Biochemistry chapter 6

Question 1

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Answer 1

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Question 3

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What are DNA and RNA ?

Answer 3

Two chemically distinct forms of nucleic acids within eukaryotic cells. These are polymers with distinct roles that together create the molecules integral to life in all organism. * The bulk of DNA is found in chromosomes in the nucleus, although some is also present in the mitochondria and chloroplasts

Question 4

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How do ATP and ADP get their names ?

Answer 4

Adenine di- and tri- phosphate gain their name from the number of phosphate groups attached to the nucleoside adenosine. These are high - energy compounds because of the energy associated with the repulsion between closely associated negative charges on the phosphate groups. Nucleotides are the building blocks of DNA

Question 5

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What are the two families of nitrogen containing bases found in nucleotides ? What do they do and contain ?

Answer 5

Purines contain two rings in their structure. There is adenine (A) and guanine (G); both found in DNA and RNA also nucleic acids. Pyrmidines contain only one ring in their structure. It contains cytosine (C), thymine (T), and uracil (U); while cytosine is found in both DNA and RNA ; thymine is only found in DNA and uracil is only found in RNA

Question 6

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What is aromatic ? What are its rules ?

Answer 6

Aromatic describes any unusually stable ring system that adheres to the following rules * The compound is cyclic * The compound is planar * The compound is conjugated (has alternating single and multiple bonds or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring The compound has 4n + 2 (where N is any integer ) pi electrons. This is called Huckels rule Below represents a conjugated compound and huckels rule {{3 2 1.png}}{{3 2 0.png}}

Question 7

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What is Watson-Crick model ? Double helix ?

Answer 7

They are the founders of the three dimensional structure of DNA. They were able to deduce the double helical nature of DNA and propose specific base-pairing that would be the basis of a copying mechanism. * Double helix is a two linear polynucleotide chains of DNA that are wound together in a spiral orientation along a common axis. {{4 1 0.png}}

Question 8

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What is B-DNA and Z-DNA?

Answer 8

The double helix of most and the right handed part of DNA is the B-DNA and it makes a turn every 3.4 nm and contains about 10 bases within that span. If you look at the picture on the other flashcard of Watson and crick you will major and minor groove. Those are meant for protein binding. * Another form of DNA is the Z-DNA for that zigzag appearance; its left handed helix that has a turn every 4.6 nm and contains 12 bases within each turn.

Question 9

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What does it mean to be dentured ? What compounds are used to denture DNA ?

Answer 9

When the conditions of the double helix nature of the DNA disrupt hydrogen bonding and base-pairing, resulting in the “melting” of the double helix into two single strands that have separated from each other. Heat, alkaline pH, and chemicals like formaldehyde also urea are commonly used to denture DNA

Question 10

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How does the aromaticity of purines and pyrimidines underscore their genetic function ?

Answer 10

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

Question 11

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If a strand of RNA contained 15% cytosine , 15% adenine , and 35% guanine and 35% uracil, would this violate Chargaff’s rule ? Why or why not ?

Answer 11

This doesn’t violate the chargaffs rule. RNA is single stranded and thus the complimentary seen in DNA does not hold true. For single stranded RNA %C does not necessarily equal %G; %A doesn’t neccesarly equal %U

Question 12

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What are Histones ? Nucleosome ?

Answer 12

The DNA that makes up a chromosome is wound around a group of small basic proteins called Histones that form in to chromatin . Also there are five Histone proteins founds in eukaryotic cells. Two copies each of the Histone proteins H2A, H2B, H3 and H4 form a Histone core and about 200 base pairs of DNA are wrapped around this protein complex of what we call nucleosome.

Question 13

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What are nucleoproteins ?

Answer 13

Histones are one example of them. These are proteins that associate with DNA. Most other nucleoproteins are acid-soluble and tend to stimulate processes such as transcription.

Question 14

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What are centromeres ?

Answer 14

A region of DNA found in the center of chromosomes

Question 15

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What is heterochromatin and euchromatin ?

Answer 15

Heterochromatin is when a small percentage of chromatin remains compacted during interphase. * In contrast, the dispersed chromatin is the euchromatin

Question 16

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What happens to the density of chromatic packaging in heterochromatin and euchromatin ?

Answer 16

* For heterochromatin its dense * For euchtromatin its not dense ( uncondensed)

Question 17

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Under the appearance of light microscopy how does the heterochromatin and euchromatin look ?

Answer 17

Heterochromatin looks light * Euchchromatin looks dark

Question 18

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What is happening to heterochromatin and euchromatin during transcriptional activity ?

Answer 18

* Heterochromatin is silent * Euchromatin is active

Question 19

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What is Helicase ?

Answer 19

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

Question 20

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What are single-stranded DNA -binding proteins ?

Answer 20

Proteins that are required to hold the DNA strands apart. These proteins bind to the unraveled strand, preventing both the reassociation of the DNA strands and degradation of DNA by nucleases

Question 21

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What is supercoiling ? DNA gyrate(DNA topiomerase II) ?

Answer 21

A wrapping of DNA itself as its helical structure is pushed ever further toward the telomeres during replication; like an old phone wire being tangledTo alleviate the tangled stress and reduce the risk of strand breakage, the topiomerase II introduced negative supercoils.

Question 22

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What is the leading strand ? what is the lagging strand ? Okazaki fragments ?

Answer 22

Leading strand in each replication fork is the strand that is copied in a continuous fashion, in the same direction as the advancing replication fork. The parental strand will be read 3’ to 5’ and its complement will be synthesized in a 5’ to 3’ manner The lagging strand is the strand that is copied in a direction opposite the direction of the replication fork. On this side of the replication fork, the parental strand has 5’ to 3’ polarity. Because the DNA polymerase can only synthesize in the 5’ to 3’ direction from a 3’ to 5’ template, small strands are produced which is called Okazaki fragments.

Question 23

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What are telomeres ?

Answer 23

Located at the very tips of chromosome and consist of repetitive sequences with a G-C content ( you know) . This repetition means that telomeres can be slightly degraded between replication cycles without loss of function.

Question 24

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Between the leading strand and lagging strand, which is more prone to mutations ? why ?

Answer 24

The lagging strand is more prone to mutation 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.

Question 25

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What are Cancer cells ? Metastasis ?

Answer 25

Proliferate excessively because they are able divide without stimulation from other cells and are no longer subject to the normal controls on cell proliferation. Metastasis is when cancer cells are able to migrate by local invasion, a migration to distant tissues by the bloodstream or lymphatic system. Over time, cancer cells tend to accumulate mutations.

Question 26

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What are oncogenes ? proto-oncogenes ? Anti-oncogenes ?

Answer 26

Mutated genes that cause cancer, also encode cell cycle related proteins. * Before the genes are mutated * They normally function to stop tumor progression, if they are mutated this would result in the loss of tumor suppression activity and therefore promote cancer.

Question 27

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What is mismatch repair ?

Answer 27

This is when cells have machinery in the G2 phase of the cell cycle and the enzymes are encoded by genes MSH2 and MLH1, which detect and remove errors introduced in replication that were missed during the S phase of the cell cycle.

Question 28

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What is a nucleotide excision repair (NER) ? Excision endonuclease.?

Answer 28

Thymine dimers are eliminated from DNA from this mechanism which is a cut and patch process. * Makes nicks(small cuts) in the phosphodiester backbone of the damaged strand on both sides of the thymine dimer and removes the defective oligionucleotide, that’s the excision endonuclease

Question 29

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When it comes to DNA polymerase(proofreading), what is the phase of that cell cycle ? And what are the key enzymes/genes used ?

Answer 29

* S phase * DNA polymerase

Question 30

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When it comes to mismatch repair, what is the phase of the cell cycle ? And what are the key enzymes/genes used ?

Answer 30

* G2 * MSH2, MLH1(MutS and mutL in prokaryotes)

Question 31

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When it comes to nucleotide excision repair, what is the phase of the cell cycle ? and what are the enzymes/genes used ?

Answer 31

* G1,G2 * Excision endonuclease

Question 32

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When it comes to Base excision repair, what is the phase of the cell cycle ? And what are the key enzymes/genes used ?

Answer 32

* G1, G2 * Glycosylase, AP endonuclease

Question 33

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What is the key structural difference in the types of lesions( any localized abnormal structural change in a bodily part) corrected by nucleotide excision repair vs those corrected by base excision repair ?

Answer 33

* Nucleotide excision repair corrects lesions that are large enough to distort the double helix * Base excision repair corrects lesions that are small enough not to distort the double helix

Question 34

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What is Recombinant DNA ?

Answer 34

First and foremost recombinant means combining of genes or characters different from what they were in the parents. * Recombinant DNA is the technology that allows a DNA fragment from any source to be multiplied by either gene cloning or polymerase chain reaction (PCR) It provides a means of analyzing and altering genes and proteins. It also provides the reagents necessary for genetic testing, such as carrier detection (detecting heterozygote status for a particular disease ) and prenatal diagnosis of genetic diseases.

Question 35

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What are restriction enzymes (restriction endonucleases ) ?

Answer 35

Are enzymes that recognize specific double-stranded DNA sequences. These sequences are palindromic(reading backwards ), meaning that the 5’ to 3’ sequence of one strand is identical to 5’to 3’ strand sequence of the strand (in antiparallel orientation) .

Question 36

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What are DNA libraries ?

Answer 36

Large collections of known DNA sequences ; in sum, these sequences could equate to the genome of the organism.

Question 37

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What are Genomic libraries ? cDNA (complimentary DNA ) vs expression libraries ?

Answer 37

Genomic libraries contain large fragments of DNA and include both coding (exon) and noncoding (intros) regions of the genome. cDNA (complimentary DNA) libraries are constructed by reverse transcribing processed mRNA. cDNA lacks noncoding regions such as introns only and only includes the genes that are expressed in the tissue from which the mRNA was isolated. For that reason the libraries are sometimes called expression libraries.

Question 38

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What is hybridization ?

Answer 38

Joining of complimentary base pair sequences. This can be DNA-DNA recognition or DNA-RNA recognition. This technique uses two single-stranded sequences and is a vital part of polymerase chain reaction and southern blotting.

Question 39

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What is a polymerase chain reaction (PCR) ? What is it used for ?

Answer 39

A automated process that can produce millions of copies of a DNA sequence without amplifying the DNA in bacteria. * PCR is used to identify criminal suspects, familial relationships, and disease causing bacteria and viruses.

Question 40

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What is a southern blot ?

Answer 40

Used to detect the presence and quantity of various DNA strands in a sample. DNA is cut by restriction enzymes and then separated by gel electrophoresis.

Question 41

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What is Gene therapy ?

Answer 41

Offers potential cures for individuals with inherited diseases. Gene therapy is intended for diseases in which a given gene is mutated or inactive, giving rise to pathology. By transferring a normal copy of the gene into the affected tissues, the pathology should be fixed, essentially curing the individual.

Question 42

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When creating a DNA library, what are some of the advantages of genomic libraries ? What about cDNA libraries ?

Answer 42

* Genomic libraries include all of the DNA in an organism’s genome, including nonvoting regions. This may be useful for studying DNA in intros, centromeres or telomeres. * cDNA libraries include only expressed genes from a given tissue but can be used to express recombinant proteins or to perform gene therapy.

Question 43

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During DNA sequencing, why does the DNA polymer stop growing once a dideoxyribonucleotide is added ?

Answer 43

Dideoxyribonucleotide lacks the 3’ -OH that is required for DNA strand elongation(the addition of length). Thus once a dideoxyribonucleic is added to a growing DNA molecule, no more nucleotides can be added because dideoyribonucleotides have no 3’ -OH groups with which to form a bond.

Question 44

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What is DNA cloning ? Recombinant vector ?

Answer 44

A technique that can produce a large amount of a desired sequence. Often, the DNA to be cloned is present in a small quantity and is part of a heterogeneous mixture containing other DNA sequences. Cloning requires that the investigator ligate the DNA of interest into a piece of nucleic acid referred to as a vector forming a recombinant vector.