Genetics Chapter 7
1 nm =
1 billionth of a meter, or 10^-9 meters
after the second round of replication in the meselson-stahl experiment, it went from 14N/15N to
14N/14N (all new- after transfer to 14N medium, new strands are made from 14N only) and 14N/15N
A 1:1 mixture of DNA from cells grown in 14N and cells grown in 15N, heated (to disrupt hydrogen bonds) and then cooled (to allow reannealing), contains
14N/14N, 14N/15N, and 15N/15N double helices.
between A and T, there are ___ hydrogen bonds
2
between C and G, there are ___ hydrogen bonds
3
nucleotides complementary to the template strand are added to the ____ end of the new strand by DNA polymerase
3'
in a DNA molecule, an OH group is attached to the _____ carbon
3' carbon
DNA's proofreading ability resides in the ______________ activity of DNA polymerases capable of removing some of the newly laid daughter strand sequence
3'-to-5' exonuclease
The structure of DNA polymerase III is such that it can only add new nucleotides to the _____ end of a primer or growing DNA strand.
3'. This is because the phosphate group at the 5' end of the new strand and the 3' -OH group on the nucleoside triphosphate will not both fit in the active site of the polymerase.
in a DNA molecule, 1-3 phosphates are attached at the ___ carbon
5' carbon
The DNA pol I enzyme possesses two activities that accomplish the removal of RNA nucleotides and their replacement by DNA nucleotides. DNA pol I first uses ________________ to remove the 5'-most nucleotide from the RNA primer. then, the newly open space is filled with the correct DNA nucleotide by ________________
5'-to-3' exonuclease activity, 5'-to-3' polymerase activity
purines
A G
the principal constituent of nuclein was eventually identified as
DNA
the major and minor grooves are regions where
DNA binding proteins can most easily make direct contact with nucleotides along one or both strands of the double helix
What enzyme catalyzes the formation of phosphodiester bonds
DNA ligase
step 3 of replication of the lagging strand
DNA ligase closes the gap between fragments A and B
step 1 of replication of the lagging strand
DNA pol III binds to the 3' end of the most recently produced RNA primer, & adds DNA nucleotides in the 5' to 3' direction until it encounters the previous RNA primer
in e. coli, daughter DNA strands are synthesized at the replication fork by
DNA pol III holoenzyme, the main DNA-synthesizing enzyme
Individual nucleotides are assembled into a polynucleotide chain by the enzyme ____________________
DNA polymerase
DNA ligase has exclusive and very high affinity for
DNA-DNA single-stranded gaps. Its single task is to form a phosphodiester bond between the two DNA nucleotides that joins the two okazaki fragments
In e. coli replication, three enzymes bind at oriC to initiate DNA replication
DnaA, DnaB, DnaC
In the structure of DNA, the 3' carbon should be attached to (2)
a hydrogen and a hydroxyl group
nuclein
a mixture of nucleic acids and proteins
to enhance their movement along template strands, DNA polymerases associate with an auxiliary protein complex known as
a sliding clamp
polymerase chain reaction (PCR) is
an automated version of DNA replication that takes place in a test tube, producing millions of copies of a short targeted segment of DNA from the original DNA molecule
rough pneumococcus strains have a mutant allele of the polysaccharide gene, which causes
an easily broken bacterial capsule, vulnerable to attack by mouse immune system antibodies
origins of DNA replication contain sequences that
attract replication enzymes
in the lagging strand, the daughter strand elongates
away from the replication fork
A 1:1 mixture of DNA from cells grown in 14N and cells grown in 15N contains
both 14N/14N and 15N/15N double helices.
To relieve strain ahead of the replication fork, topoisomerase
breaks a covalent bond in the sugar-phosphate backbone of one of the two parental strands, allowing the DNA to swivel around the corresponding bond in the other strand
topoisomerase function (2)
breaks covalent bonds in the DNA backbone, and binds ahead of the replication fork
DNA helicase function (2)
breaks h-bonds between bases, and binds at the replication fork
how was phage DNA labelled in the Hershey-Chase experiment
by growing it in a medium with radioactive phosphorous
how was phage protein labelled in the Hershey-Chase experiment
by growing it in a medium with radioactive sulfur
incorporation of a dideoxynucleotide triphosphate (ddNTP) by DNA pol into a growing strand is a ______________ event that blocks
chain-terminating event that blocks further strand elongation (absence of an OH at the 3' carbon prevents the ddNTP from forming phosphodiester bonds)
Genome sequence data do not identify any sequence consistent with a replication of origin sequence in multicellular eukaryotes. Thus, it seems likely that DNA is selected for replication in multicellular eukaryotes based on
chromatin modification rather than by the presence of specific DNA sequence
telomere length is a kind of ______________ that keeps track of _________
chronometer, the age of the cell. once the shortening reaches a critical point, the cell is directed into the apoptotic pathway
What term is used to describe the pattern of base pairing between one DNA strand and its partner in a duplex?
complementary
replisomes
complex aggregations of proteins and enzymes that assemble at each replication fork
a nitrogenous (nucleotide) base is attached to the 1' carbon of the deoxyribose molecule by a ___________ bond
covalent
deoxynucleotide monophosphates
dNMPs, where N can refer to any of the 4 nucleotide bases
deoxynucleotide triphosphates
dNTPs, free (reactive) DNA nucleotides that aren't part of a polynucleotide chain and carry a string of 3 phosphate groups at the 5' carbon
____________ & _____________ possess strikingly similar DNA replication machinery that is evolutionarily distinct from the replication machinery in ______________
eukaryotes & archaea, bacteria
when building a new strand, DNA nucleotide triphosphates (dNTPs) are recruited by DNA polymerase, which uses catalytic action to remove two phosphates in order to
form the new phosphodiester bond
DNA polymerase III determines which _______________ is complementary to the base being copied.
free nucleotide triphosphate
DNA replication is bidirectional
it progresses in both directions from the origin of replication
pyrimidines
T C
If a mutation inactivated DNA polymerase I in a strain of E. coli, would the cell be able to replicate its DNA? If so, what kind of abnormalities would you expect to find in the cell?
The cell would be able to replicate its DNA. The mutation will result in newly replicated DNA containing small segments of RNA.
If a strain of E. coli acquired a mutation that inactivated DNA polymerase III function, would the cell be able to replicate its DNA? Why or why not?
The cell would not be able to replicate its DNA because it lacks the enzyme responsible for the bulk of DNA synthesis.
DNA polymerase requires the presence of a primer sequence to provide
a 3'-OH end to which a new DNA nucleotide can be added
consensus sequence
a conserved nucleotide sequence that acts as the binding site for proteins that initiate replication
in circular chromosomes in e. coli, topoisomerase enzymes catalyze
a controlled cleavage and rejoining of DNA to allow supercoiled DNA to relax
DNA undergoes mutation at a low rate that introduces genetic variation and serves as
a foundation for evolutionary change
Mixture of heat-killed s-strain (dead pneumonia-causing) and living r-strain caused
most mice to die. Tests revealed living s-strain bacteria in the dead mice.
holoenzyme is the general term used for
multiprotein complexes in which a core enzyme is associated with additional protein components that complete its structure and lead to its function
Dideoxy sequencing produces a large number of
partial replication products, each terminated by the incorporation of a ddNTP at a different site in the sequence
Which chemical groups of nucleotides react to form the phosphodiester bond?
phosphate & OH groups
What is the name of the bond that joins one nucleotide to another in the DNA strand?
phosphodiester (covalent)
DNA polymerase III catalyzes _____________________ between the 5' phosphate of the incoming nucleotide triphosphate and the 3' hydroxyl group of the last nucleotide added to the strand.
phosphodiester bond formation
single-strand binding protein function (2)
prevents H-bonds between bases, and binds after the replication fork
RNA primers are synthesized by
primase
the ______________ protein functions as the sliding clamp in archaeal and eukaryotic replication, encircling the DNA template strand
proliferating cell nuclear antigen (PCNA) protein
essential difference between DNA & protein that made the Hershey-Chase experiment possible
proteins contain large amounts of sulfur but almost no phosphorous, and DNA contains a large amount of phosphorous but no sulfur
double-ringed nitrogenous base
purine
single-ringed nitrogenous base
pyrimidine
single-stranded binding protein prevents
reannealing (rebinding of the parental strands)
telomeres
repetitive DNA sequences that contain no genetic information, so portions (on the lagging strand, after primer removal) can be safely lost in each replication cycle, without consequence to the organism
oriC
sequence-specific origin of replication in bacteria
As soon as the base pairs separate at the replication fork,
single-strand binding proteins attach to the separated strands and prevent the parental strands from rejoining
In cancer cells, reactivation of telomerase activity appears to
stabilize telomere length, disrupting the normal program of progressive telomere shortening that would lead to apoptosis. The extended life span may allow affected cells to acquire additional mutations associated with cancer
antigen
substance that when introduced into the body stimulates the production of an antibody
telomerase is a ribonucleoprotein that synthesizes
telomeric repeat sequences to maintain telomere length in germ-line and stem cells
DNA polymerase catalyzes the formation of a phosphodiester bond between
the 3' OH group of one nucleotide and the 5' phosphate group of an adjacent molecule
a phosphate attached to the 5' carbon of the bottom sugar should be covalently linked to
the 3' OH group of the top sugar.
You can tell which end is the 3' end by the presence of __________, and the 5' end by the presence of ____________
the OH group, the phosphate group
DNA polymerase III is responsible for
the bulk of synthesis on both the leading and lagging strands
If complementary strands were to align in parallel,
the charges of complementary nucleotides would repel, and no hydrogen bonds would form
high-speed cesium chloride (CsCl) density gradient ultracentrifugation
the high speeds exert thousands of gravities of separating force, creating a graded variation in density (a density gradient) throughout the CsCl mixture. The substances migrate until they reach the point in the density gradient where their molecular density is matched by that of the gradient
Antigenic variation
the mechanism by which an infectious agent such as a protozoan, bacterium or virus alters its surface proteins in order to evade a host immune response. It is related to phase variation.
when a replication error occurs,
the mismatched DNA bases of daughter and template are unable to hydrogen bond properly. So, rotation of the daughter strand is induced into the 3'-to-5' exonuclease site. Then several nucleotides are removed before it goes back
base stacking
the offsetting of adjacent base pairs so that their planes are parallel, giving the twist to the double helix
The leading strand is made continuously from a single RNA primer located at
the origin of replication
At each replication fork, helicase moves along _________________, separating the two strands by breaking the hydrogen bonds between the base pairs.
the parental DNA
each antigenic type of pneumococcus (S/R I, II, III, IV) elicits a different immune response from the mouse immune system as a result of
the presence of several genetic differences
results of Hershey-Chase
the radioactive phosphorous (DNA) was in the bacterial pellet after centrifuge. radioactive sulfur (protein) in the phage ghosts remained suspended in the liquid
among different types of cells, the length of the S phase is variable, meaning that
the rate of progression of DNA replication varies among cells of different types
DNA regions containing A-T richness require less energy for their denaturation, because
there are only 2 hydrogen bonds between A & T
why did some scientists argue that protein must be the hereditary material and not DNA
they argued that the "20-letter alphabet" of protein could contain more info that the 4-letter alphabet of DNA
the first primers on the lagging strands are
those closest to the origin of replication
DNA polymerase I functions to (2)
to remove the RNA primer and to fill in the gaps with DNA,
in the leading strand, the daughter strand elongates
toward the replication fork
completion of DNA replication results in the formation of
two identical daughter duplexes, each composed of one parental strand and one daughter strand (semiconservative model)
bacterio(phages) are
viruses that infect bacteria. They're made of a protein shell with a tail segment that attaches to a host bacterial cell and a head segment that contains DNA
There should not be _____ bonds in the structure of DNA.
P−C (phosphate-carbon)
the lagging strand is made in segments, each with its own
RNA primer
what is the consequence of abnormal reactivation of telomerase activity in somatic cells?
aging cells will continue to proliferate, allowing them to escape programmed cell death. This is what happens in many kinds of cancer, where mutations reactivate the expression of TERT.
the 3 steps of PCR
denaturation (so DNA will denature into single strands), primer annealing (attachment of the primers to complementary sequences that bracket the target sequence), and primer extension (DNA synthesis by Taq polymerase)
telomerase activity is virtually nonexistent in
differentiated somatic cells (they have finite life spans anyway)
Notice that after one round of replication, the _____________ & _________________ models predict identical results (14N/15N), whereas the ________________ model predicts different results. (14N/14N and 15N/15N)
dispersive and semiconservative, conservative
dispersive model
each daughter duplex is a mix of parental duplex segments and daughter duplex segments
2 limitations of PCR
needing to know the sequences needed for primers, and that amplification products longer than 10 to 15 kb are difficult to produce (restricting its use to the study of selected DNA segments/ individual genes)
DNA pol I removes and replaces
nucleotides of the RNA primer
step 2 of replication of the lagging strand
once DNA pol III encounters the other RNA primer, it falls off and is replaced by DNA pol I. DNA pol I removes each RNA nucleotide and replaces it with the corresponding DNA nucleotide, from the 5' end of primer A to the 3' end of fragment B. When it encounters the 5' end of fragment A, DNA pol I falls off
In the structure of DNA, there should be _________ bond in the phosphate groups.
one P=O double
conservative model
one daughter duplex contains the two strands of the parental molecule, and the other contains two newly synthesized strands
