Lecture Notes: Introduction to Molecular Genetics (PDF)

Introduction to Molecular Genetics 09-November-2024 Semi Lecture (Semi) coverage (+ Enzymes): 1. Introduction to Molecular Genetics 2. Structure of the Nucleotide 3. Structure of DNA and RNA 4. DNA Replication 5. Information Flow: Biological Systems (Central Dogma)...

Introduction to Molecular Genetics 09-November-2024 Semi Lecture (Semi) coverage (+ Enzymes): 1. Introduction to Molecular Genetics 2. Structure of the Nucleotide 3. Structure of DNA and RNA 4. DNA Replication 5. Information Flow: Biological Systems (Central Dogma) Lecture (Finals) coverage: 6. The Genetic Code 7. Protein Synthesis 8. Mutation, Ultraviolet Light & DNA Repair 9. Recombinant DNA 10. Polymerase Chain Reaction 11. The Human Genome Project 1. Introduction to Molecular Genetics What can you say about the picture? 1. Introduction to Molecular Genetics Similarities Difference 1. Hair 1. We don’t 2. Nose look the 3. Mouth same 4. Head 5. Skin 6. Eyes 7. Lips 8. Body 1. Introduction to Molecular Genetics 1. What is the molecule responsible for all these similarities and differences? 1. Introduction to Molecular Genetics 1. What is the Molecule responsible for all these similarities and differences? DNA or Deoxyribonucleic acid a tightly wound up molecules in a structure called chromosomes in the nucleus of the cell. 1. Introduction to Molecular Genetics Thousands of genes carry the genetic information for thousands of proteins that dictate our form and some believe, our behavior!  2. The Structure of Nucleotide In the early 1950s, American biologist James Watson and British physicist Francis Crick came up with their famous model of the DNA double helix, through this now we know that deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are long polymers of nucleotides. Watson and Crick brought together data from a number of researchers (including Franklin, Wilkins, Chargaff, and others) to assemble their celebrated model of the 3D structure of DNA. 2. The Structure of Nucleotide Composition of a Nucleotide 1. Nitrogenous bases (heterocyclic amines) 2. A five carbon sugar 3. Phosphate group 2. The Structure of Nucleotide Composition of a Nucleotide 1. Nitrogenous bases 2. The Structure of Nucleotide Composition of a Nucleotide 1. Nitrogenous bases 2. The Structure of Nucleotide Composition of a Nucleotide 2. Five Carbon sugar 2. The Structure of Nucleotide Composition of a Nucleotide 3. Phosphate group 2. The Structure of Nucleotide Nucleoside = Sugar + Base 2. The Structure of Nucleotide Nucleoside The sugar + base are connected by a beta-N- glycosidic linkage that joins the 1’-carbon of the sugar and a nitrogen atom of the base (N-9 of purines and N-1 of pyrimidines). 2. The Structure of Nucleotide Nucleoside Example: The combination of Adenine and Ribose gives the nucleoside, adenosine which is a parent molecule of Adenosine Triphosphate (ATP). 2. The Structure of Nucleotide Nucleoside naming Derived from the nitrogenous bases (name) modified by the suffix − osine for the purine bases (ex: adenosine) and the suffix − idine for the pyrimidine bases. No prefix for nucleosides containing ribose but the prefix deoxy − is added for those that contains deoxyribose. 2. The Structure of Nucleotide Four (4) Nucleosides found in RNA and DNA RNA DNA adenosine deoxyadenosine guanosine deoxyguanosine cytidine deoxycytidine uridine deoxythymidine 2. The Structure of Nucleotide Nucleotides are building blocks of nucleic acids Nucleotide = Nucleoside + Phosphate 2. The Structure of Nucleotide Nucleotides are building blocks of nucleic acids Nucleotide = Nucleoside + Phosphate A nucleotide with the sugar ribose is a ribonucleotide and one having 2’deoxyribose is a deoxyribonucleotide.  2. The Structure of Nucleotide Nucleotide = Nucleoside + Phosphate Since there are two cyclic molecules in a nucleotide , the sugar and the base. The ring atoms of sugar is designated with a prime (‘) to distinguish it from the atoms of the base. What nucleoside is this? Deoxyadenosine What nucleotide is this? Ribonucleotide What nucleotide is this? The covalent bond between the sugar and the phosphoryl group is a phosphoester bond. 3. Structure of DNA and RNA A single strand DNA is a polymer of nucleotides bonded to one another by a 3’-5’ phosphodiester bonds. Sugar phosphate backbone- composed of alternating units of the five carbon sugar 2’deoxyribose and phosphoryl groups in a phosphodiester linkage. Note: Understand the anti-parallel and 3’ to 5’ properties of the DNA double helix 3. Structure of DNA and RNA Chromosomes Pieces of DNA that carry the genetic instructions or genes of an organism. Chromosome structure in Eukaryotes 3. DNA Replication DNA must be replicated before a cell divides so that each daughter cell inherits a copy of each gene. It is essential that a process of DNA replication produces an absolutely accurate copy of the original genetic information as mistakes can be made resulting in a lethal mutations. 3. DNA Replication Semiconservative replication means that since adenine can only be paired with thymine and cytosine with guanine Watson and Crick suggested that an enzyme could read the nitrogenous bases on one strand of a DNA molecule and add complementary bases to a strand of DNA being synthesized. Semiconservative because the product is the original DNA (parent) and the second strand is new (daughter). Steps in DNA Replication 1. Separation of the DNA strands by protein helicase. 2. This results to supercoiling of DNA strands, topoisomerase relieved this stress. 3. Preventing the strands coming back together, single strand binding protein binds to each strand. 4. Enyzme primase catalyzes the the synthesis of a small piece of RNA called an RNA primer that serves to ‘prime’ the process of DNA replication. Steps in DNA Replication 5. The enzyme DNA polymerase III ‘reads’ each parental strand (template) and catalyzes polymerization of a daughter strand. However, two strands of DNA are antiparallel to one another and DNA polymerase III can only catalyze DNA chain elongation in the 5’ to 3’ direction. But the replication fork proceeds in one direction and both strands are replicated simultaneously. As a result there are two mechanism for the two strands leading and lagging strand. Steps in DNA Replication For the lagging strand 1. Many RNA primers are produced. DNA polymerase III catalyzes DNA chain elongation from each of the primers. 2. The final step is the removal of the primers by DNA polymerase I replacing it with DNA nucleotides which repairs of the gaps and the DNA ligase seals the gap by the formation of the phosphoester bond between the two adjacent fragments. Steps in DNA Replication Since it is critical to produce an accurate copy of the parental DNA it is very important to avoid errors in the replication process. Good thing, DNA polymerase III is able to proofread the newly synthesized DNA and able to removed and replace a correct one if there’s an error. Key Proteins function in DNA replication: 1. DNA helicase – breaks hydrogen bonding between two strands 2. Topoisomerase – alleviates positive supercoiling 3. Single-strand binding proteins- keep the strands apart. 4. Primase – synthesizes RNA primer 5. DNA polymerase III synthesizes daughter DNA strand 6. DNA polymerase I – excises the RNA primers and fill in with DNA 7. DNA ligase – covalently links the DNA fragments together. Bacterial Chromosome Replication 4. Information Flow in Biological Systems The Central dogma of molecular biology states that in cells the flow of genetic contained in DNA is a one- way street that leads from DNA RNA Protein. 4. Information Flow in Biological Systems Transcription – a process in which a single strand of DNA serves as a template for an RNA molecule. Transcription – derived from the latin word transcribere meaning “to make a copy”. 4. Information Flow in Biological Systems Translation – a process by which the message (genetic information) is converted into protein. The genetic information in the linear sequence of a nucleotide is being translated into a protein, a linear sequence of amino acids.  CLASSES OF RNA MOLECULES 1. mRNA – carries the genetic 1. rRNA – a structural and 1. tRNA – translates the information for a protein functional component of genetic code of the mRNA into from DNA to ribosomes. A the ribosomes, which are the primary sequence of complementary RNA copy of “platforms” on which amino acids in the protein. a gene on a DNA. protein synthesis occurs. TRANSCRIPTION PROCESS POST-TRANSCRIPTIONAL PROCESSING OF RNA In eukaryotes, transcription produces a primary transcript that must undergo extensive post- transcriptional modification before it is exported out of the nucleus for translation in the cytoplasm. In prokaryotes, termination releases a mature mRNA for translation. 3 STEPS IN POST-TRANSCRIPTIONAL PROCESSING OF RNA These are addition of a 5’ cap structure and a 3’ poly(A) tail, and a RNA splicing. 3 STEPS IN POST-TRANSCRIPTIONAL PROCESSING OF RNA 1. A cap structure is enzymatically added to the 5’ end of the primary transcript. 3 STEPS IN POST-TRANSCRIPTIONAL PROCESSING OF RNA 2. Enzymatic addition of a poly(A) tail to the 3’ end of the transcript. 3 STEPS IN POST-TRANSCRIPTIONAL PROCESSING OF RNA 3. RNA splicing, involve the removal of portions of the primary transcript that are not protein coding. Bacterial genes are continuous – all the nucleotide sequences of the gene are found in the mRNA 3 STEPS IN POST-TRANSCRIPTIONAL PROCESSING OF RNA 3. RNA splicing, involve the removal of portions of the primary transcript that are not protein coding. Eukaryotic genes are discontinuous, there are extra DNA sequences within these genes that do not encode any amino acid sequences for the protein. These sequence are called introns or intervening sequences. The primary transcript both contains introns and the protein coding sequences called exons. POST-TRANSCRIPTIONAL PROCESSING OF RNA snRNPS’s – small nuclear ribonucleoproteins (read as “snurps”).