Ch.1 Flashcards
What is life?
The way a discipline defines life is intimately connected to the questions that it explores. One of the issues with defining life is that, depending upon the branch of biology where it is important, the properties of life don’t completely match. what one group thinks is an essential aspect of life, another group may not.
Evolutionary biology
study of how life on Earth changes over time through processes such as nat-ural selection and speciation. A major factor that determines the actual rate of change within a population is generation time, which is the average difference in age between a parent and its offspring
astrobiology,
which considers questions related to the possibility of life beyond Earth and the factors necessary to support life on other planets. Any definition of life that we can come up with would need to apply to entities we may discover (or meet) on other worlds.
artificial life,
which uses computer simulations, robotics, and synthetic biochemistry to simulate many of the attributes of life.
An entity is alive for evolutionary biologists only if it has properties A, B, and C.
An entity is alive for astrobiologists only if it has properties B, D, and F.
An entity is alive for artificial-life researchers only if it has properties A, D, and E.
“a self-sustaining system capable of Darwinian evolution.”
the NASA exobiology advisory board put forward a working definition of life. It did help to define what types of chemistry would constitute life on another planet. The problem with the definition is that there are many exceptions to it. There are many clearly living entities that are unable to reproduce. A mule, which is the sterile hybrid offspring of a horse and a donkey.There are also entities that science deems “non-living” that possess qualities of life such as reproduction, evolution, or something else. For example, fire can certainly make more of itself (reproduce) and it can grow and consume matter.mineral crystals can grow and maintain a highly ordered structure not unlike an organism
Seven characteristics shared by all cellular life forms.
While we can use the word entity to include a wide range of self-replicating and evolving systems, we are going to reserve the word organism for forms of life that are made of cells.
Without a strict definition of life, organisms on Earth all possess a key list of attributes. All life displays order, harnesses and utilizes energy, reproduces, responds to stimuli, exhibits homeostasis, grows and develops, and evolves.
Abiogenesis (Abiotic synthesis)
•(Spontaneous generation) An idea prevalent prior to the 19th century that complex life could be created from relatively simple ingredients.
•Organic molecules formed from in organic molecules
•Darwin figured it out before the two other guys but it was just speculation for him.
Inorganic atmospheric gases —EnergyTriggered Abiotic synthesis—> Organic molecules.
Inorganic:
-Methane
-Ammonia
-Hydrogen
-Water vapour
-Carbon dioxide
-Nitrogen
Energy:
-Lightning
-UV radiation
-Cosmic energy
Organic molecules:
-Amino acids
-Nitrogenous bases
-Sugars
-Lipids

-Still see you today and most likely, more than we think.
Spontaneous generation
= Life from nonliving matter
•Essentially abiogenesis but occurring more regularly.
•Early catalysts (clay or thermal vents)
-Favourite polymerization 
Primordial atmosphere
•In the early formation of earth, macromolecules making up all life must have been produced via abiotics synthesis.
-Beginning didn’t have organic molecules.
•Oparin-Haldane Hypothesis
-The atmosphere of primitive earth was a reducing atmosphere (lacking oxygen)
-Organic molecules that eventually formed the building blocks of life could have been formed from in organic molecules under the conditions the prevailed on primitive earth.
-First building blocks made of —> amino acids <— from macromolecules <—- made through abiotic synthesis.
Macromolecules
•Abiotic stew of inorganic matter —> simple organic molecules —> RNA nucleotides —> RNA Able to replicate itself, synthesize proteins, and function in information storage.
More complex
Amino acids —> Proteins
Nitrogenous bases —> Enzymes
Sugars —> Nucleic acids
•RNA monomers produced spontaneously from simple molecules.
•Experiment: polymers of small organic molecules produced by combining amino acid/nucleotides on hot sand, Clay, or rock.
-Can only happen in specific conditions
•Critical biological molecules are polymers.
-Nucleic acid, proteins, polysaccharides.
•2 polymers form some water. 
•Condensed reaction = polymerization
•Short polymer —> Unlinked monomer —> H2O + longer polymer.
•Polymerization
•Clay hypothesis
Protocells 
Protocells = Early “cells”
•Lipid vesicles have a many life like characteristics.
-Growth, internal chemistry, Can reproduce on their own, perform simple metabolism.
•Spontaneous formation of hollow lipid vesicles suggest how early cell-like structures have arisen
-Bi-layered structure similar to living cell membranes
•sphere Would have been able to keep or export own products
-Confining organic molecules increases rate of reaction (As get more molecules, get more reacts possible)
-Encourages evolution of cooperative relationships
•Experiment showed that vesicles form faster in the presence of a type of volcanic clay thought to be common 4 billion years ago.
-Have a catalyst (clay or rock) that favours reaction therefor increased rate of (a.k.a. Polymerization)
Formation of protocells:
•Wife reproduces: DNA molecules carry genetic information
•Life requires energy: metabolism
•Need to separate itself from the environment
-Cell membrane
-But free-floating amino acids, proteins and nucleic acid’s would not have been able to behave like cells. Because were lacking a lot of sales or structures/Functions we see them today. 
Self replicating molecules (RNA and DNA)
•Information in DNA is copied into molecules of RNA (ribonucleic acid)
-Directs production of protein molecules
•All organisms contains DNA (Deoxyribonucleic acid)
-Large, double stranded, helical molecule with instructions for cells to function.
•Why RNA?
-Polymer that stores information
-Can carry out enzymatic function
-Single strand provide template for replication.
What we know about Modern proteins and DNA
•Proteins became the dominant structural and functional macromolecules of all cells.
-Greater diversity
-Much higher rate of catalysis
•DNA is more structure complex and staple the RNA and thus evolved as a better repository of genetic information
Information flow
•Storage capacity
•Stability
•Reactivity
•Living cells require the development of a system based on nucleic acid’s that could store and pass on the information required to make proteins(Through replication)
•This flow of information, from DNA to RNA, is known as the central dogma
•The information is stored in DNA —> The information in DNA is copied into RNA —> The information and RNA guides the production of proteins.
Ribozyme binding:
•Ribozyme are RNA catalysts responsible for catalyzing critical reactions of gene expression.
•It is thought the DNA and proteins developed from RNA. 
RNA world
•First genetic material: RNA
-Single-stranded, fragile, self replicating
-Form different shapes depending on environment
-Can catalyze many different reactions (ribozymes)
-Favoured by natural selection —> RNA world
•Genetic material up all living organisms today: DNA
-Double helix: paired strands twisted around each other
-Very stable structure
-More accurately replicated. 
Primordial soup
•A solution rich an organic compounds in the primitive oceans of the earth, from which life is hypothesize to originated. 
Reducing atmosphere
•A reducing atmosphere versus an oxidizing atmosphere.
•Modern earth has an oxidizing atmosphere because it has high levels of oxygen (To the point that it’s very vital)
•Electron Rich, complex molecules cannot form in modern atmosphere —> Oxygen would take up the electrons
•A reducing atmosphere (and not the modern oxidizing atmosphere) would have been the only suitable option for the formation of early macromolecules.
-Lack of oxygen conditions favours formation of life that’ll eventually rely on oxygen to live. 
Deep sea hydrothermal vent’s
•Hot, mineral rich deep sea vents
•Where many of the earliest prokaryotes (Single cellular) (Archaea) still live (Not a lot of eukaryotes (Multicellular))
•Honeycombed, microscopic pores of hydrothermal vent’s provide a model for the evolution of early cells.
•Suggestion that earliest cell membranes would have inorganic casing composed of metal sulfides (NiS, FeS)
-Would trap and concentrate organic molecules (carbon-based) and allow complex chemical reactions
-An environment conducive to an early metabolic process mimicking the reverse citric acid cycle (In reductive conditions)
•Experiments mimicking characteristics of underwater volcanoes/vents produce more amino acids than those not mimicking them
•Complex molecules crew shuffle life may have Originated at the site of hydrothermal vent’s releasing super heated 300°C, nutrient rich water.
•Specific attention was given to alkaline hydrothermal vent’s because the water released
-Had lower temperatures (100-150°C)
-What strongly alkaline (pH 9-11), and
-Was rich in organic molecules (H2, H2S and NH3)
Evolution of metabolism
•Organic compounds synthesize from the combination of hydrogen (H2) and carbon dioxide (CO2).
-Carbon-based = organic based
•The simple to set up reactions related to the metabolic process: the citric acid cycle
•What is the most common process that translates hydrogen and carbon dioxide into organic compounds?
-Today its photo/chemosynthesis.
-Some don’t need light to perform. Will use methane or CO2 if no oxygen present in order to convert to sugars.
Photosynthesis:
-Converts CO2 to complex sugars
-Derives energy from light
Chemosynthesis:
-Converts CO2 or methane to complex sugars
-Derived energy from oxidation
Citric acid cycle
•A key component to cellular respiration
•Electrons released during oxidation use later in the respiratory pathway to generate ATP— Adenosine triphosphate (= chemical energy)
-Chemical energy used in photosynthesis or organisms that don’t use light(chemo)
•ATP is used to synthesize precursor molecules— Building blocks for amino acids and fatty acids. (more complex molecules)
Forward citric acid cycle: Oxidative
Reverse citric acid cycle: reductive
Reference lecture slide 60 
Citric acid cycle and hydrothermal vents:
•Can work forward and in reverse:
-Oxidative and reductive modes
•Oxidative mode input: Complex organic molecules
Oxidative mode output: chemical energy
•Reductive moulding put: chemical energy, carbon dioxide
Reductive mode output: large complex molecules
•Before enzymes evolved, reactions in the citric acid cycle would have been a catalyzed by iron-sulfur (Fe-S)(Fe-based & S-based) compounds (Very common in early earth), which are an abundant output product of alkaline hydrothermal vent’s. 
Oxygen revolution
•Oxygen Began accumulating ~2.7 Bya
•Forest and thetic cyanobacteria: used suns energy to split water in the hydrogen and oxygen (O2)
•Oxygen toxic to most early life:
-Because it wasn’t based to rely on to live.-obligated anaerobes (descendants)
-Present in writing Oxygen free substrates
-Some have colonized guts of animals where they produce methane gas
•Other prokaryotes adapted to oxygen rich atmosphere and began respiring aerobically (This is what really changed everything)

Stromatolites
(3.5 Bya)
-Rocks with distinctive layered structure
-Start to see some thing change in rocks around this time.
•Formed when microorganisms bind particles of sediment together, forming thin sheets.

•Look identical to live in bacterial mats
-Layers of microbes in sediment
-Top layer uses photosynthesis(bacteria able to)
-Lower layers use top layer’s by products (That’s how the layered concentrations are built over time)
•Old is traces of life on earth found in Canadian rocks, 3.95 Bya. 
Fossil
=Preserved remnant/evidence of life in the past
•Associative mostly with sedimentary rock’s:
-Rocks formed through accumulation of mud, silt, or sand
-Distinct layers of rock called strata
•Is invaluable as provides the only direct evidence about what life was like millions of years ago
•But it represents only a small fraction of the organisms that once lived on earth, and does it fast the under represents the diversity of life.
•Most fossils form in sedimentary rocks
•Sediments found in any one place form distinctive strata (layers) that usually different in color, mineral composition, particle size, and thickness
•Geologist to use the sequence of strata and her distinctive fossil assemblages to establish the geological time scale the maps the history of life on earth.
Probability of an organism or part of becoming fossilized depends on:
More likely if:
•Hard than softbodied
•Aquatic then terrestrial
•Inshore marine then offshore
•Decomposing organisms absent
—> Our understanding of the diversity and distribution of past life is biased and incomplete.

Relative versus absolute age
First evidence of life on earth
—> Indirect
•3.8 By sedimentary rocks from Greenland
•Unusual carbon isotope ratios
—> Direct
•3.5 By fossil stromatolites
•Dome shaped sedimentary rocks with peculiar layered structures
-Western Australia, southern Africa, northern Canada
•Radiometric dating
-Isotope (half-lives)
•sedimentary vs volcanic rock
Relative dating:
•sedimentary stratigraphy
-stratum = layer; graph = write, record
•Can’t tell exactly how long ago or fossil was formed 
•But can tell which fossil came first, second, etc.
Absolute dating: radiometric dating
•Radioactive isotopes and fossils and/or rocks
•Decay of one isotopic form to another at a constant rate (within their half life)
-C-12 Very common: accumulates while living, unchanged after death.
-C-14 rare: So after death, ratio C-14:C-12 Will gradually decrease
-The older the organism, the less C-14 will be left: we can use this to determine how long since the organism stopped exchanging C
•half life: 50% of atoms in a given amount of radioactive substances have decayed.
Continental drift
Understanding history of earth:
•Landmasses drift around on plates floating on hot mantle
• tectonic boundaries are sites of earthquakes and volcanic activities
•Relative position and extension of land masses have changed over time.
•Supercontinent
-1.1bya, 600mya, 250 mya
•Enormous changes in species assemblages
-New habitat, new competitors, new food sources, new climates and Enormous selective pressures.
•pangaea: Supercontinent
Pan = Everywhere/everything
Gaia = earth
Consequences of continental drift
•Changes to the environment and climate.
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v
=Opportunities for a diversification of life.
E.g., One land masses are isolated, each can develop own suit of species (Allopatric speciation)
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•Mass extinctions
-e.g., When Antarctica drifted to the poles and froze solid
Geologically active earth
•Thin crust
•Convection currents

Adaptive radiation
—> New environment opportunities created by the movement of continents and mass extinction can result in the evolution of diverse new lineage is in adaptive radiation.
Key adaptive features of prokaryotes
Advantage to: small size.
•Prokaryotes are the smallest cells known.
•Fewer resources required to grow
•Less space needed to live (tiny niches)
Advantage: binary fission
•No need to locate a mate
•Every individual can reproduce
3 key Adaptive features:
1. Small size
2. Binary fission
3. Short generational time (Able to evolve quickly)
Meaning = They are adaptable
-They have lived through many catastrophic events
•Still dominate the biosphere an outweigh in abundance all eukaryotes organisms by 10x. 
•Live wherever eukaryotes can and many places they cannot. 
Endosymbiosis theory
•Prokaryote ancestors of mitochondria and chloroplasts probably gained entry to a host cell as undisguised pray or internal parasites.
•Host (Usually the larger organism) and Endosymbionts (=Gives benefits to the host = Host becomes dependent on them) would have become a single organism overtime. 
-Both organisms benefit, always interacting with each other.
•Organelles, Coro Plast, and mitochondria all would have derive from free living prokaryotic host cells.
•Prokaryotic host cells engulfed the Endosymbionts, eventually becoming inseparable parts
—> Mitochondria: Descended from aerobic respiration
—> Chloroplasts Descended from cyanobacteria
•Photosynthesis and oxygen revolution created eventually the optimal conditions for eukaryotes to rise.
component: Membranes
Evidence: Some organelles have double membrane’s (outer membrane may be vesicular in origin)
component: Antibodies
Evidence: Susceptible to antibodies (e.g., chloramphenicol) (Indicates organelles may have bacterial origins)
component: Division
Evidence: Reproduction occurs to be a fission like process
component: DNA
Evidence: How’s own DNA which is naked and circular (Like prokaryotic DNA structure)
component: Ribosomes
Evidence: Have ribosomes which are 70s in size (identical to prokaryotic ribosomes)
