LIF101 Lecture Notes - Flow of Genetic Information PDF

LIF101 Lecture Topic (5) Wednesday 23 October 2024 Flow of genetic information, genetic code, mutations https://www.youtube.com/watch?v=M4zHVRLXkgw&ab_channel=Fr ankGregorio https://www.youtube.com/watch?v=zwibgNGe4aY&ab_channel =StatedClearly Recaps...

LIF101 Lecture Topic (5) Wednesday 23 October 2024 Flow of genetic information, genetic code, mutations https://www.youtube.com/watch?v=M4zHVRLXkgw&ab_channel=Fr ankGregorio https://www.youtube.com/watch?v=zwibgNGe4aY&ab_channel =StatedClearly Recaps About DNA  DNA carries digitized information  Four digits are used to write genetic codes Genetic information is encoded  Watson and Crick proposed structure of DNA 1953 Journal Nature in its 171st volume on pages 737–738 ( 25 April 1953) Recaps Thus, to understand the nature of genetic information we need to understand the basic DNA structure and how information flows:  Within an individual.  From one generation to the other  Within a cell 1962 Nobel Prize in Physiology and Medicine Recaps Chargaff’s Rule Adenine must pair with Thymine Guanine must pair with Cytosine Their amounts in a given DNA molecule will be about the same. T A G C Recaps DNA Double Helix 5 O 3 H-bonds 3 O 5 P P 5 O 1 G C 2 3 4 4 2 1 3 5 O P P 5 T A 3 O H-bonds O 5 P 3 P  DNA strands run anti-parellel Recaps Mark the features of DNA that makes it ideal as a genetic materials Sequence of Sequence in one nucleotides in strand serves as the DNA strands template for the could store sequence in the other genetic information ´ ´  Central dogma of Molecular biology Natureसिद्धांत of information flow Flow of Flow of information: information nucleic acid to nucleic Nucleic acid to acid protein Replication Transcription Translation DNA RNA protein Reverse Why there is no transcription In subsequent lectures we loss of will explore this flow of information information the decoding during process replication? How much of the information in DNA goes to RNA??  What guides flow of genetic information  Replication: synthesis of daughter DNA from parental DNA  Transcription: synthesis of RNA using DNA as the template  Translation: protein synthesis using mRNA molecules as the template  Reverse transcription: synthesis of DNA using RNA as the template  A gene is transcribed into RNA which is then translated into the polypeptide DNA Transcription RNA Translation Protein From DNA to protein https://www.youtube.com/watch?v=gG7uCskUOrA&ab_channel=yourgenome https://www.youtube.com/watch?v=7Hk9jct2ozY&ab_channel=WEHImovies FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN  Gene (DNA) is a linear sequence of many nucleotides  DNA is transcribed into a linear sequence of RNA  RNA is translated into a linear sequence of amino acids – polypeptides (protein) DNA RNA Protein Entire business of flow of (polypeptide chain genetic information thus depends on constructing (transferring information) one kind of polymer from another  Transcription – Step I A C G T A T C G C G T A T G C A T A G C G C A T A C G T A T C G C G T A T G C A T A G C G C A T Template DNA Strands unzip locally Transcription – Step II A C G T A T C G C G T A DNA U G C A U A G C G C A U mRNA One of the DNA strands serve as a template and copied as mRNA (messenger RNA) Transcription – Step III A C G T A T C G C G T A DNA T G C A T A G C G C A T U G C A U A G C G C A U mRNA mRNA is then releases  Transcription RNA polymerase RNA nucleotides T C C A A T A U T C T G U A G C C A U C C A C G A T A G G T T A Direction of Template transcription Strand of DNA Newly made RNA  Transcription: Steps RNA polymerase DNA of gene  In the nucleus, the DNA Promoter DNA Terminator DNA helix unzips  And RNA nucleotides line up 1 Initiation along one strand of the DNA, following the base pairing rules Area shown  As the single-stranded 2 Elongation In Figure 10.9A messenger RNA (mRNA) peels away from the gene  The DNA strands rejoin Growing RNA 3 Termination Completed RNA RNA polymerase  How does DNA/RNA code for protein? Strand to be transcribed T A C T T C A A A A T C DNA A T G A A G T T T T A G Codon - a sequence of Transcription nucleotides that codes for an A U G A A G U U U U A G amino acid RNA Start Stop Translation condon condon Met Lys Phe Polypeptide STEP III TRANSLATION  Genetic code : How can four nucleotides code for 20 amino acids? If one nucleotide codes for one amino acid then a maximum of four amino acid could be coded  If two nucleotide code for one amino acid then a maximum of 16 amino acid could be coded  If three nucleotides code for one amino acid then a maximum of 64 codons can be generated, while the number of amino acids are only 20 42 = 16 43 = 64  The dictionary of genetic code (64 potential codons) आनुवान्शिकी कोड 5’-3’ A dictionary offers translation from one language to the other.  Hallmarks of genetic code  Triplet : three consecutive nucleotides code of one amino acid  Redundant or degenerate: meaning not unique (there are more than one codon for most amino acids)  Universal: All organisms bacteria to human use the same genetic codes/dictionary  Comma-less: meaning consecutive codons are readout into an amino acid sequence without gaps Key players in decoding the genetic message DNA Leucine Messenger-RNA Transfer RNA Anti-codon Amino Codon acid  How genetic code is readout in the cell DNA A C G T A T C G C G T A T G C A T A G C G C A T 3’ U G C A U A G C G C A U 5’ mRNA 3’ Amino acid 5’ Anti-Codon 5’ 3’ tRNA C A G G U C 3’ 5’ Codon Many amino acids are specified by more than one codon- degeneracy or redundancy Codons specifying the same amino acid are called Connect the terms synonyms below about genetic codes: redundancy, degeneracy and synonymous Codon-anticodon pairing of two tRNA Leu molecules 5’- 3’ 5’- 3’ CUG Codon CUC GAC Anti- codon GAG 3’- 5’ 3’- 5’  Three codons direct chain termination  Three codons, UAA, UAG, and UGA signify chain termination.  They are not read by tRNAs but by proteins called release factors (RF1 and RF2 in bacteria and eRF1 in eukaryotes). Three Rules reading codons  Codons are read in a 5’ to 3’ direction.  Codons are non-overlapping and the message contains no gaps.  The message is translated in a fixed reading frame which is set by the initiation codon. Codons are "displayed" in RNA because it is the functional molecule that directly participates in translating the genetic code into proteins. While DNA contains the blueprint, RNA is the intermediary that communicates the codon sequence to the protein-synthesizing machinery. Meaning and consequences of non-overlapping & comma-less reading of the triplet codons Let’s consider a metaphor of a normal DNA sequence FATCATATETHERAT What is the problem here? FATATATETHERAT What is the consequence? Mutation: a change in genetic code 1. Missense mutation: An alternation that changes a codon specific for one amino acid to a codon specific for another amino acid. 2. Nonsense or stop mutation: An alternation causing a change to a chain-termination codon. 3. Frame-shift mutation: Insertions or deletions of one or a small number of base pairs that alter the reading frame.  Experimental Results:  UUU codes for phenylalanine.  CCC codes for proline.  AAA codes for lysine.  The guanine residues in poly-G firmly hydrogen bond to each other and form multistranded triple helices that do not bind to ribosomes.  Codons Amino Acids Codon copolymer Recognized Incorporated Assignment (CU)” CUC|UCU|CUC… Leucine 5’- CUC-3’ Serine UCU (UG)” UGU|GUG|UGU… Cystine UGU Valine GUG (AC)” ACA|CAC|ACA… Threonine ACA Histidine CAC  What Are Mutations? Changes in the nucleotide sequence of DNA  May occur in somatic cells (aren’t passed to offspring), but could cause diseases, such as cancer  May occur in gametes (eggs & sperm) and be passed to offspring   Change of a single nucleotide Point  Includes the deletion, insertion, mutation or substitution of ONE nucleotide in a gene Types of Gene/Point Mutations  Substitutions  Insertions  Deletions  Frameshift 1. Missense mutation: An alternation that changes a codon specific for one amino acid to a codon specific for another amino acid. 2. Nonsense or stop mutation: An alternation causing a change to a chain-termination codon. 3. Frameshift mutation: Insertions or deletions of one or a small number of base pairs that alter the reading frame. Problems and concept revision  Frameshift Mutation  Inserting or deleting one or more nucleotides  Changes the “reading frame” like changing a sentence  Proteins built incorrectly Problems THE FAT CAT ATE THE BIG RAT Delete C THE FAT ATA TET HEB IGR AT Insert A THE FAT ATA ATE THE BIG RAT Frame shift mutation  Example Point Mutation Sickle Cell disease is the result of one nucleotide substitution Occurs in the hemoglobin gene The sixth position in the normal beta chain has glutamic acid, while sickle beta chain has valine. This is the sole difference between the two Is HbS an allele of Hbb ?  Consider a gene that specifies the structure of hemoglobin. Arrange the following events in the most likely sequence in which then following events might have occurred a. Anemia is observed b. The shape of the oxygen binding site is altered c. An incorrect codon is transcribed into hemoglobin mRNA d. The ovum (female gamete) receive a high radiation dose e. An incorrect codon is generated in the DNA of the hemoglobin gene f. A mother (an X-ray technician) accidentally steps in front of an operating X- ray generator g. A child dies h. The oxygen-transport capacity of the body is severely impaired i. A wrong tRNA is attached j. Nucleotide pair substitution occurs in the DNA of the gene for hemoglobin  Question If an mRNA of human beta-globin gene is added to bacterial cell free extract then human b globin polypeptide is formed (translated) What does this observation signify with respect to genetic code?  Home assignment The amino acid sequence shown in the following table was obtained from the central region of a particular polypeptide chain in the wild type and several mutant bacterial strains Codon 1 2 3 4 5 6 7 8 9 a. Wild type phe leu pro thr val thr thr arg trp b. Mutant 1 phe leu his his gly asp asp thr val c. Mutant 2 phe leu pro thr met thr thr arg trp d. Mutant 3 phe leu pro thr val thr thr arg e. Mutant 4 phe pro pro arg f. Wild type phe leu pro ser val thr thr arg trp For each mutant, identify the nature of the mutation  Home assignment In mutant strain X of E. coli, a leucine tRNA that recognizes the codon 5’-CUG-3’ in normal cell has been so altered that is now recognizes the codon 5’-GUG-3’. A missense mutation (lets call this mutation Y) that affects amino acid 10 of a particular protein is suppressed in mutant X cells (that is when the cells are mutant for both X and Y, which now appears wild type) a. What mutational even has occurred in mutant X cells? b. What amino acid would normally be present at position 10 of the protein (without the missense mutation)? c. What amino acid is put in at position 10 if the missense mutations is not suppressed ? d. What amino acid is put in at position 10 if the missense mutations is suppressed ? Codon-anticodon pairing of two tRNA Leu molecules 5’- 3’ 5’- 3’ CUG GUG Codon CUC GAC Anti- codon GAG 3’- 5’ 3’- 5’ Problem 2: Silent Mutation Impact A mutation occurs in the third nucleotide of the codon UUU (which codes for phenylalanine, Phe) changing it to UUC. Given that both codons code for the same amino acid (Phe), what type of mutation is this, and what impact does it have on the protein's primary structure? Answer: This is a silent mutation because the codon still codes for the same amino acid (Phe). It has no impact on the protein's primary structure. Problem 3: Reading Frame Shift A mutation occurs where one nucleotide is inserted into a sequence of codons. The original sequence is as follows: 5' - AUG GCC GUA CCG - 3' What will be the new sequence of codons if a "U" is inserted between the first and second nucleotide of the second codon (GCC)? Answer: Original sequence: 5' - AUG GCC GUA CCG - 3' If a "U" is inserted after the "G" in the second codon: New sequence: 5' - AUG GUC CGU ACC G - 3' This causes a frameshift mutation, altering the reading frame from the insertion point onward, and producing a different set of codons.