Module 2b - 0

MSE 693N
Materials Science Technologies for

Applications in Life Sciences
Introduction to Life Sciences
MSE 693: Materials Science Technologies for Applications in Life Sciences Instructor: Vivek Verma
Families of Small Organic Molecules in Cells
B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
MSE 693N: Materials Science Technologies for Applications in Life Sciences Instructor: Vivek Verma
Proteins
Proteins
Introduction
• Protein
– Building block from which cells are built
– Execute several cell functions
• Shape
– Specified by its amino acid sequence
– Lowest energy conformation
– α helix and β sheets
• Functioning
– Binding to other molecules
– Binding sites are specific and versatile
– Binding strength is measured by equilibrium constant
Example of some general proteins functions
Enzymes Structural Proteins

Function: Catalysis of covalent bond Function: Provide mechanical support to
breakage or formation cells and tissues
B. Alberts et al.,Materials
MSE 693N: Essential CellTechnologies
Science Biology. for
(Garland Publishing
Applications Inc., New York, ed. Third,
in Life Sciences 2009)
Instructor: Vivek Verma
Transport Proteins
Function: Carries small molecules or Motor Proteins
ions
(Garland Publishing
(Garland Publishing
(Garland Publishing
(Garland Publishing
The Shape and Structure of Proteins
• The shape of a protein is specified by its amino
acid sequence
• A protein molecule is made from a long chain of
amino acids
– Bonds between amino acids: Peptide bonds
• Polypeptide backbone
– Repeating sequence of atoms along the chain
• Side chains
– Amino acid attached to the polypeptide chain
– Give the chain a unique property
• Hydrophobic vs. Hydrophilic
(Garland Publishing
• Noncovalent bonds
– Hydrogen bonds
– Ionic bonds
– van der Waals attractions
– Hydrophobic forces
• Conformation depending on the environment
Noncovalent Bonds Specify the Precise
Shape of Macromolecules
• Most single covalent bonds allow rotation
– Result in unlimited conformations
• Noncovalent bonds however result in
constrained shape of biological macromolecules
Noncovalent Bonds Responsible for Stable
Conformations
• Hydrogen bonds
Conformations
• Ionic bonds
Conformations
• van der Waals attractions
– Form of electrical attraction caused by fluctuating
electric charges, arising whenever two atoms come
within very short distance to each other
http://web.njit.edu/all_topics/Prog_Lang_Docs/html/autodock/AD3-12.gif
Conformations
• Hydrophobic forces
Noncovalent Bonds Mediating Interactions
Noncovalent Bonds Mediating Interactions
Depiction of Protein Structures
• N terminus purple; C terminus red
Depiction of Protein Structures
• N terminus purple; C terminus red
α Helix and β Sheets
• Result from hydrogen bonding between N–H and
C=O groups in the polypeptide backbone
– No involvement with the side chains of amino acids
• β Sheets can either form from
– Parallel chains
• Neighbouring polypeptide chains that run in the same
orientation
– Antiparallel chains
• Each section of the chain running in the direction opposite
to that of its immediate neighbour
– Both type of beta sheets produce a very rigid
structure
α Helix
α Helix
• An α helix is generated when a single
polypeptide chain turns around itself to make a
rigid cylinder
• A hydrogen bond is made between every fourth
polypeptide bond linking C=O of one peptide
bond to the N–H of another
– Gives rise to a regular helix with a complete turn
every 3.6 amino acids
β Sheets
α Helix and β Sheets
• Result from hydrogen bonding between N–H and
C=O groups in the polypeptide backbone
– No involvement with the side chains of amino acids
• β Sheets can either form from
– Parallel chains
• Neighbouring polypeptide chains that run in the same
orientation
– Antiparallel chains
• Each section of the chain running in the direction opposite
to that of its immediate neighbour
– Both type of beta sheets produce a very rigid
structure
β Sheets
α Helix: Coiled coil
• Coiled coil
– Two α helices have most
of their nonpolar side
chains on one side
– Twist around each other
with these side chains
facing inwards
Proteins Have Several Levels of Organization
Primary structure
– Amino acid sequence
• Secondary structure
– α helices and β sheets
• Tertiary structure
– Three dimensional conformation
• Quaternary structure
– Protein is formed as a complex of more than one
polypeptide
chain
• Protein domains
– Part of a polypeptide that can fold independently
into a compact, stable structure
Proteins Have Several Levels of Organization
Larger Protein Molecules Often Contain
More than One Polypeptide Chain
Larger Protein Molecules Often Contain
More than One Polypeptide Chain
• Subunit
– Each polypeptide chain in such a protein (protein
containing more than one polypeptide chain) is
called subunit
• Binding site
– Any region of a protein’s surface that interacts with
another molecule through sets of noncovalent bonds
Proteins Can Assemble in Various shapes
How Proteins Work
• All proteins bind very selectively to other
molecules
– Specificity
• Ligand
– Substance protein binds to
• Binding site
– Region of protein that associates with ligand
How Proteins Work
How Proteins Work
• • Even small changes in the amino acids
sequence can change 3-D shape and destroy
protein’s function
Antibodies (Immunoglobulins)
• Proteins produced by the immune system in
response to foreign molecules
• Y shaped molecules with two identical binding
sites
– Billions of different antibodies
– Diversity generated by changing only the length and
amino acid sequence of the loops
• Antigens
– Target of antibodies
Antibodies-To purify molecules
Antibodies- As Molecular Tags
How Proteins Work
Binding Strength
• Binding strength is measured by equilibrium
constant
– Equilibrium
• Number of binding (association) and unbinding
(dissociation) events reach steady state
– Equilibrium constant
– Equation!
Enzymes
• Enzymes are powerful and highly specific catalysts
– Will catalyse only single type of reaction
• Variety of proteins’ function is to bind to other

molecules
– Antibodies: to bacterium or virus
• Enzymes
– “Remarkable molecules that determine all of the
chemical transformations that occur in cells”
– Bind to ligands (substrate) and convert them into
products without modifying itself
Common Type of Enzymes
How Enzymes Work
• Lysozyme (example)
– Natural antibiotic in saliva, tears, egg whites

– Catalyses cutting of polysaccharide chains in cell
walls of bacteria by hydrolysis
• Due to osmotic pressure cell wall ruptures
– Free energy of severed polysaccharide is less than
free energy of intact chain
• Energy barrier
• Collision energy never exceeds energy barrier
– Transition state
• Atoms around the bond have altered geometry and
electron distribution
How Enzymes Work
• Lysozyme (example)
– Active site: fits the contours of its substrate and
catalyzes the chemical reaction
– The sugar to be broken is distorted from its most
stable conformation
How Enzymes Work: Lysozyme
How Enzymes Work- performance
• Vmax and KM measure enzyme performance
How Enzymes Work- performance
• Michaelis-Menten equation
Regulation of Enzyme Activities
• Feedback inhibition
– Enzyme acting in a reaction pathway is inhibited by a
late product of that pathway
– Large number of final product slows down activity of
enzyme acting in beginning of a reaction pathway
– Works instantaneously and is reversible
• Feedback inhibition is negative regulation
– Regulates an enzyme from acting
• Enzymes can also be subject to positive
regulation
Regulation of (Allosteric) Enzyme Activities
Regulation of (Allosteric) Enzyme Activities
• Regulatory molecule have different shape than
the regular substrate of the enzyme
• Two binding sites on enzyme
– Site for substrate
– Site that recognizes regulatory molecule
• Regulatory molecule induces conformational
change in the protein
• Many proteins are allosteric
– Two or more slightly different conformations

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MSE 693N

Materials Science Technologies for

Introduction to Life Sciences

Enzymes Structural Proteins

• Variety of proteins’ function is to bind to other

– Natural antibiotic in saliva, tears, egg whites

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