Mile-stones leading to the concept of nature of the gene: 1. The discovery of discrete units of inheritance in 1860s. - Mendel s pea experiments(

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1 Homework IV. Bioenergetics 1. Calculate the G for ATP hydrolysis in a cell in which the [ATP]/[ADP] ratio had climbed to 100:1 while the P i concentration remained at10 mm. How does this compare to the ratio of [ATP]/[ADP] when the reaction is at equilibrium and P i concentration remains at 10 mm? What would be the value of G when the reactants and prodcuts were all at standard state conditions of 1 M? 2. Calculate the free energy released when FADH 2 is oxidized by molecular O 2 under standard conditions. 3. Of the following substances, ubiquinone, cytochrome c, NAD +, NADH, O 2, H 2 O, which is the strongest reducing agent? Which is the strongest oxidizing agent? Which has the greatest affinity for electrons? 4. Suppose that you are able to manipulate th epotential of the inner membrane of an mitochondrion. You measure the ph of the mitochondrial matric and find it to be 8.0. You measure the bathing solution and find its ph to be 7.0. You clamp the inner membrane potential at +59 mv, i.e. you force the matrix to be 59 mv positive with respect to the bathing solution. Under these circumstances, can the mitochondrion use the proton gradient to drive the synthesis of ATP? Explain your answer.

2 Chap. 10 Nature of the Gene and the Genome Mile-stones leading to the concept of nature of the gene: 1. The discovery of discrete units of inheritance in 1860s. - Mendel s pea experiments( ) 2. Discovery of chromosome in The sea urchin experiment of Boveri and the round worm experiment of van Beneden led to the understanding of Meiosis. 3. Discovery of homologous chromosome in grasshopper by Sutton in 1903 (Pair of identical chromosomes). 4. Discovery of chromosome linkage and cross over in fruit fly by Morgan in Demonstration that gene could be mapped in order along length of chromosome (cross-over experiments and giant polytene chromosome in fruit fly). 6. Discovery of DNA as genetic material in Chargaff s rule 7. Determined the double helix structure of DNA by Watson and Crick.

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4 1. The discovery of discrete units of inheritance in 1860s. - Mendel s pea experiments( ) Mate or cross pea plants having different inheritable characteristics and to determine the pattern by which these characteristics were transmitted to the offspring. Severn characteristics were chosen. Trait ( ) Height Seed color Seed shape Flower color Flower position Pod color Pod shape Dominant Allele ( ) Processive Allele ( ) Tall Yellow Round Purple Along stem Green Inflated Dwarf Green Angular (Wrinkled) White At stem tips Yellow Constricted

5 Conclusions 1. The characteristics of the plants were governed by factors of inheritance, which were later termed Genes. 2. An individual plant possessed two copies of each gene that control the development of each trait, one derived from each parent. Alternative forms of the two genes are Allele. 3. The two Allele may or may not be identical. For each of the seven traits studied, one of the alleles was dominant over the other. When both are present, the recessive allele was masked by the dominant on 4. Each reproductive cell (Gamete) produced by a plant contained only one copy of a gene for each trait. Each plant arose from the union of a male and a female gamete. 5. Even though the pair of alleles remain together throughout the life of a plant, they became separated during the formation of the gametes. Model s Law of segregation 6. The segregation of one pair of alleles for one trait has no effect on the segregation of alleles for another trait. Model s Law of independent assortment.

6 2. Discovery of chromosome in The sea urchin experiment of Boveri and the round worm experiment of van Beneden led to the understanding of Meiosis. Chromosome : Visible thread of colored bodies were observed in round worms ( ). 2 in male and female gametes and 4 in the daughter cell. (Belgian: van Beneden) Meiosis - A process of generating male and female gametes. - Chromosome reduce to half (German: August Weisman) Mitosis - A process of cell division. - Each daughter cell receive the same number of chromosomes.

7 3. Discovery of homologous chromosome in grasshopper by Sutton in 1903 (Pair of identical chromosomes). Spermatogonia ( ): Cells that give rise to sperms. Spermatogonis can undergo both mitosis and meiosis. Sutton observe the change in chromosomes carefully in both mitosis and meiosis processes. Sutton found that mitotic cells has 23 chromosomes exist in look-alike pairs (homologous chromosomes) plus an extra X-chromosome. At the beginning of meiosis Sutton found that the 23 chromosomes form 11 pairs (Bivalent) plus an extra X-chromosome.

8 4. Discovery of chromosome linkage and cross over in fruit fly by Morgan in Drosophila (Fruit fly, ) - Generation time: 14 days. - Produce 1000 eggs/life. -Small, easy to maintain and breed, inexpensive. How to generate different strains (Mutants)? - Natural selection. - X-ray radiation. Characteristics: Eye color, wing length, head color etc 85 mutants were isolated and bred and crossbred. The genes did not assort independently but belongs to four linked groups. - When two genes are always expressed together they are call linked. Genes in the same chromosome are likely to be linked. Drosophila has four pairs of chromosomes Genes reside in chromosomes

9 5. Demonstration that gene could be mapped in order along length of chromosome (cross-over experiments and giant polytene chromosome in fruit fly). Genes reside in a chromosomes are not always linked. Why? During the early stage of meiosis homologous genes wrapped around each other, resulting in breakage and exchange of pieces (Corss-over, 0r genetic recombination). Same pair of genes gave the same frequency of recombination in every cross Position of a gene along the chromosome (Locus) was fixed and did not vary from one fly to the next. Physical mapping ( ) of genes in a chromosome.

10 Crossing over provides a mechanism for reshuffling alleles between maternal and paternal chromosomes. Crossing over in Drosophila genes Crossing over provides a mean to determine the relative positions of two genes. The further apart the two genes the more likely they will cross eath other.

11 Giant polytene chromosomes of larval insects. Bands (5000) indicate the positions of different genes Direct proof that genes are located in distinct loci. Puffed regions are regions where gene are actively been transcribed. Best system for direct visualization of gene expression.

12 EM of linear DNA released from the ruptured T2 bacteriaphage.

13 6. Discovery of DNA as genetic material in Chargaff s rule [A] = [T] [A] + [T] [G] + [C] [purine] = [pyrimidine] DNA

14 Fiber Diffraction

15 Watson-Crick Proposal: 1. The molecule is composed of two strainsof nucleotides. 2. The two chains spiral around each other to form a pair of right-handed helices. 3. The two chains composing two double helix run in opposite direction, I.e. antiparallel. 4. The sugar-phosphate backbone of each strand is located on the outside of the molecule with the two sets of bases projecting toward the center. 5. The bases occupy planes that are approximately perpendicular to the axis of the molecule and are, therefore, stacked on top of another like a pile of plates 6. The two stands are held together by hydrogen bonds. 7. A always pair with T and G with C, therefore the two strands are always complementary to each other. 8. Size of the molecule: 20 Å in diameter with repeat every 10 bases of pitch 34Å

16 Watson & Crick With DNA model

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18 B-DNA Major groove Wide but shallow Minor groove Narrow but deep

19 The importance of Watson-Crick Proposal: 1. The storage of genetic information: Confirm that the genetic informatioin is stored in the linear sequence 2. Self-duplicatioin and inhiritance: During replication, the two strands separated to serve as a template directing the order in which complementary nucleotides become assembled to form complementary strand. The newly synthesized two DNA molecules will be identical to each other and identical to the original one. 3. Expression of the genetic message: DNA must contain the information for its own replication. Not obvious!!!

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21 The Central dogma- The flow genetic information Replication Transcription Translation DNA mrna PROTEIN Replication ( ) DNA DNA DNA template 2 whole DNAs Transcription ( ) DNA RNA DNA template A piece of RNA Translation ( ) mrna Protein mrna : Ribosome Peptide

22 Genetic codes: With four bases how can you code for 20 a.a. Need at least 3 bases to code for one a.a. Ordering is important Start codon: AUG Initiation site Stop codons: UAA, UAG, UGA Terminating codons nonsense codons Each a.a. is coded by more than one codons Some codons are prefered.

23 Ribosome structure

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25 Transcriptional machinery: Polymerase Transcription factors promoter

26 Structure and processing of human β-globin mrna (Extron: Expressed sequence) (Intron) (Intervening sequence)

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28 Structure of transfer RNA

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30 Initiation of protein synthesis in prokaryotes 1: 30S ribosome associate with mrna, with the help of IF1 & IF2 2. f-met-trna associates with 30S ribosome and mrna by binding to GTP S joint the complex, GTP hydrolyzed, and IF2-GDP is released. Elongation Termination