Chapter 12

1. Chapter 12 DNA and RNA

2. 12-1 DNA • Griffith and Transformation • Was trying to discover why certain bacteria made people sick. • Had two strains of pneumonia bacteria isolated, both grew well in the lab, but only one could infect mice. • Disease-causing strain produced colonies with smooth edges, the non-disease-causing strain produced colonies with rough edges.

3. Griffith’s Experiments • Injected mice with disease-causing strain: mice died. • Injected with harmless strain: no illness. • Griffith wondered if disease-causing bacteria were producing a poison. • To find out, he heated a culture of disease-causing bacteria to kill them, then injected mice: mice lived. • Therefore, cause of pneumonia was probably not a chemical poison.

4. Transformation • He then mixed killed, disease-causing bacteria with a harmless culture and injected it: many mice died. • Somehow, the killed bacteria transferred their disease-causing ability to the harmless strain. • He called the process transformation because one strain of bacteria had apparently changed into the other. • Griffith hypothesized that when the live, harmless bacteria and the heat-killed, infectious bacteria were mixed, some factor transferred from the heat-killed cells to the live cells. • He thought that factor might contain a gene that could change harmless bacteria into disease-causing ones.

6. Avery and DNA • In 1944, a group of scientists led by Oswald Avery decided to repeat Griffith’s experiment to determine which molecule was responsible for transformation. • They treated heat-killed bacteria with enzymes to break down proteins, lipids, carbohydrates, and RNA one at a time: transformation occurred in each. • When DNA destroying enzymes were used, no transformation occurred, therefore, they concluded DNA was the transforming factor. • Discovered DNA is the nucleic acid that stores and transmits genetic information from one generation to the next.

9. The Hershey-Chase Experiment • Viruses are nonliving (?) particles smaller than a cell that can infect living organisms. • Bacteriophages- viruses that infect and kill bacteria. • Made of a DNA or RNA core and a protein coat. • Bacteriophages attach to the protein coat of a bacterium and inject their DNA into it. • The viral genes take over the bacteria and force it to make bacteriophages, which eventually burst out of the cell, killing it before they spread out to infect other bacteria.

10. Radioactive Markers • Hershey and Chase were trying to determine which part of the virus was infectious, the protein coat or the DNA core. This would determine whether genes were made of protein or DNA. • They grew viruses in cultures containing radioactive isotopes of phosphorus-32 and sulfur-35. • Phosphorus was the marker for DNA, sulfur the marker for protein.. • The marked viruses were allowed to infect bacteria, which were then tested for radioactivity. • Nearly all the bacteria contained 32P, the marker for DNA. • Hershey and Chase concluded that the genetic material of the bacteriophage was DNA, not protein.

12. The Structure of DNA • Scientists had to determine the structure of DNA that would allow it to: • Carry information from one generation to the next. • Put that information to work by determining the heritable characteristics of organisms. • Be easily copied. • DNA is a long molecule made up of units called nucleotides. • Each nucleotide is made of three basic parts: a 5-carbon sugar called deoxyribose, a phosphate group, and a nitrogenous base.

14. DNA contains four kinds of nitrogenous bases. • Adenine (A) and guanine (G) belong to a group of compounds called purines and have two rings in their structures. • Thymine (T) and cytosine (C) are known as pyrimidines and have one ring in their structures.

16. DNA has a backbone of sugar and phosphate from each nucleotide. This allows nucleotides to be joined in any order. • This allows it to code for all known traits. • Chargaff’s Rule • A=T and C=G • Percentages of A and T are the same, percentages of C and G are the same.

17. X-Ray Evidence • Rosalind Franklin recorded a scattering pattern of x-rays. • The X shape on the film shows the strands of DNA are twisted around each other like a string. • The angle of the twist suggests two strands.

18. The Double Helix • At the same time as Franklin, James Watson and Francis Crick were trying to model DNA by building 3D structures of cardboard and wire. • None explained the properties very well. • Watson and Crick figured out the structure after observing one of Franklin’s X-rays. • Their model was a double helix, in which two strands were wound around each other.

19. “twisted ladder” or spiral staircase. • Watson and Crick also found that hydrogen bonds formed between the nitrogenous bases and held the halves together. • H bonding can form only between certain pairs: A and T, C and G. • This principle, called base pairing, explained Chargaff’s rules.

21. 12-2 Chromosomes and DNA Replication • DNA and Chromosomes • Prokaryotic cells usually have a simple circle of DNA that is free in the nucleus. • Eukaryotic cells may have 1000x as much. • DNA Length • Many DNA strands are close to 1.6mm long, which is 1000x longer than their width. • They must be folded dramatically to fit in the cell.

22. Chromosome Structure • The nucleus of a human cell can contain 1m of DNA. • The smallest chromosome contains 30 million base pairs. • Eukaryotic chromosomes contain both DNA and protein, which is tightly packed into chromatin. • Chromatin is made of DNA tightly packed around proteins called histones. • DNA and histones form a beadlike structure called a nucleosome, which can pack with other nucleosomes to form a thick fiber, shortened by a system of loops and coils.

23. The fibers are dispersed in the nucleus for most of the cell cycle, so chromosomes are not visible. • During mitosis, the fibers of each chromosome are drawn together to form a tightly packed chromosome. • This may help separate chromosomes during mitosis and may affect gene activity and expression. • Nucleosomes can fold enormous lengths of DNA into the space of a cell nucleus. • Histone proteins have changed very little over the course of evolution, probably because DNA folding mistakes are very harmful. • Histones may also affect the way genes are “read”.

24. DNA Replication • Each strand of DNA has all the information needed to reconstruct the other half by the mechanism of base pairing. • The strands are said to be complementary because each strand can be used to construct the other strand. • If the strands are separated, the rules of base pairing allow you to reconstruct the base sequence of the missing strand

25. Duplicating DNA • A cell must duplicate its DNA in a process called replication in order to divide. • During DNA replication, the DNA molecule separates into two strands, then produces two new complementary strands following the rules of base pairing. (Replication is semiconservative.) • Each strand of DNA serves as a template (model) for the new strand. • In eukaryotic cells, replication occurs in hundreds of places and proceeds in both directions until each chromosome is copied. • DNA separates and replicates at the replication fork.

26. How Replication Occurs • DNA replication is carried out by a series of enzymes. • The first (DNA helicase) of these “unzips” the DNA by breaking the H bonds between the base pairs and unwinding the molecule. • Each strand serves as a template for the attachment of complementary bases. • Ex. A sequence of GCATTC would have a complementary sequence of CGTAAG. • The main enzyme in DNA replication is DNA polymerase, which adds individual nucleotides to the growing strand and “proofreads” it to avoid mistakes.

29. 12-3 RNA and Protein Synthesis • The Structure of RNA • A long chain of nucleotides. • Made of a 5C sugar, a phosphate group, and a nitrogenous base. • 3 differences from DNA: • Sugar is ribose, not deoxyribose. • RNA is single-stranded. • RNA uses uracil instead of thymine.

31. Types of RNA • The majority of most RNA molecules are for protein synthesis. • They control the assembly of amino acids into protein chains. • There are three main types of RNA: • Messenger RNA (mRNA) carries copies of the instructions for assembling amino acids into proteins from DNA to the rest of the cell. • Ribosomal RNA (rRNA) forms part of the ribosome where proteins are assembled. • Transfer RNA (tRNA) transfers each amino acid to the ribosome.

33. Transcription • Copying part of the nucleotide sequence of DNA into a complementary strand of RNA. • Requires RNA polymerase, which is similar to DNA polymerase. • RNA polymerase binds to DNA and separates the strands. RNA polymerase then uses one strand of DNA as a template to assemble nucleotides into a strand of RNA

35. RNA polymerase can only bind to a region of DNA called a promoter. • Promoters have specific sequence of bases that function as a starting line. • They tell the RNA polymerase where to bind to begin the RNA strand. • A similar signal on the DNA strand tells the RNA polymerase where to stop. • This completes the RNA molecule.

36. RNA Editing • RNA molecules have to be edited before making proteins. • Large pieces are frequently removed before the RNA can be functional. • The removed pieces are called introns and the remaining pieces, called exons, are spliced back together. • This may allow one gene to be spliced in different ways to code for different proteins or may play a role in evolution (small changes in DNA could have major effects in gene expression.)

37. The Genetic Code • Proteins are made by joining amino acids into a polypeptide. • Each polypeptide can contain a combination of any of the 20 amino acids in any order. • To put them in the correct sequence, mRNA has a “code” that uses the four bases A, U, C, and G in groups of three to represent each of the 20 amino acids. • Each group of three nucleotides is called a codon and specifies a single amino acid.

38. For example, the mRNA sequence UACACUGUA would be read as UAC-ACU-GUA and translate to Tyrosine-Threonine-Valine. • There are a total of 64 possible combinations, so some amino acids can be coded for by more than one codon. • The codon AUG can code for Methionine or “start” to signal where the sequence begins. • There are also three codons, UAA, UAG, and UGA that all code for “stop.” • What does the mRNA sequence AUGCCCAACGGUGAAUGA code for? • Start-proline-asparagnine-glycine-glutamate-stop

40. Translation • The ribosome “reads” the mRNA message to make a protein. • This process is known as translation. • During translation, the cell uses information from mRNA to produce proteins.

41. A- mRNA is transcribed from DNA in the nucleus and released into the cytoplasm. • B- mRNA attaches to a ribosome. As the mRNA moves through the ribosome, each codon is read by transfer RNA and the proper amino acid is attached. Each tRNA has an amino acid attached to one end and a complementary sequence (the anticodon) attached to the other end. For example, the tRNA that pairs with the codon AAC (lysine) would have a sequence of UUG.

42. C- The ribosome forms a bond between the first and second amino acids. At the same time, it breaks the bond that holds the now empty tRNA and the tRNA is released. The ribosome then moves to the next codon, where another tRNA moves in and attaches another amino acid. • D- The polypeptide chain grows until a stop codon is reached. The polypeptide is then released along with the mRNA.

46. Protein Synthesis in Eukaryotes

47. The Role of RNA and DNA • DNA contains the master plans for the cell and does not leave the nucleus. • RNA is the blueprint that leaves the nucleus and goes directly to the protein construction site. • Genes and Proteins • Most genes are nothing more than assembly instructions for proteins. • Proteins can have many roles: enzymes, pigments, cell surface antigens, growth promoters, etc. • Proteins regulate almost everything that cells do.

48. 12-4 Mutations • Mutations are changes in the DNA sequence that affect genetic information. • Mutations are usually harmful, but occasionally a favorable trait develops. • Gene mutations result from changes in a single gene. Chromosomal mutations involve changes in a whole chromosome.

49. Gene Mutations • A point mutation affects a single nucleotide. • A substitution mutation simply substitutes one nucleotide for another. • These generally affect the mRNA sequence that later codes for proteins, but sometimes do not. • They vary in how harmful they are based on where the mutation occurs, what it does, how it changes the protein, and how important the protein is.

50. Base Substitution