Protein structure and function

Dr Ashish A Prabhu
Assistant Professor
Department of Biotechnology
National Institute of Technology
Warangal, India 506004
[email protected]
Molecules of Life- Biomolecules

Chemical evolution
Biomolecules
• Proteins
• Nucleic acids (DNA & RNA)
• Carbohydrates
• Lipids

2
Protein Structure and Function
Protein Structure and Function

Stanley millers and others experiment regarding chemical evolution repeatedly produced same
molecules –that is amino acids.

Later it was found that amino acids are the structural unit of proteins

4
 Protein Structure and Function
 Proteins – Amino Acids
 Amino acids –Molecules with both a
Carboxyl and Amino Group
 Meteorites, Versatile components of Cells
Could a protein have been the initial
spark of life?
 Human body cells make tens
of thousands of distinct
proteins
 20 different amino acids – Common core
structure
 R Group contributes for difference in
Structure and Properties
 Ionize in H2O 5
Monomers and Polymers
 Monomers (One – Part)
 Small, similar molecular units
 Form large molecules by condensation/ dehydration reactions
 Immense variety of polymers can be made by a small set of monomers
 Polymers (Many – Parts)
 Long chains of monomers, result of polymerization process
 Can be a straight chain or branched
 Disassembles by hydrolysis reactions
 Each class is formed from specific set of monomers
 Every cell has thousands of different polymers (Cell Type)

6
 R – Group of AAs
 Affects reactivity
 Hydrogen to Large Carbon structures
 Contains carboxyl, sulfhydryl, hydroxyl, or amino functional groups.
 sulfhydryl group (SH) can form disulfide (S-S) bonds that help link different
parts of large proteins (Eg: Hair)
 Affects solubility: Polar or Non-Polar R groups (Hydrophilic and
Hydrophobic Amino Acids)
 Grouped into 3 General types
 Acid/ Basic
 Uncharged Polar
 Nonpolar
 Structural formula at Cellular pH => Type of Amino Acid
7
AAs – Acidic/ Basic

8
AAs – Polar Side Chain

9
AAs – Nonpolar side chains

10 10
Classification of AAs – Multiple Ways…

11
12
Essential ….Semi Essential…Non-Essential AAs…
 Classified based on nutritional requirements
 Essential AAs: Not synthesized in the body – obtained from food
1.Methionine
2. Threonine
Semi Essential AAs
3. Tryptophan 1. Arginine
4. Valine 2. Histidine
5. Isoleucine
6. Leucine
7. Phenylalanine
8. Lysine
 Non Essential AAs: Other 10 AAs not listed here – synthesized in body
13
 Amino Acids Link to Form Proteins
 Polymerization: organizes multiples simple monomers into a single
complex and ordered structure
 Condensation reactions
 Entropy? Spontaneous? Energy?
 Peptide bond: Linking AAs

14
Peptide Bonds
 Carboxyl group of one AA to Amino group of another AA
 Covalent C-N bond: Peptide Bond
 Carboxyl to carbonyl (C=O) group and Amino becomes N-H
 Stable and Planar
 Residue: AAs in a Polymer

15
 Peptide bond backbone – Properties
1. R Group orientation – Side chain interactions: amongst themselves and with H2O
2. Directionality – Free Amino: N-Terminus & Free Carboxyl: C- Terminus

16
Peptide bond backbone – Properties (Contd..)
3. Flexible: Peptide bond: cannot rotate, but the single bonds of either side
of the peptide bond can rotate

17
Oligo peptide…. Polypeptide…. Proteins
 2 AAs: Dipeptides
 3 AAs: Tripeptides
 4-50 AAs: Oligopeptide (few- peptides) or Peptides
 More than 50 AAs: Polypeptides (many- peptides)
 Proteins
 Chain of amino acids
 Complete and Functional form of the molecules
 Most proteins are large
 Some single polypeptide
 Some multiple polypeptides
 Biologically active structures
 Performs Life functions
18
 What do Proteins Look Like?
 Life
 Diversity
 Size
 Shape (Exceptions)
 Chemical properties
of their AA residues
 Structure=>Function
 Primary
 Secondary
 Tertiary
 Quaternary

19
 Proteins - Primary Structure
 Frederic Sanger (1940-50s): First Insulin
 Primary Structure: Unique sequence of AAs in
a protein
 Limitless Possibility: 20n different combinatio ns
of AAs for a polymer with a given length of n
 Fundamental to Overall Structure & 1º, 2º, 3º, 4º

20
Proteins - Secondary Structure
 Interactions between functional groups in the
peptide-bonded backbone.
 Distinctively shaped sections that are stabilized
largely by hydrogen bonding (between C=O and
N-H groups )
 Possible due to bend structure

21
 Proteins - Secondary Structure (Contd…)
 α – Helix: poly peptide backbone is
coiled (4 linear positions apart)
 β – pleated Sheet: Segments of a peptide
chain is bend 180º and fold in the same plane
(folds brings the functional groups closer)
 Ribbon diagrams
 Depends on primary structure – specifically
the geometry and Properties of AAs
 AA Proline – rarely found in α – Helix due to its
structure
 Hydrogens bonds: Week when compared
to covalent bonds

22
 Proteins - Tertiary Structure
 3D shape
 ..as the chain Bends and
Folds..
 Interactions: due to R
groups - 5 types
1. Hydrogen bonding
2. Hydrophobic Interactions
3. van der Walls interactions
4. Covalent bonding
5. Ionic Bonding
 Depends on primary and
secondary structures
23
 Proteins – Quaternary structure
 Combination of multiple polypeptide referred to as Subunits contributes for
Quaternary structure
 Identical/ Non Identical subunits (dimmer, trimer, tetramer)
 Macromolecular Machines: Protein assembly for particular function - Ribosome

24
25
 Protein Folding and Function
 Folding – Spontaneous
 Folding - Contradicts II Law of thermodynamics, Unfolded protein has more
ways to move about than folded proteins due to high ENTROPY than the folded
version; However, equalized by chemical reactions during folding releases energy
to increase the entropy in the surroundings
 Folded Structure – Less potential energy & more stable
 Folding and Structure: Crucial for Functioning of molecules/ a complete
protein
 Christian Anfinsen and Colleagues (1950s) – Structure function relationship
 Studied Unfolding & Denaturation in Ribonuclease: Cleaves Ribonucleic acid
 Chemical Compounds that break hydrogen and disulphide bonds
 Denatured Ribonuclease No longer cleaved Ribonucleic acid
 Removal of Chemicals: Reversed the Function Spontaneously
Inference: Primary sequence contains all the information for folding and folding is
essential for protein function 26
Folding is Crucial to Function

27
Molecular Chaperones – Facilitates Protein
Folding
 Special proteins of cells that facilitates protein folding
 Belong to the Family of Heat Shock Proteins
 Produced in large quantity after cells experience the denaturing
effects of high temperature
 Recognize unfolded proteins by binding to hydrophobic patches that
are not normally exposed when proteins are folded properly : Clumping
of unfolded proteins is avoided
 Chaperones help fold new proteins and denatured proteins

28
Protein shape is flexible
 Characteristic folded shape necessary for its function
 Flexible and Dynamic Shape
 Over half of the analysed proteins: Inactive state-disordered regions lacking
any apparent shape
 Until prompted: Exists in Assortment of Shapes
 What Prompts: Interactions with Ions or molecules, when chemically
modified
 Protein folding is often regulated: Ordered Active Confirmation
 Shape determines function, hence Regulated (cell signalling processes)
 Controlling and Coordinating cellular activities
Protein Function Depends on Shape: Shape depends on folding

29
 Protein shape is flexible (Contd..)
 Folding can be ‘infectious’
 Stanley Prusiner’s (1982) surprising work on folding: Infectious Prions
 Prions (proteinaceous infectious particles): Certain
normal proteins can be induced to fol into infectious
disease-causing agents.
 PrP: Alternate folded forms of normal proteins
present in healthy individuals (same primary structure
but shapes are radically different)
 Eg: ‘mad cow disease’ in cattle and human: spongiform
encephalopathies—literally, “sponge-brain-illnesses.”:
Massive degeneration of brain
How? Transmitted while consuming PrP
containing substances/ rarely inherited;
aggregation of Long fibrils=>death
All PrP illnesses are fatal30
31
Protein Functions – Diverse
 More cell functions than any other type of molecules
 Vital for Life - Life began with proteins
 Eg: Red blood cell: each contains 300 million copies of hemoglobin
(carries O2); thousands of carbonic anhydrase (CO2 from tissues to
Lungs)
 Catalysis: Speed up reactions; A protein that functions as a catalyst is
called an enzyme. Eg: Salivary Amylase, hemoglobin, carbonic anhydrase
 Catalytic function most important: Most chemical reactions that make
life possible depend on enzymes

32
 Protein Functions – Diverse (Contd…)
 Enzymes are most effective catalyst on earth Why
Are Enzymes Good Catalysts?
 Substrate: Reactants of catalysed reactions
 Enzymes hold substrate in a precise
orientation
How enzymes work?
 Emil Fischer (1894): Lock and Key Model
 Enzyme’s Active Site: the location where substrate
binds to an enzymes, clefts or cavities within the
overall shape of the protein
Did Life Arise from a Self-Replicating Enzyme?
 Skeptical: To achieve the attributes of life, proteins
would need to possess information, replicate, and
evolve (..cannot on their own..)

33
 Protein Functions – Diverse (Contd…)
 Defense: Immune system: Antibodies attack and
destroys disease causing bacterial & viruses
 Movement: Motor protein and contractile proteins
- Cell movement & Moving large molecules and
other types of cargo inside the cell. Eg: Actin and
Myosin
 Signaling: Carrying and receiving signals from cell to
cell inside the cells; Reside at cell membrane; Eg:
Glucagon: detects low sugar binds to receptors on
liver cells to trigger release of sugar into your blood.
 Structure: Structural proteins make up body
components and internal skeleton of every cell;
Eg: finger nails and hair; hemoglobin
Signaling - Ref: Chiarini et al., 2015;
 Transport: Enter or Exit the cells/ organ system;
Eg: Membrane proteins that control the passage
of specific molecules and ions Trends Pharmacological Sciences, Vol 36 (2)

34
Thank you !!

35