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Department of Chemical and

Environmental Engineering

H83BCE Biochemical Engineering

Lecture 2: Part II

Life (Its Building Blocks & Processes)


* Lipids, Fats & Steroids
* Amino Acids & Proteins

Lipids, Fats & Steroids

Lipid Properties

Non polar biological compounds, hence insoluble in water.

Present in non-aqueous biological phases

plasma and organelle membranes

Serve as polymeric biological fuel storage





When energy is needed, fat splitting enzymes are used.


Microbes use similar mechanisms for energy release as mammals.

Also act as an important mediator in biological activity.

Saturated fatty acids are relatively simple lipids:




Unsaturated fatty acid forms when a ( C C ) bond is replaced by ( C = C


)




The value of n is typically between 12 to 20

CH3 (CH2)16 COOH (stearic acid, saturated)


CH3 (CH2)7 HC = CH (CH2)7 COOH (oleic acid, unsaturated)

The long chain is insoluble in water but the carbonyl group is very
hydrophilic.
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Fats and oils are esters formed by condensation of fatty acids with glycerols

Phosphoglycerides are molecules where phosphoric acid replaces a fatty acid esterified to
one end on the glycerols.
 Phosphoglycerides also consists of hydrophilic and hydrophobic portions.

Phospholipids
A flat, double-molecular layer structure may be formed
across a small hole in a sheet submerged in lipid (or
phospholipid) solution.
 Phospholipids are fat derivatives in which one fatty acid has been
replaced by a phosphate group and one of several nitrogencontaining molecules.
 Example: Phosphatidyl ethanolamine (also known as cephalin)

Lipids and Their Interaction with Water

Representation of lipids
involved in the formation of
biological membranes.
The head groups are hydrophilic
and prefer contact with water.
Hydrophobic tails face each other.

The Basis of Membrane Formation in Water


As lipids are insoluble in water, they
initially form a monolayer on the surface
of water.
As more lipids are added, micelles form,
allowing
hydrophobic tails to interact with one
another and not water.

As more lipids are added, bilayered


vesicles eventually form,
containing two layers of lipids and an
internal compartment of water.

Biological Membranes
The hydrophobically
connected bilayers form
the basic structure of
biological membranes.
Biological plasma
membranes typically
contain appreciable
concentrations of
phospholipids and other
lipids.

http://kvhs.nbed.nb.ca/gallant/biology/cell_membrane.jpg

The membrane walls show


apparent molecular bilayer
of thickness (70 ).
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Lipid Membranes
Lipid membranes have high passive electrical resistance and capacitance.
 Hence, they are impermeable to highly charged species.
 The membrane, thus, allows the cell to contain a reservoir of charged nutrients and metabolic
intermediates.

The membrane determines which material enters, is confined and leaves the catalytic
reaction network housed in the cell.
The membranes act as a barrier.
 The bi-layer is semi-permeable.
 Toxic materials tend to be hydrophilic,
Repelled by the hydrophobic internal layer.

 Hormones are hydrophobic,


Pass straight through.

The selection of ion permeabilities can be modified by the addition of various substances
 Antibiotics and other cation-complexing molecules can increase passive ion transport

Vitamins
Substance required in trace amounts for normal cell function.
Essential vitamins
 The cell cannot survive if they are absent in the external media.
 Vitamins A, C, D, E, K, and the B vitamins (thiamine, riboflavin, niacin, pantothenic acid,
biotin, vitamin B6, vitamin B12, and folate)
 They all can be obtained from food, and vitamin D and vitamin K can be synthesised by
the body

Vitamins A, D, E, and K are lipids (water insoluble)


Vitamin C (ascorbic acid) is not (water soluble)
Many microorganisms can synthesise a number of vitamins
 Example: yeast provides ergosterol, which is converted by sunlight to vitamin D2
(calciferol).

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Hormones

Extremely potent controller of biological reaction rates.

A subgroup of hormones are Steroids:




A class of lipids with the general structure

The familiar steroid cholesterol occurs exclusively in membrane of


animal tissues.

Currently, microbes are used to carry


transformations of steroids
to yield more valuable products.


E.g.: progesterone to cortisone

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Amino Acids & Proteins

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Amino Acids
The monomeric building block of polypeptides and proteins are
the -amino acids.

H
H2N

COOH

Amino acids are optically active




possess at least one asymmetrical carbon.


Solutions of pure isomer rotates plane polarised light either to the right
(dextro- or d-) or left (levo- or l-).
H

H
H2N

COOH

L - form

HOOC

N2H

D - form

The acid (-COOH) and the base (-NH2) groups of the amino acids
can ionise in aqueous solution.
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Amino acids are positively charged (cation) at low pH and negatively


charged (anion) at high pH.
At intermediate pH value, amino acid acts as a dipolar (zwitterion)
with no net charge.
The R group differentiate the amino acids, R can be polar
(hydrophilic) or non-polar (hydrophobic)

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Simple proteins are formed by condensation reaction between amino group


from one amino acid and the carboxyl group of another, forming a peptide
bond.

OH

+ H

-H2O
OH

RH
1

H
C

C
H

O
O

R1

OH

C
N

C
R2

C
R2

Every amino acid links with the next via peptide bond.

Polypeptides are short condensation of amino acids.

As the length of the chain increases, the physicochemical characteristics will be


dominated by the R group of the residue with comparison to the amino and
carboxyl groups.

Many hormones are polypeptides




E.g. insulin and growth hormone.

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Folding a chain of amino acids


(a)

a geometric representation of amino acid chain. Each


symbol represent a side chain (a chemical group that
extends from the individual amino acids that make up
the main chain

(b)

favourable interactions between the individual amino


acid side chains dictate how the chain will fold into
specific shape

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Larger chains are called proteins


 50-100 amino acid residues

Simple proteins:
 only amino acids are present

Conjugated proteins:
 have other organic or inorganic components
 E.g. Haemoglobin, the oxygen-carrying molecule in the blood, has four
heme groups (organometallic complex containing iron).

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Proteins
Most abundant molecules within the cell,

Typically 30 70% of the cells dry weight.


Molecular weights: 6000 1 million.

Consists of (weight %):

C (50%), H (7%), O (23%), N (16%) and S(3%).

Two configurations, fibrous and globular.

A critical role of proteins is catalysis - enzymes.

Enzymes determine the rate of chemical reactions


occurring in the cell.
Found dispersed in the cytoplasm or attached to
membranes or larger assemblies.

Other membrane-associated proteins,


permeases

Aid the transport of specific nutrients to the cell.

Many single-celled organisms posses small,


hairlike extensions, flagella, whose motion
serves to propel the cell.

The flagella are driven by contractile proteins.

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Protein Structure

Described in three levels (A


fourth level is considered if more
than a single chain is present):
1.

Primary

2.

Secondary

3.

manner of extension of chain


due to hydrogen bonds.

Tertiary

4.

amino acid sequence joint by


peptide bond.

folding and bending of chain


due to hydrogen, salt and
covalent disulfide bonds, as well
as hydrophobic-hydrophilic
interaction.

Quaternary

how different chains fit together


due to same forces.

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Proteins: Primary Structure

A sequence of amino acid residues.

Every protein has not only a definite amino acid content


but also a unique sequence.


The sequence of amino acid residues in many proteins is now


known and no repeating patterns of residues have been
found.

The various side chains of amino acid residues interact


with each other, and with the immediate environment
to determine the geometrical configuration of the
protein.

This structure is dictated by the amino acid sequence.

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Secondary Structure

Two general structures:





Helices
Sheets

Appears in hair, wool and other fibrous proteins.

Due to: hydrogen bonding between atoms in closely neighbouring residues


four units down the chain.

If the H-bond occur between the C=O group of one residue and the NH
group of its neighbour, the protein chain is then coiled (-helix).

Collagen contains three -helices.





The most abundant protein in higher animals.


Rigid and stretch-resistant

E.g. skin, ligaments, eye cornea and other parts of the body.

The plate sheeted structure is stabilised by hydrogen bonds which exist


between neighbouring parallel chains.

Parallel sheets are flexible




However, they are very resistant to stretching.


Helix Protein

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Tertiary Structure

Contains sub-domains of helical and sheet regions.

Weak interactions between R groups widely separated along the


chain determine the folding to form the globular structure.



Ionic effects, hydrogen bonds, hydrophobic interactions


These interactions can be easily disrupted by changes in protein
environment

E.g.: Temperature, pH, physical forces.

Many globular proteins have their hydrophobic residues


concentrated in the molecules interior and relatively hydrophilic
groups on the outside

Oil-drop model

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Also important are covalent bonds formed by eliminating two hydrogen


atoms,

Disulfide bond formed (cysteinyl residue)


C=O
C=O

NH C S H

+
C=O

H S C NH

-2H

NH C S S C NH
C=O
Disulfide bond

These bonds cross-link within a polypeptide chain and sometimes separate


chains.

These covalent bonds are more thermal resistant.

Most of the forces holding the geometrical structure of proteins are weak and
allow the protein to flex.

The 3-D structure determines the activity and to work properly




E.g.: Lock and key model for enzyme specificity

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Enzymes
Only definite substrates are converted by a particular enzyme.

End product
+
Substrate

Enzyme-substrate
complex
Enzyme: active site on surface

Free enzyme

Enzyme has a specific site which is a geometrical compliment of the substrate.




Only substrates with the proper complimentary shape can bind to the enzyme.

Denaturation:





Structural change of protein when exposed to conditions sufficiently different from its
biological environment.
cannot perform its normal function.
Relatively small changes in temperature (or pH) may cause denaturation without
severing the covalent bond.
When the denatured protein is slowly cooled (or pH retained) to its natural value, a
reverse process (renaturation), with restoration of function, often occur.

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Quaternary Structure
Proteins may exist in more than one chain
(haemoglobin).

These chains fit together in the molecule to form


the quaternary structure.

The forces stabilising quaternary


structure are the same as those in
tertiary structure.

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