This document provides an overview of proteins and amino acids. It discusses the 20 standard amino acids that make up proteins, including their structures and classifications. It also covers key protein structures like primary, secondary, tertiary, and quaternary levels. The primary structure is the amino acid sequence. Secondary structures include alpha helices and beta sheets. Tertiary structure involves folding of the polypeptide chain into a compact 3D structure, and quaternary involves interactions between multiple polypeptide subunits.

1. PROTEINS AND
AMINO ACIDS
BY
DR. SEHRISH LODHI
M.B.B.S, M.PHIL (GENETICS AND MOLECULAR BIOLOGY)
DEMONSTRATOR, BIOCHEMISTRY DEPARTMENT
KING EDWARD MEDICAL UNIVERSITY

2. COURSE CONTENTS
• PROTEIN CHEMISTRY
• AMINO ACIDS
• STRUCTURE OF PROTEINS
• FIBROUS PROTEINS
• PROTEIN METABOLISM
• DISPOSAL OF NITROGEN
• DEGRADATION AND SYNTHESIS OF AMINO ACID

3. AMINO ACIDS
• LEARNING GOALS:
• To know the structure and naming of all 20 protein amino
acids
• To know the classification of amino acids on the basis of their
side chains.
• To know the acid and basic properties of amino acids
• To know the application of Handerson-Hasselbalch equation

4. AMINO ACIDS:
BUILDING BLOCKS OF PROTEIN
• Proteins are linear heteropolymers of -amino
acids
• There are about 300 amino acids occur in nature.
Only 20 of them occur in proteins.

5. STRUCTURE OF AMINO ACIDS

6. Proline is an IMINO ACID

7. ZWITTER ION:
• At physiological PH (7.4),
COOH group is dissociated
forming a negatively
charged carboxylate ion
(COO-) and amino group is
protonated forming
positively charged ion
(NH3
+) forming zwitter ion
• It is an isoelectric form, net
charge is zero.

8. CLASSIFICATION OF AMINO ACIDS

9. Classification on the basis of side
chain character
1. Amino acids with nonpolar side chains
2. Amino acids with uncharged polar side chains
3. Amino acids with acidic side chains.
4. Amino acids with basic side chains.

10. Amino Acids with
Nonpolar Side Chains

12. Amino Acids with
Uncharged Polar Side Chains

13. • Can form:
• H bond
• Di-sulfide bond (cysteine)
• Bonds with other structures like
phosphate group
• Can attach oligosaccharides

15. • Histidine is weakly basic, and the free amino acid is
largely uncharged at physiologic pH.
• Histidine is incorporated into a protein, Its R group can be
either positively charged (protonated) or neutral,
depending on the Ionic environment provided by the
protein.
• Histidine is the only amino acid with a side chain that can
ionize within the physiologic pH range.
• This is an important property of histidine that contributes
to the buffering role it plays in the functioning of proteins
such as Hemoglobin.

16. OPTICAL PROPERTIES OF AMINO ACIDS
• The α-carbon of amino acid is attached to four different
chemical groups is a chiral or optically active carbon atom.
• Amino acids exist in two forms, d and l, that are mirror images
of each other.
• Glycine is the exception – OPTICALY INACTIVE
• All amino acids found in proteins are of the L-configuration.

17. ACIDIC AND BASIC PROPERTIES
OF AMINO ACIDS
• Amino acids are AMPHOTERIC, that is in aqueous
solution contain both weakly acidic α-carboxyl
groups and weakly basic α-amino groups.
• Each of the acidic and basic amino acids contains an
ionizable group in its side chain.
• Thus, both free and some of the combined amino
acids in peptide linkages can act as Buffers.
• Buffers = weak acid [HA] + conjugate base [A-]

18. HENDERSON-HASSELBALCH EQUATION
• For the reaction (HA A- + H+ )
[H+] [A-]
• Ka = ─────
[HA]
• The relation between a weak acid (HA) and its conjugate base(A-) is
described by the HENDERSON-HASSELBALCH EQUATION
[A-]
• pH= pKa + log ───
[HA]
• pKa: is the pH at which half of the protons is removed from the group.
• pKa=log 1/Ka … strong acid  high Ka  low pKa
weak acid  low Ka  high pKa

19. BUFFERS
• Maximum buffering capacity of any weak acid is at
pH = pKa ---- this happens when [HA] = [A-]
• When pH > pKa ---- depronated form [HA] predominates
• When pH < pKa ---- pronated form [A-] predominates

20. TITRATION SOLUTION OF AN
AMINO ACID

21. TITRATION CURVE
OF ALANINE
• Isoelectric point, pI, is the
pH at which amino acid has
no net charge (is in isoelectric
form).
• pI is average of pK1 and pK2
• pH above pI -ve charge
• pH bellow pI +ve charge

22. TITRATION CURVE OF HISTIDINE

23. OTHER APPLICATIONS OF THE
HENDERSON-HASSELBALCH EQUATION

24. Drug Absorbtion
• Acidic drugs: HA A- + H+
• Basic drugs ; BH+ B + H+
• A drug passes through membranes
more readily if it is uncharged.
• Thus, for a weak acid, such as
aspirin, the uncharged HA can
permeate through membranes, but
A– cannot.
• For a weak base, such as morphine,
the uncharged form, B, penetrates
through the cell membrane, but BH+
does not.

25. • Therefore, the effective concentration of the permeable
form of each drug at its absorption site is determined by
the relative concentrations of the charged (impermeant)
and uncharged (permeant) forms.
• The ratio between the two forms is determined by the pH
at the site of absorption, and by the pKa of the ionizable
group.
• The Henderson-Hasselbalch equation is useful in
determining how much drug is found on either side of a
membrane that separates two compartments that differ in
pH, for example, the stomach (ph 1.0–1.5) and blood
plasma (ph 7.4).

27. STRUCTURE AND FUNCTION OF
PROTEINS
• LEARNING GOALS:
• To know the function of proteins.
• To know all the four levels of protein structure.
• To understand protein msfolding

28. FUNCTION OF PROTEINS

29. DIFFERENCE BETWEEN A PEPTIDE AND
A PROTEIN
• The basic distinguishing factors are size and structure.
• Peptides:
• are defined as molecules that consist of between 2 and 50 amino
acids,
• peptides tend to be less well defined in structure than proteins
• subdivided into
• Oligopeptides, which have few amino acids (e.g. 2 to 20), and
• Polypeptides, which have many amino acids.
• Proteins:
• are made up of 50 or more amino acids.
• Proteins are formed from one or more polypeptides joined
together.
• can adopt complex conformations known as secondary, tertiary,
and quaternary structures

30. STRUCTURE OF PROTEINS-
LEVEL OF ORGANIZATION
PRIMARY
SECONDARY
TERTIARY
QUATERNARY
Assembly
Folding
Packing
Interaction
STRUCTURE
PROCESS

31. PRIMARY STRUCTURE OF
PROTEINS
• The sequence of amino acids in a protein is called the primary
structure of the protein.
• In proteins, amino acids are joined covalently by peptide bonds.
• Each component amino acid in a polypeptide is called a “residue”.
• Peptide bonds are resistant to conditions that denature proteins, such
as heating and high concentrations of urea.
• Prolonged exposure to a strong acid or base at elevated temperatures
is required to break these bonds nonenzymically.

32. • Peptide bonds are amide linkages between the α-carboxyl
group of one amino acid and the α-amino group of another.
• All amino acid sequences are read from the N- to the C-terminal end of
the peptide.

33. DETERMINATION OF THE AMINO ACID COMPOSITION
OF A POLYPEPTIDE
I. Cation-exchange chromatography
II. Sequencing of the peptide from its N-terminal end
III. Determination of a protein’s primary structure by DNA
sequencing
• Enzymes that hydrolyze peptide bonds are termed
peptidases (proteases).
• Exopeptidases cut at the ends of proteins and are divided
into aminopeptidases and carboxypeptidases.
• Endopeptidases cleave within a protein.

34. SECONDARY STRUCTURE
OF PROTEINS
• Localized arrangement of adjacent amino acids formed as
the polypeptide chain folds are called secondary structure
of protein

35. ALPHA HELIX
• Spiral structure
• Can easily be stretched due
to tight coiling.
• Side chain extend outwards
• Stabilized by H bonding b/w
carbonyl oxygen and amide
hydrogen. 14
• Amino acids per turn – 3.6
• Alpha helical segments are
found in many globular
proteins like myoglobins,
troponin- c etc.

36. AMINO ACIDS THAT DISRUPT AN α-HELIX:
• Proline - because its secondary amino group is not
geometrically compatible. Instead, it inserts a kink in the
chain
• Charged amino acids – in large numbers, by forming ionic
bonds or by electrostatically repelling each other.
• Amino acids with bulky side chains, such as tryptophan.
• Amino acids that branch at the β-carbon , such as valine or
isoleucine,

37. BETA PLEATED SHEET
• Formed when 2 or more
polypeptides or segments of
polypeptides line up side by side.
• Individual polypeptide - β strand,
each β strand is fully extended-
inelastic.
• They are stabilized by H bond b/w
N-H and carbonyl groups of
adjacent chains.
• All peptide bonds are involved,
either interchain or intrachain
• 2 types
• parallel
• anti -parallel

39. Β-BENDS
(REVERSE TURNS, Β-TURNS)
• Permits the change of direction of the
peptide chain to get a folded structure.
• Involve four successive amino acid
residues. 1  4
• It gives a protein globularity rather
than linearity.
• H bond and ionic bonds stabilizes the
beta bend structure.
• Proline and glycine are frequently
found in beta turns.
• Beta turns often promote the formation
of antiparallel beta sheets.
• Occur at protein surfaces.

40. NON REPETITIVE STRUCTURES
• A significant portion of
globular protein’s structure
may be irregular or unique.
• They include coils and loops.
• Not random, but rather simply
have a less regular structure
• Connect two alpha helix or
beta sheath.
• Present in those area where
bend is required.

41. SUPER SECONDARY STRUCTURES
(MOTIFS)
• Present in globular protein.
• Certain groupings of secondary structural elements are
called motifs.

42. TERTIARY STRUCTURE
• Non-linear
• 3 dimensional
• Refers both to the
• folding of domains
• final arrangement of domains in
the polypeptide.
• The hydrophobic side chains are
buried in the interior, whereas
hydrophilic groups are generally
found on the surface of the
molecule.

43. DOMAINS
• Polypeptide chains containing more than 200
residues usually fold into two or more
globular clusters known as domains.
• Fundamental functional and 3 dimensional
structural unit of proteins.
• Part of protein that can fold into a stable
structure independently
• The core of a domain is built from
combinations of supersecondary structural
elements (motifs).
• Domains often have a specific function such
as the binding of a small molecule.
• Many domains are structurally independent
units that have the characteristics of small
globular proteins.

44. INTERACTIONS STABILIZING
TERTIARY STRUCTURE
• The unique three-dimensional
structure of each polypeptide
is determined by its amino
acid sequence. Interactions
between the amino acid side
chains guide the folding of
the polypeptide to form a
compact structure.
• Hydrogen bonds
• Ionic bonds
• Disulphide bridges
• Hydrophobic interactions

45. QUATERNARY STRUCTURE
OF PROTEINS
• Proteins: a single polypeptide chain -
monomeric proteins.
• Proteins: multiple polypeptide chains -
multimeric proteins.
• The arrangement of these polypeptide
subunits is called the quaternary structure
of the protein.
• Held together primarily by noncovalent
interactions.
• Subunits may either function
independently or may work cooperatively.

46. PROTEIN FOLDING
• Interactions between the side chains of
amino acids determine how a long
polypeptide chain folds into the
intricate three-dimensional shape of
the functional protein.
• Folding is a facilitated process that
requires a specialized group of
proteins, “molecular chaperones,” also
known as “heat shock proteins” (Hsp)
and ATP hydrolysis.
• The chaperones, interact with a
polypeptide at various stages during
the folding process.

47. DENATURATION OF PROTEINS
• Protein denaturation results in the unfolding and disorganization of a
protein’s secondary and tertiary structures without the hydrolysis of
peptide bonds.
• Denaturing agents include:
• Heat,
• Organic solvents,
• Strong acids or bases,
• Detergents and
• Ions of heavy metals such as lead.
• Denaturation may, under ideal conditions, be reversible. However,
most proteins, once denatured, remain permanently disordered.
• Denatured proteins are often insoluble and precipitate from solution.

48. PROTEIN MISFOLDING
• Misfolded proteins are usually tagged and degraded within
the cell
• Deposits of misfolded proteins are associated with a
number of diseases:
• A. Amyloid diseases
• B. Prion diseases
• Misfolding of proteins:
• Spontaneously
• Altered protein – mutation
• Abnormal proteolytic cleavage

49. AMYLOID DISEASES
• Amyloids: Accumulation of insoluble, long,
fibrillar protein assemblies consisting of β-
pleated sheets.
• Spontaneously aggregating proteins.
• Degenerative diseases
• Parkinson
• Huntington
• Alzheimer disease

50. A. ALZHEIMER DISEASE
• Amyloid β (Aβ), an extracellular peptide containing 40–42
amino acid residues – Neurotoxic

51. Tau (τ) protein: Helps in
the assembly of the
microtubular structure.
• Abnormal form -
hyperphosphorylated
and insoluble - block
the normal action
• A key component of
neurofibrillary
tangles inside
neurons.

52. B. PRION DISEASES
• The Prion Protein (PrP) -
causative agent of
transmissible spongiform
encephalopathies (TSEs),
including
• Creutzfeldt-Jakob
disease in humans,
• Scrapie in sheep, and
• Bovine spongiform
encephalopathy in cattle
- “mad cow” disease
• PrPC is present in normal
mammalian brains on the
surface of neurons and
glial cells.

53. CLASSIFICATION OF PROTEINS BASED
ON SHAPE
1. GLOBULAR PROTEINS
• Compact shape like a
ball with irregular
surfaces
• Enzymes are globular
2. FIBROUS PROTEINS
• usually span a long
distance in the cell
• 3-D structure is
usually long and rod
shaped