Bio1107k, Exam 2 Review Guide
Bio1107k, Exam 2 Review Guide BIOL 1107K
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This 9 page Study Guide was uploaded by Bethany B. on Wednesday September 28, 2016. The Study Guide belongs to BIOL 1107K at Georgia Gwinnett College taught by Latanya Hammonds in Fall 2016. Since its upload, it has received 7 views. For similar materials see Principles of Biology I w/Lab in Biology at Georgia Gwinnett College.
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EXAM 2 REVIEW GUIDE CHAPTER 3 CONTENT KEY TERMS: Replication—the process of copying DNA so genetic information can be passed from cell to cell or from an organism to its progeny. Mutation—any heritable change in the genetic material, usually a change in the nucleotide sequence of a gene. Transcription—the synthesis of RNA from a DNA template. Template—a strand of DNA or RNA whose squence of nucleotides is used to synthesize a compementary strand. Translation—synthesis of a polypeptide chain corresponding to the coding sequence present in a molecule of messenger RNA. Nucleotide—a constituent of nucleic acids, consisting of a 5carbon sugar, a nitrogencontaining base, and one or more phosphate groups. Phosphate Group—a chemical group consisting of a phosphorus atom bonded to four oxygen atoms. Base—a nitrogencontaining compound that makes up part of a nucleotide. Major Groove—the larger of two uneven grooves on the outside of a DNA duplex. Minor Groove—the smaller of two unequal grooves on the outside of a DNA duplex. Antiparallel—oriented in opposite directions; the strands in a DNA duplex are antiparallel. Complementary—describes the relationship of purine and pyrimidine bases, in which the base A pairs only with T and G pairs only with C. Base Stacking—stabilizing hydrophobic interactions between bases in the same strand of DNA. Supercoil—a coil of coils; a circular molecule of DNA can coil upon itself to form a supercoil. Topoisomerase—any one of a class of enzymes that regulates the supercoiling of DNA by cleaving one or both strands of the DNA double helix, and later repairing the break. Chromosome—In eukaryotes, the physical structure in which DNA in the nucleus is packaged; used more loosely to refer to the DNA in bacterial cells or archaeons. Chromatin—a complex of DNA, RNA, and proteins that gives chromosomes their structure; chromatin fibers are either 30 nm in diameter or, in a relaxed state, 10 nm. Ribosome—a complex structure of RNA and protein, bound to the cytosolic face of the RER in the cytoplasm, on which proteins are synthesized. RNA polymerase—the enzyme that carries out polymerization of ribonucleoside triphosphates from a DNA template to produce an RNA transcript. nontemplate strand—the untranscribed partner of the template strand of DNA used in transcription. Promoter—a regulatory region where RNA polymerase and associated proteins bind to the DNA duplex. TATA box—a DNA sequence present in many promoters in eukaryotes and archaeons that serves as a protein binding site for a key general transcription factor. Terminator—a DNA sequence at which transcription stops and the transcript is released. housekeeping gene—a gene that is transcribed continually because its product is needed at all times and in all cells. sigma factor—a protein that associates with RNA polymerase that facilitates its binding to specific promoters. general transcription factors—a set of proteins that bind to the promoter of a gene whose combined action is necessary for transcription. transcriptional activator protein—a protein that binds to a sequence in DNA to enable transcription to begin. enhancer A specific DNA sequence necessary for transcription. mediator complex—a complex of proteins that interacts with the Pol II complex and allows transcription to begin. Pol II—the RNA polymerase complex responsible for transcription of proteincoding genes. Initiation—the stage of translation in which methionine is established as the first amino acid in a new polypeptide chain. Elongation—the process in protein translation in which successive amino acids are added one by one to the growing polypeptide chain. primary transcript—the initial RNA transcript that comes off the template DNA strand. messenger RNA (mRNA)—the RNA molecule that combines with a ribosome to direct protein synthesis; it carries the genetic “message” from the DNA to the ribosome. polycistronic mRNA—a single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA. RNA processing—chemical modification that converts the primary transcript into finished mRNA, enabling the RNA molecule to be transported to the cytoplasm and recognized by the translational machinery. 5′ cap—the modification of the 5′ end of the primary transcript by the addition of a special nucleotide attached in an unusual chemical linkage. Polyadenylation—the addition of a long string of consecutive Abearing ribonucleotides to the 3′ end of the primary transcript. poly(A) tail—the nucleotides added to the 3′ end of the primary transcript by polyadenylation. Exon—a sequence that is left intact in mRNA after RNA splicing. Intron—a sequence that is excised from the primary transcript and degraded during RNA splicing. RNA splicing—the process of intron removal from the primary transcript. Spliceosome—a complex of RNA and protein that catalyzes RNA splicing. Lariat—a loop and tail of RNA formed after RNA splicing. alternative splicing—a process in which primary transcripts from the same gene can be spliced in different ways to yield different mRNAs and therefore different protein products. Ribosomal RNA (rRNA), found in all ribosomes that aid in translation. In eukaryotic cells, the genes and transcripts for ribosomal RNA are concentrated in the nucleolus, a distinct, dense, non–membranebound spherical structure observed within the nucleus. Transfer RNA (tRNA) that carries individual amino acids for use in translation. Small nuclear RNA (snRNA), found in eukaryotes and involved in splicing, polyadenylation, and other processes in the nucleus. Small, regulatory RNA molecules that can inhibit translation or cause destruction of an RNA transcript. Two major types of small regulatory RNA are known as microRNA (miRNA) and small interfering RNA (siRNA). Reads the template strand 3’ to 5’ but synthesizes from 5’ to 3’ Leading strand is the strand that has continuous dna synthesis. The Lagging strand has intervening coding segments (these are the okazaki fragments). It has nothing to do with the names. Growth Phase 1: transcription Sphase: DNA replication Growth Phase 2: transcription Mitosis Phase: Cell/nucleus division LESSON OBJECTIVE FOR CHAPTER 2/3: 1. Identify the four macromolecules; recognize their structures, know their monomers, bonds that link monomers to synthesize polymers, and functions within the cell. 2. Describe various carbs and their role in energy production (glucose, starch, glycogen) and cellular structure (cellulose) 3. Compare the different types of lipids in biological systems 4. Describe the levels of protein folding: primary/secondary/tertiary/quaternary structure Describe the structure of nucleic acids and discuss their importance in biological systems KEY NOTES FROM LECTURE: DNA RNA SUGAR Deoxyribose Ribose BASES A, T, C, G A, U, C, G 5’ END Monophosphate Triphosphate SIZE Very large Smaller STRANDS Double Single Scientists Griffith Avery, MacLeod, and Did Griffiths Wanted to see if it was McCarty experiment but got rid Nucleic Acid or Proteins of specific macromolecules Hershey and Chase The DNA of the phage Blender with Phages was injected into the bacterial host, but the protein coat stayed outside. Meselson and Stahl The two strands Watson and Crick Chargaff Puss CHAPTER 4 REVIEW KEY TERMS: Codon—a group of three adjacent nucleotides in RNA that specifies an amino acid in a protein or that terminates polypeptide synthesis. Anticodon—the sequence of three nucleotides in a tRNA molecule that base pairs with the corresponding codon in an mRNA molecule. aminoacyl tRNA synthetase—an enzyme that attaches a specific amino acid to a specific tRNA molecule. genetic code—the correspondence between codons and amino acids, in which 20 amino acids are specified by 64 codons. Initiation—the stage of translation in which methionine is established as the first amino acid in a new polypeptide chain. Elongation—the process in protein translation in which successive amino acids are added one by one to the growing polypeptide chain. initiation factor—a protein that binds to mRNA to initiate translation. elongation factor—a protein that breaks the highenergy bonds of the molecule GTP to provide energy for ribosome movement and elongation of a growing polypeptide chain. release factor—a protein that causes a finished polypeptide chain to be freed from the ribosome. polycistronic mRNA—a single molecule of messenger RNA that is formed by the transcription of a group of functionally related genes located next to one another along bacterial DNA. Operon—a group of functionally related genes located in tandem along the DNA and transcribed as a single unit from one promoter; the region of DNA consisting of the promoter, the operator, and the coding sequence for the structural genes. protein family—a group of proteins that are structurally and functionally related. KEY NOTES FROM LECTURE: PROTEIN FUNCTION HELICASE Unwinds parental double helix at replication forks SINGLESTRAND Binds to and stabilizes singlestranded DNA until it can be used as a BINDING PROTEIN template TOPOISOMERASE Relieves “overwinding” strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands PRIMASE Synthesizes an RNA primer at 5’ end of leading strand and of each Okazaki fragment of lagging strand DNA POL III Using parental DNA as a template, synthesizes new DNA strand by covalently adding nucleotides to the 3’ end of the preexisting DNA strand or RNA primer DNA POL I Removes RNA nucleotides of primer from 5’ end and replaces them with DNA nucleotides DNA LIGASE Joins 3’ end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand LESSON OBJECTIVES FOR CHAPTER 4: 1. Distinguish between transcription and translation. 2. Compare where transcription and translation occur in bacteria and in eukaryotes. 3. Explain the general process of transcription, including the three major steps of initiation, elongation, and termination. 4. Define “codon” and explain the relationship between the linear sequence of codons on mRNA and the linear sequence of amino acids in a polypeptide. 5. Explain how RNA polymerase recognizes where transcription should begin. Describe the role of the promoter, the terminator, and the transcription unit. 6. Explain how RNA is modified after transcription in eukaryotic cells and why. 7. Define and explain the role of ribozymes. 8. Demonstrate the correct use of the Genetic Code. 9. Describe the simplified process of translation (including initiation, elongation, and termination) and the role of ATP. 10. Describe the significance of polyribosomes. 11. Describe what determines whether a ribosome will be free in the cytosol or attached to the rough endoplasmic reticulum. 12. Explain the differences in translation of cytosolic, soluble proteins versus membrane bound proteins (secretory pathway and endomembrane system from Chapters 6 and 7) CHAPTER 12 REVIEW KEY TERMS: daughter strand—In DNA replication, the strand synthesized from a parental template strand. semiconservative replication—the mechanism of DNA replication in which each strand of a parental DNA duplex serves as a template for the synthesis of a new daughter strand. replication fork—the site where the parental DNA strands separate as the DNA duplex unwinds. DNA polymerase—an enzyme that is a critical component of a large protein complex that carries out DNA replication. leading strand—a daughter strand that has its 3′ end pointed toward the replication fork, so as the parental double helix unwinds, this daughter strand can be synthesized as one long, continuous polymer. lagging strand—a daughter strand that has its 5′ end pointed toward the replication fork, so as the parental double helix unwinds, a new DNA piece is initiated at intervals, and each new piece is elongated at its 3′ end until it reaches the piece in front of it. Okazaki fragment—In DNA replication, any of the many short DNA pieces in the lagging strand. Primer—a short stretch of RNA at the beginning of each new DNA strand that serves as a starter for DNA synthesis; an oligonucleotide that serves as a starter in the polymerase chain reaction. RNA primase—an RNA polymerase that synthesizes a short piece of RNA complementary to the DNA template and does not require a primer. DNA ligase—an enzyme that uses the energy in ATP to close a nick in a DNA strand, joining the 3′ hydroxyl of one end to the 5′ phosphate of the other end. topoisomerase II—an enzyme that breaks a DNA double helix, rotates the ends, and seals the break. Helicase—a protein that unwinds the parental double helix at the replication fork. singlestrand binding protein—a protein that binds singlestranded nucleic acids. Proofreading—the process in which DNA polymerases can immediately correct their own errors by excising and replacing a mismatched base. origin of replication—any point on a DNA molecule at which DNA synthesis is initiated. replication bubble—a region formed by the opening of a DNA duplex at an origin of replication, which has a replication fork at each end. Telomere—a repeating sequence at each end of a eukaryotic chromosome. Telomerase—an enzyme containing an RNA template from which complementary telomere repeats are synthesized. germ cells—the reproductive cells that produce sperm or eggs and the cells that give rise to them. stem cell—an undifferentiated cell that can undergo an unlimited number of mitotic divisions and differentiate into any of a large number of specialized cell types. polymerase chain reaction (PCR)—a selective and highly sensitive method for making copies of a piece of DNA, which allows a targeted region of a DNA molecule to be replicated into as many copies as desired. Oligonucleotide—a short (typically 20 to 30 nucleotides), singlestranded molecule of known sequence produced by chemical synthesis; oligonucleotides are often used as primer sequences in the polymerase chain reaction. Denaturation—the unfolding of proteins by chemical treatment or high temperature; the separation of paired, complementary strands of nucleid acid. Annealing—the coming together of complementary strands of singlestranded nucleic acids by base pairing. extension (PCR)—a step in the polymerase chain reaction (PCR) for producing new DNA fragments in which the reaction mixture is heated to the optimal temperature for DNA polymerase, and each primer is elongated by means of deoxynucleoside triphophosphates. restriction enzyme—any one of a class of enzymes that recognizes specific, short nucleotide sequences in doublestranded DNA and cleaves DNA at or near these sites. Palindromic—reading the same in both directions; describes sequence identity along the paired strands of a duplex DNA molecule; a symmetry typical of restriction sites. Palindromic—reading the same in both directions; describes sequence identity along the paired strands of a duplex DNA molecule; a symmetry typical of restriction sites. Renaturation—the base pairing of complementary singlestranded nucleic acids to form a duplex; also known as hybridization, it is the opposite of denaturation. chain terminator—a term for a dideoxynucleotide, which if incorporated into a growing daughter strand stops strand growth because there is no hydroxyl group to attack the incoming nucleotide. Sanger sequencing—a procedure in which chemical termination of daughter strands help in determining the DNA sequence. recombinant DNA—DNA molecules from two (or more) different sources combined into a single molecule. Vector—In recombinant DNA, a carrier of the donor fragment, usually a plasmid. Plasmid—In bacteria, a small circular molecule of DNA carrying a small number of genes that can replicate independently of the bacterial genomic DNA. Transformation—the conversion of cells from one state to another, as from nonvirulent to virulent, when DNA released to the environment by cell breakdown is taken up by recipient cells. In recombinant DNA technology, the introduction of recombinant DNA into a recipient cell. genetically modified organism (GMO)—an organism that has been genetically engineered, such as modified viruses and bacteria, laboratory organisms, agricultural crops, and domestic animals; also known as a transgenic organism. DNA editing—techniques that allow researchers to “rewrite” the nucleotide sequence of DNA so that specific mutations can be introduced into genes. CRISPR (clustered regularly interspaced short palindromic repeats)—a method of DNA editing in which any sequence in the genome can be replaced with any other sequence; the phrase describes the organization of the viral DNA segments in certain bacterial genomes from which the DNA editing method derives. LESSON OBJECTIVES FOR CHAPTER 12: 1. Review the scientists/experiments associated with determining the structure of DNA and the discovery of DNA as a transforming principle. 2. Elucidate the process of DNA replication including DNA polymerase, origins of replication, relevant proteins, replisome, DNA replication complex, DNA ligase, 5’ and 3’ ends and leading and lagging strand synthesis. 3. Discuss the importance of DNA proofreading and repair with regard to mutagenesis. 4. Define “point mutations”. Distinguish between basepair substitutions and basepair insertions. Give an example of each and note the significance of such changes. 5. Distinguish between a missense and a nonsense mutation. 6. Why is an insertion or deletion more likely to be deleterious than a substitution?
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