BC 1008 - Structure and
Function of Biomolecules
Devaka Weerakoon (18 L)
and
Dilrukshi de Silva (12 L)
Department of Zoology
(3 Cr – 30L + 30P)
Objectives and Learning Outcomes
• To Introduce the four basic biomolecules, their structure
and function
• What an amino acids is and their properties
• Structure of a protein
• Few examples of fibrous and globular proteins
• What an enzyme is and their functioning
• Structure of Nucleic acids
• Information storage and expression
• What a carbohydrate is and diferent types of carbohydrates
and functions
• What a lipid is and different types of lipids and their functions
Substances Found in Living Organisms
Water
Macromolecules: Giant Polymers
• There are four major
types of biological
macromolecules:
• Proteins
• Carbohydrates
• Lipids
• Nucleic acids
Macromolecules: Giant Polymers
• These macromolecules are made the same way in all
living things, and are present in all organisms in
roughly the same proportions
• An advantage of this biochemical unity is that
organisms can use these molecules interchangebly
• Macromolecules are giant polymers
• Polymers are formed by covalent linkages of smaller
units called monomers
• Molecules with molecular weights greater than
1,000 daltons (atomic mass units) are usually
classified as macromolecules
Macromolecules: Giant Polymers
• The functions of macromolecules are related to
the shape and the chemical properties of their
monomers
• Some of the roles of macromolecules include:
• Energy storage
• Structural support
• Transport
• Protection and defense
• Regulation of metabolic activities
• Means for movement, growth, and development
• Information storage
Condensation and Hydrolysis Reactions
• Macromolecules are made from smaller monomers
by means of a condensation or dehydration
reaction in which an OH from one monomer is
linked to an H from another monomer
• Energy must be added to make or break a polymer
• The reverse reaction, in which polymers are
broken back into monomers, is a called a
hydrolysis reaction
Condensation and Hydrolysis of Polymers
Condensation and Hydrolysis of Polymers
Condensation
and Hydrolysis
Reactions
How
are organic molecules
synthesized?
Molecules can be metabolized (broken down)
Structure and Function of Biomolecules
1. Introduction to proteins; Protein structure; fibrous
proteins; myoglobin and haemoglobin; immunoglobulins;
Introduction to enzymes; enzyme kinetics and inhibition;
modes of enzyme catalysis; serine proteases
2.Introduction to nucleic acids; Structure of DNA and RNA;
information storage and retrieval; the genetic code
3.Introduction to lipids; steroids and eicosanoids;
phospholipids and membranes; transport across membranes
4.Introduction to carbohydrates; linear and cyclic
structures; stereochemistry and Fischer projections;
Haworth projections; glycosidic bonds; disaccharides;
polysaccharides and complex carbohydrates
Proteins: Polymers of Amino Acids
• Proteins are polymers of amino acids. They are
molecules with diverse structures and functions
• Each different type of protein has a
characteristic amino acid composition and order
• Proteins range in size from a few amino acids to
thousands of them
• Folding is crucial to the function of a protein and
is influenced largely by the sequence of amino
acids
Protein Functions
1. Structural e.g. Collagen, elastin
2. Mobility e.g. Actin/myosin, tubulin, flagella
3. Receptors e.g. Insulin receptor
4. Ligands e.g. Insulin
5. Defense e.g. Antibodies
6. Housekeeping e.g. Enzymes of glycolysis
7. Signalling e.g. Signalling molecules
8. Enzymes e.g. Proteases
9. Storage e.g. Ovalbumin, casein
10.Transport e.g. Haemoglobin
The Monomeric Unit is the Amino Acids
• An amino acid has four groups attached to a central carbon
atom:
• Central carbon atom - a carbon
• A hydrogen atom
• An amino group (NH2)
• A carboxylic group
(COOH)
• Differences in amino acids come from the side chains, or
the R group
• Twenty amino acids used by the living organisms for
synthesis of proteins
Proteins: Polymers of Amino Acids
• Amino acids can be classified based on the
characteristics of their R groups
A. Nonpolar hydrophobic side chains
B. Polar but uncharged side chains
C. Charged hydrophilic side chains
D. Special amino acids
Non Polar Hydrophobic R groups
Charged R groups
Polar but Uncharged R groups
Unusual Amino Acids
• Cysteine has a terminal sulphydral group (SH)
• Glycine has a H atom as the side chain
• Proline - the R group forms a covalent bond with
the amino group, forming a ring (imino acid)
Two cysteines can form a Cystine
Amino Acids Display Stereoisomerism
• An isomer is a compound that has the same
molecular formula but exist in different forms
Amino Acids Display Steroeisomerism
• Compounds that carry asymmetric carbon atoms or chiral
centers show optical isomerism i.e. they can cause plane
polarized light to rotate in left or right direction
• Amino acids show stereoisomerism as all of them except
Glycine carry chiral centers
• Amino acids that exist in nature are the L forms
Special Amino Acids
•
•
•
•
Hydroxyproline
Ornithine
Citrulline
Thyroxine
Amino Acids can act as Week Acids/ Bases
CH3COOH
CH3COO- + H+
• The relationship between the chemical species
and dissociation constant is expressed by the
Henderson-Hasselbalch equation
pH = pKa + log[A-]/[HA]
Amino Acids can act as Buffers
Amino acids contain a basic amino group and an
acidic carboxyl group
Formation of Peptide Linkages
• Proteins are
synthesized by a
condensation reactions
between the amino
group of one amino
acid and the carboxyl
group of another
• This forms a peptide
linkage
• Peptide bond has
partial double bond
character
• Causes linkage to be
planar – no rotation
around peptide bond
Amino acid linkage results in a Peptide
• Dipeptide – peptide consisting of two amino acids
• Tripeptide - peptide consisting of three amino acids
• Oligopeptide - peptide consisting of several amino
acids
• Polypeptide - peptide consisting of many amino acids
• Some examples of naturally occurring peptides
• glutathione – tripeptide (glu-cys-gly) - scavenger of
free radicals
• leucine enkephalen - naturally occurring analgesic
• Oxytocin – Hormone comprising of nine amino acids
• L-aspartyl – L-phenylalanine - aspartame
The Four Levels of Protein Structure: Primary Structure
• There are four levels of protein structure: primary,
secondary, tertiary, and quaternary
• The precise sequence of amino acids is called its
primary structure
• The peptide backbone consists of repeating units of
atoms: N—C—C—N—C—C
The Four Levels of Protein Structure: Secondary Structure
• A protein’s secondary structure consists of regular,
repeated patterns in different regions in a polypeptide chain
• This shape is influenced primarily by hydrogen bonds arising
from the amino acid sequence (the primary structure)
• The two common secondary structures are the alpha helix
and the beta pleated sheet
The Four Levels of Protein Structure: Secondary Structure
• The alpha helix is a right-handed coil
• The peptide backbone takes on a helical shape due
to hydrogen bonds.
• The R groups point away from the peptide
backbone and stabilize the structure by forming H
bonds
• Fibrous structural proteins have a-helical
secondary structures, such as the keratins
found in hair, feathers, and hooves
The Four Levels of Protein Structure: Secondary Structure
• b pleated sheets form from peptide regions that lie parallel
to each other
• Sometimes the parallel regions are in the same peptide,
sometimes they are from different peptide strands
• This sheet like structure is stabilized by H bonds between
N-H groups on one chain with the C=O group on the other
• Spider silk is made of b pleated sheets from separate
peptides
Secondary Structure of Proteins
• Other elements of secondary structure include beta
turns and omega loops
The Four Levels of Protein Structure: Tertiary Structure
• Tertiary structure is the three-dimensional shape
of the completed polypeptide
The Four Levels of Protein Structure: Tertiary Structure
• The primary determinant of the tertiary structure
is the interaction between R groups
• Factors determining tertiary structure:
• The nature and location of secondary structures
• Hydrophobic side-chain aggregation and van
der Waals forces, which help stabilize them
• The ionic interactions between the positive and
negative charges and hydrogen bonding between
polar residues
• Disulfide bridges, which form between cysteine
residues
The Four Levels of Protein Structure: Quatenary Structure
• Quaternary structure
results from the ways in
which multiple polypeptide
subunits bind together and
interact
• This level of structure
adds to the threedimensional shape of the
finished protein
• Hemoglobin is an example
of such a protein; it has
four subunits
The Four Levels of Protein Structure: Summary
Bonds Contributing to the Structure of a Protein
Primary Structure
• Peptide bond (Covalent)
Irregular
contortions
Secondary, Tertiary and
from bondings
Quaternary
Structures
between
side
Noncovalent
Linkages
chains.
Hydrogen
4-20
van der Waals
Hydrophobic
Hydrophobic
clusters at the
Ionic
core of
Covalent Linkages
proteins
Disulphide Bridges
Proteins: Chaperon Proteins
• Chaperonins are
specialized proteins that
help keep other proteins
from interacting
inappropriately with one
another
• When a protein fails to
fold correctly, serious
complications can occur
• Incorrectly folded
proteins are digested by
proteosomes and the
amino acids are recycled
Proteins: Polymers of Amino Acids
• Shape or conformation is crucial to the
functioning of proteins
• The final conformation will be governed by the
type of amino acids that make up the protein
which will influence the folding pattern
• Changes in amino acids can take place due to
changes in DNA a process called mutation that
can drastically change protein structure and
therefore the function
Protein Denaturation
• Changes in temperature, pH, urea, salt
concentrations, and oxidation or reduction
conditions can change the shape of proteins.
• This loss of a protein’s normal three-dimensional
structure is called denaturation.
Protein Modification
• In some proteins further modification is needed
for functioning
• Glycosylation – adding carbohydrate moieties which
takes place in the golgi complex
• Adding lipid moieties especially in membrane
proteins
Membrane Proteins
• Lipid anchored proteins
(a) Glycolipid covalent
attachment by
glycophosphatidyl
inositol (GPI anchored
proteins)
(b) Covalent attachment of
the protein to fatty
acid like myristic acid
or palmitic acid or the
prenyl group (15-C
franesyl hydrocarbons
with repeating vinyl
groups)
Protein Modification
• In some proteins further modification is needed
for functioning
• Glycosylation – adding carbohydrate moieties which
takes place in the golgi complex
• Adding lipid moieties especially in membrane
proteins
• Covalent modification e.g. acetylation and
methylation of Lys, methylation of Arg and His,
phosphorylation of Ser, Thr or Tyr
• Sometimes they need prosthetic groups
• Sometimes cleavage is necessary for final action
Domains
• The term domain is used to describe an area of
a protein which is functionally or physically
distinct
• Steroid Hormone Receptors
Inhibitory protein complex
Hormone binding domain
DNA binding domain
Transcription activating domain
• Another example would be transmembrane
proteins that have cytosolic, transmembrane and
extracellular domains
Globular and Fibrous Proteins
Globular proteins
proteins
“spherical” shape
fibers
Fibrous
long, thin
Insulin
Hair
Hemoglobin
Wool
Enzymes
Skin
Antibodies
Nails
47
Fibrous proteins
• Proteins which are folded to a more or less rod
like shape
• They
• consist of long fibers or large sheets
• tend to be mechanically strong
• are insoluble in water and dilute salt solutions
• play important structural roles in nature
• Involved in structure: tendons ligaments blood
clots, hair, hooves feathers etc., (e.g. Collagen,
elastin, keratin and fibrin)
Fibrous Proteins
Keratin:
• Long, fiber-like shapes
• Typically structural
• Ex: a-keratins
 hair, wool, skin, and nails
 3 a-helices held together by disulfide bonds
• Ex: b-keratins
 Feathers, scales
 large amounts of beta-pleated sheet structure
Fibrous Proteins
• Collagen
• Connective tissue, skin, tendons, and cartilage
• Consists of three polypeptide chains wrapped
around each other in a ropelike twist to form a
triple helix called tropocollagen; MW approx.
300,000
• 30% of amino acids in each chain are Pro and Hyp
(hydroxyproline); hydroxylysine also occurs that
contain –OH groups for hydrogen bonding
Collagen Triple Helix
• Every third position is Gly and repeating
sequences are X-Pro-Gly or X-Hyp-Gly
• The three strands are held together by hydrogen
bonding involving hydroxyproline and
hydroxylysine
• With age, collagen helices become cross linked by
covalent bonds formed between Lys and His
residues
• Deficiency of Hyp results in fragile collagen
Globular Proteins
• Proteins which are folded to a more or less
spherical shape
• They
• Tend to be soluble in water and salt solutions
• Most of their polar side chains are on the
outside and interact with the aqueous
environment by hydrogen bonding and iondipole interactions
• Most of their nonpolar side chains are buried
inside
• Nearly all have substantial sections of a-helix
and b-sheet
Myoglobin and Hemoglobn
• Myoglobin is a protein (globin) containing a single heme
unit, which stores oxygen in cells (especially muscles)
• Hemoglobin is a multimeric protein with four sub units
• May occur intracellulary or extracellularly
• Extracellular hemoglobin has a very high molecular
weight
Both Proteins Contain a Prosthetic Group
• Porphyrins: Metal complexes
derived from porphyrin
• Many respiratory pigments are
designed around the porphyrin
molecule
• After the two H atoms bound
to N are lost, porphyrin is a
tetradentate ligand
• Two important porphyrins are
heme (Fe2+) and chlorophyll
(Mg2+)
Prosthetic Group
• Four N atoms from the porphyrin
ring are attached to the Fe2+
center
• Fifth coordination site is occupied
by a base (Histidine), of the globin
protein
• Sixth coordination site can be
occupied by
• O2 (oxyhemoglobin)
• H2O in (deoxyhemoglobin)
• CO in (carboxyhemoglobin)
• Role of the globin
• Prevent oxidation of Iron
• Reduce affinity to CO
Factors that Effect Oxygen Binding
• Binding of oxygen to Hb
displays co-operativity
• Number of factors can
influence binding of oxygen
• CO2
• pH
• Temperature
• Organic Phosphates (DPG/BPG)
Genetic Basis of Hemoglobin
• Encoded by a multigene family
 a-globin family:
a, z
 b-globin family:
b, d, e, g
• Mutations of the
Hb genes can result
in diseases such as
• Sickle cell anaemia
• Thalassemia
Composition of human hemoglobin chains at different life stages:
Embryo : z2e2, a2e2
Fetus : a2g2
Adult : a2b2 (97%), a2d2 (2-3%), a2g2 (1%)
Sickle-Cell Anemia
• Results from a single
mutation in the beta chain
Glu  Val
• (-) charge is changed to a
nonpolar (hydrophobic)
group
• This site of mutation is at
the surface of the protein in
the deoxy form of
hemoglobin.
• This results in the beta
chains ‘sticking’ together in
the deoxy form
Immunoglobulins
• The antibody molecule comprise of the immunoglobulin
domain
• Immunoglobulin domain comprise of a 100 –110 aa held
together by intra-chain disulfide bonds that forms a
compact loop within the chain (globular domain)
• 2 Heavy chains
• 2 Light chains
• The four chains are held
together by disulphide
linkages
• The quaternary structure
is Y shaped with three
arms
Functions of Antibodies
Enzymes: Biological Catalysts
• Almost all reactions in cells are catalyzed by
enzymes
• Generally most enzymes are proteins
• However RNA can also catalyse reactions
(Ribozymes)
• Enzymes accelerate reactions by lowering the free
energy of activation
• Enzymes do this by binding the transition state of
the reaction better than the substrate
• Transition state is halfway between substrate
structure and product structure
Enzymes lower
∆G‡ (Activation
energy) but do
not affect ∆G
(standard state
free energy)
for a reaction
Lect. 11-
How Enzymes Aid in the Catalytic Process
• Bind substrates
• Lower the energy of the transition state
• Directly promote the catalytic event
• Either through acidic or basic side chains that
promote addition or removal of protons
• Or through holding ions in correct position to
participate in the catalysis
• Release the products
Cofactors
• In addition to the protein part, many enzymes also
have a nonprotein part called a prosthetic group
or a cofactor
• The protein part in such an enzyme is called an
apoenzyme, and the combination of apoenzyme
plus cofactor is called a holoenzyme.
• Only holoenzymes have biological activity; neither
cofactor nor apoenzyme can catalyze reactions by
themselves
• Cofactors form an intricate part of the active site
and play a direct chemical role in the chemistry of
the reaction
64
Cofactors
• A cofactor can be either an inorganic ion or an
organic molecule, called a coenzyme
• Many coenzymes are derived from vitamins,
organic molecules that are dietary requirements
for metabolism and/or growth
• Nicotinamide adenine
dinucleotide (NADH)
N
• Metal atoms e.g. Zn++
O
O
N
• Flavin adenine dinucleotide
(FADH)
• Heme group
NADH
NH 2
O
N
N
O
OH
P
R
O
O
R S
HO
S
O-
P
O
R
R
N
+
NH 2
R
R
HO
O
OH
OH
O
FADH
NH 2
N
Me
N
NH
N
Me
O
N
N
R
R
HO
O
R
S
HO
OH
HO
P
P
O
N
OH
O
O
R
S
S
O
OH
OH
N
O
Classification of Enzymes
Class
Reactions catalyzed
Oxidoreductoases oxidation-reduction
Transferases
transfer group of atoms
Hydrolases
hydrolysis
Lyases
add/remove atoms to /from a
double bond
Isomerases
rearrange atoms
Ligases
combine molecules using ATP
66
Enzyme Action: Lock and Key Model
• An enzyme binds a substrate in a region
called the active site
• Only certain substrates can fit the active site
• Amino acid R groups in the active site help
substrate bind
• Enzyme-substrate complex forms
• Substrate reacts to form product
• Product is released
67
Enzyme Action: Induced Fit Model
• Enzyme structure flexible, not rigid
• Enzyme and active site adjust shape to bind
substrate
• Substrate molecule induced to take up a
configuration approximating the transition
state
• Shape changes also improve catalysis during
reaction
• Increases range of substrate specificity
68
Lock and Key Model vs. Induced Fit Model
E
+
S
ES complex
E +
69
P
Factors Affecting Enzyme Action: Temperature
• Little activity at low temperature
• Rate increases with temperature
• Most active at optimum temperatures (usually
37°C in humans)
• Activity lost with denaturation at high
temperatures
70
Factors Affecting Enzyme Action
Optimum temperature
Reaction
Rate
Low
High
Temperature
71
Factors Affecting Enzyme Action: Substrate Concentration
• Increasing
substrate
concentration
increases the rate
of reaction (enzyme
concentration is
constant)
• Maximum activity
reached when all of
enzyme combines
with substrate
72
Factors Affecting Enzyme Action: pH
• Maximum activity at optimum pH
• R groups of amino acids have proper charge
• Tertiary structure of enzyme is correct
• Narrow range of activity
• Most lose activity in low or high pH
73
Factors Affecting Enzyme Action: pH
Optimum pH
Reaction
Rate
3
5
7
pH
9
11
74
Regulation at Enzyme Function
• This can be achieved through two mechanisms
 Regulation of synthesis
 Regulation of degradation
• Synthesis can be regulated at two levels
 Transcription regulation
 Translation regulation
Gene
RNA
Protein
Enzyme
Modification
Functional
Enzyme
Active
Enzyme
Inactive
Enzyme
Allosteric Regulation
Stimulation & Inhibition by Control Proteins
• Enzyme is regulated by binding of specific stimulatory
or inhibitory protein
• Eg. Calcium-calmodulin
• Regulatory subunit of cAMP dependent protein kinase
Ca++ /
Calmodulin
Target
Ca++/CAM
dependent
protein Kinase
Activated
Ca++/CAM
dependent
protein
Kinase
Proteolytic Cleavage
• Some enzymes are produced as inactive
Zymogens or proenzymes
• The active site of these enzymes are masked by
a part of the molecule
• Cleavage of the masking portion by spontaneous
degradation or other proteolytic enzymes leads
to exposure of the active site and therefore
activation
 Digestive enzymes: Procarboxypeptidase,
Pepsinogen, Trypsinogen,
Reversible Covalent Modification
This result in conformational changes of the enzyme
• Covalent modification is targeted at a R group of one of the
amino acids moieties of the protein
• Phosphorylation at serine, threonine or tyrosine residues
eg. Glycogen phosphorylase
• Adenylylation at tyrosine residues eg Glutamine synthase
• Carboxymethylation at aspartic or glutamic acid residues
Compartmentalization within Organelles or Organs
• Some enzymes and enzyme complexes have fixed
locations within the cells or body
• Nucleus: DNA replication, synthesis of tRNA
and mRNA and some nuclear proteins
• Ribosomes: Protein synthesis
• Chloroplast: Photosynthesis
• Liver: Fatty acid metabolism, Gluconeogenesis,
Glucose metabolism, Glycogen synthesis
• Adipose tissue: Fat metabolism
Enzyme Kinetics
• For a given amount of enzyme the relationship
between reaction velocity and substrate
concentration
E + S
k1
k -1
ES
k2
Michaelis – Menton
rate equation
V init =
V max [S]
KM + [S]
P
Enzyme Kinetics
• Lineweaver-Burk equation and plot allows us to
determine Vmax and Km
Enzyme Inhibition
• Cause a loss of catalytic activity
• There are FOUR types of enzyme inhibition:
1. Irreversible
2. Competitive
3. Non-Competitive
4. Uncompetitive
83
Irreversible Inhibition
• A compound interferes
with the active site so as
to disable it
• Commonly it is done by
forming a stable
covalent adduct with the
enzyme
• May also block substrate
access to site
• Almost all are toxic
substances
Diisopropyl
Fluorophosphate
(DIFP)
Competitive Inhibition
When an unreactive molecule bind to an
enzyme’s active site and compete with the
substrate to bind enzyme
Vmax remain unchanged
Km appear to increase
* Increased substrate can overcome inhibition
Non-Competitive Inhibition
An inhibitor that binds to the enzyme, but not at the active
site. In this case the inhibitor is not competing for the
active site
- Binding distorts the enzyme and reduces its activity e.g.
allosteric regulation of the enzyme
This form of inhibition causes:
Vmax to drop
Km remains unchanged
* increased substrate cannot overcome a non-competitive
inhibitor
Uncompetitive inhibition
• Substrate binding to enzyme is not inhibited
• Inhibitor binds to the ES complex occurs
• ESI complex is stabilized relative to ES
complex so Km is reduced
• ESI complex is non-productive so Vmax is
lowered
How enzymes aid in the catalytic process
• Bind substrates
• Lower the energy of the transition state
• Directly promote the catalytic event
 Either through acidic or basic side chains
that promote addition or removal of protons
 Or through holding ions in correct position to
participate in the catalysis
 Or by inducing stress that makes bonds labile
• Release the products