1. How cells follow DNA directions on how to make proteins Transcript processing, protein modification, gene mutations

2. DNA = the directions in code Each chain of nucleotides is a line of code Each chain contains directions for making many different proteins Each set of directions is a gene 1 gene = 1 protein =1 trait

3. Steps in making a protein 1) Copy the Directions for one protein onto RNA (one gene) Transcription 2) Use the RNA directions to make a protein Translation

4. 1) Transcription A) RNA polymerase scans the DNA to find the gene it needs to copy B) RNA polymerase has 4 jobs 1) unwind the DNA double helix 2) breaks hydrogen bonds to separate chains 3) match RNA nucleotides to the DNA gene 4) fuse the RNA nucleotides together to make a chain of RNA http://www.youtube.com/watch?v=ztPkv7wc3yU& feature=related http://www.youtube.com/watch?v=ztPkv7wc3yU& feature=related http://www.youtube.com/watch?v=5MfSYnItYvg&f eature=related http://www.youtube.com/watch?v=5MfSYnItYvg&f eature=related

5. The chain of RNA that is made is called mRNA Or messenger RNA

6. Messenger RNA Carries coded directions out into the cell. Where mRNA binds to a ribosome.

7. 2) Translation A) Translates nucleotide code of RNA into the amino acid code of a protein B) Takes place in the cytoplasm C) Is done by a ribosome http://www.biostudio.com/demo_freeman_ protein_synthesis.htm http://www.biostudio.com/demo_freeman_ protein_synthesis.htm

8. mRNA mRNA = chain of nuclotides that make up the coded directions for making the protein Every 3 nuclotides of mRNA is a codon Each codon is the code for 1 amino acid

10. Ribosomes Made of 2 subunits. Subunits bind onto mRNA chain at start codon 3 codons at a time are inside the ribosome E is for Exit Codons in P and A sites are the ones being read

11. tRNA bring amino acids to the ribosome Match the correct amino acid in place by matching their anti-codon to the mRNA codon Fit into the E, P and A sites

12. tRNA Each tRNA only picks up ONE kind of amino acid tRNA drops off amino acids at the ribosome then moves back into the cytoplasm to pick up another amino acid(but always the same kind) aminoacyl-tRNA synthetase enzymes bind aa to tRNA

13. Steps to Translation A) Initiaion 1) Ribosome subunits bond to mRNA 2) tRNA that matches start codon binds at site P

14. B) Elongation 3) tRNA that matches 2 nd codon binds at site A 4) ribosome attaches the 2 amino acids those tRNAs carry to each other by a peptide bond http://www.phschool.com/science/biology_place/biocoach/translation/elong1.html

15. 5) Ribosome moves down mRNA chain by one codon 6) the first tRNA Moves into the E site and exits the ribosome

16. 7) the next tRNA moves into place

17. Termination 8) Ribosome moves down mRNA to stop codon 9) Release factors bind to stop codon instead of a tRNA 10) Ribosome, mRNA, tRNAs and protein all break apart

18. wobble effect There are 60 possible codons but only 45 tRNAs so only 45 anti-codons Some tRNAs can bind to more than one codon The last base in the anti-codon has some flexibility in what it binds to (wobble room) So anticodon AGU could bind to UCA or UCG

19. Mutations= changes in a cell’s DNA Caused by: 1) spontaneous errors 2) mutagens: chemicals/radiation Can happen in body cells (somatic cells) or In reproductive cells (egg & sperm)

20. Somatic cell mutations May cause no change = if mutated gene is one that is not use by that particular cell May cause cell to die May cause cancer Not passed on to children

21. Thymine dimer

22. Reproductive Cell or Early Embryo Cell Mutations Child with mutation Every cell of the child is mutated May cause miscarriage May cause a genetic disorder in child May have no effect at all

23. 2 types of mutation Gene mutation = DNA coding error may be a missense mutation where the codons code for the wrong aa …. or nonsense where stop codon or partial codon Chromosome Mutation = change in chromosome number, missing or extra chromosome pieces.

24. Gene Mutations 1) point mutations (substitutions) – change only 1 base pair a) substitution of 1 nucleotide for another b) ATT becomes ATG..(missense) c) may not cause any change = silent mutation d) may change 1 amino acid e) could be nonsense only if codes for stop e) can cause disorder

25. 2) Frameshift mutations- change all the codons a) insertion b) deletion c) THE FAT CAT = HEF ATC AT d) most always ruins protein

26. 3) tandem repeats – codons repeated over & over most often ruins protein more repeats = more problems

27. Transcripts Transcript = chain of RNA as copied from DNA template Pre-mRNA = a transcript that will become mRNA Other transcripts become tRNA or rRNA

28. Transcript processing Pre-mRNA transcript has a cap added to 5’ end cap facilitates exit through nuclear pore cap aids in translation initiation cap is attached to a UTR (untranslated region) UTR is followed by the START codon

29. Poly-A tail 3’ end of transcript gets a poly-A tail added to it Enzyme adds 50 -250 more A ribonucleotides More As added make the mRNA last longer Fewer As make the mRNA break down quicker Breakdown starts immediately on entry to cytosol Hydrolytic enzymes

30. RNA splicing Introns = in between coding regions of RNA do not code for a.a.s are cut out before mRNA leaves nucleus bacteria do NOT have introns Exons = have codons that are executed by translation….code for a.a.s Introns are cut out, exons fused together

32. Alternative splicing Exons are spliced together in different orders To make different proteins

33. spliceosome Complex of proteins and small RNAs Remove introns Joins exons in proper order RNAs in spliceosome are Ribozymes… RNA enzymes Sometimes the intron being removed IS the ribozyme

34. Evidence for RNA before DNA RNA can act as its own enzyme RNA polymerase can initiate polymerization on its own DNA polymerase can only start polymerization at a primer That is created by RNA polymerase

35. Protein location w/i the cell All translation begins in cytoplasm Some proteins need to be delivered to the ER The first few aa at leading end of those proteins = a signal peptide Signal peptide binds to a Signal Recognition Particle (SRP) SRP escorts ribosome to receptor protein on ER Protein synthesis completed on the ER and growing polypeptide chain is fed into the ER for folding & processing

37. Proteins that enter ER destined for endomembrane system (ER, golgi, lysosome, plasma membrane, nuclear membrane) or produced for secretion (insulin) (Proteins that are completed in the cytoplasm stay in cytoplasm)

39. Post-translational modification (Completed protein is modified) Amino acid modification – add functional groups Trim aa from cap end Cleave polypeptide into pieces Join 2 polypeptide into quaternary structure with disulfide bonds

40. Differences among Domains: Replication Bacteria – No histones, 1 origin, circular DNA Archaea – Have histones, 1 origin, circular DNA Eukarya – Have histones, Many origins, Linear DNA

41. Differences among Domains: Transcription Bacteria – NO transcription factors needed for RNA polymerase to recognize promoter Archaea – Require transcription factors Eukarya – Require transcription factors

42. Differences among Domains: transcription Bacteria – one type of RNA –polymerase Archaea – one type of RNA -P Eukarya – 3 types of RNA polymerase (structure of RNA-P very similar btwn Archaea and Eukarya)

43. Differences among Domains: Transcription Bacteria – terminator ends transcription… NO transcript processing (no splicing) Archaea – No conclusive evidence at this time Eukarya – different signal ends transcription depending on the type of RNA DO transcript processing for all RNA

44. Differences among Domains: Translation Bacteria – translation begins before transcription is complete Eukarya – translation in cytoplasm after transcript processing

45. Differences among Domains: Translation Bacteria – Ribosomes include 3 RNA molecules Eukarya – Ribosomes include 4 RNA molecules