24.

2 Genes
Gene (Diagram Packages P3 > D1-2) Segment of DNA that specifies a specific amino acid sequence of a protein (and since we are in the 21st century, we also know that protons of a gene may help in its expression/regulations) RNA Reminder: contains bases A, U, G and C Is single stranded, not double Does not from a double helix There are 3 types mRNA, rRNA, tRNA mRNA: messenger RNA Takes 'message' from DNA and brings it to ribosome (DNA stays in nucleus; ribosomes are in cytoplasm) tRNA: transfer RNA Transfers amino acids to the ribosome rRNA: ribosomal RNA Along with proteins makes up the ribosome, where new proteins are made (synthesized) Transcription and Translation Gene expression (production of a protein) requires 2 processes 1. Transcription 2. Translation Step 1: Transcription (in brief) (Diagram Packages P3 > D3; P4 > D2) Transcription: genetic information in nucleus on DNA is transferred (transcribed) to RNA Polynucleotide is transcribed letter by letter from DNA template (master copy) to RNA copy (actually, a mirror copy), as in A->U, T->A, C->G and G->C) The mirror copy is later used to retranslate the original message Step 2: Translation (in brief) (Diagram Packages P4 > D1) Translation: the RNA transcript (message fragment produced during step 1: transcription) directs the sequence of amino acids that are added to a polypeptide. Nucleotide vs. Amino Acid Seq. Keep in mind: nucleotide sequence is very different from amino acid sequence. The nucleotide sequence coded by mRNA helps direct the addition of amino acids by the ribosomes Step 1: Transcription in detail (Diagram Packages P3 > D2; P4 > D2) RNA polymerase: an enzyme that binds to a promoter region (region that contains special sequence of DNA that signals. 'Start here!') and opens up the double helix (unzips it) so that complementary base pairing can occur just in this region. RNA polymerase then also joins the complementary base pairs to form an RNA sequence, which results in an mRNA molecule. mRNA maturation Before entering the cytoplasm, mRNA must be processed: The original DNA and the transcribed mRNA contain Intron and Exon regions

Introns and Exons (Diagram Packages P4 > D3) Introns are genetic areas that do not code for proteins and must be removed before the mRNA leaves for the cytoplasm. They are called introns because they are intragene segments Exons are portions of the gene that are ultimately expressed. Only the exons result in a protein product. Maybe intragenons and expressons would be a better name to help remember them? Modifications to mRNA 1. A Cap and tail is added to the primary RNA: Cap is composed of an altered guanine nucleotide Tail is composed of many adenosine nucleotides. It is often referred to as a poly-A tail because poly = many and A = adenosine 2. Introns are removed and exons rejoined together Splicing done by a complex of both RNA and protein (RNA is the enzyme, and we call this complex a ribozyme) Capped, tailed, spliced (so exon only) mRNA, is now a mature mRNA fragment. Transcription Video http://www.youtube.com/watch?v=WsofH466lqk All or none? Or some Processing normally brings together all the exons of a gene; however, in some cases, some exons are kept while others are removed or not expressed o Results in a different protein for each different combination o We suspect white blood cell recognition of specific antibodies for each antigen encountered is a result of this o With a partner, take turns reviewing and then explaining all the steps in transcription. Step 2: Translation 2nd step of gene expression that leads to protein synthesis Requires Several enzymes mRNA tRNA rRNA Genetic Code Just 4 bases can produce 20 genetic codes 1. One base - 4 combination A T C G 2. If 2 base - 16 possibilities 3. If 3 bases - 64 possibilities - we have that! Genetic Code (Refer to P5 and P6 of your diagram notes!) It's Triplets! DNA code is based on a triplet code

Codon: a 3 letter (nucleotide) unit of mRNA that codes for an amino acid 61/64 code for amino acids: 3/64 code for 'stop codon' -> signals polypeptide termination Methionine codon (AUG) is also the 'start codon' -> signals polypeptide initiation. Translation Video www.youtube.com/watch?v=5bLEDd-PSTQ Why repetition? Why do some amino acids have many codons? (i.e.: several have 4 condones, and one has 6 codons!) Allow for some protection from harmful mutations (while also promoting variation) tRNA (transfer RNA) (Diagram Packages P6 > D2-3) tRNA: bring amino acids to ribosomes Is a single-stranded, 'boot-shaped' nucleic acid that loops back on itself and carries a specific amino acid to the forming polypeptide chain based on its anticodon, the CBP (complementary base pair) for a specific codon of mRNA Codon - Anticodon The anticodon of a tRNA - amino acid complex pairs with the mRNA codon The amino acid is added to the forming polypeptide chain Once the amino acid is taken from the tRNA, the tRNA leaves the area The mRNA codon sequence determines the order that tRNA - amino acids arrive at the ribosome In short Step 1: Transcription: DNA base sequence is copied into mRNA Step 2: Translation: mRNA serves as template for tRNA to bring amino acids that form a protein

And you thought they were just dots in grade 8 (Diagram Packages P7 > D1-2) Ribosome: small structural bodies found in cytoplasm and ER (Endoplasmic Reticulum) where gene translation occurs Composed of many proteins and several ribosomal RNAs (rRNAs) rRNA produced in nucleolus joins with proteins formed in cytoplasm to form 2 ribosomal subunits (the large and small subunit), which leave nucleus and join together in cytoplasm and protein synthesis Ribosome Ribosomes 1. Binding site for mRNA 2. Binding sites for 2 tRNA at a time Ribosome moves down mRNA, new tRNAs arrive and add amino acids to the growing polypeptide chain Ribosomes dissociate once protein is fully formed. Polyribosomes Often, as one ribosome moves along an mRNA molecule, another ribosome will attach to the beginning of the same mRNA Allows many proteins to be formed at the same time from one mRNA strand The entire complex is called a Polyribosome Translation in 3 steps Translation must be very orderly so that the amino acid sequence in a polypeptide is correct 3 steps involved:

Chain initiation: Steps necessary to begin translations Chain elongation: steps necessary to effect polypeptide synthesis Chain termination: steps necessary to end the process of translation Chain Initiation Step 1: small ribosomal subunit attaches to mRNA around start codon (AUG) Step 2: anticodon of the initiator tRNA - methionine complex binds with this codon Step 3: large ribosomal subunit joins with small ribosomal subunit ... In order to begin elongation Chain Elongation A ribosome has 2 binding sites for tRNA Each newly-arrived tRNA at site 2 receives a peptide from a tRNA at site 1 tRNA at site 1 leaves, and tRNA at site 2 moves to site 1 (making room for another tRNA to now arrive at site 2) This movement of ribosomes along the mRNA during protein synthesis is called translocation. Ribozymes Ribozyme: an RNA enzyme that is part of the larger ribosomal subunit Attaches peptide to newly arrived amino acid (formation of a peptide bond) Occurs over and over as protein is synthesized tRNAs that leave are now free to pickup a few amino acid and return Entire cycle of - CBP to new tRNA - transfer of peptide - translocation is rapid (15 x/ sex in E. Coli) Chain Termination Occurs when protein synthesis comes to an end Occurs at a 'stop codon' Peptide is enzymaticaaly cleaved from the last tRNA by a release factor tRNA and polypeptide leave, and ribosome dissociates into its 2 subunits With a partner Practice reviewing the entire sequence of complex events that occur in transcription and translation. Use these prompts to help out, but you should eventually be able to do it without prompts Cause of Mutation 3 general types: 1. Errors in replication 2.Mutagens 3.Transposons If it occurs In gamete, then offspring may be affected In cell (somatic), then cancer may result Errors in replication Mistakes in DNA replication occur, but are rare DNA polymerase proofreads new strand against old strand and corrects mismatched pairs Only 1 mistake out of 1,000,000,000 replicated nucleotides occur Mutagens (Diagram Packages P8 > D1) Mutagens: environmental influences that cause mutations in cells E.g. - radiation (radioactive elements and isotopes, X-rays, UV light, gamma rays), certain organic chemicals (some chemicals found in pesticides or in cigarette smoke) Mutation rate ends up being low because of repair rate and efficiency of DNA repair enzyme

Transposons segments of DNA that have ability to move within and between chromosomes Movements affects neighbouring genes by increasing their expression (up-regulating )or decreasing it (down-regulation) Jumping genes; genes that have been up- or down- regulated due to transposons Responsible for certain genetic conditions (Charcot-Marie-T Both disease ) in humans and plants(white corn kernels) Frameshift Mutations (Diagram Packages P8 > D2) There are 2 major types of mutation First is a frameshift mutation: One or more nucleotides are inserted or deleted from a sequence, resulting in an incorrect reading of mRNA that leads to an incorrect amino acid sequence in the polypeptide E.g. CCC GGG AAA TTT add a T in the 2nd position becomes CTC CGC GAA ATT T (frame has shifted 1 over) Point Mutations (Diagram Packages P8 > D3) Point Mutation: involve the substitution of one nucleotide for another Slient Mutation: Consider CTT: what does it code for? Leucine Substitute an A in the 3rd position: what does it code for? CTA - Leucine Substitute a C in the 3rd position: what does it code for? CTC - Leucine Substitude a G in the 3rd position: what does it code for? CTG Leucine The SAME amino acid! Silent Mutation Nonsense Mutation: (Diagram Packages P9 > D1) Consider TGT: Cysteine Substitute a A in the 3rd position: what does it code for? TGA STOP codon Original a.a becomes a Stop Codon Nonsense Mutation Missense Mutation (Diagram Packages P9 > D2) Substitute a G in the 3rd position: what does it code for? TGG - Tryptophan Consider the above cases. Which one(s) do you think are missense mutations? How would you define a missense mutation?

Questions & HW
How did researchers crack the code for what each codons represents?

Thinking question: at which codon position (2 or 3) do you think the most missense mutation occur? And silent mutations? Explain your answers.

Discuss with a friend: Causes and types of mutations Explain again in detail transcription and translation

Quest next class (11.27 Thursday) on section 24.2 only A separate quest will be on 24.1 and 24.3 after finishing 24.3