Iowa State University



BIOL 212 Section 1 SIExam 2 ReviewWhat is the difference between an exergonic and endergonic reaction?Exergonic: The products of the reaction have more free energy than the reactants. Because of this, energy is released. Can occur spontaneously.Endergonic: The products have more free energy than the reactants, so energy is used. Cannot occur spontaneously. In the space below, draw two graphs, each one showing the change in free energy (ΔG) during exergonic and endergonic reactions.center200025Exergonic EndergonicThe activation energy is how much energy is needed to reach the transition state, which is exactly sounds like. The amount of free energy needed to finish the reaction. Which one has a higher activation energy?Enzymes are proteins that can accelerate specific chemical reactions, sometimes speeding the reaction a million-fold! How do they do this?They facilitate reactions by bringing the reactants, or substrates together at an activation site. This allows them to reach transition state easier, lowering the activation energy.Is cellular respiration an endergonic or exergonic reaction?We are taking glucose and breaking it down into carbon dioxide, water, and energy. We use that energy to create ATP.What are oxidation and reduction reactions?Oxidation: a molecule loses a proton and electron. Reduction: a molecule gains a proton and electron.These reactions must happen together, but they release a buttload of energy.Step in respirationWhere does it occur?What are the reactants?What are the products?Net energy gainGlycolysisCytosolGlucose2 pyruvate2 NADH, 2 ATP (4 ATP are produced, but 2 are used)Pyruvate processingMitochondriaPyruvateAcetyl CoA, CO22 NADH Citric Acid CycleMitochondriaAcetyl CoA + oxaloacetate = citric acidOxaloacetate, 2 CO2 6 NADH, 2 GTP, 2 FADH2For each step in cellular respiration, fill in the location where it occurs, which molecules come in, which come out, and the net energy gain (amount of energy per glucose).As the complexes pass electrons down the electron transport chain, protons are pumped across the inner mitochondrial membrane. What does this do?Creates a gradient of protons across the inner mitochondrial membrane. Commonly known as the proton motive force (PMF)Think of it like a dam. The protons build up on the other side of the membrane and want back in, but they require a transport protein. The mitochondria harness this pressure gradient to make ATP, like the turbines of a dam.The PMF drives a turbine in the mitochondrial inner membrane called ATP synthase. As protons come through, the protein changes in configuration, allowing for ATP to be synthesized. Is photosynthesis an endergonic or exergonic reaction?The energy going into the reaction is from lightPhotosynthesis occurs in two main steps: light and dark reactions. Where do these reactions generally do and where are they located?Light reactions: occur in the thylakoid membranes and make ATP and NADPH used in dark reactions from sunlight and H2O. O2 is a byproduct. This is called the light reaction because it requires light while dark reactions do not.Dark reactions: occur in the stroma and reduce CO2 to produce sugars. This is also called the calvin cycle. This doesn’t necessarily occur in the dark, but it doesn’t require light. Which wavelengths are the best for photosynthesis? (Hint: think about the pigments most common in plants).Reds and blues are the bestThe action spectrum is the rate of photosynthesis at different wavelengths, absorption spectrum is how different wavelengths are absorbed by different pigments. Chlorophyll molecules form complexes called photosystems. There are two types in the thylakoid membrane called Photosystem II and I. What does each do?In Photosystem II, water is split, and light drives the electron to a higher energy state. It is called Photosystem II because it was discovered second. The electrons then follow an electron transport chain, pumping protons into the cell that eventually power ATP producing via the ATP synthaseLight can excite the electron again in Photosystem I and reduce NADP+ into NADPHIn the dark reactions, the enzyme rubisco fixes carbon to form carbohydrates like glucose. Rubisco is inefficient, why is this?O2 and CO2 compete for the active site of rubisco.O2 promotes photorespiration, or the breakdown of the carbon that has been fixed already.C4 plants have adapted to avoid this by developing a two-step process. CO2 is brought in and fixed by another molecule, then is transported to separate cells to be fixed by rubisco. This is meant to protect rubisco from O2 and allows plants to live in especially dry environments. What are the four phases of the cell cycle?In the table below, fill out what happens in each phase and what it looks like.Cell Cycle PhaseWhat happens here?What does it look like?Gap 1Cell growsSynthesisDNA is synthesizedGap 2Cell continues to growProphase*Chromosomes condense and nuclear membrane breaks downMetaphase*Sister chromatids arrange themselves along the middle of the cellAnaphase*Sister chromatids are separated and pulled to opposite sides of the cellTelophase*Nuclear membranes form around the separated chromosomes*these phases are all part of mitosis, or M phaseImagine we have a cell culture that takes 30 hours to double in size. You can tell right away that 10% of the cells are in mitosis. You next conduct a BrdU labeling experiment and find that 50% of cells are labeled at a given time. You finally add a drug that arrests the cell at the beginning of M phase. When reversing it, it takes 8 hours to reach S phase. How long is each phase in the cell cycle?Total length of cycle = 30 hoursM phase = 30*.1 = 3 hoursS phase = 30*.5 = 15 hoursG1 = 8 hours – 3 hours = 5 hoursG2 = 30 hours – 3 hours – 15 hours – 5 hours = 7 hoursCyclin, a portion of the Mitosis-promoting factor that induces mitosis, fluctuates throughout the cell cycle. When are the cyclin levels highest? What happens when cyclin levels are high?Cyclin is only a portion of the MPF, the cyclin-dependent protein kinase does not fluctuate, however. Cyclin levels increase during interphase and peak during M phase while CdK remains constant. When levels are high, more MPF is active and more proteins are phosphorylated. During anaphase, enzymes break down the cyclin subunits, leaving the CdK.There are three checkpoints during the cell cycle: one at the end of G1, one at the end of G2, and one at the end of M. What does each checkpoint check for?G1: checks for nutrient availability and DNA integrity. If DNA is damaged, p53 pauses the cycle or initiates apoptosis, or cell death. P53 is important for tumor suppression.G2: the cycle is stopped if chromosome replication is not complete or if DNA is damaged.M: Cell cycle stops if the chromosomes are not properly attached to the mitotic spindle. This prevents incorrect chromosome separation.On the strand below, label the 5’ and 3’ ends. Which way is DNA built?DNA is built from 5’ to 3’. Different strands run antiparallel to each other.The helical structure of DNA is stabilized by hydrogen bonds between the nitrogenous bases. Correctly match the following: Adenine, Cytosine, Guanine, ThymineAdenine = ThymineCytosine = GuanineHow I remember it is the “straight” letters and “curvy” lettersA and T form 2 hydrogen bonds while G and C form 3Because of these base pairs, one strand can act as a template for the formation of another strand.DNA replication is semiconservative. What does this mean?During the replication, the parent strand is split in half. Each half is used as a template for a new strand. If you remember, the DNA strands are antiparallel to each other. Why could this cause problems at the replication forks?One strand will be built towards the replication fork, the other will be built away from the replication for. These are referred to as the leading and lagging strands.While the leading strand is synthesized in a continuous manner, the lagging strand is not.In the table below, fill in the functions of each enzyme/structure used for DNA replication.Enzyme/StructureFunctionHelicaseUnwinds the DNA strandSSBPsHolds the DNA strand openTopoisomeraseRelieves tension further down the strandRNA PrimerAllows initiation of synthesis by providing a free 3’OH groupPrimaseSynthesizes the RNA primerDNA Polymerase IIIAdds bases to the 3’ end of the primer/strandDNA Polymerase IRemoves the RNA primer and fills the gapDNA LigaseJoins the Okazaki fragments into a continuous strand TelomeraseAdds repeating bases at the end of the lagging strand to prevent shorteningErrors in replications only occur once per one billion bases, but an incorrect base is added about once every 100,000 bases. What are some ways that errors can be fixed?DNA polymerase proofreads as it works, if there is a mismatch, the enzyme pauses and removes the mismatched base.Nucleotide excision repair recognizes damage like thymine dimers. Enzymes remove single-stranded DNA from damaged sections and lets the complimentary strand act as a template for resynthesis. Below we have a metabolic pathway. What would happen if we were to use radiation to knock out gene 2? How about gene 3? In order to grow, the cell needs the final product. 47625009969533909001022351990725104775685800114935PrecursorIntermediate 1Intermediate 2Intermediate 3Final Product Enzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 Gene 1 Gene 2 Gene 3 Gene 4Without gene 2, enzyme 2 will not be produced. There will be a buildup of intermediate 1, but the cell can still grow if given intermediates 2 or 3.Without gene 3, enzyme 3 will not be produced. There will be a buildup of intermediate 2, but will still grow if given intermediate 3.What are the 3 steps in the Central Dogma?DNAMessenger RNAProteinmRNA is produced from DNA via transcription while proteins are produced from mRNA via translation.Think of DNA, mRNA, and proteins like languages. DNA and mRNA are both made up of nucleotides, so converting between them is like transcribing in the same language.Meanwhile, proteins are made up of amino acids, so making a protein from mRNA is like translating into a new language. Each three-base code is called a triplet code or codon. Each triplet code corresponds to one amino acid, but most amino acids are coded by more than one combination. What are 2 differences between DNA and RNARNA is a single strand and uses U instead of TConvert the DNA sequence below into an amino acid sequence. Keep an eye out for the start and stop codons.5’ …ATG CCC TAC TAT CAC ATC ATT AGA GAT TAA… 3’3’ …TAC GGG ATG ATA GTG TAG TAA TCT CTA ATT… 5’5’ …AUG CCC UAC UAU CAC AUC AUU AGA GAU UAA… 3’Met-Pro-Tyr-Tyr-His-Ile-Ile-Arg-Asp-STOPIf you want more practice problems, go to , this is a random DNA sequence generator. Just be sure to look for that start codon. What are the three main types of mutations?Point mutations: a change in a single baseInsertions or deletions: involve multiple basesChromosome rearrangements: occur on the chromosome level.What is the difference between a missense and silent mutation?Missense mutations change the amino acid coded, silent mutations do not.Missense typically occur on the first nucleotide per codon, silent typically occur on the last one. Mutations can either be beneficial (increasing fitness), neutral (not affecting fitness), or deleterious (decreasing fitness). Which category(s) do most mutations fall under?Most are either neutral or deleterious. Silent mutations tend to be neutralI like to think of mutations as “if its not broken, don’t fix it”. Typically, an organism is already well adapted for its local environment, so it is very rare that a mutation would make it better. Both transcription and translation have the same names for their 3 steps: initiation, elongation, and termination. In the table below, fill in what happens in each step for each process.TranscriptionTranslationInitiationThe protein sigma guides the RNA polymerase to the DNA strand and binds to the promotermRNA strand binds to the small subunit of the ribosome.Initiator tRNA binds to the start codon.Large subunit then binds to the small, placing the initiator into the P siteElongationRNA polymerase unzips the DNA strand, building the mRNA from 5’-3’ based off the template strandAminoacyl tRNA enters the ribosome via the A site and binds to the codonPeptide bond forms between the amino acids The chain is “passed” from the tRNA in the P to the tRNA in the A siteThe ribosome moves down the mRNA strand 3 spots, opening a new codon and shifting the tRNA one site overThe tRNA in the E site is ejected from the ribosomeTerminationWhen the end is reached, the mRNA forms a hairpin-like structure due to complementary base pairs. This keeps RNA polymerase from functioning correctlyWhen the ribosome reaches the end codon, a releasing factor enters the A site. These look like aminoacyl tRNA but lack an amino acidThe peptide and mRNA strands are both released by the ribosomeThere are 61 different codons used for protein synthesis, but there are only 40 different tRNAs in humans. How does protein synthesis work if we have 20 less tRNAs?If you remember, codons tend to be redundant, almost all amino acids are coded for by multiple codons.The Wobble hypothesis states that the anticodon of the tRNA can still bind to a codon even when the third position is a nonstandard base pairing. For example, the G on the anticodon can bond with both C and USome tRNAs are able to base-pair with more than one codon. An operon is a group of genes in bacteria responsible for a single function, like a metabolic pathway. Compare and contrast the lac operon and the ara operon. How are they similar to each other in function? How are they controlled differently?Both only code for their specific genes when the sugar is present.The lac operon is controlled negatively, meaning a repressor protein prevents transcription of the genes by bonding to the operator. When lactose is present, it binds to this protein, releasing it from the operator and allowing for transcription.The ara operon is controlled both positively and negatively. When arabinose is present, it binds to an activator dimer, which guides the RNA polymerase to the initiator sequence similarly to sigma. When arabinose is not present, these dimers act as repressors, blocking the initiator and the operator for the araC gene that codes for the activators. ................
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