~Glossary~

The Biology Yak aims to create concise and understandable articles, which means some of the more technical terms are not always explained each time. Here is a list of the scientific words used, and a definition of what they mean. Contact me if you think something is missing!


 A

  • Action potential: The ‘pulse’ of signal sent down a nerve when it receives a signal
  • AID:
  • Anaerobic respiration: The process through which cells respire when no oxygen is present. This produces ethanol (in bacteria) or lactate (in mammals) as a by-product, and only produces a net gain of 2 ATP molecules per glucose respired.
    • See also: substrate level phosphorylation
  • Anterio-posterior (AP) axis: The ‘top to bottom’ axis of an animal
  • Antibody: The mobile form of BCRs (B cell receptors). Antibodies are generated and mature in the bone marrow. Each antibody is unique, and will be specific to only one epitopic antigen. This high antibody diversity is what drives innate immunity: when a new pathogen enters the host, it is likely that there will be an antibody which can recognise an antigen on the pathogen. The antibody is cloned, and these clones bind the antigen and trigger the immune system into removing the pathogen.
    • See also: antigens, B cell
  • Antigens: Distinctive (epitopic) parts of a pathogen that are recognised by antibodies. Each antibody made is unique to a specific antigen. When an antibody binds to its antigen, it gets cloned. These clones find the antigen on the pathogens and bind to all of them, which attracts the attention of the pathogen-killing cells of the immune system
    • see also- antibody
  • Antigen-presenting cell – E.g. macrophages, dendritic cells, B cells. Cells that recognise antigens from pathogens, and present them to B or T cells to activate them against that specific antigen.
    • See also: B cell, antigen
  • Archaea: The third domain of life, prokaryotic organisms distinct from bacteria and eukaryotes.
  • ATP (adenosine triphosphate): The molecule that provides power to cellular reactions. It is created from ADP (Adenosine diphosphate) and P (phosphate), in the mitochondria by glycolysis and the electron transport chain. When ATP is hydrolysed during respiration, it releases energy. This energy is used to power everything that occurs in the cell- without ATP, there would be no movement, enzymatic activity, and no life itself!

B

  • B cell/BCR:  A type of white blood cell (leukocyte), that is part of the adaptive immune system. B cells express B cell receptors (BCRs) on their cell surface. They undergo V(D)J recombination as they develop, which generates a wide range of diversity among the B cell receptors, allowing them to bind to a wide range of antigens. Differentiated B cells (plasma cells) secrete antibodies, which contain a soluble, mobile BCR
    • see also: antibody, antigen

C

  • Chromosome:  Chromosomes are structures containing histone proteins and tightly wrapped DNA. There are 26 pairs of chromosomes in humans. They provide structure for the DNA, and it remains tightly wrapped in the chromosome, until it is needed for transcription or cell duplication.
  • Cytokine: a soluble protein that can stimulate a cellular response. They are involved in cellular signaling. For example, they are released at the site of infection, and can stimulate inflammation.
  • Cytomegalovirus: A latent virus of the Herpesviridae family. Used as a vector in some vaccine designs
    • see also: vector
  • Cytosol: The jelly-like substance that makes fills up the cell, and acts as a place of reaction for many important cellular mechanisms
  • Cytotoxic: Toxic to cells

D

  • DNA: DNA is a long, antiparallel double helix molecule consisting of 4 base pairs (A,G, C,T). DNA encodes genes, which code for proteins that are essential for life. Every 3 base pairs in the sequence is a codon, which itself is specific to an amino acid. The DNA sequence contains many codons, which form strings of amino acids during translation, that in turn eventually form proteins needed in the cell.

E

  • Electron transport chain: Found within the membrane of mitochondria. This chain uses electrons to pump protons across the membrane. These protons pass back through the membrane via the enzyme ATP synthase. This generates ATP for the cell to use in energetic reactions
    • See also: mitochondria, enzymes
  • Endonuclease: An enzyme that cuts DNA. Endonucleases can be created to cut only specific sequences, and so have high useage in genetic experiments.
  • Endoplasmic reticulum: An organelle of eukaryotic cells, involved in protein modification and other functions.
    • Rough ER: Is covered in ribosomes. These synthesise proteins which are directly sent to the RER. In the RER, the proteins are modified (by glycosylation – sticking sugars on; sumoylation etc), and then sent to specific areas of the cell where they are needed
  • Enzymes– active proteins that catalyse cellular reactions. The have an active site which can cleave substrate.
  • Epigenetics– the study of how chromatin and DNA is modified. Methylation prevents DNA from being transcribed (genes from being ‘read’ and converted into proteins), which silences the gene
  • Eukaryote-  a multi- or single-celled organism that has a nucleus (from the Greek karyon- ‘kernel’), and membrane-bound organelles such as the Golgi body, endoplasmic reticulum, and mitochondria. Includes all animals, plants and fungi
    • See also: Golgi body, endoplasmic reticulum, mitochondria

F


G

  • Gene:
  • Gene conversion:
  • Golgi body

H

  • Haematopoietic stem cell: A type of stem cell that can develop into a variety of blood and immune cells. They can give rise to all the myeloid and lymphoid lineages, which include macrophages, granulocytes, T cells and B cells.
  • HLA-E (MHC-E): Human Leukocyte Antigen-E. A non-classical class Ib MHC molecule. HLA-E is class I, as it presents antigens to CD8+ T cells. However, it is non-classical as it has a very limited polymorphism, unlike classical HLA-A, -B, and -C molecules. HLA-E typically only has one polymorphism, at amino acid position 107- this varies between an arginine (R), or a glycine (G), creating two alleles: HLA-ER and HLA-EG.
    • See also: CD8+ T cells, MHC
  • Homo sapiens: The Linnaean (‘scientific’) name for modern humans
  • Horizontal gene transfer

I

  • Immune system:
  • Ion channel

J


K


L

  • Leukocytes: White blood cells, including macrophages, dendritic cells, and granulocytes.
  • Lymphocyte: A sub-division of leukocytes (white blood cells) that form part of the adaptive immune system. Lymphocytes include T cells, B cells, and Natural Killer cells
    • See also: T cell, B cell

M

  • Mamu-E: The Rhesus macaque (Macaca mulatta)-specific form of MHC-E. It is a lot more polymorphic than human MHC-E (HLA-E), and bears a lot more resemblence to class Ia MHC molecules.
  • MHC (major histocompatibility complex): The molecules that activate T cells through presentation of specific recognised antigens. These antigens are peptides either collected from the cytosol (class I) or vacuolar space (class II). The MHC gene region is one of the most heterogenous and polymorphic regions of the genome, which provides the variety in receptors needed to recognise a wide range of antigens.
    •  Class Ia: MHC-A, -B, -C. Highly polymorphic to recognise antigens from pathogens in the cell’s cytosol. Class I MHC molcules are expressed on the surface of most cells. Class I interacts with CD8+ (T cytotoxic) T cells to produce a cytotoxic response.
    • Class Ib: MHC-E, MHC-F, and MHC-G . Non-classical MHC molcules- usually have a lot less polymorphism and recognise specific peptide antigen sequences. They may be recognised by a specific group of T cells
    • Class II: Found on a limited number of immune cell surfaces. Class II interacts with CD4+ (T helper) T cells, which assist in the stimulation of other immune responses from T cells, B cells, and the innate immune system
    • see also: T cell, B cell, HlA-E
  • Mitochondria– A membrane-bound organelle found within eukaryotic cells. Originally free-living α-proteobacteria, they were endosymbiosed over 2 billion years ago but ancient proto-eukaryotes. The reason behind this endosymbiosis remains contentious, but modern day mitochondria generate ATP for cellular use, as well as iron-sulfur clusters and play a pivotal role in cell apoptosis.
    • See also: ATP, prokaryote, eukaryote

N

  • Neolithic– The period of time from ~6,000 to ~3,000 years ago

P

  • Pathogen: A virus, bacteria, protist or helminth worm that invades a host and causes harm
  • Peripheral lymphoid organ: Organs of the immune system, including lymph nodes, spleen, and tonsils.
  • Phagocyte: Leukocytes including: macrophages, dendritic cells, neutrophils and mast cells. They have absorbing, degrading capacities against pathogens. They contain enzymes such as proteases in their lysozyme that digest the pathogens that they consume.
  • Plasma cell:  Produces a specific type of antibody. Plasma cells begin as B cells, and mature into plasma cells when stimulated by their specific antigen.
  • Principle Component Analysis (PCA)– a method for analysis of multiple traits
  • Prokaryote– a single-celled organism (e.g. bacteria and archaea), which has no nucleus or membrane-bound organelles.
  • Protease: A subcategory of enzyme that digests proteins.
  • Protist- a single-celled eukaryote, for example Giardia or Monocercomonoides. They have eukaryotic features such as a nucleus and membrane-bound organelles, and so are not similar to single-celled prokaryotes such as bacteria.
  • Protozoa
  • Proto-Indo-European– The hypothesised ancestral language of over 400 languages and dialects in Europe and Asia

Q


R

  • RAG
  • RNA: Single stranded nucleic acid molecule, found across the entirely of life in several different forms.

S

  • Single nucleotide polymorphism (SNP)– A change of one base pair in a DNA sequence, which is found in over 1% of the population. Unique SNPs can arise in populations, especially when they are kept isolated from each other.
  • Stem cells. Cells that can replicate, and give rise to any type of cell in the body. Embryonic stem cells (ESC) are undifferentiated, and can be stimulated into transforming into all types of cell. They are under a lot of research, especially in areas such as cancer treatment and anti-ageing.
  • Substrate level phosphorylation– The process through which glucose is transformed into pyruvate in the cytosol of a cell. This produces 2x ATP molecules per glucose for the cell to use in energetic reactions.
    • See also: anaerobic respiration, cytosol, ATP

T

  • TCA cycle (Tricarboxylic acid cycle)
  • T cell (T lymphocyte): A cell of the adaptive immune system, that recognises antigens through interaction with MHC molecules.
    • CD4+ T cell: Interacts with MHC class II molecules. Mature into T helper (Th) cells that assist with recruitment of T cytotoxic cells, B cells, and innate immune cells such as macrophages.
    • CD8+ T cell: Interacts with MHC class I molecules. Matures into T cytotoxic (Tc) cells, that produce cytotoxins and assist with the removal of pathogen-infected cells.

U


V

  • V and DJ segment
  • Vector: A plasmid (a circular piece of DNA from a bacteria) that has been edited so that a piece of DNA/ gene can be inserted into it. This vector is then transfected into living cells, which express the gene.

W


X


Y

  • Y chromosome- In humans, the ‘male’ chromosome. It is highly reduced and contains very few functional genes.

Z

 

 

 

 

 

 

Advertisements