Exam 1 Study GuideIntroduction (Ch1)- A gene is a particular sequence of DNA that codes for a trait. Genes are located on chromosome, which are made up of DNA and proteins. Alleles are different forms of the same gene, i.e. brown eyes or green eyes.- Genotype is the actual DNA sequence in an organism. Phenotype is the traits that they portray.Structure of DNA (Ch10)- Three experiments led to the conclusion that DNA is the genetic material:1. Griffith’s Assay to TransformationGriffith worked with Pheumococcus of two strains: Smooth (S) and Rough (R). When the S strain was injected into mice, its coat prevented the immune system from recognizing the virus and the mice died. When the rough strain was injected into the mice, it did not have this coat and therefore the immune system could recognize and destroy the strain, allowing the mice to live. Griffith then heat-killed the S strain and injected it into the mice. The mice lived. However, when Griffith mixed the heat-killed Sstrain and the live R strain, the mice died. He did not prove that DNA held the genetic material, but he did suggest that the R strain was being transformed to the S strain.2. Avery, MacCleod, and McCartyWorked with the same bacteria as Griffith. They took the heat-killed S strain and removed all lipids and proteins because they knew that genes consisted mostly of proteins and nucleic acids. They separated the bacteria into three samples. One samplewas treated with protease to destroy the protein. One sample was treated with ribonuclease to destroy RNA. The third sample was treated with deoxyribonuclease to destroy DNA. The treated samples were each added to the R strain. Results showed that only the samples with DNA were transformed to the virulent S strain. The sample with the destroyed DNA only contained the R strain. They concluded that DNA is the transforming substance. Other scientists, however, were not convinced. Perhaps they did not kill the strains completely. They thought that proteins held the genetic material because they have more variation, with 20 amino acids, whereas DNA only has 4 bases.3. Hershey and ChaseUsed bacteriophages that inject their chromosomes into cells, then form another generation of phages. They grew two samples of phages – one in radioactive sulfur (35S) and the other in radioactive phosphorous (32P). Sulfur is found only in proteinand phosphorous is found only in DNA. The treated samples were then allowed to infect E. coli. Then, the protein coats of the “ghost” phages were separated from the cells. It was found that radioactive sulfur was present in the protein coats of the cells, but not in the next generation of phages. The next generation of phages contained the radioactive phosphorous, proving that DNA holds the genetic material.- Purines have 2 rings – adenine and guanine12- Pyrimidines have 1 ring – cytosine, thymine (and uracil)- Chargaff’s Ratios – the ratio of A:T = 1 and G:C = 1, but the ratio of (A/T):(G/C) varies among species- Sugar-phosphate backbone of DNA:- DNA strands are antiparallel – 3’ to 5’ on one strand and 5’ to 3’ on the other- DNA can have 1 of 3 different helical forms:o A, B – right handed. Put your right thumb up. The direction that your fingers curl is the same direction that the double helix turns. DNA is usually in the B formo Z - left handed. Pretty rare.- DNA vs RNA-H bonded on the 2’ carbon -OH bonded on the 2’ carbon Thymine Uracil Double stranded (usually) Single stranded (usually)DNA Replication and Recombination (Ch12)Meselson-Stahl Experiment – proved that DNA replication is semi-conservative.Meselson and Stahl first grew E.coli cells in a medium containing the isotope of nitrogen (15N) so that all of the DNA contained 15N. Then, they transferred the bacteria to a medium containing lighter nitrogen, 14N and allowed for DNA replication. After one round of replication, they centrifuged the DNA, to measure by density. The DNA formed one band in the tube, which was inconsistent with the conservative model of replication, which would have shown two bands – one for the DNA with 15N and one for the DNA with 14N. Meselson and Stahl allowed theE. coli to replicate again in 14N and centrifuged again. This time, they found two bands of different densities, which was consistent with the semi-conservative model of replication. Replication could not be dispersive, because that would have produced only a single strand.3- Requirements of DNA replication: template of single-stranded DNA, deoxyribonucleoside triphosphates (dNTPs – base + sugar+ phosphates), DNA polymerase, primers, free 3’ OH group to extendDNA is synthesized 5’  3’Prokaryotes can replicate in one of two ways:- Theta model- Rolling-circle modelReplication fork:DNA Polymerase I can synthesize DNA and remove RNA primers and replace them with DNA. DNA Polymerase III synthesizes DNA and is much faster than DNA polymerase I.4TranscriptionProkaryotes EukaryotesPromoter Sequence-35 consensus sequence: TTGACA-10 TATA Box-35 consensus sequence-25 TATA BoxThe 100 base pairs upstream from the core promoter contain consensus sequences that are different for different genes that vary in both length and location.Initiation The sigma factor (a protein) binds to the RNA polymerase, forming the holoenzyme which can recognize and bind to the -35 consensus sequence and the -10 TATA box within promoter sequence. The holoenzyme then begins to unwind the DNA strand.The TATAA binding protein (TBP) and transcription factor IID (TFIID) are the firsttwo things to bind in the core promoter. Then additional proteins also bind in the core promoter and specific transcription factors bind to the regulatory promoter. Enhancers can be 1000s of base pairs away upstream or downstream help initiate transcription. Many proteins stay bound to recruit more RNA polymerasesElongation RNA Polymerase starts adding complementary RNA at the transcription start site and continues to add onto the 3’ end until it reaches a termination sequence. RNA is synthesized in the 5’ to 3’ direction.Termination Rho-independent mechanism - relies on a particular sequence at the end of a gene that consists of a pair of inverted sequence of bases, which forms a “hairpin” in the secondary structure of the mRNA, which is like a speed bump. After the hair pin, a long sequence of A’s. Because A’s form only 2