final exam

Question 1

how old are the oldest fossils of life are estimated to be?

Answer 1

3.5 billion years old

Question 2

Know the usual number of bonds made by the following atoms
a. Sulfur (S)
b. Phosphorus (P)
c. Oxygen (O)
d. Nitrogen (N)
e. Carbon (C)
f. Hydrogen (H)

Answer 2

2
5
2
3
4
1

Question 3

Know how to recognize an unlikely molecule. For example (other examples are open season on quiz), which of these is unlikely in nature (and for each one, why?):
O=O H-O-H H-C=C=O H=O

Answer 3

H-C=C=O because carbon has 4 electrons to give and requires 4 bonds, but only has 3 bonds out of the 4 needed to make it stable.
H=O because hydrogen only has one electron to give while there’s 2 covalent bonds connected to the hydrogen.

Question 4

hydrogen bonds.
a. How are they formed?
b. What is their relative strength?
c. Give an example of each.
d. Which kind of bond gives water its many unique qualities?
e. Which type of bond is intramolecular and which type is intermolecular?

Answer 4

a: almost always partially positive, so it’s attracted to different partially negative pieces like (O&N)
b. weak
c. H2O
d. hydrogen bond because its partial charges make it maximally polar, which allows it to be unique among all solvents
e. intermolecular (weak)

Question 5

covalent bonds.
a. How are they formed?
b. What is their relative strength?
c. Give an example of each.
d. Which type of bond is intramolecular and which type is intermolecular?

Answer 5

a. form when two or more atoms come together to share electrons to form a more stable outer electron shell
b. strong
c. O2
d. intramolecular (strong)

Question 6

Name 4 of the five most common molecules (these are small molecules, not biomolecules) on prebiotic earth, the raw materials for the primordial soup (the starting solution of the Miller-Urey experiments).

Answer 6

Hydrogen H2, methane CH4, water H2O, ammonia NH3

Question 7

Name the kind of molecules that were predicted by Oparin to form in the high-energy reducing atmosphere of pre-biotic earth.

Answer 7

Monosaccharides, glycerol/fatty acids, nucleic acids, amino acids

Question 8

Polymerization (dehydration condensation) and depolymerization (hydrolysis) of all four biomolecules occurred chaotically in the primordial soup. What process is the only way a chemical form can persist in this chaos.

Answer 8

The molecule uses its form as a template to replicate itself

Question 9

Describe the important characteristics of the Miller-Urey experiment regarding pre-biotic earth. Be able to explain how the addition of an oxygenated environment would change the outcome of the experiment.

Answer 9

Oxidation is an important characteristic of the experiment because oxygen is very electronegative, meaning it takes electrons from others bc it’s “hungrier” as well as stronger than others. If oxidation had occurred, it would’ve prevented molecules like amino acids, glycerol/fatty acids, proteins, and nucleic acids from fully developing due to it fragmenting it or just preventing these molecules from forming at all.

Question 10

carbohydrate monomer

Answer 10

monosaccharide, (CH2O)n

Question 11

protein monomer

Answer 11

amino acid, N-C-C, different R/side chain

Question 12

lipid monomer

Answer 12

Fatty acid, # of carbon not equal to # of oxygen making it hydrophobic

Question 13

Know how to position the three phosphates (circled “P” is fine) on the appropriate carbon of the ribose.

Answer 13

connect on carbon-5 of internal ribose

Question 14

Know how to draw the internal ribose and how to number its carbon molecules.

Answer 14

pentagon with O at it’s point, clockwise 1-5 carbons, have an OH at carbon-2/3

Question 15

Know which carbon of the ribose the base attaches to.

Answer 15

carbon-1

Question 16

Know which part of a growing RNA polymer a “charged” nucleotide (the triphosphate version) attacks

Answer 16

the 3’ end where the nucleotides connect and form covalent bonds with ribose

Question 17

Describe in words what a catalyst does.

Answer 17

it speeds up a particular chemical reaction by lowering energy needed to activate a reaction, allowing it to proceed with a lower input of energy

Question 18

The persistence delivered by replication is not sufficient for evolution of chemical form. What else is
needed? Why?

Answer 18

Mutations for genetic variation are needed because without a mutation, it’ll just be the same thing being replicated over and over with no change.

Question 19

Starting with a 5mer nucleotide polymer of RNA as a template, describe template-directed polymerization of RNA. Use sketches representing three successive time points as RNA is polymerized along the template
strand: What is the relative role of hydrogen versus covalent bonds? Use the words, 3’ carbon, 5’ carbon, polymerization, triphosphate versus monophosphate nucleotide, monomer, hydrogen bonds, covalent bonds A-U, G-C.

Question 20

Be able to describe how an enzyme works: Include active site, induced fit, reactants, products, what hydrogen and covalent bonds are made and broken.

Answer 20

Enzymes are catalysts made of proteins, so it’s a protein molecule that helps a reaction lower the energy needed to start the reaction. First, substrates bind to the enzyme at its active site with an induced fit (when active site changes shape when it binds to a substrate). Enzymes are also very specific and have very specific jobs. Hydrogen bonds hold substrates in the enzyme until it makes/breaks covalent bonds between the substrates and then hydrogen bond breaks once covalent bond is made and releases substrates

Question 21

List the characteristics of an amphipathic molecule? Name one amphipathic molecule.

Answer 21

has polar and non-polar region
example: triglyceride (glycerol(polar) + 3 fatty acids(non-polar)) OR a phospholipid (phosphate group (polar) + 2 fatty acid chains (non-polar))

Question 22

What is a liposome? How is a liposome made?

Answer 22

liposome: small bubble bounded by an amphipathic molecule; small (70-300 nM) piece of water, surrounded by “lipid bilayer,” 2 lines of amphipathic molecules, an inner line with its polar heads contracting the captured piece of water, and an outer line with its polar heads facing the other way i.e. toward surrounding water. 2 lines orient their nonpolar tails toward each other and away from water
it’s made in any sort of energetic disturbance in a pool of water with amphipathic molecules in it

Question 23

Describe the circumstances (use the words, solute, inside, outside, hyperosmotic, hypoosmotic, flow of water) that would
a. lyse a red blood cell

Answer 23

there would need to be more solute inside of the cell to create a hypo-osmotic solution, so water would flow from outside of the cell into cell, eventually causing it to burst (lyse)

Question 24

Describe the circumstances (use the words, solute, inside, outside, hyperosmotic, hypoosmotic, flow of water) that would
b. shrink a red blood cell

Answer 24

there would need to be more solute outside of the cell to create a hyper-osmotic solution, so water would flow from inside of the cell to outside of the cell, causing it to shrink

Question 25

Describe the circumstances (use the words, solute, inside, outside, hyperosmotic, hypoosmotic, flow of water) that would
c. make a red blood cell happy (neither shrink nor swell/lyse)

Answer 25

there would need to be equal amounts of solute inside and outside a cell to create an iso-osmotic solution, so water would not diffuse leaving it at an equilibrium

Question 26

Describe what is meant by the “osmosis crisis?” What, exactly, caused it?

Answer 26

osmosis crisis: (low to high concentration) ever-increasing number of solute molecules (RNA polymers) inside the cell, which means that water will tend to flow in the cell by osmosis (hypo-osmotic solution). This eventually leads to the lysis of cells.
it was caused by large RNA’s not being able to diffuse to lower concentrations outside. This meant that RNA strands in cells were replicating themselves, increasing their concentration as each newly replicated polymer remained trapped in the cell’s fatty acid liposomes

Question 27

Explain how a constraining micro-environment improves replication. Use the words, RNA nucleotides, RNA polymers, ribozyme replicase, diffusion.

Answer 27

RIbozyme replicase will be able to catalyze replication of RNA faster due to all the materials needed like RNA nucleotides, RNA replicase, and RNA polymers being nearby. This causes local concentration of RNA polymers to increase, causing catalysts and reactants to collide more often, which further increases replication rate. However, because of diffusion, concentration of replicase never gets that much higher than surrounding waters. (Diffusion always keeps local concentration from increasing a lot) With the environment not being constrained, all the materials needed would diffuse and spread apart, taking longer to gather the materials needed to replicate RNA.

Question 28

The figure on p.50 of the Primer depicts the “Central Dogma”. Explain the central dogma in words using the words protein, translation, transcription, DNA.

Answer 28

Central Dogma: order of process from DNA to protein
Transcription is used to transcribe DNA into RNA (both have nucleotides so same language). Translation is then used to translate RNA into proteins (completely different so different languages).

Question 29

Be able to make a sketch and narrate in detail how replication proceeds on the leading strand using the following words (more or less in order of appearance): helicase, primase, 3’ vs 5’ carbon, RNA, DNA polymerase III, DNA polymerase I, DNA ligase.

Answer 29

First, you start with 2 strands of DNA. Then 2 helicases binds to DNA at origin of replication and starts to split up the strands by breaking the hydrogen bonds between the complementary bases as they move apart. Helicase continues to move further apart. Primase then binds to the single stranded DNA to RNA nucleotides one at a time from 5’ to 3’. DNA polymerase III then binds to the primer that is made because it can’t find where to attach without the primer. DNA polymerase III adds DNA nucleotides one at a time from 5’ to 3’. While all this is happening, DNA polymerase I attaches to the RNA primer to remove and replace the RNA nucleotides that its made of with DNA. After all of them are replaced, ligase combines the ends of the DNA polymers, completing the covalent bonds in the sugar-phosphate backbone.

Question 30

Be able to make a sketch and narrate how transcription proceeds, using the following words (more or less in order of appearance): Promoter region, RNA polymerase, template strand, RNA triphosphate nucleotide, non-template strand, GC hairpin. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step.

Answer 30

Initiation starts off with a 5’ to 3’ non-template strand antiparallel to a 3’ to 5’ template strand. RNA polymerase is bound the the promoter region of DNA and unwinds DNA at the start site. RNA polymerase adds RNA nucleotides one at a time from 5’ to 3’ to create a primer. The RNA strand eventually falls off of the DNA template while RNA polymerase keeps adding RNA. DNA reconnects behind RNA polymerase (hydrogen bonds between DNA is stronger than hydrogen bonds between RNA). Transcription continues until it reaches the GC hairpin which is formed by internal hydrogen bonds made between the RNA nucleotides as well as the poly U tail. Lastly, RNA polymerase and the RNA strand are released from DNA and DNA is able to repeat the process again.

Question 31

**Describe the function of: ribosome, mRNA, codon, anti-codon, tRNA, AUG, Methionine, P-site, A-site, peptide bond, translocate, E-site, stop codon, release factor.

Answer 31

mRNA is used to create polypeptide chains, which are used to make proteins. tRNA is used to carry amino acids to the ribosome and match them to codons (using anticodons).

Question 32

Evolution of proton pump.
a. Remind yourself how the proton pump solved the osmosis crisis.

Answer 32

proton pump solved osmosis criss because it pumped protons (H+) out of the cells, which equalized solute inside the cell and lowered the concentration of protons inside of the cell

Question 33

Evolution of proton pump.
b. What crisis does the proton pump cause?

Answer 33

energy crisis

Question 34

Evolution of proton pump.
c. What solves the crisis caused by the proton pump?

Answer 34

glycolysis

Question 35

An atom or molecule with reducing power tends to (choose one) gain / donate electrons?

Answer 35

donate

Question 36

An atom or molecule that gains an electron is oxidized / reduced?

Answer 36

reduced

Question 37

An atom or molecule that loses an electron is oxidized / reduced?

Answer 37

oxidized

Question 38

Know how to assign oxidation numbers to C, H and O within a molecule.

Answer 38

All C+H+O=0
H= +1
O= -2
solve for C

Question 39

Name the most important output of the investment phase. This is the input to the payoff phase. What characteristic of this molecule gives the payoff phase the capacity to create ATP’s?

Answer 39

The most important output of the investment phase is 2 molecules of G3P. The characteristic of this molecule that gives the payoff phase the ability to create ATP’s is that G3P’s have LOTS of reducing power, meaning that it really wants ot give away e-‘s. This allows a free Pi from the environment to bind, which creates 2 ATP’s when both Pi’s are broken off.

Question 40

Summarize glycolysis as a whole:
a. How many ATP’s are made total?
b. How many ATP’s are invested (ATP—ADP + Pi)?

Answer 40

a. 4ATP’s
b. 2 ATP’s

Question 41

Summarize glycolysis as a whole:
c. Describe the reaction that replenishes NAD+. Name the reactants that get reduced and oxidized. What are the products and where do they go next?
d. How many ATP’s does glycolysis of one glucose molecule net for the cell?

Answer 41

c. Fermentation replenishes NAD+ because it takes the NADH made from glycolysis and oxidizes it to become NAD+. Then, the NAD+ made from fermentation goes back into glycolysis (becomes a cycle).
input: NADH (from glycolysis to fermentation)
output: NAD+ (from fermentation to glycolysis)
d. 2 ATP’s

Question 42

Draw an overall (net only) input output diagram of glycolysis. This is the diagram you will use later. Include in your diagram pyruvate, NADH, NAD+, ADP, Pi, ATP, Glucose. Also include in your diagram where all the inputs come from and where all the outputs go.

Answer 42

input: 2 ADP+2Pi (from proton pump), glucose (from primordial soup), NAD+ (from fermentation)
output: 2 pyruvate (to fermentation), 2 ATP (to proton pump), NADH (to fermentation)

Question 43

Why doesn’t making energy by photosynthesis completely solve the problem caused by glucose depletion?

Answer 43

The making of energy by photosynthesis doesn’t completely solve the problem caused by glucose depletion because photosynthesis only works when there’s sunlight (during the day). Within seconds of the sun’s disappearance, electron carrier of photosynthesis is shut down and protons will gradually leak into the cell and osmosis will begin to suck in water.

Question 44

Explain how H2S-splitting photosynthesis simultaneously solves the energy and osmosis crises, at least while the sun shines

Answer 44

Osmosis crisis: electron carrier ejects protons from inside the cell to outside of the cell, which relieves osmotic stress caused by all the other large molecules
Energy crisis: When concentration of protons get too high due to the electron carrier pumping H+ out of the cell, the reverse proton pump will come into play by pumping protons back into the cell, converting ADP back into ATP to solve the energy crisis.

Question 45

C. Chlorophyll, electron-carrier protein, and reversed proton pump (Le Chatelier) solves both
osmosis and energy crises in the daylight.

Answer 45

e- carrier solves osmosis crisis and reverse H+ pump solves energy crisis during the day
chlorophyll: e- from H2S
e- carrier: e- from chlorophyll
H+ pump: ATP from H+ pump to reverse Krebs and reverse glycolysis
ADP+Pi from reverse glycolysis

Question 46

What great advantage did the evolution of oxygenic photosynthesis give to cells?

Answer 46

it allowed photosynthesis to occur anywhere there was water and light, which is good because water is everywhere

Question 47

What are the two disadvantages of H2O-splitting photosynthesis, one inconvenient, the other deadly?

Answer 47

inconvienient: oxygen in every water molecule is so electron hungry, the energy level of the electron stripped from water is significantly lower than that of an electron stripped from H2S. This causes electrons to not have enough energy to reduce NAD+ or other cofactors that are critical for reducing powers (CO2–>CnH2nOn) isn’t provided
deadly: oxygen atoms are very electron hungry. As a result, O2 gas tends to form a pair of exceedingly reactive ions (“free radicals”) that wreak havoc on unprotected cells by stealing electrons from covalent bonds and thereby altering covalent chemical structures

Question 48

What remarkable revolution was caused by the accumulation of oxygen in the atmosphere?

Answer 48

The development of the electron transport carrier (ETC) with electron carriers and oxygen as the last electron acceptor in which oxygen’s electron hunger can be exploited to convert reducing power into ATP; A cell is now able to convert reducing power from NADPH into ejected protons (& thus indirectly ATP), by using the same electron carriers, but without light

Question 49

Name the most important output of the modern Krebs cycle in the aerobic world. Explain why this output is so important.

Answer 49

reducing power created by NADH and FADH2 because its needed to run the ETC in aerobic photosynthesis

Question 50

Consider the two bacterial Domains, Archaebacteria and Eubacteria, which form an endosymbiotic union to give rise to the eukaryotes.
a. Which specific lineage evolved into mitochondria? What benefit does it get from the
symbiosis? What goodies does it give to its host?

Answer 50

Purple non-sulfur bacteria evolved into mitochondria. The benefit it got from symbiosis is a cell wall that guaranteed it food (pyruvate, ADP+Pi, and even more NADH) from its Archaebacteria host, so it was able to produce ATP by using forwad Krebs and ETC. The goodies it gives its host is lots of ATP.

Question 51

Consider the two bacterial Domains, Archaebacteria and Eubacteria, which form an endosymbiotic union to give rise to the eukaryotes.
b. Which specific lineage evolved into chloroplasts? What benefit does it get from the symbiosis? What goodies does it give to its host?

Answer 51

Cyanobacteria evolved into the chloroplast. The benefit it got from symbiosis was the protection from phagocytosis from the archaebacteria. The goodies that it gave its host was food made by photosynthesis that it allowed to occur in the cell.

Question 52

Loss of the cell wall in the Archaebacteria has important consequences.
a. What are the negative consequences of the lack of cell wall.

Answer 52

Disadvantage was the loss of the cell wall that put archaebacteria at risk of lysing from osmosis

Question 53

Loss of the cell wall in the Archaebacteria has important consequences.
b. Name two very different positive consequences of the lack of cell wall

Answer 53

1. allows DNA replication to occur at multiple points of origin
2. cells can capture food through phagocytosis or endocytosis