Chapter 6: DNA and Biotechnology Flashcards

Question

MCAT concept check DNA structure page 204 question 4 How does the aromaticity of purines and pyrimidines underscore their genetic function?

Answer 1

The aromaticity of nucleic acids make these compounds very stable and unreactive. Stability is important for storing genetic information and avoiding spontaneous mutations.

Answer 2

This does not violate Chargaff’s rule. RNA is single-stranded, and thus the complementarity seen in DNA does not hold true. For single-stranded RNA, percent C does not necessarily equal percent G; a does not necessarily equal percent U.

Answer 3

Over 6 billion

Answer 4

23 pairs of chromosomes for a total of 46 chromosomes. 23 from each parent.

Answer 5

Histones, chromatin.

Answer 6

Nucleosomes are composed of DNA wrapped around histone proteins.

Answer 7

Histones are one example of nucleoproteins (proteins that associate with DNA). Most other nucleoproteins are acid soluble in tend to stimulate processes, such as transcription.

Answer 8

A small percentage of the chromatin remains compacted during interphase and is referred to as heterochromatin. Heterochromatin often consists of DNA with highly repetitive sequences.

Answer 9

The dispersed chromatin during interphase is called euchromatin, which appears light under light microscopy. Chromatin contains genetically active DNA.

Answer 10

Heterochromatin is dark, dense, and silent. Euchromatin is light, uncondensed, and expressed.

Answer 11

DNA replication cannot extend all the way to the end of a chromosome. This will result in losing sequences and information with each round of replication. The solution to this is telomeres. A sequence of TTAGGG at the end of the DNA. The second function of telomeres: they “knot off” the end of chromosomes as they have a high G-C content. Recalling that G-C has three hydrogen bonds and A-T (or U) has only two.

Answer 12

Some of the sequence of telomeres is lost in each round of replication and can be replaced by the enzyme telomerase. Telomerase is more highly expressed in rapidly dividing cells.

Answer 13

Telomeres have a high content of guanine (TTAGGG). This makes a high content of guanine-cytosine pairing, which has three hydrogen bonds (adenine-tyrosine has two).

Answer 14

Centromeres are regions of DNA Found in the center of chromosomes. Centromeres are composed of heterochromatin, containing high content of guanine and cytosine.

Answer 15

The five histone proteins are: H1, H2A, H2B, H3 and H4. H1 is the only one not in the histone core. It is known as the “linker histone” and is the histone component that binds to the nucleosome core particle and plays a critical role in chromatin structure and DNA accessibilty.

Answer 16

High guanine and cytosine increases hydrogen bonding, making the association between DNA strands very strong at telomeres and centromeres.

Answer 17

About 3 billion base pairs (6 billion bases total)

Answer 18

The replisome or replication complex is a set of specialized proteins that assist the DNA polymerases.

Answer 19

The bacterial chromosome is a closed, double stranded, circular DNA molecule with the single origin of replication. Thus, there are two replication forks that move away from each other in opposite direction around the circle. The two replication forks eventually meet, resulting in the production of two identical, circular molecules of DNA. Eukaryotes replication must copy many more bases compared to prokaryoticic replication and is a slower process. Each eukaryotic chromosome contains one linear molecule of double stranded DNA having multiple origins of replication.

Answer 20

Helicase is the enzyme responsible for unwinding the DNA, generating two single-stranded template strands ahead of the polymerase.

Answer 21

Fluoroquinolones stops the bacteria from replicating its DNA and slows the infection. Fluoroquinolones are used for pneumonia and certain infections in the genitourinary system.

Answer 22

The genitourinary system (urogenital system) encompasses both urinary and reproductive systems.

Answer 23

Single stranded DNA binding proteins bind to the unraveled strand, preventing both the reassociated of the DNA strands and the degradation of DNA by nucleases.

Answer 24

A nuclease is an enzyme that cleaves the phosphodiester bonds between nucleotides in nucleic acids (DNA or RNA), acting like "molecular scissors" to break down these molecules.

Answer 25

Supercoiling occurs when coiling strain is applied to a strand of DNA as it unwinds during the replication process (by helicase). DNA topoisomerases introduce negative supercoils that counteract the supercoiling effect. They do so by working ahead of helicase, nicking one or both strands, relieving torsional pressure.

Answer 26

The parental strand serves as a template for the generation of new daughter strands. This is a semi conservative process because one parental strand is retained in each of the two resulting identical double stranded DNA.

Answer 27

DNA polymerases read the DNA template and synthesize the new daughter strands reading in the 3’ to 5’ direction. DNA polymerases therefor construct the strand in the 5’ to 3’ direction. The leading strand can be read immediately (3’ to 5’) and a continuous copy can be produced (5’ to 3’). The lagging strand introduces a complication. To overcome this, Okazaki fragments are made, which are short segments of DNA that are ligased together to eventually form a copy that is read in the 3’ to 5’ direction and built in the 5’ to 3’ direction.

Answer 28

The first step in DNA replication is to lay down an RNA primer. This allows a site for DNA polymerase to anchor onto to begin copying.

Answer 29

Primase synthesize a short primer, roughly 10 nucleotides long, in the 5’ to 3’ direction to start replication on each strand. These short RNA sequences are constantly being added to the lagging strand because each Okazaki fragment must start with new primer. The leading strand requires only one primer, in theory.

Answer 30

DNA polymerase READING direction is 3’-5’. Synthesis, repair, transcription, and translation occur 5’-3’.

Answer 31

DNA polymerase cannot complete synthesis of the 5’ end of the strand. Every time the DNA synthesis is carried out, chromosomes become a little shorter. This is why telomeres (high GC content TTAGGG)

Answer 32

The lagging strand is more prone to mutations because it must constantly start and stop the process of DNA replication. Additionally, it contains many more RNA primers, all of which must be removed and filled in with DNA.

Answer 33

Telomeres are the ends of eukaryotic chromosomes and contain repetitive sequences of non-coding DNA. Telomeres protect the chromosome from losing important genes from the incomplete replication of the 5’ end of the DNA strand.

Answer 34

There is no need for telomeres in the prokaryotic genome as there are no ends of DNA to protect (their DNA is circular).

Answer 35

Oncogenes promote the cell cycle while mutated tumor suppressors can no longer slow the cell cycle. Oncogenes are like an accelerator. Mutated tumor suppressor is cutting the brakes.

Answer 36

Oncogenes are mutated genes that cause cancer. Proto-oncogenes are oncogenes before they are mutated. Oncogenes primarily encode cell cycle related proteins. The abnormal alleles encode proteins that are more active than normal proteins, promoting rapid cell cycle advancement. A mutation and only one copy is sufficient to promote tumor growth and is therefore considered dominant. The first discovered was src (named after sarcoma, a category of connective tissue cancers).

Answer 37

Tumor suppressor genes, like p53 or Rb (retinoblastoma), encode proteins that inhibit the cell cycle or participate in DNA repair processes. They function to stop tumor progression, so they are sometimes referred to as antioncogenes. The loss of tumor suppression activity promotes cancer. In activation of both alleles is necessary for the loss of function even one copy of the normal protein can function to inhibit tumor formation. Multiple mutations are required. They are considered recessive.

Answer 38

Incorrectly paired bases produce unstable hydrogen bonds which can be detected by DNA polymerase. DNA polymerase can also detect the level of methylation to determine which is the correct strand: the parent strand has more methylation. Closing of the gaps with DNA ligase lacks proofreading, creating a higher likelihood for mutation on the lagging strand.

Answer 39

In G2 phase of the cell cycle, there are genes that encode for enzymes which detect and remove errors introduced in replication (during S phase). This is called mismatch repair. MSH2, MLH1 in euk. MutS and MutL in prok.

Answer 40

Thymine residues can form dimers when exposed to ultraviolet light, called thymine dimers, which distort the shape of the DNA. NER repairs this by cutting and patching. The bulge is recognized. Excision endonuclease removes the oligonucleotide, DNA polymerase fills the gap in 5’-3’ direction (reading in the 3’-5’ direction). G1 and G2 phase.

Answer 41

BER are detection systems for small, non helical deforming mutations. ONLY REMOVES THE BASE. Example. Cytosine can reanimate to uracil via thermal energy. Uracil does not belong in DNA. Detected then removed by glycosylase enzyme which creates apurinic/apyrimidinic (AP) site because glycosylase only removed the base. (Also called an abasic site). AP endonuclease replaced with proper base. BER do not hydrolyze the sugar phosphate backbone, they replace the bases attached to them to create AP sites (abasic sites).

Answer 42

Oncogene accelerates cell growth and division, tumor suppressor gene mutations is like cutting the brakes.

Answer 43

The parent strand is more heavily methylated.

Answer 44

Allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR).

Answer 45

DNA cloning produces a large amount of a desired sequence. Mutate DNA of interest forming a recombinant vector (usually bacterial or viral plasma that can be transferred to a host bacterium after insertion of the DNA of interest) Isolate a colony containing the recombinant vector. Dabble in a gene for antibiotic resistance, so that the antibiotics can then kill off all of the colonies that do not contain the recombinant vector. Grow the colony in large quantities. Restriction enzymes (restriction endonucleases) recognize specific double strand DNA sequences (which are palindromic and can therefore be excised as a double stranded unit)

Answer 46

Exon are coding Intron are non coding

Answer 47

Genomic libraries contain large fragments of DNA and include both coding (exon) and non-coding regions (intron) of the genome.

Answer 48

Expression libraries are cDNA libraries that only contain exon (or coding) genes. cDNA is complimentary DNA of an mRNA sequence.

Answer 49

Hybridization is the joining of complementary base pair sequences.

Answer 50

PCR is an automated process that can produce millions of copies of DNA sequences without amplifying the DNA in bacteria. During the process of polymerase chain reaction, the DNA of interest is denatured, replicated, and then cool to allow reannealing of the daughter strands with the parent strands. Every time this process is repeated it doubles the amount of DNA until enough copies of the DNA sequence are available for further testing. PCR requires primers that are complementary to the DNA that flank the region of interest. Primers have a high GC content for stability. The process requires heat, so DNA polymerase from Thermus aquaticus is used.

Answer 51

DNA is negatively charged, so will be attracted to the anode. Agarose gel is used (rather than polyacrylamide gel) The longer the strand, the slower it will migrate.

Answer 52

Performed with gel electrophoresis, southern blotting is used to detect the presence and quantity of various DNA strands in a sample. Southern blotting is a molecular biology technique to detect specific DNA sequences by transferring DNA fragments from a gel onto a membrane and then probing with a labeled DNA sequence.

Answer 53

Dideoxyribonucleotides contain a H at C-3 rather than a hydroxyl group, and when added to a sequence, DNA polymerase can no longer add to the chain.

Answer 54

Gene therapy is intended for disease diseases in which a given gene is mutated or inactive, giving rise to pathology. By transferring a normal copy of the gene into the effective tissues, the pathology should be fixed, essentially curing the individual. Image shows a model therapeutic human gene therapy using retrovirus as a vector (retroviral gene therapy).

Answer 55

Once DNA has been isolated, it can be introduced into eukaryotic cells. Transgenic mice are altered at their germline by introducing a clone gene into fertilized over or into embryonic stem cells. The cloned gene that is introduced is referred to as a transgene. If the transgene is a disease producing allele, the transgenic mice can be used to study the disease process. Knock out mice are where a gene has been intentionally deleted.

Answer 56

Transgenic and knockout mice approach is useful for studying dominant gene effects because the number of copies of the gene that insert into the genome cannot be controlled; the transgenic mice may each contain a different number of copies of the transgene.

Answer 57

Using embryonic stem cells for developing transgenic mice can create chimeras. Cloned genes are introduced into cultures, and one can select for cells with the transgene successfully inserted. These altered stem cells are injected into developing blastocyst and implanted into surrogates. The blastocyst itself is thus composed of two types of stem cells: the ones containing the transgene and the original blastocyst that lack the transgene: this is a chimera. This property can be readily apparent (spotting fur for example) allowing for easy identification of the chimera. Breed these to produce mice that are heterozygote and homozygous for a transgene.

Answer 58

The negative charge in DNA is primarily due to the phosphate groups in the sugar-phosphate backbone, and this backbone has a directionality, with the 5' end having a free phosphate group and the 3' end having a free hydroxyl group

Answer 59

No, prokaryotes, such as bacteria, do not have nucleosomes, which are the basic units of DNA packaging in eukaryotes, because they lack the histone proteins that form nucleosomes.

Chapter 6: DNA and Biotechnology Flashcards

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