EEB 121 Week 1-2: Domains of Life, C-value, Miller-Urey, RNA, RNP, DNA Worlds

Question 1

What are the 3 requirements for life? Where does each come from?

Answer 1

1. Source of energy: thermonuclear reactions (stars) and photo-energy (In addition, we have planetary energy, gravitation, and radioactive decay)
2. Source of carbon (and other elements for biological molecules): formed in supernovas
3. Source of liquid water: a lot of it is from “outgassing” of the mantle, but a considerable amount came from comets (big snow balls)

Question 2

What is the “Goldilocks Zone”?

Answer 2

The Goldilocks Zone is the rail around a star in which the temperature is neither too hot nor too cold for liquid water to exist. This is what actually defines the area in which you might find life

Question 3

Why did Carl Woose use small subunit rRNA to determine the relatedness of the 3 domains?

Answer 3

1. Abundant found in organellar, nuclear, and prokaryotic genomes (easy to isolate)
2. Within this molecule, there are slow portions (to compare distant organisms) and fast evolving portions (to compare closely related organisms)
3. Universally conserved structure (compared across many species)
4. Ancient and essential function in the cellular economy
5. Interaction with many other coevolved cellular RNAs and proteins

Question 4

Which domain(s) have glycerol-ester lipids?

Answer 4

Bacteria/Eukarya

Question 5

Which domain(s) have glycerol-ether lipids?

Answer 5

Archaea

Question 6

4 differences in Phospholipid Characteristics between Domains are:

Answer 6

1. Linkages: ether in Archaea, ester in Bacteria/Eukarya
2. Chains: isoprene in Archaea, fatty acid in Bacteria/Eukarya
3. Lipid layering: monolayer in Archaea; bilayer in Bacterya/Eukarya
4. Glycerol moiety: L-glycerol in Archaea; D-glycerol in Bacteria/Eukarya

Question 7

What might this tell you about the origin and relationship of the 3 domains of life?

Answer 7

Ancestor of Archaea, Bacteria, and Eukarya may have been pre-cellular since membranes are needed for cells

There might have been a point in which all three split in their common ancestors before they became independent free living cell organisms (since membranes evolved independently)

Question 8

What is problematic about using a tree structure to describe the evolution of early life?

Answer 8

It leaves out the possibility of horizontal gene transfer, 3 domains did not rise in a tree-like fashion

It suggests that all 3 came from 1 progenerator, Eukaryotes did not evolve from a progenerator shared with Archaea and BActeria

Question 9

What is the C-value?

Answer 9

The C-value is the total amount of unique DNA in the genome (also known as genome size)

Question 10

How does the C-value compare within and between species?

Answer 10

The C-value is virtually constant within a species but varies widely between species

Question 11

What are two ways of looking at the C-value paradox?

Answer 11

1. The simplification of the fact that eukaryotes have much more DNA than you would expect (Large amounts of DNA in eukaryotes and wide range in C-value. Prokaryotic genomes are relatively small and range in C-values is nominal)
2. When we look at the C-values in different eukaryotes, the C-value does not appear to be correlated with sophistication

Question 12

Large amounts of DNA are characteristics of eukaryotes. What would have allowed this expansion in the amount of DNA in eukaryotes relative to archaea and bacteria?

Answer 12

By complexing DNA with histones into nucleosomes, it dramatically increase the ability to handle large amount of DNA (this process is also known as “nuclear packaging of DNA”)

Question 13

When did the earth form?

Answer 13

4.5 billion of years ago

Question 14

When did the earliest cell evolve?

Answer 14

3.8 billion of years ago

Question 15

When did O2 increase in the atmosphere to 1%?

Answer 15

2.0 billion of years ago

Question 16

When did eukaryotes evolve?

Answer 16

1.5 billion of years ago

Question 17

What does this suggest about the potential for life to evolve?

Answer 17

Life evolves very early

Question 18

What is a plausible environment for the origins of archaea and bacteria?

Answer 18

A plausible scenario is that Archaea and Bacteria evolved in a hydrothermal vent as their energy source (the metabolic potential would be chemolithotrophic based and limited to anaerobic processes)

Question 19

What was revolutionary about the 1953 Miller-Urey experiment about the origin of life?

Answer 19

Can perform a quick reaction (weeks not centuries) creating organic molecules without oxygen. Global in nature (ocean and atmosphere portions)

Question 20

The abiotic inputs into the system included H2O, N2, NH3, CO2, CH4, H2, which were thought to exist in earth’s primitive atmosphere. What were the output molecules?

Answer 20

Amino acids and other organic compounds

Question 21

What considerations did the Miller-Urey experiment not address?

Answer 21

The Miller-Urey experiment had 5 limitations: 1. Set the location as ocean surface when life began at bottom of ocean

2. Simulates lighting which is too harsh
3. Ratio of atmosphere: ocean is not correct
4. Reaction of bio-molecules is too low
5. No compartmentalization

It did not take into consideration RNA. It did not take into account how the reaction attained the template for self-replication or self-catalysis

Question 22

Was their experiment able to satisfactorily explain the origin of life? Why or why not?

Answer 22

Proteins are good catalyst but cannot pass on information. You need an RNA molecule (that is able to self-replicate and catalyze) The question remains what allowed for inheritance

Question 23

Why is RNA a good candidate for the first “living molecule”?

Answer 23

Can act as a catalyst
Can pass on information
This allows some RNA molecules to → self-replicate

Question 24

What catalyst is required to begin an RNA World?

Answer 24

Ribozyme: RNA polymerase- can copy molecules like itself

Question 25

How is this catalyst able to close the “chicken-and-egg” loop of the Central Dogma? What important process does this allow for?

Answer 25

Tells us that proteins are not the first stage of life, or DNA either, as both are needed together to function. But RNA does both (information storage and catalytic activity in one molecule)

This allows for Darwinian Evolution

(Ribozymes function as both the template and the activation for self-replication)

Question 26

Why are proteins not a good candidate for the first “living molecule”?

Answer 26

They can’t serve as templates for replication because they can’t pass on genetic info so it can’t self replicate

Question 27

What is the hard versus the soft version of an “RNA World”?

Answer 27

Hard: RNA is the only ribozyme present, proteins used for later

Soft: Amino acids come together to form proteinoids and play a stabilizing role for RNA

Question 28

Why would it be advantageous to transition from an RNA to an RNP (ribonucleoprotein) World?

Answer 28

Proteins are better catalysts than RNA and speed up reactions. Can form many conformations and are more efficient because they have 20 amino acids versus 4 nucleobases in RNA

More properties (hydrophobic + stability)

Question 29

What catalytic activity is required to make this transition?

Primary:

Secondary:

Answer 29

Primary: Peptidyl transferase - making peptide bonds between amino acids

Secondary: Aminoacyl tRNA synthetase - charge tRNAs w/specific amino acids

Question 30

Eventually DNA took over the __________ role of the RNA molecule. Why would it have been advantageous to replace RNA with DNA for this role?

Answer 30

Eventually DNA took over the information storage role of the RNA molecule

More stable
Double stranded
Template strand that can fix errors on the other strand
H group in 2’ makes it less prone to nucleophilic attacks by alkali

Question 31

What is one line of evidence for RNA having arisen before DNA?

Answer 31

RNA rapidly evolves due to its flexibility

Catalytic activity (translate/transcribe)

Information storage

Pathways to synthesize bases is much simpler than DNA’s