Molecular Biotechnology

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Antigen

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is a substance that stimulates an immune response, especially the production of antibodies. ____are usually proteins or polysaccharides, but can be any type of molecule, including small molecules (haptens) coupled to a carrier-protein.

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polysaccharide

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(sometimes called glycans) are relatively complex carbohydrates.

They are polymers made up of many monosaccharides joined together by glycosidic linkages. They are therefore very large, often branched, molecules. They tend to be amorphous, insoluble in water, and have no sweet taste.

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dalton (Da)

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is a small unit of mass used to express atomic masses and molecular masses. It is defined to be 1/12 of the mass of one atom of carbon-12.

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Bacillus of Calmette and Guérin (BCG)

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is a vaccine against tuberculosis that is prepared from a strain of the attenuated (weakened) live bovine tuberculosis bacillus, Mycobacterium bovis that has lost its virulence in humans by specially culturing in artificial medium for years. The bacilli have retained enough strong antigenicity to become an effective vaccine for the prevention of human tuberculosis.

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secretory protein

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In eukaryotes, proteins synthesised on rough endoplasmic reticulum and destined for export. Nearly all proteins secreted from cells are glycosylated (in the Golgi apparatus, although there are exceptions (albumin). In prokaryotes, ____ may be synthesised on ribosomes associated with the plasma membrane or exported post translation.

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Glycosylated

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chemically linked to glucose

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transferase

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is an enzyme that catalyzes the transfer of a functional group (e.g. a methyl or phosphate group) from one molecule (called the donor) to another (called the acceptor). For example, an enzyme that catalyzed this reaction would be a ____:

A–X + B → A + B–X
A in this example would be the donor, and B would be the acceptor. The donor is often a coenzyme.

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Electroporation

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is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA.

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shuttle vector

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Cloning vector that replicate in cells of more than one organism, for example E. Coli and yeast. This combination allows DNA from yeast to be grown in E. Coli and tested directly for complementation in yeast. These are constructed so that they have the origins of replication of the various hosts.

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Obligate intracellular parasites

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are organisms that cannot reproduce outside their host cell, they force or compel the host to do their bidding.

examples include:

viruses
certain bacteria, including:
chlamydias
rickettsias
certain protozoa, including:
plasmodia species

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transformation

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involves the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign DNA.

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origin of replication

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is a unique DNA sequence at which DNA replication is initiated. DNA replication may proceed from this point bidirectionally or unidirectionally.

The specific structure of varies somewhat from species to species, but all share some common characteristics. This site binds a member of the pre-replication complex—a protein complex that binds, unwinds, and begins to copy DNA.

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Immunogen

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Any substance that provokes the immune response when introduced into the body.A(n)_____ is always a macromolecule (protein, polysaccharide). Its ability to stimulate the immune reaction depends on its commoness to the host, molecular size, chemical composition and heterogeneity (e.g. simlar to amino acids in a protein).

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Cytoplasm

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is a homogeneous, generally clear jelly-like material that fills cells. It consists of cytosol and the cellular organelles, except the cell nucleus. The cytosol is made up of water, salts, organic molecules and many enzymes that catalyze reactions. Plays an important role in a cell, serving as a "molecular soup" in which the organelles are suspended and held together by a fatty membrane. It is found within the plasma membrane of a cell and surrounds the nuclear envelope and the cytoplasmic organelles.

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immunogenic

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Producing immunity, evoking an immune response

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Bacterial flagellum (plural, flagella)

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a whip-like organelle that is used to move about. They may also be involved in other processes.In bacteria the filament is composed of the protein flagellin and is a hollow tube 20 nanometers thick. It is helical, and has a sharp bend just outside the outer membrane called the "hook" which allows the helix to point directly away from the cell. A shaft runs between the hook and the basal body, passing through protein rings in the cell's membranes that act as bearings

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peptidoglycan

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also known as murein, is a polymer that forms a homogeneous layer lying outside the plasma membrane and is only found in eubacteria (note: archaea have pseudo____). It serves a structural role in the cell walls of bacteria, giving them shape and strength and counteracting the osmotic pressure of the cytoplasm. It is also involved in the binary fission (reproduction) of the bacterial cell. Is a target for many antibacterial drugs, such as penicillin, which works by interfering with the formation of this layer, specifically the crosslinking enzyme transpeptidase.

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plasma membrane

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is a thin and structured bilayer of phospholipid and protein molecules that envelopes the cell. It separates a cell's interior from its surroundings and controls what moves in and out. Cell surface membranes often contain receptor proteins and cell adhesion proteins. There are also other proteins with a variety of functions. These membrane proteins are important for the regulation of cell behavior and the organization of cells in tissues.

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epitope

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is the part of a foreign organism or its proteins that is being recognised by the immune system and targeted by antibodies, cytotoxic T cells or both.

Most of these can be thought of as three-dimensional surface features of an antigen molecule. An exception are linear ____ which are determined by the amino acid sequence (the primary structure) rather than by the tertiary structure of a protein.

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cytotoxic T cells

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(a type of white blood cell) which has on its surface antigen receptors that can bind to fragments of antigens displayed by the Class I MHC molecules of virus (or other intracellular pathogen) infected somatic cells and tumor cells.

Once activated by a MHC-antigen complex, ____release the cytoxins perforin and granulysin, which forms pores in the target cell's plasma membrane; this causes ions and water to flow into the target cell, making it expand and eventually lyse. ____also release granzyme, a serine protease, that can enter target cells via the perforin-formed pore and induce apoptosis (cell death).

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MHC molecules (Major Histocompatibility Complex)

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cell surface proteins found on most cells of the body. These proteins have a distinctive structure first elucidated in 1987 by Dr. Pamela J. Bjorkman and colleagues. ____ molecules typically interact with the cell surface receptor of a type of lymphocytes known as killer T cells. The receptor on the killer T cell binds to the ____ molecule and informs the killer T cell on whether that cell is normal or not. The interesting part of the story is how the T cell can distinguish the ___ class I protein on a normal cell from that on an abnormal one. The key concept here is to appreciate that the ____molecule has within its structure a groove. Into this groove is bound a small piece of protein derived from within the cell, that was placed there during the synthesis of the ____ molecule. If this peptide of 8 or 9 amino acids happens to be a foreign peptide, such as one produced by a viral gene, or a cancer gene, the T cell will become activated, and attack the infected or cancerous cell. Of primary interest is the fact that when an organ is transplanted between non-identical people, it is the recipient's T cells reacting against the donor organ ____ proteins that causes much of organ rejection.

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protease(proteinases, peptidases or proteolytic enzymes)

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are enzymes that break peptide bonds between amino acids of proteins. The process is called proteolytic cleavage, a common mechanism of activation or inactivation of enzymes especially involved in blood coagulation or digestion. They use a molecule of water for this and are thus classified as hydrolases.

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hypervariable segment

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a portion of a gene that varies considerably from one strain to another

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Oligonucleotide,oligo,primer

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are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer base pairs. Often used as probes for detecting complementary DNA or RNA because they bind readily to their complements. Examples of procedures that use ____ are DNA microarrays, Southern blots, and fluorescent in situ hybridization (FISH).

_____ composed of DNA (deoxyoligonucleotides) are often used in the polymerase chain reaction (PCR), a procedure that can be employed to amplify almost any piece of DNA. In this instance, the ______is often referred to as a primer, or a short piece of DNA that binds to its complementary target sequence. This generates a place for a polymerase to bind and extend the primer by the addition of nucleotides to make a copy of the target sequence.

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DNA polymerase

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is an enzyme that assists in DNA replication. Such enzymes catalyze the polymerization of deoxyribonucleotides alongside a DNA strand, which they "read" and use as a template. The newly-polymerized molecule is complementary to the template strand and identical to the template's partner strand.

All ____ synthesize DNA in the 5' to 3' direction. No known _____is able to begin a new chain (de novo). They can only add a nucleotide onto a preexisting 3'- OH group. For this reason, ____ needs a primer at which it can add the first nucleotide. Primers consist of RNA and DNA bases with the first two bases always being RNA, and are synthesized by another enzyme called primase.

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cDNA (complementary DNA)

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is DNA synthesized from a mature mRNA template.____ is often used to clone eukaryotic genes in prokaryotes.____ is most often synthesized from mature (fully spliced) mRNA using the enzyme reverse transcriptase. This enzyme operates on a single strand of mRNA, generating its complementary DNA based on the pairing of RNA base pairs (A, U, G, C) to their DNA complements (T, A, C, G).

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multivalent (immunological definition)

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having multiple antigenic binding sites

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gene probe, hybridization probe

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is a short piece of DNA (on the order of 100-500 bases) that is denatured (by heating) into single strands and then radioactively labeled, usually with phosphorus (32P or 33P). The radioactive phosphorus is incorporated into one of the bases of DNA (adenine, guanine, cytosine, or thymidine) and these labeled bases are incorporated into the backbone of the DNA strands by incubation with a polymerase enzyme. This creates a short piece of radioactively labeled DNA with known sequence that will hybridize with any complementary nucleic acid strands.

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cDNA library

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refers to a complete, or nearly complete, set of all the mRNAs contained within a cell or organism. Because working with mRNA is difficult, researchers use an enzyme called reverse transcriptase which will produce a DNA copy of each mRNA strand. Referred to as cDNA these reverse transcribed mRNAs are collectively known as a ____.

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Chimera (or chimeric protein)

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is a human-engineered protein that is encoded by a nucleotide sequence made by a splicing together of two or more complete or partial genes.

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nucleotide

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a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. In the most common ____the base is a derivative of purine or pyrimidine, and the sugar is pentose - deoxyribose or ribose.

____are the structural units of RNA, DNA, and several cofactors - CoA, FAD, FMN, NAD, and NADP. In the cell they play important roles in energy production, metabolism, and signaling.

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purine

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is a heterocyclic aromatic organic compound, consisting of a pyrimidine ring fused to an imidazole ring.

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pyrimidine

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is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring.

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heterocyclic

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are organic compounds that contain a ring structure containing atoms in addition to carbon, such as sulfur, oxygen or nitrogen, as part of the ring. They may be either simple aromatic rings or non-aromatic rings. Some examples are pyridine (C5H5N), pyrimidine (C4H4N2) and dioxane (C4H8O2).

Note that compounds such as cyclopropane, an anaesthetic with explosive properties, and cyclohexane, a solvent, are not ____, they are merely cycloalkanes. The suffix '-cyclic' implies a ring structure, while 'hetero' refers to an atom other than carbon, as above.

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aromatic

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In chemistry, an ____ molecule is one in which a conjugated ring of unsaturated bonds, lone pairs, or empty orbitals exhibit a stabilization stronger than would be expected by the stabilization of conjugation alone.

This is usually considered to be because electrons are free to cycle around circular arrangements of atoms, which are alternately single- and double-bonded to one another. (These bonds may be seen as a hybrid of a single bond and a double bond, each bond in the ring identical to every other.)

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conjugated

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is the interaction between two carbon-carbon double bonds, increasing stability and thereby lowering the overall energy of the molecule. The system formed is called a conjugated system.

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unsaturated

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In organic chemistry, a ____compound has the maximum amount of hydrogens possible: i.e., no double bonds or, in a hydrocarbon chain, every carbon atom is attached to two hydrogen atoms. Of simple hydrocarbons, alkanes are saturated, and alkenes are ____.

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Transcription

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is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, ____is the beginning of the process that ultimately leads to the translation of the genetic code (via the mRNA intermediate) into a functional peptide or protein. ____has some proofreading mechanisms, but they are fewer and less effective than the controls for DNA; therefore, ____has a lower copying fidelity than DNA replication.

Like DNA replication, ____proceeds in the 5' → 3' direction (ie the old polymer is read in the 3' → 5' direction and the new, complementary fragments are generated in the 5' → 3' direction). ____is divided into 3 stages: initiation, elongation and termination.

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translation

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is the second process of protein biosynthesis (part of the overall process of gene expression). In ____, messenger RNA is decoded to produce a specific polypeptide according to the rules specified by the genetic code. ____is necessarily preceded by transcription. Similarly to transcription, _____proceeds in three phases: initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of ____).

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promoter

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is a DNA sequence that enables a gene to be transcribed. The ____ is recognized by RNA polymerase, which then initiates transcription. In RNA synthesis, ____ are a means to demarcate which genes should be used for messenger RNA creation - and, by extension, control which proteins the cell manufactures.

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ester

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In chemistry, ____ are organic compounds in which an organic group (can be symbolized by R) replaces a hydrogen atom (or more than one) in an oxygen acid. An oxygen acid is an acid whose molecule has an -OH group from which the hydrogen (H) can dissociate as an H+ ion.

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nitrite

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The ____ ion is NO2−. The anion is bent, being isoelectronic with O3.

A ____ compound is one that contains this group, either an ionic compound, or an analogous covalent one. These may be considered salts or esters of nitrous acid.

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microaerophilic

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Requiring oxygen but at a level lower than that typically found in the Earth's normal sea-level atmosphere

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gram-negative bacteria

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A common class of bacteria normally found in the gastrointestinal tract that can be responsible for disease in man (sepsis).

Bacteria are considered to be ____ because of their characteristic staining properties under the microscope, where they either do not stain or are decolourised by alcohol during Gram's method of staining.

This is a primary characteristic of bacteria that have a cell wall composed of a thin layer of peptidoglycan covered by an outer membrane of lipoprotein and lipopolysaccharide containing endotoxin.

The gram staining characteristics of bacteria have resulted in an important classification system for the identification of bacteria.

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gram-positive

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Bacteria that retain the stain or that are resistant to decolourisation by alcohol during Gram's method of staining.

This is a primary characteristic of bacteria whose cell wall is composed of a thick layer of peptidologlycan containing teichoic and lipoteichoic acid complexed to the peptidoglycan.

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urease

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An enzyme that breaks urea down into carbon dioxide and ammonia, its typically used to measure urea concentrations

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constitutive expression

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Of or relating to the synthesis of a protein or an enzyme at a constant rate regardless of physiological demand or the concentration of a substrate.

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Cytokine

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are soluble proteinaceous substances produced by a wide variety of haemopoietic and non-haemopoietic cell types, and are critical to the functioning of both innate and adaptive immune responses. Apart from their role in the development and functioning of the immune system, and their aberrant modes of secretion in a variety of immunological, inflammatory and infectious diseases, ____ are also involved in several developmental processes during human embryogenesis.

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haemopoietic

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pertaining to the formation of blood or blood cells

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Methylase

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is an enzyme that attaches a methyl group to a molecule, e.g. DNA methyltransferase which methylates C residues in DNA