This file is all about protein, its composition, functions, metabolism, importance in body, degradation and ways involved, as well as secretion with post transitional changes

2. Protein:
History of proteins:
Proteins were discovered by Jöns Jakob
Berzelius in 1838 and are among the most
actively-studied molecules in biochemistry.
The word "Protein" is derived from a Greek
word "protas" meaning "of primary
importance," because of the fundamental role
of proteins in sustaining life. Our body is
composed of nearly “10,000” types of
proteins.
Definition of protein:
Proteins are the most abundant nitrogenous organic compound
and polymers of amino acids that are linked together in one or
more long polypeptide chains typically folded into globular or
fibrous form in biologically functional way.

3. Composition of protein:
Protein are composed of amino acid that contains: Carbon,
Nitrogen, Oxygen, hydrogen. They may also contain
phosphorous and traces of other elements like: Iron, Copper,
Iodine, Manganese, Sulfur and Zinc.
Source of proteins:
Meat, Eggs, Beans, Nuts, Peas etc.
Pathway to Make a protein
DNA mRNA
tRNA
(Ribosome)
PROTEINS

4. Nuclear
membrane
Transcription
RNA Processing
Translation
DNA
Pre-mRNA
mRNA
Ribosome
Protein

5. Biological Functions of Proteins:
1- Enzymes 2- Transport proteins
3- Nutrient and storage proteins 4- Contractile or motile
proteins
5- Structural proteins 6- Defense proteins
7- Regulatory proteins
Other proteins:
1- Ligase & etc. 2- Hemoglobin
3-Lactose & etc. 4- Muscle proteins
5- glucagon 6- Antibodies
7- Hemoglobin
Protein metabolism
Definition:
The anabolic and catabolic chemical reactions and use of proteins
in the body is known as protein metabolism.

6. Protein catabolism is the breakdown of proteins into amino acids and
simple derivative compounds, for transport into the cell through
the plasma membrane and ultimately for the polymerization into new
proteins via the use of ribonucleic acids (RNA) and ribosomes. Protein
catabolism, which is the breakdown of macromolecules, is essentially
a digestion process. Protein catabolism is most commonly carried out by
non-specific endo- and exo-proteases. However specific proteases are
used for cleaving of proteins. One example is the subclass of proteolytic
enzymes called oligopeptidase.
IMPORTANCE OF PROTEIN METABOLISM:
1- To maintain the protein composition in body.
2- To remove the abnormal protein.
3- Help in growth. 4- Help in making
hormones.
5- Help in making antibodies. 6- Help in making enzymes.

7. Nitrogen pool:
The "nitrogen or amino acid pool" is a grand mixture of amino acids
available in the cell derived from dietary sources or the degradation of
protein. Tissues, proteins, hormones and enzymes are formed by amino
acid pool. Amino acid is taken up by each cell according to its own
specific needs, to be built into the cell structure and materials as
required.

8. Proteins in the body:
Proteins provide: Amino acids for protein synthesis. Nitrogen atoms for
nitrogen containing compounds. Energy when carbohydrate and lipid
resource are not available.
ENZYMATIC DEGRADATION OF DIETARY PROTEINS

9. Use of protein for energy:
Once the cells are filled in their limits with stored proteins, any
additional amino acid in the body fluid are degraded and used for
energy and stored as fat and secondarily in glycogen
This degradation occurs almost in the liver.
HORMONAL REGULATION OF PROTEIN METABOLISM:
Growth hormone: increase the synthesis of cellular protein.
Insulin: is necessary for protein synthesis.
Glucocorticoids: increase the breakdown of most tissue protein.
Testosterone: increase the protein deposition.
Estrogen & Thyroxin: increase the rate of protein metabolism.

10. Protein degradation:
The process by which protein is breakdown into simple amino acids is
known as PROTEIN DEGRADATION.
Introduction of degradation
The levels of proteins within cells are determined not only by rates of
synthesis, but also by rates of degradation.
The half-lives of proteins within cells vary widely, from minutes to
several days, and differential rates of protein degradation are an
important aspect of cell regulation.
Many rapidly degraded proteins function as regulatory molecules, such
as transcription factors.
The rapid turnover of these proteins is necessary to allow their levels to
change quickly in response to external stimuli.
In addition, faulty or damaged proteins are recognized and rapidly
degraded within cells, thereby eliminating the consequences of mistakes
made during protein synthesis.

11. Pathways of protein degradation
In eukaryotic cells, two major pathways:
1- Ubiquitin-proteasome pathway (80-90%).
(A) Ubiquitin dependent pathway.
(B) Ubiquitin independent pathway.
2- lysosomal proteolysis mediate protein degradation (receptor
dependent pathway) (10-20%).
UBIQUITIN DEPENDENT PATHWAY:
It is a cytosolic pathway for protein degradation. It requires ubiquitin
and ATP (adenine triphosphate). Mainly abnormal proteins and short
lived proteins are degraded by this pathway.
UBIQUITIN INDEPENDENT PATHWAY:
It is another cytosolic pathways for degradation and is not dependent on
ubiquitin. Mainly extracellular proteins, membrane proteins and long
lived proteins are degraded by this pathway.

12. Receptor dependent pathway:
Mainly glycoproteins and hormones are degenerated by this pathway.
Enzymes for proteins degradation:
Several enzymes are responsible for the proteins degradation
1- Protease and peptidases. 2- Cathepsins
3- Multicatalytic proteases (proteasome) 4- Magapain
5- Many others enzymes

13. Cathepsins: They are hydrolytic enzymes present in lysosome. They are
responsible for the degradation of:
1- glycoproteins Hormone. 2- Intracellular proteins.
Protease & peptidases: Several intra cellular proteases and peptidases
are involved in protein degradation.
They hydrolyzes the protein, and include:
1- Tryptase. 2- Chymase 3- Elastase 4- Collagenanse
Multicatalytic proteases (protesome): As the name tell they process
multicatalytic function. They are present in cytosol of the most
mammalian cells. Involve in intracellular protein degradation and this
includes:
1- Trypsin 2- Chymotrypsin
Magapain: High molecular mass protease which are present in:
1- Liver 2- Skeletal muscles
It degrades the protein in presence of ubiquitin.

14. The Ubiquitin-Proteasome Pathway
• The major pathway of selective protein
degradation in eukaryotic
cells uses ubiquitin as a marker that
targets cytosolic and nuclear proteins for
rapid proteolysis
• Ubiquitin is a 76-amino-acid
polypeptide that is highly conserved in all
eukaryotes (yeasts, animals, and plants).
ubiquitin PDB 1TBE

15. • Proteins are marked for degradation by the
attachment of ubiquitin to the amino group
of the side chain of a lysine residue.
• Additional ubiquitins are then added to form
a multiubiquitin chain. Such polyubiquinated
proteins are recognized and degraded by a
large, multisubunit protease complex, called
the proteasome.
• Ubiquitin is released in the process, so it can
be reused in another cycle. It is noteworthy
that both the attachment of ubiquitin and
the degradation of marked proteins require
energy in the form of ATP.
H3N+
C COO
CH2
CH2
CH2
CH2
NH3
H

lysine
20 S Proteasome








16. The ubiquitin-proteasome pathway.
Proteins are marked for rapid degradation by the covalent attachment
of several molecules of ubiquitin.
Since the attachment of ubiquitin marks proteins for rapid degradation,
the stability of many proteins is determined by whether they become
ubiquitinated.
Ubiquitination is a multistep process. (3 steps)
First, ubiquitin is activated by being attached to the ubiquitin-
activating enzyme, E1.
The ubiquitin is then transferred to a second enzyme, called
ubiquitin-conjugating enzyme (E2).
The final transfer of ubiquitin to the target protein is then mediated
by a third enzyme, called ubiquitin ligase or E3, which is responsible
for the selective recognition of appropriate substrate proteins.

17. • In some cases, the ubiquitin is first transferred from E2 to E3 and then
to the target protein
• Most cells contain a single E1, but have many E2s and multiple
families of E3 enzymes. Different members of the E2 and E3 families
recognize different substrate proteins, and the specificity of these
enzymes is what selectively targets cellular proteins for degradation by
the ubiquitin-proteasome pathway.

18. • A number of proteins that control fundamental cellular
processes, such as gene expression and cell proliferation,
are targets for regulated ubiquitination and proteolysis.
DEUBIQUITINATION

19. Explanation with example
An interesting example of such controlled degradation is provided by
proteins (known as cyclins) that regulate progression through the
division cycle of eukaryotic cells.
The entry of all eukaryotic cells into mitosis is controlled in part by cyclin
B, which is a regulatory subunit of a protein kinase called cdc2.
The association of cyclin B with cdc2 is required for activation of the
cdc2 kinase, which initiates the events of mitosis (including
chromosome condensation and nuclear envelope breakdown) by
phosphorylating various cellular proteins.
Cdc2 also activates a ubiquitin-mediated proteolysis system that
degrades cyclin B toward the end of mitosis. This degradation of cyclin
B inactivates cdc2, allowing the cell to exit mitosis and progress
to interphase of the next cell cycle.

20. • The ubiquitination of cyclin B is a highly selective reaction, targeted by
a 9-amino-acid cyclin B sequence called the destruction box. Mutations
of this sequence prevent cyclin B proteolysis and lead to the arrest of
dividing cells in mitosis, demonstrating the importance of regulated
protein degradation in controlling the fundamental process of cell
division.
H2N COO
destruction
box
chain of
ubiquitins
Primary structure of a protein
targeted for degradation

21. Review of ubiquitin pathway steps
Step 1: ubiquitin is
activated by E1
Step 2: ubiquitin
transferred to
ubiquitin-
conjugating
enzyme (E2)
Step 3:ubiquitin
target protein by
ubiquitin ligase or
E3
Protein Is Finally
Hydrolyzed

22. Lysosomal Proteolysis pathway
• The other major pathway of
protein degradation in eukaryotic
cells involves the uptake
of proteins by lysosomes.
Lysosome:
• Lysosomes are membrane-
enclosed organelles that contain
an array of digestive enzymes,
including several proteases
H+
Lysosome
ATP ADP + Pi
Vacuolar ATPase
low
internal
pH
Lumen
contains
hydrolytic
enzymes.

23. Lysosomal Enzymes
50 different degradative enzymes.
Acid hydrolases: Active at pH 5 (inside lysosome). Inactive if released
into cytosol (pH 7.2).
Acidic pH of lysosomes: maintained by a proton pump in the lysosomal
membrane, Requires ATP
Different pathways lead to the lysosome
1) Phagocytosis: Cell
“eating” of material > 250nm
2) Pinocytosis: Cell
“drinking” < 150nm
3) Receptor Mediated
Endocytosis
4) Autophagy: “self eat” of
old worn out organelles,
– important in cell
degradation during apoptosis

24. They have several roles in cell metabolism Including the digestion of
extracellular proteins taken up by endocytosis. The gradual turnover of
cytoplasmic organelles and cytosolic proteins. The uncontrolled
degradation of the contents of the cell is prevented by Containment of
proteases by Other digestive enzymes within lysosomes.Therefore, in
order to be degraded by lysosomal proteolysis, cellular proteins must
first be taken up by lysosomes.
One pathway for this uptake of cellular proteins,autophagy, involves the
formation of vesicles (autophagosomes) in which small areas of
cytoplasm or cytoplasmic organelles are enclosed in membranes
derived from the endoplasmic reticulum.
These vesicles then fuse with lysosomes, and the degradative lysosomal
enzymes digest their contents.
The uptake of proteins into autophagosomes appears to be
nonselective, so it results in the eventual slow degradation of long-lived
cytoplasmic proteins.

25. Lysosomes contain various digestive enzymes, including proteases.
Lysosomes take up cellular proteins by fusion with autophagosomes,
Autophagosomes: which are formed by the enclosure of areas of
cytoplasm or organelles. Example: (Mitochondrion)

26. Proteins are not degraded at the same rate
• ENZYME half-life
• Ornithine decarboxylase 11 minutes
• -Aminolevulinate synthetase 70 minutes
• Catalase 1.4 days
• Tyrosine aminotransferase 1.5 hours
• Tryptophan oxygenase 2 hours
• Glucokinase 1.2 days
• Lactic dehydrogenase 16 days
Importance of degradation:
• To maintain the protein composition in body
• To remove the abnormal protein
• Help in metabolism
• Help in starvation
• Help in diseases
• Help in growth

27. Protein secretion
Definition
“A secretory Protein is any protein, whether it be endocrine or
exocrine, which is secreted by a cell.”
Secretory protein includes:
1- Hormone 2- Enzymes 2- Toxins
3- Antimicrobial peptides
Secretory proteins are synthesis in endoplasmic reticulum (ER)
Steps of protein secretion
1. Protein formed by ribosomes on rough ER.
2. Protein packaged into transport vesicles, which buds from ER.
3. Transport vesicles fuse into clusters that unload protein into
Golgi complex.
4. Golgi apparatus Modifies protein -e.g. adds a carbohydrate
moieties -form a glycoprotein
5. Golgi vesicles containing finished protein formed.
6. Secretory vesicles release protein by exocytosis.

28. Step:01
When protein is assembled on ER SURFACE. IT THREADS
ITSELF THROUGH A PORE IN THE ER MEMBRANE AND INTO
CISTERNA.
ENZYMES IN THE CISTERNAE MODIFY THE NEW PROTEIN IN
A VARIETY OF WAYS.
Removing some amino acids segments,folding the protein and
stabilizing it with disulfide bridges adding carbohydrates and so
forth.
THESE CHANGES ARE CALLED POST-TRANSLATIONAL
changes.
Post-translational changes
Insulin, for example, is first synthesized as a protein 86 amino
acids long. In posttranslational modification, the chain folds back
on it, three disulfide bridges are formed, and 35 amino acids are
removed from the middle of the protein. The final insulin molecule
is therefore made of two chains of 21 and 30 amino acids held
together by Disulfide Bridge.

29. Step two
when the rough ER is finished with a protein then:
•It pinches off bubble like Transport vesicles coated with clathrin .
•Clathrin helps to select the proteins to be transported in the
vesicles.
•It also helps to mold the forming vesicles.
•Soon after the vesicles detach from the ER
•They fuse into irregularly shaped clusters.
•Now carry their material to nearest cisternae of Golgi complex.
STEP NO 3
When it contact with the Golgi complex:
The cluster fuses with it.
Then unloads its protein material in to the Golgi cisterna.

30. Step no 4
In Golgi complex further modification of protein take place.
E.g. add carbohydrates moite etc. Form glycoprotein
There is still some disagreement about how the Golgi cisternae
behave:
Some say the maturing protein is passed by transport vesicles
from one cisterna to the next.
Others say the whole cisterna migrates from one side of the
complex to the other and then breaks up into vesicles.
STEP FIVE
The final Golgi cisternae, farthest from the ER, either buds off
new coated Golgi vesicles containing the finished protein, or may
simply break up into vesicles to be replaced by younger cisternae
behind it.

31. STEP SIX
Some of the Golgi vesicles become lysosomes.
While other become secretory vesicles that migrate to the plasma
membrane and fuse with it and secrete the protein outside of the
cell membrane by a process called Exocytosis. Salivary gland, for
example, secretes mucus and digestive enzymes.
EXAMPLES OF PROTEIN HORMONES
Protein hormones include Insulin and growth hormones etc.
Protein hormones bear carbohydrate side chain and are called
Glycoprotein hormones.
•Luteinizing Hormone
•Follicle stimulating Hormone
•Thyroid-Stimulating Hormone are examples of glycoprotein
hormones

32. Hormones
• Chemical
messengers
• Globular protein
• Exert a specific
effect on tissues
Antibodies
• Y-shaped globular
proteins
• Made by
lymphocytes
• Defend body
against antigens
Haemoglobin
• Oxygen-
transporting
pigment in blood
• Conjugated protein
-globular protein
globin
-haem (non-protein
containing iron)