Title: Analysis of Biological System
1Analysis 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.
2Biochemistry
- Introduction of the biological system at
molecule level. - This section is devoted mainly to the structure
and functions of biological molecules.
3Outline 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.
4Amino 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.
5Amino 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.
6Amino 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
7Amino 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.
8Amino 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)
9Amino acid
pH effect on the charge of amino acids The
proton dissociation constants are K1, K2
(3)
(4)
represents concentration in dilute solution.
10Amino 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).
11Amino 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.
12Amino 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 .
13Amino 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.
14Standard amino acids there are 20 standard amino
acids that are commonly found in proteins.
15Amino 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
17Use 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.
18Amino 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.
20Protein
- 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.
21Heme group
Conjugated protein hemoglobin Prosthetic group
heme in green Amino acid units in red and yellow
22Protein
- 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
23Protein 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.
24Protein 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.
25Protein 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.
26Protein 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.
27Protein 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.
28Protein 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.
29Protein 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.
30Protein 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.
31Irreversible egg protein denaturation and loss of
solubility, caused by the high temperature
(while cooking it)
32Summary 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.
33Summary 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.
34Summary 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.
35Carbohydrates
- 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).
36Carbohydrates
- 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.
37Glucose
Glc in ring structure
Glucose as a straight chain
38Glucose
- 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.
39D-ribose and deoxyribose
- Ribose and deoxyribose are pentose containing
five carbon ring-structure sugar molecules
deoxyribose
D-ribose
40D-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.
41Disaccharides
- Disaccharides are formed by the condensation of
two monosaccharides via 1, 4-glycosidic linkage.
Maltose
42Disaccharides
- Common disaccharides
- - sucrose (known as "table sugar", "cane sugar",
"saccharose" or "beet sugar") , - - lactose (milk sugar)
- - maltose produced during the malting of barley.
43Oligosaccharides
- 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.
44Polysaccharides
- 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.
45Polysaccharides-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.
46Polysaccharides-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.
47Polysaccharides-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.
48Polysaccharide-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.
49Chitin poly b - (1, 4) - 2 - acetamido - 2 -
deoxi - D - glucopyranose
N-acetylation degree of chitin, i.e.
percentage of acetylated amine (amide) 78 ?10
50Chitin 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.
51Mangrove crab Ucides cordatus
52Steamed Crab
Crab Cake
53Acid washed crab shells
(Niu and Volesky, 2000, JCTB).
54Au
Chitin amide pKa lt 3.5 Cl- interference
Effect of pH (Niu and Volesky, 2003,
Hydrometallurgy).
55Summary 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.
56Lipids, 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.
57Lipids
- 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
58Fats
Fats are lipids that are esters of fatty acids
with glycerol.
glycerol
Fatty acids
fat
59Fats
- 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.
60Phospholipids
- 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.
61Steroids
- 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.
62Steroids
- 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.
63Summary 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.
64Nucleic 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.
65Nucleotides
- 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)
67Important 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.
68Deoxyribonucleic 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
69Deoxyribonucleic 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.
70DNA double-helical structure
71Double 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.
72DNA
- 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
73DNA
- 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.
74DNA Replication
- Regeneration of DNA from original DNA segments.
75DNA 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.
76Ribonucleic 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.
77Classification 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.
78Summary 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.
79Summary 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.
80Summary 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.
81Summary 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.
82Summary 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.
83Summary 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.
84Summary 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.
85Cell 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.
86Cell 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).
87Cell 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.
88Cell 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.
89Cell 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.
90Cell 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.
91Cell 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
92Cell 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.
93Cell 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.
94Cell 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.
95Nutrients 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).
96Growth 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).
97Defined medium
- - the results are more reproducible and the
operator has better control of the fermentation. - - the recovery and purification processes are
easier and cheaper.
98Growth 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).
99Summary 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.
100Summary of cell construction
Biopolymers protein Carbohydrates (polysaccharides) DNA RNA lipids
subunit
bonds for subunit linkage
functions
Characteristic three-D structure