2yr ppt

1. PRESENTATION
Department of Medical Biochemistry
Topic- Maintaining the native conformation of proteins
under the conditions of the cell
Submitted by:
Sanasam Nganthoi Devi
Group:11-21
Submitted to :
Asilbekova G.K

2. Content
• Introduction
• Properties of protein
• Native Conformation of proteins
• Proteins in their native
conformations have multiple
levels of structural organization
• Importance of Native state Protein
• Factors affecting the
conformation of proteins
• Denaturation
• Protein Denaturation
• Denaturation occurs at levels
of protein structure
• Reversibility and
irreversibility
• Nucleic acid denaturation
• Biologically-induced
denaturation
• Denaturation due to chemical
agents

3. INTRODUCTION
• Protein name is derived form a Greek word
PROTOS which means "the first or the
supreme.
• Protein are extremely complicated and
nitrogenous molecule made up of variable
number of amino acid residue joined to each
other by a specific covalent bond called
peptide bond.
• Most abundant organic molecules of the living
system.
• Its fundamental basis of structures and
function of life .

4. Properties of protein
• Solublity : Forms colloidal solution instead of true
solutions in water - large size of protein
• Molecular Weight : Depends on number of amino acid
• Shape : There is wide variety in shape - globular (
insulin ) , oval (albumin ) , fibrous or elongated (
fibrinogen )
• Acidic and basic : Depends on ratio of ( lysine +
arginine ) : ( Glut + Asp ) . Ratios greater than 1 is
basic and vice - versa

5. Native Conformation of proteins
• The native conformation is analogous
to a plane with all its parts in the
right place: when a protein is in its
native conformation, it's ready to
work.
• When something happens to knock it
out of its native conformation, its
effectiveness decreases or gets lost
all together.

6. Proteins in their native conformations have
multiple levels of structural organization
• Primary Protein-
• Primary protein structure is the linear
sequence of amino acids in a peptide or
protein.
• Primary structure of a protein is
reported starting from the amino-
terminal (N) end to the carboxyl-
terminal (C) end.
• Protein primary structures can be
directly sequenced, or inferred from

7. • Secondary Protein
• The secondary structure of a native
conformation refers to the three
dimensional organization of the
main chain atoms of a protein.
• . Main chain atoms are named in
contrast to side chain atoms, which
are the atoms in an amino
acid.Example , leucine and
Isoleucine

8. Two common types of secondary structures
• The two most common types of secondary structures that occur
in the main chain atoms of proteins resemble coils and zigzags.
The coils are called alpha helices.

9. Tertiary structures
• The tertiary structure of a native
conformation refers to the three
dimensional organization of all the
atoms—including side chain atoms—
in a protein.
• Tertiary structure looks like is to
imagine taking an amino acid
sequence with primary and secondary
structure and crumpling it up into a
ball.

10. Quatanary structures
• The quaternary structure of a native
conformation refers to the three
dimensional organization of all the
atoms in a multi-subunit protein.
• Multi-subunit proteins consist of two
or more individual amino acid chains,
each with their own primary,
secondary, and tertiary structures.

11. Importance of Native state Protein
• Native state proteins can be manufactured is important, as
attempts to create proteins from scratch have resulted in
molten globules and not true native state products.
Therefore, an understanding of the native state is crucial in
protein engineering.
• And in the protein structure side chains can bond with one
another to hold a length of protein in a certain shape or
conformation.
• Charged amino acid side chains can form ionic bonds, and
polar amino acids are capable of forming hydrogen bonds.

12. Factors affecting the conformation of proteins
• The shape is sensitive to physical and chemical
conditions around the protein molecule: -
• pH, ionic strength and temperature will affect
protein conformation.
• Binding and interaction with other molecules
(substrate, cofactors, other proteins) will also
alter protein conformation.

13. Denaturation
• Denaturation is a process in which proteins or nucleic
acids lose the quaternary structure, tertiary structure, and
secondary structure which is present in their native state,
by application of some external stress or compound such
as a strong acid or base, a concentrated inorganic salt, an
organic solvent (e.g., alcohol or chloroform), agitation and
radiation or heat.
• If proteins in a living cell are denatured, this results in
disruption of cell activity and possibly cell death.

14. Protein Denaturation
• Denatured proteins can exhibit a wide range
of characteristics, from loss of solubility to
protein aggregation.
• Protein folding is key to whether a globular or
membrane protein can do its job correctly; it
must be folded into the right shape to
function.
• Hydrogen bonds, which play a big part in
folding,

15. • Functional proteins have four levels of structural organization:
• 1) Primary structure: the linear structure of amino acids in the
polypeptide chain
• 2) Secondary structure: hydrogen bonds between peptide group chains
in an alpha helix or beta sheet
• 3) Tertiary structure: three-dimensional structure of alpha helixes and
beta helixes folded

16. • Process of denaturation:
• 1) Functional protein showing a quaternary structure
• 2) When heat is applied it alters the intramolecular bonds of
the protein
• 3) Unfolding of the polypeptides (amino acids)

17. Denaturation occurs at levels of protein structure
• In quaternary structure denaturation, protein sub-units are
dissociated and/or the spatial arrangement of protein subunits
is disrupted.
• Tertiary structure denaturation involves the disruption of:
• Covalent interactions between amino acid side-chains (such as
disulfide bridges between cysteine groups)
• Non-covalent dipole-dipole interactions between polar amino
acid side-chains (and the surrounding solvent)
• Van der Waals (induced dipole) interactions between nonpolar
amino acid side-chains.

18. • In secondary structure denaturation, proteins
lose all regular repeating patterns such as alpha-
helices and beta-pleated sheets, and adopt a
random coil configuration.
• Primary structure, such as the sequence of
amino acids held together by covalent peptide
bonds, is not disrupted by denaturation.

19. Reversibility and irreversibility
• Denaturation is reversible (the proteins can regain
their native state when the denaturing influence is
removed). This process can be called renaturation.
• Denaturation can also be irreversible. This
irreversibility is typically a kinetic, not
thermodynamic irreversibility, as a folded protein
generally has lower free energy than when it is
unfolded.

20. Nucleic acid denaturation
• Nucleic acids (including RNA and DNA) are nucleotide
polymers synthesized by polymerase enzymes during either
transcription or DNA replication.
• Following 5'-3' synthesis of the backbone, individual
nitrogenous bases are capable of interacting with one
another via hydrogen bonding, thus allowing for the
formation of higher-order structures.
• Nucleic acid denaturation occurs when hydrogen bonding
between nucleotides is disrupted, and results in the
separation of previously annealed strands.

21. Biologically-induced denaturation
• The non-covalent interactions between
antiparallel strands in DNA can be
broken in order to "open" the double
helix when biologically important
mechanisms such as DNA replication,
transcription, DNA repair or protein
binding are set to occur.
• The area of partially separated DNA is
known as the denaturation bubble

22. Denaturation due to chemical agents
• With polymerase chain reaction
(PCR) being among the most
popular contexts in which DNA
denaturation is desired, heating
is the most frequent method of
denaturation.
• Other than denaturation by heat,
nucleic acids can undergo the
denaturation process through
various chemical agents such as
formamide, guanidine, sodium
salicylate, dimethyl sulfoxide
(DMSO), propylene glycol, and

23. Conclusion
• In biochemistry, the native state of a protein or nucleic acid is
its properly folded and/or assembled form, which is operative
and functional.
• The native state of a biomolecule may possess all four levels
of biomolecular structure, with the secondary through
quaternary structure being formed from weak interactions
along the covalently-bonded backbone.
• This is in contrast to the denatured state, in which these
weak interactions are disrupted, leading to the loss of these
forms of structure and retaining only the biomolecule's

24. Reference
• H. Stephen Stoker . Organic and Biological Chemistry. Cengage
Learning.
• Brocchieri L, Karlin S . "Protein length in eukaryotic and prokaryotic
proteomes". Nucleic Acids Research.
• Sanger, F.; Tuppy, H.. "The amino-acid sequence in the phenylalanyl
chain of insulin. I. The identification of lower peptides from partial
hydrolysates". The Biochemical Journal.
• Sanger, F. "Chemistry of Insulin". Science.
• Pauling L, Corey RB, Branson HR . "The structure of proteins; two
hydrogen-bonded helical configurations of the polypeptide chain".
• Chiang YS, Gelfand TI, Kister AE, Gelfand IM .New classification of
supersecondary structures of sandwich-like proteins uncovers strict

25. Thank you for your
attention