Lec 8 Flashcards
What is life?
There are numerous definitions, some of which include organisms that other definitions consider not to be living
How long has life existed on earth?
Earliest microfossils are ~3.2-3.4 billion years old
These are likely to be fossilized creatures with cell-like walls
Living things - Definition 1
Any form that is able to grow and reproduce
CAVEAT:
-Non-living things like some minerals (crystal dendrites) are able to grow and reproduce
Living things - Definition 2
Any form that can store, transmit and express information
CAVEAT:
-Computer systems store, transmit and express information
Living things - Definition 3
Any form that is able to descend with modification
CAVEAT:
-This would include things like prions and viruses and it would not include sterile individuals like worker bees
Combined definition of living things
A living thing is any form that is able to store information, and can express this information to grow and reproduce, and can self-replicate (with the exception of sterile individuals) producing descent with modifiation
Other qualities: Metabolism, organization, self-regulation
Properties of life
Homeostasis: Ability to adjust the internal environment to maintain stable equilibrium
Structural organization: Maintain distinct parts and connections between them
Metabolism: Control chemical reactions
Growth and reproduction
Response to environmental conditions or stimuli
Respond to and evolve by natural selection
Origin of life and Natural Selection
As biologists, we are not just interested in self-replication
We also need heritable variation that leads to fitness differences
How do we study the origin of life?
We can’t use phylogenetic reconstructions, because we are looking at the original common ancestor - also known as the last universal common ancestor (LUCA)
Anything else that arose before or simultaneously left no descendants, so we can’t reconstruct origins any further back
Our goal then is to try and understand how life could have arose from the simplest molecules present on primordial earth
Big questions on the origin of life
Where do organic molecules come from?
How did complex organic reactions originate?
How did the building blocks of life assemble together?
What is the origin of information storage systems?
Abiogenesis
The emergence of life from a non-living precursor
Abiogenesis is NOT part of the Theory of Evolution
There is no full-fleshed Theory of Abiogenesis, only a collection of hypotheses
Abiogenesis requires 3 steps:
1) The origin of biological monomers
2) The origin of biological polymers
3) The evolution from molecules to cells
Where do the building blocks of life come from?
The origin of organic molecules is one of the main challenges of abiogenesis
During the last few decades several experiments have been conducted and many hypotheses have been proposed
There is no general agreement on how the first organic molecules came about
What is a plausible progression of early life?
Warm water (oceans were warmer 3 billion years ago)
Lightening, UV light, volcanic eruptions, and cosmic rays could convert atmospheric gases into molecules
Leads to a “prebiotic soup” of organic molecules in water
Eventually lipids, amino acids, and nucleotides could arise
These ultimately form a “protocell” - a self-replicating unit
Soup hypothesis (Oparin-Haldane model)
The early Earth had a chemically reducing atmosphere and ocean
Inorganic chemicals exposed to energy from lightening and volcanic eruptions produced simple organic compounds
These compounds accumulated in a “soup”
Further transformation developed more complex organic polymers and life
Miller-Urey experiment: Organic Soup Recipe
Miller and urey combined methane (CH4), ammonia (NH3), hydrogen (H2), and water (H2O) with a continuous electric current, to stimulate lightning storms believed to be common on the early earth
At the end of one week 10-15% of the carbon was in the form of organic compounds
2% of the carbon had formed 5 of the amino acids that are found in proteins
Pre-biotic conditions can result in the formation of the basic small molecules of life
Miller-Urey part II
The original vials of Miller’s experiments have been recently re-analyzed
Miller constructed 2 variations of the original apparatus - one used a spark generator and the second injected steam onto the sparks
The steam replicates what might have existed in tidal pools around volcanoes
Modern techniques revealed small amounts of 9 additional amino acids in the samples of the original apparatus
In the residues from the apparatus with the steam injector, 22 amino acids were detected, including 10 never before been identified from the original experiment
Primordial soup is a plausible explanation for the origin of organic molecules
Big questions about the origin of life do NOT include
Origin of inorganic molecules
Extraterrestrial origins
Hypothesized that organic compounds came from meteors
Early earth was showered with meteorites, comets, and interstellar ices
Complex organic compounds are found in meteorites and planetary dust
These include lipids, amino acids (90 in the Murchison meteor) and nitrogenous bases
Also amphiphilic molecules that self-assemble into vesicles (fluid-filled spaces enclosed by lipid membrane)
Deep sea vents
Favored hypothesis for origin of life
Organic compounds may form at hydrothermal vents - sulfide-rich compounds from vents mixes with CO2-rich ocean water
Alkaline vents have more moderate temperatures and porous carbonate construction
Chemical energy derives from redox reactions - electron donors (H2) react with electron acceptors CO2 producing CH4
How do simple molecules form more complex structures? The clay layer hypothesis
Chemical reactions needed to form complex organic molecules are sped up on solid surfaces
RNA chains and complex amino acid structures can self-assemble on minerals
Microscopic spaces between clay layers and ice crystals may concentrate reagents
The evolution of protocells
The studies we have discussed provide plausible mechanisms for the origin of organic molecules
-Primordial soup, deep sea vents, meteors, lay layers
We still need to understand how these complex organic molecules self-assembled into the next step towards life: Replicating vesicles
Cell is composed of lipid bilayer in aqueous solution
Lipid membranes
Early membranes would have had simple structure
Single-chain fatty acids can spontaneously form bilayers and enclosed vesicles
Vesicles can grow as they incorporate micelles (small assemblages of fatty acid molecules)
-Vesicles = aqueous balls
Transport across lipid membranes
Molecules can be easily transported across these membranes by lipid molecules that flip from inner to outer membrane at high rates
Suggests a mechanism for moving waste and nutrients in and out of simple vesicles
Lipid molecules flip and move structures across layer
Division of simple vesicles
Vesicles with multiple bilayers form spontaneously
As more micelles added, extrusions form
Vesicle will form thin, unstable strand
Strand breaks into daughter vesicles
Natural selection on vesicles
When phospholipids are experimentally introduced, they slowed down rate at which fatty acid molecules moved out of bilayer
This made phospholipid vesicles grow in size
-Addition of phospholipids makes them GROW in size
Identifies mechanism of selection on cell size and stability - incorporation of more phospholipids into membrane
Our cells are surrounded by a phospholipid bilayer
Hypercycles: Molecular mutualisms
If 2 or more molecular substrates contribute to the replication of the others, this is a molecular mutualism
-If A contributes to replication of B and B contributes to replication of A, it is a MOLECULAR MUTUALISM (both benefit)
May be important to the rise of replication in enclosed cells
Imagine 4 independent replicators, A, B, C, and D
A, B, C and D all replicate themselves in a closed loop
MOLECULAR MUTUALISM:
- B replicated more of itself when there is lots of A, and C replicated more when B is around, etc.
- However, in an open system, the benefits diffuse away - A doesn’t benefit that much from the presence of B
Imagine a change occurs to A where it sacrifices a bit of its own replication to increase the replication of B even more. Would this be favored in an open system?
NO, because this does NOT benefit A at all
Imagine our hypercycle is inside an enclosed membrane. Would A benefit from sacrificing some of itself to B?
YES
In this scenario, all the benefits A confers to B come back to it through a closed loop
Further, if all replicators are inside a membrane, then they have become a single “organism” - anything that accelerates the replication of the whole organisms will be favored
Costs vs. Benefits of membrane enclosure
COSTS: Transport of resources across membranes, building a membrane requires resources that could be used for other purposes
BENEFITS: control of internal environment, create chemical gradients to let in/exclude certain chemicals, use cell membrane as defense, partition functions efficiently
If the total benefits outweigh costs, we could see simple cells arise in this manner
-We can see this as a way for cells to arise assuming benefits>costs
Why would molecular mutualisms be favored in a closed system?
Any initial sacrifice in fitness by replicator A is regained
A chicken and egg problem of the origin of life
DNA and RNA contain the blueprints to make proteins
However, they need proteins to replicate and transcribe DNA into RNA
So which came first - nucleic acids or proteins?
RNA World
Scientists have proposed that RNA may have played roles in early life: information carrier and enzymatic molecules
RNA is now part of a complex cellular organization, but may have served both information storage and enzymatic functions in early cells
Suggests that RNA formed on mars and got to earth; best collections survived, worst died out
RNA can store information like DNA and catalyze reactions like a protein
Ribozymes are RNA molecules formed into specific shapes that catalyze biochemical reactions
Ribozymes - History
Thomas R. Cech and Sidney Altman won the Nobel Prize in chemistry for their discovery of catalytic properties of RNA in the early 1980s
Ribozymes are less stable than protein enzymes, but many existing ribozymes have been documented
Experiments have found that ribozymes can catalyze their own synthesis and can build nucleotides
Evidence for the RNA world hypothesis
Many present-day protein-based enzymes have co-factors necessary for function that are RNA nucleotides (or based on RNA nucleotides)
The deoxyribonucleotides in DNA are constructed by first building a ribonucleotide (used in RNA0, and then removing a hydroxyl group
Lab work shows that all the essential components of RNA were likely present in early earth
Ribosomes (rRNA), tRNAs, and eukaryotic spliceosomes are basically complex ribozymes
These are RNA molecules that catalyze reactions that are essential for all life forms to function
The crucial role of RNA in core cellular pathways suggest conserved processes from a long-ago RNA world
Conserved process = ancestral process
Experimental evidence for the origin of natural selection on RNA
In the 1970s Siegelman and colleagues put a 4000-bp strand of RNA into a test tube
Added more nucleotides and the replicase enzyme
Heated and incubated, and then moved a small droplet to a new test tube
The new test tube contained the replicase enzyme and free-floating nucleotides, but no primer strand of RNA
-Primer strand is necessary for replication
Repeated transfer 75 times
What did they find?
RNA was copied in each tube - that was expected
The replicase enzyme made errors, thus creating new “mutant” RNA strands different from the original 4000-bp sequence
This generated VARIATION in RNA types
The replicase enzyme just copies whatever strands are present, so this variation was heritable
Shorter strands replicated faster, but the error rate for very short (<100bp) strands was very high
What would you expect to happen to the length of RNA strands over the course of the experiment?
Converge on an intermediate strand length
What did they find?
At the end of the experiment, the RNA strands were about 200 nucleotides - small enough to replicate quickly, but not so small that they accumulated lots of errors
-Converged on good INTERMEDIATE length without a lot of errors and small enough to replicate quickly
This demonstrates natural selection on RNA strands
A follow-up experiment added a chemical that inhibits replication by replicase
Within a few hours, variants arose that could replicate successfully and more rapidly in the presence of the chemical
Strands that are short more likely to produce short strands (likewise for long)
Lon strands replicate slowly, short strands accumulate a lot of errors
How could RNA replication originate?
Experiments have shown that RNA can catalyze reactions involved in its own assembly using a ribozyme that acts as both a template and an enzyme catalyzing a reaction
-Ribozymes store information and catalyze reactions
Ribozymes can also evolve and become more efficient at catalyzing reactions
Any transmission system more efficient than RNA should be favored
Deoxyribose sugar is chemically more stable than ribose
Double-stranded structure is less vulnerable to disruption from outside molecules
DNA replication has better “proofreading” than RNA replication
Reverse complementary strands mean better repair mechanisms
DNA maintains integrity of information that’s being storesd
Consequences of using DNA for information storage
Greater molecular stability + better repair mechanisms = lower mutation rates -> DNA molecules can be bigger -> DNA can store more information (have more gene)
Having DNA store information also frees up RNA to be used in other cell functions (like a messenger system), and proteins can perform enzymatic functions
Increasing division of labor in a cell
Move from having one molecule (RNA) doing EVERYTHING with a lot of mistakes and doing things not very well to highly specialized systems for specific tasks
Where did DNA come from?
We still don’t know
Formaldehyde might play a role in converting RNA to DNA
Experiments are testing whether DNA can also act as a catalyst
This is an area of active research
Which is NOT a benefit of DNA compared to RNA as an information storage system?
It is shorter and therefore replicates faster
Evolution of complex cells
All the early cells we have been talking about are very simple - how did complex cells with modular functions arise?
-Modular functions = specializations
Natural selection favors cells better able to survive and reproduce
Horizontal gene transfer has been hypothesized to be very important to early cell evolution
Horizontal gene transfer
Exchange of genetic material between cells
NOT through mitosis (vertical gene transfer)
1) Bacterial cell encounters free DNA in the environment
2) Cell takes in some of DNA fragments
3) Some of the new DNA fragments are incorporated into the chromosome by recombination
Horizontal gene transfer: Conjugation
1) Donor produces a conjugative pilus that attaches to recipient cell
2) Pilus contracts, bringing cells together. A conjugative junction forms between the cells
3) A copy of the plasmid is passed into the recipient cell
4) Cells detach. Recipient now has a copy of the plasmid
Pilus acts as a bridge between cells, pulls them closer together so they can recombine
Horizontal gene transfer: Transduction
1) Phage attaches to bacterial host and injects its DNA
2) Cell produces new phage components
3) Host DNA is mistakenly packaged into some viral capsids
4) Cell bursts, releasing phage particles
5) Phage carrying host DNA injects that DNA into a new bacterial host
6) Transduced DNA is incorporated into the new host’s genome by recombination
Why would horizontal transfer be important to early cells?
Early cells would be simple and not have well-integrated metabolic processes
Exchanging materials with other cells might be the primary way that copies of genes were propagated
This could have big impacts on the structure of early phylogenetic trees
A common ancestral community of cells
Period of extensive exchange of genetic material and other molecules among different cell types at the base of tree of life
Increased modularity and switch to vertical transmission occurs later and gives rise to 3 main branches of life
Which is NOT true about horizontal gene transfer?
It is an important reason that offspring resemble their parents
What was the first living thing?
Once self-replicating systems were established, at least one of them started using DNA to store information and proteins to express that information
That form gave rise to all living organisms - all organisms use the same genetic code (DNA)
This was probably a population or community of cells
-Shared genetic info via horizontal gene transfer
Isotopic evidence suggests living cells arose 3.7 billion years ago
Samples from a 3.7 billion year old sedimentary rock in Greenland contain microscopic graphite particles, which appear as black dots
The graphite particles contain ratios of carbon isotopes that suggest they are derived from living cell
Microfossils from S Africa that are 3.2 billion years old
The origin of eukaryotic cells
The oldest known eukaryotic organisms date back 1.85-2.1 billion years
-Almost 2 billion years after emergence of early cells
How did these complex, integrated cells evolve?
In particular, where did membrane-bound organelles come from?
The eukaryotic transition relied on a series of endosymbiotic mergers
Emdosymbiotic mergers:
Endosymbiotic Theory is that one organism consumed another and became new organism with characters from both original organisms
Around 2 billion years ago, prokaryotes were the only living things:
1) Big, simple, blob-like; wrapped cell membrane around smaller prokaryotes
2) Photosynthetic bacteria: Converted solar energy to sugar cells
3) Took in gas and released energy
Endosymbiosis: One organism living inside the other
Blob takes in both photosynthetic and sugar-making cells = chloroplasts and mitochondria
-Structures worked together to use sunlight to get energy and O2 to break down sugar
1) Chloroplasts and mitochondria regenerate the same as they do now
2) Chloroplasts and mitochondira contain their own DNA
3) Chloroplasts and mitochondria both have an inner and outer membrane; outer membrane used to belong to blob cell, inner membrane is different
Cells that are absorbed by another cell obtain ONE more membrane than they usually have (membrane from new cell that engulfed them)
The endosymbiosis hypothesis
Organelles (particularly mitochondria and chloroplasts) originated via symbiotic or mutualistic relationships
Bacteria capable of energy production began to reside in other cells
Eventually became an obligate relationship
Mitochondria and chloroplasts unable to survive on their own outside of a cell
Mitochondria and chloroplasts have their own DNA
-Their DNA is different from nuclear DNA in the rest of the cell
Chloroplast RNA is more closely related to cyanobacteria than other eukaryotes
- Ancient mitochondria may have come from protobacteria
- Chloroplasts came from cyanobacteria
mtDNA genes more closely resemble proteobacteria than eukaryotic genes
Endosymbiosis and the eukaryotic nucleus
Nucleus may have come from archaeal ancestor and other organelles from bacteria
After rise of eukaryotic cells, DNA from other organelles migrated to nucleus
Many modern-day nuclear genes originated on chloroplast or mitochondria
Are eukaryotes more closely related to archaea or bacteria?
We’re not sure
Some eukaryotic genes are more similar to genes in bacteria, others to genes in archaea
Eukaryotic genomes could have arisen from a fusion between bacteria and archaeal cells
HGT and endosymbiosis at the base of the tree of life make it hard to separate these hypotheses
New data suggest Archaea may be paraphyletic
Eukaryotes may be NESTED WITHIN archaea (Eocyte hypothesis)
Still lots of work ongoing in this field
Endosymbiosis occurs when:
2 cells have a mutualistic relationship and cannot survive independently
What is a major transition?
Events that change the way life is organized
What might be some examples of major transitions?
Origin of self-replicating molecules (origin of heritable variation)
RNA -> DNA
Origin of first cells
Emergence of eukaryotic cells
Evolution of sexual reproduction
Emergence of multicellular organisms
Evolution of developmental complexity
Evolution of individuality
Themes of major transitions
1) Individuals give up the ability to reproduce independently to form a larger group that shares reproduction
Seen at many levels of organization (division of labor for cells, eusocial animals like bees)
2) Aggregated individuals take advantage of economies of scale and efficiencies of specialization
3) Aggregation and specialization favor increased efficiency in information acquisition, processing, transmission, and storages
How does natural selection produce major transitions?
1) Previously independent individuals join together
2) The new “individuals” reproduce faster and more efficiently due to economy of scale, division of labor, and improved information processing
Natural selection will favor something that encourages an individual from making more of itself
We need to figure out how higher-level individuals come to exist and what the individual-level benefits are at each step of the process
For example, why doesn’t coordination among different units collapse due to cheating/selfishness?
Evolution of “policing” or enforcement mechanisms that PUNISH cheaters
Constraints - higher-level individuals are “locked in” by some aspect of their biology and cannot easily change to different states
Evolution of multicellularity
CONVERGENT evolution across the tree of life
2 hypotheses for multicellularity: Staying together Model
Clonal route to multicellularity
Cells in an ancestral unicellular lineage remain together after cell replication
Likely the most common route: parents produce cells that fail to separate completely, and then offspring continue to fail to separate
No genetic differences between cells in a cluster (they are clones)
Cells that are closely related (or identical, in this case) are more likely to cooperate, because cooperation helps their genes
Doesn’t matter if the genes are inside them or another cell - any behavior that makes more copies of their genes is favored
Why would cells that are clones of each other be more likely to form multicellular clusters?
Genetically related individuals cooperate because it can increase the survival of their genes
Testing the staying together hypothesis in yeast
Start with unicellular yeast
-Single-celled organism
Create conditions that would favor multicellularity
See if it evolves
Experimental design
Unicellular yeast in asexual reproduction mode
-Just cloning themselves
Grow in test tubes with nutrients
Every day remove a small portion of solution from bottom of test tube and put in a new tube with resources
This favors yeast cells that SINK
-i.e. artificially selecting for cells that sink
Initially larger cells were favored
These had almost 2x as much DNA as standard cells
-Snowflake clusters are heavier and they will sink to bottom of tube
Between 7 and 60 days, “snowflake clusters” were observed in EVERY SINGLE REPLICATE
-A snowflake cluster is a group of cells clustered together
By the end of experiment these had outcompeted single cells and taken on a spherical form that made them sink faster
To test mechanisms of clumping, researchers looked at cell division
There were mutations in each line that caused cells to stay together after cell division
-They had mutations to keep cells in line after cell division
When clusters were split apart, they each formed new clusters, indicating cluster formation is heritable
Large clusters eventually broke off due to selection at breakpoints
2 hypotheses for multicellularity: COMING together Model
Formerly free-living cells join together in the initial stages of multicellularity
Thought to be rarer (why?)
Suggests that early cells may have been able to “choose” to be multicellular or not
Slime molds = social amoebas
Most of the time they are unicellular
Once resources in an area are depleted, up to 500,000 individual cells come together to form a “slug”
Slug travels to soil surface and breaks into multicellular fruiting bodies
Spores are enclosed at the top
These then break open and disperse through landscape
Mechanisms and benefits of multicellularity
In region of soil with highest concentration of cells cAMP is released
Signals other cells to move towards it
Slug can respond to environmental cues in ways that individual cells cannot (economies of scale)
Slug also forms a protective slime layer and can reach new food sources more quickly
Fruiting body is beneficial because it can disperse spores farther - but cells in the stalk sacrifice themselves
Genetic studies show that cells in the stalk and spores are highly genetically related
-A cell would not sacrifice itself unless it is still somehow getting its DNA out to the next generation
Cell aggregations (slugs) may DISCRIMINATE against unrelated cells
We don’t know how they do this, but genetic relatedness allows for cooperation among cells
Which is true about the evolution of multicellularity?
It is more likely to occur between genetically related cells
Evolution of multicellular INDIVIDUALS
When is a group of cells an individual organism?
Integrated and indivisible wholes that can reproduce and pass heritable variations on to their offspring
Natural selection can facilitate transitions to different levels of individuality
Key questions in the evolution of multicellular individuals
How is fitness transferred from reproductive cells (germ cells) to somatic cells?
In other words, how is it worth it for non-reproductive cells to NOT reproduce?
Maybe early on multicellular organisms were just a few cells - cheating is unlikely here
As organisms became more complex, there was natural selection to consolidate reproduction in a few cells to dissuade cheaters
-If all cells tried to produce gametes, the complex organism would die
Evolution of individuality
Volvocine algae vary in extent of multicellularity
-Unicellular, multicellular with no specialized germ cells, well-differentiated germ and somatic cells
In Volvox carteri, small somatic cells have flagella that help the algae take in nutrients, avoid sinking, and release waste
Large reproductive cells produce gametes
Whether a cell becomes somatic or reproductive depends on the expression of the regA gene
Switches from germ cell activity to somatic cell activity
May have evolved to suppress selfish reproduction and favor coordination
Compared algae:
- Existing genes took on new functions
- Chlamydomonas uses cells for swimming and reproduction, but only one at a time
- Volvox can do BOTh at the same time
- Small genetic steps led to diversity, NOT leaps
The evolution of individuality likely required
a) Cooperation among cells
b) Enforcement mechanisms to prevent cheating
c) Differentiation of somatic and reproductive cells
d) All of the above
d) All of the above
