Structure of protein

1. Protein Structure

2. Protein Functions
• Three examples of protein functions
– Catalysis:
Almost all chemical reactions in a living
cell are catalyzed by protein enzymes.
– Transport:
Some proteins transports various
substances, such as oxygen, ions, and so
on.
– Information transfer:
For example, hormones.
Alcohol
dehydrogenase
oxidizes alcohols
to aldehydes or
ketones
Haemoglobin
carries oxygen
Insulin controls
the amount of
sugar in the
blood

3. Amino acid: Basic unit of protein
COO-
NH3
+ C
R
H
An amino acid
Different side chains, R,
determine the
properties of 20 amino
acids.
Amino group Carboxylic
acid group

4. 20 Amino acids
Glycine (G)
Glutamic acid (E)
Asparatic acid (D)
Methionine (M)
Threonine (T)
Serine (S)
Glutamine (Q)
Asparagine (N)
Tryptophan (W)
Phenylalanine (F)
Cysteine (C)
Proline (P)
Leucine (L)
Isoleucine (I)
Valine (V)
Alanine (A)
Histidine (H)
Lysine (K)
Tyrosine (Y)
Arginine (R)
White: Hydrophobic, Green: Hydrophilic, Red: Acidic, Blue: Basic

5. Each protein has a unique structure!
Amino acid sequence
NLKTEWPELVGKSVEEAK
KVILQDKPEAQIIVLPVGTI
VTMEYRIDRVRLFVDKLD
Folding!

6. Protein Structure
Primary
Secondary
Tertiary
Quaternary
Assembly
Folding
Packing
Interaction
S
T
R
U
C
T
U
R
E
P
R
O
C
E
S
S

7. Protein Assembly
• occurs at the ribosome
• involves polymerization of
amino acids attached to
tRNA
• yields primary structure

8. Primary Structure
• linear
• ordered
• 1 dimensional
• sequence of amino acid
polymer
• by convention, written
from amino end to
carboxyl end
• a perfectly linear amino
acid polymer is neither
functional nor
energetically favorable 
folding!
primary structure of human insulin
CHAIN 1: GIVEQ CCTSI CSLYQ LENYC N
CHAIN 2: FVNQH LCGSH LVEAL YLVCG ERGFF YTPKT

9. Protein Folding
• yields secondary structure
• occurs in the cytosol
• involves localized spatial
interaction among primary
structure elements, i.e. the amino
acids

10. Secondary Structure
• non-linear
• 3 dimensional
• localized to regions of an
amino acid chain
• formed and stabilized by
hydrogen bonding,
electrostatic and van der
Waals interactions

11. Secondary structure
α-helix β-sheet
Secondary structures, α-helix
and β-sheet, have regular
hydrogen-bonding patterns.

12. Protein Packing
• occurs in the cytosol (~60% bulk
water, ~40% water of hydration)
• involves interaction between
secondary structure elements
and solvent
• yields tertiary structure

13. Tertiary Structure
• non-linear
• 3 dimensional

14. Protein Interaction
• occurs in the cytosol, in close proximity to other folded and
packed proteins
• involves interaction among tertiary structure elements of
separate polymer chains

15. Quaternary Structure
• non-linear
• 3 dimensional

16. Protein Function
• Catalysis – enzymes
• Structural – keratin
• Transport – hemoglobin
• Trans-membrane transport – Na+/K+ ATPases
• Toxins – rattle snake venom, ricin
• Contractile function – actin, myosin
• Hormones – insulin
• Storage Proteins – seeds and eggs
• Defensive proteins – antibodies
16

17. Forces stabilising proteins

18. • The five main forces that stabilise protein
structures. The forces are: 1. Salt Linkages 2.
Hydrogen Bonding 3. Disulfide Linkages 4.
Hydrophobic Interactions 5. Van der Waals’ Forces.
• Force # 1. Salt Linkages:
– Salt linkages (ionic bonds) result from interactions
between positively and negatively charged groups on the
side chains of the basic and acidic amino acids. For the
mutual attraction between an aspartic acid carboxylate
ion and a lysine ammonium ion helps to maintain a
particular folded area of the protein:

19. • Primary structure is when amino acids are
linked together by peptide bonds to form
polypeptide chains. There are two types of
secondary structures observed in proteins.
One type is the alpha (α) helix structure. This
structure resembles a coiled spring and is
secured by hydrogen bonding in the
polypeptide chain. The second type of
secondary structure in proteins is the beta (β)
pleated sheet.

20. • A major force stabilizing the tertiary structure is
the hydrophobic interaction among nonpolar side
chains in the core of the protein. Additional
stabilizing forces include electrostatic interactions
between ionic groups of opposite charge, hydrogen
bonds between polar groups, and disulfide bonds .
• The stabilizing forces that hold the polypeptide
subunits together are the same forces that are
responsible for tertiary structure stabilization. A
major force stabilizing the quaternary structure is
the hydrophobic interaction among nonpolar side
chains at the contact regions of the subunits.

21. Amino acids – Structures - Classification –
Zwitterions – Titration

23. ZWITTER ION: A zwitter ion is a molecule that has both positive
and negative charges.

27. C0=NH2

39. The 21st and the 22nd amino acid
• Emerging evidence suggests that enzymes responsible for
selenocysteine formation and decoding the selenocysteine
UGA codon, which by extension are critical for synthesis of the
entire selenoproteome, are essential for the development and
health of the human organism.
• Selenocysteine is an analogue of cysteine (Figure 3.5). In
place of a sulfur atom in the cysteine, selenocysteine contains
selenium (Se). Several human proteins and enzymes are
selenoproteins. Selenocysteine is located in the active sites of
enzymes that participate in oxidation–reduction reactions.

40. • Selenocysteine (Sec) and pyrrolysine (Pyl) are
rare amino acids that are cotranslationally
inserted into proteins and known as the 21st
and 22nd amino acids in the genetic code. Sec
and Pyl are encoded by UGA and UAG codons,
respectively, which normally serve as stop
signals.

41. Titration Curve

43. • Zwitterion, also known as inner salt or dipolar ion, is an
ion with a positive and a negative electrical charge at
different locations within a molecule. ... The term
zwitterion is derived from the German word zwitter,
meaning a hybrid, hermaphrodite.
An amino acid has this ability because at a certain pH value (different
for each amino acid) nearly all the amino acid molecules exist as
zwitterions. If acid is added to a solution containing the zwitterion, the
carboxylate group captures a hydrogen (H +) ion, and the amino acid
becomes positively charged

44. PEPTIDES
• A peptide is a molecule consisting of two or more amino acids
linked together by peptide bonds. The general structure of an
amino acid is: R-CH(NH2)COOH. Each amino acid is a
monomer that forms a peptide polymer chain with other
amino acids when the carboxyl group (-COOH) of one amino
acid reacts with the amino group (-NH2) of another amino
acid, forming a covalent bond between the amino acid
residues and releasing a molecule of water.
• Cyclic peptides are polypeptide chains taking cyclic ring
structure. The ring structure can be formed by linking one end
of the peptide and the other with an amide bond, or other
chemically stable bonds such as lactone, ether, thioether,
disulfide, and so on.

45. Naming of Peptides
• Peptides are named according to how many amino acid
residues they contain or according to their function:
• Monopeptide: consists of one amino acid
• Dipeptide: consists of two amino acids
• Tripeptide: has three amino acids
• Tetrapeptide: has four amino acids
• Pentapeptide: has five amino acids
• Hexapeptide: has six amino acids
• Heptapeptide: has seven amino acids
• Octapeptide: has eight amino acids
• Nonapeptide: has nine amino acids
• Decapeptide: has ten amino acids
• Oligopeptide: consists of between two and twenty amino
acids

46. • In writing the peptide structure, the amino
terminal (N-terminal) amino acid is written
first and carboxyl terminal (C-terminal) amino
acid written last.
Peptides of physiological interest :
Glutathione is a commonly occurring tripeptide (-
glutamyl cysteinyl glycine) in many living organisms.
It has a role in detoxification of toxic compounds in
physiological system.

47. Functions of peptides
• These short chains are able to penetrate the top
layer of the skin, where they go to work delivering
their anti-aging benefits, such as helping stimulate
collagen production and fight fine lines and wrinkles.
• Hormones When a peptide functions as a hormone it
carries signals from cell to cell or gland to gland.
• Antibiotics When functioning as an antibiotic
peptides help prevent the growth of microorganism
inside our bodies.
• Structural Support Once a peptide has a chain of 50
amino acids or more they form proteins.

48. • Neuropeptides When functioning as a
neuropeptides they act as signals and regulators in
the brain.
• Alkaloids This type of peptide is often found in
small animals plants and fungi. It is used in the
creation of defense mechanisms inside these
organisms.