CHEM20026 examples

specific examples used

keto iminol tautomerism

keto C=O bond strength
keto more resonance structures

enamine imminol tautomerism

enamine more resonance structures
imminol N can’t stabilise neg charge

AZT, anti-HIV drug

mimics nucleotide
triphosphorylated by enzymes
trapped in cell
incorporated into DNA or RNA
chain termination

molnupiravir

mimics base
tautomerism between mimicking C and U
introduces error into RNA replication

alfatoxin

alkylates DNA and inhibits elongation
in acidic environment
cytochrome P450 oxidase

IPTG

allolactose analogue
not degraded
precise control

Acetyl-coA

reactive thioester bond
electrophilic C1, nucleophilic C2

Claisen reaction

condensation with strong base to form enolate ion
energetically unfavourable, needs catalyst

SAM

donate methyl, adenosyl or amino butyrate groups

DsbB

controls DsbA

DsbA

controls disulfide bond formation

DsbD

controls DsbC

DsbC

shuffles positions of existing disulfide bonds

glutathione

thiol and metal buffer
used to determine redox potential of solution

zinc finger

Zn2+ stabilised by 2 Cys and 2 His residues
controls transcription, allows proteins to interact with major groove

porphyrin

-2 charge when deprotonated, all 4 N free
can coordinate a 2+ metal
chelate effect

heme

redox cycle Fe to transfer e- in oxidative phosphorylation

cytochrome c

low spin preferred in both Fe2+ and Fe3+
proteins come together by complementary electrostatics
pos binding site, incoming protein will have neg charge

SOD

Zn2+ for structural scaffold, tetrahedral
Cu2+ for redox cycling, square pyramidal

CCS metallochaperone

transports Cu(I) to SOD1 protein

ATOX1 metallochaperone

transports Cu(I) to ATP7A

ATP7A

P-type ATPase transporters
translocated from GA to PM once full of Cu(I)
maintains Cu balance in cell

plastocyanin

Cu type 1 coordination
e- shuttle for ATP synthesis in plants
entatic state

Streptavidin

selectively tagged by biotin coenzyme
fluoresce to detect avidin-biotin interactions in a cell

BirA enzyme

fuses biotin tag to protein
anytime protein interacts, it is also biotinylated

CLIA

chemiluminescent immunoassay

neo-natal jaundice

not functioning liver
can’t metabolize bilirubin

most stable bilirubin isomer

ridge-tile 4Z, 15Z

malachite green

good photothermal molecule

CTAB surfactant

binds gold seeds, maintains width, grows length

formic acid

terminates A and G at N7

DMS

terminates G at N7

hydrazine

terminates C and T at C6

hydrazine + NaCl

terminates C

first generation methods

maxam and gilbert, sanger, dye terminator

second generation methods

pyrosequencing 454, reversible terminator/illumina

TCEP

cleaves blocking group in Illumina sequencing after laser excited fluorophore

third generation methods

PacBio, Oxford Nanopore

Sybrsafe

stain DNA samples from agarose electrophoresis

Coomassie blue

Blue Native PAGE
binds unspecifically to proteins
confers overall negative charge

DTT

reduces disulfide bonds

iodoacetamide

alkylates free thiol groups to prevent re-folding

OPA, MPA

fluorescent compounds when incorporated with primary amino acid
pre-column derivatization

Ninhydrin

blue-purple compound when incorporated with primary amino acid
orange with proline
post-column derivatization

trypsin

cleaves after Lys or Arg

Chymotrypsin

cleaves after Phe, Trp or Tyr

Carboxypeptidase

cleaves C term amino acid

Cyanogen Bromide

cleaves after Met

DNFB

reagent in Sanger’s method N term analysis
reacts with N term amino acid

PITC

reagent in Edman’s method N term analysis
reacts with N term amino acid