Cell as the Basis of Life (Origin of the Cell) (HL) Flashcards
Explain how the Earth was formed?
accretion
- basically gravity pulled swirling dust leftovers from the sun’s creation and compressed the proto-Earth to in increase in temperature.
Then the proto-Earth cooled, to stratified according to density leading to a layered composition (aka the crust, upper mantle…)
Outline how water was created in Earth.
It is likely it came from extra planetary objects
- objects outside the Earth’s orbit.
Describe the Pre-Biotic Earth
In the Hadean Eon - frequent volcanic eruptions, meterorites, lightning and high temperatures; penetration of high UV radiation.
Describe the First Prebiotic Atmospheres (ADD PHOTO)
Atmosphere 1:
- Earth likely began as a region of escaping hydrogen and helium.
- Due to these being the main gases in the dusty disk from which the planets were formed.
- Molecules of hydrogen and helium move fast when warm. BECAUSE OF THAT, they eventually all escaped Earth’s gravity and drifted off into space
- THAT’S HOW THEY COOLED
Describe the Second Pre-Biotic Atmosphere
-It came from Earth itself
- Generally thought that ammonia (NH3), methane (CH4), Carbon Dioxide (CO2) and water vapour (H2O) were present sometime after the crust cooled due to volcanic outgassing.
-> Amy (ammonia nh3) Meant (methane) Carl Doesn’t (Carbon Dioxide) Wet Vipers (water vapour)
Explain the first step of Oparin and Haldane’s framework origin of life.
Inorganic “precursors” > Organic Molecules
Compare and contrast inorganic and organic molecules. (ADD PHOTO)
- Inorganic Molecules
- Do not have carbon and hydrogen within the same molecule.
- Usually have a small number of atoms
- (look like balls and half balls together)
- associated with non-living matter
- Organic molecules
- contain **carbon and hydrogen*
- can be large molecules with many atoms
-(in the pictures they look like multiple balls with tubular branches) - associated with living organism.
According to Oparin and Holdane, there was life, how did organic molecules such as carbon form from inorganic precursors?
“The early earth provided the needed conditions to form carbon compounds”
- which are again needed for organic molecules
- These conditions do not exist on Earth today
-> How was carbon formed?: The molecules in *early Earth atmos. were chemically reducing* (electron of an atom or atoms increased) in nature, meaning they are reactive gasses that transfer electrons when they react
- Due to reducing atmos, energy from volcanic reactions and lightning catalyze the basic small molecules of life (e.g. amino acids) and then they form polymers, self-replicate then form the cell (see specific card)
Outline the evidences that small organic molecules could form polymers.
Amino acids linked together form proteins (building blocks = biomolecules?)
Fatty acids (carboxylics) could assemble cell membranes.
RNA nucleotides can link together when exposed to catalysts found in clay or water
- Notice how all of these are “building blocks” discussed by Sir Calix.
Outline the process of how a cell may have been formed by an inorganic compound.
ADD IMAGE
Inorganic compounds -> Organic monomers (aka building blocks so: carboxylic/fatty acids, amino acids, carbohydrates/simple sugars, nucleotides…) -> (via anabolic reactions aka biosynthesis) polymers -> self-replication -> formation of cell.
When’s the chemical evidence of life?
3.8 billion years ago
When’s the fossil evidence of life?
3.5 billion years ago
Describe the “Great Oxygenation Event”.
- Due to early photosynthesis, it released oxygen to atmosphere.
- The oxygen concentration in the atmosphere increased from 0% to around 20%
- The increasing oxygen level eventually depleted the reducing capacity of ferrous compounds, hydrogen sulfide and atmospheric methane, and compounded by a global glaciation, devastated the microbial mats around the Earth’s surface
- caused by phototroph prokaryotes which gave oxygen as a byproduct (cyanobacteria),
Define Panspermia
a philosophical thought that life migrates naturally through space
Define Chemical Evolution
simple chemicals assembled into more complex molecular systems, from which, eventually came the first functioning cell(s).
Define Spontaneous Generation
AKA Abiogenesis. The belief that life came from non-living things
(e.g. trash can spawn a rat.)
Define life.
There are multiple definitions of life. But, there is consensus that life on earth is composed of cells.
Explain why is the cell the basic unit of life.
It is because it is the smallest structural unit that is capable of energy to sustain itself in a highly ordered state (aka living?)
Distinguish the difference between cells and subcellular components.
Cells = alive
Subcellular components = not alive
- because they’re parts of the cell
Outline the reasons why viruses are non-living.
They are not made out of cells
◎ They can not keep themselves in a stable state
◎ They do not grow
◎ They can not replicate themselves
◎ They can not perform independent metabolism
Define the NASA definition of life
a self-sustaining chemical system capable of Darwinian evolution.
Outline the reasons why explaining the origin of cells is so challenging
It is difficult to directly test hypotheses related to the origin of cells because it happened billions of years ago
Causes:
- Conditions on Earth were very different
- It’s impossible to replicate with certainty the conditions that would have existed in early earth
- Well-preserved fossils were rare
- The methods used to estimate the dates of the first living cells have ranges of uncertainty.
Explain the reason why claims (of the origins of cells) need to be tested
Karl Popper: “Scientific claims should be falsifiable”
- can be tested and discarded (falsified) if they don’t hold up their testing.
Outline the reason why viruses are not living
They are not made of cells
On Earth today, where do cells come from.
They come from other (pre-existing) cells
Outline the different implications of cells being only formed pre-existing cells
Implication 1: We can trace the origin of all the cells in our body.
Implication 2: All cells can be traced back to LUCA (last common ancestor)
Implication 3: If you keep tracing, you would eventually reach the earliest cells to have existed. There have been a first cell that arose from non-living material
Explain hypothesized process needed for the spontaneous origin of cells on Earth. (ADD PHOTO) (Oparin and Haldane)
1.) Synthesis of simple organic molecules from inorganic compounds.
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2.) Assembly of these organic molecules into polymers
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3.) The formation of a polymer
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4.) Packaging of molecules into membranes with an internal chemistry different from the surroundings (e.g. RNA, membrane-enclosed, lipid membrane)
Give (Outline? IB command terms) the experiment used for the Origin of Carbon Compounds
The Miller-Uray experiment.
Outline the conclusion of the Miller-Uray experiment.
- A variety of carbon compounds (aka organic molecules such as amino acids) were formed from inorganic compounds.
- Implications: Carbon compounds could have spontaneously formed (aka abiogenesis) on Earth
Outline the apparatus used for Miller-Urey’s original experiment. (ADD PHOTO)
1.) Water in a flask (representing ocean) is boiled so that it evaporates and moves into a larger flask.
2.) Water combines with methane, ammonia and hydrogen gases (representative of the prebiotic atmos). Sparks are fired between electrodes to simulate lightning.
3.) A cooling condenser turns stream back into liquid water
4.) Liquid water drips down into a trap, where molecules produced in the reactions can settle for collection
Outline the reasons why scientists use models.
-Artificial rep of natural phenomena that are useful when direct observation or experimentation is difficult.
-Models simplify complex systems
- via physical rep, abstract diagrams, mathematical equations or algorithms.
Explain the reason why all models have limitations and the implications of it (?)
1.) They may be oversimplified/cannot represent all aspects of a system.
2.) They are only as accurate as the scientific knowledge they are based.
- So if the knowledge is faulty, the model would be faulty as well.
Implications: all limitations need to be considered in their application
Describe the extraplanetary origin of organic compounds.
- A meteorite landed in Murchison Australia and it had organic compounds (aka compounds with carbon — LIKE WATER)
- includes many organic molecules, including amino acids, nitrogenous bases, ribose
- REMEMBER WATER HAS ORGANIC COMPOUND (HYDROGEN AND CARBON — THERE’S CARBON IF IT ISN’T PURIFIED) ??
Describe the membrane of early cells. (ADD 1 MORE PHOTO)
Membrane barrier separating the interior from its surroundings.
- Hydrophilic exteriors, hydrophobic interiors
- due to phospholipids’ hydrophilic heads and hydrophobic tails
Explain the possible formation of early cell membranes
May have formed from fatty acids instead of phospholipids
- Why?: They have have formed more readily in a pre-biotic environment
(simplicity is key there ig bc it needs to conserve energy — confirm please)
Explain why fatty acids are amphipathic (ADD PIC)
CAUSE: Each fatty acids molecule is a hydrocarbon chain with a carboxyl (COOH) group
- Carboxyl soluble in water (hydrophilic)
- Hydrocarbon tail, because of the nonpolar C-H bonds, is very hydrophobic
Define polarity
the distribution of electrical charge among the atoms connected by a chemical bond
Explain the relationship between solubility and polarity.
A polar solute will dissolve in a polar solvent whereas a non-polar solvent will dissolve in a non-polar solvent
Explain the formation of micelles (ADD GIF/PHOTO)
Fatty acids in a watery solution get attracted to one another
Explain the formation of vesicles
Fatty acid micelles at higher concentration and appropriate pH conditions can form vesicles
- captures fluids and dissolved molecules
Explain the possible formation of phospholipids (REVIEW CARD?)
- Phospholipids formed spontaneously.
- EXPLANATION HERE
- But I’m guessing they’re due to the spontaneous generation of organic molecules
Outline how the early cells membrane may have been formed. (ADD PHOTO)
Fatty acids coalesce into micelles -> Micelles coalesce to create phospholipids -> Phospholipids coalesce form membranes -> phospholipids arrange themselves back-to-back to form bilayers
Outline the person who hypothesized the formation of phospholipids
David Deamer
Outline the fourth step of the Oparin-Haldane hypothesis
Creating a cell membrane
Outline the second state of the Oparin-Haldane hypothesis
Polymerization (monomers -> polymers)
Outline what was found when putting a ground piece of the Murchison Meteorite in water.
- Because of the organic compound of the meteorite and its interaction with the water, the lipid-like molecules assembled into cell-sized membranous vesicles
Outline Deamer’s experiment that concluded that the formation of membranes was a crucial step in the origin of cells.
Where?: In a volcano with little ponds of hot acidic water
- Why?: It resembles the supposed prebiotic Earth environment.
What happened?: He poured a mixture containing organic compounds (fatty acids, amino acids, etc.) into the volcanic water
- What happened after it?: lipid membranes spontaneously formed
Define polymerization
- The assembly of these organic molecules into polymers
Define anabolic reaction
Simpler molecules form complex molecules by condensation.
Distinguish monomers from polymers.
Monomers - singular molecules, “building blocks”,
Polymers - Many parts composed of monomer subunits
Define what is a RNA polymer? (ADD PHOTO)
Polymer formed by condensation of nucleotide monomers.
Define condensation
Another word for “polymerization”
- Chemical process where two (or more?) molecules are joined tgt to make a more complex molecule
Define metabolic reactions
Biochemical reactions that transform food into energy in our body
Define a catalyst
Accelerates chemical processes
Define the term for RNA that function as a catalyst
Ribozymes
- think of it like this: ribo = protein = catalysts.
Outline the process of ribozymes’ catalyzation;
- Similar to a protein enzyme
1.) Bond to a molecule (substrate)
2.) Catalyzes reaction and changes the substrate by breaking or building chemical bonds
3.) After that, it’s ready to work on another molecule of the substrate
Asides from replicating itself, outline if RNA is also able to catalyze other essential biochemical reactions
Yes.
Outline the third step of the Oparin-Haldane hypothesis.
A self-replicating molecule
State the reason why RNA is considered to pass genetic information between generations during early Earth
It is because RNA molecules SELF-REPLICATE EASIER than DNA and one of the reasons why is that it can act as a catalyst for their own replication
- Unlike DNA, they don’t need enzymes
- ribose is also more radily available
How does RNA act as a catalyst for amino acids
The ribosome contains a ribozyme that forms the peptide bond between amino acids during transformation
Outline the unique abilities of RNA.
RNA can act both as a self-replicating molecule and as a catalyst
Explain the RNA WORLD hypothesis.
It’s the idea that RNA was forming naturally before protein/gene cycles, DNA genetic code and living cells.
It also states that RNA can act as both a carrier of genetics that can self-replicate and an enzyme
Explain how RNA could self-replicate and act as enzymes (“ribozymes”) when placed in water according to the RNA World Hypothesis
1.) If RNA is placed under less hot water with wandering nucleotides, the nucleotides would naturally do base pairing and thus create a complementary strand
2.) If the RNA is placed in hot water, the pairings would separate into separate strand and then create other complementary strands to stick to and be separated from, thus self-replicating RNA
- The formed complementary strands are the inverse of the “parent strand” but they also come with mutations (thus perhaps how the FUCA may have evolved into different forms of life)
- Through the strand’s coming together, would it be a possible explanation as to how RNA preceded DNA?
3.) The RNA act as catalysts when they pair with themselves by folding and the outward/protruding bases point outwards because they weren’t able to find partners. Then, by interacting with the other molecules in their environment, they create chemical reactions, thus, they are called Ribozymes.
Explain the evidence on how RNA may have preceded DNA.
It is in their chemical differences
- Ribose (as in Ribonucleic Acid) is readily produced in lab experiments that attempt to simulate conditions of pre-biotic Earth.
- Deoxyribose (as in DeoxyriboNucleic Acid) is harder to make and needs to be produced from ribose
How has DNA replaced RNA as a more stable storage of genetic info?
DNA is more chemically stable than chains of RNA due to the deoxyribose in the DNA.
- DNA can be longer without breakage
- The hydrogen holding together the double-helical structure of DNA add additional stability
- The use of thymine (T) than uracil enhances DNA stability.
- Because Thymine is less likely to mutate and their mutations are easier to repair
Define the term “LUCA”
Last Universal Common Ancestor
Outline what could’ve been the LUCA. (ADD PHOTO)
A small, single-celled prokaryotic
- single-celled no membrane-bound organelles
Outline what occurred in Madeline Weiss’ experiment and the conclusion of it.
What occurred:
- They compared 6.1 million protein-coding genes.
- There were only 355 coded for homologous (similar origin) protein types between the two groups.
Conclusion:
- Any genes shared between bacteria and archaea were inherited from their LUCA (rather than independently occurring)
Outline what the 355 genes in Weiss’ experiment imply about the LUCA.
LUCA was:
- an obligate anaerobe (did not use oxygen)
- be of pre-biotic Earth atmos (no oxygen, right?) + characteristics of (certain) archaea and bacteria.
-A chemoautotroph, obtaining energy from chemicals (hydrogen, converts carbon dioxide and nitrogen into essential organic compounds)
- CHEMO - chemicals, AUTOTROPH - creates food
- like phototroph BUT DIFFERENT
-> mostly from the characteristics of the archaea and bacteria with homologous protein types AND the pre-biotic earth conditions
- can also withstand extremely temperatures
Outline the various approaches used to estimate the dates of the major events in the evolution of life on Earth.
1.) Chemical Evidence
2.) Biomarkers
3.) Fossil evidence
4.) Living Organisms
Show how chemical evidence can be used as an evidence of life with example
Rocks containing fossil-like structures with isotopes suggesting may be the remains of living organisms
- how are they fossil like: they contain organic compounds with a carbon isotopic signature that could result from biological processes
Explain how evidence of microscopic life can be analyzed chemical isotopes.
Carbon occurs in three varieties: 12^C, 13^C and 14^C.
The ratio of 12^C compared to 13^C trapped in the rock serves as an indicator of living processes. THIS IS BECAUSE AUTOTROPHS PREFERENTIALLY USE 12^C OVER 13^C in the fixation of atmospheric COv2 during photosynthesis.
Define what an isotope is. (ADD PHOTO)
Atoms with the same number of protons but different numbers of neutrons, are called isotopes of the same element.
Define biomarkers
They are the molecular fossils of lipids and other organic compounds
Outline where biomarkers are encased. (ADD PHOTO)
They’re found in sedimentary rocks (aka rocks from rivers and ocean) that contain biological molecules that turned into fossil molecules
Define “molecular clock”.
the average rate at which a species’ genome accumulates mutations, (e.g. every 100 million years or something)
How were the bacteria able to reach light in order to photosynthesize (?) (PROVIDE PICTURES)
Stromatolites become covered in clay which made the bacteria able to reach the light (from shallow waters)
Outline what would be some of the earliest habitable places in earth.
The hydrothermal vents on the bottom of the sea.
Outline the reason/evidence that proves that the seafloor hydrothermal vents are some of the earliest habitable places on Earth.
There is fossilized evidence from the places that life may have been present at these location about 3.8 billion years ago
Outline the molecular clock approach (ADD PICTURE)
It uses differences in the genomes in species to tell how much time has passed since they shared a common ancestor
Outline how the hydrothermal vents were formed.
1.) They are the result of seawater filtered through the fissueres (gaps) in the ocean crust in the vicinity of spreading centers or subduction zones.
2.) The cold seawater is heated by hot magma and remerges to form the vents.
Electron microscope benefits and limitations
