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Analysis of Biological System

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Title: 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.

5
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.
6
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
7
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.
8
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)
9
Amino acid
pH effect on the charge of amino acids The
proton dissociation constants are K1, K2
(3)
(4)
represents concentration in dilute solution.
10
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).
11
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.
12
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 .
13
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.

14
Standard amino acids there are 20 standard amino
acids that are commonly found in proteins.
15
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

16
  • 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
17
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.

18
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.

19
  • 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.

20
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.

21
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

23
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.
24
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.

25
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.

26
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.
27
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.

28
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.

29
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.

30
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.

31
Irreversible egg protein denaturation and loss of
solubility, caused by the high temperature
(while cooking it)
32
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.

33
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.

34
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.

35
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).

36
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.

37
Glucose
Glc in ring structure
Glucose as a straight chain
38
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.

39
D-ribose and deoxyribose
  • Ribose and deoxyribose are pentose containing
    five carbon ring-structure sugar molecules

deoxyribose
D-ribose
40
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.

41
Disaccharides
  • Disaccharides are formed by the condensation of
    two monosaccharides via 1, 4-glycosidic linkage.

Maltose
42
Disaccharides
  • Common disaccharides
  • - sucrose (known as "table sugar", "cane sugar",
    "saccharose" or "beet sugar") ,
  • - lactose (milk sugar)
  • - maltose produced during the malting of barley.

43
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.

44
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.

45
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.

46
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.

47
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.

48
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.

49
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
50
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.

51
Mangrove crab Ucides cordatus
52
Steamed Crab
Crab Cake
53
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).
55
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.

56
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

58
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.

61
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.

62
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.

65
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.

72
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.

74
DNA Replication
  • Regeneration of DNA from original DNA segments.

75
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.

76
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.

77
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.

78
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.

81
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.

82
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.

83
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
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