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ChE 275 Winter 2014

Lecture 1 (January 6)

Class Introduction

&

Impact of Biology and Biotechnology

in Chemical Engineering

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Focus of ChE 275

Basic understanding of biochemistry, cell biologyand molecular biology.

The flow of genetic information.

Cell structure and function.

Cell regulation and control strategies.

Applications of biology in (chemical) engineering.

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Key concepts

Specific noncovalent interactions andrecognition events.

Diverse roles of hydrophobic and hydrophilic

interactions.

Selective transport of molecules.

Storage, use, and inter-conversion of chemicalenergy.

Transduction, amplification, and modulation

of external signals.

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Key concepts

Multiple levels (and time scales) by whichcells regulate protein activity.

Biopolymers: functions, synthesis, and

regulated degradation.

Reversibility, regulation and linkage of

biological reactions.

Regulation and quality control of DNA, RNA

and protein synthesis and processing.

Recombinant DNA technology.

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Assignments for ChE 275

Complete reading assignment (~ 20 pages) and

reading test (by 7:00 am) on Blackboard beforeeach MW class; OK to discuss with classmates,but complete RT independently.

First reading test on Mon Jan 13.

Lectures/class discussions will focus on keyconcepts and questions/issues raised on-line andin class.

Closed-book quiz each Monday. Copies ofprevious quizzes will be provided.

Final exam at 3:005:00 pm on March 19.

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Office Hours

Shea (Silverman 3617) - before quiz eachweek:

Monday 11:00 AM 12:00 PM

After class

TAs By appointment

Jennifer Schoborg

([email protected])

Sarah Wood

([email protected])
mailto:[email protected]:[email protected]

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Biotechnology and Bioengineering at NU

Molecular

Cellular

Tissue-level

Global;

Systems-level

AmaralBroadbelt

JewettKungLeonardMillerSheaTyo

AmaralGrzybowskiLeonardMiller

SheaTyo Leonard

MillerShea

AmaralBroadbeltJewett

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Biotechnology and bioprocess engineering

Biotechnology is broadly defined as the use ofbiological systems or organisms for a socially

desirable goal (healthcare, environment, etc.).

Bioprocess engineering is the application of chemical(and other) engineering principles to design and

optimize biological processes and biological catalysts

to bring about desired chemical transformations.

A key aspect of bioprocess engineering is the need to

develop large-scale processes that are economical to

operate and comply with FDA regulations.

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Why study biology as a chemical engineer?

1. An individual cell can be treated as a micro-factory Inputs, outputs, oxygen/mass transport, kinetics (enzyme), energy

balances (ATP, NADH, etc.), and even control systems

Capable of being optimized individually (metabolic engineering)

2. Much biological research requires systems level understanding

Biologic pharmaceuticals, disease treatment, microbial generation of

commodity chemicals, bioremediation

All levels of systems: individual cells, tissue, whole organisms,

communities of organisms

Engineers are well trained for such tasks

3. Biological commercial processes require massive scale-up

Molecular/

bench-scale

research

Pilot scale Industrial scale

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The story of penicillin Discovery of penicillin biosynthesis byPenicillium notatum. (1928)

Not useful for medicine

The Problem

A simple scratch could result in a lethal infection

In WWII, cut, burn, bullet wounds frequently were infected in battlefield conditions

Development of penicillin synthesis by Howard Florey and Ernst Chain (1939)

Grow the mold faster (reactants, optimal T)

Extract the penicillin (separations) 1stClinical Testin vivo

Pressing need for penicillin during WWIIinvolvement of industry such as Merck, Pfizer,

Squibb and USDA-NRRL.

Cartoon source: http://nobelprize.org/medicine/educational/penicillin/

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The story of penicillin

Post WWII

Low yield of penicillin fromPenicillium notatum(ca. 0.001 g/l)

and hence very inefficient process. Fermentation route vs.

chemical routeChemical route initially preferred.

Isolation of penicillin hyper-producing strain,Penicillium

chrysogenumat NRRL.

Penicillin fermentation in surface cultures.

Penicillin fermentation in roller bottles.

Development of submerged fermentation process by Pfizer.

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Penicillin

productivity

New species

Mutation and breeding Molecular biology

and breeding

Bioprocess engineering

improvements have

contributed greatly to the

increased productivity.

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Products made by biotechnology

Vitamin B2

Polymers/plastics

Ethanol Fuel

Pharmaceuticals

Vaccines

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http://www.bio.org/ind/pubs/cleaner2004/CleanerReport.pdf

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Vitamin B2synthesis

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DuPonts Sorona is one member of a family of polymers

based on Bio-PDO corn-derived chemical/1,3-propanediol.

http://www.dupont.com/sorona/technologyplatform.html

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A joint venture between DuPont and Tate & Lyle PLC has been

formed to produce 1,3-propanediol (PDO), the key building block for

DuPont Sorona polymer, using a proprietary fermentation andpurification process based on corn sugar. This bio-based method

uses less energy, reduces emissions and employs renewable resources

instead of traditional petrochemical processes.

http://www2.dupont.com/Sorona/en_US/

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U.S. National Vision goals for biomass technologies

Appl. Microbiol. Biotechnol., 64:137, 2004

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Nature Biotechnology, 22: 671, 2004

LifeCycle

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Appl. Microbiol. Biotechnol., 64:137, 2004

Integration

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l f h i bi d

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Examples of therapeutic bioproducts

Taxol

Penicillins

Erythropoietin Insulin dimer and hexamer

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Therapeutic Glycoproteins

Initially recovered from blood and other tissues (clotting

factors and growth hormone).

Production at low concentrations in primary cell culture

(urokinase).

Recombinant DNA technology developed in bacteria by

Cohen and Boyer in 1973.

Genetic engineering of animal cells to produce

recombinant proteins became routine in the 1980's.

tPA approved in 1987.

EPO sales of $1.4 billion in 1994 (still in roller bottles).

Many small reactors, but reactors in the 10,000+ L scale

are used for high-volume products.

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Monoclonal Antibodies

Polyclonal antibodies initially recovered from blood and

produced in animals (-globulin and antisera) Hybridomas for production of monoclonal antibodies were

developed by Khler and Milstein in 1975.

Production expanded from mouse ascites to stirred cultures

and hollow fiber reactors. Many of the recent advances inanimal cell culture were developed using hybridomas.

OKT3 (reversal of transplant rejection) approved in 1986.

Used in many diagnostic assays.

Production scale now exceeds 10,000 L for airlift andstirred vessels. New advances include fed-batch and high-

density perfusion systems.

New therapeutic applications require doses of 215 mg/kg

body weight and are providing much of the growth.

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U.S. Biotech: 1994-2005

Sales up 4X

R&D spending up 3X Employees up 2X

Source: Ernst & Young, LLP

2005 2006 T T Bi h D

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2005-2006 Top Ten Biotech Drugs:

US Sales >$30 BillionProduct (indications) Company 2005 sales ($

billions)

2006 sales ($

billions)

Change

Enbrel (arthritis, psoriasis,

ankylosing spondylitis)

Amgen, Wyeth, Takeda $3.7 $4.4 20%

Aranesp (anemia) Amgen $3.3 $4.1 26%

Rituxan/MabThera (non-

Hodgkin lymphoma)

Biogen Idec, Genentech, Roche$3.3 $3.9 16%

Remicade (Crohn disease,

arthritis)

Johnson & Johnson, Schering-

Plough$3.0 $3.6 20%

Procrit/Eprex (anemia) Johnson & Johnson $3.3 $3.2 -4%

Herceptin (breast cancer) Genentech, Roche $1.7 $3.1 82%

Epogen (anemia) Amgen, Kirin $2.8 $2.9 0%

Neulasta (neutropenia) Amgen $2.3 $2.7 18%

Human insulinsc(diabetes) NovoNordisk $2.5 $2.5 1%

Avastin (colon cancer) Genentech, Roche$1.3 $2.4 77%
http://www.nature.com/nbt/journal/v25/n4/fig_tab/nbt0407-380_T1.htmlhttp://www.nature.com/nbt/journal/v25/n4/fig_tab/nbt0407-380_T1.html

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Nature Biotechnology, 24: 284 (suppl.), 2006

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Cell & Tissue Culture Applications

Cultured cells as final products:

"bone-marrow" transplantation

immunotherapymesenchymal cell therapies

blood cells for transfusions

neural stem and progenitor cells

gene therapies

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Cell & Tissue Culture Applications

Cells for encapsulation (pancreas).

Cultured tissues for transplantation (skin,

chondrocytes, nerve regeneration). Functional extracorporeal or implanted

bioartificial organs (liver, kidney).

Model systems for toxicity and efficacy

testing (liver, cornea).

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Combination Devices- KeraCures KeraPac

Non-woven fabric combined with

porous microcarrier beads and

human keratinocytes (skin cells)

Placed directly on the wound,

removed several days later

Active wound care

Covers & protects

Promotes moist environment

Active agents stimulate healing

http://www.keracure.com/kerapac.asp

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Regenerative Medicine: Artificial Bladder

http://www.tengion.com/technology/platform.cfm

Tengion technology

Neo-bladder

Patients cells(autologous)

minimizes immune

rejection risk

Three phase II

clinical trials

initiated

N l bi h

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Not only can biotech create

It can also destroy.

Chlorinated

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Several species of

Dehaloccoides that are

effective in breakingdown chlorinated

chemicals have had

their genomes

sequenced.

This may allow forfurther optimization of

chlorinated compound

breakdown by

Dehaloccoides, and

may allow for use of

selected genes in otherbacteria.

Chlorinated hydrocarbons

are excellent solvents,

used in many industries.

Chlorinated

hydrocarbons are

very toxic and

accumulate in

ground water..

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Incorporation of an

NADPH-dependent

nitroreductase fromEnterobacter cloacae

and the complex XplA

enzyme (ferrodoxin and

P450 domains) from

Rhodocossus

rhodochrousallowsplants to degrade (and

get energy from) TNT

and RDX explosives.

Endogenous plant

enzymes catalyze the

remaining reactions.

Explosives

contaminates can also

permeate ground water.

Wh st d biolog as a chemical engineer?

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Why study biology as a chemical engineer?

1. An individual cell can be treated as a micro-factory

Inputs, outputs, oxygen/mass transport, kinetics (enzyme), energy

balances (ATP, NADH, etc.), and even control systems

Capable of being optimized individually (metabolic engineering)

2. Much biological research requires systems level understanding

Biologic pharmac eutic als , dis easetreatment, mi c robial generation of

com modity chemi cal s , bioremediat ion

Al l lev els of sy stems : indiv idual cell s, tis sue, whole organism s,

com munit ies of organism s

Engineers are well trained for suc h tas k s

3. Biological commercial processes require massive scale-u

M ol ec u l a r /b e n c h - s c a l e

research

Pi l o t s c a le In d u s tria l s c a le

Highly Automated Production Facilities

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g y

I t f bi l ChE D t

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Impact of biology on ChE Depts.

More than half of incoming graduate students

are interested in bio-related research. Many undergraduates are also interested in

biology; parallel growth in BME Depts.

Many of our students take jobs in bio-relatedpositions or companies.

Most ChE departments now require a class in

biology for all students (13/16 in Big 10+). Many ChE departments have changed their

name; some have developed new degrees or

majors and most have bio-related options.

E l t O t iti

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Employment Opportunities

R&D Development Commercialization

Discovery

Product Research

Process Research

Intellectual Property

Process Development

Product Development

Quality Assurance/Control

Clinical Monitors/Trainers

Medical Writers

Project Managers

Intellectual Property

Product Managers

Technical Sales

Technical/CustomerSupport

Scientific Liaisons

Medical/RegulatoryAffairs

Quality Assurance/Control

Manufacturing &

technical support

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ChE 275 Winter 2014

Lecture 1a (January 6)

Cooper and Hausman Chapter 1

This chapter introduces a lot of material in overview format.

We will go into much more detail on most of this during the

quarter. Dont worry about all of the little details.

.

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Announcements

I will post powerpoint slides on Blackboardafter lecture.

TAs will be responsible for anydispute/regrades on weekly quizzes. Seesyllabus for which TA to contact on a givenweek.

Lowest quiz will be dropped.

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Outline

Evolution

Organic molecules (amino acids, metabolites)

Macro-molecules (DNA, RNA, proteins)Membranes (phospho-lipid bilayer)

Energy source (metabolism)

Fig. 1.1 Spontaneous formation of organic molecules

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g p g

What was the bulk of

the atmosphere

composed during

pre-biotic times?

1950s

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Fig. 1.1 Spontaneous formation of organic molecules

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g p g

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Macromolecules

Nucleic Acids

RNA

DNA

Proteins

Which molecules can

replicate themselves?

Fig. 1.2 Self-replication of RNA(specific noncovalent interactions)

Which came 1st, DNA or

RNA?

Fig. 1.3 Enclosure of self-replicating RNA in a phospholipid membrane

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(also has catalytic activity)

Early membranes formed by simple

amphiphiles were likely more leaky.

Fig. 1.4 Generation of metabolic energy

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g gy

What was the source of energy to form the 1st organic molecules?

ATP ADP + Pi

G0=7.3 kcal/mol

Fig. 1.4 Generation of metabolic energy

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g gy

In what order did these mechanisms evolve?

Universal requirements for cells

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Universal requirements for cellsWhat are the minimal attributes required for

viable cells to exist?


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A. Separation of cell contentsfrom the environment.

B. Ability to transport nutrientsinto the cell.

C. Ability to replicate withreasonable fidelity.

D. Ability to generate energy tocarry out cell functions.

E. Functional molecules tocarry out cell functions.


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A. Separation of cell contentsfrom the environment.

B. Ability to transport nutrientsinto the cell.

C. Ability to replicate withreasonable fidelity.

D. Ability to generate energy tocarry out cell functions.

E. Functional molecules tocarry out cell functions.

Components

DNA

RNAProtein

Lipid bi-layers

ATP (chemicalpotential)

Conceptual model of protocell

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Conceptual model of protocell(Mansy et al.,Nature, 454:122, 2008)

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Once we have the 1stcell, where

do we go from here Prokaryotes

Eubacteria

Archeabacteria

Eukaryotes

Single-cell

Multicelled Plant

Animal

Fig. 1.7 Evolution of cells

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Species and Phylogenetic Trees

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Species and Phylogenetic Trees

What are possible

implications of this?

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Fig. 1.5 Electron micrograph ofE. coli

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Ribosomes are

present throughout

the cell.

Divide to form two

new cells; may

remain attached.

Bacillus cereus(SEM)

Streptococcus sanguis(SEM)

Diverse shapes

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------- Present

At least three classes of dynamic polymers make up the bacterial cytoskeleton.

Scientists continue to discover new things about bacteria.

Fig. 1.6 Structure of animal cells

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(both free and associated

with the rough ER)

(have their own

DNA (partial) &

ribosomes)

Nuclear pore

Eukaryotic cell nucleus and organelles

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y g

What are possible advantages for having organelles?


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y g


A. Creation of distinct environments (pH, redox, etc.).

B. Decreased diffusion distances; cells can be larger.

C. Localization of reactants for particular reactions.

D. Protect DNA from damage.

What is the evidence that mitochondria and

chloroplasts arose from prokaryotic endosymbionts?


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y g


A. Creation of distinct environments (pH, redox, etc.).

B. Decreased diffusion distances; cells can be larger.

C. Localization of reactants for particular reactions.

D. Protect DNA from damage.

What is the evidence that mitochondria and

chloroplasts arose from prokaryotic endosymbionts?

A. Their DNA and ribosomes resemble those of bacteria.

B. They are similar in size and replicate by simple division.

C. Current endosymbionts show loss of DNA (similar size).

Endosymbionts have

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small genomes

Science, 314: 259, 2006

Science, 314: 267, 2006

Endosymbionts that lost

substantial DNA may have

remained as organelles.

Experimental Biology an

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Experimental Biology an

active field

Model organismsWhat

Why

HowGrowing in the lab

Animal

PlantVirus

Microscopy (only fluorescence / 2-photon)

81

Some model organisms

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What is a genome sequence? Why useful for a model organism?82

Which of the following are reasons that

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g

biologist define and study model organisms?

A. Model organisms are easy to grow and analyze in the lab.

B. All model organisms require the same nutrients, so it is

simple to compare.

C. Model organisms have similar DNA to other organisms, so

what we learn in a model organism applies to other

organisms.

D. Model organisms are more complex than others, so if we

understand the model organism, the non-model organismsshould be easy.

E. We have lots of techniques to modify the DNA of model

organisms that can be difficult in other organisms.83

Fig. 1.13 Bacterial

l i

Bacterial modelE. coli

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colonies

Colonies formed

by mutants able to

grow under adverse

conditions can be

readily isolated.

Bacteria grow

rapidly; dilute

suspensions ofsingle cells

form colonies

in solid media.

How? Grow at high T?

Grow much faster?Tougher to select for

cells that dont grow.84

Finding a mutant that is resistant

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gto salt

1. Grow cells in high salt levels1. What size colony would you expect for

1. Normal cell?

2. Salt-resistant mutant?2. Analyze mutant

How would you find mutants with low saltresistance?

85

Fig. 1.14 EM of Saccharomyces cerevisiae

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Nuclear membrane

is not evident during

cell division; rough

ER is evident.

Good model for

studying celldivision and

organelle function,

as well as transport

into and out of the

nucleus.

86

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Fig. 1.15 Caenorhabditis

elegans

C eleganshas 959 somatic cells.

What could we study in this organism?

87

Fig. 1.16 Drosophila melanogaster

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Many genes

related todevelopment,

including of

limbs, were first

identified in

Drosophila.

Gene names are

often based on

changes in fly

appearance (e.g.,

wingless,frizzled).

88

Fig. 1.19 Zebrafish

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Fins were the precursors of limbs.

Xenopus laevis eggs.How to decide which

model system to use?

89

Fig. 1.20 Mouse as a model for human development

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Model systems are often used in sequence during drug development90

Model organisms

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If you can choose only one model organism per study, which

organism would be best suited for which study and why?

Consider simplicity (why?) and appropriateness. Organisms:E. coli(bacterium) S. cerevisiae(yeast)

C. elegans(nematode or worm)

D. melanogaster(fruit fly) M. musculus(mouse)Studies:

a) effect of a specific gene on digestive system development

b) transport of proteins through the nuclear membranec) how mutation of a specific gene affects limb development

d) role of protein misfolding in a neurodegenerative disease

e)protein synthesis on ribosomes 91

G i ll i lt

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Growing cells in culture

Unicellular organismsEasy

Why?

Multicellular organismsHardAnimal

Plant

92

Fig. 1.41 Culture of animal cells

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Normal cells stop growing when

they reach confluence.

Transformed (tumor) cells and

embryonic stem cells can growindefinitely in culture.

Lifetime in culture of normal cells

is limited due to genetic damage

and loss of telomeres.93

Animal Cell Nutritional Requirements

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q

In contrast to animal cells, yeast or bacterial cell cultures

can be grown on fairly simple media without the need toadd amino acids or various vitamins and hormones. What

is/are the primary reason(s) for this?

94

Animal Cell Nutritional Requirements

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q

In contrast to animal cells, yeast or bacterial cell cultures

can be grown on fairly simple media without the need toadd amino acids or various vitamins and hormones. What

is/are the primary reason(s) for this?

Animal cells come from organisms having multiple cell

types with specialized functions, including metabolism.

Animal cells typically live in association with other cells

and receive stimulatory factors from other cells to regulate

their growth.

Animal cells lack the enzymes to synthesize some amino

acids and vitamins (these are called essential).95

Fig. 1.12 Light micrographs of selected animal cells

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Red and

white

blood

cells

Fibroblasts

in connectivetissue

96

Fig. 1.12 Light micrographs of selected animal cells

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Isolated and cultured tissues can also serve as experimental models.

Why can cells look so different when they contain the same DNA?

Documents

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