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dna replication occurs in a 5’ to ?
3’ direction with respect to dna structure and relies on the complementary of dna strands
AT/CG RULE
the two complementary dna strands come apart at the ?
replication fork and each serves as the template strand for the synthesis of new complementary dna strands
the two newly-made dna strands
daughter strands
the two original strands
parental strands
one replicated strand and the leading strand occur in what direction ?
towards the replication fork
one replicated strand and the lagging strand occur in what direction ?
away from the replication fork
DNAaA boxes
sites for the binding of DNaA protein
at-rich regions
sites where the dna strands separate
GATC methylation sites
sites that help to regulate dna replication
initiation of replication only occurs when?
when dna is fully methylated
dna synthesis requires a ?
rna or dna primer
in the cell, both the lagging and leading replicated dna strands are synthesized by ?
DNA pol lll by using rna primers synthesized by the primase protein
primosome
coordinates the actions of helicase and primase
dna polymerase catalyzes ?
the formation of a covalent ester bond between the innermost phosphate group of the incoming deoxyribonucleoside triphosphate and 3’-OH of the sugar of the previous deoxynucleotide
the last two phosphate of the incoming nucleotide are released how ?
in the form of pyrophosphate (PP)
what polymerase is associated with the primase protein?
dna polymerase alpha
polymerase switch
dna poly a is exchanged with dna polymerase epsilon to synthesize the leading strand and the dna polymerase delta to synthesize the lagging strand
what features are dna polymerase defined by ?
synthesize dna only in the 5’ to 3’ direction
cannot start dna synthesis on an unprimed dna strand
at the 3’ ends of linear chromosomes -
the end of the strand cannot be replicated !
the telomerase protein binds to ?
telomeric repeat sequences in the telomeres at the ends of the chromosome using an rna primer
what is the name of the rna primer used in telomerase protein ?
telomeric rna
replicated the ends of the chromosomes
not all rna is ?
mrna
what is mrna translated into ?
proteins
the central dogma
dna - mrna - protein
regulatory sequences
sites for the binding of regulatory proteins that influence the rate of transcription
promoter
site for rna polymerase binding which signals the beginning of transcription
terminator
signals the end of transcription
ribosome-binding site
site for ribosome binding to mrna in bacteria which begins the translation of mrna into a protein
codons
3 nucleotide sequences within the mrna that specify particular amino acids
the sequence of codons within mrna determines the sequence of amino acids within a polypeptide
start codon
specifies the first amino acid in a polypeptide
sequence, usually a formylmethionine (bacteria)
and methionine (eukaryotes)
stop codon
specifies the end of polypeptide synthesis
the base sequence in the mrna is ?
identical to the coding or sense strand of dna
except for the sub of uracil in rna for thymine in dna
the dna strand that is actually transcribed (template) is termed the ?
template strand and is complementary to the sense strand
the mrna transcript is ?
complementary to the template strand
what enzyme catalyzes the synthesis of rna ?
rna polymerase
in e.coli, rna polymerase holoenzyme is composed of ?
rna polymerase core enzyme
five subunits, a2bb’w, sigma factor
rna polymerase core enzyme
a2bb’w
rna poly core enzyme + sigma factor =
rna polymerase holoenzyme
rna polymerase core enzyme binds loosely to the dna -
then it scans along the dna , until it encounters a promoter
when it does, the sigma factor recognizes both the 35 and 10 sequences
a region within the sigma factor that contains a helix-turn-helix structure is involved in the binding to the dna
rna polymerase does not need a ?
dna or rna primer to replicate dna to rna
e. coli has two different mech. for termination
rho-dependent termination
rho-independent termination
rho-dependent termination
requires a protein known as (rho)
rho-independent termination
uses proteins other than rho
rho-dependent termination uses the rho protein, which binds to a rho recognition site (rut), that is ?
transcribed in the rna and a stem-loop is formed by a stretch of GC nucleotide in the rna causes rna polymerase to stall and release from the dna
rho independent termination use a GC rich stem loop structure at the end of the mrna that is followed by ?
a uracil-rich sequence, auxiliary proteins (nursa)
these bind to both the rna and rna polymerase causing it to pause at the stem-loop structure and release rna polymerase from the dna
nuclear dna is transcribed by three different rna polymerases
rna pol 1
rna pol 2
rna pol 3
rna pol1
transcribes all rrna genes (no 5s rrna)
rna pol2
transcribes all mrnas
some snrnas genes needed for splicing
rna pol3
transcribes all trna genes, 5s rrna gene, microrna genes
regulatory elements are short dna sequences that affect the binding of rna polymerase to the core promoter. transcription factors (proteins) bind to these elements and influence ?
the rate of transcription
enhancers
stimulate transcription
silencers
inhibit transcription
enhancers and silencers locations
-50 to -100 region upstream of the promoter
regulatory elements are ?
cis with respect to the gene they regulate
transcription factors are ?
trans with respect to the gene that they regulate
cis acting elements
dna sequences that exert their effect only over a particular gene, like TATA box, enhancers and silencers
found near the gene that they regulate and are on the same chromosome the has the regulated gene
trans acting factors
regulatory proteins that bind to the promoter region of genes
control many genes and the genes that encode them are not located near the gene that they regulate
rna polymerase ll
five different proteins called general transcription factors
protein complex called mediator
mrnas are modified by cleavage near their 3’ end with subsequent attachment of a string of adenines to form a ?
polyadenylated (polyA) tail
-can happen in bacteria
termination according to the allosteric model is ?
aided by termination factors
termination according to the torpedo model is ?
aided by exonucleases
most eukaryotic mrnas have introns that are removed from the ?
mrna before its translated into a protein
ribosomal rna is also ?
processed from a larger precursor in bacteria
eukaryotic trna is also processed from a ?
large precursor
intron rna is spacer rna that is ?
removed from the final rna
exon rna is the rna that is ?
contained in the final rna
rna splicing occurs in ?
both bacteria and eukaryotes
but splicing using a spliceosome only happens in eukaryotes
are there spliceosomes in bacteria ?
no
does alternative splicing of mrna happen in bacteria ?
alternative splicing of mrna does not happen in bacteria
bacterial mrna does not have a ?
7-methyl-guanosine cap at their 5’ end
some bacterial mrna have a ?
polyA tail
does rna editing occur in bacteria ?
yes