Chapter 6 Flashcards

Question

What are centromeres made of?

Answer 1

They are made of double standard constitutive heterochromatin.

Answer 2

They are the middle region of a chromosome to which the microtubules attach. They are responsible for aiding in the binding of the kinetochore during mitosis and meiosis.

Answer 3

Single copy DNA are sequences that don’t repeat and hold the organisms genetic information, present in euchromatin, have a low mutation rate, found in exons Repetitive DNA are sequences that repeat, which are found near centromere’s and telomeres, they don’t contain genes, and have a high mutation rate, they are found in introns

Answer 4

It is the DNA strand that is synthesized continuously away from the origin, towards the replication fork.

Answer 5

It is synthesized in Okazaki fragments towards the origin, away from the replication fork.

Answer 6

After RNA primer removal, it seals the nick by catalyzing the formation of a phosphodiester bond to join Okazaki fragments.

Answer 7

At the start of initiation, DNA A binds to the 9-mer sequence region, inducing stress or super coiling upon the DNA, and forcing the unwinding/denaturation of the 13-mer region to form an open complex. 13-mer region is AT-rich.

Answer 8

DNA B is carried to the 13-mer region to use energy to break H bonds and separate the double stranded helix.

Answer 9

The only function that DNA C serves is to carry helicase to the 13-mer region.

Answer 10

After helicase unzips the double helix, SSBs bind to the two separated strands to prevent the DNA from reannealing.

Answer 11

Ahead of the replication fork, topoisomerase alleviates the supercoiling of the DNA by nicking one or both strands and resealing the cuts right away.

Answer 12

G1 and G2 phases.

Answer 13

They are mutated genes that cause cancer, typically only one copy of the allele is sufficient to promote cancer. Oncogenes are dominant.

Answer 14

This is the name for oncogenes before they are mutated.

Answer 15

They are genes that inhibit the cell cycle and growth. Their main function is to stop tumor progression so mutations in both copies of the allele would be needed for a complete loss of function, and to cause cancer.

Answer 16

It is a tumor suppressor gene. It is the most commonly mutated gene in cancer cells.

Answer 17

It synthesizes a short strand of RNA, that acts as a primer for DNA polymerase III.

Answer 18

It is a multi-protein holoenzyme complex, which begins synthesis of the daughter DNA strand in the 5’ to 3’ direction. Note that it reads the template strand in a 3’ to 5’ direction.

Answer 19

The main function is to initiate synthesis of a DNA strand. It delivers primase and accessory proteins to the origin of replication.

Answer 20

It has 5’ to 3’ exonuclease and polymerase activity. It removes the RNA primer, and then fills the gap by adding DNA nucleotides to the 3’ end preceding the primer.

Answer 21

Linear, many

Answer 22

Circular, one

Answer 23

In eukaryotic DNA replication, DNA polymerase alpha synthesizes the RNA primer. In prokaryotic DNA replication, primase synthesizes the RNA primer .

Answer 24

In eukaryotic DNA replication the RNA primer is removed by RNAase H. In prokaryotic DNA replication the RNA primer is removed by DNA polymerase I.

Answer 25

In eukaryotic, DNA replication, DNA polymerases Alpha, Delta, and Epsilon synthesize the DNA strands. In prokaryotic DNA replication, DNA polymerase III synthesizes the DNA strands .

Answer 26

DNA polymerase Delta adds the DNA nucleotides to the gaps where the RNA primer was removed.

Answer 27

After one round of DNA replication, each double strand contains one side that is the parental strand and the other side that is the daughter strand. After two rounds of DNA replication, there are four double strands. Two of the double strands contain only daughter genetic material. The two other strands contain half parental strand and half daughter strand genetic material.

Answer 28

Based on semiconservative method of DNA replication, after 2 rounds of division some bacteria will only contain 14N daughter DNA (genome mass 5.4 fg) and some others will contain half 14N daughter DNA and half 15N parental DNA (take AVERAGE mass: 5.45 fg).

Answer 29

It can occur if DNA is exposed to high UV radiation, causing adjacent thymine bases to dimerize creating a kink in the sequence.

Answer 30

This type of repair occurs if a base such as cytosine is converted to uracil due to radiation exposure.

Answer 31

First excision endonuclease recognizes the bulb in the sequence, and makes nicks in the phosphodiester backbone on both sides of the bulb of the damaged strand. The damaged region is removed and DNA polymerase synthesizes new nucleotides to fill in the gap, using the undamaged strand as a template. Lastly, DNA ligase seals the nick in the strand.

Answer 32

A glycosylated enzyme recognizes the mutated base and excises it without breaking the phosphodiester backbone. This leaves an abasic site or AP site, which is recognized by AP endonuclease, which removes the rest of the affected backbone. Then DNA polymerase fills in the gap by synthesizing, the DNA nucleotides using the undamaged strand . Lastly, DNA ligase seals the strand by catalyzing a phosphodiester bond.

Answer 33

It utilizes modified virus vectors that insert their own genetic material into human DNA, thus exposing the individual to the desired copy of the gene that will help cure the target disease. Basically, the modified virus is used as a mode of delivery of the target gene.

Answer 34

It is a gene which has been intentionally deleted in an organism often to find out the function of that specific gene.

Answer 35

It is a method used to compare the genomics similarities between two separate DNA fragments.

Answer 36

You denature both double stranded DNA samples, and then mix a single DNA strand from one sample with another single DNA strand from the second sample to produce a hybrid. The stronger the hybrid double-stranded DNA is, the more complementary base pairing occurred, which means that the two sample sequences were more similar to each other than different.

Answer 37

It is used to detect the presence, and quantity of a desired DNA sequence in a sample.

Answer 38

First, you cut the DNA sample with restriction enzymes, and then the fragments are separated by a gel electrophoresis. The separated fragments are transferred to a filter membrane, retaining the separation. Then radial labeled DNA probes with the desired complementary sequence, or added to the filter, which promotes binding to the target sequence of the DNA strand.

Answer 39

In the test tube, you need your target DNA strand, two short single stranded primers that are complementary to the 3’ ends of the template & coding strand, deoxyribonucleotides, and Taq DNA polymerase.

Answer 40

DNA libraries are large collections of known DNA sequences, which consist of either genomic DNA or cDNA.

Answer 41

They are large collections which contain the entire genome of an organism, including both the coding and non-coding regions of the genome. They are constructed by restriction enzyme endonuclease, and DNA ligase via cloning.

Answer 42

They are large collections, which contain only the coding regions of the organism’s genome. They are constructed by the enzyme reverse transcriptase, which reverse transcribes the mRNA into cDNA. cDNA libraries are used to sequence specific genes, produce recombinant proteins, or produce transgenic animals.

Answer 43

They are proteins from bacteria that cut DNA at specific sequences that are usually 4 to 8 base pairs long. The sequences are called a palindrome (they read the same no matter the direction that you read them).

Answer 44

They cut either in the middle leaving blunt ends or off the center, leaving overhangs called sticky ends. These sticky ends can either be 5’ or 3’.

Answer 45

A plasmid is a small and circular extra chromosomal piece of DNA naturally found in bacteria.

Answer 46

We can insert the recombinant gene into a plasmid downstream of an inducible promoter that is able to produce large quantities of the protein only when we want the gene expressed. This plasmid often contains antibiotic resistance, so that when large quantities of the plasmid are produced in bacterial colonies and an antibiotic is introduced, the vectors that don’t contain this antibiotic resistance can be killed off.

Answer 47

You cut the foreign DNA which is your target gene with a restriction enzyme, and you use the same restriction enzyme to cut the plasmid. This allows the DNA fragment to directly fit into the plasmid. Next you introduce DNA ligase which seals the nicks in the sugar phosphate backbone.

Answer 48

Target gene/DNA is micro injected into an egg cell/ova which is then implanted into a surrogate which produces all offspring with the target gene. (Homozygous transgenic offspring)

Answer 49

Transgenic, embryonic stem cells are created by micro injecting your target gene into the embryonic stem cells. These transgenic stem cells are then microinjected into a developing blastocyte. This blastocyst is injected into a surrogate who is able to produce chimera offspring which have germs lines derived from two cell lineages (one from transgenic cells & other from host blastocyst). Phenotypically, this shows on mice having patchy coats of two colors.

Answer 50

Adenine paired with thymine

Answer 51

Adenine paired with thymine

Answer 52

It is a type of DNA that forms a left-handed double helix. This is the opposite of B-DNA which makes up the human genome.

Answer 53

True, daughter strands contain the same ratio of bases as the parent strand with the exception of a few nucleotides due to DNA polymerase not being able to synthesize all the way to the end of the strand. This cause shortening of telomeres, but doesn’t harm the actual gene coding regions.

Answer 54

Sliding clamp is a protein that helps keep the DNA polymerase tightly associated with the strand.

Answer 55

1. Run through a gel electrophoresis 2. Transferred to a membrane where the RNA retains separation 3. Hybridization with a labeled complementary RNA probe

Answer 56

1. Extract proteins and put run them through a gel electrophoresis 2. Take them off the gel with the separation still intact and transfer them to a protein binding membrane such as nitrocellulose. 3. Once proteins have transferred(stuck) to the nitrocellulose membrane, you wash it with PBS. 4. Then add a blocking buffer solution whose purpose is to bind all the antibodies on the surface of the proteins non specifically. Wash again with PBS. 5. Now, add the primary antibody for your protein target which will compete with the blocking buffer and bind directly to specific protein antigens only. 6. Lastly, add secondary antibodies which are fluorescently labeled. This allows multiple secondary antibodies to bind to the primary antibody and cause signal amplification producing a brighter spot.