BIOCHEM MODULE 1 BIOCHEM C785 Western University

DNA & RNA Central DOGMA – DNA - RNA - protein  Nucleic Acid – function to encode inheritable information and pass it on through generations. RNA – less stable, temporary nucleic acid. o Easily made o Degrades rapidly outside of the nucleus Three types of RNA 1. rRNA (ribosomal) – composed of small and large sub units – binds to mRNA. 2. mRNA (messenger) – single strand copy of DNA – contains codons that specify type and order of amino acids in the polypeptide. 3. tRNA (transfer) – cloverleaf shape, carries amino acid on one end and anti-codon on other end to transfer.  Transcription – when the cell makes an RNA copy of a section of DNA and carries the information out of the nucleus to the rest of the cell. o Primary enzyme involved is RNA polymerase - Works to separate two DNA strands at the promoter (transcription start site). It then creates a short DNA-RNA hybrid that matches the correct RNA nucleotides to the DNA sequence it is transcribing. RNA is then released as a single stranded molecule. o mRNA – to form mature RNA a cap is placed on the 5’ end during transcription and a poly-A tail is placed on 3’ end after transcription termination. (This process protects mRNA from degradation once it leaves the nucleus). - Then splicing occurs – introns are cut out and remaining exons are joined together to form mature RNA that is now ready for translation.  Translation – when RNA leaves the nucleus and the information is then used to make proteins by forming a protein chain using peptide bonds. o Translation always starts with AUG codon. o Translation ends when ribosome encounters a STOP codon. Here, the ribosome then binds to a release factor protein which terminates translation. DNA contains:  Double stranded  SUGAR = deoxyribose  Contains thymine base RNA contains:  Single stranded  SUGAR = ribose  Contains uracil base DNA replication: 1. Must be separated 2. Synthesize by DNA polymerase (protein) 3. DNA polymerase matches nucleotides to parental sequence 4. If pairing is correct, then nucleotide is bonded to DNA. DNA Template DNA (Non-Coding) -------- (pneumonic TP = PAIR)  Runs in opposite direction and are complementary Non-Template (Coding) --------------- (pneumonic NTR = REPLACE)  Runs in same direction as mRNA  Strands are identical, only difference is the replacement of T with U DNA is antiparallel and has opposite 5’ and 3’ orientations COMPLEMENTARY gets PAIRED  A (adenine) pairs with T (thymine) if DNA  A (adenine) pairs with U (uracil) if RNA  C (cytosine) pairs with G (guanine)  5’ pairs to 3’ Match numbers and letters in exact same order!! Examples: 1. Template and Non-Template 2. mRNA and tRNA 3. Non-Coding and mRNA Amino Acid Sequence (read 5’ to 3’ to plug Complementary sequence Stays same, change T to U into codon table Template (Non-Coding)  Coding (Non-Template)  mRNA  tRNA complementary, RNA contains U NON-COMPLEMENTARY - REPLACE  Sequences are identical, just need to replace T with U IDENTICAL  Just match numbers and letters in exact order Gene Expression – is the transcription of new RNA. MUTATIONS  Can result from damage to DNA or errors introduced during damage repair.  Point Mutations – changes in a single base pair. Multiple kinds: 1. Silent Mutations – does not change amino acid sequence d/t redundancy in genetic code 2. Missense Mutations – codon now encodes a different amino acid 3. Nonsense Mutations – stop codon terminates translation 4. Frameshift Mutations – insertions or deletions disrupt the coding of a protein Apoptosis – programmed cell death. DNA REPAIR 1. Base Excision Repair (BER) – a single nucleotide is removed. Steps:  Recognize damage  Remove damage by excising part of one strand to leave a gap  Resynthesize the sequence using genetic information from other strand to fill the gap  Ligate to seal gap and restore continuity of DNA backbone 2. Nucleotide Excision Repair – about 30 nucleotides are removed  Thymine Dimer – when UV radiation causes two thymines that are adjacent to one another to fuse together – can only be fixed by cutting away several nucleotides. 3. Mismatch Repair – removes replication errors  Cell can distinguish newly synthesized DNA from parental DNA to remove only newly synthesized DNA to preserve parental DNA.  Proofreading: 1. DNA polymerase removes incorrect base 2. DNA polymerase inserts correct base  Mismatch: 1. Recognizes mistakes made during replication and cuts out several bases surrounding mismatched base 2. DNA polymerase