Biogeochemistry Flashcards

Question

Re: Emergence What are the modern thoughts on the Earths earliest atmosphere?

Answer 1

* 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_

Answer 2

* 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

Answer 3

* 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

Answer 4

* 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

Answer 5

1 thousand

Answer 6

* 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.

Answer 7

A reducing one

Answer 8

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

Answer 9

* 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 *

Answer 10

By electrostatic interaction and helps increase length of reaction products

Answer 11

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

Answer 12

* 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**.

Answer 13

* 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

Answer 14

* 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.

Answer 15

* **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

Answer 16

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

Answer 17

* 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.

Answer 18

* Canada * Greenland * South Africa * Western Aus

Answer 19

* 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)

Answer 20

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

Answer 21

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

Answer 22

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

Answer 23

* 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

Answer 24

* 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

Answer 25

Pyritized cyanobacterial filaments, deep sea, hydrothermal habitat

Answer 26

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

Answer 27

* 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)

Answer 28

* 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.

Answer 29

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

Answer 30

* 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

Answer 31

* 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

Answer 32

* Combining many individual organic units * Monomers * Polymers

Answer 33

* 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

Answer 34

* 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

Answer 35

* 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)

Answer 36

* 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

Answer 37

* 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.

Answer 38

* 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.

Answer 39

* 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

Answer 40

* **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

Answer 41

* 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

Answer 42

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

Answer 43

* 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

Answer 44

* Cytoplasm * Cytosol

Answer 45

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

Answer 46

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

Answer 47

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

Answer 48

* Solute (dissolved substance) concentrations * Pressure differential

Answer 49

* 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

Answer 50

* 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)

Answer 51

* **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)

Answer 52

* **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

Answer 53

500 nm and 2 um, respectively

Answer 54

* 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

Answer 55

* 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

Answer 56

* 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_

Answer 57

* 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

Answer 58

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

Answer 59

* 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

Answer 60

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

Answer 61

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

Answer 62

All of the biochemical processes occuring within a cell

Answer 63

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**

Answer 64

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

Answer 65

* 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

Answer 66

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

Answer 67

* 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.

Answer 68

* 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.

Answer 69

* 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.

Answer 70

* 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.

Answer 71

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

Answer 72

* 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

Answer 73

* 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.

Answer 74

* Phycocyanin * b-Carotene * Xanthophyll * Lycopene

Answer 75

* 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

Answer 76

* 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

Answer 77

* 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

Answer 78

* 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

Answer 79

* 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)

Answer 80

* High T's * Suggests last universal common ancestor had a hot primeval habitat

Answer 81

* 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

Answer 82

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

Answer 83

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

Answer 84

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

Answer 85

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)

Answer 86

1. Autotrophy 2. Oxygenic photosynthesis 3. Aerobic respiration

Answer 87

* 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

Answer 88

* 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

Answer 89

* 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

Answer 90

* 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)

Answer 91

* 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

Answer 92

* 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⁺

Answer 93

* 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

Answer 94

* 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

Answer 95

* 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⁺

Answer 96

* **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

Answer 97

* 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

Answer 98

* **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_

Answer 99

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

Answer 100

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

Answer 101

* 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.

Answer 102

* 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**

Answer 103

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

Answer 104

* 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)

Answer 105

* 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

Answer 106

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

Answer 107

* 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

Answer 108

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

Answer 109

* 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%)

Answer 110

* Vital * High fidelity * Morphological * Molecular * Atomic

Answer 111

* 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.

Answer 112

* 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

Answer 113

* 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.

Answer 114

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

Answer 115

* 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.

Answer 116

* 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.

Answer 117

* 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.

Answer 118

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

Answer 119

* 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

Answer 120

* 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.

Answer 121

* 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).

Answer 122

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

Answer 123

* 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

Answer 124

* 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

Answer 125

* **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

Answer 126

* **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

Answer 127

* **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**

Answer 128

* **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**

Answer 129

* 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)

Answer 130

* 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

Answer 131

* 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.

Answer 132

* 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.

Answer 133

* 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

Answer 134

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

Answer 135

* 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

Answer 136

* 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

Answer 137

* 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

Answer 138

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

Answer 139

* 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

Answer 140

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

Answer 141

* 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.

Answer 142

* 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.

Answer 143

* **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**

Answer 144

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

Answer 145

* 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.

Answer 146

* 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 ??

Answer 147

* 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

Answer 148

* 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

Answer 149

* 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

Answer 150

* 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.

Answer 151

* 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

Answer 152

* 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

Answer 153

* 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**

Answer 154

* 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

Answer 155

* 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**.

Answer 156

* 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

Answer 157

* 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)

Answer 158

* 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

Answer 159

* 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

Answer 160

* 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

Answer 161

* 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.

Answer 162

* 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)

Answer 163

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

Answer 164

* Self replicating molecule * Naked gene * **Replication and mutation** * Natural **"Darwinian" selection** of molecules * Encapsulation

Answer 165

* 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

Answer 166

* 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

Answer 167

* “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.

Answer 168

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.

Answer 169

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

Biogeochemistry Flashcards

(196 cards)