BCOR 101 Exam #1 Study Guide
BCOR 101 Exam #1 Study Guide BCOR 101
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BCOR 101 CHAPTER 1 GENETICS ANALYSIS TEXTBOOK NOTES CHAPTER 1 THE MOLECULAR BASIS OF HEREDITY VARIATION AND EVOLUTION MODERN GENETICS IS IN ITS SECOND CENTURY Three botanists Carl Correns Hugo de Vries Erich von Tschermak reached strikingly similar conclusions about the transmission of hereditary traits in plants 0 Results mirrored those of Mendel but they actually rediscovered an explanation of hereditary transmission published by Mendel 34 years prior their announcement of these re ndings allowed for the start of modern genetics Testing veri cation and expanding on the explanation of hereditary began immediately by biologists William Bateson read a publication about the appearance of the hereditary disease alkaptonuria in multiple members of unrelated families by Archibald Garrod o Bateson with the help of Garrod published the rst documented source of a human hereditary disorder Walter Sutton and Theodore Boveri used microscopy to observe chromosome movement during cell division in reproductive cells gametes 0 Saw the patterns of chromosome movement mirrored the transmission of the Mendelian hereditary units 0 Implied that hereditary units genes posited by Mendel are located on chromosomes Each chromosome carries many genes homologs carry genes for the same traits in the same order on each member of the pair Bacteria and archaea single celled organisms that do not have a true nucleus usually have a singular circular chromosome Eukaryotes nucleus which permanently contains multiple sets of chromosomes almost most eukaryotes have haploid and diploid stages in their life 0 Ex sperm and eggs are haploid and have one copy of each chromosome pair eukaryotic genomes contains two copies of each gene homologous pair in diploid state 0 Plants and animals also contain DNA in mitochondria and chloroplasts plants only Present by the dozens in each cell and each one carries one or more copies of its own chromosome Produce proteins that work with protein produced by nuclear genes to perform essential functions in cells ATP production in mitochondria which is principal energy source for cellular energy chloroplasts are necessary for photosynthesis Transmitted in cytoplasm during cell division Have evolutionary history descended from ancient parasitic bacterial invasion of eukaryotic cells Complete set of nuclear chromosomes transmitted during the celldivision process of mitosis which produce genetically identical cells meiosis creates sexual cells which are haploid in diploid organisms Gene was seen as the physical unit of heredity and revealed relationships between the observable traits of the organism phenotype and the genetic constitution of the organism genotype 1914 Oswald Avery Colin MacLeod and Maclyn McCarthy identi ed DNA as the hereditary material which began the quotmolecular eraquot in genetics 0 Spanned he second half of the 20th century and lasts until today began with the effort to discover the molecular structure of DNA James Watson Francis Crick Maurice Wilkins and Rosalind Franklin discovered the double helix structure of DNA in 1953 In 1958 common mechanism of DNA replication was found 19605 basic mechanisms of DNA transcription and mRNA translation were laid out and genetic code by which mRNA is translated into proteins was deciphered Last Universal Common Ancestor all life is descended from a common ancestor o Divided into three domains Bacteria Eukarya Archaea o Derived from model created by Carl Woese and colleagues in mid 1970s 0 Used morphology and molecular sequences to determine phylogenetic relationships between existing organisms and therefore trace the evolution of life Used the sequence of ribosomal RNA rRNA as the basis for comparison Species which are members of the same evolutionary lineage will share certain rRNA sequence changes that are not part of the species outside of the lineage Recognition of DNA as the hereditary material which stores and conveys genetic material although certain viruses use RNA as hereditary material DNA has a double helix stranded structure DNA replication contains two steps transcription and translation Three branches of modern genetics transmission genetics evolutionary genetics and molecular genetics 0 Not rigidly differentiated and there is substantial crosscommunication among all of them Vocab words genes chromosomes homologous pairs homologs haploid nucleoid diploid polyploidy mitochondria chloroplasts cytoplasmic inheritance mitosis meiosis gametes phenotype genotype alleles genomes LUCA Eukarya Bacteria Archaea deoxyribose nucleic acid DNA ribonucleic acid RNA DNA double helix DNA duplex DNA replication transcription messenger RNA mRNA translation ribosomes transmission genetics Mendelian genetics Evolutionary genetics Molecular genetics de ned at the end of the notes THE STRUCTURE OF DNA SUGGESTS A MECHANISM FOR REPLICATION O Hereditary transmission is the process of dispersing genetic information from parents to offspring 0 Completed by the generation of reproductive cells in males and females followed by the union of sperm and egg or pollen or spores at fertilization and then the development of an organism 0 Watson and Crick discovered the molecular structure of DNA as a double helix composed of two strands of DNA with an invariant sugarphosphate backbone on the outside and nucleotide bases arrayed in complementary base pairs which orient themselves toward the center of the molecule 0 Weren t the ones actively engaged in laboratory research Rosalind Franklin was one of their principal sources Franklin used an early form of xray diffraction imagery to examine the crystal structure of DNA The pattern diffracted by the xrays created a double helix 0 Watson and Crick also used research by Chargaff who had determined the percentages of the four DNA nucleotide bases and discovered that the percentages of adenosine and thymine are equal and cytosine and guanine are equal all approximately 0 Each strand of the double helix is composed of nucleotides which have three principal components a 5 carbon deoxyribose sugar a phosphate group and one of four nitrogencontaining nucleotide bases Nucleotides are linked together by a covalent phosphodiester bond Nucleotide bases are hydrophobic Hydrogen bonds form between the complementary base pairs Strands are antiparallel Vocabulary Words Chargaff39s rule complementary base pairs DNA nucleotides adenine guanine thymine cytosine phosphodiester bond hydrogen bonds strand polarity antiparallel semiconservative replication parental strand daughter strand DNA TRANSCRIPTION AND MESSENGER RNA TRANSLATION EXPRESS GENES 00000 0 Central dogma of biology summarizes the relationships between DNA RNA and proteins 0 Functional role of DNA maintaining directing and regulating the expression of genetic information 0 RNA and proteins in gene function 0 Most important idea is that DNA does not code directly for proteins DNA makes up genome of an organism and is the permanent source of genetic information in the cell by directing gene expression through transcription of DNA to RNA and then to the production of proteins 0 Two forms of RNA which play a role in transcription but are not transcribed ribosomal RNA rRNA and transfer RNA tRNA O Transcription process by which information in DNA sequence is converted into RNA sequence RNA composed of 4 nucleotides that are chemically very similar to DNA 0 Ribose sugar phosphate group one of four nitrogenous bases all identical to those in DNA except uracil which replaces thymine Certain DNA sequences most commonly promoters bind RNA polymerase and other transcriptional proteins Messenger RNA codons base pair with tRNA anticodons at the ribosome Each tRNA carries a speci c amino acid that is added to the growing polypeptide chain Genetic code contains 61 codons that specify amino acids and 3 are stop codons Genomics proteomics transcriptomics and metabolomics are new investigative strategies that can help decipher complex problems of systems biology Vocabulary words central dogma of biology ribosomal RNA rRNA transfer RNA tRNA amino acids reverse transcription template strand coding strand uracil promoters start of transcription termination sequence exons introns peptide bond polypeptide protein codon start codon anticodon stop codon genetic code genomics megabases transcriptomics transcriptome metabolomics proteomics proteome systems biology EVOLUTION HAS A MOLECULAR BASIS O 0 Four processes natural selection migration mutation and genetic drift drive the evolution of population and species The evolution of adaptive morphological characters occurs through natural selection pressures exerted on species by their environment Nonadaptive characters are neutral to natural selection evolve by other evolutionary processes Modern synthesis of evolution is the name applied to the union of transmission genetics molecular genetics Darwinian evolution and modern evolutionary genetics Phylogenetic trees describe evolutionary relationships among modern species and trace their descent from common ancestors to identify the most likely pattern of evolution Shared derived characteristics are molecular and morphological attributes that evolve in descendant species from ancient characters found in a common ancestor Molecular phylogenies trace the evolution of nucleic acid or protein sequences from common ancestors to modern species Vocabulary Words evolution natural selection migration mutation genetic drift modern synthesis phylogenetic tree cladistics clades monophyletic groups shared derived characteristics synaptomorphies homology paraphyletic group homoplasmy outgroup ingroup VOCABULARY WORDS Genes the physical unit of heredity composed of a DNA sequence that is transcribed and encodes a polypeptide or another functional molecule Chromosomes a structure composed of DNA and associated proteins that in total contain the genome of an organism Homologous pairs Chromosomes that synapse pair during meiosis Chromosomes with the same genes in the same order also known as homologous chromosomes or homologs Homologs Homologous chromosomes that have the same genes and structure and pair with one another during meiosis Haploid Possessing a single set of chromosomes n a cell or organism that possesses onehalf the number of chromosomes found in diploid cells of the organism Nucleoid the region of bacterial and archaeal cells or mitochondria or chloroplasts where the main chromosome resides Diploid the characteristic number of chromosomes Zn in somatic cell nuclei during the diploid phase of the eukaryotic life cycle Equal to twice the haploid n number of chromosomes found in the nuclei of gametes of sexually reproducing diploid species Polyploidy the presence of more than two complete sets of chromosomes in a genome Mitochondria an organelle bounded by a double membrane encoding polypeptides that interact with nuclear gene polypeptides in oxidative phosphorylation to generate ATP In many species mitochondria also participate in other metabolic processes and biochemical reactions including ion homeostasis and biosynthetic pathways Chloroplasts an organelle bounded by a double membrane where photosynthetic reactions convert light energy and C02 into xed organic carbon Cytoplasmic inheritance the random distribution of mitochondria and chloroplasts between daughter cells Mitosis the process of cell division in somatic cells that produces genetically identical daughter cells through a single nuclear division Meiosis the process of cell division occurring in germline cells Produces four haploid gametes or spores through two successive nuclear divisions in diploid species Gametes the reproductive cells produced by male and female reproductive structures sperm or pollen in male animals and plants and eggs in females Phenotype the observable physical characteristics or traits of an organism the physical manifestation of a speci c genotype Genotype the genetic composition of an organism or a cell ex all of alleles of all the genes the alleles of a single gene or a speci ed set of genes in a cell or organism Alleles an alternative form of a gene Genomes the entire complement of DNA sequences in a chromosome set of an organism LUCA stands for last universal common ancestor Eukarya one of the three domains of life separate from Archaea and Bacteria Bacteria one of the three domains of life separate from Eukarya and Archaea Archaea one of the three domains of life separate from Bacteria and Eukarya Deoxyribose nucleic acid DNA the hereditary molecule of organisms Composed of two complementary strands of nucleotides with purine bases adenine A and guanine G and pyrimidine bases thymine T and cytosine C Ribonucleic acid RNAa family of polynucleotides that are transcribed from DNA RNAs are composed of nucleotides containing the sugar ribose one or more phosphate atoms and one of four nitrogenous bases AG C and U DNA double helix the two complementary strands of DNA arranged in antiparallel orientation also known as DNA duplex DNA replication the synthesis of new DNA strands by complementary base pairing of nucleotides in a daughter strand to those in a template strand Transcription the cellular processes that synthesizes RNA strands from a DNA template strand Messenger RNA mRNAa form of RNA transcribed from a gene and subsequently translated to produce a polypeptide or protein Translation the process taking place a ribosomes to synthesize polypeptides Complementary base pairing between mRNA codons and tRNA anticodons determines the order of amino acids composing the polypeptide Ribosomes ribonucleoprotein particles composed of rRNAs and numerous proteins at which translation takes place Transmission genetics the sub eld of genetics concerned with assessment and analysis of gene transfer from parents to offspring Synonym with Mendelian genetics Mendelian genetics referring to genetic applications and analyses using the law of segregation and the law of independent assortment originally described through experiments and analysis by Gregor Mendel Evolutionary genetics the study of evolution and evolutionary processes using genetic techniques and tools Molecular genetics the sub eld of genetics that studies hereditary transmission variation mutation and evolution through the analysis of nucleic acids and proteins Chargaff39s rule the observation that the percentage of adenine equals that of thymine and that guanine percentage equals cytosine percentage in DNA Complementary base pairs the speci c pattern of purinepyrimidine pairing of nucleic acid strands ln DNA G with C and A with T in RNA uses U instead ofT DNA nucleotides DNA building blocks composed of deoxyribose sugar a nitrogenous base and one or more phosphate groups Adenine one of four nitrogenous nucleotide bases in DNA and RNA one of the two types of purine nucleotides in DNA and RNA Guanine one of four nitrogenous nucleotide bases in DNA and RNA one of two types of purine nucleotides in DNA and RNA Thymine one of four nitrogenous nucleotide bases in DNA one of two types of pyrimidine nucleotides in DNA Cytosine one of four nitrogenous nucleotide bases in DNA and RNA one of two types of pyrimidine nucleotides in DNA and RNA Phosphodiester bond a type of covalent bond formed between two nucleotides in a nucleic acid strain Formed between the 539 phosphate group of one nucleotide and the 339 OH of the adjacent nucleotide Hydrogen bonds weak electrostatic attraction formed by the sharing of a positively charged hydrogen atom by negatively charged oxygen and nitrogen atoms Hydrogen bonds form between complementary nucleotides to hold nucleic acid strands together Strand polarity 539 and 3 the orientation of a nucleic acid strand indicating its 539 phosphate and 339 hydroxyl ends Antiparallel opposite 539 and 339 orientations of two complementary nucleic acid strands Semiconservative replication the established method of DNA replication in which each strand of a parental duplex acts as a template for daughter strand synthesis and each daughter duplex is composed of one parental strand and a complementary daughter strand Parental strand the DNA strand acting as a template to direct the synthesis of a newquotdaughterquot strand of DNA Daughter strand a newly synthesized strand of DNA that is complementary to a template strand Central dogma of biology the description of the functional relationship between DNA RNA and proteins DNA to RNA to proteins Ribosomal RNA rRNA a group of RNA molecules that compose part of the structure of ribosomes Transfer RNA tRNA a family of small RNA molecules that each bind a speci c amino acid and convey it to the ribosome where the anticodon sequence undertakes complementary base pairing with an mRNA codon during translation Amino acids an aminocarboxylic acid that is a component of a polypeptide or a protein Reverse transcription the process of DNA synthesis from an RNA template by the enzyme reverse transcriptase Template strand the DNA strand serving as a template for synthesis of a complementary nucleic acid strand Coding strand the nontemplate strand of DNA that has the same 539to339 polarity as its transcript and the same sequence except for T in DNA and U in RNA Uracil one of the four nitrogenous nucleotide bases in RNA one of the two types of pyrimidine nucleotides in RNA Promoters a regulatory sequence of DNA near the 539 end of a gene that acts as the binding location of RNA polymerase and directs RNA polymerase to the start of transcription Start of transcription the DNA location at which transcription begins Termination sequence DNA sequences that serve to stop transcription also known as transcription termination Exons a nonintron segment of coding sequence of a gene Joined together following intron splicing exons correspond to the mRNA sequence that is coded into a polypeptide lntrons intervening sequences between the exons of many eukaryotic genes Present in DNA and premRNA but spliced out during premRNA processing Peptide bond a type of covalent bond that joins amino acids in polypeptide chains Formed between the amino end of one amino acid and the carboxyl end of the adjoining amino acid Polypeptide a chain of amino acids joined by peptide bonds Formed at ribosomes during translation Protein a string of amino acids encoded during translation of mRNA and linked together by peptide bonds Codon the nucleotide triplet of mRNA that encodes a single amino acid Start codon most commonly AUG encoding methionine the rst codon translate in polypeptide synthesis Anticodon the nucleotide triplet sequence of transfer RNA that pairs with an mRNA codon sequence in translation Stop codon one of three codons that bind a release factor instead a base pairing with tRNA to initiate a series of events that stops translation Genetic code the universal set of correspondences of mRNA codons to amino acids Used in translation to synthesize polypeptides Genomics the study of the structure function composition and evolution of genomes Megabases Equal to 1000 000 nucleotide bases Refers to DNA or to RNA molecules or fragments Transcriptomics the study of all the transcripts collectively known as the transcriptome within a cell tissue or organism Transcriptome set of transcripts present in a cell tissue or organism Metabolomics the study of proteins processes and interactions involved in the metabolism of organisms Proteomics the study of all the proteins collectively knowns as the proteome within a cell tissue or organism Proteome set of the proteins in a cell tissue or organism Systems biology prediction of biological functions of genes based on correlations between different data sets Evolution any change in the genetic characteristics of a population strain or species over time the theory of all organisms are related by common ancestry and have diversi ed from common ancestors over time Natural selection the evolutionary processes operating through differences in survival fecundity and relative tness of organisms with different genotypes and phenotypes Migration a process of evolution referring to the movement of organisms and genes between populations also known as gene ow Mutation an inherited change in DNA Genetic drift a process of evolution referring to random changes in allele frequencies that result from sampling errors Occurs in all populations but is strongest in small populations Modern synthesis referring to the broadbased effort beginning in the middle of the 20th century to unite Mendelian genetics with Darwin39s theory of evolution by natural selection Phylogenetic tree a diagram of evolutionary relationships among organisms or genes based on morphological or molecular characteristics Cladistics the classi cation of organisms by characteristics that are unique to the group and distinguish it from other groups lnvolves branching of new species from ancestral species Clades in phylogenetics a group of organisms de ned by characteristics that are unique to the group and distinguish the group from others Monophyletic groups a group of organisms with a single common ancestor Shared derived characteristics characteristics or traits of organisms that evolve from more ancestral characteristics or traits found in ancestral organisms Synaptomorphies similar to shared derived characteristics shared between member of the same clade molecular or morphological Homology evolutionarily related having descended from a common ancestor Paraphyletic group a group of organisms that includes some but not all the members descended from a common ancestor Homoplasmy the presence of one allele version of DNA in the organellar genomes of a cell Outgroup a species related to members of a clade but outside the clade used to root the clade lngroup a species within a clade used to compare to other members of the clade BCOR 101 CHAPTER 7 READING NOTES CHAPTER 7 DNA STRUCTURE AND REPLICATION SECTION 71 DNA IS THE HEREDITARY MOLECULE OF LIFE Hereditary molecule is the molecular substance that carries and conveys the species39 genetic information 0 Five essential characteristics of hereditary material 0 Localized to the nucleus and a component of chromosomes 0 Present in a stable form in cells 0 Suf ciently complex to contain the genetic information required to direct the structure function development and reproduction of organisms o Able to accurately replicate itself so that daughter cells contain the same information as parental cells 0 Mutable undergoing mutation at a low rate that introduces genetic variation and serves as a foundation for evolutionary change 0 DNA rst noted in 1869 by Friedrich Miescher whom isolated it from white blood cell nuclei in a mixture of nucleic acids and proteins he called nuclein 1870s microscopic studied identi ed fusiom of male and female nuclei during reproduction Chromosomes were observed in nuclei shortly after Nuceli of different species contain a different number of chromsomes Males and females contribute equal amounts of chromosomes in reproduction 1895 Edmund Wilson accurately recorded that eggs and sperm contribute the same number of chromosomes during reproduction 0 Proposed that inheritance may be effected by the physical transmission of a particular chemical compound from parent to offspring 19005 Mendel39s hereditary principles were rediscovered and disseminated through the scienti c community 0 1903 Wlater Sutton and Theodor Boveri accuratel described the paralles between homologous chromosomes and sisterchromatid separation during meiotic cell division and the inheritance of genes 0 1920 principle constituent of nuclein was identi ed as DNA and its basic chemistry was deciphered o Determined to be a polynucleotide consisting of four repaeating subunits nucleotides held together by covalent bonds 0 Nucleotides are adenine A thymine T cytosine C and guanine G o 1923 DNA localized to chromosomes which made it a candidate for the hereditry material but it is not the sole constituent of chromosomes 0 Proteins are present in high concentrations as well as RNA in the nucleus and around the chromosomes as well as many other compounds such as carbohydrates and lipids These were all considered as an option for hereditary material at one point o It was noted the proetins had 20 different amino acids whereas DNA has only 4 nucleotides Suggested that the quot20 letter alphabetquot of protein could contain more information than the quot4 letter alphabetquot of DNA Against all these thoughts 3 experiments were conducted between 1928 and 1952 combined to identify DNA as the hereditary material of organism Frederick Grif th studied strand of the bacteria pneumococcus which causes fatall pneumonia in mice Modern biology focuses on his rst few pages of his report which provided indirect evidence that DNA is the molecule responsible for conveying hereditary characteristics in bacteria The S and R forms of pneumococcus occurred in for antigenic types of bacteria identi ed as I II III and IV and each antigenic type elicits a different immune response from the mouse immune system as a result of the presence of several genetic differences Grif th39s most important observations are derived from the four injection tests that he performed using S and R bacterial strains of different antigenic types following each injection test he was able to draw blood from the injected mice and culture the blood to identify the type of bacteria growing His rst three injection results show that injecting the mice with S Strain bacteria produces illness and death that injection of heat killed S strain bacteria does not induce illness and injection of an R strain does not produce iHness Most signi cant result came when he injected a mixture of heat killed S3 strain and living R2 strained he found that the mice became ill and died from pneumonia the blood cultures resulted from the dead mice revealed living S3 bacteria Grif n proposed that this outcome was not a result of a simple mutational event and that a molecular component that he called the transformation factor is responsible for transforming R2 into S3 Also proposed the transformation factor was a molecule that carries hereditary information Shortly after Grif th Martin Dawson working with Oswald Avery developed an in vitro transformation procedure to mix living R cells with the puri ed extract of cellular material derived from heat killed S3 cells containing the transformation factor Biochemical assays were done which revealed that the S3 extract contained mostly of DNA along with small amounts of RNA and trace amounts of proteins lipids and polysaccharides Direct evidence that DNA was the transformation factor came from an experiment performed by Avery and his colleagues Colin MacLeod and Maclyn McCarty in 1944 Experiment identify the role of DNA in transformation by eliminating lipids polysaccharides protein RNA and DNA one at a time from the S3 extract ln introducing enzymes to get rid of each component the nal results revealed that transformation did not occur when DNase was added to DNA clearly indicating that transformation is blocked by the destruction of DNA Based on these observations Avery MacLeod and McCarty correctly concluded that DNA is the transformation factor and the probable hereditary material 0 Evidence in a 1952 report by Alfred Hershey and Martha Chase show that DNA but not protein is responsible for bacteriophage infection of bacterial cells 0 In their experiment Hershey and Chase took advantage of an essential difference between the chemical composition of DNA and protein to con rm the hereditary of DNA 0 Proteins contain large amounts of sulfur but almost no phosphorus and conversely DNA contains a large amount of phosphorus but no sulfur Hershey and Chase grew phage cultures and different growth medium one containing sulfur to label protein another containing phosphorus to label DNA the researchers use radioactive labeled phages from each media to infect unlabeled host bacterial cells in parallel experiments 0 After a short of a time each mixture was agitated in a blender to separate bacterial cells from the now empty phage cells the relatively large bacteria cells were easily separated from the empty phage cells by centrifuge The heavier bacteria collected in a pellet at the bottom where the later empty phages remain suspended in the supernatant testing each fraction for radioactivity revealed that virtually all the phosphorus label associated with the newly infected bacterial cells and almost none with the empty phages on the other hand the sulfur labels were found in the phage fraction and only trace amounts are found associate in the bacterial pellet The results demonstrated that phage DNA but not phage protein is transferred to host bacterial cells and directs the synthesis of phage DNA and proteins the assembly of progeny phage particles and ultimately the lysis of infected cells 0 Experiment demonstrated the transformation factor identi ed previously by Grif th was DNA it also showed that Avery MacLeod and McCarty were correct in concluding that DNA is the hereditary material SECTION 72 THE DNA DOUBLE HELIX CONSISTS OF TWO COMPLEMENTARY AND ANTIPARALLEL STRANDS DNA nucleotide has three compnents o A deoxyribose sugar 0 One of four nitrogenous bases 0 Up to three phosphate groups Deoxyribose sugar 0 5 carbons identi ed as 139239 3394 and 539 An oxygen atoms connects to the 1 carbon and to the 439 to form a pentose ring 539 carbon protrudes from the ring from the 439 carbon Nucleotide is attached to the 139 carbon by a covalent bond Hydroxyl group attached to the 339 carbon Phosphate molecule or chain is attached at the 539 carbon Hydrogen atms at 239 carbon instead of a hydroxyl group 0 00000 Four nitrogeonous bases 0 Single ring pyrimidines Cytosine and thymine 0 Double ring purines Adenine and guanine Nucleotides part of a polynucleotide chain have one phosphate group at their 539 carbon that forms the covalent phosphodiester bond with the adjacent nucleotide in the strand dAMP and dGMpP carry purines adenine and guanine while dCMP and dTMP carry the pyrimidines cytosine and thymine 0 these are deoxynucleotide monophosphates free DNA nucleotides not in a chain carry a string of 3 phosphates at the 539 carbon and are identi ed as dATP dGTP dCTP and d39lTP o collectively known as deoxynucleotide triphosphates nucleotides are assembled into the nucleotide by enzyme DNA polymerase which catalyzes the formation of the phosphodiester bond between the 339 hydroxyl group of one nucleotide and the 539 phosphate group of an adjacent nucleotide each polynucleotide chain has a sugar phosphate backbone consisting of alternating sugar and phosphate groups throughout its length DNA is most stable as a double helix and the two nucleotide strands have two rules they need to follow in their speci c relationship 0 Arrangement of the nuceotides is such that the nucleotide bases of one strand are complementary to the corresponding nucleotide bases on the second strand 0 The two strands are antiparallel in orientation Complementary base pairing joins a pyrimidine from one strand to a purine on the other 0 Chemical basis of this is due to hydrogen bonding numbers between the bases of different strands Noncovalent bonds that form between the partial charges that are associated with hydrogen oxygen and nitrogen atoms of nucleotide bases Antiparallel strand nature is essential to the formation of stable hydrogen bonds 0 Brings the partial charges of the complementary nucleotides in alignment to form hydrogen bonds In DNA distance from axis of symmetry to the outer edge of the sugar phosphate backbone is 10 angstroms 1 nm and the molecular diameter at any part of the helix is 20 angstroms 2nm Tight packing of DNA bases in the duplex leads to base stacking which imparts a twist on the double helix Base pair stacking causes major and minor grooves which partially expose the nucleotides 0 Regions where DNA binding proteins can most easily make direct contact with nucleotides along one or both strands of the double helix SECTION 73 DNA REPLICATION IS SEMICONSERVATIVE AND BIDIRECTIONAL Three attributes of DNA replication shared by all organisms 0 Each strand of the parental DNA molecule remains intact during replication 0 Each parental strand serves as a template directing the synthesis of complementary antiparallel daughter strand 0 Completion of DNA replication results in the formation of two identical daughter duplexes each composed of one parental strand and one daughter strand 0 3 proposed models of DNA replication 0 Semiconservative DNA replication propsed that each daughter duplex contains one original parental strand of DNA and one complementary newly synthesized daughter strands o Conservative DNA replication predicts that one daughter duplex contains two strands of the parental molecule and the other contains two newly synthesized daughter strands o Dispersive DNA replication predicts that each daughter duplex is a composite of interspersed parental duplex segments and daughter duplex segments MesselsonStahl Experiment 0 Proved that the semiconservative model of replication was the correct model 0 ln bacteria DNA replication is bidirectional from one origin site 0 Proved by the pulse chase labeling experiment performed byJoel Huberman and Arthur Riggs Autoradiograph evidence revealed multiple origin sites for DNA replication Eukaryotic replication origins initiate asynchronously during S pahse Eukaryotic DNA replication produces sister chromatids SECTION 74 DNA REPLICATION PRECISELY DUPLICATES THE GENETIC MATERIAL 0 Bacterial archaeal and yeast DNA replication begins at speci c locations the bind replication initiation proteins Speci c conserved sequences are found in bacteria but replication initiation is directed by chromatin state in eukaryotes 0 DNA replication begins with the synthesis of an RNA primer by primase followed by the synthesis of leading and lagging DNA strands by DNA polymerase 0 To complete replication RNA primers are removed by DNA polymerase and DNA segments are joined by DNA ligase 0 DNA polymerases not only to replicate DNA but also proofread newly synthesized DNA for accuracy o Eukaryotic and archaeal DNA replication proteins have a high degree of homology re ecting a shared common ancestry Bacteria have analogous proteins but are ancestrally more distant Eukaryotic chromosomes have repetitive sequences called teomeres at their ends that shorten with each replication in somatic cell cycles 0 Telomerase is a ribonucleoprotein that synthesizes teomeric repeat sequences to maintain teomere length in germline and stem cells SECTION 75 MOLECULAR GENETIC ANALYTICAL METHODS MAKE USE OF DNA REPLICATION PROCESSES The polymerase chain reaction PCR is used to produce large numbers of copies to target DNA sequences Dideoxynucleotide DNA sequencing is used to determine the sequence of DNA fragments Nextgeneration and thirdgeneration DNA sequencing are much faster and far cheaper methods that have paved the way for large numbers of genome sequencing projects and personal human genome sequencing VOCABULARY WORDS Bacteriophage a virus whose host is a bacterium Base stacking a phenomenon of DNA basepair interaction that rotates the base pairs around a central axis of symmetry and imparts twisting to a double helix Bidriectional DNA replication the standard method of DNA replication that synthesizes new DNA in both directions from a replication origin Clamp loader a multiprotein complex that pairs with DNA polymerase and the sliding clamp during replication Consensus sequence a nucleotide sequence in a DNA segement derived by comparing sequences of similar segments from other genes or organisms The most commonly occurring nucleotides at each position compromise the sequence Deoxynucleotide 539 monophosphate dNMPs monophosphate forms of deoxynucleotides Deoxynucleotide 539 triphosphate dNTPs thriphosphate forms of deoxynucleotides Dideoxy DNA sequencing a method of DNA sequencing devised by Fred Sanger that uses a mixture of deoxynucleotide and Dideoxynucleotide triphosphates to selectively block DNA replication producing a ladder of partially synthesized DNA strands of different lengths Dideoxynucleotide triphosphates ddNtPs rare DNA nucleotides absent oxygen molecules at the 239 and 339 carbons that are most commonly used in Dideoxynucleotide DNA sequencing DNA ligase an enzyme active in DNA replication that joins together segments of a DNA stand by catalyzing formation of phosphodiester bonds DNA polymerase the large multisubunit complex responsible for the synthesis of new strands of DNA during DNA replication or DNA repair DNA proofreading the capacity of many types of DNA polymerase to utilize a 339 to 539 exonuclease activity to remove and replace mismatched or damaged nucleotides during replication DNA replication the synthesis of new DNA strands by complementary base pairing of nucleotides in a daughter strand to those in a template strand Helicase in DNA replication the enzyme responsible for breaking down hydrogen bonds between complementary nucleotides of a DNA duplex Unwinding of the strands occurs ahead of the advancing replication fork Lagging strand in DNA replication the discontinuously synthesized strand whose Okazaki fragments are ligated to complete new strand synthesis Leading strand ln DNA replication the continuously synthesized strand Major groove the larger of two grooves formed in the DNA sugarphosphate backbone by the helical twist of the double helix and exposing certain base paIrs Minor groove the smaller of two grooves formed in the DNA sugarphosphate backbone by the helical twist of the double helix and exposing certain base paIrs Nextgeneration sequencing high throughout massively parallel DNA sequencing by synthesis Okazaki fragments a short segment of newly synthesized DNA that is part of a lagging strand that is ligated to other Okazaki fragments to complete lagging strand synthesis Origin of replication the speci c sequence at which DNA replication begins Polymerase chain reaction PCR a laboratory method for controlled replication of a speci c target sequence of DNA in successive cycle Using teo short singlestranded primers that bind to sequences on opposite sides of the target sequence exponential replication of the target sequence occurs Primase DnaG the specialized RNA polymerase that synthesizes the RNA primer during DNA replication Proliferating cell nuclear antigen PCNA in eukaryoutic DNA replication the functional equivalent of the bacterial sliding clamp that adheres DNA polymerase to the template strand and drives its progression Replication bubble a region of active bidirectional DNA replication containing replication forks on each end an origin of replication in the middle and the leading and lagging strands in each half of the bubble Replication fork in DNA replication the site of the replisome structure and the site of synthesis of the leading strand and lagging strand DNA Replisome the large molecular machine located at the replication fork that coordinates multiple reaction steps during DNA replication RNA primer in DNA replication the short singlestranded RNA segment synthesized by primase The 339 end of the RNA primer is used by DNA polymerase to begins synthesis of DNA Singlestranded binding protein in DNA replication a protein that adheres to each template strand following unwinding by helicase to prevent strand reannealing before the arrival of the replication fork Sliding clamp in bacterial DNA replication the multisubunit protein complex the joins with DNA polymerase to hold polymerase on the template and helps drive polymerase along the template Sugarphosphate backbone the alternating sugar deoxyribose or ribose and phosphate molecule pattern of nucleic acid strands formed by the formation of phosphodiester bonds linking nucleotides in the strand Supercoiled DNA the superhelical twisting of covalently closed circular DNA Telomerase the ribonucleoprotein complex whose RNA component provides a template used to synthesize repeating DNA segments that form chromosome telomeres Telomere Repeating DNA sequences synthesized by telomerase at the ends of linear chromosomes of eukaryotes contains dozens to hundreds of copies of speci c short DNA sequence repeats that buffer the coding sequence of the chromosome from loss during successive cycles of DNA replication Topoisomerase enzyme that relaxes DNA supercoiling by controlled strand nicking and rejoining CHAPTER 8 NOTES CHAPTER 8 MOLECULAR BIOLOGY OF TRANSCRIPTION AND RNA PROCESSING SECTION 81 RNA TRANSCRIPTS CARRY THE MESSAGES OF GENES RNA is single stranded but can adopt folded secondary structures essential to RNA function Nucleotides composed of a ve carbon sugar a nucleotide base and one or more phosphate groups Purines same as in DNA adenine and guanine but pyrimidines are different uracil and cytosine Sugar is ribose instead of deoxyribose Major RNA molecules Type of RNA Function Messenger RNA Used to encode the sequence of amino acids in mRNA polypeptide may be polycistronic in bacteria and archaea Encodes single polypeptides in nearly all eukaryotes Ribosomal RNA Along with numerous proteins helps form the large rRNA and small ribosomal subunits that unite for the translation of mRNA Transfer RNA tRNA Carries amino acids to ribosomes and binds there to mRNA by complementary bas pairing in order to deposit the amino acids to elongate the polypeptide Small nuclear RNA Found in eukaryotic nuclei where multiple snRNAs snRNA join with numerous proteins to form spliceosomes that remove introns from precursor mRNA microRNA miRNA Eukaryotic regulatory RNAs that have different and small interfering origins Involved in eukaryotic regulation of gene RNA siRNA expression Telomerase RNA Along with several proteins forms telomerase the ribonucleoprotein complex essential for maintaining and elongating telomere length of eukaryotic chromosomes SECTION 82 BACTERIAL TRANSCRIPTION IS A FOUR STAGE PROCESS 0 Four steps of bacterial transcription 0 Promoter recognition and identi cation 0 Initiation of transcript sequence 0 Transcript elongation o Transcription termination o A single RNA polymerase transcribes all bacterial genes This polymerase is a holoenzyme composed of a ve subunit core enzyme and a sigma subunit that aids the recognition of different forms of bacterial promoters Bacterial promoters have two consensus regions located upstream of the transcription start at approximately 10 and 35 The core enzyme of bacterial RNA polymerase carries out RNA synthesis following chain initiation by the holoenzyme Transcription of most bacterial genes terminates by an intrinsic mechanism that depends only on DNA terminator sequences Certain bacterial genes have a rhodependent mechanism of transcription termination SECTION 83 ARCHAEAL AND EUKARYOTIC TRANSCRIPTION DISPLAYS STRUCTURAL HOMOLOGY AND COMMON ANCESTRY Eukaryotic cells contain three types of RNA polymerases that transcribe mRNA an the various classes of functional RNA RNA polymerase II transcribes mRNA by interaction with numerous transcription factors that lead the enzyme to recognize promoters controlling transcription of polypeptidecoding genes Promoters recognized by RNA polymerase II have a TATA box and additional regulatory elements that bind transcription factors and RNA pol ll during transcription initiation Transcription shows similarities among all three domains of life due to the sharing of a common ancestor and the essential nature of transcription Archaeal transcription is a simpli ed version of eukaryotic transcription and is dissimilar from bacterial transcription Three archaeal transcription proteins TBP TFB and less often TFllE alpha share homology with bacterial and eukaryotic proteins and initiate transcription by interacting with RNA polymerase Eukaryotic promoter regulatory elements are recognized by their consensus sequences Tissuespeci c and developmental modi cations in transcription are regulated by enhancer and silencer sequences RNA polymerase I uses exclusive transcription factors to recognize upstream consensus sequences of ribosomal RNA genes RNA polymerase III recognizes promoter consensus sequence that are upstream and downstream of the start of transcription SECTION 84 POSTTRANSCRIPTIONAL PROCESSING MODIFIES RNA MOLECULES 539 capping of eukaryotic messenger RNA adds a methylated guanine through the action of guanylyl transferase shortly after transcription is initiated Polyadenylation at the 339 end of eukaryotic messenger RNA is signaled by an AAUAAA sequence and is accomplished by a complex of enzymes lntron splicing is controlled by cellular proteins that identify introns and exons and form spliceosome complexes that remove introns and ligate exons Consensus sequences at the 539 splice site the 339 splice site and the branch point serve as guides during intron splicing Alternative splicing is regulated by celltypespecific variation of proteins that identify introns and exons Some RNA molecules have catalytic activity and are able to selfsplice introns without the aid of proteins Ribosomal and transfer RNA molecules are generated by cleavage of large precursor molecules transcribed in bacterial archaeal and eukaryotic genomes RNA editing is a posttranscriptional altering of nucleotide sequence causing the transcripts to differ from the corresponding template DNA sequence CHAPTER 9 THE MOLECULAR BIOLOGY OF TRANSCRIPTION SECTION 91 POLYPEPTIDES ARE COMPOSED OF AMINO ACID CHAINS THAT ARE ASSEMBLED AT RIBOSOMES Polypeptides contain 20 kinds of amino acids that carry side chains giving them speci c properties Translation takes place at the ribosome where mRNA codons are coupled to transfer RNA anticodons by complementary base pairing Polypeptides have four structural levels the amino acid order primary intrachain folding secondary threedimensional functional folding tertiary and multimeric protein structure quaternary Polypeptides have an Nterminal amino end and a Cterminal carboxyl end Ribosomes are composed of two subunits that each consist of ribosomal RNA and numerous proteins Ribosomes have 3 functional sites of action the P site where the polypeptide is held the A site where tRNA molecules bind to add their amino acid to the end of their polypeptide and the E site which provides and exit point for uncharged tRNAs SECTION 92 TRANSLATION OCCURS IN THREE PHASES Bacterial translation is initiated with the binding of the ShineDalgarno sequence on the 539 mRNA end to a complementary sequence of nucleotides on the 339 end of the 16S rRNA in the small ribosomal unit The nearby start codon is the site where translation commences ln eukaryotic mRNA the 539 cap is the binding site for eukaryotic initiation factors that cause small ribosomal subunit to begin scanning in search of the start codon which is part of the Kozak sequence Archaea carry multiple translationinitiation factors that are homologous to eukaryotic initiation factors but they also produce a high proportion of leaderless mRNAs that have an unknown translationinitiation mechanism 0 During polypeptide synthesis charged tRNAs enter the A site and peptidyl transferase catalyzes peptide bond formation transferring the polypeptide from the Asite tRNA to the Psite tRNA Elongation factor proteins translocate the ribosome shifting the tRNA polypeptide complex from the A site to the P site and opening the A site for the next charged tRNA 0 Translation terminates when a stop codon enters the A site Release factor proteins rather than tRNA bind to stop codons Release factors cause release of the polypeptide and lead to the dissociation of the ribosome from mRNA SECTION 93 TRANSLATION IS FAST AND EFFICIENT An mRNA undergoes simultaneous translation by several ribosomes that attach to it sequentially to form a polyribosome Usually a ribosome will dissociate from mRNA upon encountering a stop codon but the small size of some intercistronic spacers in bacterial polycistronic mRNAs permits a ribosome to translate two or more polypeptides sequentially from the mRNA before dissociating The evolutionary evidence derived from homologies among translationally active proteins of members of the three domains of life suggests that archaea re more closely related to eukaryotes than they are to bacteria SECTION 94 THE GENETIC CODE TRANSLATE MESSENGER RNA INTO POLYPEPTIDE o The genetic code is redundant meaning that most amino acids are speci ed by more than one codon Redundancy of the genetic code is made possible by thirdbase wobble that relaxes the strict complementary basepairing requirements at the third base of the codon o Specialized enzymes called aminoacyltRNA synthetases catalyze the addition of a speci c amino acid to each tRNA SECTION 95 EXPERIMENTS DECIPHERED THE GENETIC CODE 0 In vitro experimental analysis demonstrates that the genetic code is triplet and does not contain gaps or overlaps 0 Each mRNA codon is composed of three consecutive nucleotides Of the 64 codons contained in the genetic code 61 specify amino acids are 3 are stop codons o The genetic code was deciphered by analysis of in vitro translation of synthetic messenger RNA 0 The genetic code is essential universal among living organisms The few exceptions to the genetic code are found mainly in mitochondria o Properly charged tRNAs play the central role in converting mRNA sequence into polypeptide sequence SECTION 96 TRANSLATION IS FOLLOWED BY POLYPEPTIDE FOLDING PROCESSING AND PROTEIN SORTING 0 Formation of functional proteins occurs after translation is completed and may be aided by ribosomeassociated proteins or by separate protein complexes 0 Proteins in eukaryotic cells are sorted into their cellular destinations by signal 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