Proteins

Contents
• Protein synthesis

• Protein Degradation

• Protein secretion
 Protein Synthesis

Transcription in nucleus

Translation in cytoplasm
Gene:
• A sequence of DNA nucleotides containing the information that specifies the amino acid
sequence of a single polypeptide chain is known as a gene .
• A gene is thus a unit of hereditary information

Genetic information:
• Genetic information is coded in the nucleotide sequences of DNA molecules.
• Genetic information is transferred from DNA to mRNA in the nucleus (transcription); then
mRNA passes to the cytoplasm, where its information is used to synthesize protein
(translation).

Genome:
• The total genetic information coded in the DNA of a typical cell in an organism is known as
its genome .
• The human genome contains roughly 20,000 genes.
Transcription The class of RNA molecules that specifies the
amino acid sequence of a protein and carries
this message from DNA to the site of protein
synthesis in the cytoplasm is known as mRNA
mRNA synthesis by
RNA polymerase

The subunits used to synthesize mRNA are

free (uncombined) ribonucleotide
triphosphates: ATP, GTP, CTP, and UTP.

Free ribonucleotides containing U bases pair

with the exposed A bases in DNA; likewise,
free ribonucleotides containing G, C, or A
bases pair with the exposed DNA bases C, G,
and T, respectively
mRNA • The four bases in the DNA
can be arranged in 64
Information Codons are different three-letter
triplets of combinations to form 64
in the form triplets which codes for 20
of codons nucleotides
amino acids
on mRNA • More than one triplets can
code for one amino acids
• 61 out of 64 codons are
Relationship between codons and used to specify amino acids
amino acids is called Genetic code • The other 3 are called STOP
SIGNALS or STOP CODON
 PROMOTER
• RNA polymerase binds to DNA only at
specific sites of a gene, adjacent to a
sequence called the promoter .
• The promoter directs RNA polymerase to
proceed along a strand in only one direction
that is determined by the orientation of the
phosphate–sugar backbone

TEMPLATE STRAND
• One strand, called the template strand or
antisense strand, has the correct orientation
relative to the location of the promoter to
bind RNA polymerase.
• The location of the promoter, therefore,
determines which strand will be the template
strand
• The base sequence in the RNA transcript is not identical to that in the template strand of DNA,
because the formation of RNA depends on the pairing between complementary, not identical,
bases.
• A three-base sequence in RNA that specifies one amino acid is called a codon .
• Each codon is complementary to a three-base sequence in DNA. For example, the base
sequence T—A—C in the template strand of DNA corresponds to the codon A—U—G in
transcribed RNA

SPLICING
• The entire sequence of nucleotides in the template strand of a gene is transcribed into a
complementary sequence of nucleotides known as the primary RNA transcript or pre-mRNA
• Only certain segments of most genes actually code for sequences of amino acids. These regions
of the gene are known as exons (expression regions)
• Noncoding sequences of nucleotides are known as introns
• The separation of exons from introns by spliceosome (small nuclear RNAs) is known as splicing.
• After splicing RNA becomes mature mRNA, which then goes into cytoplasm for translation
Translation
Synthesis of polypeptide
by information contained
in mRNA
Ribosomes and rRNA
• A ribosome is a complex particle
composed of about 70 to 80 different
proteins in association with a class of
RNA molecules known as ribosomal
RNA ( rRNA ).
• rRNA transcription occurs in
nucleolus
 tRNA
• tRNA helps decode a mRNA sequence into a protein.
• tRNAs bring specific amino acids to ribosomes for protein formation
• tRNA contain anticodon complementary to the codon of mRNA

• A tRNA molecule is covalently

linked to a specific amino acid by
an enzyme known as aminoacyl-
tRNA synthetase.
• There are 20 different aminoacyl-
tRNA synthetases, each of which
catalyzes the linkage of a specific
amino acid to a specific type of
tRNA.
Protein Assembly
Initiation

Elongation

Termination
1. Initiation
• The initiation of synthesis occurs when a tRNA containing the amino acid
methionine binds to the small ribosomal subunit.
• A number of proteins known as initiation factors are required to establish
an initiation complex, which positions the methionine-containing tRNA
opposite the mRNA codon that signals the start site at which assembly is
to begin.
• The large ribosomal subunit then binds, enclosing the mRNA between the
two subunits.
2. Elongation
• The protein chain is elongated by the successive addition of amino acids
• A ribosome has two binding sites for tRNA.
• Site 1 holds the tRNA linked to the portion of the protein chain that has been
assembled up to this point
• Site 2 holds the tRNA containing the next amino acid to be added to the chain.
• Following the formation of the peptide bond, the tRNA at site 1 is released
from the ribosome, and the tRNA at site 2—now linked to the peptide chain—
is transferred to site 1.
• The ribosome moves down one codon along the mRNA, making room for the
binding of the next amino acid–tRNA molecule.
• This process is repeated over and over as amino acids are addedto the
growing peptide chain, at an average rate of two to three per second.
3. Termination
• When the ribosome reaches a termination sequence in mRNA (called a
stop codon) specifying the end of the protein, the link between the
polypeptide chain and the last tRNA is broken, and the completed protein
is released from the ribosome.
• Messenger RNA molecules are not destroyed
during protein synthesis, so they may be used to
synthesize many more protein molecules.
• While one ribosome is moving along a particular
strand of mRNA, a second ribosome may become
attached to the start site on that same mRNA and
begin the synthesis of a second identical protein
molecule.
• Therefore, a number of ribosomes—as many as
70—may be moving along a single strand of
mRNA, each at a different stage of the translation
process
• Once a polypeptide chain has been assembled, it may
undergo posttranslational modifications to its amino acid
sequence.
• For example, the amino acid methionine that is used to
identify the start site of the assembly process is cleaved
from the end of most proteins.
• In some cases, other specific peptide bonds within the
polypeptide chain are broken, producing a number of
• smaller peptides, each of which may perform a different
function.
• Carbohydrates and lipid derivatives are often covalently
linked to particular amino acid side chains. These additions
may protect the protein from rapid degradation by
proteolytic enzymes or act as signals to direct the protein to
those locations in the cell where it is to function.
• The addition of a fatty acid to a protein, for example, can
lead the protein to anchor to a membrane as the nonpolar
portion of the fatty acid inserts into the lipid bilayer.
 Protein Degradation
• Different proteins degrade at different rates depending upon;
➢Structure of proteins
➢Affinity for proteolytic enzymes

• A denatured protein is more readily digested than a protein with intact

conformation
• Proteins can be targeted for degradation by the attachment of a small
peptide, ubiquitin , to the protein. This peptide directs the protein to a
protein complex known as a proteasome , which unfolds the protein and
breaks it down into small peptides
Protein Secretion
• Most protein synthesized remain inside the cell,
however some are secreted in extracellular fluid
• Proteins are large, charged molecules that cannot
diffuse through plasma membranes. Therefore,
special mechanisms are required to insert them
into or move them through membranes.
• Proteins destined to be secreted from a cell or to
become integral membrane proteins are
recognized during the early stages of protein
synthesis. For such proteins, the first 15 to 30
amino acids that emerge from the surface of the
ribosome act as a recognition signal, known as the
signal sequence or signal peptide.
Interactions Between Proteins and Ligands
Ligand
• A ligand is any molecule (including another protein) or ion that is bound to a protein by one of
the following physical forces:
(1) electrical attractions between oppositely charged ionic or polarized groups on the ligand and
the protein, or
(2) weaker attractions due to hydrophobic forces between nonpolar regions on the two molecules.
• These types of binding do not involve covalent bonds; in other words, binding is generally
reversible
Binding site
• The region of a protein to which a ligand binds is known as a binding site or a ligand-binding site
.
• A protein may contain several binding sites, each specific for a particular ligand, or it may have
multiple binding sites for the same
Binding site characteristics
1.
Chemical specificity

2. Affinity

3. Saturation

4. Competition
Chemical specificity
The ability of a protein-binding site to bind
specific ligands is known as chemical specificity

The binding between a ligand and a protein may

be so specific that a binding site can bind only
one type of ligand and no other.

Although some binding sites have a chemical

specificity that allows them to bind only one
type of ligand, others are less specific and thus
can bind a number of related ligands.

It is the degree of specificity of proteins that

determines, in part, the side effects of
therapeutic drugs
Proteins with different amino
acid sequences have different
shapes and, therefore,
differently shaped binding
sites, each with its own
chemical specificity
 Affinity
The strength of ligand–protein binding is a
property of the binding site known as affinity
Different proteins may be able to bind the
same ligand—that is, may have the same
chemical specificity—but may have different
affinities for that ligand
A protein with a high-affinity binding site for
a ligand, very little of the ligand is required
to bind to the protein
Thus affinity play an important role in
medicine as very little quantity of drug is
required to produce therapeutic effects and
avoid unwanted side effects
 Saturation
The term saturation refers to the
fraction of total binding sites that are
occupied at any given time.
When all the binding sites are
occupied, the population of binding
sites is 100% saturated.
The percent saturation of a binding
site depends upon two factors:
(1) the concentration of unbound
ligand in the solution, and
(2) the affinity of the binding site for
the ligand.
 Competition
Competition occurs between the ligands
for the same binding site
As a result of competition, the biological
effects of one ligand may be diminished
by the presence of another.
For example, many drugs produce their
effects by competing with the body’s
natural ligands for binding sites. By
occupying the binding sites, the drug
decreases the amount of natural ligand
that can be bound.
Regulation of Binding site characteristics
• There are two ways of controlling protein’s activity;
➢Changing protein shape, which alters the binding of ligands
➢Regulating protein synthesis and degradation, which determines
the types and amounts of proteins in a cell

• The two mechanisms found in cells that selectively alter protein shape
and thus function of a protein, are known as;
➢Allosteric modulation
➢Covalent modulation
Allosteric modulation
When a protein contains two binding sites, the noncovalent binding of a ligand to
one site can alter the shape of the second binding site and, therefore, the binding
characteristics of that site. This is termed allosteric (other shape) modulation and
such proteins are known as allosteric proteins
Functional (or active) site , carries out the protein’s physiological function. The
other binding site is the regulatory site . The ligand that binds to the regulatory
site is known as a modulator molecule , because its binding allosterically
modulates
The modulatory molecule when bound can change functional site;
(1) It can bind functional ligand
(2) Prevent binding of a functional ligand
(3) Increase or decrease the affinity of functional site

Functional site can also influence each other in certain proteins that are composed of more
than one polypeptide chain held together by electrical attractions between chains.
Binding of ligand to functional site of one chain can result in alteration of functional site on
other chains
The interaction between the functional binding sites of a multimeric (more than one
polypeptide chain) protein is known as cooperativity
Covalent modulation
Covalent bonding of charged chemical groups to some of the protein’s side chains is
known as covalent modulation
In most cases phosphorylation occurs, in which a phosphate group (having –ve charge)
is covalently attached to side chain of certain amino acids

This charge alters the distribution of electrical forces in the protein and produces a
change in protein conformation. If the conformational change affects a binding site, it
changes the binding site’s properties

Although the mechanism is completely different, the effects produced by covalent

modulation are similar to those of allosteric modulation
Allosteric modulation, involves noncovalent binding of modulator molecules, covalent
modulation requires chemical reactions in which covalent bonds are formed.
Two enzymes control a protein’s activity by
covalent modulation:

Protein kinase Any enzyme that mediates protein phosphorylation

Phosphoprotein An enzyme for removing the phosphate group and

returning the protein to its original shape causing
phosphatases dephosphorylation
Protein kinase

• Protein kinases are themselves allosteric proteins whose

activity can be controlled by modulator molecules.

• Therefore, the process of covalent modulation is itself

indirectly regulated by allosteric mechanisms.

• In addition, some allosteric proteins can also be modified by

covalent modulation