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Chapter Sixteen List the three components of a nucleotide. Sugar, Phosphate, Base (A, T, G, C) Distinguish between deoxyribose and ribose. Deoxyribose is the five-carbon sugar in DNA and ribose is the five-carbon sugar in RNA. List the nitrogen bases found in DNA, and distinguish between pyrimidine and purine. Adenine, Guanine, Cytosine, and Thymine are the bases. Adenine and Guanine are Purines (larger) and Cytosine and Thymine are pyrimidine (smaller). Explain the "base-pairing rule" and describe its significance. Bases complement each other. Adenine with Thymine and Guanine with Cytosine. If bases form specific pairs, the information on one strand complements that along the other. 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 double helix. Purine and pyrimidine bases are stacked. There are ten layers of nitrogenous base pairs in each turn of the helix. Hydrogen bonds hold the bases together. Explain, in their own words, semiconservative 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. Describe the process of DNA replication, and explain the role of helicase, single strand binding protein, DNA polymerase, ligase, and primase. The DNA double helix opens and a replication fork spreads in both directions away from the central initiation point. Enzymes called DNA polymerases catalyze synthesis of a new DNA strand. New nucleotides align themselves along the templates of the old DNA strands. Primers are short segments of RNA polymerized by an enzyme called primase. Helicases are enzymes that catalyze unwinding of the parental double helix to expose the template. Single-strand binding proteins are proteins that keep the separated strands apart and stabilize the unwound DNA until new complementary strands can be synthesize. Define antiparallel. The two sugar-phosphate backbones of the helix were antiparallel; that is, they ran in opposite directions. Distinguish between the leading strand and the lagging strand. Leading strand - The DNA strand that is synthesized as a single polymer in the 5’ – 3’ direction towards the replication fork. Lagging strand - The DNA strand that is produced as a series of short segments. Explain how the lagging strand is synthesized when DNA polymerase can add nucleotides only to the 3’ end. DNA polymerase removes the RNA primer and replaces it with DNA. DNA ligase catalyzes the linkage between the 3’ end of each new Okazaki fragment to the 5’ end of the growing chain. Explain the role of DNA polymerase, ligase, and repair enzymes in DNA proofreading and repair. In bacteria, DNA polymerase proofreads each newly added nucleotide against its template. Any incorrectly paired nucleotide, the enzyme removes and replaces it before continuing with synthesis. In eukaryotes, additional proteins as well as polymerase participate in mismatch repair. The damaged segment is excised by one repair enzyme and the remaining 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. Chapter Seventeen Explain how RNA differs from DNA. RNA is a single strand. The five-carbon sugar in RNA nucleotides is ribose rather than deoxyribose. The nitrogenous base uracil is found in place of thymine. In your own words, briefly explain how information flows from gene to protein. DNA transcribes into RNA and then RNA is translate depending where it’s sent. Distinguish between transcription and translation. Transcription is the synthesis of RNA using DNA. Translation is from RNA to a polypeptide. Describe where transcription and translation occur in prokaryotes and in eukaryotes. In eukaryotes transcription occurs in the nucleus and the translation occurs in the cytoplasm. In prokaryotes both occur in the cytoplasm since there is a lack of a nuclei. 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. Nucleotide triplets in mRNA are called codons. They specify which amino acid will be added to a growing polypeptide or which signals termination. Explain the process of transcription including the three major steps of initiation, elongation, and termination. RNA synthesis on a DNA templates is catalyzed by RNA polymerase. It follows the same base pairing rule as DNA replication except that in RNA uracil substitutes for thymine. Promoters, specific nucleotide sequences at the start of a gene signal the initiation of RNA synthesis. Proteins help eukaryotic RNA polymerase recognize promoter sequences. Transcription continues until a particular RNA sequence signals termination. Describe the general role of RNA polymerase in transcription. RNA polymerase transcribe genes. RNA polymerases bind to DNA at the initiation site. Distinguish among mRNA, tRNA, and rRNA. Messenger RNA copies the info stored in the strand of DNA. Ribosomal RNA makes up the ribosomes. Transfer RNA shuttles amino acids to the site of protein synthesis. Describe the structure of tRNA and explain how the structure is related to function. A tRNA molecule has a 4 leaf clover structure. One end carries an amino acid the other (anticodon) has 3 nitrogenous bases that match the codon in the mRNA. Like enzymes they attach to an animo acid in the cytoplasm and shuttles it to the ribosome. Given a sequence of bases in DNA, predict the corresponding codons transcribed on mRNA and the corresponding anticodons of tRNA. DNA=TAC mRNA=AUG tRNA=UAC Describe the structure of a ribosome, and explain how this structure relates to function. I already know this from a previous chapter. Describe the process of translation including initiation, elongation, and termination. An initiator tRNA activates translation. Additional amino acids are linked to its neighboring amino acid. When a codon codes for stop, termination occurs. Describe the difference between prokaryotic and eukaryotic mRNA. Explain how eukaryotic mRNA is processed before it leaves the nucleus. In RNA splicing, introns (non-coding regions) are removed and exons (coding regions) join. Explain why base-pair insertions or deletions usually have a greater effect than base-pair substitutions. Because mRNA is read as a series of triplets during translation, insertion or deletion of nucleotides may alter the reading of the genetic message. The nucleotides following the insertion or deletion to be improperly grouped into codons. Chapter Eighteen List and describe structural components of viruses. Genome may be Double-stranded DNA, Single-stranded DNA, Double-stranded RNA, Single-stranded RNA, Organized as single nucleic acid molecule, Either linear or circular, May have as few as 4 genes to as many as several hundred. Capsid has a Protein coat and Encloses viral genome. It’s shape may be Rodshaped, polyhedral, Complex. Its Composed of many protein subunits, Made from one or a few types of proteins. The Envelope is a Membrane that cloaks some viral capsids. Helps virus infect its host. Derived from host cell membrane. Usually virus-modified containing proteins & glycoproteins of viral origin. Bacteriophage capsids. Explain why viruses are obligate parasites. They can only reproduce inside a cell. Explain the role of reverse transcriptase in retroviruses. Transcribes DNA from RNA template Describe how viruses recognize host cells. That each type of virus has a characteristic host range, determine by specific receptors on a host cell. Distinguish between lytic and lysogenic reproductive cycles using phage T4 and phage l as examples. In the Lytic cycle, injection of a phase genome into a bacterium programs destruction of host DNA, production of new phages and digestion of the host's cell wall, releasing the progeny phages. In a Lysogenic cycle, a temperate phage insets its genome into the bacterial chromosome as a phage, which is passed on to host daughter cells until it is stimulated to leave the chromosome and initiate a Lytic cycle. Explain how viruses may cause disease symptoms, and describe some medical weapons used to fight viral infections. Viruses may damage or kill cells - infected cell may cause lysosomes to release hydrolytic enzymes. Be toxic themselves or cause infected cells to produce toxins. Cause varying degrees of cell damage depending upon regenerative ability of infected cells Weapons against viral infections: Vaccines-harmless variant or derivative of pathogenic microbe. Antiviral drugs- (1) some interfere with viral nucleic acid synthesis. (2) Mechanism for some effective drugs is unknown List some viruses that have been implicated in human cancers, and explain how tumor viruses transform cells. Retrovirus (Leukemia), Herpes virus (Burkitt's lymphoma), Papovavirus (Cervical cancer), Hepatitis B virus (Chronic hepatitis / Liver cancer). Some tumor viruses transform cells by activating cellular oncogenes, usually more than one oncogene must be activated to transform cell. List some characteristics that viruses share with living organisms, and explain why viruses do not fit our usual definition of life. Viruses either have DNA or RNA, which is essential for reproduction. But, in every organism except viruses they have DNA and RNA, that's why scientist are not sure what to classify viruses. Describe the structure of a bacterial chromosome. The bacterial chromosome is a circular DNA molecule with few associated proteins. Because bacteria has short life span, they are able to reproduce rapidly. List and describe the three natural processes of genetic recombination in bacteria. Transformation, naked DNA enters the cell from the surroundings. In transduction, bacterial DNA is carried from one cell to another by phages. In conjugation, an F-factor containing "male" cell transfers DNA to an F-cell. (Bacterial Sex.) Explain how the F plasmid controls conjugation in bacteria. Briefly describe two main strategies cells use to control metabolism. The control of gene expression enables individual bacteria to adjust their metabolism to environmental change Distinguish between structural and regulatory genes. A structural gene is a gene that codes for a polypeptide. A regulatory gene transcription of the regulatory gene produces an mRNA molecule that is translated into the repressor protein, which can then reach by diffusion. Chapter Nineteen Compare the organization of prokaryotic and eukaryotic genomes. Eukaryotic genomes are more complexly organized than prokaryotic genomes. The control of gene expression is also more elaborate in eukaryotes than in prokaryotes. In particular, selective control of genes is required for cellular differentiation. Describe the current model for progressive levels of DNA packing. Chemical modification o relocation of DNA within a genome can alter gene expression. Distinguish between heterochromatin and euchromatin. Heterochromatin is a nontranscribed eukaryotic chromatin that is so highly compacted that it is visible with a light microscope during interphase. Euchromatin- the more open unraveled form of eukaryotic chromatin, which is available for transcription. Chapter Twenty Explain how advances in recombinant DNA technology have helped scientists study the eukaryotic genome. Because of the new technology, scientists are able to manipulate and analyze genetic material. They already knows what gene goes where, now its only a matter of time where they can fix or alter a genetic disorder. Describe the natural function of restriction enzymes. Restriction is the process where foreign DNA is cut into small pieces Describe how restriction enzymes and gel electrophoresis are used to isolate DNA fragments. Have sticky ends (single-stranded ends). Sticky ends used in lab to join DNA pieces from different sources. Gel electrophoresis Used to separate restriction fragments, Separates pieces based on size through electrical field, Bigger fragments travel slower through gel, Smaller fragments travel faster, Produces pattern of bands of DNA of different lengths. List and describe the two major sources of genes for cloning. Bacterial plasmids, Foreign DNA of interest Describe how "genes of interest" can be identified with the use of a probe. Probe single-stranded DNA, Complementary to fragments of markers, Probe attaches to fragment markers Explain the importance of DNA synthesis and sequencing to modern studies of eukaryotic genomes. Uses of DNA technology in basic research (Can be used to find segments of DNA, Can be used to study details of eukaryotic gene, Can be used to map eukaryotic chromosomes, Can be used to mass produce proteins used in research). Human genome project (Map human genome, Locate disease genes). Medical uses (Diagnosis of diseases, Human gene therapy, Vaccines, Drug production insulin & erythropoietin (stimulates RBC production)). Forensic uses - DNA fingerprinting and Agricultural uses