Replication
Prokaryote
Synthesis begins at the origin Synthesis: begins at many
of replication (ORI)
OriC (origin of replication for
E. Coli) is 245 base pairs and
consists of 4 9-mer and 3 13-
mer sequences
DNAa: binds to the 13-mers
DNAc: (helicase inhibitor)
delivers DNAb (helicase) to the
template
Helicase: clamps around each
single strand of DNA and
unwinds the DNA
DNA Primase: polymerase
which is required for DNA
polymerase to begin elongation
DNA Polymerase I: removes
and replaces RNA primer
5'to 3; exonculcease activity
(RNA primer Removal)
5'to 3' polymerase activity
(replace primer with DNA)
3' to 5' exonuclease activity
(proofreading)
Polymerase II: involved in
repairing damaged DNA
3'to 5' exonuclease activity
DNA Polymerase III: multi-
subunit protein for elongation
of DNA daughter strand
main polymerase in bacteria
5' to 3' (responsible for
elongation of leading and
lagging strand)
3' to 5' exonuclease activity
DNA Ligase: ligates Okasaki
fragments
Single stranded binding
proteins: bind to single
stranded DNA in the replication
fork and prevent reannealing
Clamp protein: holds DNA
onto template
Topoisomerase: swivel DNA
allowing for free rotation of
DNA around backbones
Transcription
Eukaryote Prokaryote
RNA Molecules:
replication origins mRNA: encodes the amino acid
sequence of a polypeptide
tRNA: brings amino acids to the
ribosome during translation
rRNA: combines with ribosomal
proteins to from the ribosome
snRNA: combines with certain
proteins and is involved in RNA
processing
Helicase: clamps around each Only one single RNA
single strand of DNA and Polymerase
unwinds the DNA
DNA Primase: polymerase
which is required for DNA
polymerase to begin elongation
DNA polymerase: responsible
for elongation of leading and
lagging strands Promotor: located upstream at
-35 and -10 bp from
transcription start site
-35 consensus sequence
5'-TTGACA-3'
-10 consensus sequence
5'-TATAAT-3' (Pribnow box)
RNA polymerase and a sigma
factor bind to the -35 and -10
regions, this adhered weakly to
the bacterial DNA and slides
along until it reaches the
promotor where it binds tightly
and opens up the double helix
to expose DNA
DNA is unwound and
transcription begins
DNA Ligase: ligates Okasaki
fragments
Single stranded binding
proteins: bind to single
stranded DNA in the replication
fork and prevent reannealing
Clamp protein: holds DNA
onto template
Topoisomerase: swivel DNA
allowing for free rotation of Topoisomerase- relaxes
DNA around backbones negative supercoils
Gyrase- introduces -ve
Telomerase: synthesizes DNA
supercoils
using an RNA template to seal
intrinsic termination found in
the gaps left at the 5' end of
RNA transcript
the new DNA resulting from
extrinsic termination such as
RNA primer removal
rho proteins in prokaryotes
Translation
Eukaryote Prokaryote Eukaryote
RNA Molecules: 30S ribosomal subunit with 50S ribosomal subunit binds
mRNA: encodes the amino acid initiation factors and GTP bind forming 70S initiation complex
sequence of a polypeptide to mRNA and fMet initiator during which time the initiation
tRNA: brings amino acids to the tRNA to form 30S initiation factors are released and GTP
ribosome during translation complex hydrolyzed
rRNA: combines with ribosomal the 30S ribosome binds to the small ribosomal subunit binds
proteins to from the ribosome Shine-Dalgarno sequence to the methylated cap at the
snRNA: combines with certain (typically 5'-AGGAGG-3') 5' end of the mRNA, it then
proteins and is involved in RNA migrates to the initiation site-
processing usually the first AUG that it
encounters
Three RNA Polymerases: amino acids added one by one amino acids added one by one
RNA Polymerase I: 5.8S, 18S, by the preceding amino acid at by the preceding amino acid at
and 28S rRNA genes the C-terminus the C-terminus
RNA Polymerase II: all protein translation proceeds along the translation proceeds along the
coding genes (mRNA) and mRNA in the 5' to 3' direction mRNA in the 5' to 3' direction
some snRNAs
RNA Polymerase III: tRNA each addition involves each addition involves
genes and some snRNAs elongation factors elongation factors
Promotor: consists of a EF-Tu and GTP usher the EF-Tu and GTP usher the
collection of conserved short appropriate tRNA into the A site appropriate tRNA into the A site
sequence elements near the of the ribosome of the ribosome
transcription start site peptidyl transferase: peptide peptidyl transferase: peptide
GC Box: GGGCGG; -70 to -200 bond formation between the bond formation between the
TATA Box: TATAA; -20 to -35 two adjacent amino two adjacent amino
CAAT Box: CCAAT; -80 peptide bond formation causes peptide bond formation causes
Transcription Factors: the initiating tRNA in the P-site the initiating tRNA in the P-site
TATA box binding protein: to release its amino acid and it to release its amino acid and it
subunit of TFIID binds TATA box dissociates dissociates
of promotor the ribosome continues to the ribosome continues to
TFIID: causes distortion of move along to the next codon move along to the next codon
DNA double helix allowing for and it requires elongation and it requires elongation
recruitment of other factors and GTP factors and GTP
transcription factors
TFIIB: involved in Rna
polymerase interactions (start
site recognition)
TFIIH: contains DNA helicase peptidyl transferase: catalyzes peptidyl transferase: catalyzes
to unwind DNA and activates the formation of a peptide the formation of a peptide
RNA polymerase by bond between the first two bond between the first two
phosphorylation amino acids (fMet and Ser) of amino acids (fMet and Ser) of
TFIIE: involved in positioning a polypeptide chain on the a polypeptide chain on the
RNA polymerase ribosome ribosome
RNA polymerase II and TFIID
and other transcription factors
Termination: occurs when a Termination: occurs when a
from the basal transcription
stop codon (UAG, UAA and stop codon (UAG, UAA and
machinery
Topoisomerase- relaxes UGA) reaches the A site of a UGA) reaches the A site of a
negative supercoils ribosome. The A site accepts a ribosome. The A site accepts a
Gyrase- introduces -ve protein called a release factor. protein called a release factor.
supercoils Prokaryotes possess 3 release Eukaryotes contain a single
intrinsic termination found in factors: RF1 (recognizes UAA releasing factor: -eRF
RNA transcript and UAG), RF2 (recognizes
extrinsic termination such as UAA and UGA) and RF3 which
rho proteins in prokaryotes stimulates termination