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Evolution > Lec 8 > Flashcards

Lec 8 Flashcards

1
Q

What is life?

A

There are numerous definitions, some of which include organisms that other definitions consider not to be living

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2
Q

How long has life existed on earth?

A

Earliest microfossils are ~3.2-3.4 billion years old

These are likely to be fossilized creatures with cell-like walls

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3
Q

Living things - Definition 1

A

Any form that is able to grow and reproduce
CAVEAT:
-Non-living things like some minerals (crystal dendrites) are able to grow and reproduce

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4
Q

Living things - Definition 2

A

Any form that can store, transmit and express information
CAVEAT:
-Computer systems store, transmit and express information

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5
Q

Living things - Definition 3

A

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

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6
Q

Combined definition of living things

A

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

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7
Q

Properties of life

A

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

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8
Q

Origin of life and Natural Selection

A

As biologists, we are not just interested in self-replication

We also need heritable variation that leads to fitness differences

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9
Q

How do we study the origin of life?

A

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

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10
Q

Big questions on the origin of life

A

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?

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11
Q

Abiogenesis

A

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

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12
Q

Where do the building blocks of life come from?

A

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

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13
Q

What is a plausible progression of early life?

A

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

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14
Q

Soup hypothesis (Oparin-Haldane model)

A

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

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15
Q

Miller-Urey experiment: Organic Soup Recipe

A

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

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16
Q

Miller-Urey part II

A

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

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17
Q

Big questions about the origin of life do NOT include

A

Origin of inorganic molecules

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18
Q

Extraterrestrial origins

A

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)

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19
Q

Deep sea vents

A

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

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20
Q

How do simple molecules form more complex structures? The clay layer hypothesis

A

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

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21
Q

The evolution of protocells

A

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

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22
Q

Lipid membranes

A

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

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23
Q

Transport across lipid membranes

A

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

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24
Q

Division of simple vesicles

A

Vesicles with multiple bilayers form spontaneously

As more micelles added, extrusions form

Vesicle will form thin, unstable strand

Strand breaks into daughter vesicles

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25
Q

Natural selection on vesicles

A

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

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26
Q

Hypercycles: Molecular mutualisms

A

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
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27
Q

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?

A

NO, because this does NOT benefit A at all

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28
Q

Imagine our hypercycle is inside an enclosed membrane. Would A benefit from sacrificing some of itself to B?

A

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

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29
Q

Costs vs. Benefits of membrane enclosure

A

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

30
Q

Why would molecular mutualisms be favored in a closed system?

A

Any initial sacrifice in fitness by replicator A is regained

31
Q

A chicken and egg problem of the origin of life

A

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?

32
Q

RNA World

A

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

33
Q

Ribozymes - History

A

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

34
Q

Evidence for the RNA world hypothesis

A

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

35
Q

Experimental evidence for the origin of natural selection on RNA

A

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

36
Q

What did they find?

A

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

37
Q

What would you expect to happen to the length of RNA strands over the course of the experiment?

A

Converge on an intermediate strand length

38
Q

What did they find?

A

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

39
Q

How could RNA replication originate?

A

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

40
Q

Consequences of using DNA for information storage

A

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

41
Q

Where did DNA come from?

A

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

42
Q

Which is NOT a benefit of DNA compared to RNA as an information storage system?

A

It is shorter and therefore replicates faster

43
Q

Evolution of complex cells

A

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

44
Q

Horizontal gene transfer

A

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

45
Q

Horizontal gene transfer: Conjugation

A

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

46
Q

Horizontal gene transfer: Transduction

A

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

47
Q

Why would horizontal transfer be important to early cells?

A

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

48
Q

A common ancestral community of cells

A

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

49
Q

Which is NOT true about horizontal gene transfer?

A

It is an important reason that offspring resemble their parents

50
Q

What was the first living thing?

A

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

51
Q

The origin of eukaryotic cells

A

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?

52
Q

The eukaryotic transition relied on a series of endosymbiotic mergers

A

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)

53
Q

The endosymbiosis hypothesis

A

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

54
Q

Endosymbiosis and the eukaryotic nucleus

A

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

55
Q

Are eukaryotes more closely related to archaea or bacteria?

A

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

56
Q

New data suggest Archaea may be paraphyletic

A

Eukaryotes may be NESTED WITHIN archaea (Eocyte hypothesis)

Still lots of work ongoing in this field

57
Q

Endosymbiosis occurs when:

A

2 cells have a mutualistic relationship and cannot survive independently

58
Q

What is a major transition?

A

Events that change the way life is organized

59
Q

What might be some examples of major transitions?

A

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

60
Q

Themes of major transitions

A

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

61
Q

How does natural selection produce major transitions?

A

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

62
Q

Evolution of multicellularity

A

CONVERGENT evolution across the tree of life

63
Q

2 hypotheses for multicellularity: Staying together Model

A

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

64
Q

Why would cells that are clones of each other be more likely to form multicellular clusters?

A

Genetically related individuals cooperate because it can increase the survival of their genes

65
Q

Testing the staying together hypothesis in yeast

A

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

66
Q

2 hypotheses for multicellularity: COMING together Model

A

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

67
Q

Mechanisms and benefits of multicellularity

A

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

68
Q

Which is true about the evolution of multicellularity?

A

It is more likely to occur between genetically related cells

69
Q

Evolution of multicellular INDIVIDUALS

A

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

70
Q

Key questions in the evolution of multicellular individuals

A

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

71
Q

Evolution of individuality

A

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
72
Q

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

A

d) All of the above

Evolution (15 decks)

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