Proteins and its type on the basis of structure and amino acids

1. PROTEINS
BCH-301
INTRODUCTRY BIOCHEMISTRY
PART A

2. Contents
Introduction to amino acids
Essential and non essential amino
acids
Classification of amino acids
Peptides
Polypeptides

3. Introduction: Proteins
Proteins are the most abundant class of organic molecules found in nature.
They constitute about 50% of the cellular dry weight.
In 1839, Dutch chemist G.J. Mulder was first to be describe about proteins.
The term Protein sis derived from the Greek proteios, meaning "first" or "foremost."
The proteins are nitrogenous macromolecules that are composed of many amino
acids.
Relatively simple monomeric subunits provide the structure of thousands of
different proteins.
It’s a polymer of L α-amino acid.

4. Amino Acids
Protein Architecture-Amino acids
Proteins are polymers of amino acids with each amino acid
residue joined to its neighbour by a specific type of covalent
bond.
Proteins can be breakdown (hydrolysed) to their constituents
amino acids by a variety of methods.
The number of amino acids in a protein molecule may range
from two to several thousands.

5. Continue…
The first to be discovered was asparagine in 1806.
Last of the 20 to be found , threonine was not identified until
1938
All amino acids have trivial or common names
 In some cases derived from the sources from which they were
first isolated.

6. Classification of some proteins and their
functions
Class of proteins Functions in the body Examples
Structural Provide structural components Collagen in tendons
Contractile Movement of muscles Myosin and actin contract muscle
fibres
Transport Carry essential substances
through out the body
Haemoglobin transport oxygen
Storage Store nutrients Ferritin stores iron in liver and spleen
Hormone Regulate body metabolism and
nervous system
Growth hormone regulates body
growth
Enzyme Catalyze biochemical reaction in
the cell
Trypsin catalyze the hydrolysis of
proteins
Protection Recognize and destroy foreign
substances
Immunoglobulins stimulate immune
responses

7. Types Of Proteins
 According to their environmental condition and general
structure proteins are roughly divided in to three classes:
Fibrous Proteins
Membrane Protein
Globular Protein

8. Classification of Proteins
• Simple Proteins
• Conjugated proteins
• Derived Proteins

9. Structural Organization Of Proteins

10. Primary Structure
• Linear structure formed by the
interlinking of many amino acids.
• The primary structure is held
together by peptide bonds that are
made during the process of
protein biosynthesis.

11. Secondary Structure
• Secondary structure is the regular
arrangements of amino acids
located near to each other in
primary structure.(Structure formed
by coiling of polypeptides).
• Maintained by
• Hydrogen Bonds

12. Tertiary Structure
• Structure formed by further folding of already
coiled polypeptide(three dimensional shape of the
monomeric or multimeric molecules).
• Stabilized by
• Hydrophobic interactions
• Hydrogen bonds
• Electrostatic interactions
• Disulphide bonds

13. Quaternary Structure
• Quaternary structure is the arrangement
of multiple polypeptide subunits in the
protein
• Stabilized by
• Hydrophobic interactions
• Hydrogen bonds
• Electrostatic interactions

14. Amino Acids
• Amino acids are the group of organic compounds
containing two functional groups amino and carboxyl.
• The amino group(NH2), is basic while the carboxyl
group(COOH), is acidic in nature.
• There are 300 amino acids occur in nature. Only 20 of
them occur in proteins.
• The key elements of amino acids are carbon, hydrogen,
nitrogen and oxygen.

15. Structure of Amino Acids
(Building blocks of proteins)
Each amino acid has four different functional groups attached to the
central carbon atom, also known as the alpha (α) carbon.
Amino group (NH2)
Carboxyl group (COOH)
Side chains, R group
Hydrogen atom

17. Continue
Some are residues modified after a protein has been
synthesized; others are amino acids present in living
organisms but not as constituents of proteins.
The common amino acids of proteins have been assigned
three letter abbreviations and one letter symbols.
Used as shorthand to indicate the composition and sequence
of amino acids polymerized in proteins.

19. Continue….
For all common amino acids except glycine the α carbon is bounded to
four different functional groups
 The α-carbon of an amino acid is attached to four different chemical
groups and is, therefore, a chiral or optically active carbon atom
Because of tetrahedral arrangement of the bonding orbitals around the
α carbon atom, four different groups can occupy two unique spatial
arrangements, and thus amino acids have two possible stereoisomers.

20. Figure: Stereoisomerism in alpha-amino acids
The two stereoisomers of alanine. L- and D-alanine are
non superimposable mirror images of each other. (b, c)
‘Two different conventions for showing the
configurations in space of stereoisomers. In perspective
formulas (b) the wedge-shaped bonds project out of the
plane of the paper, the dashed bonds behind it. In
projection formulas (c)the horizontal bonds are
assumed to project out of the plane of the paper, the
vertical bonds behind. However, projection formulas
are often used casually without reference to
stereochemical configuration.

21. Amino acid residues in proteins are L
stereoisomers
Nearly all biological compounds with a chiral center occur
naturally in only one sterioisomeric form, either D or L.
Amino acid residues in protein molecules are exclusively L
stereoisomers.
D-amino acids residues have been found in only a few, generally
small peptides, including some peptides of bacterial cell walls and
certain peptide antibiotics.
Cells are able to specifically synthesize the L isomers of amino acids
.

22. Zwitter Ion
• The amine and the carboxylic acid functional groups found in amino acid
allow them to have amphoteric properties.
• Carboxylic acid group can be deprotonated to form carboxylates and alpha-
amino group can be protonated to become positive α-ammonium groups.

23. Continue…
• Both the amino and carboxyl group in an amino acid undergoes ionization
in water.
• At physiological PH 7.4, a Zwitter ion is formed.
• Contain both positive and negative charges.
• Amino group is protonated
• Carboxyl group is deprotonated
• Structure of R also Influence its solubility

24. Isoelectric pH(PI)
• The isoelectric point is the pH at
which a molecule carries no net
electrical charge or is electrically
neutral .
• Each amino acid has its isoelectric
focusing point (PI).

25. Peptide Bond
• A peptide bond is a amide
bond in which two amino
acids can be covalently
joined through a substituted
amide linage, termed a
peptide bond, to yield a
dipeptide.

27. Continue…
• Tripeptide (Three amino acids can be joined by two peptide
bonds to form a tripeptide)
• Tetrapeptide (Four amino acids can be linked to form
tetrapeptide)
• Pentapeptide (Five amino acids linked to form a pentapeptide)
• Oligopeptide (When few amino acids are joined the structure
is called as Oligopeptide.

28. Polypeptide
• A polypeptide is a single linear polymer chain of amino acids bonded
together by peptide bonds between the carboxyl and amino groups of
adjacent amino acid residues.
• When many amino acids are joined in this manner the structure is called
as polypeptide.
• Polypeptides generally have molecular weight below 10,000 while
proteins have higher molecular weight.
• Exp; Insulin hormone

29. Standard Amino Acids
• Amino acids join together to form short polymer chains or long polymer
chains called polypeptides or proteins.
• These polymers are linear and unbranched with each amino acid
attached to two neighbouring amino acids in the chain.
• Twenty two amino acids are naturally incorporated in to polypeptides
and called standard or proteinogenic amino acids. Of these, 20 are
encoded by the universal genetic code. The remaining 2 are
incorporated in to proteins by unique synthetic mechanism.

30. Non Standard Amino Acids
• A nonstandard amino acid is an amino acid that occurs naturally in cells but do
not participate in peptide synthesis
• In addition to the 20 common amino acids, proteins may contain residues
created by modification of common residues already incorporated in to
polypeptide chain.
• Aside from 20 amino acids there are many other amino acids that are called
non proteinogenic or non standard amino acids.
• They are not either in proteins for example carnitine, GABA(neurotransmitter)
are not produced directly..

31. Uncommon Amino Acids are non
strandared amino acids.
• 4-hydroxyproline
• 5-hydroxylysine
• 6-N- Methylliysine
• γ –carboxyglutamate
• Selenocysteine
• Ornithine and citrulline

32. Continue….
• Some amino acids residues in proteins may be modified transiently to
alters the protein function.
• Addition of phosphoryl, methyl, acetyl, adenylyl or other groups to
particular amino acids can increase or decrease the protein activity.

34. Classification of Amino Acids
• Amino Acids are classified as
• Non polar, aliphatic R groups (hydrophobic) with hydrocarbon side chains.
• Polar, uncharged R groups (hydrophilic) with polar or ionic side chains
• Negatively charged (Acidic) R groups
• Positively charged (Basic) R groups
• Aromatic R groups

36. Non polar, Aliphatic R groups
• The hydrocarbon R groups in this class of amino acids are nonpolar and
hydrophobic.
• The bulky side chains of alanine, Valine, leucine, and isoleucine, with their
distinctive shapes, are important in promoting hydrophobic interactions within
protein structures.
• Glycine has the simplest amino acid structure. It is most easily grouped with the
non polar amino acids, its small side chains makes no real contribution to
hydrophobic interactions.
• The minimal steric hindrance of the glycine side chain allows much more structural
flexibility than the other amino acids.

37. Continue…
• Proline has an aliphatic side chain with a distinctive cyclic structure.
• The secondary amino (imino) group in proline is held in a rigid
conformation that reduces the structural flexibility of the protein at that
point.
• Methionine, one of the two sulphur containing amino acids, has a slightly
non polar thioether group in its side chains.

39. Polar, Uncharged R groups
• The R groups of these amino acids are more soluble in water, or hydrophilic,
than those of the nonpolar amino acids, because they contain functional
groups that form hydrogen bonds with water.
• This class of amino acids includes serine, threonine, cysteine, methionine,
asparagine, and glutamine.
• The polarity of serine and threonine is contributed by their hydroxyl groups;
that of cysteine and methionine by their sulfur atom; and that of asparagine
and glutamine by their amide groups.

40. Continue…
• Cysteine has an R group (a thiol group) that is approximately as acidic as the
hydroxyl group of tyrosine.
• Cysteine is readily oxidized to form a covalently linked dimeric amino acid
called cystine, in which two cysteine molecules are joined by a disulfide
bridge.
• Disulfide bridges of this kind occur in many proteins, stabilizing their
structures.

43. Positively charged(Basic) R groups
• In positively charged amino acids R group =amine, Accepts H+, Positively charged.
• Includes; Lysine, Arginine and Histidine
• Amino acids in which the R groups have a significant positive charge at pH 7.0 are
lysine, which has a second primary amino group at the € position on its aliphatic
chain (has butylammonium side chain).
• Arginine, which has a positively charged guanidium group.
• Histidine, containing an imidazole group. Histidine is the only standard amino acid
having a side chain with a pKa near neutrality.

45. Negatively charged R groups
• In negatively charged (acidic) amino acids; R GROUP=Carboxylic acid,
Denotes H+, Negatively Charged.
• Includes Aspartate and Glutamate
• The two amino acids having R groups with a net negative charge at pH 7.0
are aspartate and glutamate, each with a second carboxyl group.
• These amino acids are the parent compounds of asparagine and glutamine,
respectively.

47. Aromatic R groups
• This class of amino acids includes Phenylalanine, Tyrosine and tryptophan.
• Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains are
relatively nonpolar (hydrophobic).
• All can participate in hydrophobic interactions, which are particularly strong
when the aromatic groups are stacked on one another.
• The hydroxyl group of tyrosine can form hydrogen bonds, and it acts as an
important functional group in the activity of some enzymes.
• Tyrosine and tryptophan are significantly more polar than phenylalanine
because of the tyrosine hydroxyl group and the nitrogen of the tryptophan
indole ring.

49. Fig: Absorption of ultraviolet light by aromatic
amino acids. Comparison of the light absorbance
spectra of the aromatic amino acids at pH 6.0. The
amino acids are present in equimolar amounts(10-3
M) under identical conditions. The light absorbance
of tryptophan is as much as fourfold higher than
that of tyrosine. Phenylalanine absorbs less light
than either tryptophan or tyrosine. Note that the
absorbance maximum for tryptophan and tyrosine
occurs near a wavelength of 280 nm.

50. Reference:
• 1. D. L. Nelson and M. M. Cox. 2017. Lehninger Principles of
Biochemistry. 5th edition. Worth Publishers, New York.
• 2. P. C. Champe., R. A. Harvey and D. R. Ferrier. 2017. Biochemistry:
Lippincott's Illustrated Reviews. 7th edition. Lippincott Williams and
Wilkins. U.S.A

51. Classification of Amino acids on
Nutritional basis
• Essential amino acids
• Non essential amino acids

52. Essential Amino Acids
Essential amino acids
• Amino acids that can not be
produced by the body by an
anabolic pathway and
therefore, need to be supplied
to the body through the diet.
• Are in meat and dairy
products.

53. Arginine Red meet, poultry, fish, dairy products

54. Arginine Role in cell division, wound healing, release of hormones

55. Deficiencies:
• A lack of essential amino acids can have adverse
consequences for the immune system results in reduced
production of antibodies.
• Make an individual more susceptible to becoming ill from
bacterial or viral infections.

56. Non essential
amino acids:
• Nonessential amino acids
that can be synthesized in
human body.
• Therefore, does not have to
be taken it through the diet.
Nonessential amino acids
Alanine
Asparagine
Aspartic acid
Serine
Cysteine
Glutamine
Glutamic acid
Glycine
Tyrosine
Proline

57. Non-Essential
Amino acids
Main Food Sources
Alanine Meat, Poultry, fish, Eggs and dairy products
Asparagine Dairy, Whey, Beef, Poultry, Whole grains
Aspartic acid Oysters, Sprouting seeds, sugar beets, molasses
Serine Soybean, Nuts Almonds, Chickpeas, meat, fish
Cysteine Broccoli, egg yolks, Garlic, Oats
Glutamic Acid Fish, Eggs, and dairy products
Glutamine Beef, Dairy products, Beans, Cabbage
Glycine Legumes, Eggs and dairy products
Tyrosine Turkey, Chicken, Milk, Yogurt, Cottage
Proline Lamb, Sausages, Dairy and egg products

58. Nonessential
amino acids
Benefits of non essential amino acids
Alanine Helps metabolize and clear toxins from the body
Asparagine For healthy brain cells and central nervous system support
Aspartic acid Produce other amino acids and essential enzymes
Serine For muscle metabolism, immune health, and good moods
Cysteine Stimulates collagen production and make the antioxidant Glutathione
Glutamic acid Provide the energy for brain and keeps the ammonia level in check
Glutamine For digestion and immune health
Glycine Heals wounds, aids in vision and hearing
Tyrosine Helps alleviate hypertension, and chronic pain
Proline Repairs tissues and regenerate skin

59. Deficiencies:
• Rare but can occur due to starvation and illness
• Deficiency in arginine is particularly common in premature
infants and thus can lead to problems in detoxifying and
eliminating ammonia from their bodies leading to state of
hyperammonemia.

60. Semi Essential amino acids:
• Semi-essential amino acids are
those that can be synthesized
by the body's metabolic
pathways, but possibly not in
sufficient quantity (especially
in children or the ill), and
therefore may have to be
supplied at least in part by the
diet.
• Example in humans are
Arginine and Histidine.

61. References:
• 1. D. L. Nelson and M. M. Cox. 2017. Lehninger Principles of
Biochemistry. 5th edition. Worth Publishers, New York.
• 2. P. C. Champe., R. A. Harvey and D. R. Ferrier. 2017. Biochemistry:
Lippincott's Illustrated Reviews. 7th edition. Lippincott Williams and
Wilkins. U.S.A

62. References:
• 1. D. L. Nelson and M. M. Cox. 2017. Lehninger Principles of
Biochemistry. 5TH edition. Worth Publishers, New York.
• 2. P. C. Champe., R. A. Harvey and D. R. Ferrier. 2017. Biochemistry:
Lippincott's Illustrated Reviews. 7th edition. Lippincott Williams and
Wilkins. U.S.A