CHAPTER 6: DNA Structure, Replication & Recombination
recombinants
(1) chromosomes that carry a mix of alleles derived from different homologous chromosomes (2) gametes with combinations of alleles not inherited from the same parent (3) recombinant plasmids.
DNA polymerase requires:
(i) a supply of the four deoxyribonucleotide triphosphates (ii) a single-stranded DNA template, and (iii) a primer of either DNA or (in cells) RNA with a free 3′ hydroxyl group.
DNA replication reflect three strict requirements for DNA polymerase action
1. The four dNTPs. 2. A single-stranded template. Double-stranded DNA must be unwound, and DNA polymerase moves along the template strand in the 3′-to-5′ direction. 3. A primer with a free 3′ hydroxyl group. DNA polymerase adds nucleotides successively to the 3′ end of the growing DNA chain. (That is, DNA polymerase synthesizes DNA only in the 5′-to-3′ direction.) However, DNA polymerase cannot establish the first link in a new chain. Polymerization therefore must start with a primer, a short, single-stranded molecule of DNA or RNA a few nucleotides long that base pairs with part of the template strand.
three parts of a nucleotide
5 carbon sugar, phosphate group, nitrogenous base
the DNA double helix can adopt two main conformations. the conformation that is most abundant in living cells is called _________ DNA
B-form
Z-form DNA
DNA in which the nucleotide sequences cause the structure to assume a zigzag shape due to the helixes spiraling to the left. The significance of this variation on DNA structure is unknown.
central dogma
DNA-transcription-RNA-translation-protein
Redundancy of Preserving the Integrity of Genetic Information
Either strand of the double helix can specify the sequence of the other. This redundancy provides a basis for checking and repairing errors arising either from chemical alterations sustained during storage or from rare malfunctions of the replication machinery.
The remarkable precision of the cellular replication machinery of Preserving the Integrity of Genetic Information
Evolution has perfected the cellular machinery for DNA replication to the point where errors during copying are exceedingly rare.
T/F: the most important mechanism for generating genomic diversity is sexually reproducing organism is mutation
False (crossing-over & independent assortment generate the most genetic diversity)
who discovered the helical structure of DNA
Rosalind Franklin, James Watons & Francis Crick
Enzymes that repair chemical damage to DNA of Preserving the Integrity of Genetic Information
The cell has an array of enzymes devoted to the repair of nearly every imaginable type of chemical damage
inversion
a 180-degree rotation of a segment of a chromosome relative to the remainder of the chromosome.
purines
a chemical group that includes the nitrogenous bases adenine and guanine.
pyrimidines
a chemical group that includes the nitrogenous bases cytosine, thymine, and uracil.
DNA polymerase
a complex enzyme that forms a new DNA strand during replication by adding nucleotides reverse complementary to a template, one by one, to the 3′ end of a growing strand.
DNA topoisomerases
a group of enzymes that help relax supercoiling of the DNA helix by nicking one or both strands to allow the strands to rotate relative to each other.
semiconservative replication
a mechanism of DNA replication in which each single strand of the parent double helix serves as template for synthesis of its complement. The result is two daughter double helixes that each contain one of the original DNA strands intact (conserved) and one completely new strand.
ribonucleic acid (RNA)
a polymer of ribonucleotides found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis. Several classes of RNA molecules exist, including messenger RNA (mRNA), transfer RNA (tRNA), ribosomal RNA (rRNA), miRNAs, piRNAs, and siRNAs.
branch migration
a process during recombination whereby Holliday junctions move away from each other and thereby enlarge the heteroduplex region between them.
heteroduplex
a region of double-stranded DNA in which the two strands have nonidentical (though similar) sequences. Heteroduplex regions are often formed as intermediates during crossing-over.
RNA primer
a short stretch of RNA that initiates DNA synthesis during DNA replication.
primer
a short, preexisting DNA oligonucleotide or RNA molecule to which nucleotides can be added by DNA polymerase.
minor groove
a space-filling representation of the DNA double helix model, the narrower of the two grooves resulting from the vertical displacement of the two backbone threads.
major groove
a space-filling representation of the DNA double helix model, the wider of the two grooves resulting from the vertical displacement of the two backbone threads.
template
a strand of DNA or RNA that is used as a model by DNA or RNA polymerase or by reverse transcriptase for the creation of a new complementary strand of DNA or RNA.
nucleotides
a subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate group, and a sugar (deoxyribose in DNA; ribose in RNA).
bacteriophages
a virus for which the natural host is a bacterial cell; literally bacteria eaters.
supercoiling
additional twisting of the DNA molecule caused by movement of the replication fork during unwinding.
Chargaff's ratio demonstrate that "in piece of double-stranded DNA, the amount of _______ equals the amount of thymine and the amount of cytosine equals the amount of _______
adenine; guanine
DNA ligase
an enzyme that forms phosphodiester bonds between DNA fragments.
anticrossover helicase
an enzyme that helps disentangle the invading strand from the nonsister chromatid, thus interrupting Holliday junction formation and preventing crossing-over.
recombinase
an enzyme that performs site-specific recombination.
DNA helicase
an enzyme that unwinds the double helix.
D-loop (deletion loop)
an unpaired bulge of a normal chromosome that corresponds to an area deleted from its paired homolog.
a virus that infects bacterial cells is called a(n).....
bacteriophage
DNA polymerase III
complex enzyme that plays the major role in synthesizing a new DNA strand during replication.
phosphodiester bonds
covalent bonds joining one nucleotide to another that form the backbone of DNA.
recombination events result in...
crossing-over only part of the time because helicases can disentangle the chromatids before holliday junctions form
site-specific recombination
crossing-over that occurs between two specific short DNA sequences, due to the action of specific enzymes called recombinases.
complementary base pairing
during DNA replication, base pairing in which a complementary strand aligns opposite the exposed bases on the parent strand to create the nucleotide sequence of the new strand of DNA; hydrogen bonding between A-T and G-C that holds the two antiparallel strands of the DNA double helix together; can also enable formation of RNA:DNA or RNA:RNA double strands. (A pairs with U in RNA.)
resection
during homologous recombination, the process whereby single-stranded 5′ ends of DNA are produced by an exonuclease at the site of double-stranded cleavage.
strand invasion
during recombination, one single-stranded DNA displaces the corresponding strand on the nonsister chromatid.
restriction enzymes
enzyme that cuts DNA at a sequence of nucleotides
exonuclease
enzyme that removes nucleotides from an end of a DNA molecule.
an enzyme that removes nucleotides from one end of a DNA molecule is called a(n):
exonuclease
Okazaki fragments
form during DNA replication, small fragments of about 1000 bases that are joined after synthesis to form the lagging strand.
Gene conversion
in a heterozygote, change in the base sequence of one allele to that of the other allele as a result of heteroduplex formation and mismatch repair during recombination.
DNA polymerase synthesizes DNA
in the 5′-to-3′ direction by adding nucleotides successively onto the 3′ end of a growing DNA chain.
integration
insertion of one DNA molecule into another.
Holliday junctions
interlocked regions of two nonsister chromatids in recombination intermediates.
Site-specific recombination
is crossing-over between two short DNA target sites catalyzed by a recombinase enzyme.
transcription factors
mediate the binding of RNA polymerase and the initiation of transcription
nucleoside
nitrogenous base + sugar
a Holliday junction is a connection between...
nonsister chromatids that is formed after strand invasion
Freidrich Miescher isolated a weakly acidic material from the nuclei of white blood cells that he named ________. the material contained mostly ___________ along with some contaminants.
nuclein; DNA
A DNA chain is a long polymer made of monomer subunits called....
nucleotides
At the DNA replication fork, DNA polymerase synthesizes
one new strand (the leading strand) continuously, while the other (lagging strand) is synthesized as multiple Okazaki fragments that are then joined by DNA ligase.
antiparallel characteristic of DNA
one strand is oriented in the 5′-to-3′ direction, while the other, complementary strand is oriented in the 3′-to-5′ direction.
elongation
phase of DNA replication, transcription, or translation when nucleotides or amino acids are added successively to a growing macromolecule.
descriptions such as 5`-3` and 3`-5` indicate the _______ of a DNA chain
polarity
the constant diameter of the double helix is ensured because hydrogen bonding is always between a __________ and a __________
purine; pyrimidine
chromosomes that carry a mix of alleles derived from different homologs are called....
recombinants
the process that causes the generation of new allelic combinations through genetic exchange between homologous chromosomes is called
recombination
The integrity and accuracy of information in DNA is preserved by
redundancy in the two strands the precision of the enzymes synthesizing DNA the action of enzymes that repair damage to DNA.
excision
removal of a segment of DNA from a larger DNA molecule.
breakage and rejoining of DNA strands to produce separate chromatids at the end of recombination is called.....
resolution
two enzymes involved in the creation of new chromatids originally joined by a Holliday junction are _________ & ___________
resolvase; DNA ligase
In B DNA, the helix has a ______-handed twist, the bases are found inside the helix and are aligned perpendicular to the central axis of the molecule, there are 10 base-pairs per turn of the helix, and the sugar-phosphate backbone twists evenly along the axis of the helix
right
which characteristic of the DNA molecule is responsible for carrying genetic information
sequence of A, G, T & C bases
phages
short for bacteriophage; a virus for which the natural host is a bacterial cell; literally bacteria eaters.
origin of replication
short sequence of nucleotides where DNA replication initiates.
when comparing the sizes of RNA molecules to DNA molecules found in nuclear chromosomes, RNA molecule will be ______ than DNA molecules
shorter
In 1928 Frederick Griffth did a number of experiments to identify the "transforming principle". notably, he found that when living ___________-type streptococcus pneumoniae bacteria were injected into mice, the mice died. in addition, he showed that when living ___________-type streptococcus pneumoniae were mixed with heat-treated smooth-type streptococcus pneumoniae and inject into mice, the mice died.
smooth; rough
telomeres
specialized terminal structures on eukaryotic chromosomes that ensure the maintenance and accurate replication of the two ends of each linear chromosome.
what did James Watson conclude from Chargaff's observation that in double-stranded DNA, adenine is found in the same amount as thymine, and that guanine is found in equal amounts as cytosine?
that thymine in one strand binds to adenine in the other and that guanine in one strand binds to cytosine in the other strand
leading strand
the DNA strand replicated continuously 5′ to 3′ toward the unwinding Y-shaped replication fork.
lagging strand
the DNA strand replicated discontinuously, 5′ to 3′ away from the Y-shaped replication fork, as small Okazaki fragments that are ultimately joined into a continuous strand.
replication fork
the Y-shaped area consisting of the two unwound DNA strands branching out into unpaired (but complementary) single strands during replication.
Griffth defined transformation as....
the ability of a molecule to confer new genetic characteristics on an organism that acquires that molecule
resolvase
the enzyme that breaks and joins DNA strands at Holliday junctions to separate nonsister chromatids during crossing-over.
DNA polymerase I
the enzyme that replaces RNA primers with DNA during DNA replication.
primase
the enzyme that synthesizes RNA primers during DNA replication.
crossing-over
the exchange of genes between homologous chromosomes, resulting in a mixture of parental characteristics in offspring.
3′ end
the final nucleotide of an RNA or DNA molecule.
5′ end
the first nucleotide of an RNA or DNA molecule.
initiation
the first phase of DNA replication, transcription, or translation needed to set the stage for the addition of nucleotide or amino acid building blocks during elongation.
polymerization
the linkage of subunits to form a multisubunit chain. For example, in DNA replication, the polymerization of nucleotides occurs through the formation of phosphodiester bonds by DNA polymerase.
deoxyribonucleic acid (DNA)
the molecule of heredity that encodes genetic information.
B-form DNA
the most common form of DNA, in which the double helix spirals to the right.
dispersive replication
the parent molecule is cut into sections such that the daughter molecules contain old DNA interspersed with newly synthesized DNA
conservative replication
the parental molecule serves as a template for the synthesis of an entirely new molecule
recombination
the process by which offspring derive a combination of alleles different from that of either parent; the generation of new allelic combinations. In higher organisms, this can occur by independent assortment and by crossing-over.
polarity
the property of having distinct ends.
independent assortment
the random distribution of the pairs of genes on different chromosomes to the gametes
how did Hershey and Chase discriminate between DNA and protein in their experiments to show that DNA was the genetic material of bacteriophage T2?
they labeled the DNA with radioactive phosphorus and the protein with radioactive sulfur
the experiments of Avery, MacLeod & McCarty were trying to determine the ________ in the experiments by Frederick Griffith
transforming substance
phosphodiester bonds link together
two sugars on adjacent nucleotides in DNA
replication bubble
unwound area of the original DNA double helix during replication.
hydrogen bonds
weak electrostatic bonds that result in a partial sharing of hydrogen atoms between reacting groups.
