Nucleic Acid Chemistry PDF

Nucleic Acid Chemistry  Objectives To be familiar with the chemical components of nucleic acid To describe how nucleotides are formed from the interaction between the base and the sugar and their nomenclature To enumerate and explain the different functions of nucleic acids To...

Nucleic Acid Chemistry  Objectives To be familiar with the chemical components of nucleic acid To describe how nucleotides are formed from the interaction between the base and the sugar and their nomenclature To enumerate and explain the different functions of nucleic acids To describe the different levels of DNA packaging and organization Chapter outline 22.1 Types of nucleic acids 22.8 Ribonucleic acids 22.2 Nucleotides: Structural 22.9 Transcription: RNA building blocks for nucleic acids synthesis 22.3 Nucleotide formation 22.10 The genetic code 22.4 Primary nucleic acid 22.11Anticodons and tRNA structure molecules 22.5 The DNA double helix 22.12Translation: Protein 22.6 Replication of DNA synthesis molecules 22.13Mutations 22.7 Overview of protein 22.14Nucleic acids and viruses synthesis 22.16The polymerase chain reaction Introduction Cells in an organism are capable of replicating Cells possess 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 an unbranched polymer in which the monomer units are nucleotides WHAT IS A NUCLEIC ACID Nucleic acids are polynucleotides—that is, long chainlike molecules composed of a series of nearly identical building blocks called nucleotides. WHAT IS A NUCLEIC ACID Nucleic acids are polynucleotides—that is, long chainlike molecules composed of a series of nearly identical building blocks called nucleotides.  Importance of nucleic acids Heredity: Passing genetic information from one generation to the next. Growth and Development: Directing the synthesis of proteins needed for growth and development. Evolution: Providing the genetic variation necessary for evolution. Energy for metabolism (ATP) Types of Nucleic acid Deoxyribonucleic acid (DNA) Found within the cell nucleus Stores and transfers genetic information Passed from existing cells to new cells during cell division Ribonucleic Acid (RNA) Occurs in all parts of a cell Primary function is the synthesis of proteins  Types of RNA Ribosomal RNA: catalyze protein synthesis. Messenger RNA: carry genetic information from genes to ribosome. Transfer RNA: Translate information in mRNA into sequence of amino acids. Components of Nucleic Acid They are polymers in which the nucleotide repeating unit is a nucleosid phosphat nucleotide Components of a e e nucleotide Nitrogen Pentose sugar sugar base Phosphate group 2- (PO43-) ribose deoxyribose Heterocyclic base THE SUGAR-PHOSPHATE BACKBONE The nucleotides are all orientated in the same direction The structural difference between ribose and pentose 2′ - deoxyribose occurs at carbon 2′ —OH group is present in ribose —H atom is present in 2′- deoxyribose Ribose is present in RNA 2′-deoxyribose is present in Nitrogen-Containing Heterocyclic Bases Phosphate The third component of a nucleotide Derived from phosphoric acid (H3PO4) Loses two hydrogen atoms, resulting in formation of a hydrogen phosphate ion (HPO42–) It is a two-step process The pentose sugar and nitrogenous base react to form a nucleoside Nucleoside Formation Nucleoside: A two-subunit molecule in which a pentose sugar is bonded to a nitrogen-containing heterocyclic base Characteristics The base is attached to C1′ position of the sugar (β- configuration) It is a condensation reaction Nucleoside Formation There are 8 nucleosides associated with nucleic acid chemistry Four RNA nucleosides / Four DNA nucleosides Nomenclature For pyrimidine bases, the suffix -idine is used Cytidine, thymidine, For purine bases, the suffix - osine is used Adenosine, guanosine Prefix deoxy- is used to Nucleotide Formation Formed by the addition of a phosphate group to a nucleoside Characteristics of phosphate addition The phosphate is attached to C5′ position and base attached to C1 Water is released when it condensation between sugar and base https://www.researchgate.net/publication/ 340583975/figure/tbl1/ AS:879445539831812@1586687564395/Naming- of-Nucleosides-and-Nucleotides.png Primary Nucleic Acid Structure Repeating units of nucleotide is the composition of nucleic acid The alternating phosphate- sugar structure is what we call nucleic acid backbone  Hydrolysis of Nucleic Acid RNA is hydrolyzed rapidly under alkaline conditions. DNA is stable under alkaline conditions. Deprotonated 2’ hydroxyl group acts as a nucleophile. DNA lacks 2’ hydroxyl group. Phosphorus atom is target of nucleophilic attack.  Nucleic acids exhibit hierarchical levels of structure: Primary structure: Nucleotide sequence and covalent bonds. Secondary structure: Regular stable structure, common to all nucleic acids. Tertiary structure: Complex folding of large nucleic acids, such as chromosomes, tRNA, and rRNA. DNA Double Helix Amounts of A,T,G, and C present in DNA molecules helped determine the three- dimensional structure of the DNA molecules Amounts of A and T were always equal Amounts of C and G were always equal Human DNA contains: 30% adenine 30% thymine 20% guanine 20% cytosine  BASIC STRUCTURAL CHARACTERISTICS OF DNA As described by Mr. Watson and Crick: The two strands are connected by Hydrogen Bonding between base pairs (Watson-Crick Base Pairs): - Adenine – Thymine = 2 Hydrogen Bonds (Easier to separate) - Cytosine – Guanine = 3 Hydrogen Bonds (Harder to separate)  BASIC STRUCTURAL CHARACTERISTICS OF DNA As described by Mr. Watson and Crick: DNA is composed of two polynucleotides, anti- parallel with each other (One strand runs from 5’ to 3’, while the other strand runs from 3’ to 5’) = Opposite Direction On the outside = Sugar-Phosphate Backbone On the inside = Hydrophobic Bases BASIC STRUCTURAL CHARACTERISTICS OF DNA As described by Mr. Watson and Crick: Two helical DNA strands. Right-handed double helix. - Diameter 20 Å - 3.4 Å per base - 10.5 bases per helical turn. - 36 Å per turn BASIC STRUCTURAL CHARACTERISTICS OF DNA As described by Mr. Watson and Crick: Backbone - Negatively charged phosphate groups provide stability Base Stacking Interactions - Van der Waals forces between stacked base pairs also contributes to stability GC content - Higher GC content leads to a more stable DNA molecule  DNA Forms - Three forms exist: A, B, and Z B form - Most stable, right- handed double helix, Watson-Crick structure, predominant form in physiological conditions A form - Right-handed double helix, wider turn, favored in solutions lacking water Z form - Left-handed helix, zigzag appearance, elongated and slender Base Pairing A pyrimidine is always paired with a purine Fits inside the DNA double strand Hydrogen bonding is most favored in A–T and G–C pairs A–T and G–C pairing is termed complementary 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′  CHARGAFF’S RULE: Content of A = Content of T Content of G = Content of C This means that in the lab, you can predict the base composition of a particular DNA by just examining one base.  Major and Minor Groves The major groove occurs where the backbones are far apart, the minor groove occurs where they are close together.  DNA Denaturation: If you want to separate the two strand  Destroy/Cut the Hydrogen Bonds = DNA Denaturation When you denature the DNA, hydrogen bonding is destroyed. (You denature the DNA from a double stranded to a single stranded DNA)  Central Dogma DNA ---------→ RNA---------→Protein.  Central Dogma Processes in the transfer of genetic information: Replication: identical copies of DNA are made Transcription: genetic messages are read and carried out of the cell nucleus to the ribosomes, where protein synthesis occurs. Translation: genetic messages are decoded to make proteins.  DNA replication The doubling process of DNA molecules The parent molecule unwinds, and two new daughter strands are built based on base pairing rules  Where is DNA replication happens A cell copies its DNA before mitosis or meiosis I DNA replication takes place in the nucleus during interphase DNA repair mechanisms and proofreading correct most replication errors  Why is DNA Replication Important? Genetic Inheritance: DNA replication ensures the faithful transmission of genetic information from one generation to the next. When a cell divides, each daughter cell needs a complete set of genetic instructions to function and develop properly. Without accurate replication, errors in the genetic code could lead to genetic disorders and other problems. Cell Growth and Repair: DNA replication is essential for cell growth, tissue repair, and maintenance. As organisms grow or replace damaged cells, they need to replicate their DNA to provide the necessary genetic material for these new cells. Cell Division: DNA replication is a prerequisite for cell division. In eukaryotic cells, such as those in humans, the cell cycle includes a phase called the S- phase, during which DNA replication occurs. Accurate replication ensures that each new cell created during cell division has an identical copy of the genetic material, allowing for the propagation of the organism.  Steps in DNA replication Step 1: Replication Fork Formation Imagine your DNA is a zipper - Before DNA can be replicated, the double stranded molecule must be “unzipped” into two single strands DNA HELICASE is an enzyme that unwind the helix and separates the strands by disrupting the hydrogen bonds The replication fork is the region of DNA where the replication process is currently taking place. (it is Y shape) Topoisomerase will break , untwist and reconnect the dna , always ahead of the replication for  Steps in DNA replication Step 2: Primer Binding Primer Binding: After DNA strands are separated, a short RNA piece, known as a primer, attaches to the 3' end of the leading strand. Starting Point: The primer always attaches as the initial point for replication on the leading strand.  Steps in DNA replication Step 3: Elongation DNA polymerase adds DNA nucleotides to the 3′ end of the newly synthesized polynucleotide strand. Leading Strand Replication: leading strand: the template strand of the DNA double helix that is oriented so that the replication fork moves along it in the 3′ to 5′ direction Replication of the leading strand proceeds in the 5' to 3' direction. DNA polymerase continuously adds complementary base pairs to the leading strand. Lagging Strand Replication: lagging strand: the strand of the template DNA double helix that is oriented so that the replication fork moves along it in a 5′ to 3′ manner The lagging strand begins replication by binding with multiple primers, which are spaced a few bases apart. DNA polymerase adds pieces of DNA, known as Okazaki fragments, between the primers. Lagging strand replication is discontinuous because Okazaki fragments are separate and need to be connected. Figure 22.1 - Continuous-Growing Strands and Okazaki Fragments Copyright ©2016 Cengage Learning. All Rights 41 Reserved. Steps in DNA replication Step 4: Termination Exonuclease Action: An enzyme called exonuclease removes all RNA primers from the original DNA strands. These primers are then replaced with the appropriate DNA bases. Proofreading: Another exonuclease "proofreads" the newly formed DNA to check for, remove, and replace any errors. DNA Ligase: DNA ligase joins Okazaki fragments together to form a single unified strand. Telomeres: The ends of linear DNA strands have repeated DNA sequences known as telomeres. Telomeres act as protective caps at the end of chromosomes to prevent fusion with neighboring chromosomes. Telomerase: A special type of DNA polymerase enzyme called telomerase synthesizes telomere sequences at the ends of the DNA strands.  Checking for Mistakes  Because so much DNA is being replicated in the many cells of the body, there is a potential for errors to occur!  DNA repair mechanisms DNA polymerases proofread DNA sequences during DNA replication and repair damaged DNA  When proofreading and repair mechanisms fail, an error becomes a mutation – a permanent change in the DNA sequence. Can alter the genetic message and affect protein synthesis Transcription Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins are said to produce messenger RNA.  DNA is transcribed to RNA Most RNA is single stranded RNA uses uracil in place of thymine RNA uses ribose in place of deoxyribose  DNA Transcription  In transcription, a strand of mRNA is assembled on a DNA template using RNA nucleotides Uracil (U) nucleotides pair with A nucleotides RNA polymerase adds nucleotides to the transcript Tscripranti on Steps in Transcription Step 1: Initiation Initiation is the beginning of transcription. It occurs when the enzyme RNA polymerase binds to a region of a gene called the promoter. This signals the DNA to unwind so the enzyme can ‘‘read’’ the bases in one of the DNA strands. The enzyme is now ready to make a strand of mRNA with a complementary sequence of bases. Step 2: Elongation Elongation is the addition of nucleotides to the mRNA strand. RNA polymerase reads the unwound DNA strand and builds the mRNA molecule, using complementary base pairs. During this process, an adenine (A) in the DNA binds to an uracil (U) in the RNA. Step 3: Termination Termination is the ending of transcription and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.  Translation The information carried by mRNA is decoded into a sequence of amino acids, resulting in a polypeptide chain that folds into a protein  mRNA is translated to protein rRNA and tRNA translate the sequence of base triplets in mRNA into a sequence of amino acids Translation Translation: The process in which mRNA codons are deciphered and a specific protein molecule is synthesized Ribosome: An rRNA–protein complex that is the site for the translation phase of protein synthesis Characteristics of ribosome structures They contain four rRNA molecules and 80 proteins in two subunits Each subunit possesses 65% rRNA and 35% protein The active site is located in the ribosomal subunit rRNA is the active site The predominance of rRNA at the active site gives it the impression of a ribozyme The mRNA binds to the small Copyright ©2016subunit of theAllribosome Cengage Learning. Rights 49 Reserved. Review for Ribosome Steps of Translation Post- Initiation Elongation Termination translational processing tRNA Another The The protein attaches tRNA polypeptide is rendered itself to the attaches continues to fully P site of a itself to the grow via functional small A site translocatio ribosomal A dipeptide n till a stop unit is formed codon is under the encountered influence of peptidyl transferase Copyright ©2016 Cengage Learning. All Rights 51 Reserved.  mRNA – The Messenger  mRNA carries protein-building information to ribosomes and tRNA for translation  Codon A sequence of three mRNA nucleotides that codes for a specific amino acid The order of codons in mRNA determines the order of amino acids in a polypeptide chain  Genetic Code  Genetic code Consists of 64 mRNA codons (triplets) Some amino acids can be coded by more than one codon  Some codons signal the start or end of a gene AUG (methionine) is a start codon UAA, UAG, and UGA are stop codons Genetic Information  From DNA to mRNA to amino acid sequence Protein synthesis Protein synthesis  What is mutation A mutation is a change in the DNA sequence of an organism. Mutations can result from errors in DNA replication during cell division, exposure to mutagens or a viral infection.  Mutations  Mutations in germ cells Passed to future generations Important for evolutionary change  Mutations in somatic cells Not passed to future generations but passed to all other somatic cells derived from it  What Causes Mutations?  Transposable elements Segments of DNA that can insert themselves anywhere in a chromosomes  Spontaneous mutations Uncorrected errors in DNA replication  Harmful environmental agents Ionizing radiation, UV  Type of mutations Point mutations involve the replacement of one base with another. Frame-shift mutations occur when a base is added or removed from the sequence.  Type of Mutation Point Mutations: 1.Substitution: A single nucleotide is replaced by another nucleotide. This can lead to changes in the amino acid sequence in a protein. 1.Missense Mutation: Results in a different amino acid being incorporated into the protein, which can alter its function. 2.Silent Mutation: The nucleotide change doesn't affect the amino acid sequence, so there's no change in the protein. 3.Nonsense Mutation: A stop codon is introduced prematurely, resulting in a truncated and often nonfunctional protein.  Type of Mutation Deletion: A section of DNA is removed, which can result in a loss of genetic material and potentially disrupt gene function. Insertion: One or more nucleotides are added to the DNA sequence, which can also disrupt the reading frame and lead to nonfunctional proteins. Duplication: A segment of DNA is duplicated, leading to extra copies of specific genes or sequences. Single-gene disorders Disorder Gene Affected Description A genetic disorder affecting the lungs, pancreas, and other organs. It is caused by mutations in the CFTR Cystic gene, which encodes a protein involved in chloride Fibrosis CFTR ion transport. A blood disorder caused by abnormal hemoglobin. It Sickle Cell is caused by a mutation in the HBB gene, which Anemia HBB encodes the beta-globin subunit of hemoglobin. Huntingto A neurodegenerative disease affecting the brain. It is n's caused by a mutation in the HTT gene, which encodes Disease HTT a protein involved in neuronal function. A bleeding disorder caused by a deficiency in clotting factors. It is caused by mutations in the F8 gene Hemophili (hemophilia A) or the F9 gene (hemophilia B), which a F8 or F9 encode clotting factors VIII and IX, respectively. A fatal genetic disorder that affects the nervous system. It is caused by a mutation in the HEXA gene, Tay-Sachs which encodes the enzyme hexosaminidase A, Disease HEXA involved in the breakdown of lipids.  Affected Disorder Chromosomes Description A genetic disorder caused by an extra copy Down Syndrome Chromosome 21 of chromosome 21. A genetic disorder affecting females, characterized by the absence or partial Turner Syndrome X chromosome absence of one X chromosome. A genetic disorder affecting males, Klinefelter Sex chromosomes characterized by the presence of an extra X Syndrome (XXY) chromosome. A genetic disorder characterized by intellectual disability, obesity, and behavioral problems. It is caused by a Prader-Willi deletion of a specific region of chromosome Syndrome Chromosome 15 15. A genetic disorder characterized by intellectual disability, seizures, and a happy Angelman demeanor. It is caused by a deletion of a Syndrome Chromosome 15 specific region of chromosome 15. A genetic disorder characterized by  Genetic engineering: The process by which an organism is intentionally changed at the molecular (DNA) level so that it exhibits different traits Recombinant DNA: DNA possessing genetic material from two different organisms 67 PCR (Polymerase Chain Reaction) https://www.youtube.com/watch?v=a5jmdh9AnS4  Viruses Minute disease-causing agents with an outer coat of protein They can reproduce only by invading host cells Host cells are caused to produce more viruses Host cells’ normal function is disrupted They attack bacteria, plants, animals, and humans Many human diseases are of viral origin Copyright ©2016 Cengage Learning. All Rights 69 Reserved.  Viruses They attach themselves to the host cell on the external surface An enzyme present in the external structure of the virus catalyzes the breakdown of the cell membrane and forms a hole They then inject their DNA or RNA into the host cell The viral nucleic acid is replicated Hundreds of new Copyright viruses are ©2016 Cengage Learning. All Rights 70 Reserved.  Vaccine A preparation containing an inactive or weakened form of a virus Antibodies produced against inactive viral or bacterial envelopes also kill naturally occurring viruses or bacteria Copyright ©2016 Cengage Learning. All Rights Reserved. MEME TIME Activity time (By Group) Activity: Exploring Innovations at the Intersection of Neuroscience, Psychology, Medicine and Genetic Engineering Topic Selection: Allow students to select a specific topic or area of interest within neuroscience and psychology and medicine that involves genetic engineering. Examples include: Gene therapy for neurodegenerative disorders Genetic manipulation of neural circuits for behavioral studies CRISPR-Cas9 applications in studying brain function Epigenetic modifications and mental health research Instruct students to summarize their findings and create a presentation or report highlighting key points. They should explain the genetic engineering techniques used, the challenges faced, References https://www.youtube.com/watch?v=8Dg0qYxXSAo https://www.youtube.com/watch?v=wlKpwoOrChw https://yulab.nju.edu.cn/_upload/article/files/73/92/1460 3e9c43f38d30ffdb8d995244/ce5597a9-5c4e-4fc6-b6b5- bc760c72bb85.pdf https://yulab.nju.edu.cn/_upload/article/files/73/92/1460 3e9c43f38d30ffdb8d995244/ce5597a9-5c4e-4fc6-b6b5- bc760c72bb85.pdf https://www.ucdenver.edu/docs/librariesprovider132/a- sync_sl/genetics/upload-2/dna-to-protein/central- dogma-of-biology-answer-key.pdf?sfvrsn=289cb5ba_2