cells and the stuff they re made of
Skip this Video
Download Presentation
Cells and the Stuff They ’ re Made of …

Loading in 2 Seconds...

play fullscreen
1 / 34

Cells and the Stuff They ’ re Made of … - PowerPoint PPT Presentation

  • Uploaded on

Cells and the Stuff They ’ re Made of …. Cells are the “ indivisible ” units of life. There is nothing smaller that is alive, nothing bigger is more alive. - J. Theriot. Metabolism: Cells consume energy from environment and use it to create ordered structures.

I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
Download Presentation

PowerPoint Slideshow about 'Cells and the Stuff They ’ re Made of …' - thi

An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.

- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
cells are the indivisible units of life
Cells are the “indivisible” units of life.

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

  • Metabolism: Cells consume energy from environment and use it to create ordered structures.
  • Replication: Cells harness energy from environment to create offspring.

Standard definition of life merges metabolism and replication:

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

Archaea, Bacteria, Eukaryota

Indiana University P575

prokaryotes and eukaryotes
Prokaryotes and Eukaryotes

Prokaryotes: absence of nuclear membrane (and other organelles)


Eukaryotes: presence of nuclear membrane


Indiana University P575

e coli as the standard ruler
E. coli as theStandard 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.

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

Indiana University P575

hierarchy of spatial scales
Hierarchy of Spatial Scales


Sperm Cell

Compound Eyes


Indiana University P575



Water Molecule


some different cell types
Some Different Cell Types

Referenced to E. coli as the standard ruler

A: Giardia lamblia

B: Plant cell

C: S. cerevisiae

D: Red blood cell

E: Fibroblast cell

F: Nerve cell

G: Rod cell

Indiana University P575

cellular interior organelles
Cellular Interior: Organelles

Red: Nucleus

Yellow: Golgi

Green: Microtubules

Indiana University P575

energy production mitochondria
Energy Production: Mitochondria

Indiana University P575

how do we know about cellular and subcellular structures
How do we know about cellular and subcellular structures?

Common techniques:

(A) fluorescence microscopy

(B) atomic force microscopy

(C) electron microscopy

Indiana University P575

cellular interiors molecular parts
Cellular Interiors: Molecular Parts

Proteins, Nucleic Acids, Lipids, Carbohydrates:

  • 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

A: DNA (nucleic acid)

B: Hemoglobin (protein)

C: Phosphatidylcholine (lipid)

D: Branched carbohydrate

Indiana University P575

examples of molecular types
Examples of Molecular Types






Indiana University P575

two great polymer languages
Two “Great Polymer Languages”


Nucleotides (4)

Amino Acids (20)


Codon (3 nucleotides)

Elements of secondary structure


Genes (~4500 in E. coli)

Fully folded proteins

Indiana University P575

macromolecular assemblies by shape
Macromolecular Assemblies (by shape)

Helical protein assemblies are ubiquitous.

Indiana University P575

macromolecular assemblies by function
Macromolecular Assemblies (by function)

Proteins, nucleic acids, lipids,

sugars acting as a team

(“-somes”): ~10 nm scale

Indiana University P575

macromolecular superstructures
Macromolecular Superstructures
  • Ribosomes on ER
  • Myosin filaments in myofibrils in muscle cells
  • Microvilli at epithelial surface

Indiana University P575

molecular representation
Molecular Representation
  • Ball-and-stick
  • Space-filling
  • Ribbon

Atomic level structure revealed through:

X-ray crystallography

Nuclear magnetic resonance (NMR)

Cryo-electron microscopy

Leading to:


Eg. Triose phosphate isomerase:

Enzyme involved in glycolysis pathway

Indiana University P575

molecular composition of bacterial cell
Molecular Composition of (Bacterial) Cell

Molecular Class % of total cell weight

Small Molecules (74%)

ions, inorganic molecules 1.2

sugars 1

fatty acids 1

individual amino acids 0.4

individual nucleotides 0.4

water 70

Medium and Big Molecules (26%)

protein 15



lipids 2

polysaccharides 2

(From Alberts, et al., MBoC)

Indiana University P575

fantastic voyage
Fantastic Voyage …

Movie available at:

See also D. Liu, “Seeing Cells on the Web”:


Indiana University P575

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

Indiana University P575

molecular census
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).

Indiana University P575

sizing up e coli
Sizing up E. coli


Nprotein, Nribosome, Nlipid, NH20, Nion !!

… back to the chalkboard.


The cell is a very crowded place!

Indiana University P575

recap hierarchy of spatial scales
Recap …Hierarchy of Spatial Scales

Hierarchy of spatial scales:





Bacterial Cell

Eukaryotic Cell

Multicellular Aggregates



Indiana University P575

spatial organization at the cellular level
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!)

Indiana University P575

hierarchy of biologically relevant time scales
Hierarchy of Biologically Relevant Time Scales

Dynamics on scales of:

  • Molecules
  • Biochemical reactions
  • Cells
  • Organisms
  • Evolution

ranging from femtoseconds

to billions of years!

Indiana University P575

e coli as the standard clock
E. coli as the standard clock

Organismal and

cellular time scales

Indiana University P575

e coli as the standard clock cont d
E. coli as the standard clock, cont’d

Subcellular time scales

Indiana University P575

central dogma of molecular biology
Central Dogma of Molecular Biology


(template for DNA, RNA)


(mRNA: template for proteins)


Biochemical networks

(computing language of cell)

Timing the machines of the central dogma: Homework!

Indiana University P575

amendments some examples
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

Indiana University P575

dna rna building blocks
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)

Indiana University P575

dna assembly
DNA Assembly

covalent bonding

hydrogen bonding

Indiana University P575

3d structure
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)!

Indiana University P575