Chapter 12: DNA Replication and Manipulation
Four Essential Components for PCR
1.Template DNA. At least one molecule of double-stranded DNA containing the region to be amplified serves as the template for amplification. 2.DNA polymerase. The enzyme DNA polymerase is used to replicate the DNA. 3.All four deoxynucleoside triphosphates. Deoxynucleoside triphosphates with the bases A, T, G, or C are needed as building blocks for the synthesis of new DNA strands. 4.Two primers. Two short sequences of single-stranded DNA are required for the DNA polymerase to start synthesis. Enough primer is added so that the number of primer DNA molecules is much greater than the number of template DNA molecules.
Denaturation
1st step for PCR; For proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive. For DNA, the separation of the two strands of the double helix. Denaturation occurs under extreme conditions of pH, salt concentration, and temperature.
Annealing
2nd Step for PCR: Also called hybridization. The act of two DNA strands coming together. Melting or denaturation is the opposite. The strands are held together by hydrogen bonds and aromatic stacking.
Replication Fork
A Y-shaped region on a replicating DNA molecule where the parental strands are being unwound and new strands are being synthesized
Southern Blot
A common technique for detecting specific DNA sequences in which restriction-enzyme fragments are separated electrophoretically, then denatured and transferred to a polymer sheet, which is incubated with a radioactive probe specific for the sequence of interest.
Lagging Strand
A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.
Probe
A labeled, single-stranded nucleic acid molecule used to find a specific gene, or other nucleotide sequence, within a mass of DNA. It hydrogen-bonds to the complementary sequence in the targeted DNA.
Polymerase Chain Reaction (PCR)
A method of producing thousands of copies (amplification) of DNA segment using the enzyme DNA polymerase
Donor DNA
A sample of DNA containing the gene of interest
Recombinant DNA
A section of DNA, often in the form of a plasmid, which is formed by joining DNA sections from two different sources.
Plasmid
A small ring of DNA that carries accessory genes separate from those of the bacterial chromosome
Proofreading
Ability of DNA polymerases to remove and replace incorrectly paired nucleotides in the course of replication.
Telomerase
An enzyme that catalyzes the lengthening of telomeres. The enzyme includes a molecule of RNA that serves as a template for new telomere segments.
DNA Polymerase
An enzyme that is a critical component of a large protein complex that carries out DNA replication. DNA polymerases exist in all organisms and are highly conserved, meaning that they vary little from one species to another because they carry out an essential function.
Helicase
An enzyme that untwists the double helix of DNA at the replication forks, separating the two strands and making them available as template strands.
Somatic Cells
Any cells in the body other than reproductive cells
Chain Terminator
Any three of the genetic code words that signal the end of a gene sentence. A terminator acts much like the period at the end of a sentence.
Restriction Enzymes
Cut DNA into shorter fragments in a predictable and controllable manner. Each recognizes a specific 4 to 6 base-pair nucleotide sequence
Telomere
DNA structure at the end of chromosomes, prevent loss of genes every time it duplicates
Sanger Sequencing
Dideoxynucleotides halt DNA polymerization at each base, generating sequences of various lengths that encompass the entire original sequence. Terminated fragments are electrophoresed and the original sequence can be deduced.
Single-stranded binding proteins
During DNA replication, molecules that line up along the unpaired DNA strands, holding them apart while the DNA strands serve as templates for the synthesis of complementary strands of DNA.
Dideoxynucleotides
Essentially the same as nucleotides except they contain a hydrogen group on the 3' carbon instead of a hydroxyl group (OH
Transgenic Organisms
Genetically modified organisms (GMOs)
Size
In gel electrophoresis, DNA fragments are separated based on their: how many adenine bases are in the fragment. sequence. size. charge. how many thymine bases are in the fragment.
Semiconservative Replication
Method of DNA replication in which parental strands separate, act as templates, and produce molecules of DNA with one parental DNA strand and one new DNA strand
Lagging
Okazaki fragments are found on the _________ strand of DNA. lagging Leading Both leading and lagging Parental
Gel Electrophoresis
Procedure used to separate and analyze DNA fragments by placing a mixture of DNA fragments at one end of a porous gel and applying an electrical voltage to the gel
Palindromic
Reads the same in both directions
recognize certain DNA sequences. Some of them will cut straight through; others will leave an overhang at both ends of the cut.
Restriction enzymes? recognize certain DNA sequences and will alternate between cutting straight through both strands of DNA and leaving some overhang at both ends. recognize certain DNA sequences and cut through the DNA, leaving some overhang at both ends. recognize certain DNA sequences. Some of them will cut straight through; others will leave an overhang at both ends of the cut. recognize certain DNA sequences and cut straight through both strands of DNA.
Oligonucleotides
Short nucleotide sequences that are used in PCR and as complementary genetic probes to identify specific gene sequences
Origin of Replication
Site where the replication of a DNA molecule begins, consisting of a specific sequence of nucleotides.
Okazaki Fragments
Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.
Germ Cells
Special cells used for reproduction. Produces gametes through meiosis.
Primer
Starter for DNA synthesis
Restriction Sites
The DNA sequence that is recognized by a restriction enzyme; the restriction enzyme cuts at this sequence, generating two DNA fragments
Template Strand
The DNA strand that provides the template for ordering the sequence of nucleotides in an RNA transcript.
Vector
The carrier of the donor fragment, and it must have the ability to be maintained in bacterial cells
Plasmid
The extrachromosomal DNA found in bacteria is called a: vector. plasmid. telomere. restriction enzyme.
Leading Strand
The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' 3' direction.
Daughter Strand
The newly made strand of DNA after DNA replication has occured
origin of replication
The point at which DNA synthesis is initiated is called the? primer. primase. start codon. replication fork. origin of replication.
RNA Primase
The primer is made by an RNA polymerase, which synthesizes a short piece of RNA complementary to the DNA template and does not require a primer.
Transformation
The recombinant DNA is mixed with bacteria that have been chemically coaxed into a physiological state in which they take up DNA from outside the cell. Having taken up the recombinant DNA, the bacterial cells are transferred into growth medium, where they multiply.
Replication Bubble
The region where two replication forks are in close proximity to eachother, producing a bubble in the replicating DNA
Extension
The solution is heated to the optimal temperature for DNA polymerase, and each primer is elongated (or "extended") by means of the deoxynucleoside triphosphates.
False
True or Fale Telomerase activity in stem cells is very low.
True
True or False A daughter strand of DNA produced during chromosome replication can be composed of leading and lagging strands from different replication bubbles.
True
True or False A transgenic organism is synonymous with a genetically modified organism, as both can contain recombinant DNA.
False
True or False DNA polymerase is the enzyme that separates the two strands of DNA during DNA replication.
True
True or False In circular DNA, the DNA molecule is not shortened during replication.
False
True or False In gel electrophoresis, DNA fragments migrate toward the negative pole of the electric field.
false
True or False In gel electrophoresis, DNA fragments migrate toward the negative pole of the electric field.
True
True or False One application of GMOs is to engineer mice that have particular diseases that scientists wish to study.
True
True or False PCR is the name of the reaction used to amplify specific sequences of DNA.
False
True or False Recombinant DNA only occurs when you take DNA from another organism and insert it into a bacterium.
False
True or False Restriction enzymes are an essential component of PCR.
False
True or False Stem cells located in the gastrointestinal tract would possess "inactive" telomerase compared to telomerase occurring in mature neurons of the brain.
True
True or False Telomerase is the name of the enzyme that replaces shortened telomeres.
False
True or False The first step of PCR is called annealing.
False
True or False The first step of PCR is called annealing?
False
True or False The semiconservative model of DNA replication means that each DNA strand consists of some newly synthesized DNA and some parental DNA.
False
True or False Transformation is the process where DNA is extracted from a plasmid.
True
True or False Synthesis of nucleic acids always occurs in the 5' → 3' direction
Stem Cells
Undifferentiated cells that can undergo an unlimited number of mitotic divisions and can differentiate into any of a large number of specialized cell types
to synthesize a strand of DNA using DNA as a template
What is the function of the enzyme DNA polymerase? to synthesize a strand of DNA using a polypeptide as a template to synthesize a strand of mRNA using DNA as a template to synthesize a polypeptide using DNA as a template to synthesize a strand of mRNA using mRNA as a template to synthesize a strand of DNA using DNA as a template
Helicase
What is the name of the enzyme that separates the two strands of DNA during replication? ligase topoisomerase helicase DNA polymerase primase
DNA fragments are joined together.
What is the result of DNA ligase's action? DNA is broken up at specific sites. DNA translation occurs. DNA fragments are joined together. DNA transcription occurs. DNA is condensed to chromosomes.
gel electrophoresis
What procedure is typically used after PCR is complete to make sure the amplification process worked properly? Sanger sequencing DNA Southern blot gel electrophoresis microarray RNA interference
The cell would eventually die as the DNA continued to shorten.
What would happen if telomerase stopped working? The cells would be able to divide indefinitely. cancer would result The cell would die immediately. The cell would eventually die as the DNA continued to shorten. None of the answer options is correct.
DNA Ligase
When the replacement is completed, the adjacent fragments are joined, or ligated, by the enzyme called DNA ligase.
They both involve complementary base pairing.
Which of the following do sticky ends and nucleic acid probes have in common? They both are used as gene vectors in genetic engineering. They both are produced by the action of restriction enzymes. They both involve complementary base pairing. They both are parts of RNA molecules.
Ligase
Which of the following enzymes is responsible for joining Okazaki fragments together? ligase topoisomerase helicase DNA polymerase primase
fish that "glow in the dark" and express fluorescent jellyfish proteins
Which of the following is an example of a transgenic organism? a patient who has received a heart valve from a pig a human infected with Hepatitis-C who "expresses" viral proteins a patient who has received a kidney transplant from a close relative a bacteria population in which a mutation conferring antibiotic resistance spontaneously arose fish that "glow in the dark" and express fluorescent jellyfish proteins
DNA Ligase
Which of the following is needed to form recombinant DNA? primase helicase Taq polymerase DNA ligase topoisomerase
Both strands get shortened at opposite ends during replication.
Which of the following is true regarding DNA replication? Only the leading strand gets shortened during replication. Only the lagging strand gets shortened during replication. Both strands get shortened at the same end during replication. Both strands get shortened at opposite ends during replication. Only the lagging strand gets shortened after every other round of replication.
because their DNA is circular so the DNA never shortens after replication
Which of the following reasons explains why bacteria can continually divide? because they are so simple because DNA replication is much quicker in bacteria than in eukaryotes because their DNA is circular so the DNA never shortens after replication because they have plasmids because they only have one chromosome
DNA polymerase can only add nucleotides to an existing chain, it cannot initiate synthesis of a new strand.
Why are primers needed for DNA replication? DNA polymerase can only add nucleotides to an existing chain, it cannot initiate synthesis of a new strand. The primers help with the proofreading function of DNA polymerase. A tiny amount of RNA is needed to tell the cell where genes are located. They help with the joining of Okazaki fragments. They help direct the placement of the telomeres.
They extend the life of cells because DNA is shortened every time it is replicated.
Why are telomeres a necessary component of linear chromosomes? They direct where DNA synthesis will begin. They fix mistakes that are made during DNA replication. They extend the life of cells because DNA is shortened every time it is replicated. They direct where DNA synthesis will end. None of the answer options is correct.
Topoisomerase II
Works upstream from the replication fork to relieve the stress on the double helix that results from its unwinding at the replication fork.
32
You run a PCR cycle for five cycles. Theoretically, how many copies of your sequence would you now have? 12 16 24 32 8
gel electrophoresis
_______ is a method for separation and analysis of macromolecules (DNA, RNA and proteins) and their fragments, based on their size and charge
Helicase
_______ moves outward from the origin of replication and breaks hydrogen bonds between DNA nucleotides. Helicase RNA primase DNA polymerase Topoisomerase II
DNA Polymerase
_______ requires both a template and an appropriately placed DNA 3' end to synthesize a nucleic acid. Topoisomerase II RNA primase Helicase DNA polymerase
RNA Primase
________ is the first enzyme to synthesize a nucleic acid at a replication fork. DNA polymerase RNA primase Topoisomerase II Helicase
Topoisomerase
_________ relieves the tension on the double helix during DNA replication. A RNA primer Topoisomerase Helicase DNA polymerase A single-stranded binding protein
False
true or false During DNA replication, the leading strand contains Okazaki fragments.