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Flashcards in Ch 11 Deck (55):
0

How old is Earth's age?

~4.5 billion years old

1

What are interdisciplinary projects?

Chemists (possible initial chemical building blocks of life)
& geologists, and atmospheric scientists (possible characteristics of environment in which life originated)

2

What were the conditions on Earth like 3.5 bya?

Ancient Earth was much hotter (Ocean temp cooled 30 C from 3. to 0.5 bya)

3

What is the last universal common ancestor, LUCA (and what was it NOT?) (4)

Common ancestor of all extant (living) organisms found on Earth that left descendant lineages that remain today

A population of organisms

NOT first life form
NOT only life-form present at that time

4

Limit of phylogenetic analyses?

Phylogenetic analyses that use extant taxa can't see beyond LUCA

5

Phylogenetic event horizon

A point in history of life beyond which phylogenetic analysis can't see

6

What are the 5 properties associated with living things?

-homeostasis (ability to adjust internal environment for stable eq.)
-structural organization (ability to maintain distinct parts and the connections b/w them)
-metabolism (control of chemical reactions)
-Growth & reproduction
-response to environmental conditions & stimuli

7

What is the two essential mechanisms by which all life are subjected to?

All life subjected to and evolved by the process of natural selection

Difference between self-replication entities and self-replicating entities subject to natural selection

8

What is the prebiotic soup hypothesis?

Atmosphere lacked oxygen
UV light and lightning might serve as source of energy -> converted atmospheric gases into a range of molecules
Other energy sources included cosmic rays, volcanic eruptions, internal heat

9

What does prebiotic soup create? How did it become richer>

Pool of molecules that existed in liquid form before life, which became richer over time in living matter. Earliest life forms emerged from prebiotic soup

Pools may have become more rich as a result of extraterrestrial objects (brought with them AA, purines, pyrimidines)

10

What did the Miller and Urey experiment test?

Stimulated condition on Earth prior to life;

Electric current = lightning; gases used (methane, hydrogen, ammonia & h2o)

experiment yielded numerous common AA

11

What reactions tempted to answer what mechanisms join amino acids together?

Fox and Huber experiment

12

Fox experiment

Demonstrated that some AA mixed at high T (120 C) in an environment free of water, then placed in water formed weak unstable bonds

13

Huber experiment

Found AA will form stable peptide bonds if in the presence of carbon monoxide- thought to be present in the ancient atm

14

What had the capacity for heredity and metabolism in early evolution (~4-3.5 bya)?

RNA

15

What three things existed in prebiotic environment or arrived by meteorites (during the RNA world period)?

Ribose, phosphate purines, and pyrimidines

16

What are the three "ingredients" for natural selection?

1st is variation
2nd is heritability
3rd is differential survival/ replication

17

Describe Spiegalman's experiment on the origin of natural selection (7 steps):

1. placed primer strand RNA into test tube
2. added more nucleotides (AGCU*) & a replicase enzyme
3. Heated & incubated mixture
4. Transferred a small drop to new test tube that did have nucleotides & replicase enzyme, *but no RNA primer*
5. New test tube is heated and incubated
6. process repeated 75 times
7. Natural selection took place on copies***

18

What was interesting about Spiegalman's experiment (on the origin of natural selection)?

The interesting this was not that the RNA was copied, Spiegalman has added replicase enzyme to ensure that this would happen. But rather that NATURAL SELECTION TOOK PLACE ON THESE COPIES, leading to a CHANGE IN THEIR CHARACTERISTICS.

**mainly because the enzyme involved errors -> new mutant forms

19

what step contained errors which produces new mutants?

RNA replication contained errors

20

What served as evidence in Spiegalman's experiment?

-differed in length and nucleotide sequence
-variation acted on by natural selection
-differential survival and replication also is present

21

What is the advantage and disadvantage of small RNA sequences? Why do we now see RNA strands greater than 100bp's?

Although it will replicate more quickly (if smaller than 50-100 nucleotides), the error rate of replication is so high they are not copied reliably.
So, short sequences would be selected AGAINST -> strands were found to be about 200bp in length.

22

What was Simper's accomplishment in his experiment, and what did he do differently?

Similar to Spiegalman's experiment, but added ACRIDINE ORGANGE (florescent dye that binds to RNA typically preventing replication by replicase enzyme) => accomplished to show evidence of Natural Selection at work.

23

What were the results of Sumper's experiment when he used the dye?

Replication was initially inhibited but soon replication occurred in variants.
It was even quicker in the presences of acridine orange & AO variants ONLY arose in the PRESENCE of acridine orange

24

Although Spiegelman and Sumper experiments demonstrated how RNA life MAY have evolved, it failed to answer what question?

Experiments required replicase; where did replicase come from?

25

What did Cech and Altman accomplished?

**Enzyme need not be proteins. RNA itself can act as an enzyme***

26

Ribozymes & its contribution to RNA world?

RNA enzymes; are much LESS STABLE than protein enzymes. Several different types are known.

In the RNA world, RNA replicated using ribozymes

27

What did Paul & Joyce experiment demonstrated?

Demonstrated that RNA can catalyze reactions involved in own assembly using R3C ribozyme. This assembly was a "self-replicating-system"

28

What did Lincoln & Joyce make later on? What did they accomplish from their experiment?

Made a perpetually self-replicating system with two different templates and 4 different substrates

New VARIANT FORMS of the template arose via various mutations which were HERITABLE

29

in the RNA world, natural selection would favor what transmission system that was more efficient?

DNA-based transmission system because it was chemically more stable **deoxyribose sugar is LESS REACTIVE**

30

what are the 5 reasons why DNA is favored?

1. double stranded structure protects the nitrogenous bases
2. proof-reading capabilities (exonuclease checks each added base)
3. repair mechanisms available since DNA is double stranded
4. DNA attributes lower mutation rates (since it allows for longer genes = more info can be transmitted)
5. DNA allows for specialization within cells (storage system/ enyme functions, etc)

31

Robinson and Miller experiment

Used formaldehyde (thought to be produced on early Earth & may have facilitated in the production of DNA) to be mixed with RNA nucleotide Uracil= similar to side chains of most amino acids

32

Why aren't viruses included in tree of life?

Because they are acellular

33

What does the phylogenetic even horizon prevent us from doing?

Prevents us from phylogenetically reconstructing the first cellular life forms.

34

Two basic cell forms

Prokaryotic (evolved early; lack membrane-bound organelles and DNA not contained in nucleus)
&
Eukaryotic (membrane-bound organelles and distinct nucleus containing DNA)

35

what are the three hypothesis of where viruses came from?

-escaped gene hypothesis
-reduction hypothesis
-relic of the RNA world hypothesis

NOTE* it's possible that more than one of these hypothesis are correct

36

Escaped gene hypothesis (of where viruses came from)

origin in selfish genetic elements that replicate within the host genome & at some point evolved necessary protein capsules/ packaging mechanisms to exist outside cells

37

Reduction hypothesis (of where viruses came from)

Origin in parasitic cellular organisms & over time their genomes became more reduced to rely on the functions of the host. eventually abandoned everything and developed a protein capsule

38

Relic of RNA world hypothesis (of where viruses came from)

Remnants of the RNA world

39

Mutualism

when members of two species interact in ways that benefit both

40

mutualistic relationships (think fitness)

fitness of all parties involved increase

41

molecular mutualism

if two or more molecular substrates each contribute in a positive way to the replication of others.

may have been important among replicators in RNA world (entities that can replicate themselves)

42

Hypercycles

Imagine four independent, RNA-based replicators labeled A, B, C, and D (Figure 11.15). Suppose that these replicators are all found in the same environment and in close proximity to one another, and that they interact in a cycle—that is, a closed loop of the form A → B → C → D → A, where an arrow from A to B indicates that A facilitates the replication of B, and so on

Type of MOLECULAR MUTUALISM

43

What are some modern world examples of hypercycles?

Earthworms and oak trees
&
Fish, water fleas and algae

44

How were hypercycles important in cell formation?

Mutations in hypercycle generate variation. Natural selection may favor variations that lead to more complex life forms

45

Mutation to A (A') makes A products with some cost to itself more accesible to replicator B. Would natural selection favor this?

NS would NOT favor this altruistic mutant because all replicators are independent entities.

***Unless the components of the hyper-cycle were enclosed in a membrane and share a collective replication rate***

46

benefits of encapsulation (4)

-controls microenvironment;
-creation of chemical gradients across membranes
-defensive mechanism against predatory replicators
-partitioning of various functions

*the benefits of the cell eventually became greater than the costs

47

How did early cells reproduce?

One hypothesis focuses on fatty acids; mutualistic relationships within cell led to the production of more fatty acids.
At higher rates of fatty acid production, the cell membrane would increase

48

what is the best way for cells to split in early reproduction?

most efficient way is for a sphere to split into two equal parts which natural selection would favor

** NS would favor any changes that lead to more rapid reproduction & increase in number or daughter cells surviving to reproduce in next generation

49

Three important facts of Horizontal Gene Transfer

- HGT led to more complex cellular organisms
- HGT may have been the primary way in which copies of genes were propagated
- means early cell life was a hodgepodge of different cell forms interchanging genetic material

50

If HGT can be disadvantagous (because you might end up with detrimental genetic material), why is it even present?

Allowed for huge amounts of variation => complexity

51

What does it mean if HGT was predominant early on in the evolution of life?

There is no single universal ancestor

52

what were essential genes responsible for?

Genes involved in energy metabolism, regulatory function, fatty acid/ lipid metabolism, synth. of nucleotides, transcription, DNA metabolism, protein binding

53

What was important when comparing the minimal gene set across organisms with small genomes?

Rather than the absolute number of genes, it is the basic functions that are most critical. From this list, we might hypothesize that DNA and RNA metabolism, the processing and folding of proteins, and energetic and intermediate metabolism, are the central building blocks that natural selection favored during early cell evolution.

54

Pal experiment tested for what?

Minimal gene set for more complex organisms; looked at E.coli- basically checked the effect of removing genes until fitness decreased