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Continuous synthesis
continuous synthesis 5'-->3' on a strand of DNA
discontinuous synthesis
synthesis of DNA on lagging strand. dna is synthesized in segments and then ligased.
semiconservative replication
replication of DNA by a mechanism by which the parental strands are conserved (remain intact) and serve as templates for the synthesis of new complementary strands
okazaki fragments
DNA sequences 100-200 NT long synthesized on lagging strand
leading strand
the strand of DNa that is synthesized continuously
lagging strand
the strand of dna that is synthesized discontinuously
helicase
enzyme that unwinds the DNA
polymerase III
holoenzyme that synthesizes DNA at the replication fork
topoisomerase
enzyme that relieves strain dring unwinding of double helix by making single nicks in the DNA that allows it to swivel
single strand binding protein
bind to the unwound DNA
keeping it straight and preventing it from base pairing itself
ligase
enzyme that links two molecules of nucleotides

forms phosphodiester bond
primase
enzyme that places primers on DNA
primer
short NT sequence with 3' OH that can initiate DNA synthesis along template
progerias
a disease that is inherited and is characterized by premature aging
holoenzyme
a form of a multimeric enzyme in which all the component polypeptides are present
central dogma
DHA <> RNA > protein
coding strand/sense strand
strand with base sequence that corresponds to mRNA 5'---3'
template strand/antisense strand
-sequence of DNA that is copied during the synthesis of mRNA
-sequence of DNA complementary to mRNA

3'-----5'
RNA
ribonucleic acid. molecule derived from DNA by transcription
poly A tail
poly adenylation
addn of a long string of adenine to the 3' end of a processed mRNA to aid in the longetivity of the transcript
5' cap
7 methylguanosine added to the 5' end of the transcript
intron
interfereing sequences in eukaryotic gene that is spliced out of premRNA
exon
segements in eukaryotic gene that are expressed
mRNA
RNA molecules that are translated on ribosomes

primary
spliceosome
RNA/protein complex that excies introns from primary transcripts of nuclear genes in eukaryotes
DNA replicates in a semiconservative fashion, what does this mean?
DNA replication is semiconservative mechanism in which each of the complementary strands in a parental double helix are conserved in the next generation. This is possible because the parental strands serve as templates for the synthesis of new complementary strands.
Meselson-Stahl had three hypotheses for how DNA replicates, what were they and how did he test them?
  1. semi-conservative- 2 complementary strands of DNa unwind and separate. each strand guides synthesis of new complementary strands
  2. conservative- parental double helix conserved, progeny is entirely new
  3. dispersive- segements of both strands of parental DNA conserved and used as atemplates. direct synthesis of new complementary strand segments join to produce new progeny
TEST used 15N heavy isotope
grew e coli cells in medium with the heavy isotope for many generations. centifuged in 6 M cscl and moved to position where its density = sald soln

the 15N cells were transferred to a medium containing 14N. DNa was extracted and observed periodically
-1 generation in 14N cells had density 1/2 of heavy DNA 1/2 light DNA
-2nd generation- 1/2 hybrid intermediate density 1/2 light

no hybrids in conservative rep
dispersive- observed shift of DNA from heavy to light in each generation
What is the origin of replication and who has this?
origin of replication- site or nucleotide sequence on a chromosome or DNA molecule at which replication is initiated

in bacteria and viral chromosomes- usually one unique replication point

eukaryoes- multiple origins present at specific sites

origins control replication of DNA caled a replicon
What is required for sucessful synthesis of DNA?
DNA polymerase
Primer DNA
templates
deoxyribonucleic acids
Mg2+ cofactor
Why does DNA pol have both polymerase and exonuclease activities?
exonuclease- cleaves nucelic acids at internal sites
5'-->3' exonuclease activity cuts back DNA strands
3' --> 5' exonuclease activity cleave mononucleotices from 3' termini

5' --> 3' proofreading
3' --> 5' DNA repair
What is a holoenzyme?
a form of a multimeric enzyme

enzyme with many subunits in which all the component polypeptides are present

DNA pol III
Leading strand synthesis
DNA is replicated continously in the 5'--> 3' direction
Lagging strand synthesis
DNA sysnthesized 5'-->3' discontinously (okazaki fragments) then connected together by ligase

replication fork created by DNa helicase splits the dna on the leading strand. DNA pol synthesizes DAN continuously in 5'->3' fashion. Lagging strand is synthesized in segments
Telomere problem
At the end of replication on a linear genome, the daughter strand has okazaki fragments and RNA primers. DNA pol removes RNA primers and replaces them. DNA can't be synthesized in locations where the primers exist because there is no room. So daughter strands grow shorter with each round of replication --> can remove important genes if telomers are too short

in germ cells this is ssolved with telomerases. these enzymes add deoxyribonucleodies to the 3' end of parent strand making it longer. primase adds primers to the externl end parent nucleotides. DNA is synthesized and ligased. RNA primer removed and no nucleotides missing.
describe all RNAs
RNA- ribonucleic acid. molecule derived from DNA by transciption

mRNA- messenger RNA- blueprint from protein. single stranded

tRNA- transfer RNA- transfers amino acids to rRNA

rRNA- ribosomal RNA. structural protein synthesis

snRNA- small nuclear located in nucleaus components of spliceosomes

miRNA- micro- gene regulation. RNA interference. Double stranded short RNA
DNA replication
  1. DNA is separated by helicase
  2. topoisomerase attaches to unwound DAN to release some strain caused byt eh unwinding. prevents tangling by nicking single bases to enable DNA strand to rotate freely
  3. single strand binding proteins attach to sing strand DNA to prevent tangling and prevent molecule from pairing with itself
  4. DNA pol III synthesized DNA 5'-3'
  5. leading strand is continous, lagging strand is discontinous and attached by ligase
Transcription steps
Initiation- RNA pol binds at promoter, localized unwinding phosphodiester bonds in RNA

elongation- addn of ribonucleotides. template strand used as template 5'->3' exact copy of coding strand

termination- 2 strategies.

rho independent RNA transcription stops when G-C rich haripin loop is creating

rho dependent- rho protein factor destabilizes template and mRNA

Eukaryotic RNA mods after transcriptions
5' cap- addn of 7 methyl guanosine to 5'. protects 5' end of transcript from attack from ribonucleases

polyadenylation- addn of 20-200 adenine to 3' end. protection fron exonuclease. length = longetivity

splicing- noncoding introns are removed with splicesosome and exons attache together
Transcription from DNA to mRNA
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