Proteins are macromolecules made of amino acid polymers known as polypeptide chains. The sequence of amino acids in a protein is determined by the gene coding for that protein. Proteins perform essential functions in living cells such as catalyzing biochemical reactions as enzymes, regulating processes as hormones, transporting molecules, providing structure, and more. After synthesis, proteins are often modified with additional functional groups which can confer new abilities like recognizing other molecules or integrating into membranes.

2. Definition
Proteins are cellular macromolecules made up of
amino acid polymers (polypeptides). The sequence of
amino acids, or primary structure of the protein, is
dictated by the nucleotide sequence of the gene
coding for that particular protein.

3. ALL PROTEINS CONTAIN:
* Carbon (C)
* Oxygen (O)
* Nitrogen (N)
* Hydrogen (H)
* Sulfur (S)

4. The word PROTEIN comes from Greek language
(prota) which means "of primary importance". This
name was introduced by Jons Jakob Berzelius in 1838
for large organic compounds with almost equivalent
empirical formulas. This name was used because the
studied organic compounds were primitive but seems
to be very important for animal nutrition.

5. Linear polymers of aa via amide linkages form
peptides (1-10), polypeptides (11-100) and proteins
(>100) eg; Aspartame (2), glutathione (3), vasopressin
(9),insulin (51).
 In the lab, proteins can be hydrolyzed (to aa) by
strong acid treatment.
 Physiologic hydrolysis is by peptidases and proteases.

6. The peptide bond
Proteins are made of amino acids linked into linear
chains, called polypeptide chains. Amino acids links
between each other by peptide bonds - this peptide
bond is formed between the carboxyl and amino
groups of neighbouring amino acids. Proteins are
formed by one or several polypeptide chains. The
sequence of the polypeptide chain is defined by a
gene with genetic code.

7. General formula
 H O
| ||
R – C – C – OH
|
NH2

8. This process can then continue to join other amino
acids and yield in an amino acid chain. When there
are few amino acids in a chain, it is called an
oligopeptide, when there are many it is called a
polypeptide. Although the terms "protein" and
"polypeptide" are sometimes used to describe the
same thing, the term polypeptide is generally used
when the molecular weight of the chain is below
10,000. An amino acid unit in a peptide is often called
a residue.

9. There are only 22 standard amino acids that exist in
living organism. Sometimes these amino acids are
chemically modified in the protein after protein
synthesis. In total the number of different proteins,
which it is possible to produce from 22 amino acids is
enormous. For example for 10 amino acid sequence it
is possible to have 2010
different sequences, which is
approximately equal to 1013
or 10 trillions of different
structures.

10. Generally speaking, proteins do everything in the
living cells. All functions of the living organisms are
related with proteins. Each protein or group of
proteins are responsible for their own specific
function.

11. Post-translational modifications
After a protein is synthesized inside the cell ,is
usually modified by addition of extra functional
groups to the polypeptide chain. These can be sugar
or phosphate groups and may confer to the protein
special functions such as: the ability to recognize
other molecules, to integrate in the plasma
membrane, to catalyze biochemical reactions, and
various other processes.

12. CLASSIFICATION OF PROTEINS BY
COMPOSITION
Simple Proteins
Albumins: blood (serum albumin); milk (lactalbumin);
egg white (ovalbumin); lentils (legumelin); kidney
beans (phaseolin); wheat (leucosin).
 Globular protein.
 Soluble in water and dilute salt solution; precipitated
by saturation with ammonium sulfate solution;
coagulated by heat; found in plant and animal tissues.

13.  Globulins: blood (serum globulins); muscle (myosin);
potato (tuberin); Brazil nuts (excelsin); lentils (legumin).
 Globular protein; sparingly soluble in water; soluble in
neutral solutions; precipitated by dilute ammonium
sulfate and coagulated by heat; distributed in both plant
and animal tissues.

14.  Glutelins: wheat (glutenin); rice (oryzenin). Insoluble in
water and dilute salt solutions; soluble in dilute acids;
found in grains and cereals.
 Prolamines: wheat and rye (gliadin); corn (zein); barley
(hordein). Insoluble in water and absolute alcohol;
soluble in 70% alcohol; high in amide nitrogen and
proline; occurs in grain seeds.

15. Protamines: sturgeon (sturine); mackerel (scombrine);
salmon (salmine); herring (clapeine). Soluble in water;
not coagulated by heat; strongly basic; high in arginine;
associated with DNA; occurs in sperm cells.
Histones: Thymus gland; pancreas; nucleoproteins
(nucleohistone). Soluble in water, salt solutions, and
dilute acids; insoluble in ammonium hydroxide; yields
large amounts of lysine and arginine; combined with
nucleic acids within cells.

16. Scleroproteins: Connective tissues and hard tissues.
Fibrous protein; insoluble in all solvents and resistant to
digestion.
 Collagen: connective tissues, bones, cartilage, and
gelatin. Resistant to digestive enzymes but altered to
gelatin by boiling water, acid, or alkali; high in
hydroxyproline.
 Elastin: Ligaments, tendons, and arteries. Similar to
collagen but cannot be converted to gelatin.
 Keratin: Hair, nails, hooves, horns, and feathers.
Partially resistant to digestive enzymes; contains
large amounts of sulfur, as cystine.

17. Conjugated Proteins
Nucleoproteins: cytoplasm of cells
(ribonucleoprotein); nucleus of chromosomes
(deoxyribonucleoprotein) viruses, and bacteriophages.
Contains nucleic acids, nitrogen, and phosphorus.
Present in chromosomes and in all living forms as a
combination of protein with either RNA or DNA.
Mucoprotein: saliva (mucin); egg white (ovomucoid).
Proteins combined with amino sugars, sugar acids, and
sulfates.
Glycoprotein: bone (osseomucoid); tendons
(tendomucoid); carilage (chondromucoid).

18. Phosphoproteins: milk (casein); egg yolk (ovovitellin).
Phosphoric acid joined in ester linkage to protein.
Chromoproteins: hemoglobin; myoglobin; flavoproteins;
respiratory pigments; cytochromes. Protein compounds with
some nonprotein pigments as heme; colored proteins.
Lipoproteins: serum lipoprotein; brain, nerve tissues, milk,
and eggs. Water-soluble protein conjugated with lipids;
found dispersed widely in all cells and all living forms.
Metalloproteins: ferritin; carbonic anhydrase;
ceruloplasmin. Proteins combined with metallic atoms that
are not parts of a nonprotein prosthetic group.

19. Derived Proteins
Proteans: edestan (from elastin) and myosan (from
myosin). Results from short action of acids or enzymes;
insoluble in water.
Proteases: intermediate products of protein digestion.
Soluble in water; uncoagulated by heat; and
precipitated by saturated ammonium sulfate; result
from partial digestion of protein by pepsin or trypsin.

20. Peptones: intermediate products of protein digestion.
Same properties as proteases except that they cannot be
salted out; of smaller molecular weight than proteases.
Peptides: intermediate products of protein digestion.
Two or more amino acids joined by a peptide linkage;
hydrolyzed to individual amino acids.

21. CLASSIFICATION BASED UPON
FUNCTION
Enzymes (catalytic proteins) Lactase, ribonuclease,
pyruvate dehydrogenase, fumarase, proteinase
Structural proteins Collagen, elastin, keratin
Regulatory or hormonal proteins Insulin, adrenaline
Transport proteins Hemoglobin, myoglobin
Genetic proteins Nucleoproteins, histones
Immune Proteins Gamma Globulin, Ig's, (Ab's)
Contractile Proteins Actin, myosin
Storage Proteins Zein, ovalbumin, casein

22. Classification by protein functions
Proteins are responsible for many different functions in
the living cell. It is possible to classify proteins on the basis
of their functions. Very often, proteins can carry few
functions and such proteins can be placed into different
groups, but despite this, it is possible to assign main group
for each protein.
 Enzymes - proteins that catalyze chemical and
biochemical reactions within living cell and outside. This
group of proteins probably is the biggest and most
important group of the proteins. Enzymes are responsible
for all metabolic reactions in the living cells. Well known
and very interesting examples are: DNA- and RNA-
polymerases, dehydrogenases etc.

23. Hormones - proteins that are responsible for the
regulation of many processes in organisms. Hormones
are usually quite small and can be classifies as
peptides. Most known protein hormones are: insulin,
growth factor, prolactin etc.
 Many protein hormones are predecessor of peptide
hormones, such as endorphin, enkephalin etc.

24. Transport proteins - These proteins are
transporting or store some other chemical
compounds and ions. Some of them are well known:
cytochrome C - electron transport; haemoglobin and
myoglobin - oxygen transport; albumin - fatty acid
transport in the blood stream etc. It is possible to
classify trans membrane protein channels as a
transport proteins as well.

25. Immunoglobulin or Antibodies - proteins that
involved into immune response of the organism to
neutralize large foreign molecules, which can be a
part of an infection. Sometimes antibodies can act as
enzymes. Sometimes this group of proteins is
considered as a bigger group of protective proteins
with adding such proteins as lymphocyte antigen-
recognizing receptors, antivirals agents such as
interferon, tumor necrosis factor (TNF). Probably the
clotting of blood proteins, such as fibrin and
thrombin should be classified as protective proteins
as well.

26. Structural proteins - These proteins are maintain
structures of other biological components, like cells and
tissues. Collagen, elastin, α-keratin, fibrin - these proteins
are involved into formation of the whole organism body.
Bacterial proteoglycans and virus coating proteins also
belongs to this group of proteins. Currently we do not
know about other functions of these proteins.
Motor proteins. These proteins can convert chemical
energy into mechanical energy. Actin and myosin are
responsible for muscular motion. Sometimes it is difficult
to make a strict separation between structural and motion
proteins.

27. Receptors These proteins are responsible for signal
detection and translation into other type of signal.
Sometimes these proteins are active only in complex
with low molecular weight compounds. Very well
known member of this protein family is rhodopsin -
light detecting protein. Many receptors are
transmembrane proteins.

28. Signalling proteins - This group of proteins is
involved into signalling translation process. Usually
they significantly change conformation in presence of
some signalling molecules. These proteins can act as
enzymes. Other proteins, usually small, can interact
with receptors. Classical example of this group of
proteins is GTPases.

29. Storage proteins. These proteins contain energy,
which can be released during metabolism processes in
the organism. Egg ovalbumin and milk casein are
such proteins. Almost all proteins can be digested and
used as a source of energy and building material by
other organisms.

30. Classification of proteins by
location in the living cell
Protein classification can be based on their
appearance in the living cell. According to this, it is
possible to classify all proteins into four main groups.
 Membrane or transmembrane proteins - these
proteins are located within cell membrane lipid bi-
layer. These proteins can be completely or partially
buried in membrane.

31. Internal proteins - these proteins are located within
living cell and all functions are related with
intercellular needs.
External proteins - these proteins function outside
the cell in which they are produced. Such type of
proteins is more common for multicellular organisms.
Virus proteins - These proteins are present only in
virus organism, usually as a coat for viral particle.

32. CLASSIFICATION BASED UPON
SHAPE
Fibrous Proteins - Long thread-like molecules whose
helical strands often form fibers or sheets; often
insoluble in water. e.g; Collagen, elastin, keratin
Globular Proteins - Generally soluble in aqueous media;
spheroid or ovoid shape; further classified on the basis
of solubility - water soluble, heat coaguble, include
proteins in blood serum, egg white, milk, and in certain
plants (pea, wheat);soluble in dilute salt solutions
 include proteins in blood serum, egg white, and in
plants such as peanuts.

33. CLASSIFICATION BASED UPON
PHYSICOCHEMICAL PROPERTIES
Simple Proteins - Yield only amino acids on hydrolysis
 Albumins, Globulins, Glutelins Soluble in dilute acids and
alkalies
 Scleroproteins Nonsoluble proteins such as Collagen
 Prolamines Soluble in alcohol, insoluble in water; found in
seeds of plants
 Histones Soluble in water, dilute acids, and alkalies; contain a
large portion of basic amino acids such as globin of
hemoglobin
 Protamines Basic proteins which are essentially large
polypeptides

34. Conjugated Proteins Yield amino acids and
nonprotein products upon hydrolysis
 Glyco- or mucoproteins Proteins plus carbohydrates;
e.g. mucin of saliva
 Lipoproteins Proteins plus a lipid; e.g. lipovitellin of egg
yolk
 Chromoproteins Proteins plus a pigmented prosthetic
group e.g. hemoglobin, myoglobin
 Metalloproteins Proteins plus a metal element such as
iron, magnesium, copper, or zinc; e.g. ferritin (Fe),
tyrosine oxidase (Cu), alcohol dehydrogenase (Zn).
 Nucleoproteins Proteins plus nucleic acid; e.g.
nucleohistone

35. Classification of proteins by
posttranslational modification
After protein translation some of them are subjected
to posttranslational modification. This modification
can be related with many different aspects of changes.
Again this classification split all proteins into
overlapped groups.
 Native proteins - these proteins are not changed
after translation.
Glyco-proteins - these proteins are modified by
covalent binding with linear or branched
oligosaccharides.

36. Cleaved proteins - the polypeptide chain of these
proteins are cleaved into two or more pieces.
Proteins with disulphide bonds. In these proteins pair
of cysteins are linked between each other by S-S or
disulphide bond (disulphide bridge)
Protein complexes. Some proteins produce protein
complexes of homo- and hetero- nature.
Chemically modified proteins - in these proteins some
residues are chemically modified by covalent bonding with
other chemical compounds.
Prions - these proteins are folded wrongly during
translation, or change their configuration straight after
translation.

37. Protein Functions
Antibodies - are specialized proteins involved in
defending the body from antigens (foreign invaders). One
way of antibody destroying antigens is by immobilizing
them so that they can be destroyed by white blood cells.
Contractile Proteins - are responsible for movement.
Examples include actin and myosin. These proteins are
involved in muscle contraction and movement.

38. Enzymes - are proteins that facilitate biochemical
reactions. They are often referred to as catalysts
because they speed up chemical reactions. Examples
include the enzymes lactase and pepsin. Lactase
breaks down the sugar lactose found in milk. Pepsin is
a digestive enzyme that works in the stomach to
break down proteins in food.

39. Hormonal Proteins - are messenger proteins which
help to coordinate certain bodily activities. Examples
include insulin, oxytocin, and somatotropin. Insulin ,
oxytocin, and somatotropin. Insulin regulates glucose
metabolism by controlling the blood-sugar
concentration. Oxytocin stimulates contractions in
females during childbirth. Somatotropin is a growth
hormone that stimulates protein production in
muscle cells.

40. Structural Proteins - are fibrous and stringy and
provide support. Examples include keratin, collagen,
and elastin. Keratins strengthen protective coverings
such as hair, quills, feathers, horns, and beaks.
Collagens and elastin provide support for connective
tissues such as tendons and ligaments.

41. Storage Proteins - store amino acids. Examples include
ovalbumin and casein. Ovalbumin is found in egg whites
and casein is a milk-based protein.
Transport Proteins - are carrier proteins which move
molecules from one place to another around the body.
Examples include hemoglobin and cytochromes.
Hemoglobin transports oxygen through the blood.
Cytochromes operate in the electron transport chain as
electron carrier proteins.

42. PLASMA PROTEIN SYNTHESIS SITE
Hepatic/Liver = almost all proteins; except Gamma
Globulins
* Plasma Cells = immunoglobulins

43. TOTAL PROTEIN: REFERENCE
RANGE
Serum 6.0 - 8.0 gm/dl
CSF 15 - 45 mg/dl
Urine negative - trace
dl = 100 mL = %

44. Hyperproteinemia
Hemolysis = Falsely INCREASES (RBC proteins
released into Serum)
Increased Total Protein
- Dyhydration/Vomitting/Diarrhea - most common
cause
- Multiple Myeloma - immunoglobulin disease state
- Excessive Hormone Secretions - example: increased
aldosterone

45. Hypoproteinemia
Decreased albumin synthesis:
a.Liver disease (specially chronic diseases).
b.Malnutrition.
c.Alcoholism
Increased albumin loss:
a.Renal disease (nephrotic syndrome).
Loss of albumin in urine (proteinuria).
b.Extensive burns:
Loss of albumin through skin .

46. Prion Diseases
Prion diseases or transmissible spongiform encephalopathies
(TSEs) are a family of rare progressive neurodegenerative
disorders that affect both humans and animals. They are
distinguished by long incubation periods, characteristic
spongiform changes associated with neuronal loss, and a failure
to induce inflammatory response.
The causative agents of TSEs are believed to be prions. The term
"prions" refers to abnormal, pathogenic agents that are
transmissible and are able to induce abnormal folding of
specific normal cellular proteins called prion proteins that are
found most abundantly in the brain. The functions of these
normal prion proteins are still not completely understood. The
abnormal folding of the prion proteins leads to brain damage
and the characteristic signs and symptoms of the disease. Prion
diseases are usually rapidly progressive and always fatal.