Bio 311C exam 3 practice questions

The inputs of non-cylic photophosphorylation, include light, water and ..... a. NADP+ b. ADP, Pi c. CO2 D. a and b e. a, b and c

D. a and b

Develop a hypothesis as to why cells have evolved to use ATP as their main energy source. How will you test this hypothesis?

Hypotheses: should be testable, specific, and narrow Hypothesis: ATP structure is compatible with the enzyme active site and enzymes could use the energy released by ATP hydrolysis. Test ATP, GTP, TTP and UTP with different enzymes that use ATP for energy coupling Hypothesis: amount of energy in ATP hydrolysis close to reaction energy levels that enzymes are capable of catalyzing. Larger minimal energy units would waste more energy. Test: compare Kcal/mol of ATP hydrolysis to individual biochemical reaction steps and other energy carriers (sugars, amino acids, redox reactants, O2...)

What will be the single most important chemical bond that supplies energy for the majority of the transportation we use today and what process make such bond?

-C-H bonds -generated by photosynthesis to fix CO2 to make carbohydrate, which is then converted to other organic molecules

What are the three important things that need to happen for a eukaryotic cell division to occur?

1. DNA replication 2. increase in cell size and volume 3. multiplication of cell organelles and cytoskeleton elements

Equilibrium is a stage when the deltaG is zero, i.e. there is no net change or the forward and reverse reactions are the same. If you consider an enzyme reaction, the products are formed from the substrate. Keq is calculated as the number of products formed per unit substrate at equilibrium. Consider the following example as 1:1 ration of reactant to product and calculate the Keq. 1. At equilibrium, the reactant remaining was 200 ug/ml and product was 800 ug/ml 2. A reaction was started with 80 mM substrate ending with 70 mM product at equilibrium

1. If the reaction is 1P-->1S, Keq=[P]/[S], [S]=200 ug/ml, and [P]=800 ug/ml, then Keq=800/200=4 2. The reaction is 1P-->1S Givens: [S]i=80 mM, [P]i=0 mM, and [P]f=70 mM. Using [S]i+[P]i=[S]f+[P]f, gives us [S]f=80mM-70mM=10 mM. Hence Keq=[P]f/[S]f, 70mM/10mM=7

What are the limiting factors of photosynthesis? List three major factors related to the structure and function of cell structures or components that limit the photosynthetic efficiency.

1. LIght 2. Water 3. CO2 levels 4. Temperature Cell Structures: Mesophyll cells (in all plants), bundle sheath cells (in C4 plants), xylem and phloem (in all plants)

What is the difference between absorption spectrum and the action spectrum in the Figure shown below? **figure in screenshots++

Absorption spectrum is for individual pigments namely Chlorophyll a, b and Carotenoids while the action spectrum shows the level of photosynthesis, which is the result of all three pigments harvesting light energy

How is the light energy converted to chemical energy in light reactions of photosynthesis?

Light energy excited electrons at the reaction center chlorophyll and the high-energy electrons are passed through electron transport chain

Given the equation for free energy change as deltaG=deltaH-T(deltaS), list three conditions that would result in the reaction to become spontaneous (same as exergonic or favorable)

Spontaneous/exergonic/-deltaG can result from: -deltaH and +T(deltaS) (exothermic and increase in energy) --deltaH greater than -T(deltaS) (exothermic outweighing a decrease in entropy) -+deltaH lesser than +T(deltaS) (endothermic outweighed by an increase in entropy)

Sprinter and marathon runners have different types of muscle tissues that use various processes to make ATP according to their needs. Speculate as to what type of ATP synthesis mechanisms operate in such individuals

Sprinters and many weightlifters develop muscle without any mitochondria, specializing in short, intense anaerobic function (glycolysis and lactic acid fermentation) Marathoners and other endurance athletes are know to develop more vascular muscle with more mitochondria and often stored fat specializing in long-term aerobic function (Krebs cycle and OxPhos)

An asian and caucasian graduate students walk in to a bar and have a few drinks. Predict who would get drunk first and why. Use the second biochemical reaction shown below to explain. Ethanol+ADH-->Acetaldehyde

There are variations in the enzyme, Aldehyde dehydrogenase (ALDH) that detoxify the acetaldehyde, among asians that are less active than typical caucasian ALDH enzyme.

Why is visible light important for photosynthesis and not the higher energy UV or lower energy infrared radiation?

Visible light is not only abundant and has the right energy level that does not damage the cells and has sufficient energy to excite elections to generate proton concentration gradient and make ATP

Which of the following product of Krebs cycle would inhibit a key enzyme glycolysis? a. ATP b. starch c. citrate d. NADH e. acetyl CoA

a. ATP c. citrate

When we exercise for a long time without rest, the muscle cells become deprived of oxygen. Which of the following is NOT produced in a muscle cell under such conditions? a. NADH b. ethanol c. ATP d. pyruvate e. lactate

a. NADH

Which of the following poison can inhibit the generation of delta[H+]? a. a poison that wold inhibit ATP synthesis b. an enzyme that would donate electrons to O2 c. cyanide like chemical that would block the electron transfer d. a chemical that would make the inner mitochondrial membrane leaky to ions e. a chemical that mimics glucose but is not hexokinase

b. an enzyme that would donate electrons to O2 c. cyanide like chemical that would block the electron transfer d. a chemical that would make the inner mitochondrial membrane leaky to ions

The initiation of the S phase and the M phase of the cell cycle depends on ... and .... to make .... a. actin; myosin; fibers b. cdk; cyclin; MPF c. ligand; enzyme; complex d. insulin; receptor; G-protein e. ADP; Pi; ATP

b. cdk; cyclin; MPF

How does the chromosome number of each daughter cell is reduced to half the original amount during meiosis? a. chromosomes do not replicate during interphase I preceding prophase I b. chromosomes replicate only once but before meiosis I but the cell divides twice c. half of the chromosomes from each gamete are lost during fertilization d. sister chromatids separate during anaphase I but not in anaphase II of meiosis e. chromosome numbers are reduced to half during crossing over in prophase I

b. chromosomes replicate only once but before meiosis I but the cell divides twice

When the photophosphorylation is happening during light reactions, the pH of stoma will ..... compared to the equilibrium state during night time. a. decrease as the protons are pumped back from thykaloid b. increase as the protons are pumped into thykaloid c. stay neutral as the protons will balance the influx and efflux d. decrease first and the increase gradually e. stay neutral as the phtophosphorylation will not affect the pH in stoma

b. increase as the protons are pumped into thykaloid

More free energy is released during the Krebs cycle than during glycolysis, but only 2 moles of ATP is produced for each mole of glucose undergoing glycolysis. Most of the remaining free energy that is produced during the Krebs cycle is used to ..... a. synthesize GTP b. reduce NAD+ and FAD c. release as heat d. oxidize pyruvate e. make ethanol

b. reduce NAD+ and FAD

An enzyme was tested with two different substrates A and B resulting in products X and Y. The Km for the substrate A was 10mM and the Km for substrate B was 100mM. From this information, we can state that... a. substrate A is less effective than substrate B to have same amount of products formed b. substrate B is less effective than substrate A to have same amounts of products formed c. there is no different between A and B in terms of products found d. X is produced less than Y with the same amount of substrate used e. Y is produced more than X with the same amount of substrate used

b. substrate B is less effective than substrate A to have same amounts of products formed

Which of the following in an anabolic process that is endergonic and endothermic? a. ATP+H2O-->ADP+Pi b. C6H12O6+6O2-->6CO2+6H2O c. CO2+H2O-->CH2O+O2 d. FADH2-->FAD+H2 e. CH4+2O2-->CO2+2H2O

c. CO2+H2O-->CH2O+O2

A chemical inhibitor that blocks the initiation of DNA replication is added to actively dividing cells. Most of the cells would be found in their .... phase of their cell cycle. a. G0 b. S c. G1 d. G2 e. M

c. G1

Which of the following statements is NOT true of glycolysis? a. ATP is used to prime the reaction b. ATP is made in this process c. acetyl CoA is an output made in cytoplasm d. NADH is produced e. Pi from cytoplasm is used to make ATP

c. acetyl CoA is an output made in cytoplasm

Which of the following statements about mitosis is NOT true? a. the chromosome number in the resulting cells is identical to parents b. DNA replicaiton is completed in S-phase c. independent assortment happens in metaphase d. two genetically identical daughter cells are formed e. it occurs in somatic cells

c. independent assortment happens in metaphase

Which of the following is NOT directly associated with photosystem II? a. release of oxygen b. harvesting of light energy by chlorophyll and other pigments c. oxidative phosphorylation d. reaction center chlorophyll e. splitting of water

c. oxidative phosphorylation

The reaction as shown below, with the reference to FAD, is a ..... process and ..... is the (oxidizing or reduction) FAD+X-H2-->FADH2+X a. reduction; X-H2; oxidizing b. oxidation; FAD; reducing c. reduction; X-H2; reducing d. oxidation; FAD; oxidizing e. oxidation; X-H2; oxidizing

c. reduction; X-H2; reducing

The energy released in aerobic respiration is originally derived from ...... a. the O2 we breath b. the ATP present in cytoplasm c. the food we eat d. the enzymes involved in glycolysis and Krebs cycle e. the CO2, ATP and NADH

c. the food we eat

When a suspension of algae is incubated in a flask in the presence of light and CO2 and then transferred to the dark, the reduction of 3-phosphoglycerate to glyceraldehyde 3-phosphate is blocked. This reaction stops when the algae are placed in the dark because.... a. the reaction requires CO2 b. the reaction is exergonic c. the reaction requires ATP and NADPH d. the reaction requires O2 e. chlorophyll is not synthesized in the dark

c. the reaction requires ATP and NADPH

How does the reduction of pyruvate to lactic acid during fermentation allow glycolysis to continue in the absence of oxygen? a. water is formed during this reaction b. this reaction is a kinase reaction c. this reaction is coupled to the oxidation of NADH to NAD+ d. this reaction is coupled to the formation of ATP e. this reaction is coupled to the reduction of NAD+ to NADH

c. this reaction is coupled to the oxidation of NADH to NAD+

Which parts or tissues of a plant allow transport of water and sugar respectively? a. stoma and xylem b. leaf and stem c. xylem and phloem d. phloem and xylem e. chloroplast and mitochondrion

c. xylem and phloem

Melting of ice at room temperature results in the following changes in free energy, enthalpy and entropy... a. +deltaG, +deltaH, +deltaS b. +deltaG, -deltaH, +deltaS c. +deltaG, -deltaH, -deltaS d. -deltaG, +deltaH, +deltaS e. -deltaG, +deltaH, -deltaS

d. -deltaG, +deltaH, +deltaS

ATP Hydrolysis yields 7.3 Kcal/mol free energy and it is coupled with many enzyme reactions that would not otherwise happen. Which of the following reaction can be coupled with ATP hydrolysis to become a favorable or spontaneous reaction? A reaction with a deltaG value of .... Kcal/mol a. -5.8 b -7.3 c. 10.5 d. 5.3 e. 0

d. 5.3

FADH2 produces less ATP each when compared to NADH because ..... a. NADH carries 4 electrons whereas FADH2 carries 2 b. NADH carries 2 electrons whereas FADH2 carries 1 c. same membrane protein that accepts electrons from these molecules binds at various sites d. FADH2 allows fewer protons transported across inner membrane and hence makes less ATP e. NADH allows fewer protons transported across inner membrane and hence makes more ATP

d. FADH2 allows fewer protons transported across inner membrane and hence makes less ATP

When mice were fed with radioactive carbon in glucose all the 6 CO2 molecules will be released during which of the following process... a. Krebs cycle and Oxidative phosphorylation b. glycolysis and acetyl CoA formation c. glycolysis and Krebs cycle d. acetyl CoA formation and Krebs cycle e. glycolysis and oxidative phosphorylation

d. acetyl CoA formation and Krebs cycle

The homologous chromosomes separate during .... and their sister chromatids separate during .... phase of meiosis a. anaphase I and telophase I b. prophase I and anaphase II c. metaphase I and metaphase II d. anaphase I and anaphase II e. telophase I and telophase II

d. anaphase I and anaphase II

Non-disjunction (unequal separation) of sister chromatids possibly resulting in many genetic disorders happen during what phase of meiosis? a, anaphase I b. prophase I c. telophase I d. anaphase II e. telophase II

d. anaphase II

Centrosomes are made of .... and they .... a. microfilaments; are the region where the membrane constricts during cytokinesis b. centrioles; are constricted regions of metaphase chromosomes c. actins; are the central region of the cell d. centrioles; determine the plane of cell division e. microtubules; are part of cilia

d. centrioles; determine the plane of cell division

Which of the following would slow down or inhibit key enzymes of Krebs cycle and glycolysis? a. excess amount of ADP and Pi b. limited amount of ATP c. excess amount of NAD+ d. excess amount of citrate e. limited amount of FADH2

d. excess amount of citrate

When RuBisCo enzymes was modified to reduce the binding of oxygen to minimize photorespiration, the enzyme activity to fix CO2 to carbohydrate was also decreased. A possible explanation to this result is the.... a. carbon fixation reaction requires O2 b. modified enzyme prefers O2 and not CO2 c. modified enzyme prefers CO2 and not O2 d. modified enzyme lost the binding to both O2 and CO2 e. carbon fixation reaction requires light and water

d. modified enzyme lost the binding to both O2 and CO2

Why is it important to reduce the chromosome numbers in half for sexual reproduction of humans? a. we do not need that many chromosomes and less is better b. skin and liver cells are sensitive to increased chromosomes number c. the sperm and egg cells start with doubt,e the chromosome number d. the sperm and egg cells fertilize and double the chromosome number e. if we continue to half the chromosome number in meiosis then we will need a small set of chromosomes after evolution

d. the sperm and egg cells fertilize and double the chromosome number

Which of the following statements about mitosis is true? a. the chromosome number in the resulting cells is halved b. DNA replication is completed in prophase c. crossing over occurs during prophase d. two genetically identical daughter cells are formed e. it consists of two nuclear divisions

d. two genetically identical daughter cells are formed

When does cyclic election flow (at Photosystem I) important for photosynthesis? a. when there is abundance ATP b. when there is a shortage of NADPH c. when there is a shortage of ATP d. when there is abundance of NADPH e. when there is equal amount of ATP and NADPH

d. when there is abundance of NADPH

Which of the following represents potential energy? a. chemical bonds b. water in a dam c. charged battery d. A and B only e. A B and C are correct

e. A B and C are correct

The free energy change of a system in deltaG=deltaH-T(deltaS). Which of the following is INCORRECT? a. deltaG can be negative if enthalpy decreases b. T is the absolute temperature and can change the deltaG c. deltaG can be negative if entropy and temperature increases d. deltaS is the change in entropy and deltaH is change in enthalpy e. a positive deltaH and negative deltaS can make deltaG negative

e. a positive deltaH and negative deltaS can make deltaG negative

When one consumes excess amounts of carbohydrates, they gain weight and store excess energy as fat. Conversion of carbohydrates to fat will involve the intermediate .... a. ATP b. starch c. citrate d. NADH e. acetyl CoA

e. acetyl CoA

The energy is stored in the form of ... in food a. citrate b. fructose c. NAD+ d. ATP e. covalent bonds

e. covalent bonds

What is the reaction between exergonic and exothermic reactions? a. they are typically unrelated, but can be coupled wit ATP hydrolysis b. every exothermic reaction leads to a subsequent exergonic one c. every exergonic reaction is also an exothermic one d. both result in a reduction of entropy in the universe e. exothermic reactions can also be exergonic processes

e. exothermic reactions can also be exergonic processes

Migratory birds store or carry limited amounts of stored energy or food but fly over long distances. Which of the following process is most utilized in such situation to make the most amount of ATP for their flying? a. glycolysis b. ethanol fermentation c. lactate fermentation d. Krebs cycle e. oxidative phosphorylation

e. oxidative phosphorylation

The phases of meiosis that cause the most variation in the four daughter cells are... a. prophase I and telophase II b. prophase II and anaphase II c. metaphase I and telophase II d. anaphase I and prophase II e. prophase I and metaphase I

e. prophase I and metaphase I

The reaction shown below is a/an .... and it occurs during the process of .... *reaction in screenshots* a. reduction.... Krebs cycle b. photophosphorylation.... glycolysis c. oxidative phosphorylation.... Krebs cycle d. substrate level phosphorylation.... Krebs cycle e. substrate level phosphorylation.... glycolysis

e. substrate level phosphorylation.... glycolysis

Suppose a thykaloid is somehow punctured so that the interior of the thykaloid is no longer separated from the stoma. This damage will have the most direct effect on which of the following processes? a. the absorption of light energy by chlorophyll b. the splitting of water c. the flow of electrons from photosystem II to photosystem I d. the reduction of NADP+ e. the synthesis of ATP

e. the synthesis of ATP

Use the cell diagram show below **screenshot** for the following questions. A. Mark at least one major event that occurs in each key stages B. Calculate the percent time spent on various stages C. Mark the control points that regulate cell division and write the rationale for such control D. Mark how the cyclin and kinase levels will change at various stages of cell cycle

A. check the book B. calculate C. G1 check point=decide if cell will divide or go to G0 S check point= to make sure if the DNA replication went OK G2 check point= to determine if the cell components are multiplied and the conditions are right for cell division M check point= check if the chromosomes have been evenly divided between the two daughter cells D. Cyclin level peaks at G2 phase- combines with CDK 2 to make MPF to initiate mitosis and then activate proteases that will degrade cyclin, which will decline in G1 and then gradually builds up in S and peaks in G2 again

Draw a bacterial cell and eukaryotic cell showing main components needed for aerobic respiration in each. Label the diagram and show the locations of where glycolysis, Krebs cycle and oxidative phosphorylation occur in each of them.

Bacteria cytoplasm: glycolysis, Krebs plasma membrane: ETC/OP Eukaryote cytoplasm: glycolysis matrix: acetyl-CoA formation and Krebs mitochondrial inner membrane: ETC/OP

Why do the respiratory poisons such as cyanide and carbon monoxide kill the cells or the organism? Elaborate as to what happens when the electron transport is blocked and why other pathways in reparation also stop

CO blocks movement of O2 into cells where it will accept electrons at the end of ETC Cyanide blocks electrons at end of ETC from moving onto 1/2 O2 When ETC is blocked, regeneration of NAD+ is stopped which inhibits citrate synthase and stops glycolysis at GDH (uses NAD+ as a substrate)

Even if a couple has a million children (or more) not even two will have identical genetic make up and traits unless they are identical twins. What are the three reasons for such genetic variation and how are identical twins born?

Crossing over (prophase I) Independent assortment (metaphase I and II) Random fertilization Identical twins are formed by a split shortly AFTER fertilization, creating two different clumps of cells with identical genomes, each developing into a separate individual

Having 3 copies of the chromosomes 21 causes down syndrome. Propose a possible way as to how this may happen during meiosis.

During anaphase II of meiosis II, sister chromatids of chromosome 21 failed to separate, resulting in one gamete with no copy of chromosome 21 and one gamete with two copies of chromosome 21. The gamete containing no copy of chromosome 21 would not produce viable offspring. The gamete containing an extra copy of chromosome 21 will produce a viable offspring after fertilization with another normal gamete. This may also happen due to uneven separation in anaphase I resulting in gametes with two copies of chromosome 21. This uneven separation is referred to as non-disjunction

The energy to make ATP in oxidative phosphorylation comes from..... a. FAD b. NADH c. NAD+ d. ATP e. the O2 we inhale

b. NADH

Methanol is toxic and any accidental drinking of methanol can make one blind or cause death. A person who drank some methanol is asked to drink ethanol as an antidote. Shown below in the enzyme reaction of Alcohol Dehydrogenase (ADH) on these two substrates. Briefly explain how this treatment works. Methanol+ADH-->Formaldehyde Ethanol+ADH-->Acetaldehyde

Formaldehyde is toxic, especially to the liver. Acetaldehyde is NOT. Ethanol competes for the same active site of ADH that methanol binds to. ADH is so busy converting ethanol to acetaldehyde that the kidneys excrete methanol from the body before a lethal amount of formaldehyde can build up

While animals will be killed by cyanide, plants are not affected by cyanide. Why?

In addition to the conventional complex IX which pumps protons against the H+ gradient, many plant mitochondria contain alternative complex IV which does not pump protons, but does use O2 to oxidize cytochrome C and is cyanide-insensitive Gleason F, Chollet R. 2011. Plant Biochemistry. Sudbury (MA): Jones & Bartlett Learning. 49 p.http://www.ncbi.nlm.nih.gov/pubmed/1883834

Label the following examples as exergonic or endergonic, exothermic or endothermic and if entropy increases or decreases based on the changes in free energy, enthalpy and entropy respectively. -osmosis -active transport -respiration -photosynthesis -amino acid biosynthesis -burning fossil fuels

Osmosis: -G -H (or H=0) +S Active transport: +G +H -S Respiration: -G -H +S Photosynthesis: +G +H -S Amino acid biosynthesis: +G +H -S Burning fossil fuels: -G -H +S

Compare and contrast substrate level phosphorylation with oxidative phosphorylation providing two similarities and tree differences

Similarities: -both make ATP by combing ADP+Pi-->ATP -couple energy from an exergonic process into the endergonic phosphorylation process Differences: -SLP produces much less ATP compared to OP -SLP driven by chemical energy source -OP happens exclusively across mitochondrial membrane, SLP happens in the cytoplasm and matrix -SLP much faster than OP -OP requires O2, SLP happens in presence or absence of O2

Compare and contrast photophosphorylation and oxidative phosphorylation with two similarities and three differences

Similarities: both make ATP and use electron transport chain, proton concentration gradient and Chemiosmosis to make ATP Differences: Oxidative phosphorylation occurs in mitochondrial inner membrane, utilizes NADH/FADH2, O2 and releases NAD+/FAD and H2O. Photophosohorylation occurs on thykaloid membrane and uses light energy to make ATP

Propose a hypothesis for chronic fatigue syndrome and how you can overcome this.

Slow catalysis or weak substrate binding of any enzyme in OxPhos. Treatment by mimicking signals that would increase expression of this enzyme

The daughter cells become haploid after what phase of meiosis? a. anaphase I b. prophase I c. telophase I d. anaphase II e. telophase II

a. anaphase I

CAM plants can keep stomata closed in daytime, reducing water loss. This is possible because they .... a. fix CO2 into organic acids during the night by PEP carboxylase b. use photosystems I and II during day and night c. use the enzyme phosphofructikinase, to fix CO2 more effectively d. fix CO2 into sugars in the bundle-sheath cells e. fix CO2 into pyretic acid in the mesophyll cells

a. fix CO2 into organic acids during the night by PEP carboxylase `

Bacteria typically have ...., whereas eukaryotes have .... a. one chromosome that is circular; many chromosomes that are linear b. several chromosomes that are circular; many chromosomes that are linear c. one chromosome that is linear; many chromosomes that are circular d. two chromosomes that are circular; eight chromosomes that are linear e. many chromosomes that are linear; one chromosome that is circular

a. one chromosome that is circular; many chromosomes that are linear

Draw a cell with two (one large and one small) sets (diploid) of homologous chromosomes going through meiosis I and II. Label the stages in which the cause of genetic variation (Q. B2) occur.

look at figures in course guide**

List 3 real life examples of how enzyme activity is affected by pH, salt concentration and temperature

pH: activation of hydrolytic enzymes by the low pH of stomach acid, high pH of bile, or low pH of lysosome. Entire activity of endomembrane system is governed by pH Salt concentration: dependence of human enzyme on correct intracellular salt concentration (too high-->dehydration and death). Likewise saltwater and freshwater fish suffer shock and death if placed in salt concentrations they're not adapted to Temperature: freezing and refrigerating food slows enzyme reaction rates in organisms that cause spoilage and in the food itself. Blanching before freezing completely deactivated enzymes and further increases shelf-life. A moderate fever increases activity of immune system and caused difficulty for invading organisms. Too high of a fever will inactivate enzymes necessary for brain function causing death.