Click the following for an Origin of Life Student Learning Guide Handout

1. Introduction

Much of our focus in this module has been on explaining the events and processes described in the table below.

FIRST Abiotic creation of monomers (the molecular building blocks of life)
NEXT Abiotically link monomers to form polymers Origin of metabolism. Create a  system for processing matter and energy and for removing wastes. Origin of heredity. Provide the system with a way to pass on instructions for maintenance, growth, and reproduction Encapsulate the system with a membrane to keep it from dissolving away, creating the first primitive cells.

In what follows, we’ll look at the origins of heredity, metabolism, and membranes. Let’s go.

2. The Origins of Heredity: The RNA World

Reproduction is a fundamental feature of any living system. In cells today (and probably all the way back to LUCA), reproduction is about passing on hereditary instructions encoded in DNA. But while DNA serves all living things as the repository (or library) of genetic information, it’s a poor candidate for having served as the first molecule of heredity. The problem is that DNA encodes information for producing proteins, but an entire team of proteins is required for production of DNA. One component couldn’t have arisen without the others already existing, and it seems beyond the realm of possibility that a system of such complexity (see the diagram below) could have spontaneously arisen, with all of its parts, all at once.

Replication of DNA at a replication fork (7): Key components of this system include 1 (DNA Helicase), 2 (DNA Polymerase), 5 (primase), and 8 (single strand binding proteins) are some of the proteins involved in this process. Click here for a tutorial about DNA replication.

A better alternative for a first hereditary molecule is RNA (ribonucleic acid).

2a.RNA v. DNA

Like DNA, RNA is a polymer composed of nucleotide monomers. But it’s different from DNA in several ways:

  1. RNA nucleotides are built around the sugar ribose, while DNA contains deoxyribose. Both are sugars that are build around five carbon atoms, but ribose has a hydroxyl group attached to the 2′ carbon (see the diagram at right and find the 2′ carbon), while deoxyribose has a hydrogen atom (which is why it’s called deoxyribose).
  2. While DNA uses the nitrogenous pyrimidine base thymine, RNA uses uracil.
  3. RNA is single stranded (unlike DNA, which is double stranded
  4. DNA’s double-stranded nature means that its three dimensional shape is always a double helix. Because RNA is single-stranded, its conformation is not constrained in the same way. Some RNA, like mRNA (messenger RNA), is a linear strand. But because the nitrogenous bases within a single RNA molecule can bond with one another, an RNA molecule can twist and bend into an unlimited number of shapes. You can see internal hydrogen bonding and the 3-D folding that results in the two representations of a transfer RNA molecule shown below.

Transfer RNA (tRNA). Notice the hydrogen bonding between complementary nucleotide bases: A and U; C and G.

tRNA: 3-D model

2b.Ribozymes are catalytic RNAs that function as enzymes

In RNA viruses and in viroids (parasitic RNAs that infect plants) RNA has an informational role. In these two cases, RNA takes on the function of DNA, and stores genetic information. But as we’ve just seen, RNA’s conformational flexibility lets it do something that DNA can’t do: fold into complex shapes. Some of these shapes result in RNAs that perform like enzymes, catalyzing chemical reactions. In other words, RNA can be both genotype and phenotype. This has been known since the 1980s, when catalytic RNAs, or ribozymes, were first discovered.

One function of ribozymes involves processing RNA or DNA through cutting or ligation (connecting together pieces of another molecule.). For example, the eukaryotic RNA processing that occurs between transcription of pre-RNA and formation of mRNA is carried out by a team of interacting RNA molecules that form a spliceosome. Spliceosomes are ribozymes that take pre-RNA and remove introns, creating messenger RNA.

RNA processing (removal of introns) is carried out by ribozymes

RNA Processing: Introns (intervening sequences, shown in black) are cut out to produce mRNA (at G)

A spliceosome is a ribozyme that carries out the processing shown in stage 1 (at left)

Ribosomes, which catalyze peptide bonds between adjacent amino acids during protein synthesis, are also ribozymes.

A ribosome catalyzing a peptide bond between two amino acids. The mRNA shows RNA in a single stranded, linear form. The ribosome made of RNA (complexed with protein) is a ribozyme.

2c. RNA doesn’t self-replicate like DNA (but let’s imagine how it could)

So, we’ve established the RNA can be genotype (information) and phenotype (action, as in ribozymes). The RNA world is a hypothetical stage in the evolution of life where RNA plays both roles, without the support of DNA (for information storage) or protein (for enzymes, structure-building, and just about everything else). But could RNA replicate without protein?

It doesn’t happen in today’s world. But let’s imagine how it could. During DNA replication, the double helix has to be unzipped by the enzyme DNA helicase. Then other enzymes, particularly DNA polymerase, use each of the separated single strands as a template for creating a new complementary strand. This is called “semi-conservative” replication.

There’s only one case in nature today where RNA is directly replicated into new RNA in a manner analogous to what’s shown above. That case involves viroids, infectious, single stranded circular RNAs that parasitize plants. Viroids don’t code for protein. They reproduce themselves by using RNA polymerase (a protein) from their hosts (the plant cells that they’ve infected).

Now imagine a viroid that could fold into a shape that would let it catalyze its own replication. If supplied with free nucleotides, that self-replicating viroid would constitute something pretty close to an RNA life-form. It would lack a metabolism, but it could self-replicate, and evolve.

2d. The RNA World

That’s essentially what the RNA world is. The RNA world would have consisted of self-replicating, evolving RNAsThis world would have emerged before cells, and before LUCA. It would have consisted of populations of RNAs that would have arisen pre-biotically. Some of these RNAs would be dependent upon one another, while others would be competing with one another (for resources such as access to the monomers required for self-assembly). During the replication process, mutations would arise, leading to a type of natural selection. Those RNA replicators that could replicate more quickly and efficiently would come to dominate their populations, just as natural selection causes beneficial alleles to spread throughout a species.

What’s the evidence for the RNA world? Theodor Diener, the discoverer of viroids, has suggested that viroids are a vestige of the RNA world (click to read Diener’s arguments, and rebuttals). In addition, scientists are working on creating RNA self-replication systems in the laboratory. For example, a ribozyme that is 189 base pairs long has been created that can synthesize complementary RNA from a 14 nucleotide RNA template. Along the same lines, RNA ribozymes have been artificially selected that are capable of copying almost any other RNA…though not itself (see this wikipedia article).

Watch the video below, which explains and animates these points.

Some of the biology described in this video (the emergence of the RNA world in tidepools, for example) runs counter to points I’ve made in the previous tutorial about the unlikelihood of life emerging in tidepools. But there’s no contradiction between the RNA world and the environments created by alkaline hydrothermal vents. For example, it’s possible that the tiny porous chambers in alkaline hydrothermal vent systems, with their constant flow of hydrogen and production of reduced carbon compounds, might have been the type of environment in which RNA nucleotides could have been synthesized and concentrated. Moreover, the presence of mineral catalysts in these micropores could have promoted the polymerization of RNA nucleotides into RNA polymers. Catalytic properties emerging in evolving RNAs in these systems could have led to the first RNA-protein systems, which in turn, could lead the the emergence of the genetic code. And at some point on the road to LUCA, DNA took over the role of genetic storage from RNA. 

ATP (adenosine triphosphate) is an RNA nucleotide. Note the three parts: phosphate groups, a ribose sugar, and the nitrogenous base adenine.

That’s not to say that there wouldn’t be difficulties in bringing this RNA world about. RNA is composed of RNA nucleotides, and these nucleotides are much more complex than the amino acids that Stanley Miller was able to synthesize in his spark chamber experiments. That makes the likelihood of their spontaneous emergence low. And, as the video you just watched acknowledged, polymerization of RNA nucleotides (even under the best laboratory conditions) is difficult. So the challenge for scientists working on the origin of life is finding a pathway from abiotically emerging monomers to self-reproducing RNAs, to LUCA, with every step along the way being gradual enough so as not to appear miraculous. The RNA world might be a step along that path, but many steps are needed to get to the RNA world, and to get from the RNA world to the world of cells.

Take the following quiz about the RNA world. Then we’ll look at the formation of cells, and then return to the alkaline hydrothermal vents where life may have first emerged.

3. The RNA World: Checking Understanding

[qwiz random = “false” qrecord_id=”sciencemusicvideosMeister1961-RNA World, Checking Understanding”]

[h]The RNA World

[i]An origin of life haiku

An RNA world

Could these self replicating

molecules evolve?

[q] DNA can only serve as an organism’s [hangman]. RNA, by contrast, can play DNA’s role, and also serve as [hangman]. Additional hint: think of two rhyming terms associated with genetics.

[c] genotype

[f] Great!

[c] phenotype

[f] Great!

[q] A conundrum associated with figuring out the origins of heredity is that DNA requires   [hangman]  in order to be replicated, but these proteins only exist because they’re coded for by [hangman].

[c] proteins

[f] Excellent!

[c] DNA

[f] Great!

[q] Whereas the sugar in DNA is  [hangman]  the sugar in RNA is[hangman].

[c] deoxyribose

[f] Great!

[c] ribose

[f] Correct!

[q] Which of the nucleotides below is found in DNA?

[textentry single_char=”true”]

[c*] B

[f] Excellent! “B” is a deoxyribonucleotide. It contains deoxyribose, the sugar in DNA.

[c] A

[f] No. “A” is a dideoxynucleotide. It’s been doubly deoxygenated. Find the molecule that’s a deoxynucleotide (deoxygenated in comparison to ribose).

[c] *

[f] No. DNA’s name (“deoxyribonucleic acid”) is a hint. Find a molecule with a sugar that, compare to ribose, has a single lost oxygen

[q] Which of the nucleotides below is found in RNA?

[textentry single_char=”true”]

[c*] C

[f] Excellent! “C” is a ribonucleotide. It contains ribose, the sugar in RNA.

[c] A

[f] No. “A” is a dideoxynucleotide. It’s been doubly deoxygenated. Find the molecule that’s a deoxynucleotide (deoxygenated in comparison to ribose).

[c] B

[f] No. “B” is a deoxynucleotide. It contains deoxyribose, the sugar in DNA.

[c] *

[f] No, that’s not correct.

[q] Three of the nitrogenous bases in DNA and RNA are the same, but there’s one difference. Whereas DNA uses the base [hangman] , RNA uses the base[hangman].

[c] Thymine

[f] Good!

[c] uracil

[f] Great!

[q] In both DNA and RNA, the bonds between complementary nucleotides are [hangman] bonds. But while DNA is always  [hangman] stranded, RNA is [hangman] stranded. 

[c] hydrogen

[f] Great!

[c] double

[f] Correct!

[c] single

[f] Good!

[q] A general name for any RNA molecule with catalytic properties is a   [hangman] .

[c] ribozyme

[f] Great!

[q] The ribozyme that carries out RNA editing shown in step “F” below is called a   [hangman]. Additional hint: the answer is derived from what’s become an obsolete move in editing film (back when it was film) or audotape (back when it was tape)
.

[c] spliceosome

[f] Good!

[q] A ribozyme that you’ve come to know well in your studies of biology (perhaps without knowing that it was a ribozyme) is shown a “2” below. It’s a [hangman].

[c] ribosome

[f] Excellent!

[q] Infectious, single-stranded particles of RNA that parasitize plants are called  [hangman] . Some biologists think that these are vestiges of the RNA [hangman] 

[c] viroids

[f] Great!

[c] world

[f] Excellent!

[q] If the RNA world ever existed, it would have been before [hangman] , the organism that’s at the base of the tree of life.

[c] LUCA

[f] Correct!

[q] For RNAs in the RNA world to be able to evolve, reproduction would have to be accompanied by  [hangman] , creating the variation that makes natural [hangman]possible.

[c] mutation

[f] Correct!

[c] selection

[f] Correct!

[q] In the diagram below, which letter would represent abiotically formed RNA nucleotides?

[textentry single_char=”true”]

[c*] a

[f] Excellent. Letter “a” represents abiotically formed RNA nucleotides.

[c] Enter word

[f] No.

[c] *

[f] No. Look for a monomer that could serve to build up the RNA (a polymer) that is the star player in this diagram.

[q] In the diagram below, which letter would represent the formation of randomly sequenced RNA molecules that have emerged through formation of sugar phosphate bonds between free RNA nucleotides?

[textentry single_char=”true”]

[c*] b

[f] Excellent. Letter “b” represents abiotically formed RNA. There was no template determining the sequence of the RNA nucleotides, so that sequence can be throught of as random.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Look for RNA molecules that seem to have formed without a template.

[q] In the diagram below, which letter represents template driven RNA synthesis?

[textentry single_char=”true”]

[c*] c

[f] Nice. Letter “c” represents RNA molecules that are being replicated based on a preexisting template.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Look for RNA molecules that seem to be forming from other RNA molecules.

[q] If letter “e” represents an amino acid, then which letter below represents the first protein that would have emerged?

[textentry single_char=”true”]

[c*] f

[f] Nice. Letter “f” represents amino acids that have, through the action of RNA, been polymerized into a protein.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Look for a molecule that would be a polymer of an amino acid (shown at “e”).

[q] At some point in the early evolution of life, RNA would have started coding for protein, a process known as translation. In the scenario proposed below, translation would have emerged before DNA, RNA, and protein became encapsulated into cells. Which letter shows translation first emerging.

[textentry single_char=”true”]

[c*] i

[f] Nice. Letter “i” represents translation in a cell-free system.

[c] m

[f] No quite. Letter “m” is translation, but it’s inside a cell. 

[c] *

[f] No. Look for an arrow that represents RNA that’s being translated into protein, but outside of a cell.

[q] At some point in the evolution of life, DNA would have taken over from RNA as the molecule of heredity. In some viruses, genetic RNA is converted into DNA through a process called reverse transcription. Which arrow represents that process?

[textentry single_char=”true”]

[c*] h

[f] Nice. Letter “h” represents reverse transcription of DNA from RNA.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Look for a DNA that’s being created based on information flowing to it from RNA. That’s reverse transcription.

[q] Once DNA emerged as the molecule of heredity, the process of DNA being transcribed into RNA would become a key process in the life of every cell. Which letter represents transcription?

[textentry single_char=”true”]

[c*] l

[f] Nice. Letter “l” represents transcription of RNA from DNA.

[c] h

[f] No. Letter “h” represents reverse transcription, not transcription.

[c] *

[f] No. Look for an arrow that indicates that information from DNA is flowing to RNA.

[x]

[restart]

[/qwiz]

4. Encapsulation: Forming Membranes and the First Cells

To encapsulate means “to enclose within.” Of all the the steps leading up to the origin of the first cells, the step of encapsulating an emerging living system within a membrane seems to be one of the most straightforward. The following video from Stated Clearly does a great job explaining how abiotically generated fatty acids could self organize to form micelles and then liposomes:  fluid-filled spheres surrounded by a lipid bilayer.

A key point that I hope you noted was that heredity, metabolism, and membranes could have all arisen at the same time, with advances in each feature promoting advances in other features.

In the quiz that follows, I threw in some concepts relating to membrane structure, which you probably learned earlier in your biology course. If you want to review, here’s a link to my tutorial about phospholipids and membrane structure (which has everything you need to know for the quiz)

5. Encapsulation, Forming Membranes Quiz

[qwiz random = “true” qrecord_id=”sciencemusicvideosMeister1961-Encapsulation, Forming Membranes”] [h]

Encapsulation: The Origin of Membranes

[i]

[q] The diagram below shows three representations of a fatty acid. The part that is attracted to water is at number

[textentry single_char=”true”]

[c*] 2

[f] Yes. Region 2 is a carboxylic acid functional group, and it has polar and hydrophilic properties that cause it to be attracted to water.

[c] Enter word

[f] Sorry, that’s not correct.

[c] *

[f] No. Region “1” is a big hydrocarbon chain. This part of the molecule would be hydrophobic (repelled by water).

[q] The molecule shown below (in three different representations) is a [hangman] acid.

[c]fatty

[f] Great!

[q] To answer the question below, think about what you’ve already learned about cell membranes and lipid bilayer. In terms of interactions with water, part 2 of the molecule below can be described as[hangman].

[c] hydrophilic

[f] Great!

[q]To answer the question below, think about what you’ve already learned about cell membranes and lipid bilayers. In terms of interactions with water, part 1 of the molecule below can be described as [hangman].

[c] hydrophobic

[f] Great!

[q] According to the video, fatty acids can form [hangman] in environments that have mineral  [hangman], and raw materials such as [hangman] monoxide and hydrogen.


[c] abiotically

[f] Great!

[c] catalysts

[f] Great!

[c] carbon

[f] Good!

[q multiple_choice=”true”] The structure shown below is a

[c] cell

[f] No. This structure spontaneously emerges when molecules like fatty acids interact with one another in a watery environment.

[c] lipid bilayer

[f] No. To be a bilayer, you have to have TWO layers. Here there’s only one.

[c*] micelle

[f] Nice job! The structure shown is a micelle.

[q] The structure shown below contains a lipid [hangman]

[c] bilayer

[f] Correct!

[q] The structure shown below is called a [hangman]

[c] liposome

[f] Correct!

[q multiple_choice=”true”] Structures like the one shown below

[c] result from dehydration synthesis reactions.

[f] No. That’s how enzymes construct polymers from monomers. What’s happening here results from the properties of the molecules shown, their interactions with each other, and their interactions with water.

[c] result from enzymes that evolved to place each molecule in a specific position.

[f] No. What’s happening here results from the properties of the molecules shown, their interactions with each other, and their interactions with water.

[c*] result as an emergent property of the molecules they’re made of, the way they interact with each other, and how they interact with water.

[f] Nice job! That’s how structures like the one shown emerge.

[q multiple_choice=”true”] The video describes a sequence in which the first membrane-like structures emerge. Which of the following best summarizes this process?

[c] micelles disaggregate into bilayered cell-like structures, each of which has an outer membrane with a bilayered structure

[f] No. While he micelles can form into bilayered membranes, they don’t do so through “disaggregation,” which would have the opposite effect.

[c*] fatty acids form micelles, which aggregate to form lipid skins, which fold in upon themselves to form fluid filled spheres with bilayered membanes.

[f] Exactly. The key point o the video is a sequence where fatty acids interact to form micelles, which interact to form lipid “skins,” which can fold in upon themselves to form fluid filled spheres with bilayer exteriors.

[c] bilayered protocells first form as other protocells with bilayered membranes stretch until their membranes touch, giving rise to new protocells, kickstarting evolution.

[f] No. Once such a system has started, it could keep going through a mechanism like the one described above. But how did the first protocells emerge?

[c] fatty acids spontaneously emerge as micelles from the primordial soup. These micelles evolve into the first cells, kickstarting evolution.

[f] No. That sounds like the kind of miraculous explanation that we’ve been trying to avoid.

[q] The diagram below shows a molecule called a  [hangman]. This molecule is composed of two [hangman] acids connected to a glycerol and a phosphate. At some point in the course of evolution, the molecule below became the key component of [hangman] in all organisms in domains eukarya and bacteria.
[c]phospholipid

[c]fatty

[c]membranes

[x][restart]

[/qwiz]

5. Origins of Life’s Chemiosmotic Metabolism

Life on Earth is based on protons flowing across membranes. If you’ve studied cellular respiration, then you know that almost all the ATP created in cellular respiration is made as protons diffuse across the ATP synthase channel of the mitochondrial inner membrane. In photosynthesis, during the light reactions, there’s a parallel flow of protons across the thylakoid membrane, through ATP synthase, and this flow creates ATP that provides the energy that makes reduction of carbon dioxide to carbohydrate possible.

Proton flow, is in turn, based upon electron flow. Photosynthesizers (mostly plants and cyanobacteria) convert light energy into a flow of electrons. The energy from that flow is used to pump protons into the thylakoid spaces in thylakoid sacs. Then the protons diffuse out through ATP synthase, generating ATP. In mitochondria, a flow of electrons from food molecules is used to pump protons into the mitochondrial intermembrane space. Then, just in photosynthesis, the protons flow out through ATP synthase, generating ATP.

So, assuming that life emerged not at the Earth’s sunlight surface, but deep in the ocean depths, how could ATP-creating proton gradients have evolved? Let’s review what’s happening in these vents about 3.8 bya.  Because of serpentinisation at alkaline hydrothermal vents, hydrogen gas was bubbling into carbon dioxide-rich seawater. With the help of iron-sulfur catalysts, the hydrogen and carbon dioxide combined into methane. Further catalytic action created monomers, which then became concentrated in the tiny, cell-sized pores within the vents. This concentration of monomers made it easier for inorganic catalysts to combine these monomers into polymers.

The image above left shows one of these tiny pores, with a cell shown on the right for comparison. Alkaline fluids, created during the process of serpentinisation in the rocks below the vents (notice the “Low [H]” label below the green inorganic vesicle on the left) would have flowed into these pores. This would have create a natural proton gradient between the acidic seawater outside the vents and the alkaline fluid inside the vents. That proton gradient is parallel to the one that cells today have to create by electron flows powered by food or sunlight. But in the vents, the gradient was there for free. Protons would flow “downhill” from outside the rocky vesicles to inside. This flow, if captured, could power the creation of phosphorylated compounds, forerunners of ATP. These compounds, in turn, could provide the chemical energy to power the creation of RNA polymers, leading to the RNA world…

Here’s a quote from biochemist Nick Lane, author of Life Ascending, which is one of my favorite biology books.

The last common ancestor of all life was not a free-living cell at all, but a porous rock riddled with bubbly iron-sulphur membranes that catalysed primordial biochemical reactions. Powered by hydrogen and proton gradients, this natural flow reactor filled up with organic chemicals, giving rise to proto-life that eventually broke out as the first living cells – not once but twice, giving rise to the bacteria and the archaea. (Nick Lane, The Cradle of Life: New Scientist, 17, October, 2009).

There are some big gaps in this account. One gap is the emergence of ATP synthase, a complex molecular machine with a spinning rotor and multiple interdependent parts. Origin of life researchers will have to continue their work to create a credible account of how this machine (shown at left in its mitochondrial form) could have arisen in a step-by-step manner (that doesn’t seem miraculous).

6. Returning to Undersea Alkaline Hydrothermal Vents: A second viewing of the Origin of Life Video (the whole thing)

Let’s return to the vents. Please watch the entire video by William Martin and Mike Russell that explains the emergence of life at alkaline hydrothermal vents. If you feel like it’s too much review (and you remember the first three minutes), then you can manually jump to 3:10.

Unfortunately, the idea of chemiosmosis at the vents isn’t portrayed or mentioned, even though it’s an essential part of the story. If you want to take a deeper dive into this material, you can read articles by Russell, Martin, and some of their collaborators (including Deborah Kelley, who discovered alkaline hydrothermal vents in 2000), at this link. A much more accessible article written by Nick Lane can be found here.

And that is as far as we’re going to go in this introductory account of life’s emergence. If you’re like me, this module is leaving you with some big questions, which I encourage you to explore. Here are just three. If you have the time and the inclination, please follow some of the suggested links if you’re interested in seeing how this work is progressing. All links open new tabs (and, please beware, some of this is very dense reading).

  1. How did the genetic code arise? See articles by Keeling, or Koonin and Novoshilov.
  2. How did the system of protein translation from mRNA evolve? See articles by Noller, or Petrov et.al.
  3. How and when did DNA take over from RNA? See Forterre et. al

7. Origins of Life: Cumulative Quiz

Let’s consolidate what we’ve learned with the following quiz. It includes information from the entire module.

[qwiz random = “false” qrecord_id=”sciencemusicvideosMeister1961-Origin of Life, Cumulative Quiz”]

[h]Origin of Life: Cumulative Quiz

[i]

[q labels = “top”]Describe the traits of LUCA.

  1. _________ celled ___________
  2. Genetic information was encoded in _____.
  3. Genes were transcribed into ______, which was translated into ________ composed of 20 ____________.
  4. Used the universal genetic code, with 64 __________.
  5. Translation was catalyzed by__________.
  6. Metabolism created _________ to power cellular work.
  7. Entire cell was surrounded by a lipid ___________.
  8. Created ATP by _____________.

[l]amino acids

[f*] Correct!

[fx] No. Please try again.

[l]ATP

[f*] Excellent!

[fx] No, that’s not correct. Please try again.

[l]chemiosmosis

[f*] Great!

[fx] No, that’s not correct. Please try again.

[l]codons

[f*] Excellent!

[fx] No. Please try again.

[l]DNA

[f*] Excellent!

[fx] No. Please try again.

[l]membrane

[f*] Excellent!

[fx] No, that’s not correct. Please try again.

[l]prokaryote

[f*] Correct!

[fx] No. Please try again.

[l]proteins

[f*] Excellent!

[fx] No, that’s not correct. Please try again.

[l]ribosomes

[f*] Good!

[fx] No, that’s not correct. Please try again.

[l]RNA

[f*] Great!

[fx] No. Please try again.

[l]Single

[f*] Good!

[fx] No. Please try again.

[q] Despite what’s commonly taught about the universality of this type of molecule for making up the lipid bilayer of membranes, LUCA’s membrane was probably NOT composed of [hangman] . That’s because one of the three domains of life, the [hangman], build their membranes out of different lipids. The diagram below might help you figure this out.

[c] phospholipids
[c]archaea

[f] Correct!

[q multiple_choice=”true”] Which of the following dates is most likely for the origin of life?

[c] 4.6 bya

[f] No.That’s way too early. That’s when the Earth was first forming.

[c] 4.1 bya

[f] No. That’s during the period of heavy bombardment. Any emerging life probably would have been destroyed by incoming meteors and comets.

[c*] 3.8 bya

[f] Excellent! You’ve chosen a date that’s between the end of the period of heavy bombardment, and before the date for the earliest fossilized life. Life clearly had to emerge somewhere in between.

[c] 3.5 bya

[f] No. As shown by fossilized stromatolites and associated microfossils from that time period, life was already well established by 3.5 bya. Choose an earlier time period.

[q] Dating of ancient structures like fossilized stromatolites is done through a method that involves measuring the decay of radioactive [hangman] of certain elements, a method known as [hangman] dating.

[c] isotopes

[c] radiometric

[q] Stanley Miller’s experiments were significant because he successfully synthesized  [hangman] acids in a simulation of the Earth’s early atmosphere.

[c] amino

[q] During the Hadean/Archaean periods when life was first emerging, the Earth was very different from today’s Earth. The sun was [hangman]; the [hangman] was closer, causing enormous [hangman]. The atmosphere lacked the gas [hangman]. The Earth was in the period of heavy bombardment, and suffered frequent impacts from [hangman] and comets.
[c] dimmer

[c] moon

[c] tides

[c] oxygen

[c] meteors

[q]Alkaline [hangman] vents, which release[hangman]gas into the environment, might have provided an environment conducive to the evolution of life.
[c] hydrothermal

[c] hydrogen

[q]Darwin speculated that life arose in a warm little  [hangman]. That’s unlikely for several reasons, one of which being that the Earth was covered by a huge [hangman], leaving very little land. In addition, constant bombardment by comets and [hangman] would have created a very hostile environment on Earth’s surface.

x

[c] Pond

[c] ocean

[c]meteors

[q]Black smoker vents are unlikely candidates for life’s emergence because the water that’s emerging from them is extremely [hangman].

[c] hot

[q]At alkaline hydrothermal vents, a process called serpentinisation results in the formation of vent fluids that are, in terms of pH, [hangman]. The same process causes the emergence of [hangman] gas. When this gas combined with carbon dioxide, it could have formed the simple hydrocarbon [hangman], which is a highly reduced compound that could serve as a source of matter and energy for building the first [hangman], the building blocks of polymers.

[c] basic

[c] hydrogen

[c]methane
[c]monomers

[q]The first membrane-bound cells might have formed as accumulation of [hangman] acids led to the formation of micelles. These micelles would aggregate together, forming fluid filled spheres, the outer “skin” of which was a lipid [hangman].
[c]fatty
[c]bilayer

[q]It’s possible that LUCA was not a membrane-bound cell, but rather population of vesicles in a porous [hangman], surviving off of flows of [hangman ] gas, and using the proton powered flow called [hangman] to power its metabolism.

[c]rock

[c]hydrogen

[c]chemiosmosis

[q] If “c” in the diagram below represents RNA, then ribonucleotides would be represented by

[textentry single_char=”true”]

[c*]B

[f] Nice. Letter “b” represents the monomers that make up RNA, which are ribonucleotides.

[c] word

[f] No.

[c] *

[f] No. Look for monomers which, if strung together, could create an RNA polymer (at “C”).

[q] In the diagram below, the only letter that could possibly represent a ribozyme would be

[textentry single_char=”true”]

[c*]D

[f] Nice. Letter “d” shows RNA that’s folded into a more complex 3-D shape, and that’s how a ribozyme would form (though in this representation, the shape is very simple).

[c] word

[f] No.

[c] *

[f] No. Look for an RNA polymer that’s folding into a more complex shape.

[q] In the diagram below, if “b” represented a ribonucleotide, then what letter could represent ribose?

[textentry single_char=”true”]

[c*]a

[f] Nice. Letter “a” shows something that goes into an RNA nucleotide, and ribose could be that something.

[c] word

[f] No.

[c] *

[f] No. Look for something that would be a component of the ribonucleotides indicated by letter “b.”

[q multiple_choice=”true”] In terms of bringing about the RNA world, which of the following steps is the one that has the most experimental evidence?

[c] From A to B

[f] No. Letter “a” to letter “b” shows (very schematically) the components of RNA (ribose, nitrogenous bases, and phosphates) coming together to form a ribonucleotide. That’s been difficult to bring about in the laboratory.

[c] From B to C

[f] No. Forming the “backbone” of RNA is not something that’s been easy to bring about in the the lab.

[c*] From C to D

[f] Excellent! Once RNA molecules have formed, it’s not hard to get them to fold up into a specific 3-D shape.

[q] In the diagram below, lipids would play a key role in which step?

[textentry single_char=”true”]

[c*]f

[f] Nice. Letter “f” shows RNA encapsulated within what looks like a cell. The membrane of that cell would be some kind of lipid.

[c] word

[f] No.

[c] *

[f] No. Remember that a cell membrane is composed of a lipid bilayer. Where do you see lipids?

[q] Fossilized cells like the ones below are found in remnants of layered bacterial mats called [hangman].

[c] stromatolites

[f] Great!

[q] According to NASA, life is a self-______________ chemical system capable of Darwinian evolution.

[hangman]

[c] sustaining

[f] Great!

[q]Isotope M has a half life of 5000 years, during which it decays into isotope N. You’re studying a sample of material that has a relative proportion of 25% M and 75% N. How old is this material?

[c] 5000 years old.

[f] No. 5000 years is one half life, during which time you’d expect half of M to decay into N, for a 50/50 ratio.

[c] 750 years.

[f] No. Here’s how to think about this. 5000 years is one half life, during which time you’d expect half of M to decay into N, for a 50/50 ratio. Based on the question, find the number of half lives, and multiply that by the duration of a half life.

[c*] 10,000 years old

[f] Excellent. If only 25% of the original material is left, then two half lives have passed, for a total of 10,000 years.

[x]

[restart]

[/qwiz]

EPILOGUE: Nick Lane’s Ten Steps to Life on Earth

Nick Lane is a British biochemist whose work has been referenced several times in this module. He has done an amazing job popularizing the most recent advances related to the origins of life. He’s been enormously influential in shaping my own understanding of living systems, and that, in turn, had deeply influenced my teaching.

Here are are his Ten Steps to the Origin of Life (taken verbatim from an article he wrote in NewScientist | 17 October 2009). 

If life did evolve in alkaline hydrothermal vents, it might have happened something like this:

1. Water percolated down into newly formed rock under the sea floor, where it reacted with minerals such as olivine, producing a hot alkaline fluid rich in hydrogen, sulphides and other chemicals. This hot fluid welled up at hydrothermal vents.

2. The early ocean was acidic and rich in dissolved iron. When upwelling hydrothermal fluids reacted with this seawater, they produced carbonate rocks riddled with tiny pores and a “foam” of iron-sulphur bubbles.

3. Inside the bubbles, hydrogen reacted with carbon dioxide to form simple organic molecules such as methane, formate and acetate. Some of these reactions were catalysed by the iron-sulphur minerals, which are still found at the heart of many proteins today.

4. The electrochemical gradient between the alkaline vent fluid and the acidic seawater leads to the spontaneous formation of acetyl phosphate and pyrophosphate, which act just like ATP, the chemical that powers living cells. These molecules drove the formation of amino acids and nucleotides, the building blocks of proteins and of RNA and DNA respectively.

5. Thermal currents within the vent pores concentrated large molecules like nucleotides, driving the formation of RNA and DNA – and providing an ideal setting for an RNA world and its evolution into the world of DNA and proteins. Evolution got under way, with sets of molecules capable of producing more of themselves starting to dominate.

6. Fatty molecules coated the iron-sulphur froth and spontaneously formed cell-like bubbles. Some of these bubbles would have enclosed self-replicating sets of molecules – the first organic cells. The earliest protocells may have been elusive entities, though, often dissolving and reforming as they circulated in the vents.

7. The evolution of an enzyme called pyrophosphatase, which catalyses the production of pyrophosphate, allows protocells to extract more energy from the gradient between the alkaline vent fluid and the acidic ocean. This enzyme is still found in many bacteria and archaea.

8. Some protocells start using ATP as well as acetyl phosphate and pyrophosphate. The production of ATP using energy from the electrochemical gradient is perfected with the evolution of the enzyme ATP synthase, found within all life today.

9. Protocells further from the main vent axis, where the natural electrochemical gradient is weaker, started to generate their own gradient to drive ATP production.

10. Once protocells could generate their own electrochemical gradient, they were no longer tied to the vents. Cells left the vents on two separate occasions, with one exodus giving rise to bacteria and the other to archaea.

What Now?

This tutorial ends this unit on the origin of life.