Questions and Answers
Match the following genetic disorders with their genetic mechanisms:
Fragile X syndrome = CGG triplet repeat expansion in the FMR1 gene Huntington's disease = CAG repeat insertion in protein sequences Sickle cell anemia = Point mutation in the beta-globin gene Cystic fibrosis = Deletion of a phenylalanine in the CFTR gene
Match the following types of blots with their uses:
Southern blot = DNA detection Northern blot = RNA detection Western blot = Protein detection In situ hybridization = Localization of nucleic acids in tissues
Match the following terms with their definitions:
Missense mutation = Change in a single amino acid in a protein Nonsense mutation = Change that results in a premature stop codon Frameshift mutation = Insertion or deletion causing a shift in reading frame Silent mutation = Change that does not alter the amino acid sequence
Match the following RNA effects with their descriptions:
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Match the following genes to their disorders:
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Match the following proteins with their roles:
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Match the following mutations with their consequences:
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Match the terms related to genetic variations with their descriptions:
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Match the following genetic variations with examples:
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Match the following concepts to their relevance in genomics:
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Match the following definitions with their relevant genetic terms:
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Match the following pairs related to diseases with their genetic concepts:
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Match the outcome of PCR with the number of cycles:
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Match the description of germ-line mutations with its outcome:
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Match the characteristic of somatic mutations with its description:
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Match the type of mutation with its effect on the amino acid sequence:
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Study Notes
DNA Repair Pathways
- Damaged base in DNA is repaired by base excision repair pathway.
- Incorrectly paired nucleotides in DNA are repaired by mismatch repair pathway.
- Bulky DNA lesions can be repaired by nucleotide excision repair pathway.
- Altered nucleotides in DNA can be changed back into their original structures by direct DNA repair pathway.
- Double-strand DNA breaks can be repaired by homologous recombination and nonhomologous end joining pathways.
Types of Mutations
- Transition: a base substitution mutation where a single purine is changed for a purine (A-G, G-A) or a pyrimidine is changed for a pyrimidine (T-C, C-T); 4 possible scenarios.
- Transversion: a base substitution mutation where a purine can switch for a pyrimidine and so on; 8 possible scenarios.
- Missense: a base substitution that changes the codon from one amino acid to another (e.g., UCA (serine) → UUA (leucine)) or changes a stop codon to a codon for an amino acid (e.g., UAA (stop) → UUA (leucine)).
- Nonsense: a base substitution that changes a codon to a stop codon.
- Silent: a base substitution that does not change the amino acid sequence.
- Neutral: a base substitution that does not affect the function of the protein.
Histone Acetylation
- Sequence with most R and K are more likely to be acetylated.
Transcriptome and Proteomics
- The set of all RNAs encoded by the genome is called transcriptome.
- PAGE (polyacrylamide gel electrophoresis) is a technique to separate a mixed sample of proteins to identify according to protein size, used for proteomics and western blotting.
Genetic Variations
- SNP (single nucleotide polymorphism) is a DNA variation in a single base pair equivalent to different alleles, used for GWA (genome-wide association).
- CNV (copy-number variation) is a section of the genome that is repeated and the number of repeats in the genome varies between individuals, used for studying diseases such as autism.
- RFLP (restriction fragment length polymorphism) is a technique used to generate genetic markers for genomic analysis, useful for mapping diseases, pedigree, and family relation.
Genome-Wide Association
- GWA is used to find SNPs in order to find genes that are causing disease in a genome.
Epigenetics
- Epigenetics is the study of heritable changes in gene function that occur without a change in the underlying DNA sequence.
- Epigenetics can affect gene expression, but not alter the DNA sequence.
Ortholog and Paralog Genes
- Ortholog: homologous genes, found in different species from a common ancestor (e.g., hemoglobin in humans and monkeys).
- Paralog: homologous genes, same organism (same individual) due to gene duplication (e.g., hemoglobin in humans).
PCR (Polymerase Chain Reaction)
- PCR is used to amplify a specific gene from a trace amount of DNA.
- If one copy of the gene is present in the starting material, after 20 cycles of PCR, 2^20 copies of the gene can be produced.
- If two copies of the gene are present in the starting material, after 20 cycles of PCR, 2^20 x 2 copies of the gene can be produced.
Somatic and Germ-Line Mutations
- Somatic mutations: occur in somatic tissue, not involved in production of germ cells, passed on to daughter cells, but not to daughters/sons.
- Germ-line mutations: occur in cells that give rise to gametes, inherited by future generations, passed on to daughters/sons.
Apoptosis and Necrosis
- Apoptosis: programmed cell death, can be triggered by viral infection, DNA damage, or mitochondrial damage.
- Necrosis: unprogrammed cell death, caused by injury, unexpected circumstances.
X Chromosome Inactivation
- X chromosome inactivation is started by long non-coding RNA, which covers the chromosome, then methyl groups attach, leading to DNA methylation and inactivation of the chromosome.
Fragile X Syndrome
- Genetic mechanism: CGG triplet repeats increased to 100's or even 1,000's of copies, can't produce enough FMR protein (fragile X mental retardation).
Huntington's Disease
- Genetic mechanism: germ line mutation where insertion of CAG repeats into the protein sequences occur (excess of glutamine), causes the progressive breakdown of nerve cells in the brain.
Other Concepts
- Southern blot: a technique used to detect specific DNA sequences.
- Northern blot: a technique used to detect specific RNA sequences.
- Western blot: a technique used to detect specific proteins.
- In situ hybridization: a technique used to detect specific RNA or DNA sequences in cells or tissues.
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Description
This study guide covers DNA repair pathways, including base excision repair, mismatch repair, nucleotide excision repair, and direct DNA repair. It also discusses transition and transversion mutations, and DNA repair mechanisms such as homologous recombination and nonhomologous end joining.