Download A: DNA

Cells and the Stuff They’re
Made of …
Lectures 3 & 4 & 5
Indiana University P575
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Cells are the “indivisible” units of life.
There is nothing smaller that is alive, nothing bigger is more alive. - J. Theriot
Standard definition of life merges metabolism and replication:

Metabolism: Cells consume energy
from environment and use it to
create ordered structures.

Replication: Cells harness energy
from environment to create
offspring.
Common ancestor several billion
years ago, gave rise to three
major cell types:
Archaea, Bacteria, Eukaryota
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Indiana University P575
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Prokaryotes and Eukaryotes
Prokaryotes: absence of nuclear
membrane (and other organelles)
Bacterium
Eukaryotes: presence of
nuclear membrane
Fibroblast
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Indiana University P575
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E. coli as the Standard Ruler
E. Coli is the “hydrogen atom” of cell biology.
“Not everyone is mindful of it, but cell biologists have two cells of interest; the
one they are studying and Escherichia coli.” – Schaechter et al.
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Easy to isolate
Able to grow in the presence of oxygen
Replicates rapidly
Easy to generate mutants
Lectures 3 & 4 & 5
Indiana University P575
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Hierarchy of Spatial Scales
Fly
Lectures 3 & 4 & 5
Bacteriophage
Compound Eyes
Sperm Cell
ATPaseIndiana University P575 DNA
Bacterium
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Water Molecule
Some Different Cell Types
Referenced to E. coli as
the standard ruler
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A: Giardia lamblia
B: Plant cell
C: S. cerevisiae
D: Red blood cell
E: Fibroblast cell
F: Nerve cell
G: Rod cell
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Cellular Interior: Organelles
Red: Nucleus
Yellow: Golgi
Green: Microtubules
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Information Processing and
Storage: Nucleus
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Energy Production:
Mitochondria
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Lipid and Protein Production:
Endoplasmic Reticulum
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Lipid/Protein Processing and
Trafficking: Golgi Appartus
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How do we know about cellular
and subcellular structures?
Common techniques:
(A) fluorescence microscopy
(B) atomic force microscopy
(C) electron microscopy
Lectures 3 & 4 & 5
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Cellular Interiors:
Molecular Parts
Proteins, Nucleic Acids, Lipids, Carbohydrates:
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Each class can be assembled by the
cell from a small number of simpler
subunits or precursor molecules
A cell needs only a restricted
repertoire of biochemical reactions
to synthesize the subunits from
food in the environment
Combinatorial assembly of subunits
gives rise to huge structural
diversity making up the stuff of
cells
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A: DNA (nucleic acid)
B: Hemoglobin (protein)
C: Phosphatidylcholine (lipid)
D: Branched carbohydrate
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Indiana University P575
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Examples of Molecular Types
Glucose
Galactose
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DNA
Hemoglobin
Indiana University P575
Phosphatidylcholine
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Two “Great Polymer Languages”
Alphabet:
Nucleotides (4)
Amino Acids (20)
Words:
Codon (3 nucleotides)
Elements of secondary structure
Sentences:
Genes (~4500 in E. coli)
Fully folded proteins
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Macromolecular Assemblies (by
shape)
Helical protein assemblies are ubiquitous.
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Macromolecular Assemblies (by
function)
Proteins, nucleic acids, lipids,
sugars acting as a team
(“-somes”): ~10 nm scale
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Macromolecular Superstructures
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(A) Ribosomes on ER
(B) Myosin filaments in myofibrils in muscle cells
(C) Microvilli at epithelial surface
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Molecular Representation
Atomic level structure revealed through:
X-ray crystallography
Nuclear magnetic resonance (NMR)
Cryo-electron microscopy
Leading to:
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(A) Ball-and-stick
(B) Space-filling
(C) Ribbon
diagrams.
Eg. Triose phosphate isomerase:
Enzyme involved in glycolysis pathway
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Indiana University P575
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Molecular Composition of
(Bacterial) Cell
Molecular Class
% of total cell weight
Small Molecules
ions, inorganic molecules
sugars
fatty acids
individual amino acids
individual nucleotides
water
(74%)
1.2
1
1
0.4
0.4
70
Medium and Big Molecules
protein
DNA
RNA
lipids
polysaccharides
(26%)
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6
1
2
2
(From Alberts, et al., MBoC)
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Fantastic Voyage …
Movie available at:
See also D. Liu, “Seeing Cells on the Web”:
http://www.lifescied.org/cgi/content/full/6/1/21
Lectures 3 & 4 & 5
Indiana University P575
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Science is built up of facts, as a house is with stones.
But a collection of facts is no more a science than a
heap of stones is a house. - Henri Poincare
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Molecular Census
Why do we care about numbers of different molecules
inside the cell?
 Quantitative understanding of cellular phenomena
requires quantitative knowledge of the numbers of key
players (molecules) involved and the spatial dimensions
over which they act.
 Molecular counts will determine rates of macromolecular
synthesis during the cell cycle (genome replication,
protein synthesis rates).
 Small or large molecular copy numbers determine the
qualitative nature of chemical reactions (stochastic vs
deterministic).
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Sizing up E. coli
Estimate:
Nprotein, Nribosome, Nlipid, NH20, Nion !!
… back to the chalkboard.
Conclusion:
The cell is a very crowded place!
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Indiana University P575
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Recap …
Hierarchy of Spatial Scales
Hierarchy of spatial scales:
Atom
DNA
Organelles
Virus
Bacterial Cell
Eukaryotic Cell
Multicellular Aggregates
Tissue
Organism
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Indiana University P575
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Spatial Organization at the
Cellular Level
Organelles (nucleus, ER, Golgi apparatus, lysosome …)
Macromolecular superstructures (myofibrils, microvilli …)
Macromolecular complexes (ATPase, replisome, proteosome…)
Proteins, nucleic acids, carbohydrates, lipids (enzymes,
DNA/RNA, polysaccharides, phospholipids…)
Amino acids, nucleotides, small sugars, fatty acids
Inorganic molecules, water, ions
(How is this organization achieved? Expenditure of energy!)
Lectures 3 & 4 & 5
Indiana University P575
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Hierarchy of Biologically
Relevant Time Scales
Dynamics on scales of:
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Molecules
Biochemical reactions
Cells
Organisms
Evolution
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ranging from femtoseconds
to billions of years!
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E. coli as the standard clock
Organismal and
cellular time scales
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Indiana University P575
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E. coli as the standard clock,
cont’d
Subcellular time scales
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Indiana University P575
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Central Dogma of Molecular Biology
DNA
(template for DNA, RNA)
RNA
(mRNA: template for proteins)
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Protein
Biochemical networks
(computing language of cell)
Timing the machines of the central dogma: Homework!
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Amendments! Some
examples…
 Cell’s heritable characteristics are not solely
determined by DNA; rather, a cell’s entire state
(protein content) determines fate of
descendants (eg. differentiation, transmission
of pathology through prions,…)
 RNA editing between mRNA synthesis and
translation
 Post-translational modification; chaperones and
proteases
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Indiana University P575
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DNA/RNA Building Blocks
DNA/RNA are nucleic acids consisting of
nucleotides (base+sugar+phosphate) subunits.
DNA: deoxyribose (sugar)
ATGC (bases)
Lectures 3 & 4 & 5
Indiana University P575
RNA: ribose (sugar)
AUGC (bases)
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DNA Assembly
covalent bonding
Lectures 3 & 4 & 5
hydrogen bonding
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3D Structure
DNA
RNA
 Base pairing yields double
helix in DNA
 Single helix and variety of
folded structures in RNA
Discovery of DNA structure and function
through combined efforts of chemists
(Franklin), biologists (Watson and Wilkins)
and physicists (Crick)!
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Indiana University P575
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