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Introduction and Biomolecules

Subtopic:

Definition of biochemical engineering

Carbohydrates
Part 1 Amino acids and protein
The central Dogma of molecular biology
Buffer solution

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What is Biochemical Engineering? What do Biochemical Engineer do?

Typical employers come

from all sectors of the
It is a subset of chemical engineering that mainly biotechnology industries,
deals with the design and construction of unit including those with
processes that involve biological organisms or interests in
molecules such as bioreactors. pharmaceuticals, food,
environment, waste
treatment, and
consulting.
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Biochemical engineer responsibilities?

• To obtain the best • To separate the desired
biological catalyst products from the
(microorganism, animal reaction mixture in the
cell, plant cell, or most economical way
enzyme) for a desired
process.

• To create the best

possible environment for
the catalyst to perform by
designing the bioreactor
and operating it in the
most efficient way.
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What are carbohydrates?

 Major class of naturally occurring organic
compounds, including sugars, starches and
cellulose.

 Play key roles as structural and storage

compounds in cells. FUNCTIONS OF CARBOHYDRATE?

The formula for a carbohydrate is (CH2O)n, where

n≥ 3.

 Classified into THREE major groups :

monosaccharide, disaccharides and
polysaccharide. 7 8

Carbohydrates - The Functions

Most important source of energy for living

organisms.
 Linked to proteins or lipids.
 Form structural tissues in plants and in
microorganisms (cellulose, lignin, murein).
 Participates in biological transport, cell- cell
recognition, activation of growth factors, modulation
of the immune system.
 DNA and RNA framework.

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Classifying carbohydrates Classifying carbohydrates

 Simple carbohydrates
1) Monosaccharides
Glucose, fructose, galactose
2) Disaccharides
Lactose, sucrose, maltose
 Complex carbohydrates
1) Polysaccharides
Starch, glycogen, cellulose

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* chaining relise on 'bridging' of oxygen atoms - glycoside bonds

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Monosaccharides
 Smallest carbohydrates, also known as simple sugars. Aldose sugars
 Monosaccharides are categorized by:
1) number of carbons (typically 3-9)
2) whether an aldehyde or ketone

 Sugar containing an aldehydes is known as an aldose.

 Sugar containing a ketones is known as a ketose.

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Aldose sugars Ketose sugars

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Ketose sugars D and L notation

 D, L tells which of the two chiral isomers we are

referring to.

 If the –OH group on the next to the bottom

carbon atom points to the right , the isomer is a
D-isomer; if it points left, the isomer is L.

 The D form is usually the isomer found in

nature.

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D and L notation D and L notation

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D notation Structural of representation of sugars

O
H C

H C OH Fisher projection: straight chain representation.

 Haworth projection: simple ring in perspective.

H C OH
 Conformational representation: chair and boat
C H 2 OH configurations.
Right = D

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Rules of drawing Haworth projections

 Draw either a six or 5-membered ring including
oxygen as one atom.
O O

HAWORTH PROJECTION
 Most aldohexoses are six-membered.
 Aldotetroses, aldopentoses, ketohexoses are 5-
membered.

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Rules of drawing Haworth projections Rules of drawing Haworth projections

 Next: number the ring clockwise starting next to  For D-sugars the highest numbered carbon
the oxygen (furthest from the carbonyl) is drawn up. For L-
5 sugars, it is drawn down. - CH2OH
O O
4 1 4 1 For D-sugars, the OH group at the anomeric
position is drawn down for α and up for β. For L-
3 2 3 2 sugars α is up and β is down.

 If the substituent is to the right in the Fisher

projection, it will be drawn down in the Haworth
projection (Down-Right Rule)
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Haworth Structure for D-Glucose Haworth Structure for D-Galactose

 Write –OH groups on the right (C2, C4) down.
Write –OH groups on the left (C3) up.
The new –OH on C1 has two possibilites: down
for  anomer, up for  anomer.

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Isomers *homework Enantiomers

 Isomerism in which two isomers are mirror
 Isomers are molecules that have the same chemical formula but images of each other (D vs L).
different structures.
Stereoisomer differs in the 3-D orientation of atoms.
Diastereomers are isomers with > 1 chiral center.
– Pairs of isomers that have opposite configurations at one
or more of the chiral centers but that are not mirror
images of each other
Epimers are a special type of diastereomer.
– Stereoisomers with more than one chiral center which
differ in chirality at only one chiral center
– A chemical reaction which causes a change in chirality at
one of many chiral center is called an epimerisation

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Disaccharides

Disaccharides
Consist of 2 monosaccharides bonded
together.

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Glycosidic Bond

 This is when two monosaccharides join to form a

Disaccharide.
 The reaction is similar to condensation.
 The reaction involves the water been given off.
Polysaccharides
>10 monosaccharides.

Most are made up of hundreds of

monosaccharides bonded together.

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Cellulose

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Protein play key roles in a living system Amino acid: Basic unit of protein

 Almost all chemical reactions in a living cell are

catalyzed by protein enzymes biocalatalyst – faster
rate reaction
 Storage and transport of biochemical molecules,
such as oxygen, ions, and so on. Nutrients and
wastes are transported into and out of the cell -
transporter
 Physical cell support and shape (collagen).
 Regulatory and information transfer (hormones eg
insulin:).
 Mechanical movement (flagella, mitosis, muscles).
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Examples of Amino acid Zwitterionic form of Amino Acids

 Zwitterion (dipolar ions) has both + and – charge

 Zwitterion is neutral overall
 Under normal cellular conditions amino acids are
zwitterions:
Amino group = -NH3+
Carboxyl group = -COO-

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pH and Ionization The peptide bond ( CO - NH linkage)

Dipeptide
Tripeptide
Peptides (4-50 amino acids)
Proteins (more than 50 amino
41 acids) 42

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Primary Structure of Proteins

 Primary structure of a proteins is the particular
sequence of amino acids connected by peptide bonds.

Proteins are linear polymers of amino acids

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Secondary Structure Basic structural units of proteins:

Secondary structure
 Secondary structure of a protein is the arrangement
of polypeptide backbone of the protein in space.
 The secondary structure includes two kinds of
repeating pattern known as helixes (α-helix, triple
helix) and sheet (β-sheet).
 Hydrogen bonding between backbone atoms are
responsible for both of these secondary structures.

Helix (α-helix, triple helix)

Sheet (β-sheet).
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Tertiary Structure Tertiary Structure

 The overall three dimensional shape that results
from the folding of a protein chain.
 Tertiary structure depends mainly on interactions
of amino acid R groups that are far apart along the
same backbone.
 Cross links between R groups of amino acids in
chain:
disulfide –S–S– +
ionic –COO– H3N–
H bonds C=O HO–
hydrophobic –CH3 H3C–

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Quaternary Structure
• The way in which two or more polypeptide
chains associate to form a single three-
dimensional protein unit. Non-covalent
forces are responsible for quaternary
structure essential to the function of
proteins.
• Example is hemoglobin that carries oxygen
in blood.
-Four polypeptide chains
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Protein Hydrolysis Hydrolysis of Dipeptide

• Break down of peptide bonds OH

• Requires acid or base, water and heat CH 3 O CH 2 O H 2O, H
+
+
• Gives smaller peptides and amino acids H 3 N CH C N CH C OH
• Similar to digestion of proteins using H heat
enzymes OH
• Occurs in cells to provide amino acids to CH2 O
CH 3 O +
synthesize other proteins and tissues +
H 3 N CH COH + H3 N CH C OH

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Denaturation Application of Denaturation

Disruption of secondary, tertiary and quaternary • Hard boiling an egg

protein structure by • Wiping the skin with alcohol swab for
heat/organics
injection
Break apart H bonds and disrupt hydrophobic
attractions • Cooking food to destroy E. coli.
acids/ bases
• Heat used to cauterize blood vessels
Break H bonds between polar R groups and
ionic bonds • Autoclave sterilizes instruments
heavy metal ions • Milk is heated to make yogurt
React with S-S bonds to form solids
agitation
Stretches chains until bonds break
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