The Origin and Chemistry of Life

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The Origin and Chemistry of Life

• Chapter 2

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Water and Life

• Water makes up a large portion of living
  organisms.
• It has several unusual properties that make it
  essential for life.
• Hydrogen bonds lie behind these important
  properties.

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Water and Life

• High specific heat capacity 1 calorie is
  required to elevate temperature of 1 gram of
  water 1C.
• 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.

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Water and Life

• Unique density behavior while most liquids
  become denser with decreasing temperature,
  waters maximum density is at 4C.
• Ice floats! Lakes dont freeze solid some
  liquid water is usually left at the bottom.

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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 viscosity.

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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.

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Water and Life

• Hydrolysis occurs when compounds are split into
  smaller pieces by the addition of a water
  molecule.
• R-R H2O R-OH H-R
• Condensation occurs when larger compounds are
  synthesized from smaller compounds.
• R-OH H-R R-R H2O

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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.

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Acids, Bases, and Buffers

• pH A measure of the concentration of H in a
  solution.
• The pH scale runs from 0 - 14.
• Represents the negative log of the H
  concentration of a solution.

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Acids, Bases, and Buffers

• Neutral solution with a pH of 7
• H OH-
• Basic solution with a pH above 7
• H lt OH-
• Acidic solution with a pH below 7
• H gt OH-

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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-).

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Organic Molecular Structure of Living Systems

• Chemical evolution in the prebiotic environment
  produced simple organic compounds that ultimately
  formed the building blocks of cells.
• Organic compounds contain carbon in the form of
  chains or rings and also contain hydrogen.
• More than a million organic compounds are known.

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Chemistry of Life

• Recall the four major categories of biological
  macromolecules
• Carbohydrates
• Lipids
• Proteins
• Nucleic acids

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Carbohydrates

• Carbohydrates are compounds of carbon (C),
  hydrogen (H) and oxygen (O).
• Usually found 1C2H1O.
• Usually grouped as H-C-OH.
• Function as structural elements and as a source
  of chemical energy (ex. glucose).

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Carbohydrates

• Plants use water (H2O) and carbon dioxide (CO2)
  along with solar energy to manufacture
  carbohydrates in the process of photosynthesis.
• 6CO2 6H2O light C6H12O6 6O2
• Life depends on this reaction it is the
  starting point for the formation of food.

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Carbohydrates

• Three classes of carbohydrates
• Monosaccharides simple sugars
• Disaccharides double sugars
• Polysaccharides complex sugars

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Monosaccharides

• Monosaccharides Single carbon chain 4-6
  carbons.
• Glucose C6H12O6
• Can be straight chain or a ring.

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Monosaccharides

• Some common monosaccharides

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Disaccharides

• Disaccharides Two simple sugars bonded
  together.
• Water released
• Sucrose glucose fructose
• Lactose
• glucose galactose

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Polysaccharides

• 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
  plants.

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Lipids

• Lipids are fatty substances.
• Nonpolar insoluble in water
• Neutral fats
• Phospholipids
• Steroids

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Neutral Fats

• Neutral fats are the major fuel of animals.
• Triglycerides glycerol and 3 fatty acids

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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.

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Phospholipids

• Phospholipids are important components of cell
  membranes.
• They resemble triglycerides, except one fatty
  acid is replaced by phosphoric acid and an
  organic base.
• The phosphate group is charged (polar).

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Phospholipids

• Amphiphilic compounds are polar and watersoluble
  on one end and nonpolar on the other end.
• They have a tendency to assemble themselves into
  semi-permeable membranes.

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Steroids

• Steroids are complex alcohols with fatlike
  properties.
• Cholesterol
• Vitamin D
• Adrenocortical hormones
• Sex hormones

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Proteins

• 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

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Proteins

• There are 20 different types of amino acids.

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Protein Structure

• Proteins are complex molecules organized on many
  levels.
• Primary structure sequence of amino acids.
• Secondary structure helix or pleated sheet.
  Stabilized with H-bonds.

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Protein Structure

• Tertiary structure 3-dimensional 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.

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Proteins

• Proteins serve many functions.
• Structural framework
• Enzymes that serve as catalysts

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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)

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Nucleic Acids

• The repeated units, called nucleotides, each
  contain a sugar, a nitrogenous base, and a
  phosphate group.

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Chemical Evolution

• Life evolved from inanimate matter, with
  increasingly complex associations between
  molecules.
• Life originated 3.5 billion years ago.

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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.

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Chemical Evolution

• Early atmosphere consisted of simple compounds
• Water vapor
• Carbon Dioxide (CO2)
• Hydrogen Gas (H2)
• Methane (CH4)
• Ammonia (NH3)
• No free Oxygen
• Early atmosphere ? Strongly Reducing

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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

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Chemical Evolution

• Possible energy sources required for chemical
  reactions
• Lightning
• UV Light
• Heat from volcanoes

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Chemical Evolution

• Simple inorganic molecules formed and began to
  accumulate in the early oceans.
• Over time

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Chemical Evolution

• Prebiotic Synthesis of Small Organic Molecules
• Stanley Miller and Harold Urey (1953) simulated
  the Oparin-Haldane hypothesis.

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Chemical Evolution

• Miller Urey reconstructed the O2 free
  atmosphere they thought existed on the early
  Earth in the lab.
• Circulated a mixture of
• H2
• H2O
• CH4
• NH3
• Energy source electrical spark to simulate
  lightening and UV radiation.

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Chemical Evolution

• Results
• In a week, 15 of the carbon in the mixture was
  converted to organic compounds such as
• Amino Acids
• Urea
• Simple Fatty Acids

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Chemical Evolution

• Conclusion life may have evolved in primordial
  soup of biological molecules formed in early
  Earths oceans.

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Chemical Evolution

• Today it is believed that the early atmosphere
  was only mildly reducing.
• Stillif NH3 and CH4 are omitted from the
  mixture
• Organic compounds continue to be produced
  (smaller amount over a longer time period).

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Chemical Evolution

• More recent experiments
• Subjecting a reducing mixture of gases to a
  violent energy source produces
• Formaldehyde
• Hydrogen Cyanide
• Cyanoacetylene
• All highly reactive intermediate molecules
• Significance?

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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.

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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.

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Chemical Evolution

• Condensation reactions occur in aqueous
  environments and require enzymes.

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Chemical Evolution

• The strongest current hypothesis for prebiotic
  assembly of biologically important polymers
  suggests that they occurred within the boundaries
  of semi-permeable membranes.
• Membranes were formed by amphiphilic molecules.
• Meteorites are common sources of organic
  amphiphiles.

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Origin of Living Systems

• Life on Earth 4 billion years ago
• First cells would have been autonomous,
  membrane-bound units capable of self-replication
  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?

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Origin of Living Systems

• RNA in some instances has catalytic activity
  (ribozymes).
• 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
  favored.

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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.

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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.

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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.

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Origin of Living Systems

• Appearance of Photosynthesis and Oxidative
  Metabolism
• 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 Earths surface.
• Land and surface waters could now be occupied.

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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)

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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.

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Precambrian Life

• Pre-Cambrian Period covers time before Cambrian
  began nearly 600 million years ago.

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Precambrian Life

• Most major animal phyla appear within a few
  million years at the beginning of Cambrian
  Period the Cambrian explosion.
• This likely represents the absence of
  fossilization rather than abrupt emergence.

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Precambrian Life

• Prokaryotes and the Age of Cyanobacteria
• Primitive characteristics of Prokaryotes
• 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 lifes history.

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Precambrian Life

• Appearance of the Eukaryotes
• Arose 1.5 billion years ago.
• Advanced Structures of Eukaryotes
• Membrane bound nucleus.
• More DNA, and eukaryotic chromatin contains
  histones.
• Membrane-bound organelles in cytoplasm.

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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 mitochondrial ribosomal RNAs
  show distinct evolutionary lineages.

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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.

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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

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Origin of Eukaryotic Cells

• Many bacteria have infoldings of the outer
  membrane.
• These may have pinched off to form the nucleus
  and endoplasmic reticulum.

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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 symbiogenesis.

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Increasing Diversity New Developments

• Photosynthesis process where hydrogen atoms
  from water react with carbon dioxide to make
  sugars and oxygen.
• 6CO2 6H2O light 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.

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Origins
http//youtu.be/jTCoKlB0s4Y