MSE 204

Introduction to Biomaterials

Module 3
Cells and Proteins

Instructor: Vivek Verma

 Topics
• Introduction to
– Biological cells
– Structure and properties of proteins

Instructor: Vivek Verma

 Basic Cell Biology
Cells
• Fundamental units of life
• 5-20 µm in diameter
• Grow and divide into two
• Have several internal components and
organelles
– Nucleus is information store (genetic) of the cell
– Cytoplasm is cell minus nucleus, contain
membrane bound organelles
• Mitochondria generate energy from food
• Chloroplasts capture light from Sunlight
– Cytosol
• Concentrated mixture of large and small molecules
Instructor: Vivek Verma
 Basic Cell Biology
• Cells
– Fundamental units of life
– 5-20 µm in diameter
– Grow and divide into two

http://www.enchantedlearning.com/subjects/animals/cell/anatomy.GIF

Instructor: Vivek Verma

 Basic Cell Biology
• Have several internal
components and
organelles
– Nucleus is information
store (genetic) of the cell
– Cytoplasm is cell minus
nucleus, contain
membrane bound
organelles
• Mitochondria generate
energy from food
• Chloroplasts capture light
from Sunlight
– Cytosol
• Concentrated mixture of
large and small molecules http://www.enchantedlearning.com/subjects/animals/cell/anatomy.GIF

Instructor: Vivek Verma

 Cell: Intracellular Compartments
• Nucleus
– Enclosed within nuclear envelope
– Contains DNA
• Encode genetic specification of the organism
• Condensed form of DNA is chromosomes
– Eucaryotes: cells with nucleus
– Procaryotes: cells without nucleus
• Mitochondria
– Generate energy from food
– Oxidation of food (e. g. sugars) to produce basic chemical
fuel adenosine triphosphate (ATP)
• Chloroplast
– Capture energy from sunlight to perform photosynthesis

Instructor: Vivek Verma

 Cell: Intracellular Compartments
• Endoplasmic Reticulum
– Materials destined for export from cell are made
• Golgi Apparatus
– Chemically modifies the molecules made in the
endoplasmic reticulum
• Lysosomes
– Intracellular digestion
– Release nutrients from food particles and breaking
unwanted molecules for recycling
• Peroxisome
– Provide isolated environment for generation and
degradation of hydrogen peroxide

Instructor: Vivek Verma

 Cytoskeleton
• Network of long, fine filament of proteins

Instructor: Vivek Verma

 Cytoskeleton

http://scienceprofonline.googlepages.com/cytoskeleton3.gif/cytoskeleton3-full.jpg
Instructor: Vivek Verma
 Cytoskeleton
• Network of long, fine filament of proteins
• Actin filaments
– Part of machinery that create contractile forces in
muscle cells
• Microtubules (MTs)
– Hollow tubes ~25 nm diameter
– Help pull duplicated chromosomes in opposite
direction and distribute them equally to daughter
cells
• Intermediate filaments
– Thickness between actin filament and MT
– Strengthen the cell machinery
Instructor: Vivek Verma
 Molecules in Cells
• Cells contain four major families of small
organic molecules
• They form monomeric building blocks for
most macromolecules
– Sugars
– Fatty Acids
– Amino Acids
– Nucleotides

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)
Instructor: Vivek Verma
 Proteins

Proteins
Instructor: Vivek Verma
 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

Instructor: Vivek Verma

 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., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
Example of some general proteins functions

Motor Proteins
B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
Example of some general proteins functions

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins
• The shape of a protein is specified by its
amino acid sequence

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins
• A protein molecule is made from a long chain
of amino acids
– Bonds between amino acids: Peptide bonds

Instructor: Vivek Verma

 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins
• 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

Instructor: Vivek Verma

 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins
• Noncovalent bonds
– Hydrogen bonds
– Ionic bonds
– van der Waals attractions
– Hydrophobic forces
• Conformation depending on the environment

Instructor: Vivek Verma

 Noncovalent Bonds
• 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

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Noncovalent Bonds

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Noncovalent Bonds
• Hydrogen bonds

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Noncovalent Bonds
• Ionic bonds

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Noncovalent Bonds
• 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
Instructor: Vivek Verma
 Noncovalent Bonds
• Hydrophobic forces

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
Noncovalent Bonds Mediating Interactions

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Macromolecules formation

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 The Shape and Structure of Proteins

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
Proteins come in a Wide Variety of Complicated Shapes

• Amino acid sequence

– Precise order of amino acids in a pure protein
• Proteins have 30 – 10000 amino acids
• X – Ray and nuclear magnetic resonance
methods are used to discover precise folding
patterns of protein

Instructor: Vivek Verma

 Depiction of Protein Structures
• N terminus purple; C terminus red

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Depiction of Protein Structures
• N terminus purple; C terminus red

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 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

Instructor: Vivek Verma

 α Helix

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 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

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 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

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 β Sheets

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 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

Instructor: Vivek Verma

 β Sheets

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
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

Instructor: Vivek Verma

Proteins Have Several Levels of Organization

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Larger Protein Molecules Often Contain
More than One Polypeptide Chain

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 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

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 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

Instructor: Vivek Verma

 How Proteins Work

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 How Proteins Work
• Even small changes in the amino acids
sequence can change 3-D shape and destroy
protein’s

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 Binding Strength
• Binding strength is measured by equilibrium
constant
– Equilibrium
• Number of binding (association) and unbinding
(dissociation) events reach steady state
– Equilibrium constant

Instructor: Vivek Verma

 Enzymes
• Enzymes are powerful and highly specific
catalysts
– Will catalyze 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

Instructor: Vivek Verma

 Common Type of Enzymes

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 How Enzymes Work- Lysozyme
Lysozyme (example)
• Natural antibiotic in saliva, tears, egg whites
• Catalyses cutting of polysaccharide chains in cell
walls of bacterial 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

Instructor: Vivek Verma

 How Enzymes Work- Lysozyme
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

Instructor: Vivek Verma

 How Enzymes Work- Lysozyme

B. Alberts et al., Essential Cell Biology. (Garland Publishing Inc., New York, ed. Third, 2009)
Instructor: Vivek Verma
 How Enzymes Work: Performance
• Vmax and Km measure enzyme performance

Instructor: Vivek Verma

 How Enzymes Work: Performance
• Vmax and Km measure enzyme performance
• Michaelis-Menten equation

Instructor: Vivek Verma