Transcription in prokaryotes — Study Path Agent

Chapter 1

Core concepts & key differences from eukaryotic transcription

1

Central dogma recap: gene, template strand, RNA product, directionality (5'→3')

2

Where/when it happens: cytosol, no nucleus; transcription–translation coupling

3

RNA types in bacteria: mRNA, rRNA, tRNA (and small RNAs overview)

4

Operons & polycistronic mRNA: why one transcript can encode multiple proteins

Chapter 2

Molecular machinery: RNA polymerase, sigma factors, and transcription units

5

Bacterial RNA polymerase: core enzyme subunits and functions (α2ββ'ω)

6

Sigma (σ) factors: promoter recognition, σ70 vs alternative σ factors

7

Promoter architecture: -35 and -10 elements, spacer length, UP element

8

Transcription unit layout: promoter, +1 start site, 5' UTR, coding region, terminator

9

DNA topology & nucleoid proteins: supercoiling effects on initiation

Chapter 3

Mechanism step-by-step: initiation → elongation → termination

10

Initiation I: closed complex formation and promoter search

11

Initiation II: open complex formation (DNA melting) and start-site selection

12

Initiation III: abortive initiation, promoter clearance, σ release/retention

13

Elongation basics: transcription bubble, NTP addition cycle, proofreading

14

Pausing/backtracking and the role of GreA/GreB (transcript cleavage factors)

15

Intrinsic (ρ-independent) termination: hairpin + U-tract mechanism

16

Rho (ρ)-dependent termination: rut sites, helicase activity, kinetic coupling

Chapter 4

Regulation of transcription in bacteria

17

Negative control: repressors and operators (e.g., lac operon logic)

18

Positive control: activators and recruitment (e.g., CAP/CRP mechanism)

19

Transcription factors & DNA binding basics: motifs, affinity, cooperativity

20

Global growth-state control: stringent response (ppGpp) and rRNA transcription

Chapter 5

RNA processing, quality control, and mRNA fate (prokaryote-focused)

21

mRNA decay pathways: RNase E, degradosome idea, and 3'→5' exonucleases overview

22

RNA surveillance & rescue systems: tmRNA (trans-translation) concept

Chapter 6

Methods, experiments, and common exam-style problem skills