Chapter 22 Nucleic Acids PDF

11/30/24 Chapter 22 Nucleic Acids 1 Chapter 22 Table of Contents 22.1 Types of Nucleic Acids 22.2...

11/30/24 Chapter 22 Nucleic Acids 1 Chapter 22 Table of Contents 22.1 Types of Nucleic Acids 22.2 Nucleotides: Building Blocks of Nucleic Acids 22.3 Primary Nucleic Acid Structure 22.4 The DNA Double Helix 22.5 Replication of DNA Molecules 22.6 Overview of Protein Synthesis 22.7 Ribonucleic Acids 22.8 Transcription: RNA Synthesis 22.9 The Genetic Code 22.10 Anticodons and tRNA Molecules 22.11 Translation: Protein Synthesis 22.12 Mutations 22.13 Nucleic Acids and Viruses 22.14 Recombinant DNA and Genetic Engineering 22.15 The Polymerase Chain Reaction 22.16 DNA Sequencing Copyright © Cengage Learning. All rights reserved 2 2 1  11/30/24 Section 22.1 Types of Nucleic Acids Cells in an organism are exact replicas Cells have information on how to make new cells Molecules responsible for such information are nucleic acids – Found in nucleus and are acidic in nature A nucleic acid is a polymer in which the monomer units are nucleotides. Two Types of Nucleic Acids: DNA: Deoxyribonucleic Acid: Found within cell nucleus – Storage and transfer of genetic information – Passed from one cell to other during cell division RNA: Ribonucleic Acid: Occurs in all parts of cell – Primary function is to synthesize the proteins Return to TOC Copyright © Cengage Learning. All rights reserved 3 3 Section 22.2 Nucleotides: Building Blocks of Nucleic Acids Nucleic Acids: Polymers in which repeating unit is nucleotide A Nucleotide has three components: – Pentose Sugar: Monosaccharide – Phosphate Group (PO43-) – Heterocyclic Base Base Phosphate Sugar Return to TOC Copyright © Cengage Learning. All rights reserved 4 4 2  11/30/24 Section 22.2 Nucleotides: Building Blocks of Nucleic Acids Pentose Sugar Ribose is present in RNA and 2-deoxyribose is present in DNA Structural difference: – a —OH group present on carbon 2’ in ribose – a —H atom in 2-deoxyribose RNA and DNA differ in the identity of the sugar unit in their nucleotides. Return to TOC Copyright © Cengage Learning. All rights reserved 5 5 Section 22.2 Nucleotides: Building Blocks of Nucleic Acids Nitrogen-Containing Heterocyclic Bases There are a total five bases (four of them in most of DNA and RNAs) Three pyrimidine derivatives - thymine (T), cytosine (C), and uracil (U) Two purine derivatives - adenine (A) and guanine (G) Adenine (A), guanine (G), and cytosine (C) are found in both DNA and RNA. Uracil (U): found only in RNA Thymine (T) found only in DNA. Return to TOC Copyright © Cengage Learning. All rights reserved 6 6 3  11/30/24 Section 22.2 Nucleotides: Building Blocks of Nucleic Acids Phospate Phosphate - third component of a nucleotide, is derived from phosphoric acid (H3PO4) Under cellular pH conditions, the phosphoric acid is fully dissociated to give a hydrogen phosphate ion (HPO42-) Return to TOC Copyright © Cengage Learning. All rights reserved 7 7 Section 22.2 Nucleotides: Building Blocks of Nucleic Acids Nucelotide Formation The formation of a nucleotide from sugar, base, and phosphate is visualized below. – Phosphate attached to C-5’ and base is attached to C-1’ position of pentose Return to TOC Copyright © Cengage Learning. All rights reserved 8 8 4  11/30/24 Section 22.2 Nucleotides: Building Blocks of Nucleic Acids Nucleotide Nomenclature Return to TOC Copyright © Cengage Learning. All rights reserved 9 9 Section 22.3 Primary Nucleic Acid Structure Sugar-phosphate groups are referred to as nucleic acid backbone - Found in all nucleic acids Sugars are different in DNA and RNA Return to TOC Copyright © Cengage Learning. All rights reserved 10 10 5  11/30/24 Section 22.3 Primary Nucleic Acid Structure Primary Structure A ribonucleic acid (RNA) is a nucleotide polymer in which each of the monomers contains ribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or uracil A deoxyribonucleic acid (DNA) is a nucleotide polymer in which each of the monomers contains deoxyribose, a phosphate group, and one of the heterocyclic bases adenine, cytosine, guanine, or thymine. Return to TOC Copyright © Cengage Learning. All rights reserved 11 11 Section 22.3 Primary Nucleic Acid Structure Primary Structure Structure: Sequence of nucleotides in DNA or RNA Primary structure is due to changes in the bases Phosphodiester bond at 3’ and 5’ position 5’ end has free phosphate and 3’ end has a free OH group Sequence of bases read from 5’ to 3’ Return to TOC Copyright © Cengage Learning. All rights reserved 12 12 6  11/30/24 Section 22.3 Primary Nucleic Acid Structure Comparison of the General Primary Structures of Nucleic Acids and Proteins Backbone: -Phosphate-Sugar- Nucleic acids Backbone: -Peptide bonds - Proteins Return to TOC Copyright © Cengage Learning. All rights reserved 13 13 Section 22.4 The DNA Double Helix Nucleic acids have secondary and tertiary structure The secondary structure involves two polynucleotide chains coiled around each other in a helical fashion The poly nucleotides run anti-parallel (opposite directions) to each other, i.e., 5’ - 3’ and 3’ - 5’ The bases are located at the center and hydrogen bonded (A=T and GΞC) Base composition: %A = %T and %C = %G) – Example: Human DNA contains 30% adenine, 30% thymine, 20% guanine and 20% cytocine Return to TOC Copyright © Cengage Learning. All rights reserved 14 14 7  11/30/24 Section 22.4 The DNA Double Helix DNA Sequence: the sequence of bases on one polynucleotide is complementary to the other polynucleotide Complementary bases are pairs of bases in a nucleic acid structure that can hydrogen-bond to each other. Complementary DNA strands are strands of DNA in a double helix with base pairing such that each base is located opposite its complementary base. Example : List of bases in sequential order in the direction from the 5’ end to 3’ end of the segment: 5’-A-A-G-C-T-A-G-C-T-T-A-C-T-3’ Complementary strand of this sequence will be: 3’-T-T-C-G-A-T-C-G-A-A-T-G-A-5’ Return to TOC Copyright © Cengage Learning. All rights reserved 15 15 Section 22.4 The DNA Double Helix Base Pairing One small and one large base can fit inside the DNA strands: – Hydrogen bonding is stronger with A-T and G-C – A-T and G-C are called complementary bases Return to TOC Copyright © Cengage Learning. All rights reserved 16 16 8  11/30/24 Section 22.4 The DNA Double Helix Practice Exercise Predict the sequence of bases in the DNA strand complementary to the single DNA strand shown below: 5’ A–A–T–G–C–A–G–C–T 3’ Answer: 3’ T–T–A–C–G–T–C–G–A 5’ Return to TOC Copyright © Cengage Learning. All rights reserved 17 17 Section 22.5 Replication of DNA Molecules Replication: Process by which DNA molecules produce exact duplicates of themselves Old strands act as templates for the synthesis of new strands DNA polymerase checks the correct base pairing and catalyzes the formation of phosphodiester linkages The newly synthesized DNA has one new DNA strand and old DNA strand Return to TOC Copyright © Cengage Learning. All rights reserved 18 18 9  11/30/24 Section 22.5 Replication of DNA Molecules DNA polymerase enzyme can only function in the 5’-to-3’ direction Therefore one strand (top; leading strand ) grows continuously in the direction of unwinding The lagging strand grows in segments (Okazaki fragments) in the opposite direction The segments are latter connected by DNA ligase DNA replication usually occurs at multiple sites within a molecule (origin of replication) DNA replication is bidirectional from these sites (replication forks) Multiple-site replication enables rapid DNA synthesis Return to TOC Copyright © Cengage Learning. All rights reserved 19 19 Section 22.5 Replication of DNA Molecules Chromosomes Upon DNA replication the large DNA molecules interacts with histone proteins to fold long DNA molecules. The histone–DNA complexes are called chromosomes: – A chromosome is about 15% by mass DNA and 85% by mass protein. – Cells of different kinds of organisms have different numbers of chromosomes. – Example: Number of chromosomes in a human cell 46, a mosquito 6, a frog 26, a dog 78, and a turkey 82 Chromosomes occur in matched (homologous) pairs. Example: The 46 chromosomes of a human cell constitute 23 homologous pairs Return to TOC Copyright © Cengage Learning. All rights reserved 20 20 10  11/30/24 Section 22.6 Overview of Protein Synthesis Protein synthesis is directly under the direction of DNA Proteins are responsible for the formation of skin, hair, enzymes, hormones, and so on Protein synthesis can be divided into two phases. – Transcription – A process by which DNA directs the synthesis of mRNA molecules – Translation – a process in which mRNA isdeciphered to synthesize a protein molecule Transcription Translation DNA RNA Protein Return to TOC Copyright © Cengage Learning. All rights reserved 21 21 Section 22.7 Ribonucleic Acids Differences Between RNA and DNA Molecules The sugar unit in the backbone of RNA is ribose; it is deoxyribose in DNA. The base thymine found in DNA is replaced by uracil in RNA RNA is a single-stranded molecule; DNA is double- stranded (double helix) RNA molecules are much smaller than DNA molecules, ranging from 75 nucleotides to a few thousand nucleotides Return to TOC Copyright © Cengage Learning. All rights reserved 22 22 11  11/30/24 Section 22.7 Ribonucleic Acids Types of RNA Molecules Heterogeneous nuclear RNA (hnRNA): Formed directly by DNA transcription. Post-transcription processing converts the hnRNA to mRNA Messenger RNA: Carries instructions for protein synthesis (genetic information) from DNA – The molecular mass of mRNA varies with the length of the protein Small nuclear RNA: Facilitates the conversion of hnRNA to mRNA. – Contains from 100 to 200 nucleotides Ribosomal RNA (rRNA): Combines with specific proteins to form ribosomes - the physical site for protein synthesis Ribosomes have molecular masses on the order of 3 million Return to TOC Copyright © Cengage Learning. All rights reserved 23 23 Section 22.7 Ribonucleic Acids Types of RNA Molecules Transfer RNA (tRNA): Delivers amino acids to the sites for protein synthesis – tRNAs are the smallest (75–90 nucleotide units) Return to TOC Copyright © Cengage Learning. All rights reserved 24 24 12  11/30/24 Section 22.8 Transcription: RNA Synthesis Transcription Transcription: A process by which DNA directs the synthesis of mRNA molecules – Two-step process - (1) synthesis of hnRNA and (2) editing to yield mRNA molecule Gene: A segment of a DNA base sequence responsible for the production of a specific hnRNA/mRNA molecule – Most human genes are ~1000–3500 nucleotide units long – Genome: All of the genetic material (the total DNA) contained in the chromosomes of an organism – Human genome is about 20,000–25,000 genes Return to TOC Copyright © Cengage Learning. All rights reserved 25 25 Section 22.8 Transcription: RNA Synthesis Steps in the Transcription Process Unwinding of DNA double helix to expose some bases (a gene): – The unwinding process is governed by RNA polymerase Alignment of free ribonucleotides along the exposed DNA strand (template) forming new base pairs RNA polymerase catalyzes the linkage of ribonucleotides one by one to form mRNA molecule Transcription ends when the RNA polymerase enzyme encounters a stop signal on the DNA template: – The newly formed RNA molecule and the RNA polymerase enzyme are released Return to TOC Copyright © Cengage Learning. All rights reserved 26 26 13  11/30/24 Section 22.8 Transcription: RNA Synthesis Post-Transcription Processing: Formation of mRNA Involves conversion of hnRNA to mRNA Splicing: Excision of introns and joining of exons – Exon - a gene segment that codes for genetic information – Intron – a DNA segments that interrupt a genetic message The splicing process is driven by snRNA Alternative splicing - A process by which several different protein variants are produced from a single gene – The process involves excision of one or more exons Return to TOC Copyright © Cengage Learning. All rights reserved 27 27 Section 22.8 Transcription: RNA Synthesis Transcriptome Transcriptome: All of the mRNA molecules that can be generated from the genetic material in a genome. – Transcriptome is different from a genome – Responsible for the biochemical complexity created by splice variants obtained by hnRNA. Return to TOC Copyright © Cengage Learning. All rights reserved 28 28 14  11/30/24 Section 22.9 The Genetic Code The base sequence in a mRNA determines the amino acid sequence for the protein synthesized. The base sequence of an mRNA molecule involves only 4 different bases - A, C, G, and U Codon: A three-nucleotide sequence in an mRNA molecule that codes for a specifi c amino acid – Based on all possible combination of bases A, G, C, U” there are 64 possible codes Genetic code: The assignment of the 64 mRNA codons to specific amino acids (or stop signals) – 3 of the 64 codons are termination codons (“stop” signals) Return to TOC Copyright © Cengage Learning. All rights reserved 29 29 Section 22.9 The Genetic Code Characteristics of Genetic Code The genetic code is highly degenerate: – Many amino acids are designated by more than one codon. – Arg, Leu, and Ser - represented by six codons. – Most other amino acids - represented by two codons – Met and Trp - have only a single codon. – Codons that specify the same amino acid are called synonyms There is a pattern to the arrangement of synonyms in the genetic code table. – All synonyms for an amino acid fall within a single box in unless there are more than four synonyms – The significance of the “single box” pattern - the first two bases are the same – For example, the four synonyms for Proline - CCU, CCC, CCA, and CCG. Return to TOC Copyright © Cengage Learning. All rights reserved 30 30 15  11/30/24 Section 22.9 The Genetic Code Characteristics of Genetic Code The genetic code is almost universal: – With minor exceptions the code is the same in all organisms – The same codon specifies the same amino acid whether the cell is a bacterial cell, a corn plant cell, or a human cell. An initiation codon exists: – The existence of “stop” codons (UAG, UAA, and UGA) suggests the existence of “start” codons. – The codon - coding for the amino acid methionine (AUG) functions as initiation codon. Return to TOC Copyright © Cengage Learning. All rights reserved 31 31 Section 22.9 The Genetic Code Practice Exercise Answers: a. 3’ GCG–GCA–UCA–ACC–GGG–CCU–CCU 5’ b. 3’ GCG–ACC–CCU–CCU 5’ Return to TOC Copyright © Cengage Learning. All rights reserved 32 32 16  11/30/24 Section 22.10 Anticodons and tRNA Molecules During protein synthesis amino acids do not directly interact with the codons of an mRNA molecule. tRNA molecules as intermediaries deliver amino acids to mRNA. Two important features of the tRNA structure The 3’ end of tRNA is where an amino acid is covalently bonded to the tRNA. The loop opposite to the open end of tRNA is the site for a sequence of three bases called an anticodon. Anticodon - a three-nucleotide sequence on a tRNA molecule that is complementary to a codon on an mRNA molecule. Return to TOC Copyright © Cengage Learning. All rights reserved 33 33 Section 22.11 Translation: Protein Synthesis Translation – a process in which mRNA codons are deciphered to synthesize a protein molecule Ribosome – an rRNA–protein complex - serves as the site of protein synthesis: – Contains 4 rRNA molecules and ~80 proteins - packed into two rRNA-protein subunits (one small and one large) – ~65% rRNA and 35% protein by mass – A ribosome’s active site – Large subunit – Ribosome is a RNA catalyst – The mRNA binds to the small subunit of the ribosome. Return to TOC Copyright © Cengage Learning. All rights reserved 34 34 17  11/30/24 Section 22.11 Translation: Protein Synthesis Five Steps of Translation Process Activation of tRNA: addition of specific amino acids to the 3’-OH group of tRNA. Initiation of protein synthesis: Begins with binding of mRNA to small ribosomal subunit such that its first codon (initiating codon AUG) occupies a site called the P site (peptidyl site) Elongation: Adjacent to the P site in an mRNA–ribosome complex is A site (aminoacyl site) and the next tRNA with the appropriate anticodon binds to it. Termination: The polypeptide continues to grow via translocation until all necessary amino acids are in place and bonded to each other. Post-translational processing – gives the protein the final form it needs to be fully functional Return to TOC Copyright © Cengage Learning. All rights reserved 35 35 Section 22.11 Translation: Protein Synthesis Efficiency of mRNA Utilization Polysome (polyribosome): complex of mRNA and several ribosomes Many ribosomes can move simultaneously along a single mRNA molecule The multiple use of mRNA molecules reduces the amount of resources and energy that the cell expends to synthesize needed protein. In the process – several ribosomes bind to a single mRNA - polysomes. Return to TOC Copyright © Cengage Learning. All rights reserved 36 36 18  11/30/24 Section 22.12 Mutations Mutation An error in base sequence reproduced during DNA replication Errors in genetic information is passed on during transcription. The altered information can cause changes in amino acid sequence during protein synthesis and thereby alter protein function Such changes have a profound effect on an organism. Return to TOC Copyright © Cengage Learning. All rights reserved 37 37 Section 22.12 Mutations Mutagens Mutations are caused by mutagens A mutagen is a substance or agent that causes a change in the structure of a gene: – Radiation and chemical agents are two important types of mutagens – Ultraviolet, X-ray, radioactivity and cosmic radiation are mutagenic –cause cancers – Chemical agents can also have mutagenic effects E.g., HNO2 can convert cytosine to uracil Nitrites, nitrates, and nitrosamines – can form nitrous acid in cells Under normal conditions mutations are repaired by repair enzymes Return to TOC Copyright © Cengage Learning. All rights reserved 38 38 19  11/30/24 Section 22.13 Nucleic Acids and Viruses Viruses Viruses: Tiny disease causing agents with outer protein envelope and inner nucleic acid core They can not reproduce outside their host cells (living organisms) Invade their host cells to reproduce and in the process disrupt the normal cell’s operation Virus invade bacteria, plants animals, and humans: – Many human diseases are of viral origin, e. g. Common cold, smallpox, rabies, influenza, hepatitis, and AIDS Return to TOC Copyright © Cengage Learning. All rights reserved 39 39 Section 22.13 Nucleic Acids and Viruses Vaccines Inactive virus or bacterial envelope Antibodies produced against inactive viral or bacterial envelopes will kill the active bacteria and viruses Return to TOC Copyright © Cengage Learning. All rights reserved 40 40 20  11/30/24 Section 22.13 Nucleic Acids and Viruses Viruses Viruses attach to the host cell on the outside cell surface and proteins of virus envelope catalyze the breakdown of the cell membrane and forms a hole Viruses then inject their DNA or RNA into the host cell The viral genome is replicated, proteins coding for the viral envelope are produced in hundreds of copies. Hundreds of new viruses are produced using the host cell replicated genome and proteins in short time Return to TOC Copyright © Cengage Learning. All rights reserved 41 41 Section 22.14 Recombinant DNA and Genetic Engineering DNA molecules that have been synthesized by splicing a sequence of segment DNA (usually a gene) from one organism to the DNA of another organism Genetic Engineering (Biotechnology): – The study of biochemical techniques that allow the transfer of a “foreign” gene to a host organism and produce the protein associated with the added gene – Bacterial strains such as E. coli inserted with circular plasmids, and/or yeast cells carrying vectors containing foreign genes are used for this purpose – Plasmids (double stranded DNA) replicate independently in bacteria or yeast Return to TOC Copyright © Cengage Learning. All rights reserved 42 42 21  11/30/24 Section 22.14 Recombinant DNA and Genetic Engineering Recombinant DNA Production using a Bacterial Plasmid Dissolution of cells: – E. coli cells of a specific strain containing the plasmid of interest are treated with chemicals to dissolve their membranes and release the cellular contents Isolation of plasmid fraction: – The cellular contents are fractionated to obtain plasmids Cleavage of plasmid DNA: – Restriction enzymes are used to cleave the double-stranded DNA Gene removal from another organism: – Using the same restriction enzyme the gene of interest is removed from a chromosome of another organism Gene–plasmid splicing: – The gene (from Step 4) and the opened plasmid (from Step 3) are mixed in the presence of the enzyme DNA ligase to splice them together. Uptake of recombinant DNA: – The recombinant DNA prepared in stept 5 are transferred to a live E. coli culture where they can be replicated, trasncribed and translated. Return to TOC Copyright © Cengage Learning. All rights reserved 43 43 Section 22.14 Recombinant DNA and Genetic Engineering Transformed cell can reproduce a large number of identical cells –clones: – Clones are the cells that have descended from a single cell and have identical DNA Given bacteria grow very fast, within few hours 1000s of clones will be produced Each clone can synthesize the protein directed by foreign gene it carries Return to TOC Copyright © Cengage Learning. All rights reserved 44 44 22  11/30/24 Section 22.15 The Polymerase Chain Reaction The polymerase chain reaction (PCR) is a method for rapidly producing multiple copies of a DNA nucleotide sequence (gene). This method allows to produce billions of copies of a specific gene in a few hours. PCR is very easy to carryout and the requirements are: – Source of gene to be copied – Thermostabel DNA polymerase – Deoxynucleotide triphosphates (dATP, dGTP, dCTP and dTTP) – A set of two oligonucleotides with complementary sequence to the gene (primers) – Thermostable plastic container and – Source of heat Return to TOC Copyright © Cengage Learning. All rights reserved 45 45 Section 22.16 DNA Sequencing DNA sequencing is a method by which the base sequence in a DNA molecule (or a portion of it) is determined. Discovered in 1977 by Fredrick Sanger Concept in DNA sequencing: Selective interruption of polynucleotide synthesis using 2’,3’-dideoxyribonucleotide triphosphates (ddNTPs). Return to TOC Copyright © Cengage Learning. All rights reserved 46 46 23  11/30/24 Section 22.16 DNA Sequencing This interruption of synthesis leads to the formation of every possible nucleotide site mixture. These nucleotides are labeled using radioactive dNTP during their synthesis. The radiolablled nucleotides are then separated on a gel by electrophoresis Return to TOC Copyright © Cengage Learning. All rights reserved 47 47 Section 22.16 DNA Sequencing Basic steps involved in DNA sequencing Step 1: Cleavage of DNA using restriction enzymes: Restriction enzymes are used to cleave the large DNA molecule into smaller fragments (100–200 base pairs). Step 2: Separation into individual components: The mixture of small DNA fragments generated by the restriction enzymes is separated into individual components via gel electrophoresis techniques. Step 3: Separation into single strands: A given DNA fragment is separated into its two strands by chemical methods to use it as a template in step 4. Return to TOC Copyright © Cengage Learning. All rights reserved 48 48 24  11/30/24 Section 22.16 DNA Sequencing Basic steps involved in DNA sequencing Return to TOC Copyright © Cengage Learning. All rights reserved 49 49 25