USMLE® STEP 1: BIOCHEMISTRY AND MEDICAL GENETICS Lecture Notes 2019 Table of Contents USMLE Step Lecture Notes 2019: Biochemistry Cover Title Page Copyright Editors Feedback Page Part I: Biochemistry Chapter 1: Nucleic Acid Structure and Organization Central Dogma of Molecular Biology Nucleotide Structure and Nomenclature Nucleic Acids Organization of DNA Review Questions Review Questions: Answers and Explanations Chapter 2: DNA Replication and Repair DNA Replication Comparison of DNA and RNA Synthesis Steps of DNA Replication DNA Repair Review Questions Review Questions: Answers and Explanations Chapter 3: Transcription and RNA Processing Transcription Types of RNA RNA Polymerases Transcription: Important Concepts and Terminology Production of Prokaryotic Messenger RNA Production of Eukaryotic Messenger RNA Alternative Splicing of Eukaryotic Primary Pre-mRNA Transcripts Ribosomal RNA (rRNA) is Used to Construct Ribosomes Transfer RNA (tRNA) Carries Activated Amino Acids for Translation Review Questions Review Questions : Answers and Explanations Chapter 4: The Genetic Code, Mutations, and Translation Translation The Genetic Code Mutations Amino Acid Activation and Codon Translation by tRNAs Translation (Protein Synthesis) Polysomes Inhibitors of Protein Synthesis Protein Folding and Subunit Assembly Translation Occurs on Free Ribosomes and on the Rough Endoplasmic Reticulum Co- and Posttranslational Covalent Modifications Posttranslational Modifications of Collagen Review Questions Review Questions : Answers and Explanations Chapter 5: Regulation of Eukaryotic Gene Expression Genetic Regulation Regulation of Eukaryotic Gene Expression Review Questions Review Questions : Answers and Explanations Chapter 6: Genetic Strategies in Therapeutics Recombinant DNA Technology Cloning Restriction Fragments of DNA: the Human Genome Project Cloning Genes as cDNA Produced by Reverse Transcription of Cellular mRNA Medical Applications of Recombinant DNA Review Questions Review Questions : Answers and Explanations Chapter 7: Techniques of Genetic Analysis Blotting Techniques Polymerase Chain Reaction (PCR) Review Questions Review Questions : Answers and Explanations Chapter 8: Amino Acids, Proteins, and Enzymes Amino Acids Protein Turnover and Amino Acid Nutrition Biochemical Reactions Review Questions Review Questions : Answers and Explanations Chapter 9: Hormones Hormones and Signal Transduction Mechanism of Water-soluble Hormones G Proteins in Signal Transduction Lipid-Soluble Hormones Review Questions Review Questions : Answers and Explanations Chapter 10: Vitamins Vitamins Vitamin D and Calcium Homeostasis Vitamin A Vitamin K Vitamin E Review Questions Review Questions : Answers and Explanations Chapter 11: Energy Metabolism Metabolic Sources of Energy Metabolic Energy Storage Regulation of Fuel Metabolism Patterns of Fuel Metabolism in Tissues Review Questions Review Questions : Answers and Explanations Chapter 12: Glycolysis and Pyruvate Dehydrogenase Overview Carbohydrate Digestion Glucose Transport Glycolysis Galactose Metabolism Fructose Metabolism Pyruvate Dehydrogenase Review Questions Review Questions : Answers and Explanations Chapter 13: Citric Acid Cycle and Oxidative Phosphorylation Citric Acid Cycle Electron Transport Chain Review Questions Review Questions : Answers and Explanations Chapter 14: Glycogen, Gluconeogenesis, and the Hexose Monophosphate Shunt Glycogenesis and Glycogenolysis Glycogen Synthesis Glycogenolysis Genetic Deficiencies of Enzymes in Glycogen Metabolism Gluconeogenesis Hexose Monophosphate Shunt Review Questions Review Questions : Answers and Explanations Chapter 15: Lipid Synthesis and Storage Fatty Acid Nomenclature Lipid Digestion Fatty Acid Biosynthesis Triglyceride (Triacylglycerol) Synthesis Lipoprotein Metabolism Hyperlipidemias Cholesterol Metabolism Review Questions Review Questions : Answers and Explanations Chapter 16: Lipid Mobilization and Catabolism Lipid Mobilization Fatty Acid Oxidation Ketone Body Metabolism Sphingolipids Review Questions Review Questions : Answers and Explanations Chapter 17: Amino Acid Metabolism Overview Removal and Excretion of Amino Groups Urea Cycle Disorders of Amino Acid Metabolism S-Adenosylmethionine, Folate, and Cobalamin Specialized Products Derived From Amino Acids Heme Synthesis Iron Transport and Storage Bilirubin Metabolism Review Questions Review Questions : Answers and Explanations Chapter 18: Purine and Pyrimidine Metabolism Overview Pyrimidine Synthesis Pyrimidine Catabolism Purine Synthesis Purine Catabolism and the Salvage Enzyme HGPRT Review Questions Review Questions : Answers and Explanations Part II: Medical Genetics Chapter 1: Single-Gene Disorders Basic Definitions Major Modes of Inheritance Important Principles That Can Characterize Single-Gene Diseases Review Questions Review Questions : Answers and Explanations Chapter 2: Population Genetics Definition Genotype and Allele Frequencies Hardy-Weinberg Equilibrium Factors Responsible for Genetic Variation In/Among Populations Review Questions Review Questions : Answers and Explanations Chapter 3: Cytogenetics Overview Basic Definitions and Terminology Numerical Chromosome Abnormalities Structural Chromosome Abnormalities Other Chromosome Abnormalities Advances in Molecular Cytogenetics Review Questions Review Questions : Answers and Explanations Chapter 4: Recombination Frequency Overview Polymorphic Markers and Linkage Analysis Gene Mapping: Linkage Analysis Review Questions Review Questions : Answers and Explanations Chapter 5: Genetic Diagnosis Genetic Diagnosis Applications of Genetic Diagnosis Review Questions Review Questions : Answers and Explanations USMLE® is a joint program of the Federation of State Medical Boards (FSMB) and the National Board of Medical Examiners (NBME), which neither sponsor nor endorse this product All rights reserved under International and Pan-American Copyright Conventions By payment of the required fees, you have been granted the non-exclusive, non-transferable right to access and read the text of this eBook on screen No part of this text may be reproduced, transmitted, downloaded, decompiled, reverse engineered, or stored in or introduced into any information storage and retrieval system, in any form or by any means, whether electronic or mechanical, now known or hereinafter invented, without the express written permission of the publisher © 2019 by Kaplan, Inc Published by Kaplan Medical, a division of Kaplan, Inc 750 Third Avenue New York, NY 10017 All rights reserved The text of this publication, or any part thereof, may not be reproduced in any manner whatsoever without written permission from the publisher 10 ISBN-13: 978-1-5062-3613-1 DIRECT VERSUS INDIRECT GENETIC DIAGNOSIS Direct genetic diagnosis is used whenever possible Its major limitation is that the disease-producing mutation(s) must be known if one is to test for them If a family carries a mutation not currently documented, as in the family above with LCAD deficiency, it will not be detected by direct mutation testing In these cases, indirect genetic testing can be used Indirect Diagnosis Direct Diagnosis Family information needed Yes No Errors possible because of recombination Yes No Markers may be uninformative Yes No Multiple mutations can be assayed with a single test Yes No Disease-causing mutation itself must be known No Yes Table II-5-1 Features of Indirect and Direct Genetic Diagnosis APPLICATIONS OF GENETIC DIAGNOSIS Genetic diagnosis is used in a variety of settings, including the ones listed below Carrier diagnosis in recessive diseases Presymptomatic diagnosis for late-onset diseases Asymptomatic diagnosis for diseases with reduced penetrance Prenatal diagnosis Preimplantation testing PRENATAL GENETIC DIAGNOSIS Prenatal diagnosis is one of the most common applications of genetic diagnosis Diagnosis of a genetic disease in a fetus may assist parents in making an informed decision regarding pregnancy termination and in preparing them emotionally and medically for the birth of an affected child There are various types of prenatal diagnosis Amniocentesis With amniocentesis, a small sample of amniotic fluid (10–20 mL) is collected at approximately 16 weeks’ gestation Fetal cells are present in the amniotic fluid and can be used to diagnose single-gene disorders, chromosome abnormalities, and some biochemical disorders Elevated α-fetoprotein levels indicate a fetus with a neural tube defect The risk of fetal demise due to amniocentesis is estimated to be approximately 1/200 Chorionic villus sampling This technique, typically performed at 10–12 weeks’ gestation, involves the removal of a small sample of chorionic villus material (either a transcervical or a transabdominal approach may be used) The villi are of fetal origin and thus provide a large sample of actively dividing fetal cells for diagnosis This technique has the advantage of providing a diagnosis earlier in the pregnancy There is a small possibility of diagnostic error because of placental mosaicism (i.e., multiple cell types in the villi) The risk of fetal demise is higher than with amniocentesis (about 1/100) Preimplantation diagnosis Embryos derived from in vitro fertilization can be diagnosed by removing a single cell, typically from the eight-cell stage (this does not harm the embryo) DNA is PCR amplified and is used to make a genetic diagnosis The advantage of this technique is that pregnancy termination need not be considered: only embryos without the mutation are implanted There is a possibility of diagnostic error as a result of PCR amplification from a single cell REVIEW QUESTIONS Select the ONE best answer The pedigree below shows a family in which hemophilia A, an Xlinked disorder, is segregating PCR products for each member of the family are also shown for a short tandem repeat polymorphism located within an intron of the factor VIII gene What is the best explanation for the phenotype of individual II-1? (A) (B) (C) (D) (E) Heterozygous for the disease-producing allele Homozygous for the disease-producing allele Homozygous for the normal allele Incomplete penetrance Manifesting heterozygote A 22-year-old woman with Marfan syndrome, a dominant genetic disorder, is referred to a prenatal genetics clinic during her tenth week of pregnancy Her family pedigree is shown below (the arrow indicates the pregnant woman) PCR amplification of a short tandem repeat (STR) located in an intron of the fibrillin gene is carried out on DNA from each family member What is the best conclusion about the fetus (III-1)? (A) (B) (C) (D) (E) Has a 25% change of having Marfan syndrome Has a 50% chance of having Marfan syndrome Will develop Marfan syndrome Will not develop Marfan syndrome Will not develop Marfan syndrome, but will be a carrier of the disease allele The pedigree below represents a family in which phenylketonuria (PKU), an autosomal recessive disease, is segregating Southern blots for each family member are also shown for an RFLP that maps 10 million bp upstream from the phenylalanine hydroxylase gene What is the most likely explanation for the phenotype of II-3? (A) (B) (C) (D) (E) A large percentage of her cells have the paternal X chromosome carrying the PKU allele active Heteroplasmy Male I-2 is not the biologic father PKU shows incomplete penetrance Recombination has occurred A 14-year-old boy has Becker muscular dystrophy (BMD), an Xlinked recessive disease A maternal uncle is also affected His sisters, aged 20 and 18, wish to know their genetic status with respect to the BMD Neither the boy nor his affected uncle has any of the known mutations in the dystrophin gene associated with BMD Family members are typed for a HindII restriction site polymorphism that maps to the 5′ end of intron 12 of the dystrophin gene The region around the restriction site is amplified with a PCR The amplified product is treated with the restriction enzyme HindII and the fragments separated by agarose gel electrophoresis The results are shown below What is the most likely status of individual III-2? (A) (B) (C) (D) (E) Carrier of the disease-producing allele Hemizygous for the disease-producing allele Homozygous for the normal allele Homozygous for the disease-producing allele Manifesting heterozygote Two phenotypically normal second cousins marry and would like to have a child They are aware that one ancestor (great-grandfather) had PKU and are concerned about having an affected offspring They request ASO testing and get the following results What is the probability that their child will be affected? (A) (B) (C) (D) (E) 1.0 0.75 0.67 0.50 0.25 A 66-year-old man (I-2) has recently been diagnosed with Huntington disease, a late-onset, autosomal dominant condition His granddaughter (III-1) wishes to know whether she has inherited the disease-producing allele, but her 48-year-old father (II-1) does not wish to be tested or to have his status known The grandfather, his unaffected wife, the granddaughter, and her mother (II-2) are tested for alleles of a marker closely linked to the huntingtin gene on 4p16.3 The pedigree and the results of testing are shown below What is the best information that can be given to the granddaughter (III-1) about her risk for developing Huntington disease? (A) (B) (C) (D) (E) 50% 25% Marker is not informative Nearly 100% Nearly 0% ANSWERS AND EXPLANATIONS REVIEW QUESTIONS Answer: A The female II-1 in this family is heterozygous for the marker (from the gel) and also has an unaffected father Her mother is a carrier and the bottom band in the mother’s pattern is associated with the diseaseproducing allele of the factor VIII gene All observations are consistent with II-1 being heterozygous (Xx) for the factor VIII gene She has no symptoms, so she is not a manifesting heterozygote (choice E) She cannot be homozygous for the disease-producing allele (choice B) because her father is unaffected Homozygosity for the normal allele (choice C) is inconsistent with the results shown on the gel She has inherited the chromosome from her mother (bottom band) that carries the mutant factor VIII allele, but from her father she has received a chromosome carrying the normal allele Note that her father is not affected, and the bottom band in his pattern is in linkage phase with the normal allele of the gene This is a case where linkage phase is different in the mother and the father Incomplete penetrance (choice D) is not a good choice because the female (II-1) does not have the disease-producing genotype She is heterozygous for the recessive and (dominant) normal allele One would expect from her genotype that she would be unaffected Answer: C The blot shows the top band in the patterns of I-1 and II-2 (the proband) is associated with the disease-producing allele Because the fetus has inherited this marker allele from the mother (II-2) and Marfan disease is dominant, the fetus will develop Marfan disease Choices A and B are recurrence risks associated with the pedigree data With no blot to examine, choice B, 50% risk would be correct Choice D would be correct if the blot from the fetal DNA showed both the bottom band (must be from mother) and the top band (from the unaffected father) Choice E is incorrect because Marfan is a dominant disease with no “carrier” status Answer: E Although II-3 has an RFLP pattern consistent with heterozygosity for the PKU allele, she has PKU The best explanation offered is that recombination has occurred, and although she is heterozygous for the restriction site generating the RFLP pattern, she is homozygous for the mutation causing PKU The restriction site is 10 million bp upstream from the phenylalanine hydroxylase gene so there is a minimum chance of recombination of 10% Although this is small, it is the most likely of the options listed The phenylalanine hydroxylase gene is not on the X chromosome (choice A) Heteroplasmy (choice B) is associated with mitochondrial pedigrees, and the phenylalanine hydroxylase gene is a nuclear one The RFLP pattern is quite consistent with I-2 being the biologic father (choice C), and he is a known carrier of the PKU mutation because he has another affected child (II-1) If II-3’s RFLP pattern showed homozygosity for the marker (identical to II-1), and she had no symptoms, incomplete penetrance (choice D) would be a good choice Answer: C The disease-producing allele of the gene is associated with the presence of the HindII site Notice that both affected males show two smaller bands (75 and 40 bp) II-3, a carrier female, also has these two smaller bands in her pattern, in addition to a larger PCR product (115 bp), representing the absence of the HindII site on her normal chromosome III-2 has only the larger PCR product (notice the density because both chromosomes yielded this product) She is homozygous for the normal allele Choice A, carrier, would be correct if her pattern had looked like those of II-3 and III-1 All the males shown are hemizygous (choice B) for the dystrophin gene because they have only one copy II-1 and III-3 are hemizygous for the disease-producing allele, and II-2 is hemizygous for the normal allele No one in the family is homozygous for the disease-producing allele (choice D) In an X-linked pattern, this would be characteristic of a female with two copies of the disease-producing allele and is very rarely seen III-2 is not a manifesting heterozygote (choice E) because she has no symptoms and is not a heterozygote Answer: E The blot indicates that both parents are heterozygous for the mutant allele Because both are phenotypically normal, the disease must be autosomal recessive If it had been X-linked recessive, the man would be hemizygous Thus, the chance they will have an affected child is 25% (0.25) Answer: A The affected grandfather has marker alleles DS2 and DS3 There is no information about which one is in linkage phase with his diseaseproducing huntingtin allele On the basis of the pedigree alone, the daughter has a 25% change of inheriting the grandfather’s disease-producing huntingtin allele (choice B); however, she would like more information Because her father (II-1) does not wish to be tested or know about his genetic status with respect to Huntington’s, it is unethical to test the daughter for the triplet repeat expansion The results would necessarily reveal the status of her father also By doing an indirect genetic test, one can see the daughter has inherited one of her marker alleles (DS2) from the grandfather via her father This means she has a 50% chance of developing Huntington’s because there is a 50% chance that DS2 is a marker for the diseaseproducing huntingtin allele in the grandfather and a 50% chance it is not (and DS3 is) Notice the result does not reveal additional information about her father (II-1) Before her testing, he had a 50% chance of having the disease-producing huntingtin allele His risk is still 50% with the information from the daughter’s test However, if the father (II-1) does develop Huntington’s in the future, that will mean that the daughter has a 100% chance of having the disease also (choice D) If her marker status had been DS1/DS1, her chances of developing Huntington’s would have been near (choice E) because she did not inherit these alleles from her grandfather One came from her grandmother (via her father) and one from her mother This result still would not reveal additional relevant information about her father (II-1), whose risk would remain 50% ... invented, without the express written permission of the publisher © 2019 by Kaplan, Inc Published by Kaplan Medical, a division of Kaplan, Inc 750 Third Avenue New York, NY 10017 All rights reserved... nitrogen-containing bases commonly found in nucleotides: purines and pyrimidines Figure I-1-3 Bases Commonly Found in Nucleic Acids Purines contain rings in their structure The purines commonly found in... containing heatdenatured DNA is slowly cooled, the two complementary strands can become base-paired again (Figure I-1-9) Such renaturation or annealing of complementary DNA strands is an important step