Biogeochemistry

Question 1

Describe how the 1950s and 1960s were hopeful years for origin of life science.

Answer 1

The 1950s and ’60s was a time when scientists began doing serious experiments on early origin of life scenarios, thusly termed the Age of Experiments.

It began with the Metabolic approaches of Melvin Calvin (1951), Harold Urey & Standley Miller (1953), and Sidney Fox, and then moved on to the Genetic approaches of James Watson and Francis Crick (1953).

Question 2

What was Melvin Calvin’s contribution to the Age of Experiments?

Answer 2

• Studied photosynthesis (hence ‘Calvin cycle’), winning Nobel prize
• In 1951 he studied prebiotic organic reactions, and found that:
• When high-energy particle radiation (reflecting cosmic rays or radioactive radiation) reacted with CO₂ and water..
• A very low yeild of organic compounds were produced.
• This discovery was very important for understanding the origins of life.
• Acted as inspiration for Miller-Urey experiment, that was more efficient.

Question 3

What was Harold Urey and Stanley Miller’s contribution to the Age of Experiments?

Answer 3

• Urey determined that Calvin’s low yeilds of organic compounds was due to an oxidising mixture, and so suggested using reducing gases similar to those of other planets in the Solar System, and possibly the early Earth.
• In 1953, over the course of a week, the Miller-Urey Experiment (Miller being Urey’s graduate student) used:
  
  • Boiling water simulating ocean
  • Methane, ammonia, hydrogen simulating primordial atmosphere
  • Electrical discharges simulating lightning
• And the products condensed and dissolved, with 10% carbon converted to organic compounds, of which 2% were amino acids. A very efficient yeild.

Question 4

What were the main findings and implications of the Miller-Urey Experiment?

Answer 4

• Experimental products were comparable with life - similar to cell constituents (e.g. most abundant glycine and alanine)
• Comparisons were also made with meteorites - e.g. similar relative abundances to Murchison meteorite (1969).
• This connection occuring between biochemical, extra-terrestrial and labratory datasets implied a possible widespread chemical evolution of the raw materials of life in the early Solar System and the Universe, given suitable prevailing conditions.

Question 5

What was James Watson and Francis Crick’s contribution to the Age of Experiments?

Answer 5

• In their quest to understand the structure of DNA they discovered the double helix, which opened doors for other areas of research that was previously not possible.
• James Watson and Francis Crick studied the structure of nucleic acids, and in 1953 proposed the structure for DNA (with the help of Rosalind Franklin).

Question 6

What makes up DNA?

Answer 6

• Collection of individual nucleotides
• DNA has two long molecular strands coiled about each other to form a double helix
• Opposing bases connected by weak hydrogen bonds

Question 7

What do nucleotides contain?

Answer 7

• A five carbon sugar molecule,
• One or more phosphate groups,
• A nitrogen-continaing compound called a nitrogenous base.

Question 8

In genetics, what do we refer to when we speak of the ‘Genetic code’?

Answer 8

• Base sequence in DNA is a set of instructions, called the genetic code, where only specific bases pair with each other:
• Adenine to thymine, guanine to cytosine. This provides a reproducable template, and..
• Enables self replication. A mechanism by which information can be passed from one molecular structure to another, to another etc.
• Directs the production of thousands of proteins (protein synthesis) - needed for the structure and function of living systems.

Question 9

Protein synthesis uses what substance?

Answer 9

RNA

• RNA different to DNA
• sugar is ribose rather than deoxyribose
• uracil is present instead of thymine
• when bonding with DNA, uracil replaces thymine and forms a base pair with the adenine of DNA

Question 10

Oil Baron, Ivor Stetson, runs a shoddy operation and has produced a large oil spill next to his drilling rig. Prior to the spill the ground water had abundant concentrations of oxygen, nitrate and sulphate. The sediment has a high permeability and consists of sand grains coated with both iron and manganese oxides.

i) Recognising that the biogeochemical reactions used by microbes are constrained by both thermodynamics and the abundance of elements in an environment, name the processes occurring in each of the sections as you progress towards the rig.

Answer 10

• Oil spill produces distinctive zones of oxidation and reduction
• Pre-spill conditions have all the materials for all the oxidation reactions
• Oil spill introduces large amount of reduced material that can then be oxidised
• As you get nearer to the oil spill the types of oxidation reactions change
• Furthest from oil spill, in most oxygen rich zone bc relative abundance of oxidants to organic matter is highest
• Oxidants become exhausted in direction of oil spill
• Oxygen exhaused at B
• Nitrate at C
• Manganese at D
• Iron at C
• All oxidants exhausted at F - just left with organic matter

Question 11

Oil Baron, Ivor Stetson, runs a shoddy operation and has produced a large oil spill next to his drilling rig. Prior to the spill the ground water had abundant concentrations of oxygen, nitrate and sulphate. The sediment has a high permeability and consists of sand grains coated with both iron and manganese oxides.

ii) For each stage list the electron acceptors and the products they would be transformed to following reduction.

Answer 11

• During aerobic respiration oil acts as electron donor and oxygen as the electron acceptor
• Where oxygen is unavailable specific microorganisms flourish until electron donors are exhausted
• Starting with NO₃^- and ending with CO₂

Question 12

What are the conditions neccessary for all oxidation and reduction reactions to take place post oil spill?

Answer 12

• Water has abundant concentrations of O₂, NO₃^- and SO₄^2-.
• Sand grains coated with both iron and manganese oxides

Question 13

Oil Baron, Ivor Stetson, runs a shoddy operation and has produced a large oil spill next to his drilling rig. Prior to the spill the ground water had abundant concentrations of oxygen, nitrate and sulphate. The sediment has a high permeability and consists of sand grains coated with both iron and manganese oxides.

iii) The area occupied by the oil spill presents conditions of what sort?

Answer 13

• Anoxic conditions similar to at bottom of water column, where lots of organic matter is being moved to, soaking up whatever oxidants are present.
• Get very little or no oxygen and perfect preservation.
• t.f. right in middle of oil spill would be perfect for preservation, even though oxygen is present at the surface, it’s not penetrating down into the center of the spill where conditions are completely anoxic.

Question 14

Re: Classification.
Fill in the table below.

Answer 14

Question 15

Summarize the Oparin-Haldane early life theory

Answer 15

• Pre-1980’s

1. Early Earth atmosphere oxygen free
2. Atmospheres of Jovian planets (captured 1’ gases)
3. Free iron in mantle (volcanic 2’ gases)
4. Reduced molecules including methane, ammonia, free hydrogen, and water vapour
5. Efficient production of organic molecules
6. Steam (Oparin),
7. UV light (Haldane),
8. Lightning (Miller-Urey)
9. Protein first approach
10. Gene-first approach

Question 16

Summarize the modern early life theory

Answer 16

• 1980s onwards

1. Early Earth atmosphere non-oxidising
2. No captured 1’ atmosphere
3. Free iron removed early to core
4. Volcanic 2’ gases
5. Carbon dioxide, nitrogen and water vapour
6. Poor atmospheric production of organic molecules
7. Vents
8. Clay mineral surfaces
9. Iron sulfur mineral surfaces
10. Extraterrestrial delivery

Question 17

The coexistence of Fe²⁺ and SO₄^2- ions under anoxic conditions has been described as “puzzling”.

Suggest how this combination of reduced and oxidised materials can come about and explain how the bacteria may fit into the overall scenario.

Answer 17

• Fe2+ is reduced and is usually found under anoxic conditions
• SO42- is oxidised and is usually found under oxic conditions
• Bacteria metabolize according to the oxidants available and the most favourable reaction
• Use mnemonic:
  
  • Oxygen
  • Nitrate
  • Magnesium
  • Iron
  • Fermantation
  • Sulphate
  • Methanogenesis
  • Acetogenesis
• The observation may suggest the initial presence of oxidised materials (Fe3+ and SO42-).
• The reduced iron is then present bc Fe3+ reduction is more favourable than SO42- reduction and the bacteria have simply not exhausted the Fe3+ supply.

Question 18

A phylogenetic analysis undertaken by Woese & Fox (1977) based upon ribosomal RNA sequence characterization revealed what?

Answer 18

That living systems represent one of three aboriginal lines of decent:

• the eubacteria, comprising all typical bacteria;
• the archaebacteria, containing methanogenic bacteria; and
• the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.

Question 19

A stream sediment was compromised by a mixture of organic compounds. Now a chemical analysis must be performed to ascertain the degree of residual contamination.

The table indicates the materials that were introduced.

Design an extraction procedure (solvent, method) to remove all possible compounds from the sediment matrix.

Answer 19

Most polar solvent mixture, such as dichloromethane and methanol or ethanol and water

Question 20

A stream sediment was compromised by a mixture of organic compounds. Now a chemical analysis must be performed to ascertain the degree of residual contamination.

The table indicates the materials that were introduced.

Design a fractionation process that will isolate the compounds for further analysis.

Answer 20

Increasing polarity of solvents, such as hexane, toluene, ethanol and then water

Question 21

What organic compounds are algae made up of?

Answer 21

C₁₅ and C₁₇

Question 22

What organic compounds are land plants made up of?

Answer 22

C₂₇, C₂₉, C₃₁

Question 23

Suggest an environment that could generate an organic assemblage of C₁₅, C₁₇, C₂₇, C₂₉ and C₃₁

Answer 23

• C15 and C17 - algae
• C27, C29 and C31 - land plants
• Near shore marine environment

Question 24

Re: Emergence

What were some of the early thoughts of the Earths earliest atmosphere?

Answer 24

• Oparin and Haldane hypothesis
  
  • Early Earth atmosphere oxygen-free
  • Efficient production of organic molecules
• 1930’s, Oparin
  
  • Argued for a mixture of methane, ammonia, free hydrogen and water vapour
  • Remneants of the primordial nebula that condensed to form the solar system
• 1950’s, Urey
  
  • Terrestrial planets small and warm
  • Lost atmospheres, later acuiring secondary atmosphere (also reducing)
  • Ideas guided Miller-Urey experiment

Question 25

Re: Emergence

What are the modern thoughts on the Earths earliest atmosphere?

Answer 25

• Presence of nebular gases still debated
• Agreement that atmosphere at time of Earth’s origin was volcanic
• Outgassing from the upper mantle
• Gases determined by internal structure of Earth and chemical composition of upper mantle
• Cold homogeneous accretion model
  
  • Presence of iron metal in the mantle
  • Nature of emitted gases was reducing
  • Methane, ammonia, and hydrogen
• Hot heterogenous accretion model
  
  • Iron metal removed from the mantle early and concentrated in the Earth’s core creating an oxidised mantle
  • Volcanic gases CO₂, water and nitrogen

Question 26

Re: emergence

was the composition of the earths early atmosphere reducing or oxidising?

Answer 26

• Composition of early atmosphere still hotly debated
• Non-oxidising atmosphere appears favourite, with CO2 a major component
• Neutral atmosphere preferred by some
• Debate is crucial to the origin-of-life question
• Non-reducing atmospheres make it difficult to explain
  
  • The generation of simple organic molecules
  • Their chemical evolution to more complex ones

Question 27

What is the accretion model?

Answer 27

• Planets formed through a process of gradual accretion
  
  • Lumps of material orbiting the young sun collided and stuck together
  • Gradually increase in size from dust grains up to tiny planets (planetesimals)
  • Craters on the moon indicated stormy early history of the solar system
  • Accretion process produced newly formed bodies which collided with the young planets

Question 28

What affect did accretion have on early atmosphere

Answer 28

• Impacts
  
  • Continuous collisions produced a molten Earth
  • Intense volcanic activity which released volatiles
  • CO2 and water were major volatiles present
• Accretion
  
  • Can help produce reducing environments
  • Impacts of meteorites and comets on the surface of the Earth
  • Delivery to Earth of volatiles, water and organic compounds
  • A major source of the building blocks of life, exclusively or in addition to endogenous synthesis

Question 29

All oceans on Earth required that how many comets brought water?

Answer 29

1 thousand

Question 30

What affect did meteorites and comets have on prebiotic molecules?

Answer 30

• Meteorites have a rich variety of organic molecules (e.g. Murchison) - and same amino acids in the same relative quantitites as those synthesized in the Miller-Urey experiment
• Observations of Halley’s and Wilson’s comets proved that comets are even richer in organic compounds than meteorites
• In the 1970’s both were seen as evidence of prebiotic processes that took place throughout the solar system, including the early Earth.
• Today, support is given to the hypothesis of exogenous delivery of organic material to the early Earth, and that this was the feedstock of life.

Question 31

Extraterrestrial infall could have helped produce what kind of atmosphere?

Answer 31

A reducing one

Question 32

How might meteorite iron metal and carbon have contributed to a early reducing atmosphere?

Answer 32

• Mixed with the Earth’s surface
• Reducing conditions in the mantle
• Consequent reduced volcanic gases
• Contribute to reducing atmosphere

Question 33

State the influence minerals can have on the origin of life.

Answer 33

• Organic building blocks could have been adsorbed and concentrated on clay mineral surfaces on ocean floor (dehydration and polymerization could take place on mineral surfaces to account for the fact that organic polymerization is not favoured in aqeous solutions).
• Act as catalysts both during polymerization and during template directed synthesis
• Act to bind reaction products through polymerization
• Protection - Bound polymers are protected from disintegration by hydrolysis
  *

Question 34

State how minerals can bind reaction products

Answer 34

By electrostatic interaction and helps increase length of reaction products

Question 35

State how minerals act as catalysts

Answer 35

Fixation of molecules about to react facilitates bond formation and speeds up reactions

Question 36

Show how hydrothermal vents inform origin of life ideas

Answer 36

• The deep-sea scenario for the origin of life was suggested after it was discovered that extant organisms flourish in hydrothermal systems
• Survive in total darkness, with no sunlight, using heat and chemical energy, mainly sulfur compounds emitted by vents
• Woese (1970s) discovered that a group of living microorganisms is the most ancient on the evolutionary scale.
• These microorganisms prefer extreme conditions - hot environments up to 120°C, anaerobic conditions, and high atmospheric pressure - and included thermophiles, hyperthermophiles and halophiles (salt lovers).
• Woese classified these as a new, third domain of life - the Archea.
• From DNA sequencing, Archeal features located on the oldest part of the tree of life - very close to the root and therefore the last common ancestor out of which all forms of life diverged.

Question 37

What is the hydrothermal-vents scenario in the context of early life on earth?

Answer 37

• Assumes direct evolutionary link between the last common ancestor and the first living systems on Earth preceding it.
• Extra polating backward implies oldest organisms on Earth are hyperthermophiles
• Life emerged in a hot environment, possibly in volcanic areas on the sea floor

Question 38

What would have been the benefits for life forming in hydrothermal vent systems?

Answer 38

• Origin of life coincided with Late Heavy Bombardment, and the deep ocean environment could have provided protection
• Physical and chemical dynamics
  
  • Gradients of temperature and pH
  • Thermodynamic non-equilibrium
  • Concentrations of various molecules
  • Highly suitable for processes of organic synthesis
• Experiments imply that high T’s and P’s in hydrothermal systems should be conductive to the production of organic molecules.

Question 39

Explain what is meant by the time window for life’s origin.

Answer 39

• Time during which chemical evolution led to first primitive living system
• End of Late Heavy Bombardment (LHB) is the oldest limit (appearence of life delayed until end of LHB)
• Although if life emerged on the ocean floor it may have been spared
• The younger boundary is determined by the evidence for the earliest life
• Time window was, geologically speaking, extremely short

Question 40

What are the basic characteristics of Archean microfossils?

Answer 40

• Confident recognition difficult
• Tiny
• Imperfectly preserved
• Simple morphologies
• Nonbiological mimics exist
• Conventional identification made on morphology alone
• Modern identification made on biogenic morphology

Question 41

Why is the conventional identification of Archean microfossils different to that of the modern?

Answer 41

• Conventional identification made on morphology alone (not enough)
• Modern identification made on biogenic morphology with an established Archean age for the samples.
• Modern identification requires geochemical signatures that are syngenetic with the alleged microfossils.

Question 42

Where will you find Archean microfossils?

Answer 42

• Canada
• Greenland
• South Africa
• Western Aus

Question 43

What are the names of the major localitites that have been found to preserve Archaean life?

Answer 43

• Isua, Greenland (3.85 Ga)
• South Africa
  
  • Onverwacht Group, Lower Barberton Greenstone belt (3.2-3.5 Ga)
  • Buck Reef Chert, Barberton Greenstone belt (3.42 Ga)
• Austrailia
  
  • Pilbara block (3.4-3.5 Ga)
  • Apex chert, Pilbara craton (3.5 Ga) (contested)
  • Sulphur Springs, Pilbara craton (3.24-3.26 Ga)

Question 44

Describe the microfossils found at Isua, Greenland

Answer 44

• 3.85 Ga
• Biogenic carbonaceous inclusions in apatites from iron formations

Question 45

Describe the microfossils found in the Onverwacht Grp of the Barberton Fm, SA.

Answer 45

• 3.2-3.5 Ga
• Cyanobacteria-like organisms, filements, traces of micro-fossils, organic mats, stromatolites in cherts/volcanic-lasts, in shallow marine environments

Question 46

Describe the microfossils found in the Pilbara block, Aus

Answer 46

• 3.4-3.5 Ga
• Shallow marine, subaerial cyanobacteria, oil inclusions (biogenic)

Question 47

Describe the microfossils found in the Apex Chert, Aus

Answer 47

• 3.0-3.4 Ga
• Cyanobacterium-like photo-autotrophs in cherts
• Kerogenous filaments in cherts, divided into cell-like compartments (Schopf 1993)
• Contested by Braiser et al. 2002
• Geological mapping of the area concluded that it was hydrothermal vent breccia not marine environment, with microfossils occuring in late-stage fissure infillings
• Filementous forms contested

Question 48

What was wrong with the filamentous forms of the Apex chert microfossils?

Answer 48

• Branched, a feature not otherwise seen until much later
• Branches secondary artefacts of crystal growth
• Cell-like structures result of silica crystalization
• Filaments are not hollow but composed of carbonaceous material around quartz crystals

Question 49

Describe the microfossils found at Sulphur Springs, Aus

Answer 49

Pyritized cyanobacterial filaments, deep sea, hydrothermal habitat

Question 50

Describe the microfossils found in the Buck Reef Chert, SA

Answer 50

• 3.42 Ga
• Carbonaceous filaments
• Biological d13C signatures, -30 per mil
• Microbial mat remains
• Shallow water organisms

Question 51

What are the oldest known stromatolites?

Answer 51

• Strelley Pool Chert, Pilbara Craton, western Aus (3.45 Ga)
• Steep Rock, Canada (3.0 Ga)
• Mozaan Grp, SA (2.8-3.0 Ga)
• Cheshire fm, Belingwe Greenstone belt, Zimbabwe (2.7 Ga)
• Campbellrand subgrp, SA (2.52 Ga)

Question 52

Describe the possible role of extraterrestrial material in kick-starting life.

Answer 52

• Thomson Helmholtz first suggested that the seeds of life reached Earth on meteorites
• Two ingredients needed for life = water and organic matter
• Liquid water stable on Earths surface since early Earth history, however organic matter was scarse at this time.
• Water mostly present as ice in outer solar system, but organic matter abundant
• Juan Oro (1961) proposed that life could have been kick-started by organic matter being delivered to the early Earth by extraterrestrial objects from the outer solar system.
• Meteorites have been found to carry amino acids (e.g. Murchison 1969), which are important building blocks for life.

Question 53

What are the biologically important molecules?

Answer 53

• Water
• Carbon (not a molecule)
• Organic macromolecules:
  
  • Lipids
  • Carbohydrates
  • Proteins
  • Nucleic acids

Question 54

Describe the water molecule and why it’s important

Answer 54

• Made up of hydrogen and oxygen, two of four elements that life on Earth relies on (carbon and nitrogen being the other two)
• Water molecules are the major component of living tissues, and generally account for 70% of their mass
• It provides a medium in which molecules can dissolve and chemical reactions can take place
• Exists as a liquid in a T range (Goldylocks zone)
• Not to cold to sustain biochemical reactions
• Not too hot to stop many organic bonds forming

Question 55

Describe the carbon element and why it’s important

Answer 55

• Life’s third most abundant element (after H and O)
• Carbon can form chemical bonds with many other atoms,
• Exhibits a great deal of chemical versitility
• Organic compounds contain other elements
  
  • Hydrogen, oxygen, nitrogen, sulfur and phosphorous
• A range of metals such as iron, magnesium and zinc also bond with carbon
• Carbon can form compounds that readily dissolve in water
• Water is essential to life on Earth

Question 56

Organic macromolecules comprise most of the molecules in a living system, and are a product of what process?

Answer 56

• Combining many individual organic units
• Monomers
• Polymers

Question 57

Describe lipids and why they’re important

Answer 57

• Any organic compounds soluble in organic solvents (e.g. fats and oils)
• Diverse group of molecules
  
  • Hydrophobic (water-hating)
  • Hydrophillic (water-loving)
  • Rarely found as individual molecules
  • Arrange themselves into weakly bonded aggregates that can be considered macromolecules
• Convenient and compact way to store chemical energy
• Weak bonding within their macromolecular structure results in a high degree of flexibility that is useful in membranes

Question 58

Describe the carbohydrate molecule and why it’s important

Answer 58

• Molecules with many hydroxyl groups (-OH) attached (e.g. sugars)
• Hydroxyl groups are polar and so make the carbohydrates soluble in water
• Large carbohydrate structures are called polysaccharides
  
  • Consists of sugar monomers connected together
  • Polymerisation occurs by reactions that involve the loss of water and result in a linear or branched network
• Used as energy stores (not as good as fat) and for structural support for organisms
• Form through condensation reaction - monomers and polymers

Question 59

Describe the protein molecules and why they’re important

Answer 59

• Long trains of amino acids linked together
• Polymerised by simple reactions that involve the loss of water
• 20 different amino acids found in living systems
• Particular sequence of amino acids that gives a protein its function
• Perhaps the most important of life’s chemicals
• Provide structure (e.g. in human fingernail and hair)
• Act as catalysts (e.g. in aiding digestion in our stomachs)
• Proteins with catalytic properties are called enzymes
• Formed during condensation (loss of water)

Question 60

Describe nucleic acids and why they’re important

Answer 60

• Largest macromolecules found (e.g. DNA and RNA)
• Collection of individual nucleotides
• Nucleotides contain
  
  • A five carbon sugar molecule
  • One or more phosphate groups
  • A nitrogen-containing compound called a nitrogenous base
• DNA has two long molecular strands coiled about each other to form a double helix
• Opposing bases connected by weak hydrogen bonds

Question 61

What is a cell?

Answer 61

• All life is made of the building blocks we call cells.
• Simple forms of life are made of only a single cell, such as the many species of bacteria and archaea.
• Complex organisms consist of vast numbers of cells working in concert with one another.
• Cells, whether living on their own or as part of a multicellular organism, are usually too small to be seen without a light microscope.
• Cells all rely on the same basic strategies to keep the outside out, allow necessary

substances in and permit others to leave,
maintain their health, and replicate
themselves.

Question 62

Are there different types of cell?

Describe nerve, plant and muscle cells.

Answer 62

• Cells share many common features, yet they can look very different.
• Cells have adapted over billions of years to a wide array of environments and functions.
• Nerve cells ‐ have long, thin extensions that can reach for meters and serve to transmit signals rapidly.
• Plant cells ‐ are brick shape and have a rigid outer layer that helps provide the structural support that trees and other plants require.
• Muscle cells – are long and tapered with an intrinsic stretchiness that allows them to change length when contracting and relaxing.

Question 63

What defines a cell?

Answer 63

• Cells are discrete packages.
• Surrounded by a cell membrane - a boundary between internal & external environments
• Also referred to as the plasma membrane
• Membranes are a framework of fat-based molecules called lipids
• Membranes are also studded with proteins that serve various functions
• Proteins up to 60% of membrane weight

Question 64

Membranes are studded with proteins that serve various functions.

What are these functions?

Answer 64

• Gatekeepers, determining what substances can and cannot cross the membrane
• Markers, indentifying the cell as part of the same organism or as foreign.
• Fasteners, binding cells together so they can function as a unit
• Communicators, sending and receiving signals from neighboring cells and the environment - friendly or alarming

Question 65

What is shown in the image

Answer 65

• A plasma membrane is permeable to specific molecules that a cell needs
• Each transport protein is specific to a certain molecule (indicated by matching colours)
• Bilayer has water on inside and outside

Question 66

Explain how a cell membrane acts as a barrier

Answer 66

Selective and semipermeable barrier that regulates flow of material into and out of the cell

Question 67

Explain how the cell membrane acts to transport material

Answer 67

• Barrier to transport and only certain substances pass through
• Blocks large molecules, like glucose and hydrophillic substances, like sodium ions
• Small, uncharged molecules, such as O2 or CO2 pass across

Question 68

What is inside a cell?

Answer 68

• Cytoplasm
• Cytosol

Question 69

What is cytoplasm?

Answer 69

• Interior within the plasma membrane
• Over 70% water
• pH maintained near neutrality

Question 70

What is the cytoplasm process?

Answer 70

• Raw materials from the external environment are enzymatically degraded
• New organic macromolecules are biosynthesized

Question 71

What is cytosol?

Answer 71

The soluble portion that contains a variety of small organic molecules and dissolved inorganic ions

Question 72

Why do cells feel pressure?

Answer 72

• Solute (dissolved substance) concentrations
• Pressure differential

Question 73

Explain how solute (dissolved substance) concentrations causes cells to feel pressure

Answer 73

• Most cells have internal concentrations that greatly exceed their external environment
• Constant tendency for external water to enter into the cytoplasm to dilute the salt content
• Creates an internal hydrostatic pressure that may reach up to 50 atmospheres
• External hydrostatic pressures are usually signif lower

Question 74

Explain how pressure differential in cells causes them to feel pressure

Answer 74

• Causes the delicate and deformable plasma membrane to stretch near the breaking point
• Were it the sole structural support, it would likely rupture and the cell would die (known as lysis)

Question 75

What are the effects of salt solutions on cells?

Answer 75

Question 76

How can cells of bacteria and Archea stay tough?

Answer 76

• Cell wall
  
  • Superimposes the plasma membrane
  • Provides extra rigidity and support for the cell
  • Governs cell morphogenesis
• Exterior armor that protects the cell from physical stress
  
  • Collision with other particales, chemical pertubants, pH changes, dissolved inorganic ions, and organic solvents
• Filters dissolved molecules passing into the cell (regulate passage of materials)

Question 77

Outline the constitution of prokaryotes

i.e. what are prokaryotes made up of and what is their form?

Answer 77

• Bacteria and Archaea
• Lack of complex parts (not large enough to differentiate many cellular processes into compartmentalized organelles)
• All posses a cell membrane that envelopes cell and seperates from external environment (plasma membrane 7-8 nm thick) - presence of both lipids and proteins within structure
• Within cytosol is a particulate fraction
• Genome, a large double-stranded molecule (the bacterial chromosome) that aggregates to form nucleoids and plasmids
• Ribosomes that manufacture proteins
• Carboxysomes as granules that serve as storage sites
• Gas vacuoles for buoyancy
• Magnetosomes, the magnetic particles found in some cells

Question 78

What is the diameter of bacteria and Archaea?

Answer 78

500 nm and 2 um, respectively

Question 79

What is the volume of a prokaryote?

Answer 79

1-3 um³

Question 80

Why is the small nature of prokaryotes beneficial?

Answer 80

• There is little to fail
• Explains why they’re found in “extreme” environments
• Extreme conditions preclude the growth of more complex organisms
• Bacteria stayed the same for a long time - no need to change

Question 81

How are the prokaryote membranes of bacteria and Archaea different from each other?

Answer 81

• In bacteria: lipid bilayer with a fatty acid portion sandwiched in the middle of two glycerol layers
• In Archaea: Fatty acid is replaced by repeating units isoprene

Question 82

Describe the relationship of prokaryote membranes with water, providing examples of how different organic membrane molecules are used by the organisms.

Answer 82

• Phospholipids
  
  • Ionized phosphate compounds at surface of glycerol give negative charge that is hydrophilic
  • Phosphate portions face both watery interior and exterior of cell
• Fatty acids
  
  • Hydrophobic nonpolar hydrocarbon chains
  • Cluster together and point inwards away from water
• Membrane fluidity
  
  • Plasma membranes are quite fluid, with a viscosity similar to light oil

Question 83

Explain the distinct make-up of Eukaryotes.

Answer 83

• Larger than Bacteria and Archaea, typically 5-100 um in diameter
• Complex structure with internal compartments
• Membranes
  
  • Most have a rigid cytoskeleton that varies in type amongst the different phyla
  • Also have a plasma membrane that contains complex lipids known as sterols
• Modify their lipid membranes with cyclic molecules (steroids)
• Contain membrane-enclosed nucleus
• Accomodates its genome in the form of DNA containing chromosomes
• Number of membrane-bound organelles that are used to segregate the various cellular functions

Question 84

What is the purpose of sterols in the plasma membranes of Eukaryotes?

Answer 84

Sterols stabalize the cell structure, making them less flexible than their prokaryotic counterparts

Question 85

Describe the membrane steroids used by eukaryotes and what are they used for?

Answer 85

• Sterols can compromise up to 25% of the total membrane lipids
• Inserted between the phospholipids of the bilayer membrane
• Ring structures of the compounds make them rigid
• Restricts movement of the fatty acid chains
• Steroid aliphatic chain can interact with distal portion of fatty acids

Question 86

Within the Eukaryote cell structure, there are a number of membrane-bound organelles that are used to segregate the various cellular functions.

What do these functions include?

Answer 86

• Mitochondria for energy production
• Chloroplasts, the chlorophyll-containing sites used by algae (and plants) for photosynthesis

Question 87

What’s the purpose of compartmentalization within the Eukaryote cell structure?

Answer 87

• Necessary for localizing the various metabolic processes
• Minimizes inherent problems of larger size
• Otaining nutrients and excreting waste products simply by diffusional processes

Question 88

What is metabolism?

Answer 88

All of the biochemical processes occuring within a cell

Question 89

Describe how metabolism proceeds.

Answer 89

1. Catabolism
   
   • Breaking down or degradative processes
   • Cells oxidise organic and/or inorganic compounds, to release chemical energy and then excrete waste products to the surroundings
   • Some of the chemical energy is utilized for cell movement, the transport of nutrients into the cell, and anabolic reactions, while the remaining energy is lost to the environment as heat
2. Anabolism
   
   1. Building up or biosynthetic processes
   2. Cells use chemical energy to convert nutrients and simple compounds into more complex structural and functional macromolecules

Question 90

What are enzymes?

Answer 90

Highly selective protein catalysits that accelerate the rate and specificity of metabolic reactions

Question 91

How do enzymes help metabolic processes?

Answer 91

• For catabolic reactions to take place initial energy needs to be invested
• Enzymes align reacting groups and break pre-existing chemical bonds
• Enzymes lower the activation energy necessary to transform a reactant into a product.
• The enzyme binds to a reactant and facilitates its transformation into a product.
• Enzyme-catalysed reactions have smaller energy barriers (activation energies) to overcome before the reaction can proceed

Question 92

What is chemical energy?

Answer 92

Chemical energy involves transfer of electrons, therefore are oxidation-reduction reactions, or redox reactions

Question 93

For metabolism to proceed, redox reactions must take place.

Explain how.

Answer 93

• An energy source acts as the primary electron donor (PED), and has the most negative electrode potential, and so gives up its electrons (is oxidised)
• Electron transfer takes place one or two at a time via a series of intermediate carrier enzymes
• The energy reciever (terminal electron acceptor, TEA) is the molecule with the most positive electrode potential, and receives the electrons (is reduced)
• After the electrons are accepted, the reduced materials (e.g. H₂O, NO₂^-, N₂, NH₃, Mn²⁺, Fe²⁺, CH₄) are waste and are discarded.

Question 94

For metabolism to proceed, the cell needs energy. How do cells obtain nutrients?

Answer 94

• Molecules have to pass across the cell membrane, which functions as a barrier - but not an impassable one
• The cell-membrane is semi-pearmeable
• Various proteins span cell membrane and permit specific molecules into the cell
• Cells can incorporate nutrients by phagocytosis.

Question 95

Explain the chemistry of photosynthesis

Answer 95

• During photosynthesis, cells use carbon dioxide and energy from the Sun to make sugar molecules and oxygen.
• Sugar molecules are the basis for more complex molecules made by the photosynthetic cell, such as glucose.
• Then, respiration uses oxygen and glucose to synthesize energy carrier molecules, such as ATP, CO2 is a waste product
• The synthesis of glucose and its breakdown are opposing processes.

Question 96

What are pigments?

Answer 96

• A pigment is a material that changes the colour of reflected or transmitted light as the result of wavelength-selective absorption.
• Biological pigments, also known as ‘biochromes’, are substances produced by living organisms that have a colour resulting from selective absorbtion of light.

Question 97

What are the functions of pigments in plants?

Answer 97

• The primary function of pigments in plants is photosynthesis.
• Other functions include attracting insects to flowers to encourage pollination.

Question 98

State which pigments are important in photosynthesis.

Answer 98

• Chlorophyll is the main photosynthetic pigment
• There are a number of chemically unique chlorophylls distinguished on the basis of their absorption spectra:
• Chlorophyll a
• Chlorophyll ß
• Bacteriochlorophyl

Question 99

What are accessory pigments?

Answer 99

• Light-absorbing compounds, found in photosynthetic organisms, that work in conjunction with chlorophyll a.
• They absorb light and pass it to the chlorophyll a photosystem.

Question 100

Name the accessory pigments

Answer 100

• Phycocyanin
• b-Carotene
• Xanthophyll
• Lycopene

Question 101

How is diversity assessed/analysed?

Answer 101

• Up until the late 1950’s phenotypic (observable, e.g. morphological, lifestyle) traits were used
• In 1970s Woese devised genotypic (genetic constitution) ways to determine relationships (e.g. the sequencing of proteins and nucleic acids)
• Molecular chronometers (e.g. ribosomal RNAs, rRNAs) reveal evolutionary relationships between life forms
• “Melting DNA” method also used

Question 102

Describe how molecular chronometers reveal evolutionary relationships between life forms.

Answer 102

• Molecular chronometers (e.g. rRNAs) exhibit sequence changes, caused by random mutations, at a constant rate (like the second hand of a clock).
• Sequence divergence - amount of sequence change in the molecule carried by two ancestrally related lineages
• Degree of divergence - reflects both the rate that mutations are fixed in the molecule and the time over which the mutational changes have occurred

Question 103

What makes an ideal molecular chronometer?

Answer 103

• Have “clock-like” / constant / regular random mutations
• Change at rates commensurate with the evolutionary distance of interest
• Rich enough in information to allow fine distinctions to be made
• Maintaining stability in overall structure
• Hence, Woese realized that ribosomal RNAs (rRNAs) meet the criteria for an ideal molecular chronometer
  
  • Small subunit rRNAs especially good

Question 104

What makes rRNAs suitable molecular chronometers?

Answer 104

• Occur in all cellular organisms that carry out protein biosynthesis (whole biosphere then)
• Feature a high degree of functional constancy
• Despite functional constraints, different positions in the three-dimesional structure of rRNAs change at different rates (allowing both distant and close phylogenetic relationships to be charted)
• Size offers at least 50 helical stalks that constitute a rich source for comparative analysis
• Genes that encode rRNAs can be sequenced relatively easily

Question 105

The molecular chronology method allowed Woese to do what?

Answer 105

• Use computer based algorithms to compare the sequence of genes encoding small subunit rRNA molecules
• Built tree of life on molecular differences
• This displays true, evolution-based phylogenetic relationships among organisms
• Allowed him to discover that life consists of three major domains (Bacteria, Archaea, Eukarya)

Question 106

Lineages at the base of the tree of life are adapted to what conditions?

Answer 106

• High T’s
• Suggests last universal common ancestor had a hot primeval habitat

Question 107

The “Melting DNA” method is another way of assessing diversity. How is this done?

Answer 107

• DNA double helix can be unzipped to produce two complimentary strands:
• Single strands of DNA from the same species can be zipped back together
• Single DNA strands from closely related sp can be partially zipped together
• Closely related sp will have similar, but not identical, sequences of nucleotides and will splice well
• Distantly-related sp will have dissimilar sequences of nucleotides and will splice poorly
• DNA hybridisation
  
  • Heat and cool DNA mixtures to see how well they bind

Question 108

What has DNA Hybridisation revealed?

Answer 108

• That species which appear similar have quite different ancestries
• e.g. owl seems to be related to hawks but are closer to nightjars

Question 109

How are same-species organisms identified today?

Answer 109

Three main taxonomic and molecular criteria are used today for deciding that two cultivated microorganisms belong to the same sp.

Question 110

Three main taxonomic and molecular criteria are used today for deciding that two cultivated microorganisms belong to the same sp.

What are these criteria?

Answer 110

1. DNA-DNA hybridization
   
   • <5% difference in the T of DNA helix dissociation for the two strains
   • >=70% DNA-DNA relatedness in whole genome reannealing tests
2. 165 rRNA gene
   
   • >97% indentity in sequence
3. Whole genome sequence comparison

Question 111

Outline the evolutionary steps of metabolism.

Answer 111

1. Reaction between H₂S and FeS at hydrothermal vents
2. Methanogenesis
3. Fermentation
4. Respiration (used sulfur)
5. Phototrophy (Sun source for energy)
6. Autotrophy (using H₂ and H₂S)
7. Photosynthetic expansion (used Fe²⁺)
8. Oxygenic photosyntheis (using H₂O) (2^nd energy rev.)
9. Aerobic respiration (3^rd energy revolution)

Question 112

What were the 3 “energy revolutions” in terms of metabolism?

Answer 112

1. Autotrophy
2. Oxygenic photosynthesis
3. Aerobic respiration

Question 113

Describe the earliest metabolism.

Answer 113

• Simple reaction in hydrothermal env
• Reaction between H₂S and FeS
• Releases enough energy to help form energy rich phosphate compounds (e.g. pyrophosphate)
• Pyrophosphate could be precursor to ATP
  
  • Can act as e- acceptor and donor
  • Simple structure
  • Can form abiotically from magma
• Reaction produces reducing power for CO₂ reduction and organic synthesis
• FeS + H₂S → FeS₂ + H₂
• Also see evolution of simple/primitive enzymes (e.g. iron sulfur protein) that could have catalysed reduction of CO2 to organic compounds, and..
• Membrane proteins capable of performing redox reactions that would have allowed stronger oxidants to be exploited

Question 114

How did methanogenesis come about in the evolution of metabolism

Answer 114

• 4H₂ + CO₂ → CH₄ + 2H₂O
• At vents, H₂ available from FeS + H₂S → FeS₂ + H₂
• T.f. methanogenesis available to earliest H₂-oxidising chemolithoautotrophs
• Suggests that methanogenesis developed from sulfur based metabolism

Question 115

How come the dominant early metabolism is not known?

Answer 115

• Short timespan mutation and adaptation possible
• Last common ancestor may have been a diverse and related population capable of gene transfer
• Rapid uptake of evolutionary adaptation
• The fact that the proteins involved in the respiration of Archaea and Bacteria are homogeneous supports this theory

Question 116

How did fermentation come about in the evolution of metabloism?

Answer 116

• The death of primitive chemolithoautotrophs led to organic debris accumulation near to vents
• Microbes fermented to utilize the reduced organic carbon as an energy source (removing dependence on H₂)
• Developed early in Bacteria and Archaea (both domains contain present day fermenters)

Question 117

What is fermentation?

Answer 117

• The partial oxidation of an organic compound using organic intermediates as electron donors and electron acceptors
• No outside electron acceptors are involved
• Typical products are acids, alcohols, ketones and gases
• e.g. C₆H₁₂O₆ → 2C₂H₅OH + 2CO₂

Question 118

How did anaerobic respiration come about in the evolution of metabolism?

Answer 118

• Fermentation was (and is) relatively inefficient, and further or complete oxidation of organic matter to CO2 would be better (right?)
• Respiration, through anaeobic pathways (e.g. using sulfur) could transfer electrons from organic matter, through fermentation, to a terminal electron acceptor
• S⁰ used by deep branching hyperthermophiles
• Other acceptors include SO₄^2- and Fe³⁺
• e.g. CH₃COO^- + 4S⁰ + 4H₂O → 4H₂S + 2HCO₃^- + H⁺

Question 119

How did phototrophy come about in the evolution of metabolism?

Answer 119

• Phototrophy was the adaptation needed to allow expansion into surrounding world, away from vents
• A rudimentary pigment, bacteriorhodopsin, was incorporated into cell membrane and illumination caused a proton gradient across membrane to give energy
• The next step involved development of more efficient bacteriochlorophylls by replacing Fe with Mg and changing the ring structure of the molecule slightly

Question 120

Describe the first autotrophs

Answer 120

• Bacteria are the likely origins of photosynthesis
• Above confusion due to gene transfer
• Highly likely in mat forming microbes
• H₂ and H₂S common electron donors
• Archaea lack photosynthetic apparatus

Question 121

Describe the photosynthetic expanison into using Fe²⁺

(Re: evolution of metabolism)

Answer 121

• Early photosynthetic growth was restricted to shallow hydrothermal vents and the continuous supply of H2 and H2S
• But other electron donors would allow colonization of new environments
• At mid ocean ridges ferrous iron allows photoferrotrophy, and the widespread supply allowed plankton to colonize shallow environments
• Fe²⁺ + 6CO₂ + 66H₂O → C₆H₁₂O₆ + 24Fe(OH)₃ + 48H⁺

Question 122

How did oxygenic photosynthesis (using H₂O) come about in the evolution of metabolism?

Answer 122

• Cynobacteria were the significant advance that would irreversibly change the world by using oxygenic photosynthesis
• Geochemical sources of reducing power (e.g. H2S, Fe2+, Mn2+, H2, CH4) limited largely to hydrothermal sources, and were in rel. low conc.s across the globe
• Early Earth potential reducing power vast if water could be utilized, since supply of water in virtually unlimited (Sunlight is also practically unlimited)
• T.f. the ideal biochemical mechanism would use the atoms of oxygen in water as a source of electrons (H₂O → O₂ + 2H⁺ + 2e^-), and biology would proliferate
• Light + nCO₂ + nH₂O → (CH₂O)n + nO₂

Question 123

What was required to happen for oxygenic photosynthesis to evolve (come about)?

Answer 123

• Required two main evolutionary events:
  
  1. A complex that could collect and store the four electrons generated
  2. Development of an oxidant with a sufficiently high electrode potential to remove electrons from water
• Chlorophyll a molecule
  
  • Able to harvest light at shorter wavelengths
  • Forms H₂O₂ but catalase oxidises it to O₂
• 6H₂O + 6CO₂ → C₆H₁₂O₆ + 6O₂

Question 124

How did aerobic respiration come about in the evolution of metabolism?

Answer 124

• Oxygen conc.s increased due to oxygenic photosynthesis
• Microbes adapted and developed enzymes to pass on electrons to O₂, and more energy could be released from the inorganic and organic materials they oxidised.
• Led to microbial expansion - greater influence on element cycling
• Aerobic respiration fully metabolises glucose

Question 125

What are the different phases in the growth cycle of organisms?

Answer 125

1. Growth begins - lag phase
2. Growth accelerates - log phase
3. Growth stalls - stationary phase
4. Growth stops - decline phase I and II

Question 126

Describe the ‘lag phase’ in the growth cycle of organisms.

Answer 126

• Growth begins
• Initial period of time when the cells adjust to their new surroundings
• Perhaps requiring the synthesis of new enzymes

Question 127

Describe the ‘log phase’ in the growth cycle of organisms.

Answer 127

• Growth accelerates
• Cells reproduce very rapidly
• Growth rates in nature slower than est. in the lab (<1% max. lab rates) bc conditions in nature not ideal and competition for nutrients exist
• Might not happen bc
  
  • cells run out of required nutrients
  • wastes build up to toxic levels
  • change in host water comp.

Question 128

Describe the ‘stationary phase’ in the growth cycle of organisms.

Answer 128

• No change in overall cell number
• Some cells grow while others die
• If conditions deteriorate many cells enter final death phase
• Adaptation frequent (response to diminished nutrients)
• Types of adaptation:
  
  • Cells become smaller to increase SA to V ratio to maximise diffusional capabilities
  • Grow at slower rate to increase cellular conc.s at given uptake rate (+ decreases metabolic demand for metalloenzymes)
  • Decrease their req. for limiting metals by altering metabolic pathways

Question 129

Describe the ‘decline phases’ in the growth cycle of organisms.

Answer 129

Growth stops

1. Decline phase I
   
   • Develop protective structures in response to starvation
2. Decline phase II
   
   • Spores are extremely durable

Question 130

Outline the evolution of complex organisms

Answer 130

• Mitochondria remsemble bacteria (purple sulfur)
• Chloroplasts resemble cyanobacteria
• Endosymbiosis theory in which eukaryotes created through combining of ancestral prokaryote with other prokaryotes in symbiotic relationship to take advantage of mutual benefit in the process:

1. Have Archaeal-type organism that injested purple bacteria (and also cyanobacteria) with intention of digesting it.
2. However, finds the bi-products beneficial and keeps the bacteria - resulting in multicellular organism.
3. Eukaryote now has factory for catching light and generating sugars and other organic compounds, and a factory for burning those compounds.
4. Then eukaryotic organisms start to populate new env.s, producing a more and more diverse biosphere, until we see the very diverse biosphere of today (e.g. w/ fungi, plants, animals)

Question 131

What are the limits on life.

Answer 131

• Water availability (water primary impediment for life)
  
  • Water facilitates biochemical reactions and acts as a transport agent for reactants and products
  • 70% of cells are water
• Organisms have temperature ranges
• Organisms have pH ranges
• Organisms have salt concentration ranges

Question 132

Give an example of an organism that has adapted to very low water conditions.

Answer 132

Xerophiles (e.g. cacti) reduce water loss with waxy surfaces and have internal solutes that accumulate glucerol

Question 133

What is the relationship between organisms and temperature?

Answer 133

• Below -20°C biochemistry of psychrophiles (bacteria <20°C) becomes too slow and membranes become rigid.
• Most organisms in nature are Mesophiles (15-45°C)
• Thermophiles (45-80°C)
• Above 121°C biochemistry of hyperthermophiles (archaea>80°C) becomes too fast and hydrolysis occurs, damaging proteins and DNA

Question 134

What are the relationships between organisms and pH?

Answer 134

Acidophiles and Alkaliphiles

• Neutrophiles (e.g. fish and bacteria >pH4, plants and insects above pH 2-3)
• Acidophile algae below pH 1
• Acidophile fungi grow near pH 0
• Acidophile archaea around pH 0
• Alkaliphiles up to pH 11

Question 135

What are the relationships between organisms and salt concentration?

Answer 135

• Most organisms require an isotonic environment or a hypotonic environment for optimum growth
• Osmotolerant - grow at reletively high salt conc. (up to 10%)
• Halophiles (bacteria that require salt for growth; >= 20%)

Question 136

What are the various degrees of preservation?

Answer 136

• Vital
• High fidelity
• Morphological
• Molecular
• Atomic

Question 137

Describe vital preservation.

Answer 137

• In the context of planetary exploration, preservation of vitality would involve the return of either dormant or living organism from another planet.
• Preservation of vitality also invokes concepts such as panspermia in which life is transported naturally from outside the Earth and is able to revive when placed in a suitable environment.

Question 138

Are there reports of vital preservation having taken place?

Answer 138

• Although controversial, there are reports of vital preservation in terrestrial geological materials:
• Revival and identification of bacterial spores in 25 to 40 Ma amber
• Isolation and growth of halotolerant bacteria from 250 Ma salt crystals

Question 139

Describe high fidelity preservation.

Answer 139

• Preservation of life without the ability of revival but with all of its chemical and morphological constituents present.
• Life has a variety of organic compounds and most are present in polymeric form.
• Both soft and hard parts are organised to be biochemically and biomechanically useful, so arrangement of constituents contains information on function.
• High fidelity preservation would preserve the constituents and their arrangements as close as possible to how they were in life.
• Examples of high fidelity pres. can sustain constituents for millenia.

Question 140

The process of high fidelity preservation includes:

Answer 140

• Desiccation or mummification (e.g. Lyuba the mammoth, 42 ka)
• Encapsulation in impervious materials such as amber

Question 141

Describe molecular preservation.

Answer 141

• Molecular reservation involves the retention of organic constituents of organisms.
• Rarely involves high fidelity chemical preservation and many of the organisms biochemicals are lost.
• Some molecular constituents resist degredation owing to inherent chemical stability which is exploited to facilitate protective roles in the living organism.
• Some molecular structures are useful bc they are diagnostic of particular organsisms known to exist under a set of specific env. conditions.

Question 142

Describe atmoic preservation.

Answer 142

• At the level of atoms, the stable isotopes of the biogenic elements C, H, N and S can preserve evidence of life.
• The signatures of life rely on the differences in stable isotope ratios brought about by biological activity.

Question 143

During atomic preservation, the signatures of life rely on the differences in stable isotope ratios brought about by biological activity.

How does this work?

Answer 143

• When a reletively unlimited source of starting materials is available for a biochemical reaction, enzymatic selectivity will lead to use of the lighter isotope.
• The difference in isotope ratios between inorganic starting materials and biogenic organic matter is called fractionation and can be used as a biosignature.
• Stable isotope ratios are exceptionally robust and their signature of life survives great durations and substantial Ts and Ps.

Question 144

Describe combined preservation.

Answer 144

Perhaps the most useful preservation events are those that represent preservation in multiple forms.

Question 145

Give an example of combined preservation.

Answer 145

• The Mid-Eocene 48 Ma Messel Oil Shale, Germany
• Almost all preservation forms present
• Anoxic lacustrine conditions led to the efficient pres. of fossil organic matter
• Fossil Tetrahedron microalgae in the shale are almost identical to their present day counterparts in morphology, molecular composition and stable isotope ratios

Question 146

Explain how preserved records are detected.

Answer 146

• For a biosignature to be useful it must be both accessible and recognizable.
• Utility of biosignature is determined by the analytical capablility available to the investigator, e.g.:
• History of stable isotope ratio mass spectrometers;
• Before the advent of stable isotope ratio mass spec. many Archean rocks would have been considered biosignature-free.
• Once stable isotope mass spec.s became available a preserved record of life could be read.

Question 147

Outline how records of organic matter are entombed.

Answer 147

• When flowing water is involved, materials can be segregated according to their density, where low density organic matter can be concentrated by selective entrainment and transport, and deposited in low energy environments.
• Fine grained minerals can produce a low porosity matrix which excludes oxidants - and the high surface areas of fine grained minerals provide sizable areas for organic adsorption.
• For organic biosignatures to be preserved their reduced (hydrogen-rich) nature should be maintained, by excluding oxygen, or oxidants, that act to convert organic matter to CO₂ and H₂O.
• Away from harmful radiation, below depths of few um for UV photons; 10 cm for solar energetic particles; and 3 m for galactic cosmic rays.
• Radiation in water causes free radicals to form, which in a radiation-rich environment will lead to oxidation of organic matter.
• Free radicals from radiation or oxygen poisoning are bad, especially so when iron is present.
• Heat causes organic metamorphism, but this can be retarded by water.
• Preservation of reduced material is more sustained at greater depths, away from oxidants that interact with the surface.
• Preservation occurs most effectively when the safe depths are reached quickly - rapid burial can transport organic matter away from near-surface degredation processes.
• The best organic host rocks are robust/impervious to alteration or metamorphism (e.g. stable minerals - silica or phosphate; clay-rich minerals have a strong association with organics and have a relative robustness to metamorphism).

Question 148

How does adsorbed organic matter promote preservation?

Answer 148

• Opportunities for degradation are reduced
• Polymerisation reactions are promoted that produce more resilient organic networks.

Question 149

How does carbon enter the long term geological carbon cycle?

Answer 149

• Surface organic matter descends
• During its passage to the deep ocean, marine organic matter decomposes in the water column, releasing CO2
  
  • 90% recycled in surface waters
  • 9% recycled in deeper waters
• Around 1% of this organic matter reaches the sea-bed intact
• Once incorporated in the sediment, degredation continues (aerobic and anaerobic organsisms)
• 0.1% of the original surface water organic matter preserved

Question 150

Name four oxygen-poor environments which produce organic rich sediments.

Answer 150

• Anoxic silled basin e.g. Black sea
• Large lake with thermal stratification e.g. Lake Tanganyka
• Coastal upwelling areas e.g. Coast of Peru
• Open ocean with poor circulation e.g. Indian ocean

Question 151

The oxygen-poor environment in the image below produces organic rich sediments.

What is this environment? Give explanations of the mechanisms that lead to low oxygen levels. Provide modern day examples and suggest typical total organic carbon levels.

Answer 151

• Anoxic silled basin
  
  • physical barrier to circulation
  • water outflow > inflow
• Freshwater surface
  
  • density stratification, poor oxygen supply, high nutrient supply
• E.g. Black Sea, organic-rich Shales, 1-15%TOC, fine laminae

Question 152

The oxygen-poor environment in the image below produces organic rich sediments.

What is this environment? Give explanations of the mechanisms that lead to low oxygen levels. Provide modern day examples and suggest typical total organic carbon levels.

Answer 152

• Large lake
  
  • Warm tropical environments, thermal stratification, no seasonal overturn, low oxygen supply
  • High productivity, high oxygen demand
• E.g. Lake Tanganyka, organic rich shales, 12 % TOC, laminae

Question 153

The oxygen-poor environment in the image below produces organic rich sediments.

What is this environment? Give explanations of the mechanisms that lead to low oxygen levels. Provide modern day examples and suggest typical total organic carbon levels.

Answer 153

• Coastal upwelling
  
  • nutrient rich subsurface waters rise to surface
• High productivity
  
  • excessive oxygen demand
  • oxygen minimum zone
  • anoxic layer
• E.g. Coast of Peru, 3-10% TOC

Question 154

The oxygen-poor environment in the image below produces organic rich sediments.

What is this environment? Give explanations of the mechanisms that lead to low oxygen levels. Provide modern day examples and suggest typical total organic carbon levels.

Answer 154

• Open ocean
  
  • poor circulation, biochemical demand, oxygen minimum zone
• Occurance
  
  • at present day in small areas
  • in past as oceanic anoxic events
• E.g. Indian ocean, 2-20% TOC

Question 155

Introduce the idea of preservation bias.

Answer 155

• Following death, a cell undergoes autolysis where the cell is destroyed by its own hydrolytic enzymes.
• Under certain conditions autolysis can be retarded by iron from volcanic ash.
• Organic components are attacked by microbes, assisted by enzymes secreted.
• In the absense of enzymes, degredation occurs more slowly
• Nucleic acids, proteins and polysaccharides are often lost on short timescales.
• There are preservation biases related to:
  
  • Burial
  • Metamorphism
  • Impacts
  • (see other cards)

Question 156

Explain the nature of preservation bias re: burial.

Answer 156

• Resistant materials such as lipids or resistant biopolymers are relatively intractable and can survive the passage into the geosphere.
• Inevitably the loss of constituents indicates that a record has suffered from preservation bias and the process must be considered when interpretations are being made.
• Those organic materials which do pass into the geosphere can lead to the formation of kerogen

Question 157

Explain the nature of preservation bias re: metamorphism.

Answer 157

• Entombed organic matter is buried and subjected to increased Ts and Ps
• Molecular architectures respond to achieve thermodynamic equilibrium
• The response represents a conversion of the biomolecule into corresponding geomolecule
• Eventually the thermal stress will lead to bond breaking events in the kerogen to produce lower molecular weight products
• Greater maturities lead to progressively lower molecular weight products
• The ultimate chemical consequence of which is methane (and eventually carbon dioxide by oxidative interaction with the mineral matrix) and graphite whose information remains only at the isotopic level.

Question 158

Explain the nature of preservation bias re: impacts.

Answer 158

• Preservation bias can be enhanced by the mechanism of access to the rock record
• Impact ejected rocks (i.e. excavated rocks) are suggested as good targets for accessing organic-rich materials that have escaped the degredation occuring at planetary surfaces through oxidation and irradiation.
• Impact excavation pressures degrade long chain hydrocarbon structures while aromatic structures are relatively well preserved.
• For planets where both biological and non-biological materials are present, impact excavation can lead to incorrect interpretations that only non-biological inputs were produced on a lifeless world.

Question 159

Describe the nature of preservation on Earth.

Answer 159

• Oxidation decreases with depth
• Surface of the Earth is bathed in oxygen gas which enables highly efficient oxidative metabolism
• Surface oxidants could diffuse into the subsurface and degrade subsurface organic matter
• At some point most aggressive oxidants will be exhausted but others can take over

Question 160

What are the key species (zones) to oxidation on Earth.

Answer 160

• O₂ (aerobic)
• NO₃^- (denitrification)
• Mn²⁺ (manganese IV reduction)
• Fe²⁺ (iron II reduction)
• SO₄^2- (sulfate reduction)
• CH₄ (methanogenesis/H₂O reduction)

Question 161

Describe the nature of preservation on the Moon.

Answer 161

• Lava encapsulation
  
  • Heating events
  • Thermal maturation
  • May alter organic matter
• Regular meteorite impacts to early lunar regolith modifies transformation process
• Lowest T step-polymerisation promoted
• Highest T step-polymer preserved
• Returned samples:
  
  • Low organic contents
  • Contamination a major issue
  • False positives likely
  • Long curation history

Question 162

Describe the nature of preservation on asteroids.

Answer 162

• Asteroids contain organic evidence of chemical evolution in the early solar system
• Organic matter is found alongside a range of mineral phases
• Mineral clasts are surrounded by a phyllosilicate-rich matrix produced by liquid water
• Organic concentrations in aqeously altered and phyllosilicate-rich chondrule accretion rims and matrix
• Organic matter only in small samples and susceptible to contamination

Question 163

Describe the nature of preservation on Mars.

Answer 163

• Oxidation decreases with depth
• Surface is highly oxidised
• Reagents include UV photons, atmospheric oxygen, mineral grain surfaces and water vapour
• Oxidising sp. such as H2O2-, OH- and O2- may diffuse into soils to depths of several cm
• Impact gardening or Aeolian processes may transport materials through oxidising zones over long timescales

Question 164

Which oxidants have been detected on Mars?

Answer 164

• Perchlorate ions (ClO₄^-) in salts
• Hydrogen peroxide (H₂O₂) in the atmosphere
• Clays and metal oxides composing surface minerals

Question 165

Describe the nature of preservation on icy moons.

Answer 165

• Liquid water, energy and organic carbon raise the possibility of active life in icy moons such as Europa
• On Europa, oxidation decreases with depth
• Energetic ions and electrons trapped in Jovian magnetosphere - can occur to depths of tens of cm
• Hydrogen is lost but oxygen is retained in tenuous atmosphere or in the ice lattice as bubbles or oxidised trace species
• Oxygen, peroxide, and oxidised surfur and carbon have been detected as trapped sp
• Bombardment related things (see other card)
• Crustal subduction must occur

Question 166

Bombardment on Europa produces:

Answer 166

• a porous regolith composed of sintered grains
• mixing of radiolytic products to depth
• collapse of pores trapping or reacting oxygen on grain surfaces

Question 167

Describe the nature of preservation on Europa (#2)

Answer 167

• The transport of materials through a subsurface water column and then ejection into space can be expected to induce some separation either based on solubility in water, charge or mass.
• The harsh radiation env. of Europa will lead to the production of surface oxidants.
• Enceladus is characterized by reletively weak irradiation, however.
• The harsh environments of the outer solar system would be expected to induce some selection for the long term preservation of organic structures.

Question 168

Breifly explain why the early 1980’s were called a time of crisis for origin of life science.

Answer 168

• Presentation of new data on the early Earth and solar system had changed ideas of prebiotic conditions
• Optimism replaced with caution
• Primordial atmosphere may not have been reducing and rich in hydrogen-containing gases, making prebiotic synthesis of organic compounds more difficult
• Time available for the emergence of the first living systems was much shorter than previously thought (emergence of cells less likely within such a short geological time frame
• New scenarios proposed for the origin and emergence of life on Earth - moving closer to the answer.

Question 169

Describe the early theories of the origin of life.

Answer 169

• Spontaneous generation: For most of human history theer has been a general belief that life can arise not only from parents but from inanimate matter, where;
• Heat and moisture could create life from soil, excremement or decaying plant and animal matter.
• Belief derived from common observations such as insects appearing in peutrifying meat and worms observed in muddy areas.
• Two approaches followed:
• Vitalism
• Materialism

Question 170

Define the term ‘vitalism’

Answer 170

Life and matter are distinct. Divine intervention appears in all ancient mythologies.

Question 171

What is ‘materialism’?

Answer 171

• Life and matter are the same.
• All objects thought to be made of one material.
• Life is spontaneously generated from the one material.
• Materialism was developed in Ancient Greece by 6th and 7th Century BC philosophers.
• Thales beleived the material was water;
• Anaximenes spoke of air as the basic element.
• Heraclitus adopted fire as the basic substance.

Question 172

What were the early theories of the origin of life that immediately followed basic materialism.

Answer 172

• In the 5th century BC, Empedocles proposed the Four Elements theory.
• Added Earth to the list of elements, to have four eternal elements or “roots”:
• Water, Earth, Fire and Air
• Empedocles believed in periodic rounds of creation and decay powered by love and harmony, and strife and seperation.
• Organisms products of mixing and seperating of the four elements.
• Only viable suggestions persist - early suggestions similar to natural selection ??

Question 173

What were the early theories of the origin of life that immediately followed the Four Elements theory.

Answer 173

• Greek Atomists, Leucippus, Democritus and Epicurus, in the 5th, 4th and 3rd centuries BC developed a materialistic approach that involved an infinite number of tiny entities or “atoms” in “void”.
• Constant motion with random collisions which generate material
• All objects made of similar stuff but differ in size and shape.
• No gods neccessary
• Constraints exist on possible combinations of atoms

Question 174

How did Plato critisize the Atomists theories?

Answer 174

• Plato (427-347 BC) believed properties and changes in atoms depended on geometric principles
• Thought movements of material elements in space insufficient to explain organisation of world and its creatures
• Preffered dualist concept where matter and form, body and soul are two different categories

Question 175

How did Aristotle critisize the Atomists theories?

Answer 175

• Artistotle (384-322 BC) acknowledged importance of chance and material necessity as explained by Atomists
• But criticised Atomists for inability to explain development and behaviour of natural organisms
• Vital processes are also driven by “final causes” involving accomplishment of specific natural ends

Question 176

What life theories did Aristotle propose?

Answer 176

• Provided ideas that persisted until the 17th century (!!)
• Living beings represent an organised whole, developed from an embryonic stage to maturity
• Directed growth: Non-random process requiring an organising principle or “soul”.
• The soul is internal and transferred from parent to offspring.
• Sexual generation where the male contributes the soul and the female the bodily material:
• The soul was carried by “pneuma” or hot air, similar to the Fifth Element, Quintessence, the element that makes heavenly bodies such as the Sun.
• Pneuma organises organisms on Earth.

Question 177

How did the idea of the Spirit change from 3rd century BC to Pre 3rd century AD?

Answer 177

• 3rd c BC - stoics believed pneuma to be a material element, but over time, pneuma changed from a carrier of soul to the spirit itself
• Post 3rd c BC - pneuma replaced by latin spirits - world soul that enters organism at birth and leaves at death to join celestial reservoir
• Pre-3rd c AD - pneuma responsible for spontaneous generation

Question 178

Briefly describe life theories between the 4th and 14th centuray AD.

Answer 178

• Saint Augustine (Father of Chistrian theology; 354-430) suggested spontaneous generation occurs by divine decree issued at creation and active for evermore (prevailed until beginning of 13th century.
• In the 12th c. Thomas Aquinas upheld Aristotle’s embryonic development and Augustine’s creation and seed principles, whereby each species produced at creation by God and unchanged thereafter.
• No remnants of Augustine philosophy in Christian though by 14th century

Question 179

Explain how scientific thought on the origin of life developed during the Scientific Revolution.

Answer 179

• The Scientific Revolution during the Mid 16th to Late 17th centuries was a period which produced new ideas in physics, astronomy, biology, human anatomy, chemistry and other sciences.
• A rejection of doctrines that had prevailed from Ancient Greece through the Middle Ages.
• Experiments revealed workings of systems such as blood circulation.
• Laid the foundation for modern science
• Produced the Mechanists

Question 180

The mechanists, what did they believe?

Answer 180

• Believed particles are inert with motion being caused by direct physical contact
• No soul or spirit
• No difference between living beings and other physical objects except the arrangement of matter
• Similar to the Greek atomists
• Mechanists believed universe was a big clock set in motion by God and left to fuunction uniterrupted

Question 181

Who was Descartes and what did he believe?

Answer 181

• Rene Descartes (1590-1650) was a leading mechanist and supporter of spontaneous generation.
• Plants, insects and worms spontaneously generate under the heat of the Sun.
• Descartes rejected explanations based on a life creating principle proposed by medeival scholars and naturalists such as van Helmont.
• Believed the living organism is a complex machine and thus can be explained by mechanistic principles
• Sexual generation, embryonic development and spontaneous generation can be explained as the working of heat and motion.

Question 182

Around the year 1600, during the Scientific Revolution, something very important happened. What was it?

Answer 182

• Development of the microscope in 1590
• First detailed account ofliving tissue made in 1644 “The Fly’s Eye”
• Widely used in late 1600’s to analyse biological structures, e.g. micrographia (Hooke 1665), red blood cells and spermatoza, microorganisms
• Microorganisms thought of as evidnce of spontaneous generation; too simplistic for sexual reproduction
• Some experiments questioned spontaneous generation

Question 183

What microscopy experiments questioned spontaneous generation?

Answer 183

• Various life stages of insects (egg, larva, pupa and adult) are all same animal
• Study of embryology - development of the chick in its egg
• Covered meat with cloth - flies laid eggs on cloth - insects cannot form spontaneously (Franseco Redi)

Question 184

What life science theories existed in the first half and end of the 17th Century?

Answer 184

• First half 17th century - mechanists believed in physical forces could organise matter
• End of 17th century - microscopy revealed eloborate inner structures
• Preformation
  
  • Germs are miniature forms of the mature organism
  • Embryonic development is the mechanical unfolding of the germ
• Pre-existence
  
  • Divine creation of germs which contain all future embryos for life

Question 185

In what way was the Preformation theory of life (proposed in the 17th century) questioned?

Answer 185

• Reformation - worms, snails, crayfish can regenerate an amputated part
• Heredity - contributions from both parents not just mother
• Size - single germ 1/1000 size of man then sixth genertion would be smaller than an atom
• Serious blows to preformation - relies on mechanical unfolding of preexisting germs

Question 186

Give an account of the contributions of Pasteur to the life science field.

Answer 186

• 1859
• Exposed boiled broths to air in vessels
• FIlter or tortuous tube revented all particles from passing through
• Nothing grew in broths unless flasks were broken open
• Living organisms that grew must come from outside
• Discredited spontaneous generation of microbes

Question 187

Give an account of the contributions of Darwin to the life science field.

Answer 187

• 19th century
• Origin of Species
  
  • Natural selection
  • New species generated from previous ones
  • No supernatural directing power
  • “Evolutionary tree”
  • Root of the tree is a single common ancestor
• Darwin’s letter of 1871
  
  • Possibility of present production of a primitive living system
  • Nonexistent chance
  • Any organic compound would be “instantly devoured or absorbed” by some living creature
  • Origin of life - had a change only on the sterile, lifeless ancient Earth.

Question 188

Describe how origin of life science became a distinct scientific discipline during the early 20th Century.

Answer 188

• Oparin
  
  • Biochemical multimolecular, multifunctional metabolic system
  • “Protein-first” or “metabolic concept”
• Haldane and Troland
  
  • Genetic theories and single reproducing molecule
  • “Gene-first” or “Gene concept”
• The two main lines of investigation thereafter
• New philosophical view:
  
  • Vitalistic (old)
  • Mechanistic (old)
  • Materialistic-evolutionary (new)

Question 189

Describe the “protein-first” (metabolic) approach?

Answer 189

• Proteins synthesized
• Proteins catalyse other molecules
• Primitive cellular system
• Coacervate or microsphere
• Growth and division

Question 190

Describe the “gene-first” (genetic) approach?

Answer 190

• Self replicating molecule
• Naked gene
• Replication and mutation
• Natural “Darwinian” selection of molecules
• Encapsulation

Question 191

A stream sediment was compromised by a mixture of organic compounds. Now a chemical analysis must be performed to ascertain the degree of residual contamination.

Describe the extraction process.

Answer 191

• Sample placed in a test tube
• Add solvent mixture (93:7 v/v DCM/MeOH)
• Add ultrasonic energy via probe
• Centrifuge and pipette off supernatant solvent
• Repeat extraction 3 times each or more
• Reduce the volume of each fraction to < 1 ml by evaporation
• Transfer concentrated fraction to preweighed vial using a pipette
• Evaporate fraction by placing vial under a stream of nitrogen
• Weigh vial to give extract weight

Question 192

A stream sediment was compromised by a mixture of organic compounds. Now a chemical analysis must be performed to ascertain the degree of residual contamination.

Describe the fractionation process process.

Answer 192

• Load extract onto column of adsorbent material
• Extract contains wide range of compound classes
• Organic solvents follow rule that like dissolves like
• Elute compound fractions with solvents of increasing solvent strength
• Important isolation and concentration step

Question 193

A stream sediment was compromised by a mixture of organic compounds. Now a chemical analysis must be performed to ascertain the degree of residual contamination.

How might one decide on a solvent?

Answer 193

• “Like dissolves like” so to isolate a compound it must be matched with a solvent of similar polarity.
• Solvents of different polarity can be used to remove other molecules.

Question 194

Label the diagram

Answer 194

Question 195

Define the term electromotive series.

Answer 195

An arrangement of metallic elements or ions according to their electrode potentials,

the order showing the tendency of one metal to reduce the ions of any other metal below it in the series.

Question 196

Give the TOC values for:

a) Anoxic silled basin
b) Large lake
c) Coastal upwelling regions
d) Anoxic open ocean areas

Answer 196

• Anoxic silled basin - 1-15%
• Large lake - 12%
• Coastal upwelling - 3-10%
• Open ocean - 2-20%