Molecular Genetics Lecture Notes PDF

Molecular Genetics Type Lecture Course Biology 30IB Topics Molecular Genetics , Biology DNA (Deoxyribonucleic Acid) Stores developmental information, Controls metaboli...

Molecular Genetics Type Lecture Course Biology 30IB Topics Molecular Genetics , Biology DNA (Deoxyribonucleic Acid) Stores developmental information, Controls metabolic activity Contains information to create proteins - foundation of bodily functions Series of nucleotides (monomers of DNA) in a double helix structure. Located in nucleii of cells. Inherited in a 50/50 split between parents. All cells will have the same information - DNA source. Usage differs between cells, with the exception of reproductive sex cells. Mitochondrial DNA (mDNA) secondary example - only inherited from mom. Genes A segment of DNA in a specific location - determines a bodily structure or function. Creates a protein to perform instructions. Molecular Genetics 1  Chromosome A packet of DNA and Proteins Formerly loose DNA that appears before mitosis (cell division) - chromatin. Condensed into chromosome - condensed DNA. Structure Theory of DNA No one had an idea of what inherited material we got from parents - protein or nucleic acid. Hershey and Chase - used bacteriophages with specific markings (sulfur for protein, phosphorous for DNA - nucleic acid) Nucleic acid was discovered and phosphorous detected in inheritance. STRUCTURE 1. Rosalind Franklin - expert of X-Ray diffraction and isolation of DNA. Used X- ray diffraction to create an outline of DNA structures. a. Maurice Wilkins - Franklin’s supervisor - gave X-ray diffraction images to James Watson and Francis Crick. 2. James Watson - biochemist who focused on molecular components of nucleotides. 3. Francis Crick - physicist who focused on structure - how molecules fit and operated. DNA + RNA DNA and RNA are nucleic acids - repeating sets of antiparallel nucleotides (Run in opposite directions, one up one down). Held together by phosphodiester bonds. Nitrogen bases - structural component - pyrimidines and purines Molecular Genetics 2  1. Pyrimidines - single ringed Nitrogen bases. (Cytosine and Thymine) 2. Purines - double ringed Nitrogen bases. (Adenine and Guanine) Structure is upheld by covalent phosphodiester bonds - cannot and should not be broken Nitrogen bases bond by hydrogen bonds - weaker, can be broken to read DNA. 5 prime and 3 prime ends are based on sugar isomers. 👉 BASE PAIRING RULE 1. Adenine pairs to Thymine (Purines to Pyrimidines) with 2 hydrogen bonds. 2. Guanine pairs to Cytosine (Purines to Pyrimidines) with 3 hydrogen bonds. Sept 06, 2024 - Chargaff’s Rule (IBO and Alberta ED) Tetranucleotide Hypothesis - DNA repeats the same set of four nucleotides, therefore we have an equal amount of each nitrogenous base. Backed by Sugar-Phosphate backbone, common to ALL living beings. ‘Struts of a ladder.’ Erwin Chargaff - wanted to prove the Tetranucleotide hypothesis - analyzed each number of nucleotide nitrogenous base. Again common in ALL living beings. Encoding/decoding and use of DNA differs from species to species. Adenine to Thymine, Guanine to Cytosine. Molecular Genetics 3  When calculating percentages therefore: A = T,G = C NumP urines = NumP yrimidines Adenine + Thymine does not usually equal Guanine + Cytosine Dividing A+T by G+C gives a common ratio (can be useful). 👉 DNA is only in chromosome form when cells undergo cell division. DNA gets packed into a shape with help from proteins →Histones. Histones perform what is known as supercoiling - coiling packets of DNA (known now as NUCLEOSOMES). Eight histones are formed as the core for DNA to wrap around (~150 pairs of DNA) An additional histome is used as a ‘glue’ for the nucleosome. Linking region forms between space of the nucleosome and DNA binds. Deoxyribonucleic Acid (DNA) Ribonucleic Acid (RNA) - Single stranded - consists of a single chain - Double stranded - double helix shape. of nucleotides. Consists of a phosphate group, pentose Consists of a phosphate group, pentose sugar, and nitrogenous bases. sugar, and nitrogenous bases. (Adenine, Guanine, Thymine, (Adenine, Guanine, Thymine, Cytosine) Uracil.) Purines (AG) and Pyrimidines (CT) Purines (AG) and Pyrimidines (UT) Responsible for containing hereditary Creates proteins and used for DNA information (nuclear DNA) replication. (mDNA and chloroplast DNA - control (mRNA, tTRNA, rRNA - messenger, transfer, Molecular Genetics 4  organelle action, metabolic activity.) ribosomal) Found in nucleus and Cytoplasm. DNA strands consist of nitrogenous bases - form coding sequences responsible for hereditary traits. Majority of DNA does not code for genes. 1. Repetitive Sequences - ‘Satellite DNA’ a. DNA sequence that contains only repeating sequences of pairs - not essential for coding. b. Consists of 5-300 base pairs - inherited 50/50 from parents, therefore essential for DNA fingerprinting (paternity tests, etc.) 2. Telomeres a. Ends of Chromosomes consisting of repeating sequences. b. Responsible for protecting chromosomes from destruction during cell division. i. Correlated with age and lifespan - longer telomeres hints at longer lives. 3. Introns a. ‘Proofread’ portion of genetic coding - responsible for protecting protein sequences. b. Removed upon successful coding - protects against errors made in copying. 4. Promoter Sites a. Sequences before constructed structural genes b. Form to initiate DNA polymerase interaction - expression and construction of Genes. DNA Replication Molecular Genetics 5  Goal of providing new cells a copy of original DNA. Duplication → semi-conservative, one parent (original) pair, one new (created) pair. Nucleic Acids are the only organic molecule capable of self-replication. 👉 1. Replication Origin (sequence to be replicated is selected) 2. Enzyme Helicase binds to rep. origin. 3. Single strands of broken DNA work as templates for created pairs. 4. DNA Primase creates RNA primers (starting point for Polymerase) 5. DNA Polymerase creates new nucleotides from 5’ to 3’. 6. When completed, Polymerase III disconnects and Polymerase I proofreads Two strands form from the original strand 1. Leading Strand a. First strand of DNA - continuous production of nucleotides that follow helicase (replication fork - 5’ to 3’) b. Preceeds Lagging Strand 2. Lagging Strand - Follows slowly behind Leading Strand. a. Creates in segments called Okazaki Fragments - works away from Helicase, antiparallel with Leading Strand. b. DNA Ligase - separate enzyme - binds Okazaki Fragments together. Protein Synthesis (RNA) Consists of two stages - Transcription and Translation DNA genetic codes direct protein synthesis - code specific animo acids.*. proteins. Molecular Genetics 6  Genes - hereditary traits. 👉 1 Gene : 1 Polypeptide Theory Most structural genes will code for only one protein. However, some proteins require the use of multiple genes (called polygenes) No gene code will code for multiple proteins. Transcription - DNA becomes mRNA (messenger) Information gathered in the nucleus and converted to mRNA 1. Helicase unwinds and breaks DNA hydrogen bonds into a Sense Strand and Anti-Sense Strand (SS and AS strands.) 2. RNA Polymerase binds to the promoter sequence in DNA (on the SS strand) a. RNA Polymerase reads coding and will use the AS strand as a template to build mRNA. Goes triplet by triplet (DNA) to create subsequent codons (RNA). b. AS coding will always start with a triplet TAC (DNA) and thus codon will always start as AUG (mRNA). 3. Polymerase continues triplet by triplet until arriving at a terminator. 4. DNA is repaired, and mRNA is processed before leaving (Eukaryotic). Translation - in Eukaryotic Cells (mRNA works with tRNA and ribosomes to create polypeptide chains - proteins). Create proteins using extracted mRNA code - ribosomes (in cytoplasm and rough ER) Molecular Genetics 7  Works alongside tRNA (transfer) to create chains based on sequences. tRNA - single stranded, w/ amino acid on 3’ end. Anticodon end aligns to codon end of mRNA to insert the correct amino acid into sequence. Ribosomes - created from rRNa and proteins. (rRNA is what brings and reads mRNA) Contains an attachment, elongation, and exit site in the Large Subunit (LSub). Smaller Subunit brings and reads mRNA like a conveyer belt (SSub). Order of Translation 1. Initiation - mRNA binds to the SSub, and tRNA binds to LSub. Amino Acid enters the elongation site (AUG - always methionine). 2. Elongation - longest step. Polypeptide chain grows as mRNA is read, tRNA aligns and releases correct and aligned amino acid. a. New tRNA will bump old tRNA out, from Elongation to Exit, Attachment to Elongation. 3. Termination - terminator codons will signal ending of polypeptide chain (STOP → UAA, UAG and UGA, do not code for any tRNA or amino acids - just stop chain.) Polypeptide chain will fold into quaternary form - functionary form. Codon code is universal - all animals/plants have the same bases Degenerative - different codes will make the same amino acids. DNA Mutations Alterations to DNA code. Not all mutations are bad - responsible for evolution and genetic diversity. Detrimental/Beneficial mutations affect the most. Molecular Genetics 8  Sources of Mutations 1. Spontaneous - internal impacts/errors in the body (free-radicals.) a. ‘Mistakes in proofreading.’ 2. Internal a. Physical - radiation, UV, X-Ray, Gamma. 3. Chemical a. Pollutants, additives, toxic agents. Targets Somatic Cells - body cells and tissue. Can result in localized or metastasized cancer (spread throughout). Gametic Cells - sperm and egg cells. If used in fertilization - zygote will be mutated, and all cells are afflicted. Beneficial Neutral Detrimental New - better protein Same protein made. No protein is made or a bad, can be added. (Mutation caused by malfunctional protein is made. degradation in code) ’AAA - AAG still code for 1. Nonsense - no protein, mRNA same amino acid.’ broadcasts an improperly placed stop codon. 2. Missense - more common, malfunctional protein - Frameshift, 1-2 bases are either added or deleted, affecting all triplets afterward. - Point Mutation, 1-2 bases exchange position, affects only specific triplet but still protein Molecular Genetics 9  - Transposition - rarer, not as important - sections of DNA are moved on the strand. DNA Technologies 1. PCR - IB Polymerase Chain Reaction Continuous copies of DNA - DNA replication in a tube. 1. Denature - DNA is heated to unravel at 95°C 2. Anneal - primers adhere to the DNA strand at 55°C 3. Extension - TAQ Polymerase builds DNAs complementary strand at 72°C 2. Restriction Endonucleases - Enzymes a. Genetic Scissors. Looks out for a specific repeating sequence, and cuts DNA at any recognized instances (restriction sites). Staggered pattern. Creates ‘sticky ends’ - two fragments of DNA that were cut by this enzyme can join together - fundamental theory of Genetic Engineering. 3. Recombinant DNA Tech - Genetic Modification (GMOs) a. Requires DNA Ligase, Restriction Enzymes, and Reverse Transcriptase. Splicing of one species genes to another species’ genes. Creates Transgenetic organisms. Recall - organisms have a universal genetic code - same nitrogenous bases..*. most organisms can adhere to base pairing rule. STEPS: 1. Reverse transcriptase reverses transcription to make cDNA (single stranded) from mRNA - code for the exact gene needed. 2. cDNA is converted to double strand DNA through DNA Polymerase - full gene is made w comp. strand. Molecular Genetics 10  3. Restriction Enzyme cuts receiver DNA gene at needed sites. 4. DNA Ligase glues gene into receiver DNA. 4. DNA Fingerprinting - use of noncoding repetitive sequences. a. Identifies the original source of DNA - vital for finding a match. (crime scenes, paternity tests, etc.) Repetitive sequences are unique to all individuals - a genetic fingerprint STEPS: 1. PCR - create many copies of found DNA 2. Restriction Enzyme cuts DNA into needed sequences. 3. Gel Electrophoresis - DNA fragments in gel face an electrical current that forces them into buffer groups. Based on size - matching buffer groups == original source DNA. Molecular Genetics 11