cells and the stuff they ’ re made of …

Lectures 3 & 4 & 5 Indiana University P575 1

Cells and the Stuff They’re Made of …

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Cells are the “indivisible” units of life.

Metabolism: Cells consume energy from environment and use it to create ordered structures.

Replication: Cells harness energy from environment to create offspring.

There is nothing smaller that is alive, nothing bigger is more alive. - J. Theriot

Standard definition of life merges metabolism and replication:

Common ancestor several billion years ago, gave rise to three major cell types:

Archaea, Bacteria, Eukaryota

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Prokaryotes and Eukaryotes

Prokaryotes: absence of nuclear membrane (and other organelles)

Eukaryotes: presence of nuclear membrane

Bacterium

Fibroblast

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E. coli as the Standard Ruler

Easy to isolate Able to grow in the presence of oxygen Replicates rapidly Easy to generate mutants

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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Hierarchy of Spatial ScalesFly Compound Eyes Sperm Cell Bacterium

Bacteriophage ATPase DNA Water Molecule

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Some Different Cell Types

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A: Giardia lambliaB: Plant cellC: S. cerevisiaeD: Red blood cellE: Fibroblast cellF: Nerve cellG: Rod cell

Referenced to E. coli as the standard ruler

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Cellular Interior: Organelles

Red: NucleusYellow: GolgiGreen: 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

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Cellular Interiors: Molecular Parts

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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Proteins, Nucleic Acids, Lipids, Carbohydrates:

A: DNA (nucleic acid)B: Hemoglobin (protein)C: Phosphatidylcholine (lipid)D: Branched carbohydrate

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Examples of Molecular Types

DNA PhosphatidylcholineHemoglobin

Glucose Galactose

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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)

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Proteins, nucleic acids, lipids, sugars acting as a team (“-somes”): ~10 nm scale

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Macromolecular Superstructures

(A) Ribosomes on ER(B) Myosin filaments in myofibrils in muscle cells(C) Microvilli at epithelial surface

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Molecular Representation

(A) Ball-and-stick(B) Space-filling(C) Ribbon

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Eg. Triose phosphate isomerase: Enzyme involved in glycolysis pathway

Atomic level structure revealed through: X-ray crystallography Nuclear magnetic resonance (NMR) Cryo-electron microscopy

Leading to:

diagrams.

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Molecular Composition of (Bacterial) CellMolecular Class % of total cell weight

Small Molecules (74%)ions, inorganic molecules 1.2sugars 1fatty acids 1individual amino acids 0.4individual nucleotides 0.4water 70

Medium and Big Molecules (26%)protein 15DNA 6RNA 1lipids 2polysaccharides 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

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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

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).

Why do we care about numbers of different molecules inside the cell?

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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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Recap …Hierarchy of Spatial Scales

Hierarchy of spatial scales:

AtomDNAOrganellesVirusBacterial CellEukaryotic CellMulticellular AggregatesTissueOrganism

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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!)

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Hierarchy of Biologically Relevant Time Scales

Dynamics on scales of:

Molecules Biochemical reactions Cells Organisms Evolution

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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Subcellular time scales

E. coli as the standard clock, cont’d

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Central Dogma of Molecular Biology

DNA (template for DNA, RNA)

RNA(mRNA: template for proteins)

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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DNA/RNA Building Blocks DNA/RNA are nucleic acids consisting of

nucleotides (base+sugar+phosphate) subunits.

DNA: deoxyribose (sugar) RNA: ribose (sugar) ATGC (bases) AUGC (bases)

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DNA Assembly

hydrogen bondingcovalent bonding

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3D Structure

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)!

DNA RNA