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β′ subunit

• coordinates catalytic Mg2+ ions

• contains important catalytic aspartates

• binds DNA

• contains the bridge helix and trigger loop

W subunit

• assemble B’

• stablilizes RNAP

• maintain the proper enzyme structure

Crab- claw structure

• B and B’ form 2 sides of a crab-claw like channel

• Dna enters between the “claws” where the active center can assess the template strand

Z-DNA

• anti/syn alternates

• sugar pucker alternates

• bp/turn 12

• glycosdiester bonds

phosphodiester bond

the covalent bond joining the 3’ oxygen of one nucleotide to the 5’ phosphate of the next nucleotide

rNTP

a ribonucleoside triphosphate used to contruct RNA: ATP, GTP, CTP, or UTP

Bridge helix

A movable α-helix in RNA polymerase that helps position nucleic acids and move the DNA-RNA hybrid during translocation.

trigger loop

A flexible active-site structure that closes around a correctly paired rNTP and positions it for catalysis.

Mg2+

A metal ion used in the RNA polymerase active site to activate the RNA 3′-OH and stabilize negative charges during catalysis.

closed complex

The initial promoter complex in which RNA polymerase has bound DNA but the DNA strands remain paired.

isomerization

a structural rearrangement that converts the closed promoter complex into an open complex

open complex

The initiation complex in which RNA polymerase has melted the promoter DNA and exposed the template strand.

DNA melting

Separation of the two DNA strands so RNA polymerase can access the template.

abortive initiation

Repeated synthesis and release of short RNAs before RNA polymerase escapes the promoter.

core enzyme

The bacterial RNA polymerase complex α2ββ′ω, which catalyzes RNA synthesis but lacks efficient promoter specificity.

ADAR1

An RNA-editing enzyme that converts adenosine to inosine in double-stranded RNA regions.

A-to-I editing

Conversion of adenosine to inosine in RNA through hydrolytic deamination.

inosine

The RNA base produced by adenosine deamination. It usually pairs with cytosine and is often interpreted as guanosine.

Zα domain

The ADAR1 domain that binds left-handed Z-DNA and Z-RNA.

helix-turn-helix motif

A DNA-binding motif containing two α-helices connected by a turn, often with one helix functioning as a recognition helix.

recognition helix

The helix that makes major DNA contacts. In the ADAR1 Zα domain, α3 serves this role.

β-hairpin

Two antiparallel β-strands connected by a tight turn. The Zα β-hairpin helps contact Z-DNA.

water mediated hydrogen bond

A hydrogen-bonding interaction in which a water molecule bridges two groups that do not contact directly.

conformation specific recognition

Protein recognition of a nucleic acid’s three-dimensional shape rather than primarily recognizing its exact base sequence.

crab claw architecture

The overall RNA polymerase shape created mainly by β and β′, which form a channel around the DNA.

sigma factor

A bacterial initiation factor that joins core RNA polymerase, recognizes promoter sequences, and helps open promoter DNA.

sigma 1

The sigma region that reduces nonspecific DNA binding. Its σ1.1 segment occupies the DNA channel before promoter DNA enters.

sigma 2

The sigma region that recognizes the −10 promoter element and helps melt the DNA.

sigma 3

The sigma region that recognizes the extended −10 element and interacts with and helps position DNA entering the active site

sigma 4

-35 element recognition. Recognizes the conserved -35 promoter element and helps determine promoter specificity.

UP element

An AT-rich promoter element upstream of −35 that binds the α-subunit C-terminal domain and strengthens transcription.

alt sigma factor

A sigma factor that redirects core RNA polymerase to a specific group of promoters in response to cellular conditions.

housekeeping genes

Genes needed for ordinary cell growth and maintenance under standard conditions.

heat shock response

a gene expression program that helps refold or reomve proteins damaged by high temp

α₂

enzyme assembly; α-CTD binds UP elements and activators

Asp residues

help stabilize mg2+

Base tautomerization

Moves a proton and rearranges double bonds, temporarily changing the donor and acceptor pattern of a base

Nonpolar aliphatic

hydrophobic packing and van der waals contacts

aromatic

base stacking, hydrophobic and van der waals contacts; Y and W can also H-bond

polar uncharged

hydrogen bonding

negative behavior

electrostatic replusion from phosphate; H-bond acceptors

positive behavior

electrostatic attraction to phosphate; often H-bond donors

hydrogen bonds

unequal sharing of electrons between atoms in a polar molecule

phi φ

measures rotation around the single covalent bond between the nitrogen atom (N) and the alpha-carbon (\(C_{\alpha }\)) in a protein's peptide backbone

Psiψ

N-Ca

primary protein structure

amino acid sequence

secondary

local backbone structures, especially alpha helices, beta sheets and turns

tertiary

complete 3d shape of one polypeptide

quaternary

arrangement of multiple polypeptide subunits

beta sheet

a common folded shape that proteins form as they build their three-dimensional structures

beta turn

4 residues reverse the chain direction favored for stability

y-turn

3 residues

negative supercoiling

stores energy favors strand separation helps DNA open during transcription

Topoisomerases I

• temporary breaks one strand and reseals it

• releives torsonial strain and supercoiling

• changes LK by one not atp used

Topoisomerases II

• breaks both strands

• changes lk by w

• can remove knots and tangles

• uses ATP

DNA gyrase

• cuts both dna strands

• introduces negative supercoils to releive tension

• uses ATP

Rho protein

Unwinds RNA-DNA hybrid and releases RNA transcript

positive supercoiling

results from overwinding and increases resistance to strand separation

negative supercoiling

results from underwinding and creates easier local strand separation

Writhe charge

left handed(+)

right handed(-)

plectonemic supercoiling

• DNA duplex coils around another part of the same duplex

• right handed and provided lower degree of DNA compaction

solenoidal supercoiling

• coiled into a tight spiral around a protein core

• left handed and increases DNA compaction

plectonemic writhe charge

right handed(-)

left handed(+)

solendoil writhe charge

right handed(+)

left handed (-)

Adenosine