Analysis of Biological System

1
Analysis of Biological System

• Despite of all their complexity, an understanding
  of biological system can be simplified by
  analyzing the system at several different levels
• the cell level microbiology, cell biology
• the molecular level biochemistry, molecular
  biology
• the population level microbiology, ecology
• the production level bioprocess.

2
Biochemistry

• Introduction of the biological system at
  molecule level.
• This section is devoted mainly to the structure
  and functions of biological molecules.

3
Outline of Biochemistry Section

• Contents-Cell construction
• Protein and amino acids
• Carbohydrates
• Lipids, fats and steroids
• Nucleic acids, RNA and DNA
• Requirements
• Understand the basic definitions,
  characteristics and functions of these
  biochemicals.

4
Amino acids and proteins

• Proteins are the most abundant molecules in
  living cells, constituting 40 - 70 of their dry
  weight. Proteins are built from a -amino acid
  monomers.
• Amino acid is any molecule that contains both
  basic amino and acidic carboxylic acid functional
  groups.

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Amino acid
a
Where "R" represents a side chain specific to
each amino acid. Amino acids are usually
classified by properties of the side chain into
four groups acidic, basic, hydrophilic
(polar), and hydrophobic (nonpolar).
a-amino acid are amino acid in which the amino
and carboxylate functionalities are attached to
the same carbon, the so-called acarbon. They
are the building blacks of proteins.
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Amino acid
Zwitterion is an amino acid having positively and
negatively charged groups, a dipolar molecule.
H
-H
-H
C
COOH
H3N
H
H
R
Zwitterion
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Amino acid
Isoelectric point (IEP) is the pH value at which
amino acids have no net charge. IEP varies
depending on the R group of amino acids. At IEP,
an amino acid does not migrate under the
influence of an electric field.
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Amino acid
pH effect on the charge of amino acids We can
arbitrarily control the pH of an aqueous solution
containing amino acids by adding base or acid.
The equilibrium reactions for the simple amino
acid (HA) are HAH HAH (1) HA
HA- (2)
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Amino acid
pH effect on the charge of amino acids The
proton dissociation constants are K1, K2
(3)
(4)
represents concentration in dilute solution.
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Amino acid
pH effect on the charge of amino acids Taking
the logs of equations 3 and 4, yields,
(5)
(6)
where pH-log(H), pK1-log(K1), and pK2-log(K2).
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Amino acid
pH effect on the charge of amino acids At
Isoelectric point (IEP), HAH A-
(7)
Equation 5 plus 6 yields
(8)
pI is the pH at the isoelectric point for
specific amino acid or protein. If R contains
acid or base group, IEP is affected by the such
groups.
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Amino acid
pH effect on the charge of amino
acids According to amino acid mass balance, the
initial amino acid concentration is
HA0 HA0 HA A- HAH (9) Combin
ing equations 3, 4 and 9, the concentration of
amino acids in neutral form HA, negatively
charged form A- and positively charged form
HAH can be calculated at specific known pH and
HA0 .
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Amino acid

• Isomerism
• Most amino acids occur in two possible optical
  isomers, called D and L.
• The L amino acids represent the vast majority of
  amino acids found in proteins.

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Standard amino acids there are 20 standard amino
acids that are commonly found in proteins.
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Amino Acids

• Essential amino acids An essential amino acid
  for an organism is an amino acid that cannot be
  synthesized by the organism from other available
  resources, and therefore must be supplied as part
  of its diet.
• Most of the pants and microorganism cells are
  able to use inorganic compounds to make amino
  acids necessary for the normal growth.
• Eight amino acids are generally regarded as
  essential for humans tryptophan, lysine,
  methionine, phenylalanine, threonine, valine,
  leucine, isoleucine.
• Two others, histidine and arginine are essential
  only in children. A good mnemonic device for
  remembering these is "Private Tim Hall",
  abbreviated as
• PVT TIM HALL
• Phenylalanine, Valine, Tryptophan
• Threonine, Isoleucine, Methionine
• Histidine, Arginine, Lysine, Leucine

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• limiting amino acid content the essential amino
  acid found in the smallest quantity in the
  foodstuff.

Protein source Limiting amino acid Wheat lysine
Rice lysine and threonine Maize lysine and
tryptophan Pulses methionine Beef methionine
and cysteine Whey none Milk none
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Use of amino acids

• Aspartame (aspartyl-phenylalanine-1-methyl ester)
  is an artificial sweetener.
• 5-HTP (5-hydroxytryptophan) has been used to
  treat neurological problems associated with PKU
  (phenylketonuria), as well as depression.
• L-DOPA (L-dihydroxyphenylalanine) is a drug used
  to treat Parkinsonism.
• Monosodium glutamate is a food additive to
  enhance flavor.

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Amino Acid (AA)-Protein
Amino acids basic unit
Peptides amino acid chain, containing 2 or more
AA.
Polypeptides containing less than 50 AA.
Protein gt 50 AA.

• Peptides (from the Greek pept??, "digestible"),
  are formed through condensation of amino acids
  through peptide bonds.

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• Peptide bond a chemical bond formed between two
  AA
• the carboxyl group of one amino acid reacts with
• the amino group of the other amino acid,
• releasing a molecule of water (H2O).
• This is a condensation (also called dehydration
  synthesis) reaction.

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Protein

• Proteins are the polymers built through the
  condensation of amino acids.
• amphoteric, isoelectric point (protein
  recovery)
• Protein constitutes 40-70 dry weight of cell.
  Its molecular weight is from 6000 to several
  hundred thousand daltons.
• Dalton is a unit of mass equivalent to a
  hydrogen atom,
• 1 dalton 1.66053886 10-27 kg.
• prosthetic groups organic or inorganic
  components other than amino acids contained in
  many proteins.
• conjugated proteins the proteins contain
  prosthetic groups.

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Heme group
Conjugated protein hemoglobin Prosthetic group
heme in green Amino acid units in red and yellow
22
Protein

• Proteins are essential to the structure and
  function of all living cells and viruses. They
  can be classified into
• structural proteins glycoprotein
• catalytic proteins enzymes
• transport proteins hemoglobin
• regulatory proteins hormones (insulin, growth
  hormone)
• - protective proteins antibodies

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Protein 3-D structure
Proteins are amino acid chains that fold into
unique 3-dimensional structures. The shape into
which a protein naturally folds is known as its
native state, which is determined by its
sequence of amino acids and interaction of
groups.
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Protein structure

• The three-dimensional structure can be described
  at four distinct levels
• Primary structure the amino acid sequence
• It is held together by covalent peptide bonds
• Each protein has not only a definite amino acids
  composition, but also a unique sequence.
• The amino acid sequence has profound effect on
  the resulting three-dimensional structure and on
  the function of protein.

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Protein structure

• Secondary structure highly patterned
  sub-structures
• a-helix and ß-pleated sheet
• It is the way that the polypeptide chain is
  extended and is a result of hydrogen bonds
  between protein residues.
• Secondary structures are locally defined, meaning
  that there can be many different secondary motifs
  present in one single protein molecule.
• Two major types of secondary structure are
  a-helix and ß-pleated sheet.

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Protein structure
Secondary structure a-helix
- Formed within the same protein chain. -
Hydrogen bonding can occur between - the
a-carboxyl group of one residue and - the NH
group of its neighbor four units down the same
chain. - The helical structure can be easily
disturbed since hydrogen bond is unstable.
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Protein structure
Secondary structure ß-pleated sheet

• - within the same protein molecule
• consists of two or more amino acid sequences
  that are arranged
• adjacently and in parallel, but with
  alternating orientation
• -Hydrogen bonds can form between the two strands.
  
• -Hydrogen bonds established between the N-H
  groups in the backbone of one strand
• with the CO groups in the backbone of the
  adjacent, parallel strand(s).
• - The sheet's stability and structural rigidity
  and integrity are the result of
• multiple such hydrogen bonds arranged in this
  way.

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Protein structure

• Tertiary structure the overall shape of a
  single protein molecule
• The tertiary structure is a result of interaction
  between R groups widely separated along the
  chain. The folding or bending of an amino acids
  chain induced by interaction of R groups
  determines the tertiary structure.
• It is held together primarily by hydrophobic
  interactions but hydrogen bonds, ionic
  interactions, and disulfide bonds are usually
  involved too.
• The tertiary structure has a profound effect on
  its function.

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Protein structure

• Quaternary structure the shape or structure that
  results from the union of more than one protein
  molecule, which function as part of the larger
  assembly or protein complex.
• Only protein with more than one polypeptide chain
  has quaternary structure. This structure has an
  important role in the control of their catalytic
  activity.
• these tertiary or quaternary structures are
  usually referred to as "conformations," or
  folding and transitions between them are called
  conformational changes.
• The mechanism of protein folding is not entirely
  understood.

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Protein Denaturation

• Protein Denaturation A protein that is not in
  its native state and their shape which allows for
  optimal activity.
• Proteins denature when they lose their
  three-dimensional structure - their chemical
  conformation and thus their characteristic folded
  structure.
• Proteins may be denatured at the secondary,
  tertiary and quaternary structural levels, but
  not at the primary structural level.
• This change is usually caused by heat, acids,
  bases, detergents, alcohols, heavy metal salts,
  reducing agents or certain chemicals such as
  urea.
• The proteins can regain their native state when
  the denaturing influence is removed. Such
  denature is reversible. Some other denature is
  irreversible.- direct purification processes.

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Irreversible egg protein denaturation and loss of
solubility, caused by the high temperature
(while cooking it)
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Summary of amino acids and protein

• Amino acids are basic building blocks of
  proteins.
• They contain acid carboxyl group and base amino
  group as well as side group R.
• They can be neutral, positively or negatively
  charged.
• They are 21 basic amino acid and 10 essential
  amino acids for human being.

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Summary of amino acids and protein

• Proteins are amino acid chain linked through
  peptide bond.
• They can be classified into structural protein,
  catalytic protein, transport protein , regulatory
  and protective proteins in either globular or
  fibrous forms.

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Summary of amino acids and protein

• Protein has three-dimensional structure at four
  level.
• - Primary structure the sequence of amino
  acids.
• - Secondary structure a way that the
  polypeptide chain is extended. a-helix and
  ß-pleated sheet formed by hydrogen bond.
• - Tertiary structure the overall shape of a
  protein molecule and the result of interaction
  between R groups mainly through hydrophobic
  interaction.
• - Quaternary the interaction between different
  polypeptide chains of protein. This structure is
  important to the active function of protein
  especially enzyme.
• Protein can be denatured at its three dimensional
  structure. Protein denature could be reversible
  or irreversible.

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Carbohydrates

• Carbohydrates
• Carbohydrates (monosaccharides) are represented
  by the general formula (CH2O)n, where n3 and are
  synthesized from carbon dioxide and water through
  photosynthesis.
• Certain carbohydrates are an important storage
  and transport form of energy in most organisms.
• Carbohydrates are classified by the number of
  sugar units
• monosaccharides (such as glucose),
• disaccharides (such as maltose),
• Oligosaccharides (fructo-oligosaccharides), and
• polysaccharides (such as starch, glycogen,
  cellulose, and chitin).

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Carbohydrates

• Monosaccharides are the simplest form of
  carbohydrates containing three to nine carbon
  atom. They consist of one sugar and are usually
  colorless, water-soluble, crystalline solids.
• Monosaccharides are either aldehydes or ketones
  with many hydroxyl groups added, usually one on
  each carbon except the functional group.
• Imoportant monosaccharides include glucose,
  ribose and deoxyribose.

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Glucose
Glc in ring structure
Glucose as a straight chain
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Glucose

• Glucose (Glc) is one of the main products of
  photosynthesis and starts cellular respiration.
• The cell uses it as a source of energy and
  metabolic intermediate. Glucose is the source for
  glycosis and citric acid cycle in metabolic
  pathway.
• The natural form (D-glucose) is also referred to
  as dextrose, especially in the food industry.
  D-glucose is in the form of a ring (pyranose)
  structure. The L-form plays a minor role in
  biological systems.
• Glc is produced commercially via the enzymatic
  hydrolysis of starch.

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D-ribose and deoxyribose

• Ribose and deoxyribose are pentose containing
  five carbon ring-structure sugar molecules

deoxyribose
D-ribose
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D-ribose and Deoxyribose

• D-ribose is a component of the ribonucleic acid
  (RNA) that plays central role for protein
  synthesis.
• Ribose is critical to living creatures. It is
  also a component of adenosine triphosphate (ATP),
  and nicotinamide adenine dinucleotide (NAD), that
  are critical to metabolism.
• Deoxyribose is a component of DNA that is
  important genetic material.

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Disaccharides

• Disaccharides are formed by the condensation of
  two monosaccharides via 1, 4-glycosidic linkage.

Maltose
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Disaccharides

• Common disaccharides
• - sucrose (known as "table sugar", "cane sugar",
  "saccharose" or "beet sugar") ,
• - lactose (milk sugar)
• - maltose produced during the malting of barley.

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Oligosaccharides

• Oligosaccharides refer to a short chain of sugar
  molecules
• - Fructo-oligosaccharides (FOS), which are found
  in many vegetables, consist of short chains of
  fructose molecules.
• - Galacto-oligosaccharides (GOS), which also
  occur naturally, consist of short chains of
  galactose molecules.

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Polysaccharides

• Polysaccharides are formed by the condensation of
  more than two monosaccharides by glycosidic
  bonds.
• Polysaccharides have a general formula of
  Cn(H2O)n-1 where n is usually a large number
  between 200 and 500.
• They are very large, often branched, molecules.
• They tend to be amorphous, insoluble in water,
  and have no sweet taste.
• When all the constituent monosaccharides are of
  the same type they are termed homopolysaccharides
  when more than one type of monosaccharide is
  present they are termed heteropolysaccharides.
• Examples include storage polysaccharides such as
  starch and glycogen and structural
  polysaccharides such as cellulose and chitin.

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Polysaccharides-starch

• Starch is a combination of two polysaccharides
  called amylose and amylopectin.
• Amylose is constituted by glucose monomer units
  joined to one another head-to-tail forming
  alpha-1,4 linkages.
• Amylopectin differs from amylose in that
  branching occurs, with an alpha-1,6 linkage every
  24-30 glucose monomer units.
• In general, starches have the formula (C6H10O5)n,
  where "n" denotes the total number of glucose
  monomer units.

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Polysaccharides-starch

• Starches are insoluble in water.
• They can be digested by hydrolysis, catalyzed by
  enzymes called amylases, which can break the
  glycosidic bonds between the 'alpha-glucose'
  components of the starch.
• The four major resources for starch production
  and consumption in the USA are
• corn, potatoes, rice, and wheat.
• Dietary sources of starch are pasta and bread.

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Polysaccharides-glycogen

• Glycogen is storage form of glucose in animal
  cells.
• Glycogen is a highly branched polymer of 10,000
  to 120,000 Glc residues and molecular weight
  between 106 and 107 daltons.
• Most of Glc units are linked by a a-1,4
  glycosidic bonds,
• approximately 1 in 12 Glc residues also makes a
  a-1,6 glycosidic bond with a second Glc which
  results in creating of a branch.

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Polysaccharide-Cellulose

• Cellulose (C6H10O5)n is a long-chain
  polysaccharide of beta-glucose.
• The molecule weight is between 50,000 to 1
  million daltons.
• The linkage between glucose monomer in cellulose
  is ß-1,4 glycosidic linkage.
• It forms the primary structural component of
  plants and is not digestible by humans. Only a
  few microorganism can hydrolyze enzyme.

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Chitin poly b - (1, 4) - 2 - acetamido - 2 -
deoxi - D - glucopyranose
N-acetylation degree of chitin, i.e.
percentage of acetylated amine (amide) 78 ?10
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Chitin structure

• Chitin is important structural polysaccharides in
  the cell wall of microorganisms and animal
  shells.
• Chitin can be obtained from fungi, insect,
  lobster, shrimp and krill, but the most important
  commercial sources are the exoskeletons of crabs
  obtained as waste from seafood industrial
  processing.

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Mangrove crab Ucides cordatus
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Steamed Crab
Crab Cake
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Acid washed crab shells
(Niu and Volesky, 2000, JCTB).
54
Au
Chitin amide pKa lt 3.5 Cl- interference
Effect of pH (Niu and Volesky, 2003,
Hydrometallurgy).
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Summary of Carbohydrates

• Carbohydrates are the energy sources for cell
  living.
• Carbohydrates include monosaccharide,
  disaccharide, and polysaccharides.
• Important monosaccharides are glucose and
  ribose.
• - Glucose is the energy source for cell
  metabolism
• - Ribose is the unit for forming nucleotides and
  nucleic acid.
• Important polysaccharides are storage starch,
  glycogen, and structural cellulose and chitin.

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Lipids, fats and steroids

• Lipids, fats and steroids
• Lipids are hydrophobic biological compounds that
  are insoluble in water, but soluble in nonpolar
  solvent such as benze, chloroform and ether.
• They are present in the nonaqueous biological
  phase such as plasma membrane.
• Cells can alter the mix of lipids in their
  membrane to compensate for changes in temperature
  or to increase their tolerance to the presence of
  chemical agents such as ethanol.

57
Lipids

• fatty acids The major component in most lipids
  made of a straight chain of hydrophobic
  hydrocarbon group, with a carboxyl group
  (hydrophilic) at the end.
• A typical saturated fatty acid has the form of
  CH3-(CH2)n COOH
• Where n is typically between 12 and 20, such
  as acetic acid CH3COOH.
• A typical unsaturated fatty acid contain double
  CC- , or triple bonds on the hydrocarbon chain,
  such as Oleic acids
• CH3-(CH2)7-HCCH-(CH2)7-COOH

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Fats
Fats are lipids that are esters of fatty acids
with glycerol.
glycerol
Fatty acids
fat
59
Fats

• Fats play a vital role in maintaining healthy
  skin and hair, insulating body organs against
  shock, maintaining body temperature, and
  promoting healthy cell function.
• They also serve as energy stores for the body and
  can serve as biological fuel-storage molecules.
• In food, there are two types of fats saturated
  and unsaturated.
• Fats are broken down in the body to release
  glycerol and free fatty acids.
• glycerol can be converted to glucose by the
  liver and thus used as a source of energy.
• The fatty acids are a good source of energy for
  many tissues, especially heart and skeletal
  muscle.

60
Phospholipids

• Phospholipids such as glycerophospholipids are
  built on a glycerol core to which are linked two
  fatty acid-derived "tails" by ester linkages and
  one "head" group by a phosphate ester linkage.
  Phospholipids are key components to control the
  entry or exit of molecules in the cell membrane.

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Steroids

• A steroid is a lipid characterized by a carbon
  skeleton with four fused rings.
• Different steroids vary in the functional groups
  attached to these rings.

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Steroids

• Hundreds of distinct steroids have been
  identified in plants and animals.
• Their most important role in most living systems
  is as hormones-regulate the cell metabolism.
• In human physiology and medicine, the most
  important steroids are cholesterol functioning
  chiefly as a protective agent in the skin and
  nerve cells, a detoxifier in the bloodstream, and
  as a precursor of many steroids.

63
Summary of lipids

• Lipids are energy storage in cell membrane and
  regulators of cell metabolism.
• - fat, phospholipids and steroids.
• - Important components in cell membrane to
  compensate for changes in temperature or increase
  the cell tolerance for some chemicals.

64
Nucleic acids, RNA and DNA

• Nucleic acid is a complex, high-molecular-weight
  biochemical macromolecule composed of nucleotide
  chains that convey genetic information.
• The most common nucleic acids are
  deoxyribonucleic acid (DNA) and ribonucleic acid
  (RNA).
• Nucleic acids are found in all living cells and
  viruses.

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Nucleotides

• Nucleotides are the building blocks of DNA and
  RNA.
• Serve as molecules to store energy and reducing
  power.
• The three major components in all nucleotides are
  phosphoric acid, pentose (ribose and
  deoxyribose), and a base (purine or purimidine).
• Two major purines present in nucleotides are
  adenine (A) and guanine (G), and three major
  purimidines are thymine (T), cytosine (C) and
  uracil (U).

66
(No Transcript)
67
Important Ribonucleotides

• Adenosine triphosphate (ATP) and guanosine
  triphosphate (GTP), which are the major sources
  of energy for cell work.
• - The phosphate bonds in ATP and GTP are
  high-energy bonds.
• - The formation of phosphate bonds or their
  hydrolysis is the primary means by which cellular
  energy is stored or used.
• nicotinamide adenine dinucleotide (NAD) and
  nicotinamide adenine dinucleotide phosphate
  (NADP).
• The two most common carriers of reducing power
  for biological oxidation-reduction reactions.

68
Deoxyribonucleic acid (DNA)

• Deoxyribonucleic acid (DNA) is formed by
  condensation of deoxyribonucleotides .

3
The nucleotides are linked together between the
3 and 5 carbons successive pentose rings by
phosphodiester bonds
5
69
Deoxyribonucleic acid (DNA)

• DNA is a very large threadlike macromolecule (MW,
  2X109 D in E. coli).
• DNA contains adenine (A) and guanine (G), thymine
  (T) and cytosine (C).
• DNA molecules are two stranded and have a
  double-helical three-dimensional structure.

70
DNA double-helical structure
71
Double helical DNA structure

• The main features of double helical DNA structure
  are as follows .
• The phosphate and deoxyribose units are on the
  outer surface, but the bases point toward the
  chain center. The plane of the bases are
  perpendicular to the helix axis.
• - The diameter of the helix is 2 nm, the helical
  structure repeats after ten residues on each
  chain, at an interval of 3.4 nm.
• The two chains are held together by hydrogen
  bonding between pairs of bases.
• Adenine (A) - thymine (T), guanines (G) -
  cytosine (C).
• - The sequence of bases along a DNA strand is not
  restricted in any way and carries genetic
  information, and sugar and phosphate groups
  perform a structure role.

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DNA

• Genetic code is the relation between the
  sequence of bases in DNA (or its RNA transcripts
  ) and the sequence of amino acids in protein.
• (Biochemistry, Lubert Stryer, 1988)
• - Codon refers to a sequence of three bases on a
  mRNA.
• - There are maximum 64 codons.
• - These codons, when expressed, represent a
  particular amino acid or stop signal for
  protein synthesis.
• e.g. -CGCCGCTGC-
• -GCGGCGACG-
• -CGCCGCUGC-

DNA
mRNA
arg
arg
sys
73
DNA

• The sequence of the codons determines the
  sequence of amino acids for a protein synthesis.
• Some other combinations of codons regulate when
  the gene is expressed.
• Gene each sequence of codons generating a unique
  protein.
• A DNA molecule contains lots of genes.

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DNA Replication

• Regeneration of DNA from original DNA segments.

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DNA Replication

• DNA helix unzips and forms two separate strands.
• Each strand will form a new double strands.
• The two resulting double strands are identical,
  and each of them consists of one original and one
  newly synthesized strand.
• - This is called semiconservative replication.
• The base sequences of the new strand are
  complementary to that of the parent strand.

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Ribonucleic acid (RNA)

• Ribonucleic acid (RNA) is formed by condensation
  of ribonucleotides.
• RNA is a long, unbranched macromolecule and may
  contain 70 to several thousand nucleotides. RNA
  molecule is usually single stranded.
• RNA contains adenine (A), guanine (G), cytosine
  (C) and uracial (U). A-U, G-C in some double
  helical regions of t-RNA.

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Classification of RNA

• According to the function of RNA, it can be
  classified as
• Messenger RNA (m-RNA) synthesized on chromosome
  and carries genetic information to the ribosomes
  for protein synthesis. It has short half-life.
• Transfer RNA (t-RNA) is a relatively small and
  stable molecule that carries a specific amino
  acid from the cytoplasm to the site of protein
  synthesis on ribosomes.
• Ribosomal RNA (r-RNA) is the major component of
  ribosomes, constituting nearly 65. r-RNA is
  responsible for protein synthesis.
• Ribozymes are RNA molecules that have catalytic
  properties.

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Summary of Cell Construction

• Cells contain biologically important chemicals
  such as protein, carbohydrates, lipid and nucleic
  acids.
• Protein
• Proteins are amino acid chain linked through
  peptide bond.
• They can be classified into structural protein,
  catalytic protein, transport protein and
  protective proteins in either globular or fibrous
  forms.

79
Summary of Cell Construction

• Protein
• Protein has three-dimensional structure at four
  level.
• - The primary structure is determined by the
  sequence of amino acids. It is held together by
  peptide bonds.
• - The secondary structure is a way that the
  polypeptide chain is extended, including a-helix
  and ß-pleated sheet formed by hydrogen bonds.
• - The tertiary structure is the overall shape of
  a protein molecule, formed by the hydrophobic
  interaction of R chain.
• - Interaction between different polypeptide
  chains. Only protein with more than one
  polypeptide chain has quaternary structure.
• Protein can be denatured at its three dimensional
  structure. Protein denature could be reversible
  or irreversible.

80
Summary of Cell Construction

• Carbohydrates are the energy sources for cell
  living.
• Carbohydrates include monosaccharide,
  disaccharide, and polysaccharides.
• Important monosaccharides are glucose and
  ribose.
• - Glucose is the energy source for cell
  metabolism
• - Ribose is the unit for forming nucleotides and
  nucleic acid.
• Polysaccharides are made of monosaccharides
  through glycosidic bonds.

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Summary of Cell Construction

• Lipids fats, phospholipids and steroids
• Lipids are hydrophobic biological compounds that
  are insoluble in water.
• They are present in the nonaqueous biological
  phase such as plasma membrane.
• Cells can alter the mix of lipids in their
  membrane to compensate for changes in temperature
  or to increase their tolerance to the presence of
  chemical agents.
• Steroids are regulators.

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Summary of Cell Construction

• Nucleotides are basic units of nucleic acids DNA
  and RNA.
• Nucleotides include pentose, base and phosphoric
  acid.
• Bases include purine or pyrimidine.
• Two major purines present in nucleotides are
  adenine (A) and guanine (G), and three major
  pyrimidines are thymine (T), cytosine (C) and
  uracil (U).
• Ribonucleotides
• - adenine triphosphate (ATP) stores energy.
• - NAD and NADP are important carriers of
  reducing power.

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Summary of Cell Construction

• DNA
• DNA contains genetic information.
• DNA contains adenine (A) and guanine (G), and
  thymine (T), and cytosine (C). A-T G-C
• DNA has a double helical structure.
• The bases in DNA carry the genetic information.

84
Summary of Cell Construction

• RNA
• RNA functions as genetic information-carrying
  intermediates in protein synthesis.
• It contains adenine (A) and guanine (G), and
  cytosine (C) and uracil (U).
• m-RNA carries genetic information from DNA to the
  ribosomes for protein synthesis.
• t-RNA transfers amino acid to the site of protein
  synthesis
• r-RNA is for protein synthesis.

85
Cell Nutrients

• Nutrients required by cells can be classified in
  two categories
• - Macronutrients are needed in concentrations
  larger than 10-4 M.
• C, N, O, H, S, P, Mg 2, and K.
• - Micronutrients are needed in concentrations
  less than 10-4 M.
• Mo, Zn, Cu, Mn, Ca, Na, vitamins,
• growth hormones and metabolic precursors.

86
Cell Nutrients- Macronutrients

• Carbon compounds are the major sources of
  cellular carbon and energy.
• Heterotrophs use organic carbon sources such as
  carbohydrates, lipid, hydrocarbon as a carbon
  source.
• Autotrophs can use carbon dioxide as a carbon
  source. They can form carbohydrate through light
  or chemical oxidation.
• In aerobic fermentations, about 50 of substrate
  carbon is incorporated into cell mass and about
  50 of it is used as energy sources.
• In anaerobic fermentation, a large fraction of
  substrate carbon is converted to products and a
  smaller fraction is converted to cell mass (less
  than 30).

87
Cell Nutrients- Macronutrients

• Carbon sources
• - In industrial fermentation, the most common
  carbon sources are molasses (sucrose), starch
  (glucose, dextrin), corn syrup, and waste sulfite
  liquor (glucose).
• - In laboratory fermentations, glucose, sucrose
  and fructose are the most common carbon sources.
  Ethanol, methanol and methane also constitute
  cheap carbon sources.

88
Cell Nutrients- Macronutrients

• Nitrogen compounds are important sources for
  synthesizing protein, nucleic acid.
• Nitrogen constitutes 10 to 14 of cell dry
  weight.
• The most commonly used nitrogen sources are
  ammonia or ammonium salts such as ammonium
  chloride, sulfate and nitrate, protein, peptides,
  and amino acids. Urea can be cheap source.
• In industrial fermentation, nitrogen sources
  commonly used are soya meal, yeast extract,
  distillers solubles, dry blood and corn steep
  liquor.

89
Cell Nutrients- Macronutrients
Oxygen constitutes about 20 of the cell dry
weight. - Molecular oxygen is required as
terminal electron acceptor in the aerobic
metabolism of carbon compounds. - Gaseous
oxygen is introduced into growth media by
sparging air or by surface aeration. -
Improving the mass transfer of oxygen in a
bioreactor is a challenge in reactor control.
90
Cell Nutrients- Macronutrients
Hydrogen 8 of dry cell weight source
carbohydrates. Phosphorus 3 of cell dry
weight - present in nucleic acids and in the
cell wall of some gram-positive bacteria. - a
key element in the regulation of cell metabolism.
- sources Inorganic phosphates. The
phosphate level should be less than 1 mM for the
formation of many secondary metabolites such as
antibiotics.
91
Cell Nutrients- Macronutrients

• Sulfur 1 of cell dry weight
• - present in protein and some coenzymes.
• - source Ammonium sulfate, Sulfur containing
  amino acids such as cysteine
• some autotrophs can use S0 and S2 as energy
  sources.
• Potassium a cofactor for some enzyme and is
  required in carbohydrate metabolism.
• cofactor any of various substances necessary to
  the function of an enzyme, such as metal ions.
• - source potassium phosphates.
• Magnesium a cofactor for some enzyme and is
  present in cell walls and membranes. Ribosomes
  specifically requires Mg2 .
• - sources Magnesium sulfate or chloride

92
Cell Nutrients- Micronutrients

• Micronutrients could be classified into the
  following categories (required less than 10-4 M)
• most widely needed elements.
• trace elements needed under specific growth
  conditions .
• - Trace elements rarely require.
• - Growth factor.

93
Cell Nutrients- Micronutrients

• Micronutrients could be classified into the
  following categories
• most widely needed elements are Fe, Zn and Mn.
  Such elements are cofactors for some enzyme and
  regulate the metabolism.
• trace elements needed under specific growth
  conditions are Cu, Co, Mo, Ca, Na, Cl, Ni, and
  Se. For example, copper is present in certain
  respiratory-chain components and enzymes.

94
Cell Nutrients- Micronutrients
-Trace elements rarely required are B, Al, Si,
Cr, V, Sn, Be, F, Ti, Ga, Ge, Br, Zr, W, Li and
I. These elements are required in concentrations
of less than 10-6M and are toxic at high
concentration. - Growth factor is also
micronutrient. Growth factor stimulates the
growth and synthesis of some metabolites. e.g.
Vitamin, hormones and amino acids. They are
required less than 10-6M.
95
Nutrients for S. cerevisiaethanol production

• glucose (40g/L), NH4Cl (1.32 g/L), MgS04.7H2O
  (0.11 g/L), CaCl2.2H2O (0.08 g/L), K2HPO4 (2.0
  g/L).

96
Growth medium

• There are two types of growth medium defined
  medium and complex medium.
• Defined medium contains specific amounts of pure
  chemical compounds with known chemical
  compositions.
• glucose (40g/L), NH4Cl (1.32 g/L), MgS04.7H2O
  (0.11 g/L), CaCl2.2H2O (0.08 g/L), K2HPO4 (2.0
  g/L).

97
Defined medium

• - the results are more reproducible and the
  operator has better control of the fermentation.
• - the recovery and purification processes are
  easier and cheaper.

98
Growth medium

• Complex medium contains natural compounds whose
  chemical composition is not exactly known.
• - yeast extract, peptone, molasses or corn
  steep.
• - high yields providing necessary growth factor
  vitamins, hormones and trace metals.
• - Complex media is less expensive than defined
  media.

glucose (40g/L), yeast extract, NH4Cl (1.32 g/L),
MgS04.7H2O (0.11 g/L), CaCl2.2H2O (0.08 g/L),
K2HPO4 (2.0 g/L).
99
Summary of Cell Nutrients
Nutrients that required by cell living can be
categorized into macronutrient that are required
higher than 10-4M, micronutrients that less than
10-4M. Macronutrients include N, C, O, H, S, P,
K and Mg. They are major components in cell dry
weight. Micronutrients are classified into most
widely needed elements, needed under specific
conditions and rarely needed one. Growth medium
can be either defined or complex.
100
Summary of cell construction
Biopolymers protein Carbohydrates (polysaccharides) DNA RNA lipids
 subunit        
bonds for subunit linkage
functions
Characteristic three-D structure