Genetics Exam 3

Origin of replication (prokaryote)

One origin of replication (OriC) on circular chromosome.

Origin of replication (eukaryote)

Many origins of replication on each linear chromosome.

Helicase (prokaryote)

DnaB; unwinds DNA at the replication fork.

Helicase (eukaryote)

MCM complex; unwinds DNA at the replication fork.

Single-strand binding proteins (prokaryote)

SSB proteins; stabilize unwound DNA strands.

Single-strand binding proteins (eukaryote)

RPA proteins; stabilize unwound DNA strands.

Primase (prokaryote)

DnaG; synthesizes short RNA primers.

Primase (eukaryote)

DNA polymerase α; has primase activity to start new strands.

Main DNA polymerase (prokaryote)

DNA polymerase III; synthesizes leading and lagging strands.

Main DNA polymerases (eukaryote)

DNA polymerase ε (leading) and δ (lagging).

Primer removal (prokaryote)

DNA polymerase I removes RNA primers and fills in DNA.

Primer removal (eukaryote)

Flap Endonuclease

DNA ligase (prokaryote)

Seals nicks between Okazaki fragments.

DNA ligase I (eukaryote)

Seals nicks between Okazaki fragments.

Topoisomerase (prokaryote)

DNA gyrase relieves supercoils ahead of the fork.

Topoisomerases (eukaryote)

Topoisomerase I and II relieve supercoiling.

End-replication problem

Eukaryotes solve it using telomerase; prokaryotes don’t have this issue because DNA is circular.

DNA polymerase proofreading

3′→5′ exonuclease activity in both prokaryotic and eukaryotic polymerases.

RNA polymerases in prokaryotes

One RNA polymerase transcribes all RNA types.

RNA polymerases in eukaryotes

Pol I makes rRNA, Pol II makes mRNA, Pol III makes tRNA.

Promoter (prokaryote)

-35 region and -10 (Pribnow box).

Promoter (eukaryote)

TATA box (at about -25).

Initiation factor (prokaryote)

Sigma (σ) factor; helps RNA polymerase recognize the promoter.

Initiation factors (eukaryote)

General transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH).

Helicase during transcription (eukaryote)

TFIIH acts as a helicase to unwind DNA at promoter.

Elongation (both)Transcription

RNA polymerase adds ribonucleotides 5′→3′ complementary to template DNA strand.

Termination (prokaryote)Transcription

Rho-dependent or intrinsic termination.

Termination (eukaryote)Transcription

Polyadenylation signal (AAUAAA) triggers cleavage and release.

RNA processing (prokaryote)

None; mRNA is ready immediately.

RNA processing (eukaryote)

5′ cap, 3′ poly-A tail, and intron splicing to form mature mRNA.

Transcription location (prokaryote)

Cytoplasm (can be coupled with translation).

Transcription location (eukaryote)

Nucleus (separate from translation).

Ribosome size (prokaryote)

70S (30S + 50S subunits).

Ribosome size (eukaryote)

80S (40S + 60S subunits).

Start codon (both)

AUG.

First amino acid (prokaryote)

N-formylmethionine (fMet).

First amino acid (eukaryote)

Methionine (Met).

Initiation site (prokaryote)Translation

Shine-Dalgarno sequence helps ribosome bind before AUG.

Initiation site (eukaryote)Translation

Kozak sequence surrounds start codon for recognition.

Initiation factors (prokaryote)

IF1, IF2, IF3.

Initiation factors (eukaryote)

eIFs (e.g., eIF2, eIF4).

Elongation factors (prokaryote)

EF-Tu, EF-G.

Elongation factors (eukaryote)

eEF1, eEF2.

Energy source for translation

GTP (used in initiation, elongation, and termination).

Coupling with transcription (prokaryote)

Yes; translation can begin while mRNA is still being transcribed.

Coupling with transcription (eukaryote)

No; transcription in nucleus, translation in cytoplasm.

Termination (prokaryote)Translation

Release factors RF1, RF2 recognize stop codons (UAA, UAG, UGA).

Termination (eukaryote)Translation

Single release factor eRF recognizes all stop codons.

Mnemonic for ribosome size

'70S small bacteria, 80S elegant eukaryotes.'

Ribosome size (prokaryote) 

70S (30S + 50S subunits)

Ribosome size (eukaryote)

 80S (40S + 60S subunits)

Start codon (both) 

AUG

First amino acid (prokaryote)

N-formylmethionine (fMet)

First amino acid (eukaryote)

Methionine (Met)

Initiation site (prokaryote)Translation

Shine-Dalgarno sequence helps ribosome bind before AUG

Initiation site (eukaryote)Translation

→ Kozak sequence surrounds start codon for recognition

Initiation factors (prokaryote)Translation

→ IF1, IF2, IF3

Initiation factors (eukaryote) Translation

eIFs (e.g., eIF2, eIF4)

Elongation factors (prokaryote)Translation

EF-Tu, EF-G

Elongation factors (eukaryote)

eEF1, eEF2

Energy source for translation

GTP (used in initiation, elongation, and termination)

Coupling with transcription (prokaryote)

Yes; translation can begin while mRNA is still being transcribed

Coupling with transcription (eukaryote)

No; transcription in nucleus, translation in cytoplasm

Termination (prokaryote) Translation

Release factors RF1, RF2 recognize stop codons (UAA, UAG, UGA)

Termination (eukaryote)Translation

Single release factor eRF recognizes all stop codons

Mnemonic for start sequences

Shiny bacteria” → Shine-Dalgarno for prokaryotes; “Kozak eukaryote” → Kozak for eukaryotes

Mnemonic for ribosome size

“70S small bacteria, 80S elegant eukaryotes”

70S ribosome composition

Made of 30S (small) and 50S (large) subunits

16S rRNA function

Base-pairs with Shine-Dalgarno sequence to align mRNA

23S rRNA function

Catalyzes peptide bond formation (peptidyl transferase activity)

5S rRNA function

Structural role in stabilizing the ribosome

mRNA function

Carries genetic code from DNA to ribosome

Shine-Dalgarno sequence

Ribosome binding site upstream of AUG start codon

Start codon in prokaryotes

AUG (codes for N-formylmethionine, fMet)

tRNA function

Brings amino acids to ribosome and matches them to mRNA codons

Aminoacyl-tRNA synthetase function

Charges tRNA with correct amino acid using ATP

Initiator tRNA in prokaryotes

Carries N-formylmethionine (fMet)

Initiation Factor 1 (IF1)

Blocks A site to prevent premature tRNA entry

Initiation Factor 2 (IF2)

Brings initiator fMet-tRNA to P site using GTP

Initiation Factor 3 (IF3)

Prevents 50S binding until initiation complex is ready

Elongation Factor Tu (EF-Tu)

Delivers charged tRNA to A site (uses GTP)

Elongation Factor Ts (EF-Ts)

Regenerates EF-Tu-GTP form

Elongation Factor G (EF-G)

Moves ribosome along mRNA (translocation step)

Release Factor 1 (RF1) and 2

Recognizes UAA and UAG stop codons

Release Factor 3 (RF3)

Uses GTP to release polypeptide from ribosome

Energy for tRNA charging

ATP

Energy for translation steps

GTP

A site (ribosome)

Entry site for aminoacyl-tRNA

P site (ribosome)

Holds growing polypeptide chain

E site (ribosome)

Exit site for empty tRNA

Peptidyl transferase center

Part of 23S rRNA; catalyzes peptide bond formation

Coupling of transcription and translation

Occurs simultaneously in prokaryotes