The formation of a peptide bond between glycine and alanine is
shown in Figure 5.8. The product is called dipeptide, the reaction
can be eliminated a water molecule. Amino Acid and Protein3
EGAK
Slide 4
4
Slide 5
The portion of each amino acids remaining in the chain is
called an amino acid residue Chains containing a few amino acid
residues are collectively referred to as oligopeptides. If the
chain is very long, it is called a polypeptide. Oligopeptides and
polypeptides are formed by polymerization of amino acids via
peptide bonds In writing the sequence of an oligopeptide or
polypeptide that the convention is to always write the N-terminal
amino acid (the residue has a free -amino group) to the left, and
the C-terminal to the right. (the residue has a free -carboxyl
group) Amino Acid and Protein5
Slide 6
Large peptide chain. Protein polypeptide chain are typically
more than 100 amino acid residue. All proteins are polypeptides.
This is why understanding the nature of polypeptides and the
peptide bond is so important a part of biochemistry. Small peptide
chains are common and often have important biologic roles. For
example the hormone glucagon has 29 residues, vasopressin has 9
residue and thyrotropin- releasing hormone has 3 residue Amino Acid
and Protein6
Slide 7
CONFORMATION OF PROTEINS Every protein in its native state has
a unique three- dimentional structure, which referred to as its
conformation. The function of a protein arises from its
conformation. Protein structures can be classified into four levels
of organization : primary, secondary, tertiary, and quartenary.
Amino Acid and Protein7
Slide 8
8
Slide 9
The primary structure is the covalent backbone of the
polypeptide formed by the specific sequence. This sequence is coded
for by DNA and determines the final three dimensional from adopted
by the protein in its native state Amino Acid and Protein9
Slide 10
The secondary structure is the spatial relationships of
neighboring amino acid residue. 1. Secondary structure is dictated
by primary structure. The secondary structure arises from
interactions of neighboring amino acids. Because DNA coded primary
sequence dictated which amino acids are near each other, secondary
structure often form as the peptide chain comes off the ribosome.
Amino Acid and Protein10
Slide 11
2. Hydrogen bonds, these formation very important
characteristic of secondary structure, (H-bond) between the CO-
group of one peptide bond and the NH group of another nearby
peptide bond. (a). If the H-bonds form between peptide bonds in the
same chain, either helical structure such as the -helix develop or
turn such as -turns are formed. (b). If the H-bonds form between
peptide bonds in different chains, extended structures form, such
as the -pleated sheet. Amino Acid and Protein11
Slide 12
3. The -helix is rod like structure with the peptide bond
coiled tightly inside and the side chain of the residue protruding
outward. (a). Characteristics (1.) Each CO is hydrogen-bonded to
the NH of a peptide bond that is four residues away from it along
the same chain 2.) There are 3.6 amino acid residue per turn of the
helix, and the helix is right-handed (turn in a clockwise around
the axis) (b). Helical structures in proteins were predicted by
Linus Pauling from his studies of fibrous proteins. However, the
-helix can also be important in the structure globular proteins,
although those chains are much shorter than the chains in fibrous
proteins Amino Acid and Protein12
Slide 13
Amino Acid and Protein13 -Helix -Sheet
Slide 14
Tertiary structure refers to the spatial relationships of more
distant residues 1. Folding. The secondary ordered polypeptide
chains of soluble proteins tend to fold into globular structure
with the hydrophobic side chain in the interior of the structure
away from the water and the hydrophilic side chains on the outside
in contact with water. This folding is due to associations between
segments -helix, extended -chains, or other secondary structures
and represent a state of lowest energy (greatest stability) Amino
Acid and Protein14
Slide 15
2. The conformation result from: a.Hydrogen bonding within a
chain or between chains b.The flexibility of the chain at points of
instability, allowing water to obtain maximum entropy and thus
govern the structure to some extent c.The formation of other non
covalent bonds between side chain groups, such as salt linkages, or
- electron interaction of aromatic rings d.The sites and numbers of
disulfide bridges between Cys residues within the chain Amino Acid
and Protein15
Slide 16
Amino Acid and Protein16
Slide 17
Quartenary structure refers to the spatial relationships
between individual polypeptide chains in a multi chain protein;
that is, the characteristic noncovalent interaction between the
chains that form the native conformation of the protein as well as
occasional disulfide bonds between the chains 1. Many proteins
larger than 50 kdal have more than one chain and are said to
contain multiple subunits, with individual chains known as
protomers. 2. Many multisubunit proteins are composed of different
kinds of functional subunits. Amino Acid and Protein17
Slide 18
Denaturation Denaturation is the organization of the overall
molecular shape of a protein. It can occur as an unfolding of
uncoiling of helices, or as separation of subunits. Denaturation is
usually is accompanied by a major loss in solubility. Several
reagents or physical force like heat, UV radiation, shaking,
ethanol, heavy metals, and strong acids and bases that cause
denaturation. Amino Acid and Protein18
Slide 19
Amino Acid and Protein19 denaturation renaturation
Slide 20
The gene-encoded primary structure of polypeptide is the
sequence of its amino acids. Primary structure are stabilized by
covalent peptide bonds. Its secondary structure results from
folding of polypeptide into hydrogen- bonded motifs can form
supersecondary motifs. Secondary structure (higher orders) are
stabilized by weak force-multiple hydrogen bond, electrostatic bond
(salt bond), and association of hydrophobic R groups. Tertiary
structure concern the relationships between secondary structure
domains. Quartenary structure of proteins with two or more
polypeptides (oligometric proteins) is a feature based on the
spatial relationships between various types of polypeptide Amino
Acid and Protein20