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The Origin and Chemistry
of Life
Chapter 2
Water and Life
 Water makes up a
large portion of living
 It has several
unusual properties
that make it
essential for life.
 Hydrogen bonds lie
behind these
important properties.
Water and Life
 High specific heat capacity – 1 calorie is
required to elevate temperature of 1 gram of
water 1°C.
 Moderates environmental changes.
 High heat of vaporization – more than 500
calories are required to convert 1 g of liquid
water to water vapor.
 Cooling produced by evaporation of water is
important for expelling excess heat.
Water and Life
 Unique density
behavior – while
most liquids become
denser with
water’s maximum
density is at 4°C.
 Ice floats! Lakes
don’t freeze solid –
some liquid water is
usually left at the
Water and Life
 Water has high
surface tension.
 Because of the
hydrogen bonds
between water
molecules at the
water-air interface,
the water molecules
cling together.
 Water has low
Water and Life
 Water acts as a
solvent – salts
dissolve more in
water than in any
other solvent.
 Result of the dipolar
nature of water.
Water and Life
 Hydrolysis occurs when compounds are split
into smaller pieces by the addition of a water
 R-R + H2O
R-OH + H-R
 Condensation occurs when larger compounds
are synthesized from smaller compounds.
 R-OH + H-R
R-R + H2O
Acids, Bases, and Buffers
 Acid: Substance that liberates hydrogen ions
(H+) in solution.
 Base: Substance that liberates hydroxyl ions
(OH-) in solution.
 The regulation of the concentrations of H+ and OH- is
critical in cellular processes.
Acids, Bases, and Buffers
 pH – A measure of the concentration of H+ in a
 The pH scale runs from 0 - 14.
 Represents the negative log of the H+
concentration of a solution.
Acids, Bases, and Buffers
Neutral solution with a pH of 7:
[H+] = [OH-]
Basic solution with a pH above 7:
[H+] < [OH-]
Acidic solution with a pH below 7:
[H+] > [OH-]
Acids, Bases, and Buffers
 Buffer: Molecules that prevent dramatic
changes in the pH of fluids.
 Remove H+ and OH- in solution and transfers them
to other molecules.
 Example: Bicarbonate Ion (HCO3-).
Chemistry of Life
 Recall the four major categories of biological
Nucleic acids
 Carbohydrates are compounds of carbon (C),
hydrogen (H) and oxygen (O).
 Usually found 1C:2H:1O.
 Usually grouped as H-C-OH.
 Function as structural elements and as a
source of chemical energy (ex. glucose).
 Plants use water (H2O) and carbon dioxide
(CO2) along with solar energy to manufacture
carbohydrates in the process of
 6CO2 +6H2O
C6H12O6 + 6O2
 Life depends on this reaction – it is the starting point
for the formation of food.
 Three classes of carbohydrates:
 Monosaccharides – simple sugars
 Disaccharides – double sugars
 Polysaccharides – complex sugars
 Monosaccharides –
Single carbon chain
4-6 carbons.
 Glucose C6H12O6
 Can be straight
chain or a ring.
 Some common monosaccharides:
 Disaccharides –
Two simple sugars
bonded together.
 Water released
 Sucrose = glucose
+ fructose
 Lactose =
glucose + galactose
 Polysaccharides – Many simple sugars
bonded together in long chains.
 Starch is the common polymer in which sugar is
usually stored in plants.
 Glycogen is an important polymer for storing sugar
in animals.
 Found in liver and muscle cells – can be converted
to glucose when needed.
 Cellulose is the main structural carbohydrate in
 Lipids are fatty substances.
Nonpolar – insoluble in water
Neutral fats
Neutral Fats
 Neutral fats are the major fuel of animals.
 Triglycerides – glycerol and 3 fatty acids
Neutral Fats
 Saturated fatty acids occur when every carbon
holds two hydrogen atoms.
 Unsaturated fatty acids have two or more
carbon atoms joined by double bonds.
 Phospholipids are
important components
of cell membranes.
 They resemble
triglycerides, except
one fatty acid is
replaced by phosphoric
acid and an organic
 The phosphate group is
charged (polar).
 Amphiphilic compounds are polar and water–
soluble on one end and nonpolar on the other
 They have a tendency to assemble themselves into
semi-permeable membranes.
 Steroids are
complex alcohols
with fatlike
 Cholesterol
 Vitamin D
 Adrenocortical
 Sex hormones
 Proteins are large complex molecules
composed of amino acids.
 Amino acids linked by peptide bonds.
 Two amino acids joined – dipeptide
 Many amino acids – polypeptide chain
 There are 20 different types of amino acids.
Protein Structure
 Proteins are
complex molecules
organized on many
 Primary structure
– sequence of
amino acids.
 Secondary
structure – helix or
pleated sheet.
Stabilized with Hbonds.
Protein Structure
 Tertiary structure – 3dimensional structure of
folded chains. Eg. Disulfide
bond is a covalent bond
between sulfur atoms in
two cysteine amino acids
that are near each other.
 Quaternary structure
describes proteins with
more than one polypeptide
chain. Hemoglobin has
four subunits.
 Proteins serve many functions.
 Structural framework
 Enzymes that serve as catalysts
Nucleic Acids
 Nucleic acids are complex molecules with
particular sequences of nitrogenous bases that
encode genetic information.
 The only molecules that can replicate themselves –
with help from enzymes.
 Deoxyribonucleic acid (DNA)
 Ribonucleic acid (RNA)
Nucleic Acids
 The repeated units,
called nucleotides,
each contain a
sugar, a nitrogenous
base, and a
phosphate group.
Chemical Evolution
 Life evolved from inanimate matter, with
increasingly complex associations between
 Life originated ~3.5 billion years ago.
Chemical Evolution
 Origin of Life
 Oparin-Haldane Hypothesis (1920s)
 Alexander Oparin and J.B.S. Haldane proposed an
explanation for the chemical evolution of life.
Chemical Evolution
 Early atmosphere consisted of simple
Water vapor
Carbon Dioxide (CO2)
Hydrogen Gas (H2)
Methane (CH4)
Ammonia (NH3)
No free Oxygen
Early atmosphere → Strongly Reducing
Chemical Evolution
 Such conditions conducive to prebiotic
synthesis of life.
 Present atmosphere is strongly oxidizing.
 Molecules necessary for life cannot be synthesized
outside of the cells.
 Not stable in the presence of O2
Chemical Evolution
 Possible energy
sources required for
chemical reactions:
 Lightning
 UV Light
 Heat from volcanoes
Chemical Evolution
 Simple inorganic molecules formed and began
to accumulate in the early oceans.
Over time:
Chemical Evolution
 Prebiotic Synthesis of Small Organic Molecules
 Stanley Miller and Harold Urey (1953) simulated the
Oparin-Haldane hypothesis.
Chemical Evolution
 Miller & Urey reconstructed the
O2 free atmosphere they
thought existed on the early
Earth in the lab.
 Circulated a mixture of
Energy source: electrical spark to
simulate lightening and UV
Chemical Evolution
 Results:
 In a week, 15% of the carbon in the mixture was
converted to organic compounds such as:
Amino Acids
Simple Fatty Acids
Chemical Evolution
 Conclusion: life may have evolved in
“primordial soup” of biological molecules
formed in early Earth’s oceans.
Chemical Evolution
 Today it is believed that the early atmosphere
was only mildly reducing.
 Still……if NH3 and CH4 are omitted from the
 Organic compounds continue to be produced
(smaller amount over a longer time period).
Chemical Evolution
 More recent experiments:
 Subjecting a reducing mixture of gases to a violent
energy source produces:
Hydrogen Cyanide
 All highly reactive intermediate molecules
Chemical Evolution
 All react with water and NH3 or N2 to produce a
variety of organic compounds:
Amino Acids, Fatty Acids, Urea, Sugars,
Aldehydes, Purine and Pyrimidine Bases
Subunits For Complex Organic Compounds.
Chemical Evolution
 Formation of Polymers
 The next stage of chemical evolution required the
joining of amino acids, nitrogenous bases and
sugars to form complex organic molecules.
 Does not occur easily in dilute solutions.
 Water tends to drive reactions toward
decomposition by hydrolysis.
Chemical Evolution
 Condensation reactions occur in aqueous
environments and require enzymes.
Chemical Evolution
 The strongest current
hypothesis for prebiotic
assembly of biologically
important polymers
suggests that they
occurred within the
boundaries of semipermeable membranes.
 Membranes were
formed by
 Meteorites are
common sources of
Origin of Living Systems
 Life on Earth: 4 billion years ago
 First cells would have been autonomous,
membrane-bound units capable of selfreplication requiring: Nucleic Acids
 This causes a biological paradox.
 How could nucleic acids appear without the enzymes
to synthesize them?
 How could enzymes exist without nucleic acids to
direct their synthesis?
Origin of Living Systems
 RNA in some instances has catalytic activity
 First enzymes could have been RNA.
 Earliest self-replicating molecules could have
been RNA.
 Proteins are better catalysts and DNA is more
stable and would eventually be selectively
Origin of Living Systems
 Protocells containing protein enzymes and
DNA should have been selectively favored over
those with only RNA.
 Before this stage, only environmental
conditions and chemistry shaped biogenesis.
 After this stage, the system responds to natural
selection and evolves.
 The system now meets the requirements for
being the common ancestor of all living things.
Origin of Living Systems
 Origin of metabolism in the earliest organisms:
Probably primary heterotrophs.
Derived nutrients from environment.
Anaerobic bacterium-like.
No need to synthesize own food.
 Chemical evolution had supplied an abundant
supply of nutrients in the early oceans.
Origin of Living Systems
 Over time, nutrient supply began to dwindle as
the number of heterotrophs increased.
 At that point, a cell capable of converting
inorganic precursors to a required nutrient
(autotrophs) would have a selective advantage.
 The evolution of autotrophic organisms
required gaining enzymes to catalyze
conversion of inorganic molecules to more
complex ones.
Origin of Living Systems
 Appearance of Photosynthesis and Oxidative
 Early photosynthetic organisms probably used
hydrogen sulfide or other hydrogen sources to
reduce glucose.
 Later, autotrophs evolved that produced oxygen.
 Modern photosynthesis
6CO2 + 6H2O → C6H12O6 + 6O2
 Ozone shield formed which restricted the amount
of UV radiation reaching Earth’s surface.
 Land and surface waters could now be occupied.
Origin of Living Systems
 As oxygen accumulated in the atmosphere, it
reacted with water to form caustic substances
like hydrogen peroxide.
 Many life forms could not handle the new
environment and were ultimately replaced by those
that could tolerate the new environment and
eventually by those that could take advantage of the
surplus of oxygen (eukaryotes).
 The Great Oxygen Event (GOE)
Origin of Living Systems
 Atmosphere slowly changed from a reducing to
a highly oxidizing one.
 Oxidative (aerobic) metabolism (more
efficient) appeared using oxygen as the
terminal acceptor and completely oxidizing
glucose to carbon dioxide and water.
Precambrian Life
 Pre-Cambrian
Period covers time
before Cambrian
began nearly 600
million years ago.
Precambrian Life
 Most major animal phyla
appear within a few
million years at the
beginning of Cambrian
Period: the “Cambrian
 This likely represents
the absence of
fossilization rather than
abrupt emergence.
Precambrian Life
 Prokaryotes and the Age of
 Primitive characteristics of
 A single DNA molecule,
lacking histones, not bound
by nuclear membranes.
 No mitochondria, plastids,
Golgi apparatus and
endoplasmic reticulum.
 Cyanobacteria peaked one
billion years ago
 Dominant for two-thirds
of life’s history.
Precambrian Life
 Appearance of the Eukaryotes
 Arose 1.5 billion years ago.
 Advanced Structures of
 Membrane bound
 More DNA, and
eukaryotic chromatin
contains histones.
 Membrane-bound
organelles in cytoplasm.
Endosymbiotic Theory
 Lynn Margulis and
others propose that
eukaryotes resulted
from a symbiotic
relationship between
two or more bacteria:
 Mitochondria and
plastids contain their
own DNA.
 Nuclear, plastid and
ribosomal RNAs
show distinct
evolutionary lineages.
Endosymbiotic Theory
 Plastid and mitochondrial ribosomal DNA are
more closely related to bacterial DNA.
 Plastids are closest to cyanobacteria in
structure and function.
 A host cell that could incorporate plastids or
mitochondria with their enzymatic abilities
would be at a great advantage.
Endosymbiotic Theory
 Energy producing bacteria came to reside
symbiotically inside larger cells.
 Eventually evolved into mitochondria.
 Photosynthetic bacteria came to reside
symbiotically in cells.
 Eventually evolved into chloroplasts.
 Mitochondria & chloroplasts have own DNA
(similar to bacterial DNA).
 Animation
Origin of Eukaryotic Cells
 Many bacteria have
infoldings of the
outer membrane.
 These may have
pinched off to form
the nucleus and
Precambrian Life
 Heterotrophs that ate cyanobacteria provided
ecological space for other types of organisms.
 Food chains of producers, herbivores and
carnivores accompanied a burst of evolutionary
activity that may have been permitted by
atmospheric changes.
 The merging of disparate organisms to produce
evolutionary novel forms is called
Increasing Diversity – New
 Photosynthesis – process where hydrogen atoms
from water react with carbon dioxide to make sugars
and oxygen.
 6CO2 +6H2O
C6H12O6 + 6O2
 Autotrophs make their own food using energy from the
sun, carbon dioxide & water.
 Build-up of oxygen in the atmosphere allows evolution of
other organsisms.
 Heterotrophs obtain their energy from the environment.
 Sexual reproduction – allows for frequent genetic
recombination which generates variation.
 Multicellularity – fosters specialization of cells.