CHAPTER 16 OBJECTIVES
-List the three components of a nucleotide.
A phosphate, a sugar and a base.
-Distinguish between deoxyribose and ribose.
Deoxyribose and Ribose are both five-carbon sugar components that alternate with phosphate groups to form the backbone of the polymer and bind to the nitrogenous bases. However, deoxyribose is present in DNA whereas ribose is found in RNA.
-List the nitrogen bases found in DNA, and distinguish between pyrimidine and purine.
Adenine, Guanine, Thymine and Cytosine. Purine include Adenine and Guanine whereas pyrimidine include Thymine and Cytosine.
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-Explain the "base-pairing rule" and describe its significance.
The base-pairing rule says explains that A must pair with T and that G pairs with C. It is significant because it explains Chargaff’s rule, it suggests the general mechanisms for DNA replication. If bases of specific pairs, the information on one strand compliments the other, it dictates the combination of complementary base pairs, but places restriction on the linear sequence of nucleotides along the length of a DNA strand. The sequence of the bases can be highly variable, which makes it suitable for coding genetic information. Also, though hydrogen bonds between paired bases are weak bonds, collectively they stabilize the DNA molecule.
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-Describe the structure of DNA, and explain what kind of chemical bond connects the nucleotides of each strand and what type of bond holds the two strands together.
DNA is a helix with a uniform width of 2 nm. This width suggested that it had two strands. Purine and pyramidine bases are stacked .34 nm apart. The helix makes one full turn every 3.4 nm along its length. There are ten layers of nitrogenous base pairs in each turn of the helix. Enzymes link the nucleotides together at their sugar-phosphate groups. Hydrogen bonds hold the bases together.
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-Explain, in your own words, semiconservative replication
Watson and Crick’s model is a semiconservative model for DNA replication. They predicted that when a double helix replicates, each of the two daughter molecules will have one old or conserved strand from the parent molecule and one newly created strand.
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-Describe the process of DNA replication, and explain the role of helicase, single strand binding protein, DNA polymerase, ligase, and primase.
DNA replication begins at special sites called origins of replication that have a specific sequence of nucleotides. Specific proteins required to initiate replication bind to each origin. The DNA double helix opens at the origin and replication forks spread in both directions away from the central initiation point creating a replication bubble. Then, new nucleotides align themselves along the templates of the old DNA strands. DNA polymerase links the nucleotides to the growing strands. Exergonic hydrolysis of the phosphate bond drives the endergonic synthess of DNA and provides the required energy to from the new covalent linkages between the neucleotides. Helicases are enzymes which catalyze unwinding fo the parental double helix to expose the template.Ligase and primase are enzymes that play an important role in the replication of DNA.
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-Define antiparallel
The sugar phosphate backbones of the two complementary DNA strands run in opposite directions; that is, they are antiparallel.
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-Distinguish between the leading strand and the lagging strand.
The leading strand is the DNA strand which is synthesized as a single polymer in the 5’ -> 3’ direction towards the replication fork. The lagging strand is the DNA strand that is discontinuously synthesized against the overall direction of replication.
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-Explain how the lagging strand is synthesized when DNA polymerase can add nucleotides only to the 3’ end.
Lagging strand is produced as a series of short segments called Okazaki fragments, which are each synthesized in the 5’ -> 3’ direction. Okazaki fragments are 1000 to 2000 nucleotides long in bacteria and 100 to 200 nucleotides lon in eukaryotes. The many fragments ligated by DNA ligase , a linking enzyme that catalyzes the formation of a covalent bond between the 3’ end of each new Okazaki fragment to the 5’ end of the growing chain.
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-Explain the role of DNA polymerase, ligase, and repair enzymes in DNA proofreading and repair.
If a segment of DNA becomes damaged, excision repair can help. The damaged segment is excised by one repair enzyme and the remainding gap is filled in by base-pairing nucleotides with the undamaged strand. DNA polymerase and DNA ligase are enzymes that catalyze the filling in process.
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CHAPTER 17 OBJECTIVES
-Explain how RNA differs from DNA.
Ribonucleic acid (RNA) links DNA’s genetic instructions for making proteins to the process of protein synthesis. It copies or transcribes the message from DNA and then translates that message into a protein RNA, like DNA, is a nucleic acid or a polymer of nucleotides. RNA structure differs from DNA in the following ways: the five carbon sugar in RNA nucleotides is ribose rather than deoxyribose and the nitrogenous base uracil is found in place of thymine.
-In your own words, briefly explain how information flows from gene to protein.
Information flows from gene to protein through two major processes, transcription and translation. Transcription is the synthesis of RNA using DNA as a template. A gene’s unique nucleotide sequence is transcribed from DNA to a complementary nucleotide sequence in mRNA. The resulting mRNA carries this transcript of protein building instructions to the cell’s protein synthesizing machinery. Translation is the synthesis of a polypeptide, which occurs under the direction of mRNA.
-Distinguish between transcription and translation.
Transcription- The transfer of information from DNA molecule into an RNA molecule. Translation- The transfer of information from an RNA molecule into a polypeptide, involving a change of language from nucleic acids to amino acids.
-Describe where transcription and translation occur in prokaryotes and in eukaryotes.
In Prokaryotes, both transcription and translation occur in the cytoplasm. On the other hand, in Eukaryotes, Transcription occurs in the nucleus and translation in the cytoplasm.
-Define codon, and explain what relationship exists between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide.
A codon is a three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code. For each 3 letters it equals an amino acid. It consists of three bases coding for 61 amino acids.
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-Explain the process of transcription including the three major steps of initiation, elongation, and termination.
Initiation- The RNA polmerses attaches to promoter regions on the DNA and begins to unzip the DNA into two strands. A promoter region for mRNA transcriptions contains the sequence T-A-T-A (called TATA Box). Elongation- Occurs as the RNA polymerase unzips the DNA and assembles RNA nucleotides using one strand of the DNA as a template. As in DNA replication, elongation of the RNA molecules occurs in the 5’ à 3’ direction. In contrast to DNA replication, new nucleotides are RNA nucleotides (rather than DNA nucleotides), and only one DNA strand is transcribed. Termination- Occurs when the RNA polymerase reaches a special sequence of nucleotides that serve as a termination point. In eukaryotes, the termination region often contains the DNA sequence AAAAAAA
-Describe the general role of RNA polymerase in transcription.
It pry the two strands of DNA apart and hook together the RNA nucleotides as they base-pair along the DNA template
-Distinguish among mRNA, tRNA, and rRNA.
mRNA (Messenger RNA)- Is a single strand of RNA that provides the template used for sequencing amino acids into a polypeptide.tRNA (Transfer RNA)- Is a short RNA molecule (consisting of about 80 nucleotides) that is used for transporting amino acids to their proper place on the mRNA template.rRNA (Ribosomal RNA)- Nolecules are the building blocks of ribosomes. The nucleolus is an assemblage of DNA actively being transcribed into rRNA
-Describe the structure of tRNA and explain how the structure is related to function.
Interactions among various parts of the tRNA molecules reslt in base-pairings between nucleotides, folding the tRNA in such a way that it forms a three-dementional molecule. (In two dimensions, a tRNA resembles the three the three-leaflets of a clover leaf.) The 3’ end of the mRNA. Exact base-paring between the third nucleotides of the tRNA anticodons and the third nucleotide of the mRNA codon is often not required. This “wobble” allows the anticodon of some tRNAs to base-pair with more than one kind of codon. As a result, about 45 different tRNAs base-pair with 64 different codons.
-Given a sequence of bases in DNA, predict the corresponding codons transcribed on mRNA and the corresponding anticodons of tRNA.
AAA GTA CTC ATG GAT
CCC UGC AGA CGU UCG
Proline Cysteine Arginine Leucine Serine
-Describe the structure of a ribosome, and explain how this structure relates to function.
Ribosomes have three binding sites—one for the mRNA, one for a tRNA that carries a growing polypeptide chain (P site, for “polypeptide), and one for a second tRNA that delivers that next amino acid that will be inserted into the growing polypeptide chain (A site, for “amino acid”)
-Describe the difference between prokaryotic and eukaryotic mRNA.
Prokaryotic: mRNA is produced by transcription. Eukaryotic: First it produces Pre-mRNA, and then develops mRNA, but it later has to go from the nucleus to the cytoplasm
-Explain how eukaryotic mRNA is processed before it leaves the nucleus.
mRNA must be translocated from nucleus to cytoplasm
CHAPTER 18
-List and describe structural components of viruses.
Viral Genomes- Their genomes may consist of double stranded DNA, single stranded DNA, double stranded RNA, or single stranded RNA. Capsids and Envelopes- The protein shell that encloses the viral genome is called a capsid. They are built from a large number of protein subunits called capsomeres. Influenza viruses, and many other viruses found in animals, have viral envelopes, membranes cloaking their capsids. They are derived from membrane of the host cell.
-Explain why viruses are obligate parasites.
Viruses are obligate intracellular parasites; they can only reproduce within a host cell. An isolated virus is unable to replicate itself- or do anything else, for that matter, except infect an appropriate host cell.
-Explain the role of reverse transcriptase in retroviruses.
Retro viruses are equipped with a unique enzyme called reverse transcriptase, which can transcribe DNA from an RNA template, providing an RNA – DNA information flow.
-Describe how viruses recognize host cells.
Viruses identify their host cells by a “lock-and-key” fit between proteins on the outside of the virus and specific receptor molecules on the surface of the cell.
-Distinguish between lytic and lysogenic reproductive cycles using phage T4 and phage l as examples.
A reproduction cycle of a virus that culminates in death of the host cell is known as a lytic cycle. It begins when the tail fibers of a T4 virus stick to specific receptor sites on the outer surface of an E.coli cell. The sheath of the tail then contracts, thrusting a hollow core through the wall and membrane of the cell. The phage injects its DNA into the cell, leaving an empty capsid as a “ghost” outside the cell. Once infected, the E.coli cell quickly begins to transcribe and translate the viral genes. Nucleotides salvaged from the cell’s degraded DNA are recycled to make copies of the phage genome. The phage parts come together, and three separate sets of proteins assemble to form phage heads, tails, and tail fibers. The phage then directs production of an enzyme that digests the bacterial cell wall. With a damaged cell wall, osmosis causes the cell to swell and finally burst, releasing 100 to 200 phage particles.
In contrast to the lytic cycle, the lysogenic cycle reproduces the viral genome without destroying the host. Infection of an E.coli cell by lambda begins when the phage binds to the surface of the cells and injects its DNA. Within the host, the lambda DNA molecules forms a circle. What happens next depends on the type of reproductive mode; lytic or lysogenic. During lysogenic cycle, the lambda DNA molecule is incorporated into a specific site of the host cell’s chromosomes, and it is then known as a prophage. Bacteria reproduce normally, copying the prophage and transmitting it to daughter cells. Then many cell divisions produce a colony of bacteria infected with prophage.
-Explain how viruses may cause disease symptoms, and describe some medical weapons used to fight viral infections.
Some viruses damage or kill cells by causing the release of hydrolytic enzymes from lysosomes. Some viruses cause the infected cells to produce toxins that lead to diseases symptoms, and some have toxic components themselves, such as envelope proteins. Vaccines are harmless variants or derivatives of pathogenic microbes that stimulate the immune system to mount defenses against the actual pathogen. Adenine arabinosideis is an antiviral drug that interferes with viral nucleic acid synthesis. Another is acyclovir, which seems to inhibit herpesvirus DNA synthesis.
-List some viruses that have been implicated in human cancers, and explain how tumor viruses transform cells.
Some viruses that have been implicated in human cancers are hepatitis B, Epstein-Barr, papilloma and HTLV-1. All tumor viruses transform cells through the integration of viral nucleic acid into host cell DNA.
-List some characteristics that viruses share with living organisms, and explain why viruses do not fit our usual definition of life.
An isolated virus is biologically inert, unable to replicated its genes or regenerate its own supply of ATP. Yet it has a genetic program written in the universal language of life. Although viruses are obligate intracellular parasites that cannot reproduce independently, it is hard to deny their evolutionary connection to the living world.
-Describe the structure of a bacterial chromosome.
The major component of the bacterial genome is one double stranded DNA molecule arranged in a circle. It has a dense region of DNA called nucleoid. Many bacteria also have plasmids, which have a small number of genes.
-List and describe the three natural processes of genetic recombination in bacteria.