Exam 5

Question 1

How did life begin?

Answer 1

After the earth cooled, there was little free oxygen in the atmosphere and lots of energy available (lightening, volcanoes, UV light)
Organic molecules could form spontaneously in the oceans
History of life is a series of speciation and extinction events

Question 2

The first cells (types, genetic molecules, energy)

Answer 2

Prokaryotes (bacteria/archaea)
Used RNA for functions now performed by DNA and proteins (RNA world)
Obtained energy by absorbing and breaking down organic molecules and later by engulfing and digesting smaller cells

Question 3

Why did the increase in atmospheric oxygen occur and why is it considered the most important environmental change in the history of life?

Answer 3

Photosynthesis

Question 4

Evolutionary Milestones

Answer 4

1. Photosynthesis
2. Evolution of eukaryotes
3. Multicellularity
4. Internal skeleton
5. Eukaryotes move on to land
6. Reptiles evolved from early tetrapods
7. Asteroid impact/ Environmental change
8. Mammals diversified
9. Human evolution

Question 5

1. Photosynthesis

Answer 5

Evolved 1st in prokaryotes (eg cyanobacteria)
Released oxygen into atmosphere
O2 initially reacted with iron and minerals, but eventually built up in the oceans and atmosphere

Question 6

The Oxygen Catastrophe

Answer 6

Newly “oxic” environment caused mass extinction of anaerobic life
Reacted with methane (a greenhouse gas), which removed greenhouse gas from the atmosphere and precipitating a snowball ice age
Organisms that could withstand the catastrophe survived, allowing for eventual evolution of aerobic respiration and formation of the ozone layer which facilitated colonization of land

Question 7

2. Evolution of Eukaryotes

Answer 7

Key: Much greater metabolic efficiency
Evolved from prokaryotes that engulfed/ were invaded by other cells
Engulfed cell lived and reproduced inside host cell (endosymbiosis)
The 2 cells became co-dependent
The engulfed cell’s descendants became organelles (chloroplasts, mitochondria)

Question 8

Evidence that chloroplasts and mitochondria used to be free-living prokaryotes

Answer 8

1. Both contain DNA
2. Both reproduce independently of the rest of the cell
3. Both contain ribosomes resembling those of bacteria
4. Both have double membranes

Question 9

3. Multicellularity

Answer 9

Key: enabled organisms to grow larger and enabled specialized structures to form
2 types: simple and complex multicellularity

Question 10

Simple multicellularity

Answer 10

Aggregation of cells

Question 11

Complex multicellularity

Answer 11

Communication between cells, specialized parts

Question 12

What hurdles need to be overcome for multicellularity to evolve?

Answer 12

Preventing overpopulation of cells (controlling cell division)
*Cancer is a disease that represents a breakdown in the ability to overcome this hurdle

Question 13

4. Internal skeleton

Answer 13

Key: better support and allows greater range of body shapes
Better locomotion
Precursor to jaws

Question 14

5. Eukaryotes move onto land

Answer 14

Algae and plants moved first
Then invertebrates (worms, insects)
Then 1st tetrapods (4 legged animals) evolved from lobe-finned fish but required moisture

Question 15

What is evidence that limbs evolved while animals were still living in water?

Answer 15

Fish fossil found with fingers, gills, and fish-like tail

Also tetrapod arm found in streambed

Question 16

What was the advantage for moving onto land?

Answer 16

Escape predators in water

Access to more resources

Question 17

6. Reptiles evolved from early tetrapods

Answer 17

Able to live in dryer habitats

Some evolved to large size (dinosaurs)

Question 18

7. Asteroid impact/ Environmental change

Answer 18

Drove dinosaurs to extinction
Smaller animals survived
Birds and mammals both evolved from reptiles prior to extinction of dinosaurs, and they diversified following the extinction

Question 19

Mammal-like reptiles

Answer 19

Mammals descended from pre-dinosaur reptiles
Upright stance
Transition to mammalian teeth, jaws, and ears
Mammals have variety of teeth, reptiles have all one type of tooth
Reptiles have 3 bones on each side of the lower jaw and 1 bone in each ear, while mammals have 1 bone on each side of the lower jaw and 3 bones in each ear

Question 20

What is the advantage of using marsupials over rodents for studying development?

Answer 20

Have development outside the uterus

Question 21

Why do embryos sometimes illustrate the same changes during development that occurred over millions of years of evolution?

Answer 21

Early embryonic development is highly conserved over time

Question 22

Key points of life history

Answer 22

1st tetrapods evolved from fish
Ancestors of reptiles, birds, and mammals branched off next
Both birds and mammals evolved from reptiles

Question 23

8. Mammals diversified

Answer 23

Primates evolved from insectivores
Had forward-facing eyes, which is an advantage for binocular vision and depth perception
Had opposable thumb
Most recent common ancestor of humans and chimps was about 6 mya

Question 24

9. Human evolution

Answer 24

Human and chimp lineages diverged about 6 mya
Many different hominin species have existed, often simultaneously
Human family tree is a twiggy bush rather than a linear progression
Few older hominin fossils have been found because they died in forests that do not fossilize well and are hard to find fossils in

Question 25

Important transitions in hominin evolution

Answer 25

1st bipeds (walk on 2 legs) appeared early in hominin evolution (advantage= can see farther, keep cooler, carry food, and better for long-distance travel)
1st manufactured stone tools about 2 mya
Fire about .5 mya

Question 26

Why is it hypothesized that the first genetic material was RNA rather than DNA?

Answer 26

When modern cells make proteins, they first copy genes from DNA into RNA and then use the RNA as a blueprint to make proteins. This last stage could have existed independently at first. Later on, DNA could have appeared as a more permanent form of storage, thanks to its superior chemical stability.

Also, the RNA versions of enzymes, called ribozymes, also serve a pivotal role in modern cells. The structures that translate RNA into proteins are hybrid RNA protein machines, and it is the RNA in them that does the catalytic work. Thus, each of our cells appears to carry in its ribosomes “fossil” evidence of a primordial RNA world

Question 27

Modern RNA and DNA molecules contain a nucleobase, ribose sugar, and phosphate, all of which combine into a nucleotide. What were the difficulties with understanding how both ribose and phosphate originally became available and incorporated into the genetic material? What are the current hypotheses concerning both the ribose and the phosphate? How do scientists think the three subunits began to assemble into nucleotides (or at least the C and U nucleotides)?

Answer 27

Ribose is unstable and rapidly breaks down in an even mildly alkaline solution. Phosphorus is abundant in the earth’s crust but mostly in minerals that do not dissolve readily in water, where life presumably originated. So it is not obvious how phosphates would have gotten into the prebiotic mix. The high temperatures of volcanic vents can convert phosphate-containing minerals to soluble forms of phosphate, but the amounts released, at least near modern volcanoes, are small. A completely different potential source of phosphorus compounds is schreibersite, a mineral commonly found in certain meteors. The corrosion of schreibersite in water releases its phosphorus component. This pathway seems promising because it releases phosphorus in a form that is both much more soluble in water than phosphate and much more reactive with organic (carbon-based) compounds.

Simply mixing the three components in water does not lead to the spontaneous formation of a nucleotide—largely because each joining reaction also involves the release of a water molecule, which does not often occur spontaneously in a watery solution. For the needed chemical bonds to form, energy must be supplied. The new proposed pathway does not generate exclusively the “correct” nucleotides. But amazingly, exposure to ultraviolet light destroys the “incorrect” nucleotides and leaves behind the “correct” ones. The end result is a remarkably clean route to the C and U nucleotides.

Question 28

How is it hypothesized that the first cells copied their genetic information, given that they probably lacked enzymes made of protein? There are two hypotheses, one that includes a catalyst (i.e. a molecule that functions like an enzyme) and one that does not.

Answer 28

RNA sequences in the very first organisms could have directed its own replication by having catalytic RNA sequences.

Or, small changes to the chemical structure of the sugar component in DNA/RNA—changing one oxygen-hydrogen pair to an amino group (made of nitrogen and hydrogen)—made the polymerization hundreds of times faster, so that complementary strands formed in hours instead of weeks.

Question 29

What were the earliest cell membranes probably like?

Answer 29

Primitive membranes were probably made of simpler molecules, such as fatty acids. These membranes would still pose a formidable barrier to the entry of nucleotides and other complex nutrients into the cell. So, vesicles probably brought nutrients in and out

Question 30

What role might a ‘volcanic area’ have play in the origin of life?

Answer 30

In one possible scenario, the protocells circulated between the cold and warm sides of a pond, which may have been partially frozen on one side (the early earth was mostly cold) and thawed on the other side by the heat of a volcano. The temperature differences would cause convection currents, so that every now and then protocells in the water would be exposed to a burst of heat as they passed near the hot rocks, but they would almost instantly cool down again as the heated water mixed with the bulk of the cold water. The sudden heating would cause a double helix to separate into single strands. Once back in the cool region, new double strands—copies of the original one—could form as the single strands acted as templates

Question 31

According to the article, what key step in the relationship between the host cell and its internal symbiont resulted in the two cells becoming a single individual?

Answer 31

Both must benefit from the relationship and have many years of evolution

Question 32

The article states that ‘all mitochondria are descended from one original mitochondrion.’ What do you think is the evidence for this, based on the context where the statement is made?

Answer 32

Similarity of mitochondrial dna sequences in all living organisms.

Question 33

Look at the tree on the last page of the reading. Why do some of the branches merge together? What is the tree illustrating here?

Answer 33

Convergence represents individuals of different species setting up symbiotic relationships and forming new organisms. The tree is illustrating an interconnected tree of life in which organisms have multiple ancestors, even from different domains.

Question 34

Chloroplasts and mitochondria are argued to be the result of two separate endosymbiotic events. Given your knowledge of biology, which one do you think happened first?

Answer 34

I think chloroplasts happened first because plants came along before animals, which have mitochondria.

Question 35

Given what you learn in the article about the structure of a fish fin, why might it be a relatively simple step for a cell to switch from producing dermal bone to producing endochondral bone? Did the fish cells have to evolve a new ability that fish cells weren’t otherwise able to do?

Answer 35

In both cases, the Hox genes tell a clump of embryonic cells that they need to end up at the far end of an appendage. But when their cells reached their addresses, some of them became endochondral bone instead of fin rays. It may have been a simple matter to shift from one kind of tissue to another. No new abilities had to be evolved in this fish cells.

Question 36

What do the Hoxa-13 and Hoxd-13 genes do in mice? And in fish?

Answer 36

Mice: tell certain cells in the tetrapod limb bud that they will develop into hands and feet

Fish: control cells that became dermal bone rather than the endochondral bone found in our own limbs.

Question 37

**Check out this comparison of dermal and endochondral bone development. Clearly there are lots of differences between the two. Given your understanding of genetics, how could just two Hox genes be responsible for such a large number of differences in bone development?

Answer 37

idk

Question 38

***Your body contains both dermal bone (e.g. parts of the skull and pelvis) and endochondral bone (e.g. long bones). Based on what you read in the NY Times article, do you think your Hox genes were involved in the development of your dermal bone, endochondral bone, or both?

Answer 38

idk, both

Question 39

How are mass extinction events defined?

Answer 39

At least 50% of the species on the planet go extinct.

Question 40

How fast is the actual rate of dying during a typical mass extinction?

Answer 40

Over tens of thousands of years.

Question 41

Although the precise events that precipitated most extinction events aren’t known for sure, the likely causes of these events overlap. What causal features do the extinction events tend to share?

Answer 41

Climate change (Asteroids, volcanoes, temperature changes)

Question 42

According to the video, what is the ‘normal’ (i.e. estimated average) number of extinctions per year, outside of mass extinctions?

Answer 42

10-25 species per year

Question 43

Which past extinction event is considered the biggest in terms of diversity of life lost from the planet?

Answer 43

The great dying

Question 44

Organisms exhibit vast differences in both the numbers and identities of genes they have in their genomes, suggesting that there must be ways to acquire ‘new’ genes. The article describes one common source of new genes. Explain how they arise.

Answer 44

Gene duplication/Fusion: Ex-During the duplication process parts of an existing gene are lost. It should have been a fatal mistake since the prologues of genes contain sequences called promoters, which switch them on or off. Instead it fused with a copy of another gene, which gave it a new lease on life.

Question 45

Why are the types of genes described in the article difficult to find and often overlooked using existing methods of analysis?

Answer 45

They are difficult to find because the genes are organized in a very unusual way. For example, in other mammals like elephants, rats, and platypuses, the copies tend to sit next to the originals in a tandem series. But in humans, chimps, and gorillas, they disperse across the genome.
They also have a different architecture; Imagine a gene, G1, which gets copied into a different part of the genome, producing G2. Now, another duplication event copies G2, creating yet another copy of G1 along with some of the new DNA surrounding it. This happens again and again; with each new duplication event, the core genes picks up more flanking material. “It builds an inverse Oreo cookie”.
They aren’t found in lab animals like flies and mice.
Most traditional sequencing methods rely on reading small sections of DNA that can then be combined into a coherent whole. But since duplicated genes are almost identical to their originals, their pieces often get mistaken for parts of their ancestors and assembled incorrectly.

Question 46

Based on your general understanding of biology, explain the likely reason behind this observation: “When two parts of the genome are nearly identical, they can often lead to massive rearrangements, where sequences are doubled, lost, or shuffled.” Why/when does this rearrangement occur?

Answer 46

Similar sequences of DNA are recognized by the same molecules, so if one is cut by an enzyme, the other may be too even though it wasn’t the target gene. This can lead the two genes to be “cut and pasted” into each other, mixing, doubling, and deleting the potentially wrong sequences.

Question 47

CRISPR-Cas9 is a relatively new tool for modifying genomes. It works by inserting a segment of reference RNA into a nucleus of an egg cell. The reference RNA guides an enzyme (Cas9) to the part of the genome containing the complementary sequence in the DNA; the enzyme then cuts the DNA at that specific location. Suppose you are a biologist trying to understand the role of a particular gene by knocking out that gene using CRISPR-Cas9 and observing the effects on an organism. Given what you have learned in this article, what is a potential complication of using this technique to elucidate a gene’s function?

Answer 47

The RNA and enzyme may potentially go to the wrong part of the genome if two genes have very similar sequences like in duplicated genes. The enzyme may bind and cut the wrong gene instead of the target gene, and thus the target genes function will not be studied, but rather the similar gene’s will.