Topics 1-4: Biological molecules
Lipids




Made
of
Bonds
Prope
rties
S&F
Insoluble in water
High solubility in non-polar solvents
Simple lipids, compound lipids, and lipid derivatives
Non-polymer
Simple Lipid
(triglycerides)
 Glycerol
 3 fatty acids
Compound Lipid
(phospholipids)
 Esters of 2 fatty acids
 An alcohol
 Additional small charged
group (eg choline, serine)
Ester linkage btw OH
Ester linkage; phosphoester
group of Glycerol and
linkage btw 3rd OH group of
COOH group of a fatty
glycerol and phosphate
acid by condensation
group
 Melting point
 Amphipathic
increases with
 Aggregate in aqueous
hydrocarbon chain
environment to shield
length and degree of
hydrophobic tails from
saturation
water
 Saturated fats (no
 Micelle: small, spherical
double bonds)
droplet; monolayer
 Unsaturated fats
 Bilayer: 2D sheet
(contains double
 Liposome/vesicle: hollow
bonds)
sphere formed when
bilayer folds back on itself
Structure
Function
Structure
Function
Hydrophobic Allow motile Amphipathic  Forms a
organisms hydrophobic selectively
fatty acid;
to keep
permeable cell
their mass hydrophilic
membrane;
phosphate
to a
boundary btw
head
minimum
cell & external
environment
 Does not
 Liposome/
affect cells’
water
vesicle:
potential
storage and
transport of
 Good
cellular
thermal
products
insulator
 Micelles:
transport fats
Weak
Adipose
Hydrophobic  Maintain
hydrophobic tissue
interaction
integrity of
interaction cushions & btw fatty
membrane
protects
acid tails
bilayer
Compound Lipid (glycolipids)



Glycerol
2 hydrocarbon tails
A polar, short
carbohydrate chain
Glycosidic bond btw OH
group of glycerol and C atom
on carbohydrate chain

Amphipathic due to
soluble carbohydrate
chain and insoluble
hydrocarbon tails
Structure
Carbohydra
te chain
attached to
lipid
Hydrocarbo
n tails
Function
 Found on cell
surface
membrane
facing
external
environment
 Serves as a
marker in
cell-cell
recognition
 Involves in
cell-cell
adhesion as
a result of
binding
Hydrophobic
interaction
btw fatty acid
tails serve to
Topics 1-4: Biological molecules
vital organs
anchor the
 Permit lateral
against
glycolipids at
movement:
physical
cell surface
membrane
impact
membrane
fluidity
Lower
Aid
Contain
Important for
density than buoyancy of choline
synthesis of
water
aquatic
acetycholine
animals
Higher
Efficient
proportion energy
of C and H to store:
O atoms
releases
38kJ/g upon
oxidation
Large
Release
number of C- metabolic
H bonds
water
Kink: a bend in the hydrocarbon chain caused by a C=C double bond; prevents the molecules from
packing closely enough, thus weakening hydrophobic interactions and lowering the melting point
Lipid derivative: eg. Steroids, ketone bodies, fatty alcohols, carotenoids
Cholesterol: made up of 3 fused 6-membered and one 5-membered ring. Intercalated in
phospholipid membrane; interferes in hydrophobic interactions.
Carbohydrates

Contains a carbonyl (C=O) group and multiple hydroxyl (OH) groups
Monosaccharide
Disaccharide
 (CH2O)n
 Formed from 2
monosaccharides in a
 Important as energy
condensation reaction, by a
source/respiratory substrate
glycosidic bond
 Building blocks for synthesis of
 Maltose α(1, 4)
disaccharides and
polysaccharides
 Lactose β(1, 4)
 Aldo sugar (C=O on 1C)/
 Sucrose α(1, 2) [not a reducing
ketone (C=O on 2C)
sugar due to lack of a Free
Anomeric Carbon; both
 May exist as linear or ring
anomeric C1 of glucose and
structures, in dynamic eqm
anomeric C2 of fructose are
 Ring structure incorporated
used in formation of C-O-C]
into di/polysaccharides
Anomeric Carbon: Carbon that is bonded to 2 Oxygen atoms
Polysaccharide
 Macromolecular
polymers
 Serve as storage
materials (eg. Starch
and glycogen)
 Serve as structural
materials (eg.
cellulose) for
structural support
Glycosidic Bond: bond formed when the anomeric hydroxyl group of one sugar unit and any
hydroxyl group on the other sugar react to form a C-O-C bond with the elimination of a water
molecule
Topics 1-4: Biological molecules
α-glucose: anomeric hydroxyl group lies below the plane of the ring
β-glucose: anomeric hydroxyl group lies above the plane of the ring
Found in
Main
function
Monomer
Glycosidic
bond
S&F
Starch
Plants (as starch granules)
Storage
α-glucose
Amylose α(1, 4)
Amylopectin α(1, 4) & α(1,
6)
Structure
Large molecule
Composed of 10-1000 of
glucose monomers
Molecules are highly
branched
Anomeric carbon involved
in glycosidic bond
formation, leaving few free
anomeric OH groups
Structure
Function
Amylose
Can be easily
molecules hydrolysed
linked by
by enzymes
α(1, 4)
present in
glycosidic
plants and
bonds
most org
Amylose
Compact
molecules shape is ideal
are packed for storage
in a helical
coil
Iodine test Blue-black colouration
Glycogen
Animals (liver, skeletal
muscles in the form of
cytoplasmic granules)
Storage
Cellulose
Plants (cell wall)
α-glucose
α(1, 4) & α(1, 6)
β-glucose
Β(1, 4)
Support
Function
Structure
Function
Insoluble; ideal as storage
Alternate
 β(1, 4) result in
material as it does not
inverted βlong, unbranched
exert osmotic pressure
glucose units
chains
within cells and living org
linked by β(1, 4)  not easily
glycosidic bonds hydrolysed by
Large number of glucose
molecules act as a large
acid/ enzyme
store of carbon and energy
 stable structural
(respiratory substrate)
support
Compact shape allow for
easy storage; supplies
larger number of free ends
available for hydrolysis by
amylase at any one time
Makes it an unreactive and Long and
Allows extensive
chemically-stable
unbranched
hydrogen bonds to
compound, ideal as a
with OH groups form btw parallel
storage substance
projecting
chains, which are
outwards from grouped into
Structure
Function
cellulose chains microfibrils
Glucose
Can be
resulting in high
unit linked
hydrolysed by
tensile strength
by α(1, 4)
glycogen
glycosidic
phosphorylase;
bonds
Coiled
helically;
compact
Microfibrils
Higher tensile
associate into
strength; stability
macrofibrils
Cellulose fibres Withstand forces
laid down in
exerted in all
different
directions; full
orientation in
permeability to
different layers water and solutes
Red-violet colouration
None
Topics 1-4: Biological molecules
Proteins



contain C, H, O, N and S
polymers (polypeptide) made of 20 amino acids
polypeptides (pp) folded and coiled into a unique 3D conformation
• Haemoglobin
• Ion protein channel
• Enzyme
• Ribosome
Catabolism
Transport
Structural
Regulatory
• collagen
• muscle
• hair and nails
• Hormone
• Antibody
• Receptor
Amino Acid




Contains amine group (-NH2), acidic carboxyl group (-COOH), H atom, variable R group (size,
charge, polarity and hydrophobicity of R group determine the type and location of bonds
present at higher levels of the protein)
Able to form an electrically neutral, dipolar Zwitterion -> amphoteric (act as buffers)
Non-polar(hydrophobic) /polar uncharged(hydrophilic; no net charge) / polar
charged(hydrophilic)
Glycine: smallest R group-H. Proline: bulky aa residue; does not fit readily into secondary
structure, producing kinks Cysteine: forms strong covalent disulphide bridge with another
cysteine aa residue.
Denaturation: Loss of the specific 3D conformation of a protein molecule, when the bonds that
maintain the conformation of the protein is broken and the protein unfolds and can no longer
perform its normal biological function
Primary Struture
Secondary Structure
Tertiary Structure
Quatenary Structure
• specific linear
sequence and
unique number of
amino acids that
constitute the pp
chain
• joined by peptide
bond (-CONH-)
• formed in N to C
direction
• peptide bond only
• regular coiling and
folding of regions
of the pp chain to
form repeated
patterns,
maintained by
regularly spaced H
bonds btw CO&NH
• α-helix & β-pleated
sheet
• Hydrogen bond
only
• further bending ,
twisting and folding of
the pp chain with the
secondary structures
to give a precise
overall 3D
conformation of a
protein
• Ionic, Hydrogen,
disulfide bonds and
hydrophobic
interactions btw Rgroups
• overall protein
structure that results
from the association of
two or more pp chains
to form a functional
multimeric protein
• eg. collagen,
haemoglobin
• Ionic, Hydrogen,
disulfide bonds and
hydrophobic
interactions
Topics 1-4: Biological molecules
α-helix
Extended spiral spring (3.6 residues per
turn)
Formation  Pp backbone forms repeating helical
structure
 stabilised by intra-chain H bonds
 btw O atom of nth C=O is H bonded to
(n + 4th) NH on the linear sequence
Special
 H bonds formed are parallel to main
features
axis of helix
 R groups of aa residues project
outside the helix, perpendicular to
the main axis
Examples α-keratin
Shape
Shape
Primary
Collagen
Globular
α-chain, containing 141 aa
β-chain, containing 146 aa
 Each pp consists of 8 α helices
connected by non-helical segments
 Stabilized by H bonds
 Also contains a haem prosthetic
group
Tertiary
 Each pp chain is folded such that the
hydrophilic aa residues are located
at the surface of a subunit while
hydrophobic ones are buried in the
interior of the molecule -> soluble
 Allows formation of a hydrophobic
cleft to allow the haem prosthetic
group (an Fe ion held in a porphyrin
ring structure) to bind
 Each haem group will allow for the
binding of 1 molecule of oxygen
Quaternary  Tetrameric
 2 pp chains in each dimer(αβ) are
held together by hydrophobic
interactions, though ionic and H
bonds also occur
 4 subunits form a spherically shaped
molecule held by multiple noncovalent interactions
Secondary
β-pleated
Extended zigzag, sheet-like conformation
 stabilised by H bonds btw carbonyl and
amine groups of the peptide backbone
 can occur within the same pp chain(intra)
or btw neighbouring pp chains(inter)
 Antiparallel/parallel
 Aa with bulky R groups cause steric
hindrance -> aa residues in β-pleated
usually have smaller R groups
Silk fibroin
Haemoglobin
Fibrous
 Repeating tripeptide sequence of
Glycine-X-Y, where X is often proline and
Y is often hydroxyproline/hydroxylysine
 Each pp chain is >1000 aa residues long
 Every 3rd residue (glycine) passes
through the centre of triple helix
 Each collagen pp assumes a left-handed
helical conformation with about 3
residues per turn, known as the collagen
helix
 Each chain is called an α-chain
 Each collagen molecule consists of 3 αchains, held by extensive H bonding
 3 parallel α-chains wind around one
another with a gentle right-handed,
rope-like twist to form a tropocollagen,
aka right-handed triple helix
 Bulky proline residues are located on
the outside of the triple-helix
Topics 1-4: Biological molecules
Function
 Reversible binding to oxygen
 As Fe2+ binds to O2, the iron ion is
pulled closer
 Creating a strain on the other
haemoglobin subunits, such that the
previously obscured haem groups of
other subunits are not revealed
 Hence, remaining subunits have
changed their shape/conformation
to allow oxygen to bind more readily
by increasing their affinity to oxygen
= cooperative binding
 Many tropocollagen lie side by side
(staggered), linked by covalent crosslinks giving rise to a collagen fibril
 Arrangement is stabilised by
hydrophobic interactions
 Structural support
 Strong, insoluble fibers with great tensile
strength
 Well-packed rigid triple structure is
responsible for its characteristic tensile
strength (supertwisted)
 Staggered arrangement confers greater
strength to collagen
Enzymes






Biological catalysts that speed up reactions by lowering the activation energy of reaction,
thereby allowing more substrate molecules to attain the transition state
Effective in small amounts
Remain chemically unchanged at the end of reaction and can be used repeatedly
Specific to substrate of group substrates
Speed up the rate at which chemical eqm is reached but does not alter the eqm itself
Rate of reaction is affected by [E], [S], temperature and pH
Aa residues
Function
Active Catalytic  Directly involved in catalytic activity – making/breaking of chemical
site
bonds
 Facilitate reaction often by acting as donors or acceptors of H+ of other
groups on the substrate
Binding Hold substrate(s) in position while catalysis takes place by associating with
substrate transiently through non-covalent bonds
Structural
Involved in maintaining the specific 3D conformation of the active site, and
the enzyme on a whole, which is esp important for proper functioning of
the globular protein
Non-essential
No specific function
Active site: site on enzyme where the substrate molecule(s) binds to; unique 3D conformation of
active site ensures only substrates with a complementary conformation will enter and undergo
specific reactions.
Topics 1-4: Biological molecules
Enzymes lower activation energy by:
1. Orientating the substrates in close proximity, in the correct orientation, to undergo
chemical reactions
2. Straining critical bonds in the substrate molecule(s), allowing the substrates to attain
their unstable transition state configuration
3. Providing a microenvironment that favours the reaction due to presence of specific
amino acids/ions on active site
Induced fit Hypothesis
E+S
E-S Complex
Product
formed
• When a complementary substrate enters the enzyme active site, it is
held by weak bonds to the R groups of binding aa residues
• substrate binding induces a conformation change in the active site
• enzyme changes its shape slightly so that AS fits more snugly around
the substrate, binding the substrate more firmly
• AS aa residues are moulded into a precise conformation and position
such that the chemical groups of catalytic aa residues are close to the
chemibal bonds in the substrate
• stretching britical bonds, or bringing reacting groups in close proximity
• stabilizing the transition state and lowering activatino energy of the rxn
• catalysis is facilitated where the substrate is converted to product
• product is released as it is no longer complementary to AS
• AS is available for other substrates
When explaining factors affecting rate of reaction:
[E] or [S]
pH
1. Name limiting factor
2. Availability of enzyme active site
3. Frequency of effective collision between
E and S
4. Rate of formation of E-S complex
5. Rate of formation of products
Temperature:
1.
2.
3.
4.
Change in kinetic energy of E and S
Frequency of effective collisions btw E and S
Rate of formation of E-S complex
Likeliness of over activation energy barrier
1. Concentration of H+ ions
2. Less/more H+ ions to neutralise negative
charges present in enzyme
3. Alteration of ionisation of aa disrupts
the ionic/H bonds that maintain the 3D
conformation of the enzyme
4. Denaturation
5. No E-S complex can be formed
Topics 1-4: Biological molecules
5. Rate of formation of products
6. Optimum temperature
a) Thermal agitation
b) Disrupt bonds
c) Effect on 3D conformation of enzyme, and AS
Vmax: the maximum rate at which an enzyme is able to perform the reaction at a specific [E] and
excess substrates
Km (Michaelis constant): the affinity of the enzyme for its substrate; [S] that allows a reaction to
proceed at half Vmax
The lower the Km value, the higher the affinity of the enzyme for its substrate
Competitive Inhibition
Inhibitor
Structurally similar to substrate
Bind to
Active site
Equivalent to Increase in [S]
Effect on Vmax Same. At high [S], S can out-compete I
Effect on Km increase
Non-competitive Inhibition
Structurally not similar to substrate
Any other part, alters 3D conformation of E
Decrease in [E]
Decrease
Same
Allosteric regulation:




Usually occurs in multi-subunit enzymes
Regulation of an enzyme by the binding of molecules at an allosteric site
Activators stabilise the active form of the enzyme, increasing the affinity of E for S
Inhibitors binds to the same region, stabilizing the inactive form of the enzyme, and
decreasing the affinity of E for S
Control and Regulation of Metabolic Pathways


Controlled by multi-enzyme complex
o Biological reactions may proceed with no accumulation of products in cells, as
products become substrates of subsequent reactions
o Reactants are modified in series of small steps enabling controlled release of energy
and minor adjustments to be made to molecules
o Each step is catalysed by a specific enzyme, so each enzyme act represents a point
of control of the overall pathway
o Spatially arranged so that product of one reaction is ideally located to become the
substrate of the next enzyme, permitting the build up of high local [S] and
biochemical reactions can proceed rapidly
o Sequencing of reactions greatly increase the efficiency of the enzyme pathway
End-product inhibition is when accumulation of end-products act as inhibitors on the
enzyme(s) controlling the preceding step(s) of the pathway