chapter 5 Flashcards
what was griffith’s contribution
demonstrated that cells carry a “transforming” molecule
what was avery, mcleod, mccarty’s constribution
demonstrated that DNA is the genetic material
what was watson and crick’s contribution
double-helix model of DNA
-two strands of DNA are antiparallel and the bases are stacked on one another
-two strands connected by A-T and G-C with 10 base pairs per helix turn
what are the four basic molecular genetic processes
- transcription
- RNA processing
- mRNA translation
- replication
what is the difference in structure in ribose and deoxyribose
in the 2’ position, ribose has an OH
in the 2’ position, deoxyribose has just an H
purines
A+G
2 rings
prymidines
U+T+C
one ring
what is at the 5’ end of a DNA molecular
phosphate group
what is at the 3’ end of a DNA molecule
OH group
what are the building blocks of a nucleotide
phosphate, sugar, base
what connects nucleotides in a DNA molecule
H bond
how can protein interaction bend DNA
the conserved C-terminal domain of the TATA box-binding protein (TBP) binds to the minor groove of specific DNA sequences rich in A and T, untwisting and sharply bending the double helix
how can the G+C content of DNA affect the melting temperature
the temp at which DNA denatures increases with the proportion of G+C base pairs
the Tm is a function of the G·C content of the DNA; the higher the G+C percentage, the greater the Tm
what does topoisomerase I do
- relieves torsional stress on DNA
- associates with parental DNA strand ahead of the large T-antigen
what did meselson-stahl contribute
the idea that DNA replication is semiconservative
what direction is DNA synthesized
5’—->3’
what are the three requirements for DNA synthesis
- a primer strand with a free 3’ terminus
- a template strand that is base-paired to the primer
- a source of dNTPs
what is DNA polymerase’s job in DNA synthesis
DNA polymerase catalyzes formation of a phosphodiester bond between the 3’ oxygen of the primer stand and the alpha phosphate of a correctly base-paired dNTP
what does DNA polymerase I do
catalyzed the reaction that adds a single nucleotide to the growing complement strand
when a nucleotide is added, what happens
two terminal phosphates are cleaved off, released as pyrophosphate
what are the general properties of DNA polymerases
- depend on a single stranded nucleotide
- can add free nucleotides ONLY to the 3’ - OH end of an EXISTING polynucleotide (DNA or RNA)
- direction of synthesis is 5’ to 3’
where does DNA synthesis begin in a bacterial chromosome
a site termed the origin of replication
how does DNA synthesis proceed in a bacterial chromosome
bidirectionally (this results in 2 replication forks)
note: the replication forks eventually meet at the opposite side of the bacterial chromosome, ending its replication
how is eukaryotic DNA synthesis different than prokaryotic
- there is more DNA
- the chromosomes are linear
- the DNA is complexed with proteins
- eukaryotic chromosomes contain multiple origins of replication allowing the genome to be replicated in a few hours
what enzyme does proofreading
DNA polymerases
note: ALL DNA polymerases have 3’ to 5’ exonuclease activity that allows for proofreading
what does helicase (viral large T antigen) do
unwinds the parental DNA strands, beginning at a replication origin
what does DNA polymerase ε (Pol ε) (epsilon) do
extends the LEADING strand up to the replication fork
what does PCNA do
-sliding clamp
keeps Pol ε stable and associated with the replication fork
forms complexes with DNA Pol ε and Pol δ, preventing dissociation from the DNA template
what does RPA do
multiple copies of RPA bind the lagging strand (and leading) by keeping it stable and orienting it in the optimal position for replication by Pol δ
binds to single-stranded DNA that has been unwound
maintains ssDNA (single-stranded DNA) template for copying by DNA polymerases
what does primase RNA polymerase-DNA polymerase α (Pol α) complex do
synthesizes primers for LAGGING STRAND synthesis
helicase is what kind of molecule
hexamer (6 identical subunits)
PCNA–Pol δ complex does what
binds the 3’ end of each primer and extends the primer to synthesize most of an okazaki fragment
what shape is PCNA
donut!
double-stranded DNA passes through the hole in the center
what is RFC and what does it do
“clamp loader”
binds to PCNA before the “clamp” is opened and opens the ring so that it can encircle a short region of DNA synthesized by Pol α
what does the Pol delta RFC PCNA complex do
displaces the primase-Pol alpha complex following primer synthesis
DNA polymerase alpha is the only polymerase to
associate with primase
what does DNA polymerase alpha/primase complex do
synthesizes a short RNA/DNA hybrid
-10 RNA nucleotides followed by 20 to 30 DNA nucleotides
what is the primer synthesized by Pol alpha-primase used for
used by DNA polymerase delta or epsilon for the processing elongation of the leading (epsilon) lagging (delta) strands
what is polymerase switching and when does it occur
the trade-off that occurs when polymerase alpha is done synthesizing the primer
after the RNA-DNA primer hybrid is made, polymerase switching occurs and Pol alpha is replaced by Pol delta (lagging) and Pol epsilon (leading)
