Unit 3 // AOS1 Textbook Definitions Flashcards
The definitions of specific words that comes directly from the textbook.
Protein
A biomacromolecule made of amino acid chains folded into a 3D shape
Polypeptide
A long chain of amino acids. Proteins can be made of one or many polypeptides
Proteome
All the proteins that are expressed by a cell or organism at a given time
Enzyme
An organic molecule, typically a protein, that catalyses (speeds up) specific reactions
Peptide hormone
A protein signalling molecule that regulates physiology or behaviour
Antibody
A protein produced by plasma cells during the adaptive immune response that is specific to an antigen and combats pathogens in a variety of ways. Also known as immunoglobulin
Carboxyl group
The functional group on amino acid molecules that contains a hydroxyl group (OH) and an oxygen double-bonded to a carbon atom
Amino group
The functional group of amino acid molecules that is made up of one nitrogen and two hydrogens (NH2)
R-group
The variable portion of an animo acid and molecule. It can be one of twenty variations and determines the identity of the amino acid
Hydrophobic
Having a tendency to repel and be insoluble in water
Hydrophilic
Having a tendency to be attracted to and dissolve in water
Monomer
A molecule that is the smallest building block of a polymer
Polymer
A large molecule that is made up of small, repeated monomer subunits
Condensation reaction
A reaction where two monomers join to form a larger molecule, producing water as a by-product
Peptide bond
The chemical bond linking two amino acids
Primary structure
The first level of protein structure, which refers to the sequence of amino acids in a polypeptide chain
Secondary structure
The level of protein structure where the amino acid chain forms either alpha-helices, beta-pleated sheets, or random coils
Tertiary structure
The functional 3D shape of a polypeptide chain
Quaternary structure
The level of protein structure where the multiple polypeptide chains bond together, or other non-protein groups are added to form a fully functional protein
Alpha helix
An organised coil secondary structure of proteins
Beta-pleated sheet
An organised folded secondary structure of proteins
Random coil
An irregular secondary structure of proteins that is neither an alpha helix nor a beta-pleated sheet
Disulphide bond
A strong covalent bond occurring between two sulphur atoms
Prosthetic group
A non-protein group bound to a protein. For example, a vitamin or ion
Nucleic acid
The class of macromolecule that includes DNA and RNA. All nucleic acids are polymers made out of nucleotide monomers
Polymer
A large molecule that is made up of small, repeated monomer subunits
Nucleotide
The monomer subunit of nucleic acids. Made up of a nitrogen-containing base, a five-carbon sugar molecule (ribose RNA and deoxyribose in DNA) and a phosphate group
Monomer
A molecule that is the smallest building block of a polymer
DNA (deoxyribonucleic acid)
A double-stranded nucleic acid chain made up of nucleotides. DNA carries the instructions for proteins which are required for cell and organism survival
RNA (ribonucleic acid)
A single stranded nucleic acid chain made up of nucleotides. Includes mRNA, rRNA, and tRNA
Phosphodiester bond
A strong covalent bond linking a five-carbon sugar to a phosphate group
Condensation reaction
A reaction where two monomers join to form a larger molecule, producing water as a by-product
Sugar-phosphate backbone
A strong covalently linked chain of five-carbon sugar molecules and phosphate groups in a nucleic acid chain
Chromosome
A structure made of protein and nucleic acids that carries genetic information
Gene
A section of DNA that carries the code to make a protein
Genome
The complete set of DNA housed within an organism
Antiparallel
A characteristic of DNA strands describing how each strand runs in an opposite direction to the other. One strand runs in a 3’ -> 5’ direction and the other runs in a 5’ -> 3’ direction
Complementary base pairing
Describes which nucleotides can form hydrogen bonds with each other. C pairs with G, a pairs with T (or U in RNA)
Double helix
The structure of double-stranded DNA in the nucleus of eukaryotic cells, where each DNA strand wraps around a central axis
Nuclear DNA
DNA that is located in the nucleus of a cell
Messenger RNA (mRNA)
RNA molecules that are produced during transcription and carry genetic information from the nucleus to the ribosomes
Transfer RNA (tRNA)
RNA that recognises specific codons on the mRNA strand and adds the corresponding amino acid to the polypeptide chain during protein synthesis
Ribosomal RNA (rRNA)
RNA that is a key structural component of ribosomes, which assembles proteins
Transcription
The process whereby a sequence of DNA is used as a template to produce a complementary sequence of mRNA
Translation
The process where an mRNA sequence is read to produce a corresponding amino acid sequence to build a polypeptide
Genetic code
The set of rules by which information is encoded in genetic material
Triplet
The sequence of three nucleotides in DNA coding for one amino acid
Codon
The sequence of three nucleotides in mRNA coding for one amino acid
Start codon
The sequence of three nucleotides in mRNA that signals the start of translation
Promoter
The sequence of DNA to which RNA polymerase binds
RNA polymerase
The enzyme responsible for constructing a pre-mRNA sequence from a DNA sequence during transcription
TATA box
A type of promoter region
Introns
Non-coding regions of DNA that do not code for proteins. They are spliced out during RNA processing
Exons
Regions of DNA that code for proteins and are not spliced out during RNA processing
Termination sequence
A sequence of DNA that signals the end of transcription
Operator
A short region of DNA that interacts with repressor proteins to alter the transcription of an operon
Repressor protein
A protein coded for by a regulatory gene that prevents gene expression by binding to its operator
Gene expression
The process of reading the information stored within a gene to create a functional product, typically a protein
Leader region
The segment of DNA or mRNA that immediately precedes the coding region. Also known as the leader segment or leader sequence
Precursor messenger RNA (pre-mRNA)
The immediate product of transcription of a DNA sequence. Requires modifications before it can undergo translation
Transcription factor
Proteins that bind to the promoter region and control the functioning of RNA polymerase
Template strand
The strand of DNA transcribed by RNA polymerase to produce a complementary pre-mRNA strand
Coding strand
The strand of DNA not transcribed by RNA polymerase, contains an identical sequence to the mRNA strand produced (except thymine is replaced with uracil in mRNA)
Ribosome
An organelle made of rRNA and protein that is the site of protein synthesis. Can be free in the cytosol or attached to the rough endoplasmic reticulum
5’ methyl-G cap
A molecule added to the 5’ end of pre-mRNA during RNA processing
3’ poly-A tail
A chain of adenine nucleotides added to the 3’ end of pre-mRNA during RNA processing
Splicing
Process where introns are cut out of a pre-mRNA molecule, and exons are joined together
Spliceosome
The enzyme that removes introns from the pre-mRNA molecule and joins exons together during RNA processing
Alternative splicing
The process where different exons may be spliced, resulting in a single gene producing multiple different mRNA strands
Anticodon
The sequence of three nucleotides on a tRNA molecule that recognises a specific sequence of three nucleotides (codon) on an mRNA strand
Exocytosis
A type of bulk transport that moves large substances out of a cell
Gene regulation
The control of gene expression, typically achieved by switching transcription on or off
Structural gene
A segment of DNA that doesn’t code for regulatory proteins, but instead codes for proteins that play a role in the structure or function of a cell or organism
Regulatory gene
A segment of DNA responsible for producing proteins that control the expression of other genes
Activator protein
A protein coded for by a regulatory gene that increases gene expression
Operon
A cluster of linked genes that all share a common promoter and operator and are transcribed at the same time
trp operon
A series of genes within certain species of bacteria that encode for the production of the amino acid tryptophan
trp operon repression
Mechanism for gene regulation within the trp operon whereby repressor proteins stop the initiation of transcription when tryptophan levels are high
Conformational change
A change in the three-dimensional shape of macromolecules such as proteins
trp operon attenuation
Mechanism for gene regulation within the trp operon whereby the premature ceasing of translation stops transcription when tryptophan levels are high
Attenuator sequence
Part of the leader region within the trp operon that allows for attenuation
Terminator hairpin
A loop formed in mRNA in the presence of tryptophan that ceases transcription of the trp operon
Antiterminator hairpin
A loop formed in mRNA when tryptophan is not present that ensure the transcription of the structural genes in the trp operon
Vesicle
A small fluid-filled organelle enclosed in a phospholipid membrane that transports substances around the cell
Bulk transport
A type of active transport that uses vesicles to move large molecules or groups of molecules into or out of the cell
Active transport
The movement across a semipermeable membrane requiring an energy input
Secretory products
The substances inside a vesicle that are being transported out of the cell
Plasma membrane
The phospholipid bilayer with embedded proteins which separates the intracellular environment from the extracellular environment
Rough endoplasmic reticulum (RER)
A membranous organelle shaped like a series of connected, flattened cylinders that folds and transports proteins via its attached ribosomes
Golgi apparatus
An organelle made of flattened sacs of membrane involved in modifying, sorting, and packaging proteins. Also known as the Golgi body or Golgi complex
Mitochondrion (pl. mitochondria)
A double-membrane-bound organelle that is the sire of the second and third stages of aerobic cellular respiration
Catalyst
A substance capable of increasing the rate of a reaction without being used up
Catalyse
To increase the rate of a reaction
Substrate
The reactant of a reaction catalysed by an enzyme
Reactant
A molecule that undergoes a transformation into a product. When enzymes are involved, the reactant is called a substrate
Product
The transformed molecule created in a reaction
Enzyme-substrate complex
The structure formed when an enzyme and substrate are bound together
Activation energy
The energy required to initiate a reaction
Collision theory
Explanation of chemical reactions that states that in order to react molecules must hit one another
Biochemical pathway
A series of enzyme-catalysed biochemical reactions in which the product of one reaction becomes the substrate of the next reaction. Also know as metabolic pathway
Optimal
The point at which for a given condition (e.g. temperature), the maximum function of an enzyme occurs. Also known as optimum
Denature
The disruption of a molecule’s structure by an external factor such as heat
Saturation point
The point at which a substance (e.g. an enzyme) cannot receive more another substance (e.g. substrate)
Limiting factor
A factor that prevents the rate of reaction from increasing
Limiting reagent
A reactant that prevents the rate of reaction from increasing
Enzyme inhibitor
A molecule that binds to an prevents an enzyme from functioning
Competitive inhibition
The hindrance of an enzyme by blocking the active site and preventing the substrate from binding
Non-competitive inhibition
The hindrance of an enzyme by binding to an allosteric site and changing the shape of the active site to prevent the substrate from binding
Allosteric site
A region on an enzyme that is not the active site
Reversible inhibition
Enzyme inhibition that involves weaker bonds that can be overcome
Irreversible inhibition
Enzyme inhibition that involves stronger bonds that cannot be broken
Cofactor
Any organic or inorganic molecule, such as a coenzyme or metal ion, that assists enzyme function
Coenzyme
A non-protein organic cofactor that assists enzyme function. They release energy and are recycles during a reaction
ATP
Adenosine triphosphate, a high energy molecule that, when broken down, provides energy for cellular processes
ADP
Adenosine diphosphate, the unloaded form of ATP
Endonuclease
An enzyme that breaks the phosphodiester bond between two nucleotides in a polynucleotide chain
Recognition site
A specific target sequence of DNA upon which restriction endonucleases act
Restriction endonuclease
Any enzyme that acts like molecular scissors to cut nucleic acid strands at specific recognition sites. Also known as a restriction enzyme
Sicky end
The result of a staggered cut through double-stranded DNA by an endonuclease resulting in overhanging nucleotides
Blunt end
The result of a straight cut across the double-stranded DNA by an endonuclease resulting in no overhanging nucleotides
Overhanging nucleotides
Unbonded nucleotides on the ends of the DNA strand resulting from a staggered cut
Ligase
An enzyme that joins molecules, including DNA or RNA, together by catalysing the formation of phosphodiester bonds
Polymerase
An enzyme that synthesises a polymer from monomers, such as forming a DNA strand from nucleic acids
Primer
A short, single strand of nucleic acids that acts as a starting point for polymerase enzymes to attach
Virus
A non-cellular, infectious agent composed of genetic material enclosed in a protein coat that requires a host cell to multiply
Bacteriophage
A virus that infects prokaryotic organisms
CRISPR-Cas9
A complex formed between gRNA and Cas9 which can cut a target sequence of DNA. Bacteria use this complex for protection from viruses and scientists have modified it to edit genomes
CRISPR-associated protein 9 (Cas9)
An endonuclease that creates a blunt end cut at a site specified by guide RNA (gRNA)
CRISPR
Short, clustered repeats of DNA found in prokaryotes which protect them against viral invasion
Spacer
Short sequences of DNA obtained from invading bacteriophages that are added into the CRISPR sequence
Protospacer
A short sequence of DNA extracted from a bacteriophage by Cas1 and Cas2, which has yet to be incorporated into the CRISPR gene
Protospacer adjacent motif (PAM)
A sequence of two-six nucleotides that is found immediately next to the DNA targeted by Cas9
Guide RNA (gRNA)
RNA which has a specific sequence determined by CRISPR to guide Cas9 to a specific site
Genetic modification
The manipulation of an organism’s genetic material using biotechnology
Deleterious mutation
A change in DNA that negatively affects an individual
Gene therapy
Repairing genetic mutations by replacing a defective gene with a healthy one
Single guide RNA (sgRNA)
Guide RNA utilised by scientists to instruct Cas9 to cut a specific site when using CRISPR-Cas9 in gene editing
Gene knockout
A technique in gene editing where scientists prevent the expression of a target gene to understand its function in an organism
Zygote
The diploid cell formed by the combination of two haploid gamete cells
Gene knock-in
A technique in gene editing where scientists substitute or add a nucleotides in a gene
Embryo
An early stage of development in an organism. In humans, used to refer to the organism during the first eight weeks of development
Differentiation
The process in which cells develop specialised characteristics, typically transforming them from one cell type to another more specialised cell type
Polymerase chain reaction (PCR)
A laboratory technique used to produce many identical copies of DNA from a small initial sample
Amplify
To increase the quantity of a molecule by making many copies
Taq polymerase
A heat-resistant DNA polymerase enzyme isolated from the bacteria Thermus aquaticus, which amplifies a single-stranded DNA molecule by attaching complementary nucleotides
Elongate
To synthesise a longer polynucleotide
Thermal cylinder
A laboratory apparatus which alters the temperature in pre-programmed steps for temperature-sensitive reactions like PCR
Anneal
The joining of two molecules, for example two complementary DNA strands during the cooling phase of PCR
Forward primer
A DNA primer that binds to the 3’ end of the template strand and reads the DNA in the same direction as RNA polymerase
Reverse primer
A DNA primer that binds to the 3’ end of the coding strand and reads the DNA in the reverse direction to RNA polymerase
Gel electrophoresis
A technique that separates DNA fragments based on their molecule size
Well
An indent in the gel into which a DNA sample is loaded
Standard ladder
A mixture of DNA fragments of known length that are used to infer the size of fragments in a sample
Agarose gel
A sponge-like gel used in gel electrophoresis that contains pores for DNA fragments to move through
Buffer
An ion-rich solution that carries electrical current through the agarose gel
Electrode
Conductors of electricity that are attached to both ends of a gel allowing an electrical current to pass through it
Band
A line seen in the gel after running gel electrophoresis that corresponds to a collection of DNA fragments of a specific size
Ethidium bromide
A fluorescent dye that binds to DNA fragments in a gel and allows them to be easily visualised under ultraviolet light
Kilobase (kb)
A unit of measurement that corresponds to one thousand nucleotides. May also be written as kbp
Base pair (bp)
A unit of measurement that corresponds to one nucleotide
Lane
The column of the gel corresponding to each sample of DNA
Genetic testing
Screening an individual’s DNA for anomalies that may make them susceptible to a particular disease or disorder
DNA profiling
The process of identification on the basis of an individual’s genetic information
Homozygous
Having identical alleles for the same gene on homologous chromosomes
Heterozygous
Having different alleles for the same gene on homologous chromosomes
Short tandem repeats (STR)
Short, repeated sequences of nucleotides found in the non-coding regions of nuclear DNA
Plasmid
A small, circular loop of DNA separate from the chromosome, typically found in bacteria
Recombinant plasmid
A circular DNA vector that is ligated to incorporate a gene of interest
Bacterial transformation
The process by which bacteria take up foreign DNA from their environment. Scientists use this process to introduce recombinant plasmids into bacteria
Insulin
A hormone secreted by the pancreas to control blood glucose levels
Diabetes
A disease where the body cannot properly produce or respond to insulin
Gene of interest
A gene scientists want to be expressed in recombinant bacteria. This gene often encodes a protein we wish to produce in commercial quantities. Also known as the desired gene
Vector
A means of introducing foreign DNA into an organism. Plasmids are a popular vector in bacterial transformation
Plasmid vector
A piece of circular DNA that is modified to be an ideal vector for bacterial transformation experiments
Antibiotic resistance gene
Gene which confers antibiotic response
Origin of replication (ORI)
A sequence found in prokaryotes that signals the start site of DNA replication
Reporter gene
Gene with an easily identifiable phenotype that can be used to identify whether a plasmid has taken up the gene of interest
Heat shock
A method that involves rapidly increasing and decreasing the temperature to increase membrane permeability in order to enhance the likelihood of bacterial transformation
Electroporation
A method that involves delivering an electric shock to bacterial membranes to increase their membrane permeability and increase the likelihood of transformation
Fusion protein
A protein made when separate genes have been joined and are transcribed and translated together
Genetic engineering
The process of using biotechnology to alter the genome of an organism, typically with the goal of conferring some desirable trait
Genetic engineering technologies
Refers to the artificial alteration of an organism’s genome via the exchange of foreign genetic material, typically from one organism. This is often done external to the organism via the use of a transfer vector such as a plasmid. Also known as genetic recombination technologies
Silenced
Describes a gene that is prevented from being expressed
Genetically modified organism (GMO)
An organism with genetic material that has been altered using genetic engineering technology
Host organism
The organism researches wish to genetically modify
Cisgenic organisms
A genetically modified organism that contains foreign material from a sexually compatible donor organism, typically from the same species
Transgenic organism
A genetically modified organism that contains foreign genetic material from a separate species (or recombinant DNA from the same species that has been manipulated before introduction)
Plant tissues culture
A range of techniques used to grow plant cells, tissues, or organs under sterile conditions using a nutrient culture medium, such as an agar plate or nutrient broth of known composition. It is widely used to produce clones in a plant
Transgene
A gene that has been artificially introduced into the genome of a separate organism (usually of another species)
