Overview

of Cellular & Molecular

Biology

Engineering Analysis

Shuler, Ch 2: An overview of Biological Basics

The domains of life

Prokaryotes

Eubacteria
(bacteria)

Arechaebacteria
(archae)

Single-cell


Single-cell

Similar
metabolism

Single-cell
Eukaryotes

mulGcellular

Similar gene
expression

Similar
biotech
tools

Universal features of a living organism

Barrier, eg, lipid bilayer membrane
Energy conversion, eg, electron transfer
and energy capture mechanisms (light,
inorganic/ organic chemicals)
Catabolism and anabolism, convert
organic compounds to construct building
blocks
Transport system, to control import/
export of materials and signals
Reproduc9ve informa9on: to reproduce
with high delity yet allow exibility to
evolve
Conserved features: evoluGon not
revoluGon

MAIN DIFFERENCES BETWEEN

PROKARYOTIC AND EUKARYOTIC CELLS:

1. Chemical components of the cell wall

2. Nucleus containing chromosomal DNA
3. Subcellular organelles in the cytoplasm

Engineering math
Mass balances
Mass acGon kineGcs
ReacGon stoichiometry
Separable dierenGal equaGons

Engineering analysis:
Material & energy balances
Help account for what is changing in a process
IN

PROCESS

OUT

Examples:
Corn ethanol as biofuel, how much corn, energy and water are
needed to produce 100 M gallons/ year?
A patient is on kidney dialysis for a given transfer rate and blood
composition, how long do they need to be attached to the machine?

Engineering analysis
Help account for what is changing in a process

IN

PROCESS
Generation,
consumption

OUT

Accumulation = In Out + Generation Consumption

Accumulation = 0 steady state
EXAMPLES: bank account; population of a city, mass of a person
Need to quantify IN & OUT (using process variables),
not always the same units (convert)

Example - New York City

Input =

People moving in

Generation =

Consumption =
Accumulation =

Output =

Births

Deaths
Change in populaGon

AccumulaGon = In Out + GeneraGon ConsumpGon

People moving out

Corn Ethanol Process

ANNUAL capacity in 2008 of 8 Billion gallons, expected to be 11 Billion
Gallons by 2011 which means 4 billion bushels of corn by 2011
DAILY usage of gasoline in US is 390 million gallons/day in 2007!!
Corn
100,000 bushels/day
(energy, water to produce)

Ethanol
275,000 gallons/day
Distiller Dry Grain
(waste yeast/corn)
860 tons/day
CO2

Yeast &
enzymes
Energy

Water
What closed system to use ?

Corn Ethanol Process

Water
Corn

Enzymes
(glucoamylase)

Yeast &
Enzymes
(-amylase)

Mill
Cooler

200 Proof **
Ethanol

Slurry Tank

Liquefaction

CO2

Fermentation
Molecular Sieve
DDG

Whole stillage
to dryer

Distillation

What closed system to use ?

Stoichiometric calcula9on of
biological reac9ons

Cell composiGon
C Hx Ny Oz (someGmes C Hx Ny Oz Pw )

1 mol of biological material is dened as the
amount containing 1 mol of C

Examples
Bacteria x=1.6 to 2

y=0.2 to 0.26

z=0.27 to 0.45
C H1.6 N0.2 O0.27

Animal
C H1.98 N0.26 O0.49

hEn 3701

Cellular building blocks

Carbohydrates (monosaccharides); l-amino acids; nucleoGdes; fajy acids/ lipids

Monomers polymerize to make more complex structures (eg, protein, cell membrane)
Average Composition of a Cell (pg/cell)

Animal cell

Bacteria

Wet weight

3500

1.5

Dry weight

600

0.3

Protein

250

0.17

Carbohydrate

150

0.015

Lipid

120

0.015

DNA

10

0.015

RNA

25

0.075

Water

1.2
-9

Volume

4 x 10 cm

Typical Elemental composition (%of dry mass)

C

Bacteria

50

13

25

Yeast

48

32

Other
minerals
8

0.5

You can measure cells (dry weight) if you can write mtl balance for main IN and OUT, you can
obtain the elemental composiGon

Engineering analysis of a cell

Glucose (C6H12O6) and ammonia (NH3) form a sterile soluGon (no live cells) fed
conGnuously into a vessel containing a microorganism. Assume complete bio-
reacGon. The product formed from the reacGon contains ethanol, cells
(CH1.8O0.5N0.2 ) and water. The gas produced is CO2 . If the reacGon occurs
anaerobically (without the presence of oxygen) what is the minimum amount
of kg of feed (glucose and ammonia) required to produce 4.6 kg of ethanol ?
Only 60 % of the moles of glucose are converted to ethanol.

IN

cell

OUT

BIOLOGICAL SYSTEMS USED IN

BIOTECHNOLOGY

o Bacteria
o Fungi (yeast, molds)
o Cell lines: insect, plants and mammalian
o MulGcellular organisms: plants or animals
o Viruses: insect, plants and mammalian

Viruses

Very small (30 to 200 nm)

Parasites: FuncGon only inside other cells
Use either DNA or RNA as geneGc material
Viruses infect other cells and can alter the
hosts DNA
Importance in Biotechnology

Vectors for recombinant DNA technology

Vaccines: weakened or dead virus
Drug discovery: anGviral agents

Topic 2

Typical bacterial cell

Two avors: gram-posiGve (one membrane) and gram-nega9ve (two membranes, E. coli)

No organelles, no
compartmentalized
membrane enclosed
space

Sieve

barrier

(lipid bilayer)

(not lipid bilayer)

Peptydoglycan
(cell wall)!

Staphylococcus

E. coli

Gram positive

Gram
negative

Plasma
membrane!

Peptydoglycan !

Plasma membrane!
Periplasm!
Lipopolysaccharide & prot!
(Outer membrane)!

Gram negaGve

Moving beyond single bacterial cells:

EukaryoGc cells
Compartmentaliza9on: space and funcGon
(organelles)
Increased gene9c complexity (combinatorial
gene regulaGon, epigeneGcs)
Dieren9a9on: distribuGon of funcGons in
Gme and space
Development into mulG-cellular organisms,
Gssues, organs: survival based on organisms,
not cell

CompartmentalizaGon
Compartmentalization of Space for Specialiased Functions

Eukaryo9c cell

DierenGaGon

Differentiation: Example
Life Cycle of Streptomycetes-a soil bacterium
Even some bacteria can differentiate, e.g. Streptomyces, Bacillus can
formSpore-forming
spores. Mold (an eukaryote)
can
alsoBsporulate.
bacteria
(eg,
acillus, Streptomyces)

18 hours

30 hours

10 hours
Free spore

2 Days

3 Days
4 to 10 Days
Adapted from Schauer et al., 1988

Animal Cell
Cilia
Plasma
Membrane

Peroxisome
Nucleus

Smooth Endoplasmic

InformaGon processing
Genetic code
DNA as heritable information storage
Universal (almost) linear chemical code

Information processing of life

DNA replication: Templated polymerization to
replicate heritable information
Transcription
Translation
nucleotide
tRNA
Aminoacids

DNA

mRNA
protein

rRNA

What is a gene?

Genome
s
ize
o
f
s
ome
o
rganisms
Genome Size of Some Organisms
Genome (bp)
Size

Phylum

Species

Algae

Prenomas salina

Mycoplasma

M. pneumoniae

Bacterium

E. coli

4.6 x 106

Bacillus subtilis

4.2 x 106

Estimate Number of
Genes

6.6 x 105
8 x 105

4300

Yeast

S. cerevisiae

1.21 x 107

Slime mold

D. discoideum

5.4 x 107

Nematode

C. elegans

8.0 x 107

Insect

D. melanogaster

1.4 x 108

Bird

G. domesticus

1.2 x 109

Amphibian

X. laevis

3.1 x 109

Mammal

H. sapiens

3.3 x 109

35,000-50,000

Flowering plant

Arabidopsis thaliana

1.3 x 108

25,000-28,000

Hordeum vulgare
(Barlay)

7000

5.0x 109

Genome size does not correlate completely to complexity of an organism

Heredity and diversity

Chemical Basis of Heredity: DNA
Replication

How a

8/22/2006

Fidelity in
Flexibility

(Template
strads)

How are living systems diversified?

Flexibilit

Combi

Whe
indiv
gen

Variati

Allo
mod

Fidelity in reproducing genetic information

Flexibility and adaptability for evolution
Flexibility in two ways
Combinatorial assortment of genetic materials
of Genetic
Alteration
Modes
When passing
genetic information
to offspring, different
individual offspring receive different combination of

Intragenic
mutation
genetic materials
create new genes

Variation in genetic materials

Gene Duplication

Allow for changes in the genetic materials, or the

modification of the genetic information

Make more copies, closely related genes

Segment shuffling

A segment of a gene is broken and rejoined to

give hybrid gene

 Molecular & cellular biology basics

TranscripGon (DNA mRNA)

TranslaGon (mRNA protein)
Proteins, post-translaGonal modicaGon & sorGng
Cell growth & death