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Chapters 16 and 17

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Before the end of the semester we will be covering Historical DNA experiments Structure of DNA/RNA DNA Replication Protein Synthesis (Transcription and Translation) Mutations Gene Expression (if time) No more labs this semester! Your final will be comprehensive Both multiple choice and short answermore info to come!

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Important Historical Experiments In the 1940s little was understood about inheritance and how it worked. It was believed the genetic material was either DNA or protein. It was understood that chromosomes are made of both DNA and protein Initial experiments suggested it was proteinlittle was understood about DNAs structure or function (proteins were identified as being more complex)

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Avery, McLeod, McCarty 1944 goal was to identify if inherited substance was either DNA, RNA, or protein used chemicals and bacteria that only allowed one of the above to be active at a time Results determined that the transforming agent was DNA Scientific community still skeptical

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Hershey and Chase 1952 used bacteriophages to confirm DNA is the genetic material bacteriophages were tagged with radioactive isotopes (DNA--P; protein--S) it was shown that the DNA was able to infect the bacteriophages, not the protein by tracking the radioactivity

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Watson and Crick 1953 discovered the shape of DNA molecule was a double helix using pictures of the molecule, they built a model sugar/phosphate backbone nitrogen bases in the interior strands are antiparallel helix uniform in diameter (base-pairing rules)

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Wilkins and Franklin 1953 Franklin used x-ray diffraction to photograph DNA (her pictures were used by Watson and Crick) Wilkins was working closely with Franklin in her lab and allegedly showed Watson and Crick the photograph that helped them build their model Watson, Wilkins, and Crick were awarded the Nobel Prize for science in 1962. Rosalind Franklin died in 1958 of cancer and was never given a Nobel Prize.

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Using the original papers published in Nature in 1953, identify the characteristics of a DNA molecule. What important characteristics did they (Watson, Wilkins, Crick, and Franklin) discover? List/highlight as many as you can.

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Deoxyribonucleic Acid (DNA) Classified as a nucleic acid (biological molecule) Genetic material organisms inherit from their parents Copied prior to cell division (mitosis/meiosis) Shape of a double helix Made up of nucleotides (building blocks) 5-carbon sugar (deoxyribose), phosphate, nitrogen base

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Base-Pairing Rules: A T C G Directionality Complementary strands Antiparallel: each strand runs in an opposite direction Designated 5 and 3 ends (carbon on sugar) Two types of bases Purines: two carbon rings Guanine, Adenine Pyrimidines: one carbon ring Cytosine, Thymine, Uracil

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Ribonucleic Acid (RNA) mRNA (messenger RNA)instructions (from DNA) for making protein tRNA (transfer RNA) carries amino acids rRNA(ribosomal RNA)makes up ribosomes 5-carbon sugar (ribose) Single stranded (one gene) Uracil instead of thymine A U

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Both RNA and DNA Have adenine, cytosine, and guanine Made of nucleotides Sugar and phosphate backbone Nitrogen bases perpendicular to backbone Held together by hydrogen bonds

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Biochemical Gymnastics: DNA Replication Occurs during S-phase of Interphase in the cell cycle Semi-conservative process. Each new strand of DNA produced is made of one parental and one new strand (described by Watson and Crick) Each strand serves as a template for the new strand In prokaryotes DNA is circular In eukaryotes DNA is linear

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DNA Replication (Overview) Begins at the origin of replication (specific sequences of DNA nucleotides) Proteins recognize this sequence and attach to the DNA and separate the two strands creating a bubble At either end of this bubble is the replication fork Replication then proceeds in both directions from the origin until both strands are copied. In prokaryotes replication starts in one spot, in eukaryotes multiple spots

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The Players. Helicase: enzyme that unwinds and unzips the helix at the replication forks. Single-strand Binding Protein (SSBPs): binds to unpaired DNA strand to keep them from re-pairing Topoisomerase: enzyme that relieves tension ahead of the replication fork (from untwisting of strand) Primase: enzyme that synthesizes the RNA primer for replication DNA Polymerase: several enzymes that catalyze the synthesis of new DNA (in eukaryotes there are 11 total); also checks for errors Ligase: links new fragmented DNA segments together

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Replication only occurs in the 5 to 3 direction Nucleotides added only to 3 end of molecule This is problematic for one side of the DNA molecule Leading strand: continuous strand Single RNA primer Lagging strand: discontinuous in fragments (Okazaki fragments) multiple RNA primers

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The steps 1. Origin of replication is located 2. Bubble forms in DNA helix by Helicase 3. Primase synthesizes primer to begin replication Need RNA primer to have something to add nucleotides to. 4. DNA Nucleotides are added by DNA polymerase to primer to begin new strand 5. Replication proceeds in the 5 to 3 direction on both sides of the molecule Leading and lagging strands 6. Replication continues until the entire molecule is copied http://highered.mheducation.com/sites/0035456775/student_view0/chapter12/dna_replication.html http://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html

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Ending Replication After every round of replication some of the DNA molecule is lost due to polymerase not being able to replicate it. To avoid excess loss of DNA, the ends of eukaryotic chromosomes have telomeres (long repeating sequences) Excess DNA nucleotides (no genetic info) Acts as a buffer to actual genes (does shorten over time thought to be evidence of aging)

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Chapter 18

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Gene Expression: process by which DNA directs the synthesis of proteins occurs in two parts: Transcription and Translation this process dictates the presence of specific traits (genotype/phenotype) occurs in all organisms Watson and Crick describes this as the central dogma (DNA RNA Protein)

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Transcription synthesis of RNA (mRNA) using DNA as a template (protein instructions) occurs in nucleus (eukaryotes) or cytoplasm (prokaryotes) Prokaryotes can begin translation before transcription is finished Eukaryotes have an extra step during transcription before translation can begin

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DNA is a template strand, which is used to produce mRNA instructions (for protein) mRNA is complementary to DNA uses different nucleotides (uracil) RNA polymerase unzips DNA and joins complementary RNA nucleotides to copy instructions reads 5 to 3, no primer needed promoter: DNA sequence where RNA polymerase attaches and initiates transcription http://www.dnalc.org/resources/3d/13- transcription-advanced.html

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3 Stages Initiation RNA polymerase joins to the promoter and begins to unwind helix helped by transcription factors (proteins), creates a transcription-initiation complex Elongation RNA polymerase unwinds/untwist 10-20 nucleotides at a time nucleotides added to 3 end as mRNA is built, the molecule peels away from DNA and the double helix reforms Termination in prokaryotes there is a terminator sequence (stop signal) eukaryotes transcribe a specific sequence to stop transcription (creates pre-mRNA)

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RNA Modifications (eukaryotes only) RNA processing: enzymes in the nucleus modify pre-mRNA To help protect from degradation 5 cap (modified G sequence) 3 (poly-A tail) RNA splicing: removal of large portions of the RNA molecule (cut and paste) eukaryotes have long stretches of non-coding DNA interspersed with coding segments introns: non-coding segments exons: coding segments eventually expressed

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RNA Splicing introns are removed and exons are joined together snRNPs: join together to form a spliceosome Once finished, completed mRNA leaves nucleus to begin translation

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Translation synthesis of a polypeptide using mRNA as instructions occurs on ribosomes (rRNA) in cytoplasm tRNA: transfers amino acids to growing protein each associated with a particular amino acid anticodon: complementary RNA sequence to mRNA

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instructions for producing a protein uses three letters on mRNA (triplet code) codon: mRNA triplet (3 nucleotides) methionine is start stop codons UAA, UAG, UGA

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3 stages Initiation mRNA, tRNA, and ribosome start with amino acid methionine (initiator tRNA) translation initiation complex Elongation amino acid added to chain via sites on ribosome (A-P-E) elongation factors help process; reads 5-3 requires energy Termination stop codons end synthesis, codes for release factor release factors bind and protein is released via hydrolysis Protein is then folded into appropriate shape with help of chaperonin proteins http://www.dnalc.org/resources/3d/16- translation-advanced.html

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Oops! Mutation: change to genetic information Ultimate source of new genes May be spontaneous or result from mutagens Point mutations: change in single nucleotide (substitution) silent: change doesnt alter amino acid sequence missense: changes one amino acid into another (minor changes) nonsense: change codon for amino acid into a stop codon (premature end to translation) Frameshift mutation: add/lose nucleotides resulting in change to reading frame of codons (not multiples of 3) Insertion or Deletion http://www.bozemanscience.com/mutations/