Biology Unit 3 AOS 1 Proteins & Genetic Code

3’ poly-A tail

a chain of adenine nucleotides added to the 3’ end of pre-mRNA during RNA processing

5’ methyl-G cap

a molecule added to the 5’ end of pre-mRNA during RNA processing

Activator Protein

a protein coded for by a regulatory gene that increases gene expression

Active Site

the part of an enzyme where the substrate binds

Active Transport

the movement of molecules across a semipermeable membrane requiring an energy input

ADP

adenosine diphosphate, the unloaded form of ATP

Affinity

the tendency of a molecule/atom to bind or react with another molecule/atom

Agarose Gel

a sponge-like gel used in gel electrophoresis that contains pores for DNA fragments to move through

Alpha Helix

an organised coiled secondary structure of proteins

Allosteric Site

a region on an enzyme that is not the active site

Alternative Splicing

the process where different exons may be spliced, resulting in a single gene producing multiple different mRNA strands

Aneuploidy

when a cell or organism varies in the usual amount of chromosomes in its genome by the addition or loss of a chromosome

Anneal

the joining of two molecules, for example two complementary DNA strands during the cooling phase of PCR

Antibiotic Resistance Gene

gene which confers antibiotic resistance

Anticodon

the sequence of three nucleotides on a tRNA molecule that recognises a specific sequence of three nucleotides (codon) on an mRNA strand

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

Anti-terminator Hairpin

a loop formed in mRNA when tryptophan is not present that ensures the transcription of the structural genes in the trp operon

Apoptosis

the controlled death of cells in the body. Also known as programmed cell death

Attenuator Sequence

part of the leader region within the trp operon that allows for attenuation

Band

a line seen in the gel after running gel electrophoresis that corresponds to a collection of DNA fragments of a specific size

Beta-Pleated Sheet

an organised folded secondary structure of proteins

Blunt End

the result of a straight cut across the double-stranded DNA by an endonuclease resulting in no overhanging nucleotides

Buffer

an ion-rich solution that carries electrical current through the agarose gel

Bulk Transport

a type of active transport that uses vesicles to move large molecules or groups of molecules into or out of the cell

catalyst

a substance capable of increasing the rate of a reaction without being used up

Chimeric

an organism or cell containing genetic material from another organism or cell

Chromosome

a structure made of protein and nucleic acids that carries genetic information

Cisgenic Organisms

a genetically modified organism that contains foreign genetic material from the same species

Coding Strand

d the strand of DNA not transcribed by RNA polymerase, contains an identical sequence to the mRNA strand produced

Codon

the sequence of three nucleotides in mRNA coding for one amino acid

Coenzyme

a non-protein organic cofactor that assists enzyme function. They release energy and are recycled during a reaction

Cofactor

any organic or inorganic molecule, such as a coenzyme or metal ion, that assists enzyme function

Collision Theory

An explanation of chemical reactions that states that in order to react molecules must hit one another

Competitive Inhibition

the hindrance of an enzyme by blocking the active site and preventing the substrate from binding

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)

Condensation Reaction

a reaction where two monomers join to form a larger molecule, producing water as a by-product

Conformational Change

a change in the three-dimensional shape of macromolecules such as proteins

CRISPR

short, clustered repeats of DNA found in prokaryotes which protects them against viral invasion

Cas-9

an endonuclease that creates a blunt end cut at a site specified by guide RNA

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

Denature

the disruption of a molecule’s structure by an external factor such as heat

DNA

a double-stranded nucleic acid chain made up of nucleotides. DNA carries the instructions for proteins which are required for cell and organism survival

Disulphide Bond

a strong covalent bond occurring between two sulphur atoms

Double Helix

the structure of double-stranded DNA in the nucleus of eukaryotic cells, where each DNA strand wraps around a central axis

DNA Profiling

the process of identification on the basis of an individual’s genetic information

Electrode

conductors of electricity that are attached to both ends of a gel allowing an electrical current to pass through

Electroporation

a method that involves delivering an electric shock to bacterial membranes to increase their membrane permeability and increase the likelihood of bacterial transformation

End Product Inhibition

a form of inhibition where the final product in a series of reactions inhibits an enzyme in an earlier reaction in the sequence

Endonuclease

an enzyme that breaks the phosphodiester bond between two nucleotides in a polynucleotide chain

Enzyme

an organic molecule, typically a protein, that catalyses (speeds up) specific reactions

Enzyme Inhibitor

a molecule that binds to and prevents an enzyme from functioning

Enzyme-Substrate Complex

the structure formed when an enzyme and substrate are bound together

Exocytosis

a type of bulk transport that moves large substances out of a cell

Exon

regions of DNA that code for proteins and are not spliced out during RNA processing

Forward Primer

regions of DNA that code for proteins and are not spliced out during RNA processing

Gel Electrophoresis

a technique that separates DNA fragments based on their molecular size

Gene

a section of DNA that carries the code to make a protein

Gene Knock-in

a technique in gene editing where scientists substitute or add nucleotides in a gene

Gene Knockout

a technique in gene editing where scientists prevent the expression of a target gene to understand its function in an organism

Gene Regulation

the control of gene expression, typically achieved by switching transcription on or off

Genetic Engineering

the process of using biotechnology to alter the genome of an organism, typically with the goal of conferring some desirable trait

Genetic Modification

the manipulation of an organism’s genetic material using biotechnology

Genetically Modified Organism

an organism with genetic material that has been altered using genetic engineering technology

Genome

the complete set of DNA housed within an organism

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

Introns

non-coding regions of DNA that do not code for proteins. They are spliced out during RNA processing

Irreversible Inhibition

enzyme inhibition that involves stronger bonds that cannot be broken

Ligase

an enzyme that joins molecules, including DNA or RNA, together by catalysing the formation of phosphodiester bonds

Limiting Factor

a factor that prevents the rate of reaction from increasing

Limiting Reagent

a reactant that prevents the rate of reaction from increasing

Monomer

a molecule that is the smallest building block of a polymer

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

Nucleic Acid

the class of macromolecule that includes DNA and RNA. All nucleic acids are polymers made out of nucleotide monomers

Nucleotide

he monomer subunit of nucleic acids. Made up of a nitrogen-containing base, a five-carbon sugar molecule (ribose in RNA and deoxyribose in DNA), and a phosphate group

Optimal

the point at which for a given condition (e.g. temperature), the maximum function of an enzyme occurs.

Organic

a compound containing a carbon-hydrogen bond

Peptide Bond

the chemical bond linking two amino acids

Phenotype

the physical or biochemical characteristics of an organism that are the result of gene expression and the environment

Phosphodiester Bond

a strong covalent bond between nucleotides, linking a fivecarbon sugar to a phosphate group

Polypeptide

a long chain of amino acids. Proteins can be made of one or many polypeptides

Polymerase Chain Reaction

a laboratory technique used to produce many identical copies of DNA from a small initial sample

Polyploidy

when an organism contains additional sets of chromosomes in its genome

Primary Structure

the first level of protein structure, which refers to the sequence of amino acids in a polypeptide chain

Primer

a short, single strand of nucleic acids that acts as a starting point for polymerase enzymes to attach

Promoter

the sequence of DNA to which RNA polymerase binds

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

Quaternary Structure

the level of protein structure where multiple polypeptide chains bond together, or other nonprotein groups are added to form a fully functional protein

R-Group

the variable portion of an amino acid molecule. It can be one of twenty variations and determines the identity of the amino acid

Random Coil

an irregular secondary structure of proteins that is neither an alpha helix nor a beta-pleated sheet

Rate

the speed at which a chemical reaction proceeds

Reading Frame

the order in which nucleotide triplets or codons are divided into a consecutive, non-overlapping sequence

Recognition Site

a specific target sequence of DNA upon which restriction endonucleases act

Recombinant Plasmid

a circular DNA vector that is ligated to incorporate a gene of interest

Regulatory Gene

a segment of DNA responsible for producing proteins that control the expression of other genes

Reporter Gene

A gene with an easily identifiable phenotype that can be used to identify whether a plasmid has taken up the gene of interest

Repressor Protein

a protein coded for by a regulatory gene that prevents gene expression by binding to its operator

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

Reversible Inhibition

enzyme inhibition that involves weaker bonds that can be overcome

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