Chapter9.Heredity1. Define heredity genetics, genome, gene, phenotype, and genotype.Genetics is the science that studies the inheritance of biological characteristics by living thingsThis subject, also known as heredity,is a wide-ranging science that examines:_the transmission ofbiological properties (traits)from parent to offspring._theexpression andvariation ofthose traits,the structure and function of thegenetic material, and_how this material changes or evolves.The genome is the sum total of genetic material carried within a cellAll chromosomes containa series of basic informational“packets"called genes.Agene canbedefined from more than one perspective.Genesfall into three basic categories: structural genesthat code for proteins, genes that code for RNA, and regulatory genes that control geneexpression.The sum of all of these types of genes constitutes an organism's distinctive geneticmakeup, or genotype. The expression of the genotype creates traits (certain structures orfunctions) referred to as the phenotype.2.Discuss the basic nature of genetic material in eukaryotes, prokaryotes,and virusesAlthough most of the genome exists in the form of chromosomes, genetic material can appear innonchromosomal sites as well. For example, bacteria and some fungi contain tiny extra pieces ofDNA (plasmids),and the mitochondria and chloroplasts of eukaryotes are equipped with their ownfunctional chromosomes.Genomes of cells are composed exclusively of DNA,but viruses containeither DNA or RNAastheprincipal genetic material.Although the specificgenome ofan individualorganism is unique,the general pattem of nucleic acid structure and function is sim ilar among allorganisms.3.Explain how DNA is organized and packaged.Ingeneral,a chromosome isadiscretecellular structurecomposedof a neatlypackaged DNAmolecule. The chromosomes of eukaryotes and bacterial cells differ in several respects. Thestructure of eukaryotic chromosomes consists of a DNA molecule tightly wound aroundhistone proteins, whereas a bacterial chromosome is condensed and secured into a packet bymeans of a different type of protein.Eukaryotic chromosomes are located in the nucleus, theyvary in number from a few to hundreds; they can occur in pairs (diploid) or singles (haploid);and they are linear in format In contrast, most bacteria have a single, circular chromosome,although some have multiple chromosomes and afew have linear chromosomes.4.Describethechemical structureofDNAand its significanceThe basic unit of DNA structure is a nucleotide, composed of phosphate, deoxyribose sugar,and a nitrogen base. Each deoxyribose sugar bonds covalently in a repeating pattern with twophosphates.Oneofthebondsisto thenumber5(read“fiveprime")carbonon deoxyribose,andtheother is to the 3carbon, which specifi es the order and direction of each strand.This formationresults in an elongate strand with a sugar-phosphate backbone. Other important considerations ofDNA structure concern the nature of the double helix itself.The two strands are not oriented in the1
1 Chapter 9. Heredity 1. Define heredity, genetics, genome, gene, phenotype, and genotype. Genetics is the science that studies the inheritance of biological characteristics by living things. This subject, also known as heredity, is a wide-ranging science that examines: _ the transmission of biological properties (traits) from parent to offspring, _ the expression and variation of those traits, _ the structure and function of the genetic material, and _ how this material changes or evolves. The genome is the sum total of genetic material carried within a cell. All chromosomes contain a series of basic informational “packets” called genes. A gene can be defined from more than one perspective. Genes fall into three basic categories: structural genes that code for proteins, genes that code for RNA, and regulatory genes that control gene expression. The sum of all of these types of genes constitutes an organism’s distinctive genetic makeup, or genotype. The expression of the genotype creates traits (certain structures or functions) referred to as the phenotype. 2. Discuss the basic nature of genetic material in eukaryotes, prokaryotes, and viruses. Although most of the genome exists in the form of chromosomes, genetic material can appear in nonchromosomal sites as well. For example, bacteria and some fungi contain tiny extra pieces of DNA (plasmids), and the mitochondria and chloroplasts of eukaryotes are equipped with their own functional chromosomes. Genomes of cells are composed exclusively of DNA, but viruses contain either DNA or RNA as the principal genetic material. Although the specifi c genome of an individual organism is unique, the general pattern of nucleic acid structure and function is sim ilar among all organisms. 3. Explain how DNA is organized and packaged. In general, a chromosome is a discrete cellular structure composed of a neatly packaged DNA molecule. The chromosomes of eukaryotes and bacterial cells differ in several respects. The structure of eukaryotic chromosomes consists of a DNA molecule tightly wound around histone proteins, whereas a bacterial chromosome is condensed and secured into a packet by means of a different type of protein. Eukaryotic chromosomes are located in the nucleus; they vary in number from a few to hundreds; they can occur in pairs (diploid) or singles (haploid); and they are linear in format. In contrast, most bacteria have a single, circular chromosome, although some have multiple chromosomes and a few have linear chromosomes. 4. Describe the chemical structure of DNA and its significance. The basic unit of DNA structure is a nucleotide, composed of phosphate, deoxyribose sugar, and a nitrogen base. Each deoxyribose sugar bonds covalently in a repeating pattern with two phosphates. One of the bonds is to the number 5’(read “five prime”) carbon on deoxyribose, and the other is to the 3’ carbon, which specifi es the order and direction of each strand. This formation results in an elongate strand with a sugar-phosphate backbone. Other important considerations of DNA structure concern the nature of the double helix itself. The two strands are not oriented in the
same direction. One side of the helix runs in the opposite direction of the other, in what is called anantiparallel arrangement. The order of the bond between the carbon on deoxyribose and thephosphates is used to keep track of the direction of the two sides of the helix. Thus, one helix runsfrom the 5'to 3'direction, and the otherruns from the 39 to 59direction.This characteristic is asignificant factor in DNA synthesis and translation. As apparently perfect and regular as the DNAmolecule may seem, it is not exactly symmetrical The torsion in the helix and the stepwise stackingofthe nitrogen bases producetwodifferent-size surfacefeatures,themajorandminorgrooves.5. List the nitrogen bases and explain their bonding patterns.The nitrogen bases, purines and pyrimidines, attach by covalent bonds at the 1'position ofthe sugar.They spanthe center ofthemoleculeand pairwithappropriatecomplementarybasesfrom the other strand, thereby forming a double-stranded helix. The paired bases are soaligned as to be joined by hydrogen bonds. Such weak bonds are easily broken, allowing themolecule to beunzipped'into its complementary strands.This feature is of great importancein gainingaccessto the information encoded inthe nitrogen base sequence.Pairing of purinesand pyrimidines is not random; it is dictated by the formation of hydrogen bonds betweencertain bases.Thus, in DNA,the purine adenine(A)pairs with the pyrimidine thymine (T),and the purine guanine(G)pairs with the pyrimidine cytosine (C)6.Describe the process of DNAreplication as it occurs in prokaryotic cellsDNA replication requires a careful orchestration of the actions of 30 different enzymes,which separatethestrands of theexistingDNAmolecule,copy itstemplate, andproduce twocomplete daughter molecules.A simplified version ofreplication includes thefollowing:1.uncoilingtheparentDNAmolecule, beginningat a predetermined point of origin,2. unzipping the hydrogen bonds between the base pairs, thus separating the two strands andexposingthe nucleotide sequence ofeach strand (which is normallyburied in the centerof thehelix) to serve as templates; and3.synthesizingtwo new strandsby attachment of thecorrect complementarynucleotides toeach single-stranded template.9.2ApplicationsoftheDNACode:TranscriptionandTranslation1.Present anoverview of themainaspects oftheflowofgenetic information incellsAlthough thegenomeis full of critical information,the DNAmolecule itself cannotperformcell processes directly.Instead, its information is conveyed to RNAmolecules,which carry outthe instructions it contains. The concept that genetic information flows from DNA to RNA toprotein has long been a central theme of molecular biology.It states that the master code ofDNA is first used to synthesize RNA via a process called transcription, and the informationcontained in the RNAis then used to produce proteins in a process known as translation.Theprincipal exceptions to this pattern are found in RNA viruses, which convert RNA to otherRNA, and in retroviruses, which convert RNAto DNA.2. Explain the relationship between the structure ofDNA and the structure of proteins.Thefinalkeypoints that connectDNAandproteinfunction are1).DNA is a blueprint that indicates which kinds of proteins to make and how to make them2
2 same direction. One side of the helix runs in the opposite direction of the other, in what is called an antiparallel arrangement. The order of the bond between the carbon on deoxyribose and the phosphates is used to keep track of the direction of the two sides of the helix. Thus, one helix runs from the 5’ to 3’ direction, and the other runs from the 39 to 59 direction. This characteristic is a significant factor in DNA synthesis and translation. As apparently perfect and regular as the DNA molecule may seem, it is not exactly symmetrical. The torsion in the helix and the stepwise stacking of the nitrogen bases produce two different-size surface features, the major and minor grooves. 5. List the nitrogen bases and explain their bonding patterns. The nitrogen bases, purines and pyrimidines, attach by covalent bonds at the 1’ position of the sugar. They span the center of the molecule and pair with appropriate complementary bases from the other strand, thereby forming a double-stranded helix. The paired bases are so aligned as to be joined by hydrogen bonds. Such weak bonds are easily broken, allowing the molecule to be ‘unzipped’ into its complementary strands. This feature is of great importance in gaining access to the information encoded in the nitrogen base sequence. Pairing of purines and pyrimidines is not random; it is dictated by the formation of hydrogen bonds between certain bases. Thus, in DNA, the purine adenine (A) pairs with the pyrimidine thymine (T), and the purine guanine (G) pairs with the pyrimidine cytosine (C). 6. Describe the process of DNA replication as it occurs in prokaryotic cells. DNA replication requires a careful orchestration of the actions of 30 different enzymes, which separate the strands of the existing DNA molecule, copy its template, and produce two complete daughter molecules. A simplified version of replication includes the following: 1. uncoiling the parent DNA molecule, beginning at a predetermined point of origin; 2. unzipping the hydrogen bonds between the base pairs, thus separating the two strands and exposing the nucleotide sequence of each strand (which is normally buried in the center of the helix) to serve as templates; and 3. synthesizing two new strands by attachment of the correct complementary nucleotides to each single-stranded template. 9.2 Applications of the DNA Code: Transcription and Translation 1. Present an overview of the main aspects of the flow of genetic information in cells. Although the genome is full of critical information, the DNA molecule itself cannot perform cell processes directly. Instead, its information is conveyed to RNA molecules, which carry out the instructions it contains. The concept that genetic information flows from DNA to RNA to protein has long been a central theme of molecular biology. It states that the master code of DNA is first used to synthesize RNA via a process called transcription, and the information contained in the RNA is then used to produce proteins in a process known as translation. The principal exceptions to this pattern are found in RNA viruses, which convert RNA to other RNA, and in retroviruses, which convert RNA to DNA. 2. Explain the relationship between the structure of DNA and the structure of proteins. The fi nal key points that connect DNA and protein function are: 1). DNA is a blueprint that indicates which kinds of proteins to make and how to make them
This blueprintexists in the order of triplets along the DNA strands2).The order of triplets directs a protein's primary structure—the order and type of aminoacids in the chainwhich determines its characteristic shape and function.3). Proteins contribute significantly to the phenotype by functioning as enzymes and structuralmolecules.TripletsSinglenucleotide3524?DNACodonmRNA(copyofone strand)Aminoacids2354Variations intheorderandtypeswill dictate the shapeand function of the protein.igure9.9SimplifiedviewoftheDNA-protein3. Describe the different types of RNA and their basic functions in genetic expression.Ribonucleic acid (RNA ) is an encoded molecule like DNA, but its general structure isdifferent in several ways:1).It is a single-stranded molecule that can assume secondary and tertiary levels of complexitydue tobonds within themolecule,leading to specialized forms of RNA(mRNA,tRNA,andrRNA)2). RNA contains uracil, instead of thymine, as the complementary base-pairing mate foradenine. This does not change the inherent DNA code in any way because the uracil stillfollows the pairing rules.3). Although RNA is a single helix that consists of alternating sugar and phosphate molecules,the sugarinRNAis riboseratherthan deoxyribose.There are many functional RNA: most prominently, messenger RNA, transfer RNA, ribosomes,several types of enzymes, and a storehouse of raw materials. The many functional types of3
3 This blueprint exists in the order of triplets along the DNA strands. 2). The order of triplets directs a protein’s primary structure—the order and type of amino acids in the chain—which determines its characteristic shape and function. 3). Proteins contribute significantly to the phenotype by functioning as enzymes and structural molecules. 3. Describe the different types of RNA and their basic functions in genetic expression. Ribonucleic acid ( RNA ) is an encoded molecule like DNA, but its general structure is different in several ways: 1). It is a single-stranded molecule that can assume secondary and tertiary levels of complexity due to bonds within the molecule, leading to specialized forms of RNA (mRNA, tRNA, and rRNA). 2). RNA contains uracil, instead of thymine, as the complementary base-pairing mate for adenine. This does not change the inherent DNA code in any way because the uracil still follows the pairing rules. 3). Although RNA is a single helix that consists of alternating sugar and phosphate molecules, the sugar in RNA is ribose rather than deoxyribose. There are many functional RNA: most prominently, messenger RNA, transfer RNA, ribosomes, several types of enzymes, and a storehouse of raw materials. The many functional types of
RNArangefrom small regulatory pieces to large structural ones.All types of RNA areformedthrough transcription of a DNA gene, but only mRNA is further translated into proteinTABLE9.2Major Types of Ribonucleic Acid Involved in Protein SynthesisTranslatedRNATypeContains Codes ForFunction in CellYesMessenger (mRNA)Sequence of amino acids in proteinCarries the DNA master.codetotheribosonNoTransfer (tRNA)A cloverleaf RNA to.carry amino.acidsBrings aminoacidstoribosomeduring translatiorNoRibosomal (rRNA)Several largestructural rRNAmoleculesForms:the major part of a ribosomgandparticipatesinproteinsynthesiNoPrimerAn RNAthat can begin DNAreplicationPrimesDNA4. Explain what happens during transcription.During transcription, an RNA molecule is synthesized using the codes on DNA as a guide ortemplate.A large enzyme complex RNA polymerase, is responsible for this process.Transcription proceeds in three stages:initiation elongation, and termination.Initiationrequires the RNA polymerase to recognize a region on a gene called the promoter region.This region consists of two sets of DNA sequences located just before the initiation site.Theprimary function of the promoter is to provide aposition for initial binding of the RNApolymerase.Priorto thefirst synthesis step of transcription, theRNApolymerasebegins to separatethetwo strands of the DNA helix and forms an open“bubble'of sorts.This bubble serves as thespace where the bonds between the nucleotides of mRNA will actually be made.Only onestrand of DNA—the template strand is transcribed. This is the one that carries a messagethat can be translated into a protein.As elongation proceeds, the polymerase moves thetranscription bubble forward, exposing subsequent sections of DNA.It simultaneously bringsin nucleotidesthatare complementarytothe DNA templateand continuestoassemble themRNA strand. As with replication, this occurs in the 5'to 3' direction with regard to thegrowing mRNA. DNA that has already been transcribed rewinds back into its double helixstructure.The part of the mRNA strand that is already assembled remains attached to theenzymecomplexbuthangsoutofthewayof theprocessingmachineryAttermination, thepolymeraserecognizesanother codeonDNAneartheendof thegenethat signals the separation and release of the completed mRNA.It will go immediatelyto thetranslation phase on the ribosome.5.Describethegenetic code,codons,and anticodons,and howtheyrelatetooneanother.In fact the language of DNA exists in the order of groups of three consecutive bases, ortriplets, on one DNA strand The message of this transcribed strand is later read as a series oftriplets called codons. This compact molecule acts as a translator that converts RNA languageinto protein language.The bottom loop of the cloverleaf exposes a triplet, theanticodon,thatbothdesignatesthespecificityofthetRNAandcomplementsmRNA'scodons.6. Relate the participants and steps in translation (protein synthesis).In translation, all of the elements needed to synthesize a protein, from the mRNA to thetRNAs with amino acids, are brought together on the ribosomes. The process occurs in fivestages: initiation, elongation, termination, and protein folding and processingThe mRNA molecule leaves the DNA transcription site and is transported directly to4
4 RNA range from small regulatory pieces to large structural ones. All types of RNA are formed through transcription of a DNA gene, but only mRNA is further translated into protein. 4. Explain what happens during transcription. During transcription, an RNA molecule is synthesized using the codes on DNA as a guide or template. A large enzyme complex, RNA polymerase, is responsible for this process. Transcription proceeds in three stages: initiation, elongation, and termination. Initiation requires the RNA polymerase to recognize a region on a gene called the promoter region. This region consists of two sets of DNA sequences located just before the initiation site. The primary function of the promoter is to provide a position for initial binding of the RNA polymerase. Prior to the first synthesis step of transcription, the RNA polymerase begins to separate the two strands of the DNA helix and forms an open ‘bubble’ of sorts. This bubble serves as the space where the bonds between the nucleotides of mRNA will actually be made. Only one strand of DNA—the template strand —is transcribed. This is the one that carries a message that can be translated into a protein. As elongation proceeds, the polymerase moves the transcription bubble forward, exposing subsequent sections of DNA. It simultaneously brings in nucleotides that are complementary to the DNA template and continues to assemble the mRNA strand. As with replication, this occurs in the 5’ to 3’ direction with regard to the growing mRNA. DNA that has already been transcribed rewinds back into its double helix structure. The part of the mRNA strand that is already assembled remains attached to the enzyme complex but hangs out of the way of the processing machinery. At termination, the polymerase recognizes another code on DNA near the end of the gene that signals the separation and release of the completed mRNA. It will go immediately to the translation phase on the ribosome. 5. Describe the genetic code, codons, and anticodons, and how they relate to one another. In fact, the language of DNA exists in the order of groups of three consecutive bases, or triplets, on one DNA strand. The message of this transcribed strand is later read as a series of triplets called codons. This compact molecule acts as a translator that converts RNA language into protein language. The bottom loop of the cloverleaf exposes a triplet, the anticodon, that both designates the specifi city of the tRNA and complements mRNA’s codons. 6. Relate the participants and steps in translation (protein synthesis). In translation, all of the elements needed to synthesize a protein, from the mRNA to the tRNAs with amino acids, are brought together on the ribosomes. The process occurs in five stages: initiation, elongation, termination, and protein folding and processing. The mRNA molecule leaves the DNA transcription site and is transported directly to
ribosomes.Ribosomal subunits are specifi cally assembled ina waythatforms sites tohold themRNA and tRNAs.The ribosome thus recognizes these molecules and stabilizes reactionsbetweenthemWiththemRNAmessageinplaceontheassembled ribosome,thenextstepintranslationinvolves entrance of tRNAs withtheiraminoacids.Thepool of cytoplasm around the regioncontains a completearrayof tRNAs,previously charged byhavingthe correct aminoacidattached.The step in which the complementarytRNAmeets with the mRNAcode is guided bythe two sites on the large subunit of the ribosome called the P site (left)and the A site (right)Think of these sites as recessed spaces tucked within the two subunits of the ribosome, witheach site accommodating a tRNA.The ribosome also has an exit or E site where used tRNAsare released.Ingeneral, the ribosome shifts its readingframe alongthe mRNAfrom one codonto the next This brings each succeeding codon into place on the ribosome and makes a spacefor the next tRNA to enter Then, a peptide bond is formed between the amino acids on theadjacent tRNAs, and the polypeptide grows in length. The termination of protein synthesis isnot simplyamatter of reachingthelast codononmRNA.It isbrought about bythepresenceofat least one special codon occurring just after the codon for the last amino acid. Terminationcodons—UAA,UAG,and UGA-arecodonsfor which there isnocorresponding tRNA.Alsotermed nonsense or stop codons, they carry a necessary message: Stop here. When this codonis reached, a special enzyme breaks thebond between the final tRNA and the finishedpolypeptide chain, releasing it from the ribosome.Beforenewlymadeproteinscan carry outtheirstructural orenzymaticroles,theyoftenrequire finishing touches.Evenbefore the peptide chain is released from theribosome, itbeginsfoldingupon itselftoachieve itsbiologically activetertiary conformation.13.Distinguish major points of difference between prokaryotic and eukaryotic transcriptionandtranslation.Eukaryotes sharemany aspects of proteinsynthesis with prokaryotes.But theydodiffer insignificant ways.The start codon in eukaryotes is also AUG, but it codes foran alternateform ofmethionine. Another difference is that eukaryotic mRNAs code for just one protein,unlikebacterialmRNAs,whichoften containinformationfrom several genes in series.Prokaryotic and eukaryotic cells also vary in location and structure of genes.The presence ofDNA in the nucleus ofeukaryotic cells means that eukaryotic transcription and translation cannotbe simultaneous as it is in prokaryotes. The mRNA transcript must pass through pores in thenuclear membrane and becarried to theribosomes inthe cytoplasm or on the endoplasmicreticulumfortranslationA eukaryotic gene contains the code for a protein, but located along the gene are one to severalintervening sequences of bases,called introns,that do not codefor protein.Introns areinterspersed between codingregions, called exons,that will betranslated intoprotein.9.3GeneticRegulationof Protein SynthesisandMetabolism1. Explain the functions ofoperons in bacterial genetic control.An operon is a section of DNA that contains one or more structural genes along with acorresponding operator gene that controls transcription.Many catabolic operons are induciblemeaning that the operon is turned on (induced)by the substrate of the enzyme for which the
5 ribosomes. Ribosomal subunits are specifi cally assembled in a way that forms sites to hold the mRNA and tRNAs. The ribosome thus recognizes these molecules and stabilizes reactions between them. With the mRNA message in place on the assembled ribosome, the next step in translation involves entrance of tRNAs with their amino acids. The pool of cytoplasm around the region contains a complete array of tRNAs, previously charged by having the correct amino acid attached. The step in which the complementary tRNA meets with the mRNA code is guided by the two sites on the large subunit of the ribosome called the P site (left) and the A site (right). Think of these sites as recessed spaces tucked within the two subunits of the ribosome, with each site accommodating a tRNA. The ribosome also has an exit or E site where used tRNAs are released. In general, the ribosome shifts its reading frame along the mRNA from one codon to the next. This brings each succeeding codon into place on the ribosome and makes a space for the next tRNA to enter. Then, a peptide bond is formed between the amino acids on the adjacent tRNAs, and the polypeptide grows in length. The termination of protein synthesis is not simply a matter of reaching the last codon on mRNA. It is brought about by the presence of at least one special codon occurring just after the codon for the last amino acid. Termination codons—UAA, UAG, and UGA—are codons for which there is no corresponding tRNA. Also termed nonsense or stop codons, they carry a necessary message: Stop here. When this codon is reached, a special enzyme breaks the bond between the final tRNA and the finished polypeptide chain, releasing it from the ribosome. Before newly made proteins can carry out their structural or enzymatic roles, they often require finishing touches. Even before the peptide chain is released from the ribosome, it begins folding upon itself to achieve its biologically active tertiary conformation. 13. Distinguish major points of difference between prokaryotic and eukaryotic transcription and translation. Eukaryotes share many aspects of protein synthesis with prokaryotes. But they do differ in significant ways. The start codon in eukaryotes is also AUG, but it codes for an alternate form of methionine. Another difference is that eukaryotic mRNAs code for just one protein, unlike bacterial mRNAs, which often contain information from several genes in series. Prokaryotic and eukaryotic cells also vary in location and structure of genes. The presence of DNA in the nucleus of eukaryotic cells means that eukaryotic transcription and translation cannot be simultaneous as it is in prokaryotes. The mRNA transcript must pass through pores in the nuclear membrane and be carried to the ribosomes in the cytoplasm or on the endoplasmic reticulum for translation. A eukaryotic gene contains the code for a protein, but located along the gene are one to several intervening sequences of bases, called introns, that do not code for protein. Introns are interspersed between coding regions, called exons, that will be translated into protein. 9.3 Genetic Regulation of Protein Synthesis and Metabolism 1. Explain the functions of operons in bacterial genetic control. An operon is a section of DNA that contains one or more structural genes along with a corresponding operator gene that controls transcription. Many catabolic operons are inducible, meaning that the operon is turned on (induced) by the substrate of the enzyme for which the