amino acid whose
side chain (R) forms a covalent bond
with its amino group, and this results
in what's called the proline kink.
How do amino acids bond together and what is
the name of the bond (linkage)?
What determines the final shape
(conformation) of the protein
polymer?
The final conformation of the
protein is determined by the
sequence of the amino acids it
contains.
What is an amino terminus (Aterminus)?
An amino terminus is the free amino group at
one end of the polypeptide.
What is a carboxyl terminus (Cterminus)
A carboxyl terminus is the free carboxyl
group at one end of the polypeptide.
Globular Proteins
Are composed of one or more polypeptide
chains that take on a rounded or spherical
shape.
Many enzymes and other functional proteins
are globular.
collagen
e.g.:
keratin
haemoglobin
Globular proteins may be described
in terms of four levels of
structure:
1) The primary structure of protein
2) The secondary structure of protein
3) The tertiary structure of protein
4) The quaternary structure of protein
What is the primary structure of
protein?
Is the sequence of amino acids in
the polypeptide chain.
STRUCTURE
• Primary (1º)
– Description: The linear sequence of amino acids
(AAs) as determined by the genetic code (DNA).
– Bonding:
Covalent peptide bonds between AAs.
H2O
H2O
H2O
H2O
What is the secondary structure of protein?
In certain regions, a hydrogen bond forms between the
electronegative oxygen of the carboxyl group of one peptide
bond and the electropositive hydrogen of an amino group,
that is four bonds away.
1) αhelix: A type of polypeptide secondary structure
characterized by a tight coil that is stabilized by hydrogen
bonds.
α helix
2) β-pleated sheet: polypeptide secondary
structure that form between parallel stretches of a
polypeptide, and are (the stretches) stabilized by
hydrogen bonds.
STRUCTURE
• Secondary (2º)
– Description: The twisting and folding of the linear
primary (1º) structure.
– Bonding:
Hydrogen bonds between charged AAs.
– Forms:
triple helix
(e.g. keratin)
(e.g. fibrin)
(e.g. collagen)
What is the tertiary structure of protein?
Is the complex folding (super coiling) of the
polypeptide that is stabilized by side chain
interactions (R-group - R-group interactions)
that include all of the following:
1.
2.
3.
4.
5.
Ionic bonds between oppositely charged side
chains
Hydrogen bonds between certain polar side
chains
Van Der Waals forces between non-polar groups
Proline kinks
Disulfide bridges: when the sulfur containing Rgroups of two cysteine residues are close they
form a disulfide bridge (-S-S-) these are strong
stabilizers of the tertiary structure
Disulfide bridges:
What is the quaternary structure of
protein?
Is the clustering (aggregation) of two or
more polypeptides of the tertiary
structure.
→
→
→
What is protein denaturation?
Protein denaturation is the change in the
three-dimensional shape of a protein.
Denaturation could be due to changes in:
1.
Temperature (heat denatures the protein in
hair allowing to straighten curly hair,
barbecuing meat & boiling an egg)
2. pH (gastrin works best at pH 2 and is
denatured in the small intestine at pH 10)
3. Ionic concentration
4. Exposing the protein to liquids (water, alcohol)
What are chaperone proteins?
Chaperone proteins are special proteins
that aid a growing polypeptide to fold
into the tertiary structure.
Nucleic Acids
The two nucleic acids DNA and RNA are
essential for all living things.
DNA consists of sugar, phosphate groups
linked together through sugar phosphate
Bonds, and four nitrogenous bases: adenine
(A), guanine (G), cytosine (C), and
thymine (T) [in case of RNA uracil (U) is
used instead of thymine (T) and the sugar
is also different, ribose instead of
deoxyribose].
DNA



All living things have chromosomes
inside the nuclei of their cells, the
Chromosomes are made of DNA.
The number and sequence of amino acids in
a protein chain, determines the unique
characteristics of that particular protein.
The sequence of the nucleotides (or in
other words the nucleotides’ bases) of a
gene, is the determining factor that codes
for the corresponding sequence of amino
acids of that particular protein, this one
gene is called one protein hypothesis.
DNA Structure
What is a nucleotide?
A nucleotide
includes a
sugar
molecule,
a phosphate
group, and a
nitrogenous
base bonded
together.
The Nitrogenous Bases
Adenine
Cytosine
Guanine
Thymine
Uracil
Purines
(Double rings)
Pyrimidines
(Single rings)
The Nitrogenous Bases


Are adenine (A), guanine (G), cytosine (C),
and thiamine (T) [in case of RNA uracil (U)
is used instead of thiamine (T)].
The nitrogenous bases of the adjacent
nucleotides are paired as follows:
A-T or T-A
G-C or C-G
Since there are 4 bases and each codon
that codes for an amino acid is made of 3
Bases, then there is a probability
of 64
3
Codes of base triplets (4 =64),which are
more than enough to code for the 20
available amino acids.