Allele
An allele designates an alternative version of a gene, located at a specific chromosomal locus. These variants emerge due to mutations or genetic variations within the DNA sequence, leading to distinct genetic information across individuals within a population. Alleles can manifest diverse phenotypic traits, fostering genetic diversity and inheritance patterns. For instance, in humans, eye color is determined by alleles of genes such as OCA2 and HERC2, where variations in these alleles contribute to different eye colors like blue, brown, or green. Each gene inherits two alleles, one from each parent, which can be either identical (homozygous) or distinct (heterozygous), influencing trait expression and genetic outcomes. Inheritance of these alleles follows principles like dominance, recessiveness, and codominance.

Autosomal
Autosomal refers to the chromosomes numbered 1 to 22 in humans, excluding the sex chromosomes (X and Y). These chromosomes contain genetic information for a wide range of traits and characteristics, including physical features, metabolic processes, and susceptibility to inherited disorders.

Polymorphism
A polymorphism is a naturally occurring genetic variation within a population, typically present at a frequency of 1% or more. It often involves differences in DNA sequences, such as single nucleotide substitutions or variations in repetitive DNA segments. Unlike mutations, which are rare genetic changes occurring at a frequency of less than 1%, polymorphisms are common and may or may not have a significant impact on an individual's phenotype. Polymorphisms contribute to genetic diversity and serve as the basis for natural selection and adaptation within populations.

Homozygous
Homozygous refers to a genetic condition where an individual carries two identical alleles for a particular gene, either both dominant or both recessive, at a specific locus on a pair of homologous chromosomes. In a homozygous state, the alleles may be identical due to inheritance from both parents or arising from a mutation. Homozygosity often results in uniform expression of a trait.

Heterozygous
Heterozygous refers to a genetic condition where an individual carries two different alleles for a particular gene, one dominant and one recessive, at a specific locus on a pair of homologous chromosomes. In a heterozygous state, the individual inherits one allele from each parent, resulting in diverse genetic combinations. Heterozygosity often leads to variable expression of a trait, influenced by the dominance or recessiveness of the alleles.

Nucleotide
A nucleotide is the fundamental building block of nucleic acids, such as DNA and RNA, comprising three main components: a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil), a pentose sugar (ribose in RNA or deoxyribose in DNA), and a phosphate group. These components form the backbone of the nucleic acid structure, with the nitrogenous base varying among nucleotides and determining the genetic information encoded within the molecule. Nucleotides play crucial roles in genetic replication, transcription, and translation processes, serving as carriers of genetic information and energy currency within cells.

Codon
A codon is a sequence of three nucleotides in mRNA that specifies a particular amino acid or serves as a start or stop signal for protein synthesis. Each codon corresponds to a specific amino acid or a signal for the initiation or termination of translation during protein synthesis. The genetic code is degenerate, meaning that most amino acids are encoded by more than one codon, providing redundancy and robustness to the translation process. Codons are essential for the accurate and efficient translation of genetic information from nucleic acids to proteins.

Riboflavin
Also known as vitamin B2, is a water-soluble vitamin essential for various physiological processes in the body, including energy metabolism, cellular growth and repair, and antioxidant defense. As a precursor to the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), riboflavin plays a crucial role in numerous enzymatic reactions involved in the metabolism of carbohydrates, fats, and proteins. Additionally, riboflavin acts as an antioxidant, scavenging reactive oxygen species and protecting cells from oxidative damage. Dietary sources of riboflavin include dairy products, meat, fish, poultry, eggs, green leafy vegetables, and fortified grains. Riboflavin deficiency can lead to various health problems, including fatigue, skin disorders, and impaired growth and development. Supplementation with riboflavin may be beneficial for individuals with certain genetic conditions, such as defects in the flavin-containing monooxygenase 3 (FMO3) enzyme, by potentially stabilizing residual enzyme activity and enhancing metabolic function.

Amino Acid
Amino acids are organic compounds that serve as the building blocks of proteins and play fundamental roles in various physiological processes within living organisms. Structurally, amino acids consist of a central carbon atom (the α-carbon) bonded to a hydrogen atom, an amino group (-NH2), a carboxyl group (-COOH), and a side chain (R group) that determines the unique properties of each amino acid. There are 20 standard amino acids encoded by the genetic code, each differing in their side chain composition and chemical properties. These amino acids are linked together via peptide bonds to form polypeptide chains, which ultimately fold into complex three-dimensional protein structures. Amino acids are essential for protein synthesis, enzyme function, neurotransmitter synthesis, and numerous other biological processes critical for life. They can be obtained through dietary sources or synthesized de novo within the body.

Exon
Exons are segments of DNA that contain coding regions within a gene and are transcribed into mRNA during the process of gene expression. In eukaryotic organisms, genes are composed of both exons and introns. Exons typically encode the amino acid sequence of a protein or functional RNA molecule. During mRNA processing, introns are removed through a process called splicing, leaving only the exons to be joined together to form the mature mRNA transcript. This mature mRNA is then translated into a protein by ribosomes.

Recessive
"Recessive" describes an allele that exerts its phenotypic effect only when present in a homozygous state, meaning both copies of the gene are identical. In heterozygous individuals, where one copy of the dominant allele is present, the dominant phenotype typically masks the expression of the recessive allele. This genetic trait often manifests as a less common phenotype in populations due to its hidden nature in heterozygotes.

Gene
A gene is a fundamental unit of heredity that encodes the instructions necessary for the synthesis of functional molecules, typically proteins or RNA molecules, which play essential roles in various biological processes. Genes consist of specific sequences of nucleotides within the DNA molecule, organized along chromosomes in the cell nucleus. These sequences serve as templates for the transcription of messenger RNA (mRNA), which is then translated into proteins through a complex process involving ribosomes and transfer RNA (tRNA). The expression of genes is tightly regulated and can be influenced by various internal and external factors, ultimately contributing to the development, growth, and functioning of organisms.

Precursor
A precursor refers to a substance or molecule that precedes and serves as a starting material or intermediate in a biochemical or metabolic pathway leading to the synthesis or formation of another compound. Precursors play crucial roles in various biological processes, serving as building blocks or substrates for the biosynthesis of complex molecules such as proteins, nucleic acids, lipids, and secondary metabolites. In biochemical pathways, precursors are often transformed or modified through enzymatic reactions, ultimately yielding the final products essential for cellular functions and physiological processes.

TMA
TMA (Trimethylamine): Trimethylamine is a volatile organic compound (VOC) with a distinct fishy odor, produced by the metabolic breakdown of nitrogen-containing compounds such as choline, carnitine, and certain amino acids by gut bacteria. It is primarily synthesized in the liver and then excreted through bodily fluids, including urine, sweat, and breath.

TMAO
TMAO (Trimethylamine N-Oxide): Trimethylamine N-oxide is an oxidized derivative of trimethylamine formed through the enzymatic oxidation of trimethylamine by flavin-containing monooxygenase 3 (FMO3) in the liver. Unlike trimethylamine, TMAO is odorless and less volatile, making it less noticeable in bodily fluids such as urine and sweat. TMAO has been implicated in various physiological processes, including osmoregulation, protein stabilization, and the regulation of cellular functions. Additionally, elevated levels of TMAO in the bloodstream have been associated with cardiovascular diseases and metabolic disorders, suggesting a potential role in human health and disease.

Mutation
A mutation refers to any alteration or change in the nucleotide sequence of DNA or RNA, leading to variations in the genetic information encoded by an organism's genome. Mutations can occur spontaneously or be induced by external factors such as radiation, chemicals, or errors during DNA replication or repair processes. These alterations can manifest in different forms, including substitutions, deletions, insertions, or rearrangements of nucleotides, which may affect the structure, function, or regulation of genes. Mutations serve as the raw material for evolutionary change, driving genetic diversity and contributing to the development of traits, diseases, and adaptations in organisms.

DNA
DNA (Deoxyribonucleic Acid): DNA is a double-stranded helical molecule that encodes the genetic instructions necessary for the development, functioning, growth, and reproduction of all known living organisms and many viruses. Composed of nucleotides containing a sugar-phosphate backbone and nitrogenous bases (adenine, thymine, cytosine, and guanine), DNA carries the hereditary information that determines an organism's traits and characteristics through the sequence of its nucleotide bases. The unique sequence of nucleotides in DNA molecules dictates the sequence of amino acids in proteins, the regulation of gene expression, and ultimately, the phenotype of an organism.

Protein
Proteins are intricate molecules formed from one or more chains of amino acids, bonded together by peptide connections. They are indispensable players in numerous biological functions, acting as structural components, enzymes, hormones, antibodies, and more. The specific sequence of amino acids determines each protein's distinct structure and function. Within cells, proteins are synthesized through the intricate process of genetic transcription and translation. This mechanism involves transcribing the genetic information encoded in DNA into messenger RNA (mRNA), which is then translated by ribosomes into the precise sequence of amino acids required for protein assembly, enabling cells to fulfill their diverse functions.

Enzyme
An enzyme is a specialized protein that acts as a catalyst, facilitating and accelerating biochemical reactions within living organisms. Enzymes achieve this by lowering the activation energy required for reactions to occur, thereby speeding up the conversion of substrates into products. Each enzyme is highly specific, recognizing and binding to particular substrates at its active site, where the catalytic process occurs. Enzymes play crucial roles in metabolic pathways, signal transduction, and other cellular processes, enabling organisms to maintain homeostasis and carry out essential functions.

Coenzyme
A coenzyme is a non-protein organic molecule that works in conjunction with enzymes to facilitate and regulate biochemical reactions. Coenzymes participate in enzymatic reactions by donating or accepting chemical groups, electrons, or functional components, thereby enabling enzymes to catalyze specific reactions more effectively. Coenzymes are often derived from vitamins or other essential nutrients and serve as cofactors or prosthetic groups for various enzymes. By interacting with enzymes, coenzymes enhance their catalytic activity and contribute to the overall efficiency of cellular processes, including metabolism, DNA replication, and energy production.

Substrate
In biochemistry, a substrate refers to the specific molecule upon which an enzyme acts to catalyze a chemical reaction. Substrates bind to the active site of an enzyme, where the enzyme facilitates the conversion of the substrate into one or more products. The interaction between the substrate and the enzyme is highly specific, with the substrate molecule possessing a complementary shape and chemical properties that enable it to fit into the active site of the enzyme. Substrate binding typically induces conformational changes in the enzyme, leading to the formation of an enzyme-substrate complex and the initiation of the catalytic process. Substrates can vary widely depending on the type of enzyme and the reaction it catalyzes, ranging from small molecules like sugars and amino acids to complex macromolecules such as proteins and nucleic acids.
In the context of trimethylaminuria (TMAU), the substrate, trimethylamine (TMA), undergoes enzymatic oxidation mediated by flavin-containing monooxygenase 3 (FMO3), resulting in the conversion of TMA into its oxidized form, trimethylamine N-oxide (TMAO), a less odorous and more water-soluble compound, which can then be excreted from the body.

Genotype
The genotype refers to the genetic constitution or genetic makeup of an organism, typically in terms of the specific alleles present at one or more loci on its chromosomes. It represents the complete set of genes or genetic information that an individual inherits from its parents. The genotype determines the potential range of traits or phenotypic characteristics that an organism can express.

Phenotype
The phenotype refers to the observable traits or characteristics of an organism that result from the interaction between its genotype and the environment. It encompasses all aspects of an organism's physical appearance, behavior, and physiology, including morphology, biochemical properties, and developmental patterns. The phenotype is influenced by both genetic factors (genotype) and environmental factors, such as nutrition, temperature, and exposure to stressors.

Haplotype
A haplotype refers to a specific combination of alleles or genetic markers that are inherited together on the same chromosome from a single parent. It represents a distinct genetic configuration or sequence of DNA variations within a particular genomic region. Haplotypes can span multiple genes or genetic loci and are often associated with specific phenotypic traits or disease susceptibilities. Analysis of haplotypes is important in population genetics, evolutionary studies, and genetic association studies to understand the inheritance patterns and genetic diversity within populations.

Microbiota
This term refers to the collection of microorganisms, including bacteria, fungi, viruses, and other microbes, that inhabit a particular environment, such as the human body. In the context of the gut, the gut microbiota refers specifically to the microorganisms residing in the gastrointestinal tract.

Gut Microbiota
This is a subset of the overall microbiota and specifically refers to the microorganisms that inhabit the gastrointestinal tract, from the mouth to the colon. The gut microbiota plays a crucial role in various physiological processes, including digestion, metabolism, immune function, and even mental health.

Intestinal Bacteria
This term specifically refers to the bacteria that reside in the intestines, which is a part of the gastrointestinal tract. Intestinal bacteria are a significant component of the gut microbiota and are involved in many of its functions.

Microflora
This is an older term that was commonly used to refer to the microbial community inhabiting a particular environment, such as the gut. While it's still occasionally used, microbiota has become the preferred term in scientific literature.

Microbiome
Refers to the collective genetic material of all the microorganisms present in a particular environment. It includes the genetic material of the microorganisms themselves, as well as their metabolites and other substances they produce.
So, while "microbiota" refers to the organisms themselves, "microbiome" refers to their collective genetic material and functional capabilities.

Last updated : March 2024