DNA Structure, Complementarity, and Replication

  • DNA Complementarity

    • DNA complementarity refers to the base pairing rules.
    • Base pair matching rules:
    • Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds.
    • Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.
    • Example:
    • If a DNA strand has the sequence 5'-ATGCTA-3', the complementary strand is:
      • a) 5'-TACGAT-3'
      • b) 3'-TACGAT-5' (correct answer)
      • c) 5'-UACGAU-3' (not applicable as U is in RNA)
      • d) 3'-ATGCTA-5' (not a valid complement)

  • DNA Structure

    • Characteristics of DNA:
    • The DNA double helix consists of two strands that are antiparallel.
      • Answer: d) DNA strands are antiparallel (one 5'->3', one 3'->5').
    • Sugar-phosphate backbone is on the outside, and nitrogenous bases are on the inside.
    • Strands do not run parallel to each other.

  • DNA Replication

    • Enzymes Involved:
    • DNA polymerase is primarily responsible for synthesizing new DNA strands. (Answer: b)
    • Other enzymes include:
      • Helicase: unwinds the DNA helix.
      • Ligase: joins Okazaki fragments.
    • Central Dogma of Molecular Biology:
    • Describes the flow of genetic information:
      • b) DNA -> RNA -> Protein. (Correct)

  • Base Pairing Incorrectness

    • Identify incorrect pairing:
    • a) Adenine with Thymine (2 hydrogen bonds) (correct)
    • b) Guanine with Cytosine (3 hydrogen bonds) (correct)
    • c) Adenine with Uracil (in RNA) (correct)
    • d) Guanine with Thymine (incorrect) (Correct answer)

  • Percentage of Bases

    • If a double-stranded DNA molecule is 30% adenine:
    • Cytosine would be 20% (20% due to complementary base pairing).

  • 5' End Characteristics

    • The 5' end of a DNA strand is characterized by:
    • A free phosphate group on the 5' carbon of the sugar (Answer: a).

  • Semiconservative DNA Replication

    • DNA replication is described as semiconservative because:
    • Each new DNA molecule contains one original strand and one new strand (Answer: b).

Gene Expression, Transcription, Translation, and Alternative Splicing

  • Transcription

    • Defined as:
    • c) Making RNA from DNA (correct).
    • Enzyme responsible for transcription:
    • RNA polymerase (Answer: b).
    • If the DNA template strand is 3'-TACGCA-5', the mRNA sequence will be:
    • 5'-AUGCGU-3' (correct answer).

  • Alternative Splicing

    • Definition:
    • Producing different mRNA transcripts from the same gene by including/excluding different exons (Answer: b).
    • Clinical significance:
    • Alternative splicing can lead to multiple protein isoforms from one gene with different drug-metabolizing activities (Answer: b).

  • Translation

    • The ribosome:
    • c) Reads mRNA codons and assembles amino acids into protein (correct answer).
    • Codon Definition:
    • b) A three-nucleotide sequence in mRNA that codes for a specific amino acid (correct).

Introns, Exons, and Mutations

  • Introns and Exons

    • True statement:
    • b) Exons are expressed in the final protein; introns are removed during splicing (correct).

  • Nonsense Mutation

    • Results in:
    • b) A premature stop codon, leading to a truncated protein (correct).

  • CYP2D6 Alternative Splicing

    • May create enzyme variants with altered substrate specificity (Answer: a).

  • Genetic Variation - Mutations, SNPs, Polymorphisms

    • A single nucleotide polymorphism (SNP) is defined as:
    • a) A DNA sequence variation occurring in >1% of the population at a single base pair position (correct).
    • Difference between mutation and polymorphism:
    • c) Polymorphisms typically occur in >1% of the population; mutations are rarer (correct).

  • Common Genetic Variants

    • The MOST common genetic variant in the human genome is:
    • b) Single nucleotide polymorphisms (SNPs) (correct).

  • Synonymous (Silent) Mutation

    • Does not change the amino acid sequence due to codon degeneracy (Answer: c).

  • Missense Mutation

    • Results in:
    • b) A different amino acid being incorporated into the protein (correct).

  • Functional Consequences in Drug Metabolism

    • c) Nonsynonymous SNP in the active site of a metabolizing enzyme (likely to have functional consequences) (correct).

Copy Number Variations (CNVs) and Pharmacogenetics

  • Copy Number Variations (CNVs)

    • Defined as:
    • b) Deletions or duplications of large DNA segments (1kb to several Mb) (correct).

  • CYP2D6 Gene Deletion & Phenotypes

    • Results in:
    • b) Poor metabolizer phenotype (correct).

  • Pharmacogenetics vs Pharmacogenomics

    • Pharmacogenetics studies single genes/variants; pharmacogenomics studies genome-wide variation (Answer: b).

  • Pharmacodynamic Genes

    • Primarily affect drug targets, receptors, and downstream signaling pathways (Answer: b).

  • Examples of Pharmacokinetic and Pharmacodynamic Genes

    • Pharmacokinetic gene example: c) CYP2D6 (drug metabolizing enzyme).
    • Pharmacodynamic gene example: d) VKORC1 (warfarin target enzyme).

Chromosomal Nomenclature and Genetic Markers

  • Chromosomal Nomenclature

    • In chromosomal nomenclature:
    • "p" refers to the short arm of the chromosome (Answer: b).
    • "q" refers to the long arm of the chromosome (Answer: b).
    • Example: The CYP2D6 gene location (22q13.2) means:
      • b) Chromosome 22, long arm, region 1, band 3, sub-band 2 (correct).

  • Notation of Genetic Variants

    • Correct description of a deletion on the short arm of chromosome 5:
    • d) Both b and c (5p- and del(5p)).
    • Notation "46,XY" indicates:
    • a) A normal male karyotype with 46 chromosomes (correct).
    • Centromere location affects chromosome arms:
    • b) Metacentric chromosomes have the centromere in the middle; acrocentric have it near one end (correct).

  • Term "Locus"

    • Refers to:
    • a) A specific physical location of a gene on a chromosome (correct).

Haplotype and Linkage Disequilibrium

  • Haplotype

    • Defined as:
    • a) A set of alleles at multiple loci on the same chromosome inherited together (correct).

  • Diplotype

    • Defined as:
    • b) Two haplotypes (one from each parent) that make up an individual's genotype (correct).
    • Haplotype phasing importance:
    • b) Different haplotype combinations can result in different phenotypes even with the same genotype (correct).

  • CYP2C19 Heterozygosity

    • In a patient heterozygous at two CYP2C19 SNP positions (681G>A and 636G>A), phasing is necessary to evaluate:
    • b) Whether variants are on the same or different chromosomes (correct).

  • CYP2C19*2 Haplotype Definition

    • Defined by:
    • b) Multiple SNPs that travel together including 681G>A as the defining variant (correct).

Linkage Disequilibrium (LD)

  • Linkage Disequilibrium (LD)
    • Defined as:
    • b) Non-random association of alleles at different loci (Answer: b).
    • Tag SNPs:
    • a) SNPs that mark a particular haplotype block and can represent multiple other SNPs in LD (correct).
    • Complete Linkage Disequilibrium:
    • b) Two alleles always occur together (perfect correlation) (correct).
    • Reasons why a tag SNP may not be the causative variant:
    • b) The tag SNP marks a haplotype block; the causative variant may be another SNP in LD (correct).

Mendelian Inheritance Patterns

  • Autosomal Recessive Inheritance

    • An affected individual must have:
    • b) Two copies of the variant allele (homozygous) (correct).

  • Autosomal Dominant Inheritance

    • An individual with one copy of the variant allele:
    • b) Will express the trait/disorder (correct).

  • Carrier Probability in Autosomal Recessive Inheritance

    • If both parents are carriers, the probability their child will be affected:
    • b) 25% (correct).

  • X-linked Recessive Traits

    • Predominantly affect males; females are usually carriers (Answer: b).

  • CYP2D6 Inheritance

    • Poor metabolizer phenotype follows:
    • b) Autosomal recessive inheritance (need two non-functional alleles) (correct).

Genetic Concepts and Population Genetics

  • Codominance

    • Means:
    • b) Both alleles are expressed equally in the heterozygote (correct).

  • Incomplete Penetrance

    • Means:
    • a) Not all individuals with a disease genotype develop the disease phenotype (correct).

  • Hardy-Weinberg Equilibrium

    • Equation:
    • p2+2pq+q2=1p^2 + 2pq + q^2 = 1 describes expected genotype frequencies in a population at equilibrium (correct).
    • Assumptions of Hardy-Weinberg equilibrium include:
    • a) Random mating, no migration, no mutation, no selection, large population (correct).

  • Expected Frequencies in Hardy-Weinberg Equilibrium

    • If frequency of the CYP2C9*3 allele (q) is 0.1, the expected frequency of *3/*3 homozygotes is:
    • a) 0.01 (q2q^2) (correct).
    • If p(frequencyof∗1allele)=0.7p (frequency of *1 allele) = 0.7 and q(frequencyof∗2allele)=0.3q (frequency of *2 allele) = 0.3, the expected frequency of 1/2 heterozygotes:
    • b) 0.42 (2pq) (correct).

  • Violations of Hardy-Weinberg Equilibrium

    • c) Natural selection favoring one allele (correct).

  • Differing Pharmacogene Allele Frequencies Between Populations

    • Due to:
    • b) Migration, genetic drift, founder effects, and possibly selection (correct).

Pharmacogenomics Applications

  • Investigating Functionally Significant SNPs

    • To determine if a novel SNP in CYP2D6 is functionally significant, assess:
    • b) If it changes amino acid sequence, is in a conserved region, and test enzyme activity (correct).

  • Assigning a Diplotype

    • To assign a diplotype from SNP data, you need:
    • b) Phasing information to determine variants on same chromosome (correct).

  • Importance of Tag SNPs in Pharmacogenomics

    • Based on:
    • b) Being in linkage disequilibrium with other SNPs in a haplotype block (correct).

  • Inferring Haplotype from Defining SNP

    • From detecting the defining SNP (1846G>A) for CYP2D6*4 allele, one can infer:
    • b) The entire *4 haplotype is likely present due to LD (correct).

  • Understanding Haplotype vs Genotype in Phenotypes

    • Importance of understanding haplotypes:
    • b) Heterozygous variants on same chromosome may retain functional copy; if on different chromosomes, may have no functional copies (correct).

  • Functional Relevance of Synonymous SNPs

    • A synonymous SNP in an exon might still be functionally relevant because:
    • b) It could affect mRNA splicing, mRNA stability, or translation efficiency (correct).

  • Designing Pharmacogenomic Panels

    • To minimize cost while maximizing information, use:
    • b) Tag SNPs to capture haplotype variation (correct).

  • Variability in Drug Clearance

    • A drug metabolized by CYP2D6 shows variability in clearance likely due to:
    • b) Genetic polymorphisms in CYP2D6 (poor to ultrarapid metabolizers) (correct).

  • Alternative Splicing Outcomes

    • Could produce:
    • b) Multiple protein isoforms with different catalytic activities (correct).