Topic 3 - Key Terms

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abasic site - Where there is no base attached to the deoxyribose sugar residue in a DNA strand. (T3P2)

alleles - Variants of a gene that may be followed genetically, usually through their phenotypic effect, but also using a molecular assay, such as PCR. (Note: there is a discussion of this terminology in Topic 3 Part 1 Section 1, 'Mutations and alleles'.) (T3P1)

alpha-melanocyte-stimulating hormone (α-MSH) - A peptide hormone of the melanocortin family that is bound by the melanocortin 1 receptor (MC1R). (T3P3)

apurinic site - Where a purine base has been lost from a DNA strand. (T3P2)

base excision repair (BER) - The process of scanning and removal of single damaged bases or nucleotides, particularly depurinated or deaminated bases. (T3P2)

candidate gene - A gene that, from the known or predicted biochemical properties of its product, is possibly responsible for a particular phenotype. (T3P3)

codons - Three consecutive nucleotides along a DNA molecule (or in the mRNA molecule transcribed from it) that specify either a particular amino acid, or the end of the protein synthesis. (T3P1)

dominant - Refers to a gene allele that determines phenotype in a heterozygous cell or organism, masking the effect of any recessive alleles of the same gene that may be present. (T3P3)

double-strand break (DBS) repair - Process of repair of a DNA molecule in which both strands have been broken. It can occur by two distinct mechanisms: homologous end-joining, and non-homologous end-joining. (T3P2)

epistatic - Where the phenotype of one gene 'over-rides' that of the other, the gene whose phenotype is expressed is said to be epistatic to the other gene. (T3P1)

exon - Coding regions of a gene, i.e. parts of a gene that after transcription into RNA are spliced together by the removal of intervening introns (in eukaryotic cells) to be used as the template for protein synthesis. (T3P1)

frameshift mutation - A mutation in which one or more nucleotides (but not a multiple of three nucelotides) are inserted or deleted from an open reading frame. (T3P1)

genome-wide association studies (GWAS) - Studies using a large number of sequence variants within the genome as genetic markers, and seeking to identify variants that are closely linked to an unidentified gene, thereby locating it within the genome. (T3P1)

homologous end-joining - A mechanism of double-strand break repair that uses the double helix of a homologous chromosome to guide accurate repair. (T3P2)

hypostatic - In an epistatic interaction between genes, the gene whose phenotype is suppressed is said to be hypostatic to the other gene. (T3P1)

intron - Non-coding regions of a gene (located between exons) that are transcribed, but are spliced out of the primary transcript before the mature mRNA is used in protein translation. Common in eukaryotic genes but rare in prokaryotes. (T3P1)

melanocortin 1 receptor (MC1R) - A G-protein-coupled receptor that binds the peptide hormone α-MSH, and transduces a signal across the cell membrane, ultimately stimulating the expression of tyrosinase. (T3P3)

microsatellites - Microsatellites are short stretches of repeated sequences, such as repeated dinucleotides or trinucleotides, which are dispersed around the genome. (T3P3)

mismatch repair (MMR) - A form of DNA repair that identifies mismatched bases in a DNA molecule and replaces the mismatched base with the correct base. (T3P2)

missense mutation - A nucleotide change in an open reading frame that leads to a change of an amino acid residue in the encoded protein. (T3P1)

modifier gene - A gene that interacts with another gene to modify (but not mask) its effect and influence phenotype. (T3P1)

molecular chaperones - Proteins that play an important role in the folding of proteins, ensuring that proteins adopt the correct conformation and preventing inappropriate protein aggregation. (T3P1)

mutation - A heritable sequence change in a gene or chromosome; the process by that gives rise to such an alteration. (Note: there is a discussion of this terminology in Topic 3 Part 1 Section 1, 'Mutations and alleles'.) (T3P1)

neutral mutations - Changes in DNA sequence that are not subject to selection; for example a mutation that does not result in a change in the function of the encoded protein (or RNA). (T3P1)

non-homologous end-joining (NHEJ) - A mechanism of double-strand break repair that does not make use of sequence homology between the DNA termini that are joined. (T3P2)

nonsense mutation - A nucleotide change in an open reading frame that changes a codon that encodes an amino acid into a stop codon. (T3P1)

nucleotide excision repair (NER) - A DNA repair mechanism that recognises damaged or modified bases (such as thymidine) and excises the damaged nucleotide prior to repair of the DNA molecule. (T3P2)

null mutations - Mutations which completely abolishes function, for example by preventing expression of a protein or expression of a protein with no function. (T3P1)

open reading frame (ORF) - A nucleic acid sequence with series of codons that do not include any stop codons. (T3P1 and T5P2)

pleiotropy - A cellular process, signal or gene, that has more than one effect, or more than one phenotypic outcome. At the genetic level, describes a situation where a single mutation affects two or more apparently unrelated phenotypic traits. (T3P1)

polymerase chain reaction (PCR) - A laboratory technique for amplifying a few copies of a DNA sequence (template) to generate thousands or millions of copies by a series of in vitro reactions using DNA polymerase. The reaction typically consists of 30–40 cycles that each has three parts: denaturation of DNA template, annealing of primers, and synthesis of DNA. (T3P3)

QTL analysis - QTL analysis (quantitative trait locus analysis) is a form of genetic mapping that looks for associations between genome sections defined by neutral marker loci and a contribution to the overall trait being studied. (T3P3)

quantitative trait locus (QTL) - Quantitative trait loci (QTLs) are stretches of DNA linked to, or containing, the genes that underlie a specific trait. (T3P3)

restriction fragment length polymorphisms (RFLPs) - A restriction fragment length polymorphism (RFLP) is a difference between two homologous DNA sequences that can be visualised as DNA fragments of different lengths after digestion of the DNA samples in question with specific restriction endonucleases. (T3P3)

silent mutations - A mutation that leads to no change in the amino acid sequence of the protein. (T3P1)

simple sequence repeats - Short stretches of DNA sequences repeated in a tandem fashion many times. Microsatellites are an example of simple sequence repeats. (T3P3)

single nucleotide polymorphisms (SNPs) - Loci within the genome where different individuals differ at single base pairs. (T3P3)

Southern blotting - Southern blotting (named for molecular biologist Ed Southern, who devised the technique) is a technique in which DNA fragments are first separated by agarose gel electrophoresis, before transferring them to a membrane for detection of specific sequences by hybridising with a tagged or labelled DNA probe consisting of the sequence of interest. (T3P3)

splicing - The process by which introns are removed from the primary mRNA transcript. (T3P1)

start codon - The start codon is the first codon of an open reading frame. It is normally the methionine codon, ATG. (T3P1)

stop codon - Stop codons do not correspond to an amino acid, and therefore cause translation to terminate. The three stop codons are UGA, UAA and UAG. (T3P1)

transition - A mutation that involves the substitution of a purine (A or G) for a purine, or a pyrimidine (C or T) for a pyrimidine. (T3P1)

transmembrane domains - Transmembrane domains are regions of a protein which traverse a membrane. (T3P3)

transposable elements - Transposable elements are segments of DNA which can excise from one location in the genome and insert in another location. (T3P3)

transversion - A mutation that involves the substitution of a purine (A or G) for pyrimidine (C or T), or vice versa. (T3P1)