DNA Structure and Replication Flashcards
what was believed to be genetic material in the 1940s
protein
what is the transforming agent in bacterial transformation?
DNA
explain Griffith’s in vivo transformation experiments
he injected a mouse with four different bacterium
Control: inject with virulent IIIS, mouse dies
-Inject with non virulent IIR, mouse lives
Heat killed: inject with killed IIIS, mouse lives
Critical experiment: inject with living IIR and killed IIIS, mouse dies, tissue analysis shows live IIIS
explain Avery-MacLeod-McCarty in vivo transformation experiments
treated IIIS filtrate with different neutralizing agents for protein, RNA, lipids, carbs, and DNA to see which was the transforming agent
IIR v IIIS
-which is virulent/impact on injected mice
IIIS is virulent and killed mice
what was the discovery of transforming non-virulent IIR cells into virulent IIIS cells
discovery of transformation
what is transformation used by to transfer DNA
bacteria
in Avery, MC^2 destroying which material led to transformation not occurring? why is this important?
when DNA was destroyed transformation did not occur.
proved that DNA was the transforming agent
explain Hershey-Chase bacteriophage experiment
labeled protein phages and DNA phages separately then traced each radioactive label in the course of infection
DNA contains large amounts of [what], whereas protein contains large amounts of [what]?
DNA: phosphorus
Protein: sulfur
what were phage proteins labeled with in hershey-chase?
DNA phages?
Proteins: 35S
DNA: 32P
what was infected bacteria labeled with in hershey-chase? what did it prove was the genetic material in T2 phages?
infected bacteria were labeled with 32P which proved genetic material in T2 is DNA not protein
dNMPs and dNTPs
dNMPs: monophosphates-part of the nucleotide chain
dNTPs: triphosphates-not part of the nucleotide chain
T/F dNTPs and dNMPs are both part of the polynucleotide chain
FALSE. only dNMPs are
chemical structural difference between DNA and RNA
DNA has an H on the 2’ carbon whereas RNA has an OH on the 2’ carbon
structural difference between nucleosides and nucleotides
Nucleoside: Nitrogenous base + Pentose sugar
Nucleotide: Nucleoside + Phosphate group
nomenclature difference between nucleosides and nucleotides
Nucleoside: ends with ‘SINE’
Nucleotide: ends with ‘ACID’
most significant nucleoside phosphate
NTP(precursor for ATP)
assembly of polynucleotide chains(3 componants)
-individual nucleotides assemble through DNA polymerase
-phosphodiester bond forms between 3’ hydroxyl group and paired 5’ phosphate group
-each chain has a sugar phosphate backbone alternating sugar and phosphate groups
3 required properties of genetic code
must replicate
must encode information
must be able to change/mutate
complementary vs antiparallel sequences?
Complementary: bases of one strand pair with corresponding base of the other strand(EX: A-T, C-G)
Antiparallel: the 2 strands are antiparallel to each other with respect to 5’ and 3’ ends
Chargaff’s rules
-A=T AND G=C
-(A+G) = (C+T)
-(G+C) ≠ (A+T)
how do chargaff’s rules correlate to the base composition studies critical conclusions?
it showed a specific chemical affinity between nitrogenous bases
base stacking definition
creates gaps among sugar-phosphate backbone that partially exposes nucleotides
major vs minor grooves
Major is wider and deeper than minor grooves
B-DNA properties
-most common
-right handed twist
-low salt conditions
A-DNA properties
-mainly in bacteriophage and in vitro
-high salt/dehydration
-base tilted in relation to axis
-grooves modified
Z-DNA properties
-found near transcription start sites
-zigzag conformation
-left handed helix
-no major groove
what are the 3 forms of DNA
A-DNA
B-DNA
Z-DNA
3 attributes of DNA replication shared by all organisms
-each strand of parental DNA remains intact
-each parental strand serves as template for complimentary daughter strand
-completion results in formation of tw identical daughter duplexes composed of one parental and one daughter strand
basics of DNA replication
semiconservative
bi-directional
main synthesis- polymerase III
direction 5’ - 3’
start at point(s) of origin
3 theoretical models of DNA replication
Semiconservative
Conservative
Dispersive
what is the origin of replication in prokaryotes
location where DNA replication begins
what is the replication fork in prokaryotes
located at the end of the replication bubble where replication is complete
what is the replication bubble in prokaryotes
expands around the origin of replication as DNA replication proceeds bi-directionally from it
main differences in DNA replication between prokaryotes and eukaryotes
Eukaryotic DNA replication is more complex
-more DNA
-linear chromosomes
-DNA complexed with proteins
what is a consensus sequence
comparing a region of DNA between related species and determining the most common nucleotide found at a specific position of DNA
why do prokaryotes have only one origin of replication
because bacterial DNA is a circle so origin of replication meets up with the terminus of replication
steps of DNA replication in bacteria(7 steps)
-helicase breaks H bonds, topoisomerase calms supercoiling
-single-stranded binding prevents reannealing
-primase synthesizes RNA primers
-polymerase III synthesizes daughter strand
-polymerase III elongates leading strand and lagging strand
-polymerase I removes and replaces RNA primer
-DNA ligase joins okazaki fragments
what is RNA priming
universal initiation of DNA replication
what are Okazaki fragments
discontinuous strands of replicated DNA
how are okazaki fragments combined after being synthesized
combined by DNA ligase
Function of DNA polymerase I
remove primer and fill gaps
Function of DNA polymerase II
repairs DNA damage from external forces
and damage at replication fork
Function of DNA polymerase III
proofreading and DNA polymerization
Function of DNA polymerase IV and V
repair DNA damages caused by external forces
what is the function of the sliding clamp
clamp onto double-stranded DNA during replication to anchor polymerase III
why does proofreading need to occur
detect mismatches
cut out wrong nucleotides
what activity allows DNA polymerase to work
presence of sliding clamp
what causes supercoiling?
what controls it?
it is torsional stress caused by the unwinding of chromosomes during replication.
controlled by topoisomerases
how many telomeres are important in chromosomes
4 (one cap on each chromosome end)
main characteristics of telomeric sequences
contain special repeat: TTAGGG
T/F prokaryotes have telomeres
FALSE
what causes the gap in telomeres? what enzyme fixes it?
gap is caused by telomerase adding extra telomeric sequence to the lagging strand.
polymerase fills the gap
telomerase activity steps (4 steps)
-telomeric repeat added to lagging strand
-repeats fold back and form G-G bond
-polymerase fills the gap formed
-hairpin turn is cleaved and removed
-telomerase synthesizes new telomeric sequence on the end
difference between PCR amplification and dye terminator sequencing(sanger sequence)
PCR does not contain ddNTPS which are present in sanger sequence
What is the most commonly used DNA polymerase?
What is it isolated from?
Where does it naturally occur?
Taq
isolated from Thermus Aquaticus
found naturally in hot springs
fill in the blank: cancer cells maintain _____ activity and are ______
telomerase, imortalized
what do groves in DNA allow for
DNA binding proteins can make direct contact with nucleotides
semiconservative DNA replication
each daughter duplex has one daughter and one parental strand
conservative DNA replication
one daughter duplex has both daughters, the other has both parents
dispersive DNA replication
each daughter duplex contains interspersed daughter ant parental segments
main enzyme groups that control DNA replication and their basic functions
Helicases-unwind and stabilize
Gyrases-cut and stabilize
RNA polymerase-synthesize RNA primers
DNA polymerase-synthesize DNA
Ligase-stitch fragments
