Challenges coming from
molecular biology
Trento, March 25, 2009
Molecular biology - microbiology
17th century
 Robert Hooke – non-living cell walls
 Antonie van Leeuwenhoek - live cell, microscope
"the Father of Microbiology"
1838 - Matthias Jakob Schleiden and Theodor Schwann
--- cell theory (functional units of life)
Molecular biology - genetics
17th century
 Robert Hooke – non-living cell walls
 Antonie van Leeuwenhoek - live cell, microscope
1838 - Matthias Jakob Schleiden and Theodor Schwann
--- cell theory (functional units of life)
1865 Gregor Mendel – laws of heritability "the Father of Genetics"
1900 Correns, deVries and Tschermak – rediscover
Wilhelm Johannsen - "gene"
Molecular biology
17th century
 Robert Hooke – non-living cell walls
 Antonie van Leeuwenhoek - live cell, microscope
1838 - Matthias Jakob Schleiden and Theodor Schwann
--- cell theory (functional units of life)
1865 Gregor Mendel – laws of heritability
1900 Correns, deVries and Tschermak – rediscover
Warren Weaver 1938 --- MOLECULAR BIOLOGY
(biology at a molecular level)
Molecular biology
1941 George Wells Beadle & Edward Lawrie Tatum
- "one gene, one enzyme" hypothesis
Nobel Prize in Physiology or Medicine 1958
1944 Oswald Avery, Colin MacLeod, Maclyn McCarty
- DNA is the material of which genes and chromosomes are made
1953 James D. Watson and Francis Crick
- double-helix structure for DNA
Nobel Prize in Physiology or Medicine 1962
Central dogma of molecular biology
Francis Crick 1958
replication
DNA
transcription
RNA
translation
Protein
RNA virus
Howard Temin
David Baltimore
reverse transcriptase
(retrovirus)
ribozyme
Nobel Prize in Chemistry 1989
Nobel Prize in Physiology or Medicine 1975
Sidney Altman
Thomas R. Cech
prion
Nobel Prize in Physiology or Medicine 1997 Stanley Prusiner
cells with nucleus, organelles
cells without nucleus
Cells as “tiny chemical factories”
food
membrane
food,
energy
output
DNA
(information)
Biological macromolecules
DNA and RNA
 deoxyribonucleic acid
store the hereditary information (genes) for the
development and functioning of living organisms
 ribonucleic acid
single stranded
Proteins
 Building blocks + Execute cell functions
 catalysis (enzymes)
 transport (channels, pumps)
 transport as tiny molecular machines (kinesin, dynein,
myosin)
 signaling (carry messages)
 antibodies, toxins, hormones, etc.
 regulators, protein-protein interactions
Proteins
Amino group
Carboxyl group
Side chain
20 different amino acids
Peptide bond
Proteins
 Primary structure - amino acid
sequence of the peptide chains
(peptide bonds).
 Secondary structure - alpha helix
and strands of beta sheet
 Tertiary structure – 3D structure
 Quaternary structure – protein
complex
Enzymes
 biocatalysis (modify chemical reaction rates)
 specific to substrates
 proteins (+ RNAs)
 active site (catalytic/active and binding sites)
Biomembranes – phospholypid bilayer, proteins
proteins in the
membrane
DNA
mRNA
polypeptide
substrate
protein
activity
network
physiology
product(s)
A
B
C
D
E
F
Macromolecules - focus of molecular biologists
gene
Genes
Genetic code
Genetic code
gene
Black box
Proteins
“Play” with the box
 PHYSIOLOGY – observations, perturb the system


Alan L. Hodgkin Andrew F. Huxley
1914 - 1998
1917 -
Nobel Prize in Physiology or Medicine 1963
input
Black
box
squid giant axon
output
How action potentials in neurons are initiated and propagated
-- biophysical characteristic of cell membranes
“Play” with the box
 PHYSIOLOGY – observations, perturb the system
 BIOCHEMISTRY – protein identification, selection
 GENETICS – “naughty child” (mutants)
Challenges – modeling mol. biol.
 Signal transduction
 Metabolism
 Transport mechanisms, molecular motors
 Gene expression
 Biological oscillations
Signal transduction
Signal transduction pathways
Metabolism
breakdown of complex compounds
thousands of reactions catalyzed by enzymes
construction of complex compounds
Metabolic pathways
 series of biochemical
reactions
(catalyzed by enzymes)
 requiring cofactors
 pathways are connected
(form a complicated
network)
Challenges
 Signal transduction
 Metabolism
 Transport mechanisms, molecular motors
 Gene expression
 Biological oscillations
Cytoskeleton, filaments
Polymerization
Dynamic instability
Molecular motors
Chemical energy
Mechanical force
Source:
- Free energy of nucleotide hydrolysis
- Ion gradients
- “walking motors” (kinesin)
- rotating engines (bacterial flagellar motor)
“Walking motors”
 moving on actin filaments and microtubules
 transport (of vesicules, organelles, RNAs), signaling
Bacterial movement
Flagella of Escherichia coli observed in transmission
electron microscope. Bar, 1 m.
Challenges
 Signal transduction
 Metabolism
 Transport mechanisms, molecular motors
 Gene expression
 Biological oscillations
Biochemical oscillations
 System properties rise and
fall in a regular rhythmic
fashion
Regulatory feedback loops
+
Positive feedback
loop
Negative feedback
loop
-
Y
X
X
Y
+
-
+
-
Y
X
-
Y
X
+
Origin of oscillations
 Negative feedback
 Time delay
 Physical constraint (transcription, translation, transport
time)
 Long chain of reaction intermediates (e.g. metabolic
pathway)
 Dynamic hysteresis (positive feedback, overshootundershoot)
 ‘nonlinear’ kinetic rate laws
 Appropriate time scale
Time-delayed negative feedback
Circadian rhythm
Time Delayed Negative Feedback Loop
POSITIVE
ELEMENTS
transcription
translation
NEGATIVE
ELEMENTS
clock genes
transcription
clock controlled genes
translation
rhythmic metabolism
and behavior
Cell cycle
E2F
Wee1
Rb
p55cdc
Kip1
Cdh1
Bottom-line
Black
box
A
B
C
D
E
F
Thank you for your attention!
ADDITIONAL FIGURES
 Extension for a better understanding…
amino acids
folded protein
binding site (“pocket” on the surface)
Membrane
transport
Ion channels
Hydrophobic
molecules
Small
uncharged
polar
molecules
Large
uncharged
polar
molecules
ions
bricks
H2O
build up
break down
nutrient
macromolecules
energy
CO2
+
H2O
Metabolism