Important words and concepts from Chapter 16, Campbell & Reece, 2002 (1/29/2005):
by Stephen T. Abedon (abedon.1@osu.edu) for Biology 113 at the Ohio State University
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Course-external links are in brackets Click [index] to access site index Click here to access text's website Vocabulary words are found below |
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(1) Chapter title: The Molecular Basis of Inheritance
(a) [the molecular basis inheritance (Google Search)] [index]
HISTORY OF UNDERSTANDING OF DNA
(2) Chromosomes (see also chromosome)
(a) Chromosomes consist of DNA and protein
(b) Which is the hereditary material? The history of our understanding is outlined in the efforts of the following:
(i) Griffith, 1928
(ii) Avery, MacLeod, and McCarty, 1944
(iii) Hershey and Chase, 1952
(iv) Chargaff
(c) [chromosomes (Google Search)] [index]
(a) Griffith discovered a hereditary molecule that was transmittable between bacteria
(b) See Figure 16.1, Transformation of bacteria
(c) [Griffith 1928 (Google Search)] [index]
(4) Avery, MacLeod, and McCarty, 1944
(a) Avery et al. found that Griffith's transmittable hereditary molecule is DNA
(b) In particular, they showed that the transmittable hereditary molecule was susceptible to the DNA hydrolyzing enzyme known generically as DNase
(c) [Avery MacLeod McCarty, DNase OR DNase, DNase, DNase (Google Search)] [index]
(a) Hershey and Chase showed that the hereditary material in T2 bacteriophages is DNA, thereby generalizing Avery, MacLeod, and McCarty's observation
(b) See Figure 16.2, The Hershey-Chase experiment
(c) [Hershey Chase, Alfred Day Hershey (Google Search)] [the bacteriophage ecology group (Microdude)] [index]
(6) Chargaff (Chargaff's rule) (see also Chargaff's Rule)
(a) Chargaff found that different species of organisms have different DNA nucleotide compositions
(b) Chargaff's rule states that the fraction of nucleotides that makes up an organism's DNA always behaves the rule: the fraction of A's = the fraction of T's, and the fraction of G's = the fraction of C's (i.e., the fractions of A + T + G + C = 1; A = T and G = C; 2 * (A + G) = 1, etc.)
(c) [Chargaff, Chargaff's rule (Google Search)] [index]
(a) Franklin and Wilkins are responsible for supplying an X-ray diffraction of DNA, essentially an in-this-case crude molecular picture of the molecule, that indicated the basic structural features that DNA possesses:
(i) The periodicity of DNA
(ii) The molecule's uniform width
(iii) That the nitrogenous bases stacked 0.34 nm apart
(b) See Figure 16.4, Rosalind Franklin and her X-ray diffraction photo of DNA
(c) [Franklin Wilkins DNA, DNA X-ray diffraction (Google Search)] [index]
(a) Watson and Crick, in 1953, published the double helix model of DNA's structure
(b) J. D. Watson and F. H. C. Crick (1953). Molecular Structure of Nucleic Acids. Nature, vol. 171 (25 April 1953), pages 737-738
(c) This paper was, arguably, the single most important contribution to biology (and perhaps even chemistry as well) of the twentieth century
(d) See Figure 16.5, The double helix
(e) The Watson and Crick model:
(i) Explains DNAs periodicity
(ii) Explains DNAs uniform width
(iii) Explains Chargaff's rule
(iv) Explains how DNA is replicated
(f) (you will not be held responsible for the above history)
(g) [Watson Crick, double helix (Google Search)] [annotated version of Watson & Crick, 1953!, (nice index of gifs and html files but I have no idea who the author is)] [index]
IMPORTANT DNA PROPERTIES
(9) Base sequence (see also base sequence)
(a) The sequence of bases in a DNA molecule represent information
(b) This sequence is effectively unconstrained by the structure of the double helix
(c) As a consequence, much of the DNA in a chromosome (i.e., that which makes up genes) represents unique nucleotide sequences
(d) The rest consists of various repeated sequences which typically are species specific
(e) [base sequence (Google Search)] [index]
(10) Strand complementarity (see also strand complementarity)
(a) Because of base pairing and the making up of a double helix of DNA of two separate strands, there exists a redundancy of information carried by the double helix
(b) Note, however, that the two DNAs do not possess the same sequence
(c) Instead, each possesses the complementary sequence of the other
(d) Another way of saying this is that through base pairing one strand is capable of specifying the sequence of the other strand, and vice versa
(e) This sequence complementarity forms the basis of DNA-templated DNA polymerization (i.e., DNA replication)
(f) [strand complementarity (Google Search)] [index]
(11) 5' --> 3' polarity (see also 5' to 3' polarity)
(a) Recall that the sugars of nucleic acids are numbered with primes (i.e., 1' through 5')
(b) Recall additionally that the backbone of polymerized nucleic acids consists of the 3' through 5' carbons alternating with a covalently bonded phosphate group
(c) See Figure, Incorporation of a nucleotide into a DNA strand
(d) [5' 3' polarity (Google Search)] [index]
(12) Antiparallel strands (see also antiparallel)
(a) Recall additionally that the two DNA strands that make up a double helix are arranged antiparallel
(b) That is, starting from one end of the double helix, one strand runs in the 5' --> 3' direction while the other runs in the 3' --> 5' direction
(c) See Figure, The two strands of DNA are antiparallel
(d) This antiparallel nature of DNA impacts on DNA replication
(e) [antiparallel strands (Google Search)] [index]
DNA REPLICATION
(13) 5' --> 3' direction of synthesis (see also 5' to 3' direction)
(a) During DNA synthesis, incoming subunits arrive with phosphates
(b) They attach to the 3' -OH exposed at the end of the growing new strand
(c) This supplies the phosphate making up the sugar-phosphate backbone of DNA
(d) It also constrains the growth of the new DNA strand to the 5' to 3' direction
(e) That is, for each DNA molecule there exists a 5' end at which no synthesis is occurring (directly, anyway) and a 3' end at which synthesis may occur
(f) See Figure, Incorporation of a nucleotide into a DNA strand
(g) [5' 3' direction of synthesis (Google Search)] [index]
(14) Semiconservative DNA replication (see also semiconservative replication)
(a) The specific mechanism by which DNA is replicated is termed semiconservative
(b) Despite the long, confusing word used to describe it, this is actually the simplest mechanism by which template-dependent DNA replication might occur
(c) In short, semiconservative DNA replication consists of each strand of DNA in a double helix specifying the polymerization of a new strand which, in turn, remains attached (via base pairing) to its parent strand
(d) This parent-daughter strand forms a new double helix that consists of both a parental strand of DNA and a newly synthesized strand of DNA
(e) (note that above I am using the term "strand" synonymous to "single molecule of DNA", i.e., one-half of a double helix)
(f) NOTE THAT KNOWING THAT SEMICONSERVATIVE DNA REPLICATION IS HOW ORGANISMS REPLICATE THEIR DNA OR THAT THIS IS SIMPLEST OF THE POSSIBLE MEANS OF DNA REPLICATION IS NOT THE SAME THING AS UNDERSTANDING HOW SEMICONSERVATIVE DNA REPLICATION WORKS
(g) See Figure 16.7, A model for DNA replication: the basic concept
(h) [semiconservative DNA replication (Google Search)] [index]
(15) Nucleosides (see also nucleoside)
(a) The incoming subunit, in fact, does not carry just one phosphate
(b) Instead it carries three phosphates (i.e., their structure is analogous to that of ATP)
(c) Nucleosides that carry a single phosphate are called nucleotides and this is what remains following the addition of a nucleoside triphosphates to a growing DNA (or RNA) polymer
(d) The hydrolytic removal of two of these phosphates supplies the energy employed to attach the subunit to the 3' -OH of the growing DNA strand
(e) See Figure, Incorporation of a nucleotide into a DNA strand
(f) [nucleoside -HIV (Google Search)] [index]
SOME ENZYMES AND PROCESSES INVOLVED IN DNA REPLICATION
(16) DNA polymerase (see also DNA polymerase)
(a) The enzyme that catalyzes this template-directed conversion of nucleosides into an elongated DNA strand is called DNA polymerase
(b) Note that DNA polymerase can elongate a strand of DNA only in the 5' --> 3' direction
(c) See Figure, Incorporation of a nucleotide into a DNA strand
(d) See Figure, The two strands of DNA are antiparallel
(e) NOTE THAT REPLICATION DNA IS POLYMERIZED BY DNA POLYMERASE WHEREAS TRANSCRIPTION OF RNA (NEXT CHAPTER) IS POLYMERIZED BY RNA POLYMERASE
(f) [DNA polymerase (Google Search)] [index]
(17) RNA priming (see also RNA priming)
(a) DNA polymerase attaches new nucleotides with high fidelity (thus reducing errors)
(b) This high-fidelity nucleotide addition requires the existence of a 3' -OH
(c) This means that DNA polymerase cannot initiate DNA replication since, at the start of DNA replication, the to-be-synthesized DNA strand does not yet possess a 3' -OH (i.e., the strand does not yet exist)
(d) This problem of how to initiate DNA replication in the absence of a 3' -OH is solved by priming using RNA
(e) See Figure, Priming DNA synthesis with RNA
(f) [RNA priming (Google Search)] [index]
(18) Primase (see also primase)
(a) DNA replication is initiated with RNA by an enzyme called primase
(b) Primase can initiate template-directed polymerization without a 3' -OH
(c) Thus, DNA polymerase uses a RNA 3' -OH to initiate replication
(d) The RNA is then eventually replaced by DNA
(e) Note that replacing the RNA with DNA at the very ends of linear chromosomes is a problem because no matter what, the very end will never have a 3' -OH
(f) (this problem explains, at least in part, the problem of telomere erosion in eukaryotes)
(g) See Figure, Priming DNA synthesis with RNA
(h) [primase (Google Search)] [index]
(19) Origins of replication (see also origin of replication)
(a) One place that primase acts is at certain DNA sequences called origins of replication
(b) This is the site of priming of the leading strand of DNA replication
(c) See Figure: Origins of replication in eukaryotes
(d) [origins of replication (Google Search)] [index]
(20) Proofreading (see also proofreading)
(a) In addition to all of the above (and much not mentioned) another problem run into during DNA replication is that template directed replication is not sufficient to achieve the high fidelity of DNA replication that organisms achieve
(b) That is, the interaction between complementary bases is not precise enough to allow the level of DNA replication fidelity most organisms shoot for
(c) An additional level of fidelity is achieved by what is known as proofreading
(d) During DNA replication, the newly attached bases are checked to make sure they really are the correct, complementary bases
(e) Those that are not correctly paired are removed and replaced
(f) In prokaryotes this is yet another function of the DNA polymerase while eukaryotes (in all their complexity) use additional proteins
(g) RNA viruses, like HIV and influenza virus, by the way, do not employ proofreading and consequently possess much higher mutation rates than do most DNA-based organisms; this high mutation rate allows HIV (and influenza virus, etc.) to evolve maddeningly quickly
(h) [proofreading replication (Google Search)] [index]
REPLICATION FORK
(21) Replication fork (see also replication fork)
(a) One role of these replication origin proteins is to open up the double helix so that both strands are exposed as single-stranded DNA, i.e., as potential templates
(b) The local "bubble" created by this separation of strands about the origin is bordered at each end with a replication fork
(c) It is at these replication forks that the parent double helix is unwound and daughter DNA strands are synthesized, thus converting one double helix into two
(d) See Figure: Origins of replication in eukaryotes
(e) [replication fork (Google Search)] [index]
(22) The replication fork, a summary
(a) See Figure, A summary of DNA replication
(b) Note:
(ii) Single-stranded binding protein
(iii) Proofreading
(c) [replication fork (Google Search)] [index]
(23) Helicase (see also helicase)
(a) The enzyme that opens the replication fork is called helicase
(b) This name refers to the fact that the double helix is unwound (helically, get it?) at the replication fork
(c) [helicase (Google Search)] [index]
(24) Single-strand binding protein (see also single-strand binding protein)
(a) An unwound double helix is unstable
(b) To prevent the individual strands from reannealing prior to the synthesis of the new daughter strand, a protein is employed to stabilize the single-stranded DNA
(c) This protein is called single-strand binding protein
(d) [single strand binding protein (Google Search)] [index]
LEADING- VS. LAGGING-STRAND SYNTHESIS
(25) Leading strand (see also leading strand)
(a) Note that because of the antiparallel nature of the double helix, as the replication fork opens, for one DNA strand the opening occurs in the 3' --> 5' direction while for the other DNA strand the opening occurs in the 5' --> 3' direction
(b) See Figure, Synthesis of leading and lagging strands during DNA replication
(c) Note that both new daughter strands are laid down in a 5' --> 3' direction antiparallel to each template (parent) strand
(d) As a consequence, for only one daughter strand will the replication fork be opening such as to allow unimpeded 5' --> 3' synthesis
(e) This unimpeded strand is called the leading strand
(f) [leading strand (Google Search)] [index]
(26) Lagging strand (see also lagging strand)
(a) The other strand must be replicated in the direction leading away from the replication fork
(b) Consequently, the replication of this other strand is discontinuous
(c) Its replication must wait for the replication fork to sufficiently open up the DNA so that a reasonably large number of nucleotides are exposed (on the order of 100 to 1000, depending on system)
(d) Then, at the replication fork RNA synthesis must be primed, thus priming DNA synthesis which then proceeds in the 5' --> 3' direction
(e) At the other end DNA polymerase eventually (i.e., a fraction of a second later) bumps into the RNA from a previous priming
(f) This RNA is stripped away by the DNA polymerase and replaced with DNA
(g) The new segment of DNA is then ligated to the downstream DNA strand
(h) This represents the complex synthesis of the lagging strand
(i) See Figure, Synthesis of leading and lagging strands during DNA replication
(j) [lagging strand (Google Search)] [index]
(27) Okazaki fragments (see also Okazaki fragments)
(a) The fragments of DNA synthesized to make up the lagging strand are called Okazaki fragments for their discoverer
(b) [Okazaki fragment or fragments (Google Search)] [index]
(28) DNA ligase (see also DNA ligase)
(a) The enzyme that ligates together the Okazaki fragments is called DNA ligase
(b) [DNA ligase (Google Search)] [index]
(29) Telomeres (telomerase) (see also telomere and telomerase)
(a) The end of a linear chromosome presents an additional DNA replication problem: At the end of a chromosome RNA priming cannot supply a 3' -OH
(b) Why not? There is no sequence beyond the end of the chromosome to template the polymerization of the priming RNA sequence
(c) As a consequence, the ends of linear chromosomes tend to erode with every replication (i.e., the very ends aren't replicated so are lost, and this effect is cumulative so that each chromosomal replication results in a loss of additional DNA)
(d) To guard against this erosion, eukaryotes possess regions of DNA at the end of their chromosomes called telomeres that serve essentially as DNA-erosion buffers
(e) That is, the telomeres, which are otherwise not important for chromosome functioning, erode rather important parts (e.g., protein-coding regions)
(f) To replace eroded telomeres, eukaryotes employ an enzyme called telomerase
(g) Telomerase, however, is mostly found in cells that are immortal (e.g., germ line cells) or in the developing organism
(h) The absence of telomerase places an upper limit on how many times the cells in your body may divide, thus providing an additional level of protection against uncontrolled cell growth such as that seen with cancer
(i) See Figure, Telomeres and telomerase
(j) [telomere or telomeres, telomerase (Google Search)] [index]
(30) (Review transcription if you have time)
VOCABULARY
(31) Vocabulary [index]
(b) Base sequence
(c) Chargaff
(d) Chromosomes
(e) DNA ligase
(f) DNA polymerase
(g) Helicase
(h) Lagging strand
(i) Leading strand
(j) Nucleosides
(m) Primase
(n) Proofreading
(o) Replication fork
(p) RNA priming
(q) The replication fork, a summary
(r) Semiconservative DNA replication
(s) Single-strand binding protein
(u) Telomerase
(v) Telomeres
(w) 5' --> 3' direction of synthesis
(32) Practice questions [index]
(a) How does the fact that DNA is synthesized in a 5' to 3' direction impact on the synthesis of DNA at the replication fork?
(b) Name three types of protein (specific/actual names) normally found at replication forks?
(c) Show the reaction catalyzed by DNA polymerase, the reaction that results in DNA replication (i.e., nucleotide addition to the being-synthesized DNA strand). Be specific, showing all major chemical players (by name only is OK) including specifically (hint, hint, hint!) the relevant functional groups and to what they are attached (additionally, note that there are two reactants plus a number of products, only one of the latter, the obviously important product of DNA replication, must be included for you to achieve full credit for this modified question). Don't worry about the various accessory proteins also found at replication forks.
(d) What two roles do nucleosides play in DNA replication?
(e) Describe the direction in which DNA replication occurs (i.e., in which a growing DNA strand is lengthened).
(f) The process of checking newly attached bases during DNA replication, to make sure the correct base really was inserted, is called __________.
(g) Following the opening of the replication fork, the newly separated DNA strands are kept from interacting by what protein while they await replication (i.e., the passage of DNA polymerase)?
(h) What supplies the energy used to polymerize DNA during DNA replication?
(i) Diagram semiconservative DNA replication in a manner distinguishing this form of synthesis from, for example, conservative DNA replication. Limit your diagram to showing the parental double helix and the two resulting double helices, i.e., don't answer this question by drawing a replication fork. For example, draw the parental double helix like so:
(i) ╤╤╤╤╤╤╤╤╤╤
(ii) ╧╧╧╧╧╧╧╧╧╧
(j) What is the problem that is solved by the formation of Okazaki fragments?
(k) Explain what "strand complementarity" means with regard to the DNA double helix.
(l) What is the lagging strand during semiconservative DNA replication and why is it called that?
(m) Name three enzymes involved in DNA replication and describe what each does.
(n) What aspect of DNA replication makes it necessary for linear chromosomes to have telomeres?
(o) Viruses whose genomes consist of RNA (not DNA) tend to have high rates of mutation. This is because the fidelity of genome replication in these viruses is controlled solely by the physical interaction between nitrogenous bases. What aspect of nucleic acid replication is absent in these viruses, but is found in the much-higher fidelity replicating bacteria and eukaryotes?
(p) What is the function of single-strand binding protein? (binding to single-stranded DNA is not a sufficient answer)
(q) Why must DNA polymerase be capable of stripping RNA off of DNA strands?
(r) What is the name given to the site of priming of the leading strand of DNA replication?
(s) Name at least one substrate of the enzyme primase.
(t) Phosphates are attached to what carbon on nucleoside triphosphates?
(i) 1'
(ii) 2'
(iii) 3'
(iv) 4'
(v) 5'
(vi) none of the above
(u)
What is the significance of the
circled hydroxyl group? 
(v) What enzyme employed during replication most likely has the following substrates: DNA (serving as template), RNA nucleoside triphosphates (ATP, GTP, CTP, UTP), and a growing RNA polymer?
(i) Helicase
(ii) Primase
(iii) DNA polymerase
(iv) Ligase
(v) Single-strand binding protein
(w) What are origins of replication?
(x) For the lagging strand, which does not occur
(i) DNA is synthesized in the 3' to 5' direction
(ii) DNA is synthesized in the 5' to 3' direction
(iii) Okazaki fragments are found
(iv) Primase is employed
(v) RNA is stripped away
(y) In prokaryotes, which enzyme is responsible for proofreading?
(i) Single-strand binding protein
(ii) Helicase
(iii) Primase
(iv) DNA polymerase
(v) RNA polymerase
(z) In all cellular organisms what aspect of what molecule serves as the primary information storage molecule?
(aa) Name the hydroxyl group required for the addition of a new nucleotide to a growing strand of DNA.
(bb) The DNA molecules within a double helix are arranged antiparallel. How does this arrangement affect the actual process of semiconservative DNA replication?
(cc) An incoming subunit during DNA replication (a DNA polymerase substrate) carries how many phosphates?
(dd) What is the name of the enzyme primarily responsible for the synthesizing nucleotide subunits (from nucleoside triphosphates) into a strand of DNA?
(ee) In semiconservative DNA replication, what is another name for the strand that is synthesized continuously?
(ff) What does DNA ligase do?
(gg) Where are telomeres found?
(hh) What does it mean for a DNA strand to display 5' --> 3' polarity?
(ii) What does it mean for the DNA strands making up the double helix to be antiparallel?
(jj) The enzyme that catalyzes this template-directed conversion of nucleoside triphosphates into an elongated DNA strand is called ___________.
(kk) The enzyme primase supplies what specific functional group that is necessary for template-directed DNA synthesis?
(ll) Why does the lagging strand lag during DNA synthesis?
(mm) How is the instability of the unwound double helix avoided during semiconservative DNA replication?
(nn) During DNA replication, the newly attached bases are checked to make sure they really are the correct, complementary bases, and those that are not are removed and replaced. This process is called __________.
(oo) Where on chromosomes does telomerase act?
(pp) During DNA replication, the newly attached bases are checked to make sure they really are the correct, complementary bases. This process is known as __________.
(qq) During DNA replication, to prevent the strands of ssDNA, separated at the replication fork, from reannealing prior to the synthesis of the new daughter strand, a protein is employed that binds to these strands. That protein is called __________.
(rr) Matching: (a) DNA ligase, (b) DNA polymerase, (c) Helicase, (d) Primase. (use each only once)
(i) Does not require a 3' OH: __________
(ii) Links Okazaki fragments: __________
(iii) Responsible for removing RNA in prokaryotes: __________
(iv) Unwinds replication fork: __________
(ss) During what process is RNA is stripped away and replaced with DNA?
(tt) In what direction is the leading strand during DNA replication laid down?
(uu) (bonus) Draw an incoming nucleic acid monomer as employed by DNA polymerase to effect DNA replication. Note: indicate the nitrogenous base simply with a "G".
(vv) What is semiconservative DNA replication.
(33) Practice question answers [index]
(a) There is both a leading strand and a lagging strand, the former synthesizes DNA in the 5' to 3' direction continuously as the replication fork is opened while the latter is synthesized discontinuously as Okazaki fragments.
(b) primase, DNA polymerase, helicase, single-strand binding protein.
(c) nucleoside triphosphate + 3'-OH --[DNA polymerase]--> DNA strand with one additional nucleotide + residual phosphates.
(d) Nucleosides supply (i) the subunit and incoming phosphates as well as (ii) the chemical energy necessary to achieve polymerization of DNA by dehydration synthesis.
(e) 5' to 3' direction
(f) Proofreading
(g) single-strand binding protein
(h) the two additional phosphates attached to the incoming nucleoside triphosphates. Note that ATP is not a correct answer since ATP is a ribonucleotide and the question specifically asked about DNA replication.
(i) For example:
Semiconservative DNA replication:
╤╤╤╤╤╤╤╤╤╤ → ╤╤╤╤╤╤╤╤╤╤ + ┬┬┬┬┬┬┬┬┬┬
╧╧╧╧╧╧╧╧╧╧ ┴┴┴┴┴┴┴┴┴┴ ╧╧╧╧╧╧╧╧╧╧
Conservative DNA replication:
╤╤╤╤╤╤╤╤╤╤ → ╤╤╤╤╤╤╤╤╤ + ┬┬┬┬┬┬┬┬┬┬
╧╧╧╧╧╧╧╧╧╧ ╧╧╧╧╧╧╧╧╧ ┴┴┴┴┴┴┴┴┴┴
(j) the simultaneous, semiconservative synthesis of DNA templated by the two strands of unwound DNA occurs in the 5' --> 3' direction off of one strand but the replication fork opens in the 3' --> 5' direction for the other strand. To replicate DNA in this strand, DNA must be synthesized away from the opening replication fork. Synthesis in this direction can only occur until the DNA polymerase collides with already-synthesized DNA. The resulting fragment is termed an Okazaki fragment. The problem solved is the synthesis of this other-strand of DNA.
(k) It means that each strand of DNA making up a double helix can specify the nucleotide sequence of the other strand, i.e., is the complement of the other strand, but is not the same sequence as the other strand.
(l) the lagging strand is the replicating DNA that must be synthesized in the 3' --> 5' direction; this is accomplished not by polymerizing in the 3' to 5' direction but instead via the employment of Okazaki fragments synthesized essentially backward, i.e., in the 5' to 3' direction away from the opening replication fork
(m) DNA polymerase = template-directed DNA polymerization and proofreading, primase = templated-directed synthesis of the RNA primers of DNA replication, helicase = opening of the replication fork by unwinding the DNA, single stranded binding protein = stabilization of not-yet-replicated single stranded regions of DNA found at the opening replication fork.
(n) The requirement for RNA priming makes it impossible to replicate one strand at the end of a linear chromosome
(o) Proofreading
(p) Single-strand binding protein prevents the reannealing of complementary DNA strands, i.e., the reformation of the double helix once the replication fork has been opened
(q) On the lagging strand DNA polymerization is repeatedly primed by RNA and the completion of Okazaki fragments requires the removal of this RNA and its replacement of with DNA (DNA synthesis is then completed on the lagging strand with the action of DNA ligase)
(r) The site of priming of the leading strand is the origin of replication; in eukaryotes there is more than one origin of replication and therefore more than one leading strand
(s) Answers include: the DNA template, the RNA triphosphates, and the growing RNA primer
(t) (v) 5' carbon
(u) This is the 3' OH that is required for DNA polymerase catalyzed DNA replication
(v) (ii) Primase
(w) Origins of replication are DNA sequences at which primase acts to initiate DNA replication particularly of the leading strand
(x) (i) DNA is synthesized in the 3' to 5' direction
(y) (iv) DNA polymerase
(z) Nucleotide sequence of DNA
(aa) 3'
(bb) It means that one strand is replicated continuously (leading strand) while the other is replicated discontinuously (lagging strand; Okazaki fragments)
(cc) 3
(dd) DNA polymerase
(ee) Leading strand
(ff) DNA ligase repairs nicks in DNA, e.g., when RNA is excised on the lagging strand during semiconservative DNA replication and is replaced by DNA, one ends up with two adjacent strands of DNA that are then tied together using DNA ligase
(gg) Telomeres are found at the ends of eukaryote chromosomes
(hh) It means that DNA nucleotides are added onto the 3' hydroxyl group of a polynucleotide that begins with the 5' carbon of ribose at the other end (i.e., the end to which nucleotides are not added)
(ii) It means that the polynucleotides are arranged 5' --> 3' for one strand but 3' --> 5' for the other strand, moving in the same direction along a double helix
(jj) DNA polymerase
(kk) Primase supplies a 3' hydroxyl group to DNA polymerase
(ll) The lagging strand lags because DNA can synthesized continuously in the 5' --> 3' direction on only one of the two strands during semiconservative DNA replication; the other strand, the lagging strand, must be have its DNA synthesized in the 5' --> 3' direction in spurts as new template becomes available as the double helix is unwound at the replication fork
(mm) Single-stranded binding protein stabilizes the single-stranded DNA created upon the unwinding of the double helix
(nn) Proofreading
(oo) Telomerase acts at the end of chromosomes, adding telomeres
(pp) Proofreading
(qq) Single-strand binding protein
(rr) (i) (d) Primase, (ii) (a) DNA ligase, (iii) DNA polymerase, (iv) Helicase
(ss) DNA replication; bumping of DNA polymerase into already replicated Okazaki fragment, etc.
(tt) 5' --> 3' direction
(uu) There should be three phosphates attached to deoxyribose at the 5' carbon and a "G" attached at the 1' carbon
(vv) Semiconservative DNA replication refers to the laying down of newly synthesized DNA strands onto complementary template strands such that a single double helix gives rise to two double helices, each of which consists of parental strand and one daughter strand of DNA