Bio 204 Midterm 2

Describe four different ways that Eubacteria and Eukaryotes differ in their mechanisms of protein synthesis.

1. Eubacteria- Transcribed mRNA often codes for multiple proteins Eukaryote- mRNA translate into a single protein 2. Eubacteria- Transcription and translation occur next to each other, as the mRNA has barely come off the DNA before it attached to a ribosome for translation. Eukaryote- Transcription and translation occur in different parts of the cell: transcription in the nucleus, where DNA resides. Transcribed mRNA must exit the nucleus before it can dock on ribosome. 3. Eubacteria- Control transcription by protein repressors, which binds to sections of DNA called operators to turn off transcription. Stop and Go gene regulation. Eukaryote- Use operators and activators, which bind to the enhancers, thereby activating transcription. Eukaryotic activators exert their influence far from the initiation site of RNA polymerase. Expands the number of different proteins that can activate a particular gene, giving more metabolic flexibility. Transcription factors are small molecules and protein which bind to activators and speeds up initiation of transcription. Gene is regulated in continuous graded fashion. 4. Eubacteria- No splicing, no protein cap, no poly A-tail Eukaryote- "mRNA processing". First, protein cap placed on the 5' end of mRNA to prevent degrading of mRNA when its shipped out of the nucleus. Second, adenosine nucleotides added to 3' end, forming a poly-A tail used as a handle by nuclear pore when mature transcript is sent out of nucleus. Gene splicing, the removal of introns and splicing together of exons, occurs to produce the mature mRNA transcript.

List two of the four ways Eubacteria and Eukaryote differ in their mechanisms of protein synthesis

1st- In Eubacteria, transcribed mRNA codes for multiple protein In Eukaryotes, mRNA translates into a single protein 2nd- In Eubacteria, transcription and translation occur right next to each other, as the mRNA has barely come off the DNA before it attached to the ribosome for translation. In Eukaryotes, transcription and translation occur in different parts of the cell: transcription in the nucleus, where DNA resides. Transcribed mRNA must exit the nucleus before it can dock on ribosome.

Use sketches to help you describe the first phase of glycolysis. Start with glucose (not the detailed structure, just depict glucose as a circle as we did in lecture). What happens to the glucose molecule? Use the words, glucose, investment (what is invested?), phosphorylation, ATP, ADP, splitting, glyceraldehyde-3-phosphate.

2 ATP are invested. They give up their phosphate (phosphoralation). The 2 ADP leave. Glucose splits into 2 G3P's, each containing one phosphate = investment phase SKETCHES

Compare and contrast the three main structural elements of the eukaryotic cell, microtubules, microfilaments, and intermediate filaments. For each kind of element, name its main functional protein and what distinguishes it from the other two.

Actin (Micro) Filament- Tensile structure Composed of Actin Dynamic- part of cell movement Small Microtubules- Compression Composed of Tubulin Dynamic Large Intermediate- Intermediate sized Compression and tension Composed of Vimentin Static

What is the disadvantage of the loss of the cell wall of Archaebacteria?

Cells are more vulnerable to osmosis-induced bursting and mechanical insults.

Draw a sketch of a membrane oriented vertically with "Reducing Power" increasing in the vertical axis (label this) to describe in detail how H2S-splitting photosynthesis solves the osmosis problem. Use the words, chlorophyll, light, photon, electron, H2S, S, H+, electron carrier, reducing power, NADH, inside cell, outside cell, H+ gradient. Explicitly explain how photosynthesis relieves the osmosis problem.

Chlorophyll captures light energy and absorbs a photon. 2 electrons of an H2S molecule abandon the H2S turning S to H+. The newly freed electrons are turned over to an electron carrier. It ejects a proton from inside to outside the cell relieving osmotic pressure. SKETCH

What is so important about cyanobacteria from an evolutionary perspective?

Cyanobacteria were utilized by archaebacteria to produce food by photosynthesis. Chloroplasts descended from cyanobacteria.

What specified lineage within the Eubacteria evolved into chloroplasts?

Cyanobacterium

Does Kreb Cycle in the modern aerobic world use O2? If not what does?

No, the ETC uses it to provide ATP

Why doesn't making energy by photosynthesis completely solve the energy crisis.

Photosynthesis can't work at night. Within seconds of the sun's disappearance, the electron carrier of photosynthesis shuts down. Protons gradually break into the cell, and osmosis sucks water in.

Describe the calcium pump. Which way does calcium go? What energy required?

located in the membrane. it pumps Ca out. It's powered by the hydrolysis of ATP

Describe 3 different ways that RNA has maintained its role as middle-man in the overall process of protein synthesis

mRNA- middleman between DNA and protein tRNA- middleman between mRNA and amino acids rRNA- Middleman between polypeptide chain and ribosome

Use the knowledge you've gained (including Le Chatelier's principle) to make predictions about our cell. Make a prediction for if a Martian (or a cell biologist!)... a. darkens the cell, then injects into it superabundant pyruvate, NADH and ATP. What would happen and why? b. darkens the cell, chemically (and continuously) reduces all NADH to NAD+, and finally injects superabundant glucose. What process would be forced into action and what products would it produce?

??????

Draw a sketch (as usual, include all inputs and where they come from, and all outputs and where they go) to help you explain how the electron transport chain (ETC) really brought cellular life into the fast lane. a. What is the one direct function of the ETC? b. Where does the ETC get its electrons? c. What is the name of the last electron carrier in the ETC? d. What does it do with its electron? e. Name at least one additional electron carrier. f. How many total ATP's can be generated from the oxidative breakdown of one molecule of glucose? g. How does this compare to the anaerobic breakdown of the same glucose?

A) pumping out protons B) NADH and FADH2 C) CYTC D) gives it to oxygen E) COQ F) 32-36 G) 18X

The electron transport chain (ETC) really brought cellular life into the fast lane. A) What is the one direct function of the ETC B) Where does the ETC get its electrons? C) How many total ATP's can be generated from the oxidative breakdown of one molecule of glucose? D) How does this compare to the anaerobic breakdown of the same glucose?

A) to eject protons out of the cell to equalize the ion concentration B) 2 electrons from NADH and 2 electrons from FADH2 C) 36 ATPS D) This is an 18-fold increase over what glycolysis can make in the absence of oxygen (2 ATPs net gain)

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? b. Which specific lineage evolved into chloroplasts? What benefit does it get from the symbiosis? What goodies does it give to its host?

A. Purple bacteria it brings in photosynthetic and electron-transport chain capacities. Host spits out pyruvate waste product into the purple bacterium and gets 18 times as many ATPs. Purple bacteria gets unlimited reactants into its Krebs Cycle, doesn't have to capture food, or perform glycolysis to get pyruvate. B. Cyanobacteria, Host utilizes it to produce food by photosynthesis. Gains protection against phagocytosis by predacious archaebacteria.

Please narrate and make a sketch to describe how amino acid tRNA sythetase places the correct amino acid onto tRNA a. What are the three different kind of reactants that the enzyme work with? b. What happens to those reactants? Be sure to mention all hydrogen and covalent bonds made and broken.

Amino acid and ATP are brought into the active site of the charger enzyme by hydrogen bonding. ATP loses 2 phosphates (by breaking its covalent bonds) to provide energy to bond tRNA to amino acids covalently. Charged tRNA is released and is covalently bonded to its correct amino acid. ATP -> hydrolysis-> attaches a.a. to tRNA a. ATP, tRNA, amino acid b. ATP covalent bond is broken and creates energy for tRNA to covalently bond to its specific amino acid. Hydrogen bonds hold reactants to charger enzyme. The products are ADP, Pi, and the covalently bonded tRNA and AA. SKETCH

Draw a sketch of an entire cell that shows how photosynthesis solves the energy problem. Use the words, electron carrier, NAD+, NADH, H-gradient, original H+ pump, ADP, ATP, Krebs cycle in reverse, carbon fixation.

As the electron carrier accepts the electrons, protons pump out of the cell creating a high H+ gradient. THe proton pump will then run in reverse making ATP from ADP. SKETCH

Rank in order of reducing power CH2O CH4 CO2

CH4- greatest CH2O-Middle CO2- least

How does the cell make food as a dividend of photosynthesis? Sketch the pathways and use the words, proton pump, ATP, electron carrier, reducing power, NADH, carbon fixation, carbohydrate, "reverse Krebs cycle", glycolysis, and pyruvate in your narrative. Be sure to distinguish the different roles of reducing power and ATP as sources of energy during photosynthesis. Also be sure to make clear whether processes are going in forward or reverse mode (and do not forget arrow heads).

CO2, ATP, and reducing power (NADH and FADH2) are inputs. The reducing power fixes CO2 into pyruvate by adding electrons. ATP provides the energy for the covalent bonds between the added carbons to the CO2 molecule. SKETCH

What evolutionary crisis does glycolysis solve? What caused the crisis?

Energy crisis from the depletion of ATP because of the proton pump.

Know the three ways we learned in lecture to identify which player in a redox reaction is being reduced, and which is being oxidized.

First, if one of the molecules sees a "reduced" charge, e.g., it goes from no charge to minus charge, or from positive charge to zero charge, it is almost certainly reduced (conversely, if its charge goes positive it has likely been oxidized). Second, if a molecule picks up a hydrogen atom, it has usually been reduced (conversely, a molecule that has lost a hydrogen has likely been oxidized). Third, if a molecule loses an oxygen atom, it has been reduced (conversely if a molecule receives an oxygen, it has been oxidized). Using these three tricks, you should be able to identify which molecule reduces which (and conversely which molecule oxidizes which).

Describe the big picture of Kreb's cycle in the modern aerobic world. What are its reactants and where do they come from? What are its products and where do they go?

Glycolysis piles up pyruvate and sends Krebs cycle in forward mode (Le Chateliers Principle). Krebs cycle takes pyruvate and converts it to ATP and reducing power. Because of the presence of oxygen, which will take electrons from anything no matter how low its reducing power is, the ETC sucks electrons from NADH and FADH2. This the reason Krebs can go in forward mode. The inputs of the process is pyruvate from glycolysis, (2) ADP + P from the running cell, and NAD+ and FAD+from the ETC. The outputs are ATP which supplies cellular process with CO2, CO2, and reducing power (NADH and FADH) which hands its electrons to the ETC.

Know which side (in or out) of every living prokaryotic cell has more hydrogen, sodium, potassium, and calcium

Hydrogen, Calcium, and Sodium- greater on outside Potassium- greater on inside

Know which side (in our out) of every living prokaryotic cell has more hydrogen, sodium, potassium, and calcium.

Hydrogen, Sodium, Calcium = high outside Potassium = high inside

Explain how H2S-spliting photosynthesis simultaneously solves the energy crisis and osmosis crisis, at least while the sun shines.

It solves the osmosis crisis because in the process of handling an electron, the electron carrier ejects a proton. It solves the energy crisis because the original proton pump responds to the excess proton concentration on the outside of the cell by turning around and growing in reverse (Le Chateliers Principle). Protons flow into the cell and pulls the phosphate from the water, converting ADP into ATP. This reversal is a way to generate ATP entirely independently of glycolysis, and is more efficient. The highly efficient volume ejection of protons by photosynthesis relieves the ATP powered proton pump of its osmosis related duties, and transforms the function of the pump, by driving it in reverse, to being an energy source.

Describe the sodium/potassium pump. What is pumped out, what is pumped in? Where does the energy come from? How can this pump help solve the osmosis problem if it is pumping solute both out and in?

NA+ out and K+ in. This removes solute because 3 NA+ ions leave for every 2 K+ ions pumped in for a net outflow of 1 ion. Energy comes from ADP —> ADP + Pi Na pump causes a gradient outside the cell. Food comes in through diffusion. The co-transporter protein takes Na+ and molecule of glucose from outside cell to inside

Know how to find two RNA molecules in NAD+

NOTES

What is the most important output of the modern Krebs cycle?

Reducing Power

Which enzyme catalyzes the capture of CO2 from the atmosphere in the Calvin cycle?

Rubisco

Be able to identify in a detailed depiction of the Reverse Krebs cycle a. where CO2 is being fixed. b. where energy is being added. c.where (on which Carbon) a reactant is being reduced by NADH or FADH2

SKETCH

Describe with sketches the following: a. the original function of the proton pump b. its new function in the sunlight with photosynthesis. In your two descriptions you must identify every input and where it came from, as well as every output and where it goes. Finally for each function, identify the most important output, i.e., the primary function.

SKETCH

Know how to answer each part of the Group Study that is due Friday. In particular, know each new evolutionary alteration to the four processes (glycolysis, Krebs cycle, electron transport chain, and proton pump), including inputs and where they come from, outputs and where they go to, and most important function.

SKETCH

Know how to answer each part of the Group Study that is due Friday. Use a sketch to describe each stage in the evolutionary history of glycolysis, Krebs cycle, and the proton pump, including for each stage inputs and where they come from, outputs and where they go, and most important function. Start with the primordial soup and end with aerobic breakdown of glucose. Don't forget to describe processes in the light as well as the dark.

SKETCH

Make a sketch to help you describe aerobic metabolism in the dark in Eukaryotes. Starting with glucose outside the cell, use arrows between labeled processes put circles around each process) and indicate all inputs and outputs (indicate which outputs are the most important) to summarize the aerobic pathway. Start by drawing a cell with its cytosol (Archaebacterial host), and a large mitochondrion (symbiont) as we did in lecture. Pay close attention to the membranes separating these two regions. Map onto this sketch in its proper place: phagocytosis, outer membrane, inner membrane, intermembrane space, glucose, glycolysis, pyruvate, Krebs cycle, NADH/FADH2, NAD+, FADH, electron transport chain, protons, proton pump, ATP, ADP + Pi

SKETCH

Please make a sketch for each A-E below. Each sketch should show the process in a circle, placed appropriately within the cell. It should include all the inputs into that process and where they come from, as well as all outputs from that process and where they go. Note that these inputs and outputs will not be listed in the question! Thus, you should start practicing right away. A. Proton pump solves the osmosis crisis, thereby causing energy crisis. B. Glycolysis (and fermentation) of glucose from primordial soup solves energy crisis, causes food crisis. C. Chlorophyll, electron-carrier protein, and reversed proton pump (Le Chatelier) solves both osmosis and energy crises in the daylight. D. Products of photosynthesis make glucose for use in the night. E. Night-time is STILL anaerobic glycolysis and fermentation. Almost identical to B. What's different?

SKETCH

Use sketches of the cell membrane oriented vertically (with reducing power as the vertical access) to help you describe how the Electron Transport Chain likely evolved. Use the words, inside cell, outside cell, reducing power chlorophyll, light, electron, electron donor, NADH, H2O, O2, protons, reverse proton pump.

SKETCH

Draw an overall (net only) input output diagram. 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.

SKETCHES

What is meant by the endosymbiotic theory of the origin of the Eukaryotes?

Several key organelles of Eukaryotes, including the mitochondria and chloroplasts, were formerly bacteria that were taken inside another cell in endosymbiosis, which means another cell begins to live inside another cell.

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

Since H20 is virtually everywhere, when it is used as the electron donor it means that photosynthesis could be performed almost anywhere on earth where water and light are present.

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

The Electron Transport Chain because O2 grabs the electrons from the procession of carriers because it is electron hungry.

What other classes of molecule are synthesized from precursors produced by the Krebs cycle.

The building blocks of fats (fatty acids and glycerol, nucleic acids (ribose and bases) and proteins (amino acids) and produced by the Krebs cycle.

What pathway takes reducing power (NADH, FADH2) , ATP, and CO2 as its inputs. What does that pathway produce as outputs? Where do those outputs go?

The cell can makes its own food by the reversed Krebs cycle, which uses reducing power, ATP, and CO2 as inputs. Excess pyruvate from the reversed Krebs cycle, in addition to ATP and NADH from photosynthesis, ultimately synthesizes the food, i.e. glucose.

What new evolutionary crisis does glycolysis create?

The food crisis

What are the two disadvantages of H20-splitting photosynthesis, one inconveinent and one deadly?

The inconvenient disadvantage is that photosynthesis requires an unwieldly two step electron excitation, because the energy level of the electron stripped from that of water is markedly lower than that of the electron of H2S. Since the electron is not energetic enough to reduce NAD+ or another cofactor, the cell had to evolve an additional molecule of chlorophyll to take an additional photon from the sun, thereby ejecting more energy into the low energy electron and giving it reducing power. The deadly problem is that )2 tends to form a pair of exceedingly reactive ions that wreck havoc on unprotected cells when the iron supply runs low and contributes to many intracellular problems.

What is the advantage of the Calvin cycle over the reverse Krebs cycle? (why is it more efficient?)

The latter part of glycolysis is not pushed backward, and the enzymes never have to go in reverse. The key point is that three out of the ten enzymes in glycolysis do not have to go both ways when carbon fixation is by the calvin cycle. Because fewer enzymes have to go back and forth, the overall efficiency is increased.

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

The most important output is G3P, and the characteristic is the ability to be phosphorylated. This is important because the reducing power allows the G3P to bring the phosphates out of water without ATP.

Please narrate and make a sketch to describe how translation proceeds, using the following words: ribosome, mRNA, codon, anti-codon, tRNA, AUG, Methionine, P-site, A-site, peptide bond, translocate, E-site, stop codon, release factor. Be sure to explicitly state how hydrogen and covalent bonds are made and broken for each step.

The small subunit of the ribosome comes upon the start codon (AUG) on the mRNA strand. A tRNA attaches because of its complimentary anti-codon (UAC) and the amino acid methionine is attracted to the codon AUG. After the started tRNA is in place, then the large subunit joins the cluster. The start codon is in the P-Site. The next codon (CCU) attracts its tRNA and anti-codon (GGA) and the amino acid Leucine. (hydrogen bonds between anti-codon and codon). The covalent bond between methionine and its tRNA is broken, and at the same time a peptide bond is formed between Methionine and Leucine. The mRNA strand then translocates 3 nucleotides to the right, and the leftmost tRNA that is translocated to the E-Site is ejected from the ribosome without its amino acid. This process continues until the stop codon comes into the A-Site, and then a release factor slides into the A-Site, and releases everything. SKETCH

Two advantages of Archaebacteria?

There is replication at multiple points of origin. The cells can capture relatively large food particles by phagocytosis and digest it at its leisure.

Use sketches to describe the second phase of glycolysis. How does glyceraldehyde-3-phosphate get phosphorylated without ATP? Where exactly does the phosphate come from? Use the words, glyceraldehyde-3-phosphate, NAD+, NADH, reduction, oxidation, ATP, ADP, harvesting, pyruvate.

Two G3P's have such a high reducing power that they are able to take a free floating phosphate from water and attach it. It uses reducing power for energy to make the P bond. NAD+ is reduced by G3P and becomes NADH. Finally, 4 ADP molecules take 1 phosphate off 2 G3P's. 4 ATP produced (2 net). Stripped G3P becomes pyruvate. SKETCHES

Does Krebs Cycle produce CO2? If not, what does?

Yes, Forward Krebs Cycle

Consider glycolysis as a whole. a. How many ATP's are made total? b. How many ATP's are invested (ATP---ADP + Pi)? 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?

a. 4 b. 2 c. NAD+ gets replenished by the fermentation of pyruvate. The fermentation oxidizes the NADH becomes NAD+. Byproducts are lactate and ethanol. They are secreted from cell. D) 2

The amino-acyl tRNA enzymes match up specific amino acids with tRNA molecules, in preparation for translation of mRNA into protein. Please describe the specificity of this process. In particular, a. In principle, how many different tRNA molecules are there? b. How many different synthetases are used to prepare for translation? c. To how many different amino acids can a particular synthetase bind? d. To how many different tRNA molecules can a particular synthetase bind?

a. 64 in principle, 61 in practice b. 20 c. 1 d. 1-6

9.) Evolution or proton pump. a. Remind yourself how the proton pump solved the osmosis crisis. b. What crisis does the proton pump cause? c. What solves the crisis caused by the proton pump?

a. equalized the total number of solutes inside vs. outside by ejecting one proton of H+ by using the energy source of hydrolized ATP to ADP plus Pi b. Energy crisis, because of the depletion of ATP c. Glycolysis

Loss of the cell wall in the Archaebacteria has important consequences. a.What are the negative consequences of the lack of cell wall. b.Name two very different positive consequences of the lack of cell wall. c.How did the loss of the cell wall lead to a symbiotic relationship with Eubacteria?

a.Cells are more vulnerable to osmosis-induced bursting and mechanical insults. b. Replication, at multiple points of origin, take in large food particles by phagocytosis and digests it at its leisure. c. As the archaebacteria began to take in living cells for food by endocytosis the possibility for endosymbiosis, or when a cell begins to live inside another occurs.

Which specified lineage within the Eubacteria evolved into mitochondria?

purple bacteria