Chapters 12 and 13

1. Chapters 12 and 13 0 DNA and Protein Synthesis

2. Discovery of the Role of DNA A. 1928 - Frederick Griffith discovers transformation in bacteria : * discovered that “something” was able to transform harmless (non – virulent) bacteria into harmful (virulent)

3. Discovery of the Role of DNA (cont’d) animation • 1944 -Oswald Avery and colleagues show that DNA can transform bacteria • 1952 - Alfred Hershey and Martha Chase use bacteriophage to confirm that DNA (not protein) is the genetic material

4. Discovery of the Role of DNA (cont’d) D. 1953 - James Watson and Francis Crick propose a structural model for the DNA molecule Based On: X-Ray crystallographyimages prepared by Maurice Wilkins and Rosalind Franklin Chargaff’s Rule: # of Adenines = # of Thymines # Guanines = # of Cytosines

5. DNA and RNA are Polymers of Nucleotides • Both are nucleic acids made of long chains of nucleotide monomers • A nucleotide (building block of a nucleic acid) has 3 parts: • A phosphate (PO4-) group that is negatively charged • A 5-Carbon sugar (deoxyribose in DNA or ribose in RNA) • A nitrogen-containing base

6. Thymine, Cytosine, Adenine, and Guanine DNA (deoxyribonucleic acid) bases: purines pyrimidines • Pyrimidines: single ring bases • Purines: double ring bases • Complimentary bonding pattern: • Adenine + Thymine (share 2 hydrogen bonds) • Cytosine + Guanine (share 3 hydrogen bonds)

7. RNA: ribonucleic acid Similar to DNA except: • Sugar in RNA = ribose • Base “uracil” instead of thymine • Single stranded Figure 10.2C, D

8. Twist The Structure of DNA • Two polynucleotide strands wrapped around each other in a double helix • A sugar-phosphate backbone • Steps made of hydrogen-bound bases (A=T, C G)

9. DNA REPLICATION: • Helicase enzyme splits H bonds between bases… unzips a portion of DNA • DNA polymerase binds to each strand • DNA polymerase adds complimentary nucleotides to each parent strand • Replication continues until both parent strands are copied • DNA polymerase “proof-reads” molecule for mistakes replication fork: location where DNA helix is still together. Next place to be unzipped replication bubble: location where DNA is being copied

10. Each strand of the double helix is oriented in the opposite direction (“anti-parallel”) “prime” #’s refer to carbons in the sugar At one end, the 3’ carbon has an (OH) and at the opposite, a 5’ carbon has the PO4- Why does this matter? DNA polymerase can only add nucleotides to the 3’ end. A daughter strand can only grow from 5’  3’ Therefore, only one daughter strand is made continuously (leading strand) The other strand (lagging strand) is made in a series of short pieces (Okazaki fragments), later connected by DNA ligase Bioflix movie A Structural Problem with DNA Replication

11. Replication in Living Cells: Prokaryote v. Eukaryote Prokaryote: * one single loop of DNA * regulatory proteins bind to a starting point on the 1 chromosome * bi-directional replication until all is copied • Eukaryote: • much more DNA to copy • replication begins at many points, bi-directional replication • after replication is finished, replicated chromatin threads condense into chromosomes

12. When DNA can repair mistakes and when it can’t DNA enzymes work like a spell checker • Cut out wrong sequences • Undamaged strand is template • Only 2 or 3 stable changes per year Mutations: some severe, others are not • Inheritable changes occur in gametogenesis • Now the “wrong” sequences are copied • Ex: cystic fibrosis (CF): a deletion of 3 nucleotides in a certain gene • Ex: sickle cell anemia: one nucleotide substitution in the hemoglobin gene • Mutagen: a mutation causing substance (can break DNA) • Ex: x-rays, radioactivity, nicotine

13. Protein Synthesis: the transfer of information from: DNA  RNA  Proteins “gene expression”: A gene is a linear sequence of many nucleotides. 3 Types: • Structural genes: have info to make proteins • Regulatory genes: code for proteins which are on/off switches for other genes • Genes that code for tRNA, rRNA, histones DNA vs. RNA • single stranded • A U C G • ribose sugar • 3 types of RNA: • messenger, transfer, ribosomal • double stranded • A T C G • deoxyribose sugar mRNA (messenger):copies DNA’s message in nucleus  brings it to cytoplasm tRNA (transfer):carries amino acids to mRNA so protein can be made rRNA (ribosomal): major part of the ribosome. Helps link amino acids from tRNA’s together  assemble protein

14. Protein Synthesis is Two Steps: • Transcription: The DNA of the gene is transcribed into mRNA • Translation: decoding the mRNA and assembling the protein

15. 1. Transcription: Eukaryote • DNA sequence (message for protein) is transcribed by mRNA • Only one strand (bottom; non-coding strand) is needed as a template Steps: RNA polymerase splits H bonds in DNA section RNA polymerase attaches to a promoter region on DNA to begin transcription RNA polymerase travels along bottom strand of DNA. RNA nucleotides join in a complimentary pattern (A=U, C=G) A termination signal reached, transcription over mRNA strip detaches from DNA, DNA helix closes up mRNA is processed: Intronsare cut out, Exonsare glued together, cap and tail are added. Mature mRNA leaves nucleus through pores cytoplasm for next step (translation)

16. 2. Translation: the synthesis of proteins using mRNA, tRNA and ribosomes • The Genetic Code: the language in which instructions for proteins are written in the nucleotide sequences • Each triplet of mRNA nucleotides is a “codon” because it will “code” for 1 amino acid • Ex: AUG GUC CCU AAU CCU Met – Val – Pro – Asn – Pro • Original strand of DNA (coding strand): ATG GTC CCT AAT CCT • Only difference: U is substituted for T • Use the Genetic Codechart to “decode” mRNA message

17. The Genetic Code is the Rosetta Stone of Life • Nearly all organisms use exactly the same genetic code • More than one codon for most amino acids = degenerate nature…a change (mutation) in gene does not always mean a different amino acid. • what does CAU code for? ACU? UAU? GCC? • how many codons for Leu? • what is special about AUG and it’s amino acid, Methionine? • what is special about UAA, UAG, and UGA? HIStidine…THReonine…TYRosine…ALAnine

18. An exercise in translating the genetic code: Step 1: fill in corresponding DNA bases to dark blue strand (non-coding) Step 2: Transcribe the dark blue strand into mRNA (pink) Step 3: Translate the codons into correct amino acids (use chart) G A A A T G T G T T T A Coding strand (gene we want copied) transcription translation

19. An exercise in translating the genetic code: answers Step 1: fill in corresponding DNA bases to dark blue strand (non-coding) Step 2: Transcribe the dark blue strand into mRNA (pink) Step 3: Translate the codons into correct amino acids (use chart)

20. How Does Translation Happen? Need: tRNAs and ribosomes (rRNA) tRNA: single stranded RNA, folded up * 2 parts: anticodon and aa attachment site • Ribosome: 2 protein subunits and ribosomal RNA * allows aa’s to attach by making peptide bonds * travels along mRNA strip, tRNA’s join and bring correct amino acids • Confused? • Watch demo on board and videos animation bioflix animation

21. Put It All Together:

22. Mutations can change the message of genes • Mutations: • changes in DNA base sequence • caused by errors in DNA replication, recombination, or by mutagens • substituting, inserting, or deleting nucleotides also alters a gene “point mutation”…may or may not alter amino acid sequence “frame-shift mutation”…most devastating to protein structure

23. Chromosomal Mutations: • affect chromosome structure and shape • can occur during crossing over (prophase 1) • 4 types: deletion, duplication, inversion, translocation • Genetic Mutations: Harmful of helpful? • can be both • depends on environment • Harmful Examples: • a) defective proteins from defective genes can disrupt normal cell function (ex: regulation of cell cycle  cancer) • b) sickle cell anemia (one point mutation in hemoglobin gene). Cells form sickle shape, can’t carry oxygen, can block blood vessels, painful. • Helpful Examples: • new proteins made by mutations can give an advantage in a certain environment • ex: antibiotic resistant bacteria, peppered moths

25. Please make the following changes: On multiple choice section 2: #7 “A” + “C” Cross out: “the growing molecule” PUT IN: “the parent strand”