PROTEINS
Lali Shanshiashvili
• Structure and Function;
• Amino Acids ;
• Primary Structures of Proteins;
• Three-Dimensional Structure in Function;
• Globular Proteins;
• Fibrous proteins;
The relationship between structure
and function is a fundamental part of
biochemistry.
This is especially important when
studying proteins!
Protein functions:
1. Many proteins function as enzymes, the
biochemical catalysts. Enzymes catalyze nearly all
reactions that occur in living organisms.
Protein functions:
• 2. Some proteins bind other molecules for storage
and transport.
• For example, hemoglobin binds and transports O2
and CO2 in red blood cells; other proteins bind
fatty acids and lipids.
Protein functions:
3. Several types of proteins serve as pores and
channels in membranes, allowing for
the passage of small, charged molecules.
Protein functions:
4. Some proteins, such as tubulin, actin, and
collagen, provide support and shape to cells and
hence to tissues and organisms.
5. Assemblies of proteins can do mechanical work,
such as the movement of flagella, the separation
of chromosomes at mitosis, and the contraction of
muscles.
6. Many proteins play a role in information flow in
the cell. Some are involved in translation whereas
others play a role in regulating gene expression by
binding to nucleic acids.
7. Some proteins are hormones, which regulate
biochemical activities in target cells or tissues; other
proteins serve as receptors for hormones.
8. Proteins on the cell surface can act as receptors
for various ligands and as modifiers of cell-cell
interactions.
9. Some proteins have highly specialized functions.
For example, antibodies defend vertebrates against
bacterial and viral infections, and toxins, produced by
bacteria, can kill larger organisms.
General structure of amino acids
The 20 amino acids are called the common,or
standard, amino acids. Despite the limited number
of amino acids, an enormous variety of different
polypeptides can be produced by connecting the
20 common amino acids in various combinations.
• In the 20 common amino acids the amino group
and the carboxyl group are bonded to the same
carbon atom: the α-carbon atom. Thus, all of the
standard amino acids found in proteins are α -
amino acids. Two other substituents are bound to
the α -carbon— a hydrogen atom and a side chain
(R) that is distinctive for each amino acid.
In the physiological pH range of 6.8 to 7.4, amino
acids are zwitterions, or dipolar ions, even though
their net charge may be zero.
• The mirror-image pairs of amino acids are
designated D (for dextro, from the Latin dexter,
“right”) and L (for levo, from the Latin laevus,
“left”).
Amino acids with nonpolar side chains
• Glycine (Gly, G) is the smallest amino acid. Since its R group is
simply a hydrogen atom, the a-carbon of glycine is not chiral. The
two hydrogen atoms of the a-carbon of glycine impart little
a
hydrophobic character to the molecule.
• Glycine plays a unique role in the structure of many proteins
because its side chain is small enough to fit into niches that cannot
accommoda-te any other amino acid.
• Proline (Pro, P) differs from the other 19 amino acids because its
three-carbon side chain is bonded to the nitrogen of its a-amino
group as well as to the a-carbon creating a cyclic molecule.
• The cyclic structure of proline makes it much less hydrophobic than
valine, leucine, and isoleucine.
• Alanine, valine, leucine, and isoleucine play an important
role in establishing and maintaining the three-
dimensional structures of proteins because of their
tendency to cluster away from water.
Amino acids with uncharged polar side chains
Cancer
Tylosin
Rinise
rises
Serine (Ser, S) and threonine (Thr, T) have uncharged polar side chains
containing b-hydroxyl groups. These alcohol groups give a hydrophilic
character to the aliphatic side chains. The hydroxyl groups of serine
and threonine have the weak ionization properties of
primary and secondary alcohols.
targets for PhaspPolartian
Amino acids with acidic side chains
Aspartate (Asp, D) and glutamate (Glu, E) are dicarboxylic amino acids
and have negatively charged hydrophilic side chains at pH 7.
In addition to α-carboxyl groups, aspartate possesses a b-carboxyl
group and Glutamate possesses a g-carboxyl group.
Aspartate and glutamate confer negative charges on proteins because
their side chains are ionized at pH 7.
Aspartate and glutamate are sometimes called aspartic acid and
Glutamic acid.
Asparagine (Asn, N) and glutamine (Gln, Q) are the amides
of aspartic acid and glutamic acid, respectively.
I
Amino acids with basic side chains
Histidine (His, H), lysine (Lys, K), and arginine (Arg, R) have hydrophilic
side chains that are nitrogenous bases. The side chains can be
positively charged at physiological pH.
has no tRNA
not insert triplets no
post fucional
Translation during
More than 200 different amino acids are found in
living organisms. 2ms that if activate
will
Demination causes disess
Arginine citruline
citrulini No
Asinal urea ornithine
Peptide bonds link amino acids in proteins
• The linear sequence of amino acids in a
polypeptide chain is called the primary structure.
• Higher levels of structure are referred to as
secondary, tertiary, and quarter.
The linkage formed between amino acids is an amide bond called a
peptide bond.
This linkage can be thought of as the product of a simple
condensation reaction between the a-carboxyl group of one amino
acid and the a-amino group of another.
• A water molecule is lost from the condensing amino acids in the
reaction.
Linked amino acids in a polypeptide chain are called amino acid
residues. The names of residues are formed by replacing the ending –
ine or -ate with -yl.
A glycine residue in a polypeptide is called glycyl and a glutamate
residue is called glutamyl. In the cases of asparagine, glutamine, and
cysteine, -yl replaces the final -e to form asparaginyl, glutaminyl,
and cysteinyl, respectively.
The free amino group and free carboxyl group at the opposite ends of
a peptide chain are called the N-terminus (amino terminus) and the
C-terminus (carboxyl terminus), respectively.
At neutral pH each terminus carries an ionic charge. Amino acid
residues in a peptide chain are numbered from the N-terminus to the
C-terminus .
In a similar manner, we can write the
second dissociation reaction as
and the dissociation constant K2 as
• Typical values for pK 2 are in the range of 9.0 to 9.8. At
physiological pH, the a-carboxyl group of a simple amino acid (with
no ionizable side chains) is completely dissociated, whereas the a-
amino group has not really begun its dissociation.
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Amphoteric – capable of donang and accepng protons, thus able to serve as an acid or
base
Modicaon of an amino acid dependent on pH
Glycine Titraon Prole
Two stages in traon corresponding to deprotonaon of the two tratable groups
Two disnct buering zones
Buer – a system capable of resisng changes in pH, consisng of conjugate acid-base pair in
which the rao of proton acceptor to proton donor is near unity
All amino acids have at least two pKa’s
pK1 – deprotonaon of carboxyl (1.8 to 2.4)
pK2 – deprotonaon of amino (9.0 to 11.0)
Isoelectric point (pl) - the pH at which a solute has no electric charge, and thus does not move in an
electric eld
For an amino acid with only two tratable groups it’s equal to the average of the pKa values
Amino Acids with Ionizable R-Groups
The titration curve
o o
a o
• Titration of glycine, a simple amino acid. The isoelectric point,
pI, the pH where glycine has a net charge of 0, can be
calculated as (pK1 + pK2)/2.
Titrations of glutamic acid
0 0 a
Titrations of lysine.
If you use a pdf file - pp.17-27
If you use a printed book – pp.1-6
