2.+Biological+basics_cells

Overview of Cellular & Molecular Biology

Engineering Analysis

Shuler, Ch 2: An overview of Biological Basics

The domains of life

Prokaryotes

Eukaryotes

Eubacteria (bacteria) Arechaebacteria (archae)

Single-‐cell mulGcellular

Single-‐cell Single-‐cell

Similar metabolism

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 fidelity yet allow flexibility 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 differenGal equaGons

Engineering analysis: Material & energy balances

•  Help account for what is changing in a process

PROCESS IN 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

PROCESS Generation, consumption

Accumulation = In – Out + Generation – Consumption Accumulation = 0 è 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)

IN OUT

Input = People moving in Output = People moving out

Generation = Births

Consumption = Deaths

Accumulation = Change in populaGon

Example - New York City

AccumulaGon = In – Out + GeneraGon – ConsumpGon

Corn Ethanol Process

Energy

Corn 100,000 bushels/day (energy, water to produce) Ethanol

275,000 gallons/day

Distiller Dry Grain (waste yeast/corn) 860 tons/day CO2

Water

Yeast & enzymes

•  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!!

What closed system to use ?

Corn Ethanol Process

Mill Corn

Water Enzymes

(glucoamylase)

Slurry Tank Liquefaction Cooler

Yeast & Enzymes (α-amylase)

Fermentation

Distillation Whole stillage to dryer

CO2

Molecular Sieve DDG

200 Proof ** Ethanol

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 defined 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

Cellular building blocks ChEn 3701 8/22/2006

Prof. W-S Hu Lecture Notes 4

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

Volume 4 x 10-9 cm3

Typical Elemental composition (%of dry mass)

Other mineralsSPONHC

0.51329748Yeast

82513750Bacteria

• 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 DNA

mRNA

proteinAmino-acids

tRNA rRNA

Gene: functional unit of genetic information• Old dogma:

- one gene, one protein, - now overlapping segments of DNA for different proteins

• Gene: segment of DNA sequence corresponding to a single protein (or to a single catalytic or structural RNA molecule)

•  Carbohydrates (monosaccharides); l-‐amino acids; nucleoGdes; fajy acids/ lipids •  Monomers polymerize to make more complex structures (eg, protein, cell membrane)

•  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.

cell

IN OUT

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

BIOLOGICAL SYSTEMS USED IN BIOTECHNOLOGY

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

•  Vectors for recombinant DNA technology •  Vaccines: weakened or dead virus •  Drug discovery: anGviral agents

Importance in Biotechnology

Typical bacterial cell

ChEn 3701 8/22/2006


Structure of the cells:chemical bonds, materials,

organelles and cells

ChEn 3701, Fall 2006Topic 2

Three Domains of life

Prokaryotes

Eukaryotes

Eubacteria(bacteria)

Archaebacteria(archae)

Similar in metabolism

Similar in gene expression machinery

Single-cell

multicellular

Unicellular

No organelles, no compartmentalized membrane enclosed space

(lipid bilayer)

(not lipid bilayer)

Sieve barrier

Gram-positive and negative bacteria

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

Staphylococcus

Gram positive

E. coli

Gram negative

Peptydoglycan (cell wall)!

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)

•  Differen9a9on: distribuGon of funcGons in Gme and space

•  Development into mulG-‐cellular organisms, Gssues, organs: survival based on organisms, not cell

CompartmentalizaGon

ChEn 3701 8/22/2006


Moving beyond simple microbial cells

1. Compartmentalization in space and function:-organelles

2. Differentiation:-distribution of functions in space and time (e.g. spores)

3. Increased genetic complexity -ploidity, combinatorial gene regulation

4. Development into tissue, organs, and multicellular organisms

-Survival is based on “organism” not “cells.”

Differentiation: ExampleLife Cycle of Streptomycetes-a soil bacterium

10 hours

18 hours 30 hours

2 Days

3 Days4 to 10 Days

Free spore

Adapted from Schauer et al., 1988

Even some bacteria can differentiate, e.g. Streptomyces, Bacillus can form spores. Mold (an eukaryote) can also sporulate.

Compartmentalization of Space for Specialiased Functions

Filamentous Cytoskeleton

CiliaPlasma

MembranePeroxisome

NucleusNucleolus

Smooth Endoplasmic Reticulum

Mitochondrion

Golgi Vesicles

Small Membrane Vesicles

Lysosome

Centrioles

Rough Endoplasmic

Reticulum

Animal CellEukaryo9c cell

DifferenGaGon

ChEn 3701 8/22/2006


Moving beyond simple microbial cells

1. Compartmentalization in space and function:-organelles

2. Differentiation:-distribution of functions in space and time (e.g. spores)

3. Increased genetic complexity -ploidity, combinatorial gene regulation

4. Development into tissue, organs, and multicellular organisms

-Survival is based on “organism” not “cells.”

Differentiation: ExampleLife Cycle of Streptomycetes-a soil bacterium

10 hours

18 hours 30 hours

2 Days

3 Days4 to 10 Days

Free spore

Adapted from Schauer et al., 1988

Even some bacteria can differentiate, e.g. Streptomyces, Bacillus can form spores. Mold (an eukaryote) can also sporulate.

Compartmentalization of Space for Specialiased Functions

Filamentous Cytoskeleton

CiliaPlasma

MembranePeroxisome

NucleusNucleolus

Smooth Endoplasmic Reticulum

Mitochondrion

Golgi Vesicles

Small Membrane Vesicles

Lysosome

Centrioles

Rough Endoplasmic

Reticulum

Animal Cell

Spore-‐forming bacteria (eg, Bacillus, Streptomyces)

InformaGon processing

ChEn 3701 8/22/2006


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

Volume 4 x 10-9 cm3

Typical Elemental composition (%of dry mass)

Other mineralsSPONHC

0.51329748Yeast

82513750Bacteria

• 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 DNA

mRNA

proteinAmino-acids

tRNA rRNA

Gene: functional unit of genetic information• Old dogma:

- one gene, one protein, - now overlapping segments of DNA for different proteins

• Gene: segment of DNA sequence corresponding to a single protein (or to a single catalytic or structural RNA molecule)

What is a gene?

Genome size of some organisms

ChEn 3701 8/22/2006


Sex (mating type) Enhances Genetic Material Exchange

Sex also introduces ploidity. Bacteria also have more primitive form of sex, but not ploidity

Yeast can differentiate as well as having different ploidity in their life cycle

AutosomeSex chromosome Autosomes: 22 parental, 22

maternal

Combinatorial assortment in meiosis: among the autoxomes somroriganate from paternal, others maternal

Diploidity greatly increases genetic diversification among individuals in a population

Biological Scales: LengthOther scales: time, mass, “complexity”, genome Genome Size of Some Organisms

5.0x 109Hordeum vulgare(Barlay)

25,000-28,000

35,000-50,000

7000

4300

Estimate Number of Genes

1.3 x 108Arabidopsis thalianaFlowering plant

3.3 x 109H. sapiensMammal

3.1 x 109X. laevisAmphibian

1.2 x 109G. domesticusBird

1.4 x 108D. melanogasterInsect

8.0 x 107C. elegansNematode

5.4 x 107D. discoideumSlime mold

1.21 x 107S. cerevisiaeYeast

4.2 x 106Bacillus subtilis

4.6 x 106E. coliBacterium

8 x 105M. pneumoniaeMycoplasma

6.6 x 105Prenomas salinaAlgae

Genome (bp)Size

SpeciesPhylum

Genome size does not correlate completely to “complexity” of an organism

Heredity and diversity

ChEn 3701 8/22/2006


Chemical Basis of Heredity: DNA Replication

(Template strads)

How are living systems diversified?

• Fidelity in reproducing genetic information• Flexibility and adaptability for evolution

– Flexibility in two ways• Combinatorial assortment of genetic materials

– When passing genetic information to offspring, different individual offspring receive different combination of genetic materials

• Variation in genetic materials– Allow for changes in the genetic materials, or the

modification of the genetic information

Modes of Genetic Alteration

– Intragenic mutation• create new genes

– Gene Duplication• Make more copies, closely related genes

– Segment shuffling• A segment of a gene is broken and rejoined to

give hybrid gene– Horizontal Transfer

• Entire segment of gene moves from one cell to another (may not be the same species)

A segment of chromosome can also be shuffled

ChEn 3701 8/22/2006


Chemical Basis of Heredity: DNA Replication

(Template strads)

How are living systems diversified?

• Fidelity in reproducing genetic information• Flexibility and adaptability for evolution

– Flexibility in two ways• Combinatorial assortment of genetic materials

– When passing genetic information to offspring, different individual offspring receive different combination of genetic materials

• Variation in genetic materials– Allow for changes in the genetic materials, or the

modification of the genetic information

Modes of Genetic Alteration

– Intragenic mutation• create new genes

– Gene Duplication• Make more copies, closely related genes

– Segment shuffling• A segment of a gene is broken and rejoined to

give hybrid gene– Horizontal Transfer

• Entire segment of gene moves from one cell to another (may not be the same species)

A segment of chromosome can also be shuffled

Molecular & cellular biology basics

•  TranscripGon (DNA à mRNA) •  TranslaGon (mRNA à protein) •  Proteins, post-‐translaGonal modificaGon & sorGng •  Cell growth & death

2.+Biological+basics_cells

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