Transcript Document

Lecture Outline
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Molecular biology - the chemical basis
of terrestrial life
Cellular biology - “life as we know it”
The origin of life on Earth
Implications for astrobiology
Carbon (C) is a unique element, key role in
organic chemistry and molecular biology
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Strong C-C bonds provide the structural support for
very large 3D molecules
 C can simultaneously form strong bonds with H and
O thus allowing large and complex molecules
 CO2 is a gas allowing easy C transport and
interactions
 Organic (C structured) compounds are 50x more
numerous than inorganic ones
 Not particularly abundant in the Earth’s mantle,
[C/O]Mantle=10-3[C/O]Cosmic (carbon starvation?)
Liquid Water: Essential for Life
Essential for terrestrial biology
 Water is a flexible solvent
 Lots of local order in water
 Cells are mostly water
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Water is an excellent solvent
Likes Water
 OH
 COO Sugars
 Polar solvents
Doesn’t like water
 CH3
 CH2-CH2-
Four major classes of bio-molecules
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Proteins: chains of amino acids that are the
functional “machines” of biology
 Nucleic Acids: lengthy sequences of
nucleotides which store, copy & implement
protein structures
 Carbohydrates: energy storage & structure
 Lipids: energy storage & cell membranes
All 4 types of bio-molecules are long polymers
made of a set of identical “building blocks”
The
®
Lego
Principle
• Biology is largely built from on a
small number of components:
- 20 L amino acids
- 5 nucleotide bases
- a few D sugars & fatty acids
• A common property of biology
(and mass-produced children’s toys)
throughout the universe??
Nucleic Acids:
Three key self-propagation mechanisms
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DNA (info archive)storage and replication
 DNA to RNA (blueprint) transcription
 RNA to protein (hardware) construction
 RNA only ?? (RNA World Hypothesis)
The functioning of these mechanisms requires
a genetic code/language, a bio-energy supply and
carrier (ATP, Adenosine Triphosphate), a
“building tool” (ribosome) and water as a
medium.
All above are universal features of terrestrial life!
Amino acids are the “lego” building
block components of proteins
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13 to 27 atoms of C, O, N, H & S
A COOH (carboxy) end that “loses” a H+
ion
A NH2 (amino) end that “takes” a H+ ion
More than 170 known, but only 20 are
coded by nucleic acids and “used” to
make proteins
19 are l-chiral (left-handed) & one is
symmetric
Carboxy & amino ends “plug” together to
form a peptide bond and thus make long
chains:
H3N+ + COO- -> OC-NH + H2O
Amino Acids
The 4 levels of protein structure
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Peptide bond chains of 100s of amino acids
 Chain winds to form an -helix or folds to
form a -sheet stabilized by H bonds
 Fold into specific 3D shapes set by disulfide
bonds and hydrophobic interactions
 Also such proteins may combine as subunits
to form a larger and more complex protein
Protein
Structure
Protein functions = many and diverse
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Structure
Enzymes
Hormones
Transportation
Protection
Sensors
Toxins
Gates
Movement
Proteins comprise
>50% of the mass of
many cells (the rest
being largely water).
More than 104 human
proteins are known.
Genetic information
specifies proteins and
nothing else.
Nucleic acids (DNA and RNA)
Very long chains (again) of nucleotides
 Each nucleotide is made of a
phosphoric acid, a sugar and a base
 Sugar is d-ribose in RNA & deoxy-dribose in DNA
 RNA bases are Cytosine, Uracil,
Adenine & Guanine; DNA bases = C, A,
G & Thymine
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DNA structure & replication
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Consists of two nucleotide chains/strands
wrapped around each other in a spiral helix
A on one strand matches T on the other
Similarly G and C pair between strands
When the strands are separated, they can
each regenerate their partner & thus copy the
information they encode
A codon consists of 3 sequential bases and
specifies one amino acid (or start/stop)
DNA Nucleotides
RNA structure & transcription
Consists of a single chain/strand of
nucleotides
 Organized in the same 3 base codons
as DNA except that U replaces T
 DNA generates/transcribes messengerRNA (mRNA) which provides the
“working blueprint” for protein synthesis
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Protein synthesis/construction
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mRNA carries the amino acid sequence information
for the protein
transfer-RNA (tRNA) provides the raw material amino
acids by binding them to anti-codon (complementary
base triplets)
Ribosome macromolecule/protein reads mRNA to
select specified amino acids from tRNA and extrudes
them in a chain as it moves along the mRNA
ATP energizes the individual bondings by transfer of
a phosphate group to a X-OH component
mRNA, tRNA & ribosome are reusable for additional
syntheses, but ATP degrades to ADP & must be reenergized
What is Life?
Definition of Life (many possibilities)
Metabolism (chemical activity)
 Growth/development
 Energy utilization
 Local entropy reduction
 Preservation of information/identity
 Procreation
 Mutation
 Spatial boundaries
 Functional in abiotic environments
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Cells
Cells are alive, satisfy all definitions of life
 All “normal” life forms are cellular
 Most terrestrial life is unicellular
 Cells are enclosed by a membrane
 Within cells the processes of molecular
biology occur in an aqueous solution
 Cells organize/utilize a large number of
biomolecules & their interactions -> life
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Two fundamental classes of cells
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Prokaryotes: no nucleus &
relatively little internal structure
Eukaryotes: nucleus containing
cell’s DNA, defined by an inner
membrane, & complex internal
structures
Quite different in many ways
Major clue to the evolution of life
on Earth
Properties of prokaryotes
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No nuclear membrane
Single circular strand of DNA
mRNA generated from start to stop codons
No internal organelles & little structure
Relatively small (0.1-10m diameters)
Ancient,oldest life forms (3.9 Gyr ago ?)
Two evolutionary branches (split 3.5 Gyr ?)
Archaea
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“Third kingdom”
Archaea differ more from bacteria than we do from
bacteria
Structurally like bacteria; however, archaea have
metabolic pathways similar to eukaryctes
Use a wide variety of energy sources including
ammonia, metal ions, free hydrogen
Many extremophiles are archaea
No pathogens or parasites!
Methanogens in our guts
http://www.ucmp.berkeley.edu/
archaea/archaea.html
Two typical prokaryotes
Properties of eukaryotes
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DNA segregated into nucleus by membrane
Multiple linear stands of DNA
An intermediary mRNA is “edited” into exon
and intron segments -> final mRNA
Complex internal structure/many organelles
Relatively large (10-100m diameters)
Relatively recent (appeared 2-3 Gyr ago)
Unicellular and all multi-cellular life forms
Exon/intron editing during transcription
Typical eukaryote internal structures
Major eukaryote organelles
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Nucleus
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Cytoskeleton
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Flagellum
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Lysosome
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Mitochondrium*
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Peroxysome
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Endoplasmic reticulum 
Golgi apparatus
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Plastids
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DNA, DNA->mRNA
Internal transport/support
Movement
Digestion/waste removal
Food+oxygen -> ATP
Fat metabolism
Protein & lipid synthesis
Protein & lipid storage
photosynthesis
Origin of biochemistry
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First produce the macromolecule building blocks
 Happened very fast, 4 Gyr ago (Earth just cooled)
 Possible locations/environment
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Shallow tidal pools or lagoons (Darwin)
Deep sea hydrothermal vents
On wet clay surfaces
Deep underground?
Proteins or nucleic acids first?? (chicken & egg issue)
 RNA biology first (no DNA or proteins)? RNA world?
Oparin-Haldane Hypothesis
Urey-Miller Experiment (1953)
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water (H2O)
methane (CH4)
ammonia (NH3)
hydrogen (H2)
no oxygen
+ sparks
YIELDS
amino acids! (>2% of
C in one week)
Urey-Miller experiment issues &
subsequent developments
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Seminal influence on origin of life studies
 Many variations on details work also
 All DNA/RNA bases later produced in (HCN) experiments
 No progress in assembling building blocks into “useful”
macromolecules by similar techniques
 Now believed that Earth’s primordial atmosphere was
CO2 dominated & had little CH4 which very much reduces
the amino acid yields
 U-M conditions resemble oceanic hydrothermal vents
 Clay surfaces may facilitate macromolecule assembly
Origin of cellular life
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Also very very fast (3.7 - 3.9 Gyr)
Requires formation of enclosing lipid membranes
Simple protein membranes have been formed
spontaneously in lab experiments
Membranes need to effectively isolate important
macromolecules & their reactions but not seal off
environment completely (complex function)
Speculative possibility of noncellular ancestors??
Prokaryote microfossil dated at 3.7 Gyr
Mitochondria and Lysosomes
*Mitochondria have
their own internal
DNA (loop) and
reproduce separately
from the cell!
Note internal complexity
of these organelles, likely
endosymbionts.
General Characteristics of the
Molecular Biology of Terrestrial Life
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Extraordinarily complex & inter-connected chemical
processes, vastly richer than any other known
chemical systems
Basic biochemistry shared by all known terrestrial
organisms as well as many of its details
Carbon based and water dependent
Hierarchically structured (using much simpler
subcomponents), polymerized macromolecules
Few (4) general classes of compounds but many
individual ones with highly specialized and specific
biological functions
Implications for Extraterrestrial Life
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Requires no exotic conditions or constituents
 Appears to have happened only once on Earth
 Intricate complexity -> origin problem
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No obvious route of gradual development
Jump in complexity wrt other natural chemistry
Absence of theoretical or empirical alternative
biochemistries -> one type of life only??
 Physical mechanism for evolutionary adaptation
and development once started
Evolution of cellular life
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Last Common Ancestor = prokaryote, anaerobic
heterotrophe, maybe ≤ 250 genes, resembling present day
mycoplasmas (<500 genes)
 Even simpler RNA-only cells a possibility?
 Split into Archaea and Bacteria classes (3.5 Gyr ?)
 Anaerobic autotrophs/chemoautrophs next
 Photoautotrophs, cyanobacteria (2.7 - 2.5 Gyr)
 O2 respiration by 2.2 Gyr (high octane biology!)
 Eukaryotes w ~6000 genes, evolved via endosymbiont
“colonization”? (3 - 2 Gyr)
 Multicellular life consisting of eukaryotes (1 Gyr)
Implications for extraterrestrial life
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Multiple hurdles:
Biochemistry (proteins & nucleic acids)
 Cells
 Autotrophism (chemo/photo-synthesis, food)
 Internal organelles
 Oxygen respiration
 Multicellular cooperation
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Appearance time is often interpreted to imply
probability/improbability of each development
Convergence or Divergence of Cosmic and
Biological Evolution? (How similar to here?)
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Large/coarse scales -> convergence
 But on some small/fine scales -> divergence
 Divergence might begin on the scale of
planetary systems since known extrasolar
systems are unlike the Solar System
 However it might not occur until far finer
levels of detail <- assumption!