Key Concepts in Bacterial and Eukaryotic Gene Expression

Nucleoid

The region of a bacterial cell that houses the chromosome; DNA is in direct contact with cytoplasm and not membrane-bound.

Loop domains

One of the two major forces that compact bacterial chromosomes.

Negative DNA supercoiling

One of the two major forces that compact bacterial chromosomes.

Nucleosome

146 bp wrap around a histone octamer.

Histone H1

The linker histone that stabilizes the 30 nm fiber.

Acetylation

Modification that neutralizes lysine's positive charge on histone tails.

CTCF protein

DNA-binding factor that shapes loop domains by dimerizing at CCCTC sequences.

Constitutive heterochromatin

Permanently silent chromatin, e.g., centromeres.

Facultative heterochromatin

Chromatin that can switch states, such as an inactive X chromosome.

Condensin

Multi-protein complex that uses ATP to condense metaphase chromosomes.

Cohesin

Multi-protein complex that uses ATP for sister chromatid cohesion.

Unique sequence class

DNA sequences that have single or few copies.

Moderately repetitive sequence class

DNA sequences that have hundreds/thousands of copies, e.g., rDNA.

Highly repetitive sequence class

DNA sequences that have thousands-millions of short repeats, such as satellite DNA.

Human chromosome 22 compaction

About 10,000-fold during metaphase compared to fully extended DNA.

DNA gyrase

Enzyme that adds negative supercoils to bacterial DNA.

Histone H3/H4 acetylation

Histone variant or PTM associated with active euchromatin.

SMC proteins

Structural Maintenance of Chromosomes proteins that dimerize to clamp and extrude DNA loops.

10 nm fiber

Chromatin fiber diameter that corresponds to 'beads-on-a-string'.

Nucleosomes per 11 nm DNA length

~1 nucleosome every 200 bp (core + linker).

Heterochromatin transcriptional state

Generally inactive/silent.

Inactive X chromosome

Example of facultative heterochromatin in mammals.

Histone H3 serine-10 phosphorylation

Histone tail modification often correlated with chromosome condensation during mitosis.

Chromatin

Term that describes DNA plus its associated proteins.

Nucleolar organizer regions (NORs)

Location where ribosomal DNA genes are clustered in eukaryotes.

Spliceosomes

Molecular machines that remove most introns in eukaryotic pre-mRNA.

5′ and 3′ splice sites

GU at the 5′ end, AG at the 3′ end, plus a branch-point A.

Group I self-splicing initiation

Free guanosine attacks the 5′ splice site, releasing exon 1.

5′ capping advantages

Protects against 5′ → 3′ exonucleases and promotes ribosome recognition.

Alternative splicing

Contribution to proteome size by generating multiple protein isoforms from one gene.

Deamination

RNA editing type that converts cytosine to uracil in apolipoprotein B mRNA.

Degenerate genetic code

Description of the genetic code where multiple codons specify the same amino acid.

Stop codons

UAA, UAG, UGA.

Inserting three nucleotides outcome

Frame restored (no shift), protein gains one extra amino acid.

Silent mutation

Nucleotide change that does not alter the amino acid due to code degeneracy.

CBC20/CBC80 heterodimer

Cap-binding proteins that assist nuclear export.

Typical poly-A tail length

~250 adenines in mammals.

Self-splicing introns discovery

First discovered in Tetrahymena thermophila rRNA genes.

SR proteins

Components that recognize splice sites for exon definition.

Splice-site mutations diseases

Classes of diseases often involving β-thalassemia, spinal muscular atrophy, some cancers.

σ (sigma) factor

Subunit of bacterial RNA polymerase that confers promoter specificity.

-10 consensus sequence

5′ TATAAT 3′.

Rho-independent terminator structure

GC-rich stem-loop followed by ~8 U residues in RNA.

RNA polymerase III

RNA polymerase that transcribes tRNA genes in eukaryotes.

CTD phosphorylation

Event that marks the transition from initiation to elongation in Pol II.

Basal transcription

Low-level transcription driven only by core promoter + general transcription factors.

Mediator

Protein complex that links activator TFs to Pol II.

Cis-acting element

DNA sequence that affects transcription of the same molecule, e.g., enhancer.

Torpedo model

Model where 5′→3′ exonuclease Xrn2 degrades RNA downstream of the poly-A site.

RNA chain elongation

Bacterial transcription stage that requires no primer or helicase.

Adjacent genes transcription direction

Determined by the orientation of their individual promoters.

Rifampicin

Antibiotic that inhibits bacterial transcription by binding β subunit of RNA polymerase.

Average speed of bacterial RNA polymerase

≈ 43 nucleotides s⁻¹ at 37 °C.

CTD phospho-cycling

Ensures Pol II re-use for rapid re-initiation on active genes.

TFIID

General TF that contains the TATA-binding protein.

P-site

Site on the ribosome that holds the growing peptide chain.

Shine-Dalgarno sequence

Sequence that aligns bacterial mRNAs with the 16S rRNA for initiation.

Kozak's optimal consensus

GCC(A/G)CCAUGG with purine at -3 and G at +4 around AUG in vertebrates.

EF-Tu

Elongation factor that delivers aa-tRNA to the A-site in bacteria.

23S rRNA

Catalyzes peptide-bond formation in the large ribosomal subunit.

Translation termination in eukaryotes

eRF1 recognizes stop codon; eRF3-GTP promotes polypeptide release.

Wobble base

Third codon position where non-Watson-Crick pairing is tolerated.

Coupling of transcription and translation in bacteria

Both occur in the cytoplasm without a nuclear envelope.

Tetracycline

Antibiotic that blocks aminoacyl-tRNA binding in the A-site.

Alkaptonuria

Metabolic disorder that led Garrod to propose the gene-enzyme link.

Beadle & Tatum experiment

Proved 'one gene-one enzyme' by mapping Neurospora mutants to enzymatic steps.

Aminoacyl-tRNA synthetase error rate

< 1 mis-charged per 10,000 tRNAs.

First step of tRNA charging

Amino acid activated by ATP forming aminoacyl-AMP.

30S ribosomal subunit

Ribosomal subunit that 'decodes' codon-anticodon pairing accuracy.

Bacterial ribosome amino acid addition speed

~15-20 aa s⁻¹ at 37 °C.

Class-I/II release factors

Exhibit structural mimicry to tRNA to fit A-site.

E-site

Site occupied by a de-acylated tRNA just before leaving the ribosome.

Puromycin

Mimics aa-tRNA, enters A-site, causes premature chain termination.

Isoacceptor tRNA pair

tRNA^Leu‐AAU and tRNA^Leu-GAG both carry leucine but have different anticodons.

eEF-2-GTP

Energy-dependent factor that drives ribosome translocation in eukaryotes.

Loop domains and negative DNA supercoiling

The two major forces that compact bacterial chromosomes.

146 bp

The number of base pairs that wrap around a histone octamer in a nucleosome, making ~1.65 left-hand turns.

Constitutive vs facultative heterochromatin

Constitutive is permanently silent (e.g., centromeres); facultative can switch, such as an inactive X chromosome.

Condensin and cohesin

Multi-protein complexes that use ATP to condense metaphase chromosomes; condensin for loop compaction and cohesin for sister chromatid cohesion.

Unique, moderately repetitive, and highly repetitive sequences

Unique: single or few copies; moderately: hundreds/thousands (e.g., rDNA); highly: thousands-millions, short repeats (satellite DNA).

10,000-fold

The compactness of human chromosome 22 during metaphase compared to fully extended DNA.

High levels of histone H3/H4 acetylation

The histone variant or post-translational modification associated with active euchromatin.

1 nucleosome every 200 bp

The average number of nucleosomes per 11 nm DNA length.

Heterochromatin

Generally inactive/silent transcriptional state.

Inactive X chromosome (Barr body)

An example of facultative heterochromatin in mammals.

GU and AG

The sequences that define the 5′ and 3′ splice sites in pre-mRNA, plus a branch-point A.

Group I self-splicing

Initiates when free guanosine attacks the 5′ splice site, releasing exon 1.

5′ capping

Two advantages include protecting against 5′ → 3′ exonucleases and promoting ribosome recognition.

Inserting three nucleotides

Results in frame restored (no shift), protein gains one extra amino acid.

250 adenines

The typical length of a poly-A tail when first added in mammals.

Tetrahymena thermophila

The organism where self-splicing introns were first discovered.

SR proteins and U1 snRNP

The components that recognize splice sites for exon definition.

β-thalassemia, spinal muscular atrophy, some cancers

Disease classes that often involve splice-site mutations.

5′ TATAAT 3′

The -10 consensus (Pribnow box) sequence.

Rho-independent terminator

Structure characterized by a GC-rich stem-loop followed by ~8 U residues in RNA.

CTD phosphorylation by TFIIH

The event that marks the transition from initiation to elongation in Pol II.

5′→3′ exonuclease Xrn2

The enzyme that degrades RNA downstream of the poly-A site in the torpedo model.

Orientation of individual promoters

Determines whether adjacent genes are transcribed in opposite directions.

≈ 43 nucleotides s⁻¹

The average speed of bacterial RNA polymerase at 37 °C.

GCC(A/G)CCAUGG

Kozak's optimal consensus around AUG in vertebrates, with purine at -3 and G at +4.