Tables from Exam 3 Chapters 11-15

Replication models, DNA polymerases, components required for bacterial replication, important enzymes, classes of RNA, and introns

Theta replication model

• circular DNA template

• no breakage of nucleotide strand

• 1 replicon

• unidirectional or bidirectional

• produces two circular molecules

Rolling-circle replication model

• circular DNA template

• breakage of nucleotide strand

• 1 replicon

• unidirectional

• produces one circular molecule and one linear molecule (that may circularize)

Linear eukaryotic

• linear DNA template

• no breakage of nucleotide strand

• many replicons

• bidirectional

• produces two linear molecules

DNA Polymerase I

• moves both directions

• removes and replaces primers

DNA polymerase II

• only moves 3’ to 5’

• repairs DNA

DNA polymerase III

• only moves 5’ to 3’

• elongates DNA

DNA polymerase IV

• no exonuclease activity

• repairs DNA

Initiator protein

Binds to origin and separates strands of DNA to initiate replication

DNA helicase

Unwinds DNA at replication fork

Single-strand-binding proteins

Attach to single-stranded DNA and prevent secondary structures from forming

DNA gyrase

Moves ahead of replication fork, making/resealing breaks in the double-helix to release the torque that builds up from unwinding at the replication fork

DNA primase

Synthesizes a short RNA primer to provide a 3’-OH group for the attachment of DNA nucleotides

DNA ligase

Joins Okazaki fragments by sealing breaks in the sugar-phosphate backbone of newly synthesized DNA

Replication licensing factors

Mark origin of replication sites, ensure that replication initiates only once during the cell cycle to prevent chaos

Holliday junctions

Produced by gyrase enzymes; critical to the recombination mechanism. Initiated by a single-strand DNA break, then this mechanism moves down the chromosome and resolves it

Ribosomal RNA (rRNA)

• prokaryotic and eukaryotic cells

• located in cytoplasm

• structural and functional components of the ribosome

Messenger RNA (mRNA)

• prokaryotic and eukaryotic cells

• located in nucleus and cytoplasm

• carries genetic code for proteins

Transfer RNA (tRNA)

• prokaryotic and eukaryotic cells

• located in cytoplasm

• helps incorporate amino acids into polypeptide chain

Pre-messenger RNA (pre-mRNA)

• eukaryotic cells

• located in nucleus

• precursor to mRNA

Small nuclear RNA (snRNA)

• eukaryotic cells

• located in nucleus

• processing of pre-mRNA

Small nucleolar RNA (snoRNA)

• eukaryotic cells

• located in nucleus

• processing and assembly of rRNA

Micro RNA (miRNA)

• eukaryotic cells

• located in nucleus and cytoplasm

• inhibits translation of mRNA

Small interfering RNA (siRNA)

• eukaryotic cells

• located in nucleus and cytoplasm

• triggers degradation of other RNA molecules

Piwi-interacting RNA (piRNA)

• eukaryotic cells

• located in nucleus and cytoplasm

• suppresses the transcription of transposons in reproductive cells

Long noncoding RNA (lncRNA)

• eukaryotic cells

• located in nucleus and cytoplasm

• performs a variety of functions

CRISPR RNA (crRNA)

• prokaryotic cells

• assists in destruction of foreign DNA

Group I introns

• located in genes of bacteria, bacteriophages, and eukaryotes

• self-splicing

Group II introns

• located in genes of bacteria, archaea, and eukaryotic organelles

• self-splicing

Nuclear pre-mRNA introns

• located in protein-encoding genes in the nucleus of eukaryotes

• spliceosomal (not self-splicing)

Transfer RNA introns

• located in tRNA genes of bacteria, archaea, and eukaryotes

• enzymatic splicing (not self-splicing)

amino acids

building blocks of proteins, required for protein synthesis in bacterial cells

aminoacyl-tRNA synthetases

attach amino acids to tRNAs, required for protein synthesis in bacterial cells

ATP

needed to provide energy for binding amino acids to tRNAs in bacterial protein synthesis

Release factors 1, 2, and 3

bind to ribosome when the stop codon is reached and terminate translation, required for synthesis of protein in bacterial cells

synonymous codons

Several codons that encode for the same amino acids

stop codons

3 codons that terminate translation

sense codons

61 codons that encode amino acids