BIO 93 MIDTERM 2 REVISION: Cellular Respiration, Photosynthesis, and Molecular Biology, Exams of Advanced Education

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BIO 93 MIDTERM 2 REVISION

Which of the following is true concerning photosynthesis and cellular respiration? - In cellular respiration, glucose is oxidized and oxygen is reduced, while in photosynthesis, carbon dioxide is reduced and water is oxidized. Which of the following is true about enzymes? - Enzymes lower the activation energy for a reaction Which of the following is true for cellular respiration? - To proceed into the Citric Acid Cycle oxygen is required Which of the following is true for all exergonic reactions? - The reaction proceeds with a net release of free energy If a drug was administered that specifically makes the inner membranes of mitochondria and thylakoids more permeable to small, charged ions, what would be the effect on ATP production? - ATP production would decrease in both plants and animals What is meant by the description "antiparallel" regarding the strands that make up DNA? - The 5' to 3' direction of one strand runs counter to the 5' to 3' direction of the other strand. Transcription in eukaryotes requires which of the following in addition to RNA polymerase? - several transcription factors Cytosine makes up 42% of the nucleotides in a sample of DNA from an organism. Approximately what percentage of the nucleotides in this sample will be thymine? - 8% Suppose you are provided with an actively dividing culture of E. coli bacteria to which radioactive thymine has been added. What would happen if a cell replicates once in the presence of this radioactive base? - DNA in both daughter cells would be radioactive. The genetic code is essentially the same for all organisms. From this, one can logically assume which of the following? - A gene from an organism can theoretically be expressed by any other organism. If one strand of DNA is 5'-CGGTAC-3', then the corresponding complementary strand would be - 3'-GCCATG-5' If one strand of DNA is 5'-CGGTAC-3', then the corresponding RNA transcript would be

• 3'-GCCAUG-5'

Accuracy in the translation of mRNA into the primary structure of a polypeptide depends on specificity in the - bonding of the anticodon to the codon and the attachment of amino acids to tRNAs. If a point mutation occurred in the TATA box upstream of a DNA sequence coding for a gene, what would be the immediate consequence during the initiation step of transcription? - Transcription factors would be unable to bind, preventing the recruitment of RNA polymerase II. Which of the following is the first event to take place in translation in eukaryotes? - the small subunit of the ribosome recognizes and attaches to the 5' cap of mRNA A karyotype is an image of all the chromosomes in the cell. Based on what you know about the cell cycle, at what stage of the cell cycle are chromosomes in a karyotype imaged? - Mitosis The main role of mitosis is to: - Generate cellular clones by copying a cell's DNA and evenly dividing it between two diploid daughter cells. A cell with a diploid number of 24 would have __ pairs of chromosomes and division via mitosis would result in __ cells containing chromosomes __ each. - 12, 2, 24 p53 is an extremely important tumor suppressor. A loss of function mutation in this gene would be expected to cause cancer by: - Increasing cell cycle activity by decreasing production of proteins that inhibit the cell cycle A nonsense mutation occurs in one of the genes responsible for degrading cyclins. What would be the most likely effect of this mutation? - Increased cell cycle activity resulting in increased cell division What do you think is the best way to uncontrollably increase cell division? - express an oncogene to overstimulate cell cycle What do you think is the best way to uncontrollably increase cell division? - express a tumor suppressor gene that is mutated to remove inhibitory signaling of cell cycle Which of the following statements about enzymes is TRUE? - - Enzymes speed up reaction rate by increasing the energy available

• Enzymes can be synthesized on free or bound ribosomes*

In cellular respiration, glycolysis - - is an endergonic reaction because it requires an enzyme

• takes place in both the cytoplasm and the mitochondrial matrix
• produces the electron carriers NADH and FADH
• generates ATP* Explanation: In cellular respiration glycolysis takes place in the cytoplasm and the Citric Acid cycle occurs in the mitochondrial matrix. This process generates NADH and ATP but not FADH2. It also produces pyruvate but this is not converted to acetlyCo-A until pyruvate enters the mitochondrion. This process does require enzymes but it is exergonic not endergonic since the products have lower energy than the reactants. Which stage/s of cellular respiration occurs in the mitochondrion? - - All
• glycolysis and oxidative phosphorylation
• citric acid cycle and chemiosmosis* Explanation: Glycolysis occurs in the cytoplasm but the rest of cellular respiration occurs in the mitochondrion including the citric acid cycle, electron transport and chemiosmosis (which together are oxidative phosphorylation). In substrate-level phosphorylation, ATP synthesis is mediated by enzymatic transfer of a phosphate group from a substrate molecule to ADP. - - true*
• false Explanation: Substrate level phosphorylation occurs both in glycolysis and in the citric acid cycle. However, it only accounts for a small percentage of the ATP synthesized in cellular respiration. Chemiosmosis depends most directly on: - - pumping of sodium ions
• co-transport of H+ ions and sucrose
• passive diffusion of H+ ions*
• exocytosis of H+ ions Explanation: ATP synthesis is powered by flow of H+ ions across the inner mitochondrial membrane through a protein complex called the ATP synthase. What do lactic acid fermentation and oxidative phosphorylation have in common? - - Both regenerate NAD+ from NADH*
• Both produce large quantities of ATP
• Both break down sugars to carbon dioxide
• Both produce alcohol
• Both create a hydrogen ion gradient Explanation: In the absence of oxygen ATP can be made and NAD+ converted to NADH during glycolysis. However to regenerate NAD+ needed for more glycolysis the electrons from NADH are moved back onto pyruvate to make lactic acid. In the presence of oxygen, glycolysis makes some ATP and NADH, and the rest of the electrons are harvested from pyruvate during the citric acid cycle to make more NADH, FADH2 (ATP also made by substrate level phosphorylation). During oxidative phosphorylation the NADH and FADH2 carrier donate their electrons to the pumps in

the electron transport chains and release H+ to matrix, thus powering the pumps and generating NAD+ and FAD. The pumps move H+ ions into the intermembrane space and these travel back into matrix down their concentration gradient through the ATP synthase protein complex which combines ADP+Pi to make ATP. What are the high energy molecules that enter the Calvin cycle? - - water

• NADH
• NADPH*
• glucose
• oxygen Explanation: NADPH is carrying high-energy electrons to be used in creating glucose in the Calvin cycle. Carbon dioxide is the source of carbon and oxygen is produced by the light reactions but it is released to atmosphere and does not contribute to Calvin cycle. NADH is the electron transporter in cellular respiration. Where are chlorophyll molecules located? - - cytoplasm
• stroma
• outer chloroplast membrane
• thylakoid membrane*
• vascular system Explanation: Chlorophyll molecules are in the thylakoid membranes inside chloroplasts. Two batches of radish seeds of equal weight were put in two different Petri dishes with identical amounts of water and light. Dish A was grown in normal air. Dish B was grown in pure oxygen. After 10 days you removed all the water and measured the dry weight of both dishes and found that: - - Dish A was heavier than Dish B*
• Dish A was lighter than Dish B
• Dish A and Dish B both produced seedlings and had same weight
• Seeds germinated and produced seedlings only in Dish A
• Seeds germinated and produced seedlings only in Dish B Explanation: This requires that you remember that photosynthesis requires not only water and light but CO2 which is present in air but not in pure oxygen. Therefore seeds in both dishes can germinate and produce seedlings since before leaves are formed cellular respiration using energy stored in the seeds are used to produce ATP and CO is released so both loose weight and would be the same weight early on. However, after 10 days the seedlings in air would have leaves and be able to fix carbon and gain weight. In contrast, the seedlings in pure oxygen would have leaves but they would not gain weight since they cannot fix carbon without any CO2. So dish grown in air would be heavier than the dish grown in pure oxygen. Chemiosmosis is important in synthesis of ATP in which of the following processes? - - Photosynthesis
• Cellular respiration
• Glycolysis
• Both photosynthesis and cellular respiration*

• to produce a primer for DNA polymerase to extend Explanation: Because the double helix has a twist, pulling the strands apart creates torsional stress ahead of the fork; this is relieved by topoisomerase (also called DNA gyrase). Without topoisomerase, torsional stress would eventually halt replication by preventing helicase from continuing to separate the DNA strands. Topoisomerases break PDE bonds in the backbones, helicase disrupts hydrogen bonds, not covalent bonds, that hold the two strands together. SSBs prevent re-annealing of the strands, and RNA primase makes the RNA primer. One DNA strand must be replicated discontinuously because: - - phosphodiester bonds between DNA nucleotides can only be broken on one strand at a time
• RNA polymerase can only bind on one side of the replication fork at a time
• there are multiple origins of replication
• the two strands have complementary sequence
• the two DNA strands have opposite polarity* Explanation: Phosphodiester bonds are formed not broken during replication. When the RNA primer is removed, phosphodiester bonds involving RNA bases are broken, but this can happen on both strands at the same time. DNA replication occurs on both sides of the fork. While there are multiple origins or replication in mammals and the strands are indeed complementary, these facts do not explain why one strand is synthesized discontinuously. Because replication is 5' to 3' and the strands are anti-parallel (opposite polarity), DNA synthesis must be discontinuous. Gene expression patterns - - are static once a cell has differentiated
• are the same in a liver cell and a neuron
• are the same between individuals of a particular species
• are determined in part by the availability of specific transcription factors* Explanation: Gene expression patterns are controlled in part by cellular differentiation, but are also affected by environmental factors - they are definitely dynamic, not static. While the liver cells and neurons in one organism will have the same genes, they will not express these genes in the same pattern. Gene expression patterns in my liver and your liver would be similar, but different - they would be affected by what we each ate for lunch, our difference in age, diseases we might have, etc. Transcription factors generate gene expression patterns by binding to some but not all gene promoters and then recruiting RNA polymerase to the genes whose promoters they bind. Nuclear pores prevent immature mRNA from moving to the cytosol. All of the following features would be present in an mRNA that is allowed to pass through a nuclear pore EXCEPT: - - introns*
• 5' cap
• poly A tail
• an AUG start codon
• Stop codon Explanation: Introns are spliced out in the nucleus before the mRNA is allowed to pass through the nuclear pore. All the other items would be present in an mRNA in the

cytosol (mRNA code for proteins so would have a start and stop codon - rRNA or tRNA would not as they function as RNA). Alternative splicing of mRNA is a mechanism for: - - stabilizing mRNA transcripts

• translating the mRNA in the opposite direction (3' to 5')
• splicing mRNA in the cytosol rather than the nucleus
• addition of a 3' cap to the primary RNA transcript
• producing different proteins from a single gene* Explanation: Alternative splicing refers to the ability to splice out exons with the introns in some cases to make different but related proteins from two different mRNA transcribed from the same gene. The cap is on the 5' end. Alternative splicing does not increase mRNA stability. The other two options (translating 3' to 5' and splicing in the cytosol) never happen. The sequence of the template strand of a piece of DNA is 5' AAA TGC CCT GAT 3'. The sequence of the RNA transcript would be: - - 5' AAA TGC CCT GAT 3'
• 5' AAA UGC CCU GAU 3'
• 5' AUC AGG GCA UUU 3'*
• 5' UUU ACG GGA CUA 3'
• 5' TTT ACG GGA CTA 3' Explanation: Remember that the new nucleotides will be polymerized 5' to 3' and will be anti-parallel to the template. This means the template is "read" 3' to 5' by the polymerase. You can write the complementary strand 3' to 5' right above the template then write it backwards to get the answer. By convention, DNA and RNA are always presented 5' to 3' when one strand is shown. The energy for mRNA translation comes from: - - the triphosphates on the incoming amino acid
• the triphosphates on the ribosomal RNA
• ATP and GTP*
• ATP
• the negative potential across the plasma membrane Explanation: Translation requires ATP to charge the tRNA - the energy in the aminoacyl bond is used by the ribosome to form the peptide bond. GTP is required to form the initiation complex, for ribosomal translocation, to increase the fidelity of codon-anti- codon pairing, and to disassemble the ribosome when the stop codon is reached. A tRNA molecule: - - is a complex of RNA and proteins
• has secondary structure because complementary bases form covalent bonds
• can pass through the nuclear pore*
• is transcribed from a RNA template
• is translated on free ribosomes Explanation: tRNA functions as pure RNA. Their secondary structure is the result of intramolecular hydrogen bonding (non-covalent bonds) between complementary bases. As they are transcribed from a DNA template in the nucleus and function in the cytosol,

• may contain different numbers of genes
• may contain different alleles of the same genes*
• remain associated during meiosis II Explanation: Each member of a homologous chromosome pair is inherited from one of your parents (one from each). The centromere is in the same relative position on homologus chromosomes and they have the same genetic loci in the same order. However, your mom and dad may have given you different versions (alleles) of the same gene. Homologous chromosomes separate during meiosis I and are no longer associated in meiosis II. Histones are associated with DNA: - - only during mitosis and meiosis
• when DNA is exported to the cytosol for transcription
• at all times except briefly during DNA synthesis and when genes are transcribed*
• in order to recruit ribosomes to DNA
• because they are attracted by DNA's positive charge Explanation: Histones are always associated with DNA except when the DNA is being copied by DNA or RNA polymerase. DNA has a negative charge and histones have a positive charge that helps neutralize this to facilitate DNA packing. DNA is not exported to the cytosol and ribosomes do not bind to DNA. A human liver cell that is not dividing has - - 23 pairs of homologous chromosomes*
• 22 pairs of homologous chromosomes
• 92 chromatids
• 46 pairs of homologous chromosomes Explanation: A liver cell has 46 chromosomes but 23 pairs of homologous chromosomes. Chromatids are present only during cell division. Which of the following sequences is in ORDER, from early to late, in the cell cycle? Not all events in the entire cell cycle are shown in any of the sequences - - interphase, prophase, G2, DNA replication, mitosis
• prophase, metaphase, S phase, anaphase, telophase
• G1, S, G2, DNA replication, prophase
• Interphase, S, G1, prophase, metaphase
• G1, S, prophase, metaphase, cytokinesis* Explanation: G1 is followed by S which is when DNA replication occurs. This is followed by G2 and then mitosis in which prophase is before metaphase and metaphase is before cytokinesis. A cell undergoing mitosis with a mutation in an orc1 gene has 4 centrosomes. This is most likely to disrupt: - - spindle formation*
• nuclear envelope break down
• pairing of sister chromatids
• crossing over Explanation: Accurate chromosome segregation during mitosis requires formation of a microtubule spindle apparatus. This requires 2 centrosomes that are located a the two

poles. If there are 4 centrosomes, then the spindle is not likely to form correctly. This should not affect nuclear envelop breakdown. Pairing of sister chromatids and crossing over occurs in meiosis, not mitosis. Each sister chromatid at metaphase of mitotic cell division is attached to a mitotic spindle fiber at a structure called the - - centriole

• kinetochore*
• MTOC
• aster fibers Explanation: The kinetochore is a structure of proteins associated with specific sections of chromosomal DNA at the centromere. In telophase of mitosis, the mitotic spindle breaks down and the chromatin uncoils. This is the opposite of what happens in - - S-phase
• anaphase
• metaphase
• prophase*
• interphase Explanation: During prophase the chromosomes have condensed and the mitotic spindle forms. One hallmark characteristic of a cancer cell is: - - anchorage dependence
• normal cell cycle control
• anchorage independence*
• expression of proto-oncogene
• density-dependent inhibition The process of crossing over: - - results in the exchange of genetic material between sister chromatids
• exchanges sections of non-sister chromatids that have different genetic loci
• occurs during both mitosis and meiosis
• takes place during meiosis I*
• reduces genetic variability Explanation: Crossing over occurs between non-sister chromatids during prophase of meiosis I and increases the genetic diversity of the gametes. Crossing-over exchanges sections of non-sister chromatids that have the SAME genetic loci. Crossing over does not occur during mitosis. Meiosis I is sometimes referred to as the "reduction division." This makes sense because: - - the length of prophase I is reduced relative to the length of prophase II
• the number of chromosomes is reduced in meiosis I*
• cells perform more reduction reactions than oxidation reactions during meiosis I
• the number of different proteins required for meiosis I is reduced relative to meiosis II Explanation: The term "reduction" refers to the reduction in the number of chromosomes/cell; if you are confused about how to count chromosomes, count