Transcript Analysis of Biological System

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.
Biochemistry
Introduction of the biological system at
molecule level.
This section is devoted mainly to the structure
and functions of biological molecules.
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.
Amino acids and proteins
Proteins are the most abundant molecules
in living cells, constituting 40% - 70% of
their dry weight. Proteins are built from α amino acid monomers.
Amino acid is any molecule that contains
both basic amino and acidic carboxylic
acid functional groups.
Amino acid
H
H2N
α
C
COOH
R
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).
α-amino acid are amino acid in which the amino and carboxylate
functionalities are attached to the same carbon, the so-called α–
carbon.
They are the building blacks of proteins.
Amino acid
Zwitterion is an amino acid having positively and negatively
charged groups, a dipolar molecule.
H
H3N+
C
H
-H+
COOH
H3N+
C
+H+
R
H
-H+
COO-
H2N
C
+H+
R
Zwitterion
R
COO-
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.
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+ = H++AH
(1)
HA = H++A-
(2)
Amino acid
pH effect on the charge of amino acids
The proton dissociation constants are K1, K2
[ A ][ H  ]
K1 
[ HA]
(3)
[ HA][ H  ]
K2 
[ HAH  ]
(4)
[ ] represents concentration in dilute solution.
Amino acid
pH effect on the charge of amino acids
Taking the logs of equations 3 and 4, yields,
[ HA]
pH  pK1  log
[ HAH  ]
[ A ]
pH  pK 2  log
[ HA]
(5)
(6)
where pH=-log(H+), pK1=-log(K1), and pK2=-log(K2).
Amino acid
pH effect on the charge of amino acids
At Isoelectric point (IEP),
[HAH+] = [A-]
(7)
Equation 5 plus 6 yields
pI  pH  ( pK1  pK2)
(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.
Amino acid
pH effect on the charge of amino acids
According to amino acid mass balance, the initial
amino acid concentration is [HA]0
[HA]0 = [HA] + [A-] + [HAH+]
(9)
Combining 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 [HA]0 .
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.
Standard amino acids: there are 20 standard amino
acids that are commonly found in proteins.
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
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
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.
Amino Acid (AA)-Protein
Amino acids: basic unit
Peptides: amino acid chain, containing 2 or more AA.
Polypeptides: containing less than 50 AA.
Protein: > 50 AA.
Peptides (from the Greek πεπτος, "digestible"), are formed through
condensation of amino acids through peptide bonds.
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.
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.
Conjugated protein: hemoglobin
Prosthetic group: heme in green
Amino acid units in red and yellow
Heme group
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
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.
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.
Protein structure
Secondary structure: highly patterned sub-structures
α-helix and β-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 α-helix and
β-pleated sheet.
Protein structure
Secondary structure: α-helix
- Formed within the same protein chain.
- Hydrogen bonding can occur between
- the α-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.
Protein structure
Secondary structure: β-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 C=O 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.
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.
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.
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.
Irreversible egg protein denaturation and loss of solubility,
caused by the high temperature (while cooking it)
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.
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.
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. α-helix and β-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.
Carbohydrates
Carbohydrates:
• Carbohydrates (monosaccharides) are represented by the general
formula (CH2O)n, where n≥3 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).
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.
Glucose
Glucose as a straight chain
Glc in ring structure
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.
D-ribose and deoxyribose
Ribose and deoxyribose are pentose containing
five carbon ring-structure sugar molecules
D-ribose
deoxyribose
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.
Disaccharides
Disaccharides are formed by the condensation of two
monosaccharides via 1, 4-glycosidic linkage.
Maltose
Disaccharides
Common disaccharides:
- sucrose (known as "table sugar", "cane
sugar", "saccharose" or "beet sugar") ,
- lactose (milk sugar)
- maltose produced during the malting of
barley.
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.
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.
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.
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.
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 α-1,4 glycosidic
bonds,
• approximately 1 in 12 Glc residues also makes a
α-1,6 glycosidic bond with a second Glc which
results in creating of a branch.
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 β-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.
Chitin:
poly [b - (1, 4) - 2 - acetamido - 2 - deoxi - D glucopyranose ]
H
H
CH2OH
O
H
H
HN
C O
CH3
CH3
C OH
HN
O
H
H
O
H
CH2OH
O
n
N-acetylation degree of chitin, i.e.
percentage of acetylated amine (amide) 78 10 %
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.
Mangrove crab: Ucides cordatus
Steamed Crab
Crab Cake
Acid washed crab shells
(Niu and Volesky, 2000, JCTB).
Au
Au uptake (mmol/g)
0.25
0.2
Chitin amide: pKa < 3.5
Cl- interference
pH 3.4
0.15
pH 2.4
0.1
pH 4.5
0.05
0
0
0.5
1
1.5
2
2.5
3
Equilibrium Au concentration (m m ol/L)
Effect of pH (Niu and Volesky, 2003, Hydrometallurgy).
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.
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.
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 –C=C- ,
or triple bonds on the hydrocarbon chain, such as Oleic
acids:
CH3-(CH2)7-HC=CH-(CH2)7-COOH
Fats
Fats are lipids that are esters of fatty acids with glycerol.
glycerol
Fatty acids
fat
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.
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.
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.
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.
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.
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.
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).
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.
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
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.
DNA double-helical structure
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.
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.
DNA
e.g. -CGCCGCTGC-GCGGCGACG-CGCCGCUGCarg
arg
sys
mRNA
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.
DNA Replication
Regeneration of DNA from original DNA segments.
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.
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.
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.
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.
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 α-helix and β-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.
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.
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.
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.
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.
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.
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.
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%).
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.
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.
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.
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.
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
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.
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.
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.
Nutrients for S. cerevisia
ethanol 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).
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).
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.
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).
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.
Summary of cell construction
Biopolymers
subunit
bonds for
subunit
linkage
functions
Characteristic
three-D
structure
protein
Carbohydrates
(polysaccharides)
DNA
RNA
lipids