Agenda: 1. High-Yield Science: Enzyme Kinetics 2. Science Passage Strategy 3. Science Questions: Type and Rephrase 4. Science Questions: Investigate and Match In this lesson, you’ll learn to: • Explain the significance of key aspects of the double-reciprocal Lineweaver– Burk format, including axes, intercepts, units, and slopes • Identify Vmax and Km on both Michaelis–Menten and Lineweaver–Burk plots • Plot the effects of competitive inhibition on both graph types Enzyme activity is often graphed using a Michaelis–Menten plot. However, enzyme activity may also be graphed using an alternative format, the Lineweaver–Burk plot. HMG-CoA reductase is the rate-limiting enzyme of cholesterol synthesis. Statins, such as atorvastatin (Lipitor), simvastatin (Zocor), and rosuvastatin (Crestor) are routinely used to treat patients with high cholesterol because they are competitive inhibitors of HMG-CoA reductase. How would the use of a statin affect the Lineweaver–Burk plot of HMG-CoA reductase? A Michaelis–Menten plot clearly shows the asymptotic behavior of a plot of an enzyme’s kinetics. What is the plot’s basic shape? How does it display KM and Vmax? Reaction Velocity Substrate Concentration [S] V (s/µmol) A Lineweaver–Burk plot shows the same information as a Michaelis– Menten plot. How does it display KM and Vmax? What are the benefits of a Lineweaver–Burk plot, compared to a Michaelis–Menten plot? 1 Needs Review 1 [S] (mM–1) Why does a competitive inhibitor increase an enzyme’s KM while leaving its Vmax unchanged? V (s/µmol) A competitive inhibitor will have the effect of increasing the slope of a Lineweaver–Burk plot. Why? 1 Needs Review 1 [S] (mM–1) A competitive inhibitor will have the effect of increasing the slope of a Lineweaver–Burk plot. Why? Reaction Velocity Needs Review Substrate Concentration [S] Reflect: What are 3 things from this lesson you recalled and what are 3 things you need to review more? I knew: I need to review: 1. 1. 2. 2. 3. 3. The content in this lesson can be found in Biochemistry Review Chapter 2: Enzymes. In this lesson, you’ll learn to: • Preview a science passage at a glance, determining likely topic and difficulty • Utilize the highlight, outline and interrogation methods as they apply to science passages Science Topics • Organic Chemistry Reactions (Organic Chemistry Review Chapter 1) • Biology and Behavior (Behavioral Sciences Review Chapter 1) • Translation (Biochemistry Review Chapter 7) Science Knowledge MCAT Expertise MCAT Science Science Knowledge Skills Data and Statistical Analysis Scientific Reasoning and Problem Solving Experimental and Research Design MCAT Strategy—Science Passages PREVIEW for difficulty Decide whether to read the passage now or later CHOOSE your approach Decide whether you will Highlight, Outline, or Interrogate the passage READ and DISTILL the meaning of each paragraph Use keywords and science terms to identify the most important and testable content, and use the approach you choose to extract major takeaways from each paragraph Needs Review In this section, you’ll learn to: • Preview a science passage at a glance, determining likely topic and difficulty Practice Passage 1 – Chem/Phys Styrene is used extensively in the manufacture of plastics, rubber, and resin. It is a colorless liquid with a sweet, aromatic odor at low concentrations and a sharp, disagreeable odor at high concentrations. Because its metabolite is reactive, styrene is classified as a mutagen. Studies have not yet proven definitively that exposure leads to cancer, but a causal link is strongly suspected; the U.S. National Toxicology Program describes styrene as “reasonably accepted to be a human carcinogen.” Styrene can be synthesized in the lab either by reacting sulfuric acid with compound A (1-phenylethanol), characterized by a mild hyacinth odor, or using zinc metal with compound B (1-phenyl-1,2 dibromoethane) in ethanol; Compound B can be synthesized by generating Br2 gas in situ from the reaction of potassium bromate and hydrobromic acid and irradiation with a lamp. The preferred method for styrene production on an industrial scale involves taking compound C (ethylbenzene) through a dehydrogenation reaction catalyzed by an amalgam of iron(III) oxide and potassium carbonate. Needs Review Practice Passage 2 – Psych/Soc In evolutionary psychology, a supernormal stimulus, or “superstimulus,” is an evolutionarily novel concentration of engaging factor that produces a stronger response than a typical one. Certain systems that govern the reaction to rewarding stimuli can be overloaded and their negative feedback component overridden. This hypothesis provides explanations for the number of excessive behaviors in society, often conceptualized as “behavioral addictions:” drug addiction, internet addiction, food addiction, and so on. The neurocircuitry and endocrinology underlying hunger and satiety may represent the best studied system in this regard. They clearly produce a physiological balance under certain conditions with regular stimulus, such as when a laboratory mouse fed rodent chow its whole life maintains a normal weight, but are dysregulated in other conditions that contain superstimuli, such as when that mouse fed a high-fat, high-carbohydrate diet becomes obese. The signals that encode hunger and satiety alter the brain’s dopaminergic reward system in multiple ways, affecting hypothalamic neurocircuits and neuropeptides in combination with peripheral hormones, to modulate midbrain dopaminergic activity and alter reward value. Ghrelin, a peptide hormone produced in the stomach, allows for preferential promotion of food-seeking and food-consuming behavior. It also increases the amplitude of dopamine release via AgRP/NPY neurons (agouti-related peptide/neuropeptide Y). Finally, by acting on the hippocampus, ghrelin promotes dopamine induced synaptic plasticity and future silencing of the reward cue. Needs Review Practice Passage 3 – Bio/Biochem It is well established that 1α(OH)2D3 (1,25D3), the active metabolite of vitamin D, negatively affects breast cancer cells by inhibiting cell proliferation and curtailing invasiveness, both through apoptosis and potentiating differentiation. 1,25D3 downregulates estrogen receptor α expression and inhibits estrogenmediated signalling in these cells Furthermore, lower circulating levels of vitamin D in women have been positively linked with enhanced breast cancer risk and disease mortality. Vitamin D action is mediated by the nuclear receptor and transcription factor Vitamin D receptor (VDR). A polymorphism in the VDR gene found on exon 2 in the 5' coding region results in different translation initiation sites. A thymine (T) to cytosine (C) conversion in the first translation initiation codon ATG generates long and short variants of VDR. In the VDRff variant, initiation of translation occurs at the first ATG site, giving rise to a full-length VDR protein comprised of 427 amino acids. Conversely, in the VDRFF variant, translation begins at the second ATG site, resulting in a truncated protein with three fewer amino acids. Researchers have proposed that this polymorphism may be implicated in the differential response to vitamin D treatment for breast cancer. MCF-7 cells with transfected vector, VDRff, or VDRFF were treated with estradiol in the presence or absence of 1,25D3 for 4 days and dyed with crystal violet. Absorbance at 570 nm was used to assay for cell proliferation. The results are displayed below (** indicates p <0.01). Adapted from: Alimirah, F, Peng, X, Murillo, G, Mehta, RG (2011). Functional significance of vitamin D receptor FokI polymorphism in human breast cancer cells. PLoS One. 6(1): e16024. doi:10.1371/journal.pone.0016024. Needs Review In this section, you’ll learn to: • Utilize the highlight, outline and interrogation methods as they apply to science passages Practice Passage 1 – Highlight Styrene is used extensively in the manufacture of plastics, rubber, and resin. It is a colorless liquid with a sweet, aromatic odor at low concentrations and a sharp, disagreeable odor at high concentrations. Because its metabolite is reactive, styrene is classified as a mutagen. Studies have not yet proven definitively that exposure leads to cancer, but a causal link is strongly suspected; the U.S. National Toxicology Program describes styrene as “reasonably accepted to be a human carcinogen.” Styrene can be synthesized in the lab either by reacting sulfuric acid with compound A (1-phenylethanol), characterized by a mild hyacinth odor, or using zinc metal with compound B (1-phenyl-1,2 dibromoethane) in ethanol; Compound B can be synthesized by generating Br2 gas in situ from the reaction of potassium bromate and hydrobromic acid and irradiation with a lamp. The preferred method for styrene production on an industrial scale involves taking compound C (ethylbenzene) through a dehydrogenation reaction catalyzed by an amalgam of iron(III) oxide and potassium carbonate. Needs Review Practice Passage 2 – Outline In evolutionary psychology, a supernormal stimulus, or “superstimulus,” is an evolutionarily novel concentration of engaging factor that produces a stronger response than a typical one. Certain systems that govern the reaction to rewarding stimuli can be overloaded and their negative feedback component overridden. This hypothesis provides explanations for the number of excessive behaviors in society, often conceptualized as “behavioral addictions:” drug addiction, internet addiction, food addiction, and so on. The neurocircuitry and endocrinology underlying hunger and satiety may represent the best studied system in this regard. They clearly produce a physiological balance under certain conditions with regular stimulus, such as when a laboratory mouse fed rodent chow its whole life maintains a normal weight, but are dysregulated in other conditions that contain superstimuli, such as when that mouse fed a high-fat, high-carbohydrate diet becomes obese. The signals that encode hunger and satiety alter the brain’s dopaminergic reward system in multiple ways, affecting hypothalamic neurocircuits and neuropeptides in combination with peripheral hormones, to modulate midbrain dopaminergic activity and alter reward value. Ghrelin, a peptide hormone produced in the stomach, allows for preferential promotion of food-seeking and food-consuming behavior. It also increases the amplitude of dopamine release via AgRP/NPY neurons (agouti-related peptide/neuropeptide Y). Finally, by acting on the hippocampus, ghrelin promotes dopamine induced synaptic plasticity and future silencing of the reward cue. Needs Review Practice Passage 3 – Interrogate It is well established that 1α(OH)2D3 (1,25D3), the active metabolite of vitamin D, negatively affects breast cancer cells by inhibiting cell proliferation and curtailing invasiveness, both through apoptosis and potentiating differentiation. 1,25D3 downregulates estrogen receptor α expression and inhibits estrogenmediated signalling in these cells Furthermore, lower circulating levels of vitamin D in women have been positively linked with enhanced breast cancer risk and disease mortality. Vitamin D action is mediated by the nuclear receptor and transcription factor Vitamin D receptor (VDR). A polymorphism in the VDR gene found on exon 2 in the 5' coding region results in different translation initiation sites. A thymine (T) to cytosine (C) conversion in the first translation initiation codon ATG generates long and short variants of VDR. In the VDRff variant, initiation of translation occurs at the first ATG site, giving rise to a full-length VDR protein comprised of 427 amino acids. Conversely, in the VDRFF variant, translation begins at the second ATG site, resulting in a truncated protein with three fewer amino acids. Researchers have proposed that this polymorphism may be implicated in the differential response to vitamin D treatment for breast cancer. MCF-7 cells with transfected vector, VDRff, or VDRFF were treated with estradiol in the presence or absence of 1,25D3 for 4 days and dyed with crystal violet. Absorbance at 570 nm was used to assay for cell proliferation. The results are displayed below (** indicates p <0.01). Adapted from: Alimirah, F, Peng, X, Murillo, G, Mehta, RG (2011). Functional significance of vitamin D receptor FokI polymorphism in human breast cancer cells. PLoS One. 6(1): e16024. doi:10.1371/journal.pone.0016024. Lesson Review PREVIEW for difficulty • Decide whether to read the passage now or later CHOOSE your approach • Decide whether you will highlight, outline or interrogate the passage READ for keywords • Use keywords and science terms to identify the most important and testable content DISTILL the meaning • Use the approach you choose to extract major takeaways from each paragraph Reflect: What are 3 things from this lesson you recalled and what are 3 things you need to review more? I knew: I need to review: 1. 1. 2. 2. 3. 3. The content in this lesson can be found in Organic Chemistry Review Chapter 1: Nomenclature, Behavioral Sciences Review Chapter 1: Biology and Behavior, and Biochemistry Review Chapter 7: RNA and the Genetic Code. In this lesson, you’ll learn to: • Identify the question type using the question stem and answer choices • Rephrase the question stem to determine the task(s) to be carried out Science Topics • Amino Acids, Peptides, and Proteins (Biochemistry Review Chapter 1) • Enzyme Structure, Function, and Regulation (Biochemistry Review Chapter 2) • Nucleic Acid Structure and Function (Biochemistry Review Chapter 6) • Transcription and Translation (Biochemistry Review Chapter 7) Science Knowledge MCAT Expertise MCAT Science Science Knowledge Skills Data and Statistical Analysis Scientific Reasoning and Problem Solving Experimental and Research Design TYPE the question Use the question stem and answer choices to identify the question type and difficulty and decide whether to do it now or later REPHRASE the stem Simplify the phrasing of the question stem to determine the specific tasks required to answer it INVESTIGATE potential solutions Use prior knowledge and the passage, if necessary, to predict what you can about the answer MATCH your prediction to an answer choice Look for an answer choice that is synonymous with your prediction Needs Review Type By: • Reading the question AND answers • Identifying the question type and difficulty • Deciding to attack now or later Look in the question stem and answer choices for: • Science “buzzwords” • Passage references (e.g., “paragraph 3,” “Experiment 2”) • Length, complexity, and structure • Numbers or formulas • Common question and answer patterns Using what you find, determine: • The science being tested • How hard the question will be for you • How long the question will take you Rephrasing a Science Question • Determine the task to be accomplished based on the question type • Simplify the phrasing of the original question stem • Translate the question into specific pieces of information you either know or can locate in the passage Needs Review Question Stem A scientist has an unknown sample of an amino acid that has been determined to have an amino group, a carboxyl group, optical activity, and multiple amino groups on its side chain. Of the following values, its most likely isoelectric point is: The different antigenic blood types (A, B, and O) are inherited through allelic genes. The actual molecular difference between two blood types is in the carbohydrate that is attached to a common molecular backbone. The best explanation for how genes determine blood type, therefore, is that each gene: A mixture composed of four organic compounds: pentanone, pentane, pentanoic acid, and ethanol, is separated by column chromatography using silica gel with cyclohexane as the eluent. What is the most likely order of elution of the four compounds, from first to last? A scientist uses a fluorescent marker to tag a large protein before placing it near a macrophage. Once the macrophage phagocytoses the protein, which of the following organelles will most likely fluoresce when viewed under a microscope? Rephrase Needs Review 1. If a point mutation occurs that changes one nucleotide in an mRNA molecule, the final protein product is LEAST likely to be affected if the altered nucleotide is in the A. B. C. D. original start codon. original stop codon. first letter of a codon. third letter of a codon. 2. Which set of graphs best depicts the optimal temperature and pH range for pepsin activity? A. B. C. D. Needs Review 3. A segment of a DNA strand has the base sequence: 5′—GTTCATTG—3′ What would be the base sequence of the RNA strand transcribed from this DNA? A. B. C. D. 5′—CAATGAAC—3′ 5′—GTTCATTG—3′ 5′—CAAUGAAC—3′ 5′—CAAGUAAC—3′ 4. Which of the following is a possible interpretation of the repetitive nerve stimulation studies in Figure 1? A. People with Lambert–Eaton myasthenic syndrome experience increasing weakness with repetitive stimulation. B. People with myasthenia gravis experience increasing weakness with repetitive nerve stimulation. C. People with myasthenia gravis experience decreasing weakness with repetitive nerve stimulation. D. People with Lambert–Eaton myasthenic syndrome experience slower nerve conduction than people with myasthenia gravis. Needs Review 5. Which of the following is the most likely reason for the production of faulty prelamin A in individuals with progeria? A. The mutation causes a termination sequence in the DNA to appear earlier than is normal. B. The point mutation causes a stop codon to appear earlier in protein sequencing than is normal. C. The DNA splices and reforms at the lamin A gene, removing part of the protein’s template strand. D. The protein that is sequenced from prelamin A is less stable as a result of the mutation, and it denatures. Lesson Review When Typing the question, look in the question stem and the answer choices for: • • • • • • • Science “buzzwords” Passage references (e.g., “paragraph 3,” “Experiment 2”) Length, complexity, and structure “Yes/No” patterns in the answer choices Numbers or formulas Figures, tables, or other graphics Anything else that has made similar questions easy, hard, or otherwise notable for you in the past Using what you find, determine: • • • • The science being tested How hard the question will be for you How long the question will take you Whether you should skip the question for now Then, Rephrase the question stem to determine the task(s) to be carried out by: • Eliminating any extraneous information, or “fluff” • Identifying the core topic(s) being tested So you can decide: • Whether content knowledge is enough to answer the question • Whether you require additional information from the passage • The steps required to convert the relevant information into a viable prediction Use your experience with similar questions to avoid mistakes. Reflect: What are 3 things from this lesson you recalled and what are 3 things you need to review more? I knew: I need to review: 1. 1. 2. 2. 3. 3. The content in this lesson can be found in Biochemistry Review Chapter 1: Amino Acids, Peptides, and Proteins , Biochemistry Review Chapter 2: Enzyme Structure, Function, and Regulation , Biochemistry Review Chapter 6: DNA and Biotechnology, and Biochemistry Review Chapter 7: RNA and the Genetic Code In this lesson, you’ll learn to: • Determine the best method to investigate potential solutions • Make strong predictions for MCAT style questions • Match your prediction to an answer choice Science Topics • Amino Acids, Peptides, and Proteins (Biochemistry Review Chapter 1) • Enzyme Structure, Function, and Regulation (Biochemistry Review Chapter 2) • Nucleic Acid Structure and Function (Biochemistry Review Chapter 6) • Transcription and Translation (Biochemistry Review Chapter 7) Science Knowledge MCAT Expertise MCAT Science Science Knowledge Skills Data and Statistical Analysis Scientific Reasoning and Problem Solving Experimental and Research Design TYPE the question Use the question stem and answer choices to identify the question type and difficulty and decide whether to do it now or later REPHRASE the stem Simplify the phrasing of the question stem to determine the specific tasks required to answer it INVESTIGATE potential solutions Use prior knowledge and the passage, if necessary, to predict what you can about the answer MATCH your prediction to an answer choice Look for an answer choice that is synonymous with your prediction Needs Review In this section, you’ll learn to: • Determine the best method to investigate potential solutions Investigate and Match by: • Deciding whether to refer back to the passage • Determining whether you can make a focused prediction • Matching to the correct answer or eliminating the incorrect answers 1. Which of the following statements about DNA methylation is the most accurate? 2. Polymerase chain reaction amplifies DNA by first unwinding it using heat rather than DNA helicase. What bonds must be broken in order for this reaction with heat to proceed? 3. Which of the following can be inferred from the passage? 4. Which of the following processes is demonstrated in the regulation of enzyme A, as described in the passage? 5. A person has a mutation in the promoter site of the gene for the lactase enzyme, rendering the promoter site nonfunctional. What symptom(s) will occur? I. Less digestion of lactose by the person II. More digestion of lactose by the person’s symbiotic gut bacteria III. Malnutrition due to glucose deficiency Needs Review 6. If a point mutation occurs that changes one nucleotide in an mRNA molecule, the final protein product is LEAST likely to be affected if the altered nucleotide is in the A. B. C. D. original start codon. original stop codon. first letter of a codon. third letter of a codon. 7. Which set of graphs best depicts the optimal temperature and pH range for pepsin activity? A. B. C. D. Needs Review 8. A segment of a DNA strand has the base sequence: 5′—GTTCATTG—3′ What would be the base sequence of the RNA strand transcribed from this DNA? A. B. C. D. 5′—CAATGAAC—3′ 5′—GTTCATTG—3′ 5′—CAAUGAAC—3′ 5′—CAAGUAAC—3′ 9. Which of the following is a possible interpretation of the repetitive nerve stimulation studies in Figure 1? A. People with Lambert–Eaton myasthenic syndrome experience increasing weakness with repetitive stimulation. B. People with myasthenia gravis experience increasing weakness with repetitive nerve stimulation. C. People with myasthenia gravis experience decreasing weakness with repetitive nerve stimulation. D. People with Lambert–Eaton myasthenic syndrome experience slower nerve conduction than people with myasthenia gravis. Needs Review 10. Which of the following is the most likely reason for the production of faulty prelamin A in individuals with progeria? A. The mutation causes a termination sequence in the DNA to appear earlier than is normal. B. The point mutation causes a stop codon to appear earlier in protein sequencing than is normal. C. The DNA splices and reforms at the lamin A gene, removing part of the protein’s template strand. D. The protein that is sequenced from prelamin A is less stable as a result of the mutation, and it denatures. Needs Review In this section, you’ll learn to: • Make strong predictions for MCAT style questions • Match your prediction to an answer choice Practice Passage (Questions 11–15) Hutchinson-Gilford progeria syndrome (HGPS) is a rare genetic disease that affects one in eight million live births. Individuals with progeria exhibit symptoms of aging at an early age and generally only live until their teenage years or, occasionally, their early 20s. Affected individuals experience stunted growth, musculoskeletal degeneration, loss of hair, and have a characteristic appearance. Progeria typically results from a point mutation in position 1824 of the LMNA gene coding for lamin A. A cytosine is replaced with a thymine, resulting in a shortened mRNA transcript that codes for a faulty version of unprocessed prelamin A. During post-translational processing, prelamin A is incapable of losing its farnesyl group (a 15-carbon isoprenoid), preventing the conversion of prelamin A to mature lamin A. Figure 1 shows the post-translational processing that results in mutant prelamin A, also known as progerin. The farnesyl group locks progerin to the nuclear rim. While bound to the nuclear rim, progerin cannot offer the necessary structural support to the nuclear envelope. As a consequence, the nuclear envelope is misshapen. The structure of the nuclear envelope is essential for the proper manipulation of chromatin during mitosis. Figure 1. Mutant prelamin A post-translational processing Needs Review Normal prelamin A post-translational modification consists of four steps. The processing begins with the farnesylation of the cysteine of the CaaX box (cysteine and three aliphatic amino acids located at the carboxyl terminus of prelamin A) by farnesyltransferase (FTase). Shortly thereafter, the –aaX portion of the CaaX box is removed. Next, the product is methylated. Finally, the carboxyl terminal as well as the modified farnesyl group is sliced off by the peptidase ZMPSTE24. Figure 2 illustrates normal prelamin A post-translational processing. FTase inhibitors have been tested with animal models and shown to reverse the malformation of the nuclear envelope caused by progerin. Figure 2. Normal prelamin A post-translational processing Needs Review 11. Why is the malformation of the nuclear envelope reversed in animal models when FTase inhibitors are used? A. FTase inhibitors catalyze the upstream cleavage of the modified farnesyl group. B. No progerin is made in the presence of FTase inhibitors. C. Normal prelamin A is created when FTase inhibitors are present. D. FTase inhibitors physically prevent progerin from locking to the nuclear rim 12. One of the three amino acids found at the carboxyl terminus of prelamin A could be: A. B. C. D. tyrosine. tryptophan. phenylalanine. alanine. Needs Review 13. What is the most likely reason for the production of faulty prelamin A in individuals with progeria? A. The mutation introduces a new splice site, resulting in loss of RNA from one of the exons of prelamin A. B. The point mutation causes a stop codon to appear earlier in protein sequencing than is normal. C. The DNA splices and reforms at the lamin A gene, removing part of the protein’s template strand. D. The protein that is sequenced from prelamin A is less stable as a result of the mutation, and it denatures. 14. Which of the following is most likely to result in stunted growth and musculoskeletal degeneration? A. Structurally supported nuclear envelopes B. Loss of the farnesyl group by prelamin A C. Methylation of prelamin A during posttranslational processing D. The improper manipulation of chromatin during mitosis Needs Review 15. What change occurs in DNA when a point mutation changes a cytosine to a thymine? A. One fewer hydrogen bond is formed between base pairs. B. A pyrimidine is changed into a purine. C. An −OH group is added to deoxyribose. D. The phosphate backbone is deformed due to base pair mismatch Lesson Review INVESTIGATE means… • Use prior knowledge and the passage, if necessary • Predict what you can about the answer or decide to use elimination. • Be flexible if your initial approach fails Don’t be afraid to change your approach if: • You find or remember new information • The question is harder or easier than you first thought • The question is taking you too long MATCH means… • Search the answer choices for a response that is synonymous to your prediction • Eliminate answer choices that diverge from your prediction or are factually inaccurate • Select an answer and move on Reflect: What are 3 things from this lesson you recalled and what are 3 things you need to review more? I knew: I need to review: 1. 1. 2. 2. 3. 3. The content in this lesson can be found in Biochemistry Review Chapter 1: Amino Acids, Peptides, and Proteins , Biochemistry Review Chapter 2: Enzyme Structure, Function, and Regulation , Biochemistry Review Chapter 6: DNA and Biotechnology, and Biochemistry Review Chapter 7: RNA and the Genetic Code