Cell as the Basis of Life (Origin of the Cell) (HL)

Question 1

Explain how the Earth was formed?

Answer 1

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…)

Question 2

Outline how water was created in Earth.

Answer 2

It is likely it came from extra planetary objects
- objects outside the Earth’s orbit.

Question 3

Describe the Pre-Biotic Earth

Answer 3

In the Hadean Eon - frequent volcanic eruptions, meterorites, lightning and high temperatures; penetration of high UV radiation.

Question 4

Describe the First Prebiotic Atmospheres (ADD PHOTO)

Answer 4

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

Question 5

Describe the Second Pre-Biotic Atmosphere

Answer 5

-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)

Question 6

Explain the first step of Oparin and Haldane’s framework origin of life.

Answer 6

Inorganic “precursors” > Organic Molecules

Question 7

Compare and contrast inorganic and organic molecules. (ADD PHOTO)

Answer 7

- 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.

Question 8

According to Oparin and Holdane, there was life, how did organic molecules such as carbon form from inorganic precursors?

Answer 8

“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)

Question 9

Outline the evidences that small organic molecules could form polymers.

Answer 9

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.

Question 10

Outline the process of how a cell may have been formed by an inorganic compound.

Answer 10

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.

Question 11

When’s the chemical evidence of life?

Answer 11

3.8 billion years ago

Question 12

When’s the fossil evidence of life?

Answer 12

3.5 billion years ago

Question 13

Describe the “Great Oxygenation Event”.

Answer 13

• 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),

Question 14

Define Panspermia

Answer 14

a philosophical thought that life migrates naturally through space

Question 15

Define Chemical Evolution

Answer 15

simple chemicals assembled into more complex molecular systems, from which, eventually came the first functioning cell(s).

Question 16

Define Spontaneous Generation

Answer 16

AKA Abiogenesis. The belief that life came from non-living things

(e.g. trash can spawn a rat.)

Question 17

Define life.

Answer 17

There are multiple definitions of life. But, there is consensus that life on earth is composed of cells.

Question 18

Explain why is the cell the basic unit of life.

Answer 18

It is because it is the smallest structural unit that is capable of energy to sustain itself in a highly ordered state (aka living?)

Question 19

Distinguish the difference between cells and subcellular components.

Answer 19

Cells = alive

Subcellular components = not alive
- because they’re parts of the cell

Question 20

Outline the reasons why viruses are non-living.

Answer 20

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

Question 21

Define the NASA definition of life

Answer 21

a self-sustaining chemical system capable of Darwinian evolution.

Question 22

Outline the reasons why explaining the origin of cells is so challenging

Answer 22

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.

Question 23

Explain the reason why claims (of the origins of cells) need to be tested

Answer 23

Karl Popper: “Scientific claims should be falsifiable”
- can be tested and discarded (falsified) if they don’t hold up their testing.

Question 24

Outline the reason why viruses are not living

Answer 24

They are not made of cells

Question 25

On Earth today, where do cells come from.

Answer 25

They come from other (*pre-existing*) cells

Question 26

Outline the different implications of cells being only formed pre-existing cells

Answer 26

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*

Question 27

Explain hypothesized process needed for the spontaneous origin of cells on Earth. (ADD PHOTO) (Oparin and Haldane)

Answer 27

1.) Synthesis of **simple organic molecules from inorganic compounds.** l v 2.) Assembly of **these organic molecules into polymers** l v 3.) The **formation of a polymer** l v 4.) **Packaging of molecules into membranes with an internal chemistry different from the surroundings** (e.g. RNA, membrane-enclosed, lipid membrane)

Question 28

Give (Outline? IB command terms) the experiment used for the Origin of Carbon Compounds

Answer 28

**The Miller-Uray experiment**.

Question 29

Outline the conclusion of the Miller-Uray experiment.

Answer 29

- *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**

Question 30

Outline the apparatus used for Miller-Urey’s original experiment. (ADD PHOTO)

Answer 30

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

Question 31

Outline the reasons why scientists use models.

Answer 31

-**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.

Question 32

Explain the reason why all models have limitations and the implications of it (?)

Answer 32

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

Question 33

Describe the extraplanetary origin of organic compounds.

Answer 33

- 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) ??

Question 34

Describe the membrane of early cells. (ADD 1 MORE PHOTO)

Answer 34

Membrane barrier *separating the interior from its surroundings.* - *Hydrophilic exteriors, hydrophobic interiors* - due to *phospholipids’ hydrophilic heads and hydrophobic tails*

Question 35

Explain the possible formation of early cell membranes

Answer 35

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)

Question 36

*Explain why fatty acids are amphipathic* (ADD PIC)

Answer 36

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

Question 37

Define polarity

Answer 37

the *distribution of electrical charge* among the atoms connected by a chemical bond

Question 38

Explain the relationship between solubility and polarity.

Answer 38

A polar solute will dissolve in a polar solvent whereas a non-polar solvent will dissolve in a non-polar solvent

Question 39

Explain the formation of *micelles* (ADD GIF/PHOTO)

Answer 39

*Fatty acids in a watery solution get attracted to one another*

Question 40

Explain the formation of vesicles

Answer 40

**Fatty acid micelles at higher concentration and appropriate pH conditions can form vesicles** - captures fluids and dissolved molecules

Question 41

**Explain the possible formation of phospholipids** (REVIEW CARD?)

Answer 41

- Phospholipids formed *spontaneously*. - EXPLANATION HERE - But I’m guessing they’re due to the spontaneous generation of organic molecules

Question 42

Outline how the early cells membrane may have been formed. (ADD PHOTO)

Answer 42

Fatty acids coalesce into micelles -> Micelles coalesce to create phospholipids -> Phospholipids coalesce form membranes -> phospholipids arrange themselves back-to-back to form bilayers

Question 43

Outline the person who hypothesized the formation of phospholipids

Answer 43

David Deamer

Question 44

Outline the fourth step of the Oparin-Haldane hypothesis

Answer 44

Creating a cell membrane

Question 45

Outline the second state of the Oparin-Haldane hypothesis

Answer 45

Polymerization (monomers -> polymers)

Question 46

Outline what was found when putting a ground piece of the Murchison Meteorite in water.

Answer 46

- Because of the organic compound of the meteorite and its interaction with the water, *the lipid-like molecules assembled into cell-sized membranous vesicles*

Question 47

Outline Deamer’s experiment that concluded that the formation of membranes was a crucial step in the origin of cells.

Answer 47

**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*

Question 48

Define polymerization

Answer 48

- *The assembly of these organic molecules into polymers*

Question 49

Define anabolic reaction

Answer 49

*Simpler molecules form complex molecules* by condensation.

Question 50

Distinguish monomers from polymers.

Answer 50

**Monomers** - singular molecules, “building blocks”, **Polymers** - Many parts composed of monomer subunits

Question 51

Define what is a RNA polymer? (ADD PHOTO)

Answer 51

Polymer formed by *condensation of nucleotide monomers.*

Question 52

Define condensation

Answer 52

**Another word for “polymerization”** - Chemical process where two (or more?) molecules are joined tgt to make a more complex molecule

Question 53

**Define metabolic reactions**

Answer 53

Biochemical reactions that *transform food into energy in our body*

Question 54

Define a catalyst

Answer 54

Accelerates chemical processes

Question 55

Define the term for RNA that function as a catalyst

Answer 55

*Ribozymes* - think of it like this: ribo = protein = catalysts.

Question 56

Outline the process of ribozymes’ catalyzation;

Answer 56

- 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

Question 57

Asides from replicating itself, outline if RNA is also able to catalyze other essential biochemical reactions

Answer 57

Yes.

Question 58

Outline the third step of the Oparin-Haldane hypothesis.

Answer 58

*A self-replicating molecule*

Question 59

State the reason why RNA is considered to pass genetic information between generations during early Earth

Answer 59

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

Question 60

**How does RNA act as a catalyst for amino acids**

Answer 60

*The **ribosome contains a ribozyme** that forms the peptide bond between amino acids during transformation*

Question 61

Outline the unique abilities of RNA.

Answer 61

RNA can act both as a *self-replicating molecule and as a catalyst*

Question 62

Explain the RNA WORLD hypothesis.

Answer 62

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**

Question 63

Explain how RNA could self-replicate and act as enzymes (“ribozymes”) when placed in water according to the RNA World Hypothesis

Answer 63

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.**

Question 64

Explain the evidence on how RNA may have preceded DNA.

Answer 64

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*

Question 65

How has DNA replaced RNA as a more stable storage of genetic info?

Answer 65

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*

Question 66

Define the term “LUCA”

Answer 66

Last Universal Common Ancestor

Question 67

Outline what could’ve been the LUCA. (ADD PHOTO)

Answer 67

A small, single-celled *prokaryotic* - single-celled no membrane-bound organelles

Question 68

Outline what occurred in Madeline Weiss’ experiment and the conclusion of it.

Answer 68

**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)

Question 69

Outline what the 355 genes in Weiss’ experiment imply about the LUCA.

Answer 69

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

Question 70

Outline the various approaches used to estimate the dates of the major events in the evolution of life on Earth.

Answer 70

1.) **Chemical Evidence** 2.) **Biomarkers** 3.) **Fossil evidence** 4.) **Living Organisms**

Question 71

Show how chemical evidence can be used as an evidence of life with example

Answer 71

*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**

Question 72

Explain how evidence of microscopic life can be analyzed chemical isotopes.

Answer 72

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.

Question 73

Define what an isotope is. (ADD PHOTO)

Answer 73

Atoms with the **same number of protons but different numbers of neutrons**, are called isotopes of the same element.

Question 74

Define biomarkers

Answer 74

They are the **molecular fossils of lipids and other organic compounds**

Question 75

Outline where biomarkers are encased. (ADD PHOTO)

Answer 75

They’re found in ***sedimentary rocks (aka rocks from rivers and ocean)* that contain *biological molecules that turned into fossil molecules***

Question 76

Define “molecular clock”.

Answer 76

the **average rate at which a species' genome accumulates mutations,** (e.g. every 100 million years or something)

Question 77

How were the bacteria able to reach light in order to photosynthesize (?) (PROVIDE PICTURES)

Answer 77

**Stromatolites become covered in clay** which made the bacteria able to reach the light (from shallow waters)

Question 78

Outline what would be some of the earliest habitable places in earth.

Answer 78

The hydrothermal vents on the bottom of the sea.

Question 79

Outline the reason/evidence that proves that the seafloor hydrothermal vents are some of the earliest habitable places on Earth.

Answer 79

**There is fossilized evidence** from the places that life may have been *present at these location about 3.8 billion years ago*

Question 80

Outline the molecular clock approach (ADD PICTURE)

Answer 80

It uses *differences in the genomes in species to tell how much time has passed since they shared a common ancestor*

Question 81

Outline how the hydrothermal vents were formed.

Answer 81

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.*

Question 82

Electron microscope benefits and limitations

Answer 82