 Transcript Processing  Protein Folding  RNAi  Gene Repair

 Transcription factor recognizes TATA Box and binds to DNA  RNA polymerase bonds to DNA  RNA polymerase separates strands and strings together complementary nucleotides (using U instead of T)  Primary transcript has been created when terminator region is reached

 Transcription: › Creates molecule to carry protein instructions from DNA › Creates exact replica complementary to DNA

 Alteration of ends of transcript: › 5’ end capped with modified guanine  Keeps RNA from degrading in the cytoplasm › Cleavage factors and stabilizing factors bind to 3’ end › Poly A polymerase binds and cleaves 3’ end and adds poly A tail made of adenine

 RNA splicing: › Nucleotides removed › Introns = non-coding regions › Exons = coding regions to be expressed › Small nuclear ribonucleoproteins (snRNPs) = proteins that detect adenine at branching site › Spliceosomes remove the intron and bind the two exons

 The sequence of amino acids defines a protein’s primary structure.

 Blueprint for each amino acid is characterized by base triplets › Found in the coding region of genes  Ribosomes recognize triplets and create proteins

 Covalent bonds between amino acids help stabilize the protein  Shape and stability also maintained by chemical forces

 Chaperone proteins: › Prevent nearby proteins from inappropriately associating and interfering with proper folding › Surround protein in protective chamber during folding › Ex) bacteria: GroEL and GroES › Use ATP › Also assist in refolding proteins

Chaperone proteins protecting folding proteins

 Models of protein folding: › Diffusion Collision Model:  Nucleus is formed  Secondary structures collide and pack together › Nuclear Condensation Model:  Secondary and tertiary structures are made simultaneously

 RNAi = RNA Interference  RNAi is used to: › Silence specific genes › Fix gene expression problems in mammals › Also known as: › Cosuppression › Post Transcriptional Gene Silencing › Quelling

 Types of small silencing RNA: › Small interfering RNA (siRNA)  Endogeneous: derived from cell  Exogeneous: delivered by humans › Micro RNAs (miRNA) › PIWI-interacting RNAs (piRNA)  RNAi breaks up mRNA before it is synthesized.

 Allows singling out of genes to determine function.

 Could halt progression of: › Cancer › HIV › Arthritis › All other diseases

 DNA can be damaged by: › Radiation (gamma, x-ray, and ultraviolet) › Oxygen radicals from cellular respiration › Environmental chemicals (hydrocarbons) › Chemicals used in chemotherapy

 Four major types of DNA damage: › Deamination: amino acid group lost › Mismatched base › Backbone break › Covalent cross-linkage between bases Deamination in DNA

 Repairing damaged bases: › Direct chemical reversal › Excision repair mechanisms:  Base excision repair (BER)  Nucleotide excision repair (NER)  Mismatch repair (MMR)

 Chemical Reversal › Ex) glycosylase enzymes remove mismatched T and restore correct C

 Excision repair mechanisms: › Base excision repair:  DNA glycosylases identify damaged bases  DNA glycosylases remove damaged bases  Deoxyribose phosphate backbone component removed, creating gap  Gap filled with correct nucleotide  Break in strand ligated

 Excision repair mechanisms: › Nucleotide excision repair:  Protein factors identify damage  DNA is unwound  Faulty area is cut out and the bases are removed  DNA is synthesized to match that of the opposite, correct strand  DNA ligase adds synthesized DNA

 Excision repair mechanisms: › Mismatch repair  Corrects mismatches of normal bases (A&T, C&G) by:  Identifying mismatched bases  Cutting mismatched bases

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