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Bioprocess Engineering
Chap. 2 An Overview of Biological Basics
1. Microbial Diversity
(1) psychrophiles: cells grow at low temp (<20o C)
(2) mesophiles: cells grow with the temp optima in the range of 20-50o C
(3) thermophiles: cells grow at temp greater than 50o C
(4) aerobic: cells require oxygen for grow and metabolism
(5) anaerobic: cell growth inhibited by the presence of oxygen
(6) facultative: organisms switch the metabolic pathways to allow them to grow
under either circumstance
(7) cyanobacteria: grow in an environment with only little moisture and a few
dissolved minerals (formerly called blue-green algae), photosynthetic,
convert CO2 into organic compounds
(8) coccus: cells with a spherical or elliptical shape
(9) bacillus or rods: cylindrical cells
(10) spirillum: spiral-shaped cells
2. Naming Cells
(1) dual name (binary nomenclature):
a. genus: a group of related species
b. species: includes organisms that are substantially alike
c. example: Escherichia coli
(2) names are given in Latin
(3) two primary cell types:
a. prokaryotes:
(i) have a simple structure with a single chromosome
(ii) have no nuclear membrane and no organelles
(iii) 0.5-3 um
b. eucaryotic
(i) have a more complex internal structure
(ii) more than one chromosome (DNA molecule) in the nucleus
(iii) have a true nuclear membrane and a variety of organelles
(iv) fungi (yeasts and molds), algae, protozoa, animal and plant cells
(v) 5-10 times larger than prokaryotes in diameter
(4) gram stain (developed by Hans Christan Gram in 1884)
a. procedures:
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(i) first requires fixing cells by heating,
(ii) the basic dye, crystal violet, is added, all bacteria will stain purple
(iii) iodine is added, followed by the addition of ethanol
b. types:
(i) Gram-positive cells remain purple: do not have an outer membrane,
easier for protein excretion
(ii) Gram- negative cells become colorless (E. coli): have an outer
membrane
3. Viruses
(1) very small and are obligate parasites of other cells
(2) from 30 to 200 nm
(3) contain either DNA (DNA viruses) or RNA (RNA viruses) as genetic material,
which is covered by a protein coat called “capsid”
(4) bacteriophages: viruses infecting bacteria
(5) bacteriophages attach to the host cell wall with tail fibers and inject the viral
nuclear material into the host cell
(6) reproduction of viruses:
a. lytic cycle: host cells lyse or break apart and phage particles released
b. lysogenic cycle: phage DNA incorporated into host DNA and the host
may continue to multiply
(7) bacteriophages can be used as vectors to ioncorporate foreign DNA into host
cell
4. Cell Construction
(1) living cells composed of high-MW polymeric compounds such as proteins,
nucleic acids, polysaccharides, and storage materials (fats,
polyhydroxybutyrate, glycogen)
(2) cells also contain inorganic salts (NH4+, PO4(3-), K+, Ca(2+), Na+, SO4(2-))
and metabolic intermediates (pyruvate, acetate), and vitamins
(3) Elemental composition of typical bacteria cell: 50%C, 20%O, 14%N, 8%H,
3%P, 1%S, etc.
(4) More than 2000 rxns taking place in a cell
5. Amino acids and proteins
(1) Proteins are the most abundant organic molecules in living cells, 40-70% of
their dry weight
(2) Proteins are polymers built from amino acid monomers
(3) a-amino acids are the building block of proteins (structure: p.27)
(4) they differ from each other by R group (side chain)
(5) the a. a. sequence determines a protein’s primary structure
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(6) two major types of proteins
a. fibrous proteins
b. globular proteins
(7) biological functions of proteins
a. structural proteins: glycoproteins, collagen, keratin
b. Catalytic proteins: enzymes
c. Transport proteins: hemoglobin, serum albumin
d. Regulatory proteins: hormones (insulin, growth hormone)
e. Protective proteins: antibodies, thrombin
(8) Enzymes:
a. more than 2000 enzymes are known
b. enzymes are highly specific in their function and have extraordinary
catalytic power
c. each enzyme contains one or more active site for substrate binding during
catalysis
d. some enzymes are regulated and are called regulatory enzymes
e. most enzymes are globular proteins
(9) Amino acids
a. there are 20 a.a.
b. only L-amino acid are found in proteins
c. a.a. have acidic (COOH) and basic (NH2) groups
d. zwitterions
e. the pH value at which a.a. have no net charge is called the isoelectic point
(pI), which varies depending on R group of a.a.
(10) Peptide bond
a. the condensation rxn between two a.a. results in the formation of a
peptide bond
b. peptides contain 2 or more a.a. linked by peptide bonds
c. polypeptides usually contain less than 50 a.a.
d. larger a.a. chains are called proteins
(11) conjugated proteins:
a. proteins containing prosthetic groups (organic and/or inorganic
components)
b. hemoglobin is a conjugated protein and has 4 heme groups, which are
iron-containing complexes.
(12) structure of proteins
a. primary structure: the linear a.a. aequence
b. secondary structure:
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(i) a result of H-bonding between residues not widely separated
(ii) two major type:
1. helixes:
(a) either a-helix or triple helix
(b) in a-helix, H-bonding occur between the a-carboxyl
group of one residue and the NH group of its neighbor 4
units down the chain
(c) triple helix present in collagen consisting of 3 a- helixes
2. sheets:
(a) ß-sheet is more stable
(b) The H-bonds between parallel chains stabilize the sheet
structure and provide resistance to stretching
c. Tertiary structure:
(i) a result of interaction between R groups widely separated along the
chain
(ii) R groups may interact by covalent, disulfide, or H bonds
(iii) Hydrophobic and hydrophilic interactions may also present
(iv) Disulfide bonds are critical in proper chain folding
d. Quaternary structure:
(i) only proteins with more than one polypeptide chain have quaternary
structure
(ii) hemoglobin
(iii) the forces can be disulfide bonds or other weak interactions
(13) Antibodies (Ab) or Immunoglobulins
a. proteins bind to particular molecules with high degree of specificity
b. the foreign molecule is called the antigen (Ag)
c. form an antigen-antibody complex, which precipitates from the serum
and is called “precipiyin”
d. the complex formation is called the “immune response”
e. Ab usually has two binding sites
f. 5 major classes of immunoglobulins in human blood plasma: IgG (most
abundant), IgA, IgD, IgM, IgE, MW are about 150kd except for IgM
(900kd) (A Dalton is a unit of mass equivalent to H atom)
g. immunoglobulins have 4 polypeptide chains: 2 heavy chains (H) (about
430 a.a.) and 2 light chains (L) (about 214 a.a.), these chains are linked
by disulfide bonds into a Y-shaped, flexible structure
6. Carbohydrates: Mono- and Polysaccharides
(1) play key roles as structural and storage compounds in cells
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(2) general formula: (CH2 O)n, n≧3
(3) synthesized through photosynthesis
CO2 +H2O=CH2 O+O 2 (p.35)
(4) monosaccharides
a. contain 3-6 carbon atoms
b. either aldehydes or ketones (p.36 Table 2.5)
c. D-ribose and deoxyribose (p.37) are 5 carbon ring-structure and are
essential components of RNA and DNA
(5) Disaccharides are formed by the condensation of two monosaccharides
a. Sucrose is a disaccharide of a-D-glucose and ß-D-fructose
b. Lactose is a disaccharide of ß-D-glucose and ß-D- galactose (p.38)
(6) polysaccharides are formed by the condensation of more than 2
monosaccharides by glycosidic bonds
a. amylose: a straight chain of glucose linked by a-1,4-glycosidic linkages
and is water insoluble and constitutes about 20% of starch
b. amylopectin: s branched chain of D-glucose, branching occurs by
a-1,6-glycosidic linkages. Water soluble
(7) Glycogen:
a. a branched chain of glucose that resembles amylopectin
b. highly branched and contains about 12 glucose units in straight-chain
segments
(8) Cellulose:
a. long, unbranched chain of D-glucose with MW between 50000 and 1
million daltons
b. the linkage is a ß-1,4-glycosidic linkage, which is resistant to enzymatic
hydrolysis
7. Lipids, Fats, and Steroids
(1) lipids
a. hydrophobic, water- insoluble molecules
b. soluble in nonpolar solvents such as benzene, cloroform, and ether
c. major component is fatty acid, which is made of straight chain of
hydrocarbon (hydrophobic) groups, with a carboxyl group (hydrophilic)
at the end
d. fatty acid: CH3 -(CH2 )n-COOH, n=12 to 20
e. unsaturated fatty acids contain double C=C bonds, such as oleic acid
(2) Fats:
a. serve as biological fuel-storage molecules
b. esters of fatty acids with glycerol
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c. formation of fatty acid (p.41)
(3) Steroids
a. hormones that are important regulator of animal development and
metabolism at very low conc.
b. A well –known steroid, cholesterol, is present in membranes of animal
tissues
8. Nucleic Acids, RNA and DNA
(1) nucleic acid
a. nucleic acids play central role in reproduction of living cells
b. nucleotides are the building blocks of DNA and RNA and also serve as
molecules to store energy and reducing power
c. three major components in nucleotides are phosphoric acid, pentose
(ribose or deoxyribose), and a base (purine or pyrimidine)
d. purines: adenine (A) and guanine (G)
e. pyrimidines: thymine (T), cytosine (C), and uracil (U)
(2) Deoxyribonucleic acid (DNA)
a. stores and preserves genetic information
b. contains A, T, C, G
c. formed by condensation of nucleotides between the 3’ and 5’ carbons’
successive sugar rings by phosphodiester bonds
d. has a double-helical 3-D structure
e. the sequence if bases in DNA carries genetic information
f. the base sequence of DNA is written in the 5’→3’ direction
g. the phosphate and deoxyribose units are on the outer surface, but the
bases point toward the chain center
h. the diameter of the helix is 2nm with interval of 3.4nm (10 residues)
i. two chains are held together by H-bonding between pairs of bases: A-T (2
H-bonds) and G-C (3 H-bonds)
j. DNA replication: regeneration of DNA from original DNA segments.
Semiconservative
k. Some cells contain circular DNA segments in cytoplasm that are called
“plasmids”. Plasmids are easily moved in and out if cells and are often
used for genetic engineering
(3) Ribonucleic acid (RNA)
a. plays a central role in protein synthesis
b. transcribe the genetic information in DNA and translate in protein
synthersis
c. the templates for RNA synthesis are DNA molecules
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d. RNA molecules are the templates for protein synthesis
e. Transcription: formation of RNA molecules from DNA
f. Translation: formation of peptides and proteins from RNA
g. Messenger-RNA (m-RNA): genetic information-carrying intermediates
h. Transfer-RNA (t-RNA) and ribosomal-RNA (r-RNA): involve in part of
the machinery of protein synthesis
i. RNA consists of nucleotides joined by 3’-5’ phosphodiester bonds
j. RNA molecules are usually single-stranded
k. Ribosome: the organelle in cytoplasm where proteins are synthesized
9. Cell Nutrients
(1) microorganisms are classfied in 2 categories on the basis of the carbon
sources:
a. heterotrophs: use organic compounds as carbon and energy source
b. autotrophs: use CO2 as carbon source
(i) chemoautotrophs: utilize CO2 as a carbon source and obtain energy
from oxidation of inorganic compounds
(ii) PhotoautotrophsL use CO2 as carbon source and utilize light as an
energy source
(2) Nutrients required by acells can be classified in two categories:
a. macronutrients: needed in conc. larger than 10-4 M
b. micronutrients: needed in conc. less than 10-4 M
(3) Growth media
a. complex media: contain natural compounds whose chemical composition
is not exactly known
b. defined media: contain the exact amount and type of nutrients