Biochemistry Chapter 8 PDF

Chapter 8 DNA, RNA, and the Flow of Genetic Information © 2023 W. H. Freeman and Company  CHAPTER 8 DNA, RNA, and the Flow of Genetic Information  Ch.8 Learning Goals By the end of this chapter, you should be able to: 1. Identify the bases for DNA and RNA and dis...

Chapter 8 DNA, RNA, and the Flow of Genetic Information © 2023 W. H. Freeman and Company  CHAPTER 8 DNA, RNA, and the Flow of Genetic Information  Ch.8 Learning Goals By the end of this chapter, you should be able to: 1. Identify the bases for DNA and RNA and distinguish between nucleosides and nucleotides. 2. Distinguish between DNA and RNA in both structure and function. 3. Explain how DNA is replicated. 4. Explain how information flows from DNA to protein. 5. Identify some key differences between bacterial and eukaryotic genes.  Ch.8 Outline 8.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar–Phosphate Backbone 8.2 A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure 8.3 The Double Helix Facilitates the Accurate Transmission of Hereditary Information 8.4 DNA Is Replicated by Polymerases That Take Instructions from Templates 8.5 Gene Expression Is the Transformation of DNA Information into Functional Molecules 8.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point 8.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons  The Central Dogma DNA and RNA = long linear polymers called nucleic acids Nucleic acids carry information in a form that can be passed from one generation to the next. central dogma = the flow of genetic information from DNA to RNA to proteins  Section 8.1 A Nucleic Acid Consists of Four Kinds of Bases Linked to a Sugar–Phosphate Backbone deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) = linear polymers that are well suited to function as carriers of genetic information nucleotide = each monomer unit within the polymer Each nucleotide consists of: – a sugar. – a phosphate. – one of four bases. Polymeric Structure of Nucleic Acids The sequence of the bases constitutes a form of linear information.  DNA and RNA Differ in the Sugar Component and One of the Bases ribose = the sugar in RNA – The 2′-carbon atom of the sugar is linked to hydroxyl (–OH) group. deoxyribose = the sugar in DNA – The 2′-carbon atom of the sugar is linked to a hydrogen atom. – Absence of a 2′–OH increases resistance to hydrolysis. Ribose and Deoxyribose  The Backbones of DNA and RNA Backbones of DNA and RNA consist of sugars linked by phosphodiester bridges. The 3′–OH of one sugar is esterified to a phosphate group which is joined to the and the 5′–OH of an adjacent sugar. Backbone is constant in a nucleic acid. Each phosphodiester bridge has a negative charge. – repels nucleophilic species that can hydrolyze the backbone Sugar–Phosphate Backbones of Nucleic Acids  The Bases of DNA and RNA Bases are attached to the 1′ carbon atom of the sugar. Two of the DNA bases are derivatives of purines = adenine (A) and guanine (G). Two of the DNA bases are derivatives of pyrimidines = cytosine (C) and thymine (T). RNA contains the pyrimidine derivative uracil (U) instead of thymine (T). Purines and Pyrimidines  Nucleotides Are the Monomeric Units of Nucleic Acids nucleoside = a unit consisting of a base bonded to a sugar – RNA nucleosides = adenosine, guanosine, cytidine, and uridine – DNA nucleosides = deoxyadenosine, deoxyguanosine, deoxycytidine, and thymidine nucleotide = a nucleoside joined to 1+ phosphoryl groups by an ester linkage – nucleoside triphosphates are the precursors of DNA and RNA  N-β-Glycosidic Linkages The C-1′ of the sugar is attached to the N-9 of a purine or the N-1 of a pyrimidine by N-β- glycosidic linkage.  DNA Molecules Are Very Long and Have Directionality DNA molecules must comprise many nucleotides to carry the necessary genetic information. E. coli genome = a single DNA molecule consisting of two strands of 4.6 million nucleotides each  Some DNA Molecules Can Be Extremely Large Humans have ~3 billion nucleotides in each strand of DNA. – divided among 24 chromosomes (22 autosomal and 2 sex chromosomes (X and Y)) The Indian muntjac has a similar sized genome distributed on 3 chromosomes.  DNA Chains Have Directionality DNA chains have directionality (polarity). – One end has a free 5′–OH group or a 5′–OH group attached to a phosphoryl group. – The other end has a free 3′–OH group. By convention, nucleic acid sequences are written from left to right in the 5′-to-3′ direction.  The Structure of a Nucleic Acid Chain Can Be Simplified Nucleic acid chains are represented by only the identity of the bases.  Which statement is true? (1 of 2) a. Each phosphodiester bridge in a nucleic acid backbone has a positive charge. b. Nucleosides consist of a base bonded to a sugar. c. The bases in DNA are adenine (A), thymine (T), guanine (G), and uracil (U). d. Nucleic acids are written in the 3′-to-5′ direction. e. RNA contains the sugar deoxyribose, whereas DNA contains ribose. © Macmillan Learning, 2023  Which statement is true? (2 of 2) a. Each phosphodiester bridge in a nucleic acid backbone has a positive charge. *b. Nucleosides consist of a base bonded to a sugar. c. The bases in DNA are adenine (A), thymine (T), guanine (G), and uracil (U). d. Nucleic acids are written in the 3′-to-5′ direction. e. RNA contains the sugar deoxyribose, whereas DNA contains ribose. © Macmillan Learning, 2023  Section 8.2 A Pair of Nucleic Acid Strands with Complementary Sequences Can Form a Double-Helical Structure The double helix: – forms because bases on two separate nucleic acid strands form specific base pairs. – is stabilized by hydrogen bonds and van der Waals interactions. – facilitates the replication of genetic material. X-Ray Diffraction Photograph of a Hydrated DNA Fiber Features of the Watson–Crick Model features deduced from diffraction patterns are: – two helical, antiparallel polynucleotide strands are coiled around a common axis in a right-handed helix – the sugar–phosphate backbones are on the outside and the purine and pyrimidine bases lie on the inside of the helix – bases are nearly perpendicular to the helix axis – adjacent bases are separated by ~3.4 Å – the helical structure repeats every 34 Å, with ~10.4 bases per turn of helix – there is a rotation of nearly 36 degrees per base – the diameter of the helix is about 20 Å Watson–Crick Model of DNA  Structures of the Base Pairs Proposed by Watson and Crick When guanine pairs with cytosine and adenine with thymine, the base pairs have essentially the same shape. Base pairs are held together by weak hydrogen bonds.  If a segment of DNA has the sequence ATCGGCTAAGC, what is the complementary sequence (written in the 3′-to-5′ direction)? (1 of 2) © Macmillan Learning, 2023  If a segment of DNA has the sequence ATCGGCTAAGC, what is the complementary sequence (written in the 3′-to-5′ direction)? (2 of 2) TAGCCGATTCG © Macmillan Learning, 2023  Base Compositions Experimentally Determined for a Variety of Organisms In the 1940s, Erwin Chargaff observed that the A:T and G:C ratios were each nearly 1:1 in a variety of organisms while the A:G ratio varied. TABLE 8.1 Base compositions experimentally determined for a variety of organisms Organism A :T G: C A: G Human being 1.00 1.00 1.56 Salmon 1.02 1.02 1.43 Wheat 1.00 0.97 1.22 Yeast 1.03 1.02 1.67 Escherichia coli 1.09 0.99 1.05 Serratia marcescens 0.95 0.86 0.70  Stacking of Base Pairs Base stacking contributes to the stability of the double helix because: – double helix formation is facilitated by the hydrophobic effect. – stacked base pairs attract one another through van der Waals forces.  DNA Can Assume a Variety of Structural Forms B-form = right-handed double helix made up of anti-parallel strands held together by Watson–Crick base pairs – most DNA under physiological conditions A-form = similar to B-form, but wider and shorter with tilted base pairs relative to the helix axis – seen in RNA double helices and RNA–DNA hybrid helices Z-form = left-handed double helix with zigzagged phosphoryl groups – unknown biological role, but Z-DNA-binding proteins have been isolated B-Form, A-Form, and Z-Form DNA  Sugar Pucker Explains Many Structural Differences Between B- Form and A-Form DNA In A-DNA, C-3′ lies out of the plane formed by the other four atoms of the ring (C-3′ endo). – leads to an 11-degree tilting of the base pairs In B-DNA, C-2′ lies out of the plane (C-2′ endo).  Comparison of A-, B-, and Z-DNA TABLE 8.2 Comparison of B-, A-, and Z-DNA B A Z Shape Intermediate Broadest Narrowest Rise per base pair 3.4 Å 2.3 Å 3.8 Å Helix diameter ~20 Å ~26 Å ~18 Å Screw sense Right-handed Right-handed Left-handed Glycosidic bond* anti anti Alternating anti and syn Base pairs per turn of helix 10.4 11 12 Pitch per turn of helix 35.4 Å 25.3 Å 45.6 Å Tilt of base pairs from 1 degree 19 degrees 9 degrees perpendicular to helix axis *Syn and anti refer to the orientation of the N-glycosidic bond between the base and deoxyribose. In the anti ori- entation, the base extends away from the deoxyribose. In the syn orientation, the base is above the deoxyribose. Pyrimidines can be in anti orientations only, whereas purines can be anti or syn.  The Major and Minor Grooves Are Lined by Sequence-Specific Hydrogen-Binding Groups Major and minor groove arise because glycosidic bonds of a base pair are not diametrically opposite each other. Major groove is wider and deeper than the minor groove. Hydrogen-bond donor and acceptor atoms in the grooves enable interactions with proteins. – essential for replication and transcription The Major and Minor Groove  Some DNA Molecules Are Circular and Supercoiled DNA molecules must be compacted to fit inside cells. E. coli has a circular DNA molecule that is twisted into a superhelix by the process of supercoiling. Supercoiling is biologically important. – Supercoiled DNA is more compact than relaxed DNA. – Supercoiling may hinder or favor the capacity of the double helix to unwind and interact with other molecules. Relaxed and Supercoiled Circular DNA Forms  Single-Stranded Nucleic Acids Can Adopt Elaborate Structures (1 of 2) stem-loop = common structural motif seen in nucleic acids – occurs when two complementary sequences within a single strand form a double helix – can include mismatched base pairs or unmatched bases  Single-Stranded Nucleic Acids Can Adopt Elaborate Structures (2 of 2) stem-loop = common structural motif seen in nucleic acids – occurs when two complementary sequences within a single strand form a double helix – can include mismatched base pairs or unmatched bases more elaborate structures may form, often stabilized by Mg2+ ions Stem-Loop Structures Identify a stem loop structure. (1 of 2) © Macmillan Learning, 2023 Identify a stem loop structure. (2 of 2) © Macmillan Learning, 2023 Complex Structure of an RNA Molecule  Section 8.3 The Double Helix Facilitates the Accurate Transmission of Hereditary Information Separation of the double helix yields two single-stranded templates. Because of the base-pairing rules, the sequence of one strand determines the sequence of the partner strand. semiconservative replication = process by which each replicated DNA molecule contains one parent strand and one newly-synthesized daughter strand Semiconservative Replication  The Double Helix Can Be Reversibly Melted During replication or transcription, the two strands of the double helix must be separated. In the laboratory, DNA strands can be separated by heating a solution of DNA or adding acid or alkali. In cells, helicases use chemical energy to disrupt the helix. melting = dissociation of a double helix melting temperature (Tm) = temperature at which half of the helical structure is lost annealing = renaturation of a double helix – occurs when the temperature is lowered below Tm  Monitoring the Melting Process hypochromism = effect where bases stacked in a double helix absorb less ultraviolet light at 260 nm than bases in a single-stranded molecule Melting can be monitored by measuring the increase in absorption of 260 nm light. Hypochromism  DNA replication: (1 of 2) a. is called conservative because each new helix retains both of the parental strands. b. only occurs when the temperature is increased above the Tm. c. requires hydrogen bonds to be disrupted. d. is accompanied by a decrease in absorption of 260 nm light. e. results in second-generation daughter molecules that do not contain any of the original parental strands. © Macmillan Learning, 2023  DNA replication: (2 of 2) a. is called conservative because each new helix retains both of the parental strands. b. only occurs when the temperature is increased above the Tm. *c. requires hydrogen bonds to be disrupted. d. is accompanied by a decrease in absorption of 260 nm light. e. results in second-generation daughter molecules that do not contain any of the original parental strands. © Macmillan Learning, 2023  Section 8.4 DNA Is Replicated by Polymerases That Take Instructions from Templates DNA polymerase catalyzes phosphodiester-bridge formation in a step-by-step manner (DNA)n + dNTP ⇌ (DNA)n+1 + PPi where dNTP is any deoxyribonucleotide and PPi is a pyrophosphate ion Key Characteristics of DNA Synthesis key characteristics include: – the reaction requires four deoxynucleoside 5′-triphosphates and Mg2+. – the new DNA strand is assembled on a preexisting DNA template (the template strand) – DNA polymerases require a primer to begin synthesis – chain elongation proceeds in the 5′-to-3′ direction – many DNA polymerases have nuclease activity to remove mismatched nucleotides DNA Polymerases Catalyze Strand Elongation  The Genes of Some Viruses Are Made of RNA Some viruses have RNA genomes that are replicated by RNA-directed RNA polymerases. – example = tobacco mosaic virus retroviruses = viruses with single-stranded RNA genomes that are converted to DNA double helices by reverse transcriptase – example = human immunodeficiency virus 1 (HIV-1) Flow of Information from RNA to DNA in Retroviruses  Section 8.5 Gene Expression Is the Transformation of DNA Information into Functional Molecules DNA is expressed in two steps: – Step 1: an RNA copy (messenger RNA, mRNA) is made that encodes directions for protein synthesis – Step 2: information in mRNA is translated to synthesize functional proteins  Several Kinds of RNA Play Key Roles in Gene Expression major kinds of RNA that are involved in gene expression: – messenger RNA (mRNA) = template for protein synthesis – transfer RNA (tRNA) = carries amino acids in an activated form to the ribosome for peptide-bond formation – ribosomal RNA (rRNA) = major component of ribosomes that serves as the actual catalyst for protein synthesis  RNA Molecules in E. coli TABLE 8.3 RNA molecules in E. coli Sedimentation Number of Type Relative amount (%) coefficient (S) Mass (kDa) nucleotides Ribosomal RNA 23 1.2 × 103 3700 (rRNA) 80 16 0.55 × 103 1700 5 3.6 × 101 120 Transfer RNA (tRNA) 15 4 2.5 × 101 75 Messenger RNA 5 Heterogeneous (mRNA)  All Cellular RNA Is Synthesized by RNA Polymerases transcription = synthesis of RNA from a DNA template RNA polymerase catalyzes the initiation and elongation of RNA chains (RNA)n residues + ribonucleoside triphosphate ⇌ (RNA)n+1 residues + PPi  RNA Polymerase RNA polymerase doesn't require a primer.  Key Requirements of RNA Polymerase RNA polymerase requires: – a double- or single-stranded DNA template. – four ribonucleoside triphosphates (ATP, GTP, UTP, and CTP). – a divalent metal ion (Mg2+ or Mn2+). RNA and DNA Synthesis Similarities The direction of synthesis is in the 5′-to-3′ direction. mechanism of elongation = 3′–OH at the terminus of the growing chain makes a nucleophilic attack on the innermost phosphoryl group of the incoming nucleoside triphosphate Synthesis is driven by pyrophosphate hydrolysis. RNA Polymerase Catalyzes the Strand-Elongation Reaction RNA Polymerases Take Instructions from DNA Templates Early evidence found that TABLE 8.4 Base composition (percentage) of RNA synthesized the base composition of from a viral DNA template the newly synthesized DNA template (plus, or RNA is the complement coding, strand of ϕX174) RNA product of the DNA template A 25 U 25 strand. T 33 A 32 G 24 C 23 C 18 G 20 Complementarity Between mRNA and DNA If a template strand of DNA has the sequence 3′–TCAAGGCGA–5′, what is the corresponding mRNA sequence (written in the 5′-to-3′ direction)? (1 of 2) © Macmillan Learning, 2023 If a template strand of DNA has the sequence 3′–TCAAGGCGA–5′, what is the corresponding mRNA sequence (written in the 5′-to-3′ direction)? (2 of 2) 5′–AGUUCCGCU–3′ © Macmillan Learning, 2023 Transcription Begins Near Promoter Sites and Ends at Terminator Sites promoter sites = regions along DNA templates that specifically bind RNA polymerase and determine where transcription begins – typically vary from an idealized single sequence, or consensus sequence, by only 1–2 residues – prokaryote examples: Pribnow box, –35 region – eukaryote examples: TATA box (Hogness box), CAAT box Promoter Sites for Transcription in Prokaryotes and Eukaryotes  Transcription Termination Prokaryote termination occurs when RNA polymerase synthesizes a terminator sequence or by the action of the protein rho. Terminator sequence is a stem-loop structure followed by a sequence of U residues. – Structure forms by base-pairing of self-complementary sequences that are rich in G and C. Less is known about eukaryote termination. A Stem-Loop Structure at the 3′ End of an E. coli mRNA Transcript  Modification of Eukaryotic mRNA in eukaryotes, mRNA is modified: – a "cap" structure (guanosine nucleotide attached to mRNA with a 5′-5′ triphosphate linkage) is attached to the 5′ end – a sequence of adenylates (a poly(A) tail) is added to the 3′ end  Transfer RNAs Are the Adaptor Molecules in Protein Synthesis Transfer RNAs (tRNAs): – bring amino acids to the mRNA. – contain an amino-acid attachment site and a template recognition site. – have several regions of base-paired segments in multiple stem loons. – are called aminoacyl-tRNAs when an amino acid is attached by an aminoacyl-tRNA synthetase. codon = three coding bases on the mRNA template anticodon = three complementary bases on the tRNA General Structure of an Aminoacyl- tRNA  Attachment of an Amino Acid to a tRNA Molecule The amino acid is attached to 3′–OH group of the ribose at the 3′ end of the tRNA molecule. CCA terminus = region at the 3′ end tRNA sequence that contains two cytidylates followed by an adenylate Section 8.6 Amino Acids Are Encoded by Groups of Three Bases Starting from a Fixed Point genetic code = the relation between the sequence of bases in DNA and the sequence of amino acids in proteins Features of the genetic code: – three nucleotides encode an amino acid – nonoverlapping – has no punctuation – has directionality – is degenerate (most amino acids are encoded by more than one codon)  The Genetic Code TABLE 8.5 The genetic Sixty-one code First position Second position Third position triplets specify (5' end) U C A G (3' end) Phe Ser Tyr Cys U amino acids. U Phe Ser Tyr Cys C Leu Ser Stop Stop A Leu Ser Stop Trp G Three triplets Leu Pro His Arg U C Leu Pro His Arg C are stop Leu Pro Gln Arg A codons that Leu Pro Gln Arg G lle Thr Asn Ser U designate A lle Thr Asn Ser C lle Thr Lys Arg A termination of Met Thr Lys Arg G translation. G Val Val Ala Ala Asp Asp Gly Gly U C Val Ala Glu Gly A Val Ala Glu Gly G Note: This table identifies the amino acid encoded by each triplet. For example, the codon 5'-AUG-3' on mRNA specifies methionine, whereas CAU specifies histidine. UAA, UAG, and UGA are termination signals. AUG is part of the initiation signal, in addition to coding for internal methionine residues.  For the codon AAA, click on the amino acid. (1 of 2) TABLE 8.5 The genetic code First position Second position Third position (5' end) U C A G (3' end) Phe Ser Tyr Cys U U Phe Ser Tyr Cys C Leu Ser Stop Stop A Leu Ser Stop Trp G Leu Pro His Arg U C Leu Pro His Arg C Leu Pro Gln Arg A Leu Pro Gln Arg G lle Thr Asn Ser U A lle Thr Asn Ser C lle Thr Lys Arg A Met Thr Lys Arg G Val Ala Asp Gly U G Val Ala Asp Gly C Val Ala Glu Gly A Val Ala Glu Gly G Note: This table identifies the amino acid encoded by each triplet. For example, the codon 5'-AUG-3' on mRNA specifies methionine, whereas CAU specifies histidine. UAA, UAG, and UGA are termination signals. AUG is part of the initiation signal, in addition to coding for internal methionine residues.  For the codon AAA, click on the amino acid. (2 of 2) TABLE 8.5 The genetic code First position Second position Third position (5' end) U C A G (3' end) Phe Ser Tyr Cys U U Phe Ser Tyr Cys C Leu Ser Stop Stop A Leu Ser Stop Trp G Leu Pro His Arg U C Leu Pro His Arg C Leu Pro Gln Arg A Leu Pro Gln Arg G lle Thr Asn Ser U A lle Thr Asn Ser C lle Thr Lys Arg A Met Thr Lys Arg G Val Ala Asp Gly U G Val Ala Asp Gly C Val Ala Glu Gly A Val Ala Glu Gly G Note: This table identifies the amino acid encoded by each triplet. For example, the codon 5'-AUG-3' on mRNA specifies methionine, whereas CAU specifies histidine. UAA, UAG, and UGA are termination signals. AUG is part of the initiation signal, in addition to coding for internal methionine residues.  The Genetic Code Is Highly Degenerate synonyms = codons that specify the same amino acids – most differ only in the last base of the triplet biological significance of degeneracy: – decreases probability of mutating to chain termination – minimizes the deleterious effects of mutations  Codon Bias codon bias = nonrandom use of synonymous codons in different organisms – may help regulate translation  Messenger RNA Contains Start and Stop Signals for Protein Synthesis ribosomes = large molecular complexes assembled from protein and ribosomal RNA mRNA is translated into proteins on ribosomes. Stop codons are read by proteins called release factors rather than tRNA molecules. The Start Signal for Protein Synthesis In prokaryotes: – an initiator tRNA carries a modified amino acid, formylmethionine (fMet), and recognized AUG. – the initiating AUG codon is preceded by the purine-rich Shine–Dalgarno sequence which base pairs with a complementary sequence in ribosomal RNA. In eukaryotes, the AUG nearest the 5 end is the initiator codon. reading frame = order of the three nonoverlapping nucleotides – established by the location of the initiator codon Initiation of Protein Synthesis The Genetic Code Is Nearly Universal Most organisms use the same genetic code because there is strong selection against deleterious mutations. Some genomes are translated by different code – example: in ciliated protozoa, codons that are stop codons in most organisms encode amino acids – example: mitochondria also use variations in the genetic code because mitochondrial DNA encodes a distinct set of tRNAs that recognize alternative codons Distinctive Codons of Human Mitochondria TABLE 8.6 Distinctive codons of human mitochondria Codon Standard Code Mitochondrial code UGA Stop Trp UGG Trp Trp AUA lle Met AUG Met Met AGA Arg Stop AGG Arg Stop  Section 8.7 Most Eukaryotic Genes Are Mosaics of Introns and Exons eukaryotic genes are discontinuous – exons = coding regions – introns = noncoding regions The average human gene has 8 introns, while some have more than 100. Intron size ranges from 50 to 10,000 nucleotides. RNA Processing Generates Mature RNA Eukaryotic pre-messenger RNA (pre-mRNA) contains exons and introns. Following modifications, introns are spliced out and coding sequences are linked at the 3' end. spliceosomes = assemblies of proteins and small nuclear RNA molecules (snRNAs) that carry out splicing  The Spliceosome Recognizes Specific Sequences Within the Intron That Specify the Splice Sites Introns almost always begin with a GU and end with an AG that is preceded by a pyrimidine-rich tract.  Most genes in eukaryotes: (1 of 2) a. are continuous. b. are transcribed and spliced to generate a primary transcript, which is then modified by cap and poly(A) addition. c. are randomly spliced to generate multiple proteins. d. contain introns that may or may not encode for protein. e. contain exons ordered in the same sequence in mRNA as in DNA. © Macmillan Learning, 2023  Most genes in eukaryotes: (2 of 2) a. are continuous. b. are transcribed and spliced to generate a primary transcript, which is then modified by cap and poly(A) addition. c. are randomly spliced to generate multiple proteins. d. contain introns that may or may not encode for protein. *e. contain exons ordered in the same sequence in mRNA as in DNA. © Macmillan Learning, 2023 Many Exons Encode Protein Domains Many exons encode discrete structural elements, binding sites, and catalytic sites. exon shuffling = process by which new proteins arise in evolution by the rearrangement of exons alternative splicing = process allowing the generation of multiple proteins from a primary transcript