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) → RNase H and FEN1 remove RNA primers

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 (adds telomeres); prokaryotes don’t have this issue because DNA is circular

DNA polymerase proofreading → 3′→5′ exonuclease activity in both prokaryotic and eukaryotic polymerases

Mnemonic for polymerases → “ε is efficient (leading), δ deals with delays (lagging)”

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 (“R-M-T = I-II-III”)

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

Termination (prokaryote) → Rho-dependent or intrinsic (hairpin) termination
Termination (eukaryote) → 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)

Mnemonic for polymerases → “Pol I = rRNA, Pol II = mRNA, Pol III = tRNA”

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) → Shine-Dalgarno sequence helps ribosome bind before AUG
Initiation site (eukaryote) → 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) → Release factors RF1, RF2 recognize stop codons (UAA, UAG, UGA)
Termination (eukaryote) → 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

30S subunit contents → 16S rRNA + 21 proteins

50S subunit contents → 23S rRNA + 5S rRNA + 34 proteins

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)

Stop codons → UAA, UAG, UGA

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) → Recognizes UAA and UAG stop codons

Release Factor 2 (RF2) → Recognizes UAA and UGA 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