Molecular Biology: Key Terms and Glossary

The 26S proteasome recognises a K48-linked ubiquitin chain, returns the ubiquitin for reuse, unfolds the substrate, and hydrolyses it inside a sealed core that is not the lysosome.

The 2′-OH is the extra hydroxyl of ribose, absent from DNA, that makes RNA easier to hydrolyse and able to catalyse, which is why these notes treat DNA as the stabler archive.

32P and 35S are the labels Hershey and Chase used for phage DNA and phage protein; most of the phosphorus entered the cell and most of the sulphur stayed outside, a strong enrichment rather than a perfect separation.

Allolactose is the inducer of the *lac* operon, an isomer made as a side reaction by β-galactosidase; lactose itself does not bind the repressor.

Alpha satellite is the tandem repeat of about 171 bp that builds human centromeres, together with the histone variant that marks them.

Alternative splicing produces more than one mRNA from a single pre-mRNA by including, skipping, or shifting exons, while the two chemical steps of splicing stay the same.

Alu elements are primate SINEs of about 300 bp, present in about a million copies and together about a tenth of the human genome.

Anfinsen’s refolding of ribonuclease is used here to show that the sequence encodes the native structure of many small proteins, so chaperones solve a kinetic problem and do not add missing information.

The antiterminator is the *trp* leader hairpin formed by segments 2 and 3 when a ribosome stalls on the tandem tryptophan codons, and that hairpin keeps the terminator from forming.

The AP site is a deoxyribose in the backbone that has lost its base, whether by spontaneous hydrolysis or because a glycosylase removed the base, and base-excision repair cuts at that sugar.

ApoB-48 is the shortened apolipoprotein B of chylomicrons, produced in the intestine when one cytidine in the mRNA is deaminated to uridine and a stop codon appears; the liver does not edit that site and makes ApoB-100.

Attenuation at the *trp* operon is early termination decided by where the ribosome sits on the leader RNA, choosing an antiterminator hairpin or a terminator hairpin. If no ribosome translates that leader, the terminator still forms, so attenuation is not simply a failure of translation.

B-form DNA is the physiological right-handed duplex these notes use for length, with a rise of about 0.34 nm per base pair and about 10.5 base pairs per turn.

The branch point is the adenosine inside an intron whose 2′-OH attacks the 5′ splice site in the first step of splicing.

BRCA2 helps load Rad51 onto single-stranded DNA that is coated with the eukaryotic single-strand binding protein, so loss of BRCA2 impairs homologous recombination.

A bromodomain is a module that binds acetyl-lysine, so an acetyl mark can recruit proteins as well as loosening the histone tail’s hold on DNA.

The C-value is the amount of DNA in a haploid, unreplicated genome, and these notes treat it as a poor measure of complexity, an onion genome of about 16 Gb being several times the human haploid figure of about 3.1 Gb.

In this chapter cAMP is the ligand CAP must bind before CAP can activate *lac* transcription, and the nucleotide is low while glucose is being used.

The cap is an inverted 7-methylguanosine joined 5′–5′ to the first nucleotide of a pol II transcript while serine 5 of the CTD is phosphorylated. The same three letters in capitals name the catabolite activator protein, which is a different term.

CAP, also called CRP, is the dimeric activator that binds about 61.5 bp upstream of the *lac* start only when it holds cAMP, and then recruits polymerase to a weak promoter. The same three letters with only the first capitalised name the mRNA cap, a different term.

Cas9 is an RNA-guided nuclease that cuts both strands beside a PAM when the guide pairs there; without that adjacent motif the match is not a substrate, and cellular repair, not the cut itself, writes the final sequence.

cDNA is DNA copied from messenger RNA by reverse transcriptase, so the introns are already gone and the collection represents transcripts of the cells that were sampled, not the whole genome.

In these notes the central dogma means that the stored genome is nucleic acid, DNA or in some viruses RNA, and that reverse transcription copies RNA into DNA, whereas a protein sequence is not copied back into a nucleic acid.

Chargaff’s rules, in these notes, are the equalities of adenine with thymine and of guanine with cytosine in double-stranded DNA, read here as the pairing rule that made a DNA genome chemically credible.

A corepressor is a small molecule that makes a repressor bind DNA, as tryptophan does for TrpR, the opposite of an inducer that makes a repressor let go.

CpG is the dinucleotide at which vertebrate cells place regulatory 5-methylcytosine; promoter CpG islands usually stay unmethylated where the gene can be expressed.

CPSF is the factor that recognises the AAUAAA cleavage signal and directs the cut that creates the 3′ end of a typical mRNA before the poly(A) tail is added.

The CTD is the repeated carboxyl-terminal tail of the largest subunit of RNA polymerase II; phosphorylation of serine 5 near the promoter recruits capping, and phosphorylation of serine 2 towards the 3′ end recruits splicing and cleavage factors.

Dam methylates adenine in GATC sites, and until that mark appears the new strand is the one *E. coli* mismatch repair cuts; human cells do not use Dam methylation as that signal.

Dicer cuts the loop from a precursor microRNA, or cuts long double-stranded RNA, to leave a short duplex of about 21–23 bp that can be loaded as a guide.

DnaA is the initiator protein that, when it holds ATP, binds *oriC* and opens the DNA; how much active DnaA is available helps restrict initiation to once per cycle.

DNMT1 methylates the new strand of a hemimethylated CpG after replication, and that copying of an existing mark is what these notes mean by epigenetic maintenance.

An E3 ligase chooses the protein that will receive ubiquitin, after E1 has activated ubiquitin with ATP and E2 has carried the thioester.

eEF2 is the eukaryotic factor that drives translocation after the peptide bond, moving the peptidyl-transfer RNA into the P site, and diphtheria toxin stops that step by modifying eEF2.

EF-Tu is the bacterial GTPase that brings aminoacyl-transfer RNA to the A site and hydrolyses GTP when the codon–anticodon pair is accepted.

Euchromatin is the more open chromatin state, enriched for genes that are active or able to be activated, and it tends to be replicated earlier in S phase.

An exon is a segment of a split gene that is retained in the mature mRNA.

The exon-junction complex is the protein deposit left about 20–24 nucleotides upstream of a newly joined exon–exon boundary, a mark that the intron was removed.

FEN1 cuts at the base of the short flap raised when the lagging-strand polymerase runs into the previous Okazaki fragment, removing RNA that must not remain in the chromosome.

fMet is N-formylmethionine on the bacterial initiator transfer RNA, delivered to the P site at the start codon, and it is not the methionine inserted by the elongator RNA at later AUG codons.

A glycosylase cleaves the glycosidic bond of a damaged base that does not strongly distort the helix, leaving an AP site for the rest of base-excision repair.

GroEL is the bacterial chaperonin, two rings of seven subunits, that closes a client chain inside a chamber with its lid so the chain can fold away from other proteins.

DNA gyrase is the bacterial type II topoisomerase that introduces negative supercoils, and fluoroquinolones inhibit it; eukaryotic topo II relaxes and decatenates but does not write that underwinding.

H1 is the linker histone bound where DNA enters and leaves the nucleosome, and it is not a subunit of the histone octamer.

The Hayflick limit is the finite number of divisions normal human somatic cells complete in culture, classically on the order of fifty population doublings for fibroblasts. These notes do not treat that limit as a complete theory of ageing, nor telomerase as enough by itself for malignant transformation.

A helix–turn–helix protein reads DNA by laying its second helix in the major groove, the fold of LacI and CAP and the relative of eukaryotic homeodomains.

Heterochromatin is the compact, transcription-poor state of the same DNA, often later-replicating; constitutive heterochromatin stays compact in most cells, whereas facultative heterochromatin is conditional.

Hsp70 binds short hydrophobic peptides on an unfolded chain and lets them go again when ATP is hydrolysed, offering another chance to fold without dictating the final shape.

Inducer exclusion is the shutting of lactose permease by the unphosphorylated glucose-specific IIA protein of the phosphotransferase system, so inducer does not enter while glucose is available.

An intrinsic terminator is a GC-rich hairpin in the new RNA followed by a run of U, which pauses the polymerase and lets the weak RNA–DNA hybrid fall apart without a release protein.

An intron is a transcribed segment that is removed before the mRNA is finished; in a typical human protein-coding gene the introns are much longer than the exons.

A K48 linkage joins ubiquitin units through lysine 48, and a chain of usually four or more is the canonical signal for the proteasome, which a lysine-63 chain is not.

A Kozak context is the short neighbourhood of a eukaryotic AUG, above all a purine three bases before it and a G immediately after it, that makes the scanning small subunit prefer that start.

Ku is the heterodimer that recognises the two broken ends non-homologous end joining will bring together and seal.

LacI is the *lac* repressor, made from its own gene, that binds the operator and an auxiliary site and loops the DNA until allolactose lowers its affinity for those sites.

The lariat is the branched intron freed by splicing, held in a 2′–5′ link at the branch adenosine, and later debranched and degraded.

A leucine zipper is a coiled coil with leucine at every seventh residue that dimerises the protein; the leucines do not touch the DNA, and the basic regions of the dimer do.

A LINE is a long interspersed repeat, mostly a transposon or its fossil; a few human LINE-1 copies can still move, and SINEs use that machinery.

The linking number counts how many times one strand of a closed duplex winds about the other, and supercoiling is the difference from the relaxed winding of about one turn per 10.5 base pairs.

A long read is a single-molecule sequence, commonly tens of kilobases, able to cross a repeat or a whole splice isoform that short reads split apart, with a higher raw error on one pass.

MCM is the eukaryotic replicative helicase, loaded once per cycle as an inactive double hexamer and only later activated to unwind DNA.

Mediator is the large complex that bridges DNA-bound activators to RNA polymerase II, and it is not itself a sequence-specific DNA-binding protein.

MutS recognises a base mismatch or a very small loop so mismatch repair can excise the new strand; eukaryotes use MutS homologues for the same recognition step.

NHEJ, non-homologous end joining, reseals a double-strand break without copying a sister chromatid, often gaining or losing a few nucleotides, and it is the usual choice in G1.

Nonsense-mediated decay destroys an mRNA in which a stop codon sits more than about 50 nucleotides upstream of the last exon–exon junction, because a junction complex is still bound downstream of that stop.

A northern blot detects an RNA with a nucleic-acid probe and reports whether that RNA is present, roughly how abundant it is, and how long it is, which is not the same information as a protein blot.

A nuclear receptor binds a hormone and then reads a response element as a dimer through its zinc modules; the steroid ligand is not itself a transcription factor.

The nucleosome core is two copies each of H2A, H2B, H3, and H4, wrapped by about 147 bp in about 1.7 left-handed turns. The figure of about 180–200 bp is that core plus linker DNA, not the stretch on the octamer.

O1 is the principal operator of the *lac* operon, overlapping the transcription start, where bound LacI blocks RNA polymerase.

An Okazaki fragment is one short piece of lagging-strand DNA, about 1,000–2,000 nucleotides in bacteria and about 100–200 in eukaryotes, made because both strands of the fork are polymerised only 5′ to 3′.

An operon is a cluster of neighbouring genes transcribed from one promoter into a single mRNA, the arrangement these notes use for many bacterial pathways.

ORC is the origin recognition complex that marks potential eukaryotic origins and, with its loading partners in G1, seats MCM without yet starting the fork.

*oriC* is the single origin of *E. coli*, about 245 bp, with DnaA-binding sites and an AT-rich element that unwinds so two forks can leave in opposite directions.

The PAM is the short motif the Cas protein demands next to the guide match before it will cut; for the Cas9 used in these notes that motif is NGG.

PCNA is the eukaryotic sliding clamp, a ring loaded at a primer–template junction so that pol δ and enzymes that finish the lagging strand stay associated with the DNA.

Peptidyl transferase is the ribosomal activity that transfers the growing chain onto the amino acid in the A site, and the catalyst is 23S or 28S ribosomal RNA rather than a ribosomal protein.

A plasmid is an extra circular DNA with its own origin, often carrying an accessory gene such as antibiotic resistance, and it is the natural relative of a cloning vector.

RNA polymerases I, II, and III divide nuclear transcription: pol I makes the large ribosomal RNA precursor, pol II makes pre-mRNA and most spliceosomal small RNAs other than U6, and pol III makes transfer RNA, 5S ribosomal RNA, and U6, and none of these numerals is a DNA polymerase.

Pol III is the bacterial enzyme that copies most of the chromosome, polymerising at its α subunit and proofreading at a separate ε subunit, and the numeral does not mean RNA polymerase III.

Pol δ is the eukaryotic replicative polymerase that runs into the previous Okazaki fragment, peels up a flap, and is held on the DNA by PCNA.

Pol ε is the eukaryotic replicative polymerase that copies most of the leading strand after pol α has handed over the primer, and it is not an RNA polymerase.

Polarity, as a Chapter 1 term, means that a nucleic-acid chain has distinct 5′ and 3′ ends and that synthesis adds nucleotides only at a 3′-OH. Chapter 6 uses the same word for a different event, in which an early nonsense codon lets Rho terminate and abort downstream genes of an operon.

Polycistronic describes an mRNA that carries several open reading frames, each with its own ribosome-binding site, so each frame can be translated.

A polysome is a set of ribosomes translating one mRNA at the same time, each making its own chain; on a eukaryotic mRNA they form only after export from the nucleus.

Puromycin resembles the aminoacylated end of transfer RNA, takes the nascent chain in the peptidyl-transferase centre, and releases it, on both bacterial and eukaryotic ribosomes.

Rad51 is the eukaryotic recombinase that, with ATP, coats a resected 3′ overhang as a filament and uses that filament to invade a homologous duplex.

A release factor is a protein, not a transfer RNA, that reads a stop codon in the A site and hydrolyses the finished polypeptide from the P-site RNA.

A reporter replaces a hard-to-measure product with an easy signal, such as colour from *lacZ*, light from luciferase, or fluorescence from GFP, and the signal reports the construct that was introduced.

Rho is the ATP-dependent hexameric helicase that binds bare, C-rich sites on the transcript and pulls the RNA out of a paused polymerase.

Rise is the axial advance per base pair, about 0.34 nm in B-form DNA, one of the two numbers these notes multiply by genome length to obtain a contour length.

Sanger sequencing reads one template by stopping chains with a dideoxynucleotide that lacks a 3′-OH, and a clean read in these notes is about 500–900 nucleotides.

The seed sequence is nucleotides 2–8 of an animal microRNA guide, where partial pairing is often enough to repress translation and shorten the mRNA without cutting it.

A selectable marker, often a gene for antibiotic resistance, allows only cells that have taken up the vector to form colonies, and an empty vector carries the marker too.

Semiconservative replication gives each daughter duplex one parental strand and one new strand, the pattern shown by one intermediate-density band after a single generation in light medium and by intermediate plus light DNA after a second.

The Shine–Dalgarno sequence is a short purine-rich stretch upstream of a bacterial AUG that base-pairs with the 3′ end of 16S ribosomal RNA and thereby places the start codon in the P site.

A short read, in the cluster method these notes describe, is one of a very large number of sequences, commonly about 100–300 nucleotides, obtained by synthesis on amplified fragments.

Sigma is the subunit that lets bacterial RNA polymerase find a promoter and open it, after which the elongating enzyme is usually the core alone; σ54 is the exception that cannot melt DNA until an activator hydrolyses ATP.

A SINE is a short interspersed repeat that does not encode its own reverse transcriptase and depends on LINE proteins to move.

A snRNP is one of the small nuclear ribonucleoproteins of the spliceosome, U1, U2, U4, U5, and U6, that recognise the splice sites and branch point and rearrange for the two chemical steps.

A Southern blot detects DNA, usually after it has been cut, with a labelled nucleic-acid probe, and a band reports presence and rough fragment size rather than a finished sequence.

A sticky end is the short single-stranded overhang left by a staggered restriction cut, able to base-pair with a matching overhang and hold the fragments for ligation.

SWI/SNF is an ATP-dependent remodeller that slides, ejects, or unwraps nucleosomes; it can read acetyl-lysine and it does not itself write histone marks.

Taq polymerase is the heat-stable DNA polymerase from *Thermus aquaticus* that survives the strand-separation step of PCR and therefore need not be added every cycle; it has no proofreading exonuclease.

The TATA box is a pol II promoter motif, consensus TATAAA, often centred about 25–30 bp before the start, and many pol II genes do not have it.

Telomerase is a reverse transcriptase that lengthens the 3′ overhang at a linear chromosome end by copying an RNA template carried in the enzyme, and it does not copy the rest of the chromosome.

TFIIH is the general transcription factor that opens a pol II promoter and phosphorylates the polymerase tail, and the same helicase subunits open DNA during nucleotide-excision repair.

Thymine is the DNA base that stands where uracil stands in RNA, so a uracil produced by deamination of cytosine is recognised as damage rather than as a normal DNA base.

A thymine dimer is a cyclobutane bridge between adjacent pyrimidines, usually thymines, formed by ultraviolet light; it distorts the helix and is removed by nucleotide-excision repair.

Transformation is the heritable change Griffith observed when a heat-stable substance from dead pneumococci altered living cells, and the experiment does not identify which molecule carried the trait.

The transforming principle is the activity Avery, MacLeod, and McCarty fractionated and identified as DNA, a conclusion that was resisted because a trace of protein was hard to exclude and protein was then the favoured candidate.

TriC, also called CCT, is the eukaryotic cytosolic chaperonin, eight different subunits in each ring and a built-in lid, and actin and tubulin do not fold without it.

TrpR is the *trp* repressor, which occupies its operator only when tryptophan is bound, so a high tryptophan concentration turns repression on.

Ubiquitin is the 76-residue protein whose terminal glycine is joined to a lysine of a substrate or of another ubiquitin, and a single ubiquitin is not by itself an instruction to destroy the protein.

A UP element is an AT-rich stretch upstream of −35, roughly from −40 to −60, contacted by the carboxyl-terminal domain of the α subunit on some strong promoters.

UvrABC is the bacterial set of proteins that finds a bulky distortion, cuts on both sides, and releases an oligonucleotide of about twelve nucleotides, far more than a glycosylase removes.

A western blot detects a polypeptide with an antibody and reports apparent mass and a rough amount, not whether the polypeptide is catalytically active.

Wobble is flexible pairing between the third base of a codon and the first base of the anticodon, so that U reads A or G, G reads U or C, and inosine reads U, C, or A, and cells therefore need only on the order of forty transfer RNAs rather than 61.

A writer is an enzyme that puts a chemical mark on a histone, and a reader is a protein that binds one such mark; these notes refuse a legend in which each mark has a single meaning on every residue.

Classical xeroderma pigmentosum is an inherited failure of nucleotide-excision repair, so sun-exposed skin does not clear dimers and skin cancers are very frequent. The variant form is not an excision defect; it is loss of DNA polymerase η, which normally copies past a thymine dimer.

*Xist* is the long non-coding RNA that is transcribed from, and coats in cis, the X chromosome to be silenced, recruiting Polycomb to that chromosome only. It is one worked example, not a mechanism these notes assign to every long non-coding RNA.

A zinc finger of the C2H2 kind is a small module held by zinc on two cysteines and two histidines, and a chain of such fingers can read successive groups of bases.

The −10 element is the promoter hexamer, consensus TATAAT in these notes, that σ70 contacts about ten bases upstream of the start.

The −35 element is the second σ70 hexamer, consensus TTGACA, spaced about 17 bp upstream of the −10 element, and that spacing matters as much as the sequence match.