•Aromatic rings – have alternating single and double bonds; flat and have absorbance in the UV
• Biopolymer - a polymeric substance occurring in living organisms
• N-glycosidic bond – covalent bond between sugar and base in
• Peptide Bond – covalent bond between amino acids in peptides and proteins which is planar and rigid.
• Phosphodiester bond – covalent bond between nucleotides in RNA/DNA
• Residue – generic name for a subunit in a polymer (more often used for proteins – also as “amino acid
residue”)
• B-DNA – standard double helix structure of DNA
• Base-pairing –hydrogen bonding between bases
• Electrophoresis – separation of molecules by electric current in permeable matrix
• Major Groove – wide groove in B- DNA
• Electrostatic repulsion - repulsing between charged atoms of the same charge
• Minor Groove – narrow groove in B- DNA
• Deamination – loss of amine
• dsDNA – double stranded DNA
• ssDNA –single stranded DNA
• Tm/Melting point – when 50% of the molecule is unfolded/separated
Central Dogma of Molecular Biology - flow of genetic information within a biological system
(DNA>RNA>Protein)
• Chromosome – DNA molecule with part or all of the genome
• Epigenetics – DNA modifications that do not change the DNA sequence can affect gene activity
• Genome – the complete genetic composition of a cell or species
• Proteome - the complete set of proteins expressed by an organism, cell or tissue type.
• Transcriptome – the set of all RNA molecules in one cell or a population of cells.
• Ligase – enzyme, joins pieces of DNA
• Semi-conservative DNA replication – DNA contains one older and one newly replicated strand
• Helicase – enzyme, unwinds DNA
• Topoisomerase/gyrase – enzyme,
• Supercoiling – overwinding DNA
that relieves supercoiling
• Replication fork – structure where DNA is being replicated on the lagging and leading strands
• Primase – RNA polymerase that makes primers for replication
• ssBP/single stranded binding proteins – bind to ssDNA and protect from tangling/reforming dsDNA
• Initiation – polymerisation starts
• Chain elongation – main phase of polymerisation
• Termination – polymerisation stops
• Okazaki fragments – DNA fragments being generated on the lagging strand
Promoter – DNA sequence near start site of transcription, bound by sigma factor which recruits RNA
polymerase II complex
• RNA polymerase II complex – collection of proteins that make an RNA copy of DNA
• Sigma Factor – common bacterial transcription factor
• Transcription factor – protein that binds DNA and regulates transcription
• Transcription bubble – local unwinding of DNA for transcription
• Transcriptional activator – molecule that increases transcription
• Transcriptional repressor - molecule that decreases transcription
• Transcription start site – DNA sequence where transcription begins
• aa – abbreviation for amino acid
• Peptidyl transferase – enzyme component of the ribosome that transfers the activated amino acids from
tRNA to the growing peptide chain
• aa-tRNA synthetase – enzyme that binds tRNA and charges it with the correct, activated amino acid
• Anticodon – sequence in tRNA that recognises the codon in mRNA
• Ribosome – RNA-protein complex that catalyses peptide bond formation and guides correct sequence
assembly in protein translation
• Codon – sequence of 3 bases that specifies a given amino acid
• Start Codon – Codon that signals the start of protein synthesis – encodes Met
• Genetic Code – set of codons and corresponding amino acids
• Stop Codon – Codon that signal the end of translation; no tRNAs recognise these codons
• mRNA/tRNA/rRNA – messenger (encodes proteins), transfer (links mRNA to correct amino acid) and
ribosomal (forms the ribosome) RNA
• Release/terminal factor – protein that binds the stop codon to terminate translation
• Alpha Helix– form of protein secondary structure that forms a right handed helix
• Sidechain – functions groups which distinguish amino acids from each other
• Beta Strand –extended form of protein secondary structure Beta Sheet – Assembly of beta strands
• Polypeptide – protein or peptide
• Beta turn – form of protein secondary structure, often formed between beta strands in a beta sheet
• Protein Folding – process of forming tertiary structure
• Secondary structure – local interactions in the polypeptide chain with defined hydrogen bonding patterns
and backbone bond angles
• Quaternary structure – arrangement of folded protein subunits
• Primary structure – protein sequence
• Tertiary structure – overall fold of a protein (or protein subunit)
• Activation energy – The energy required to initiate a reaction
• Pyrophosphate (PPi) – released by hydrolysis of NTPs into NMPs; spontaneously forms phosphates (2Pi);
provides energy for unfavourable reactions
• Catalyst – speeds up reaction rates (not used up/doesn’t affect equilibrium)
• Enzyme – biological (usually protein) catalyst
• Reaction rates – speed of a reaction
• Substrate – molecule on which an enzyme reacts