The Origin and Chemistry of Life

1
The Origin and Chemistry of Life

• Chapter 2

2
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.

3
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.

4
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.

5
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.

6
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.

7
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

8
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.

9
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.

10
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-

11
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-).

                                                                                          
12
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.

13
Chemistry of Life

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

14
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).

15
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.

16
Carbohydrates

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

17
Monosaccharides

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

18
Monosaccharides

• Some common monosaccharides

19
Disaccharides

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

20
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.

21
Lipids

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

22
Neutral Fats

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

23
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.

24
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).

25
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.

26
Steroids

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

27
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

28
Proteins

• There are 20 different types of amino acids.

29
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.

30
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.

31
Proteins

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

32
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)

33
Nucleic Acids

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

34
Chemical Evolution

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

35
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.

36
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

37
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

38
Chemical Evolution

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

39
Chemical Evolution

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

40
Chemical Evolution

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

41
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.

42
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

43
Chemical Evolution

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

44
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).

45
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?

46
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.

47
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.

48
Chemical Evolution

• Condensation reactions occur in aqueous
  environments and require enzymes.

49
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.

50
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?

51
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.

52
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.

53
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.

54
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.

55
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.

56
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.

57
Precambrian Life

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

58
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.

59
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.

60
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.

61
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.

62
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.

63
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

64
Origin of Eukaryotic Cells

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

65
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.

66
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.

67
Origins