How Genes Work

1. How Genes Work 15

2. Key Concepts • Most genes code for proteins. • DNA is transcribed to messenger RNA by RNA polymerase, and then messenger RNA is translated to proteins by ribosomes. In this way, genetic information is converted from DNA to RNA to proteins. • Each amino acid in a protein is specified by a group of three bases in messenger RNA.

3. Key Concepts • Mutations are random changes in DNA, ranging in extent from single bases to large chromosome regions, that may or may not produce changes in the phenotype.

4. Introduction • While the work of early geneticists, including Mendel, Watson & Crick, and others, illuminated the structure of DNA and genes, and the method of inheritance, biologists still did not understand how gene expression occurred. • Gene expression is the process of translating the information in DNA into functioning molecules within the cell.

5. What Do Genes Do? • Early advances showed that genes carry the instructions for making and maintaining an individual. • In order to infer what a particular gene does, George Beadle and Edward Tatum proposed damaging a gene, creating a mutant, and then observing the resulting effect on the mutant’s phenotype. • Nonfunctioning alleles are now called knock-out, null, or loss-of-function alleles.

6. The One-Gene, One-Enzyme Hypothesis • To test their hypothesis, Beadle and Tatum damaged genes in the bread mold Neurosporacrassa, and observed that defects in particular genes resulted in the mold’s inability to produce specific proteins. • The results of their experiments inspired their one-gene, one-enzyme hypothesis, which proposed that each gene contains the information needed to make an enzyme.

7. Testing the One-Gene, One-Enzyme Hypothesis • Srb and Horowitz further tested the one-gene, one-enzyme hypothesis by examining the production of the amino acid arginine by N.crassa. • Arginine is produced via a metabolic pathway requiring the action of three different enzymes. Srb and Horowitz hypothesized that different genes lead to the synthesis of each of the three enzymes.

9. Testing the One-Gene, One-Enzyme Hypothesis • To test their hypothesis, Srb and Horowitz used radiation to create thousands of mutant individuals and then performed a genetic screen, which allowed them to select those mutants incapable of producing arginine. • The results supported the one-gene, one-enzyme hypothesis. • Three distinct mutants were produced, each deficient in one of the three enzymes in the arginine metabolic pathway. • Biologists finally understood what most genes do: They contain the instructions for making proteins.

14. One-Gene-One-Enzyme Hypothesis

15. The Central Dogma of Molecular Biology • Francis Crick proposed that DNA is an information storage molecule, and that the sequence of bases in DNA is a kind of code in which different combinations of bases could specify the 20 amino acids. • A particular stretch of DNA (a gene) contains the information to specify the amino acid sequence of one protein. • The information encoded in the base sequence of DNA is not directly translated into the amino acid sequence of proteins.

16. RNA—the Intermediary between Genes and Proteins • François Jacob and Jacques Monod proposed that RNA molecules act as a link between genes, found in the cell’s nucleus, and the protein-manufacturing centers, located in the cytoplasm. • Messenger RNA (mRNA) was found to carry information from DNA to the site of protein synthesis. • The enzyme RNA polymerase synthesizes RNA according to the information provided by the sequence of bases in a particular stretch of DNA.

18. The Central Dogma • The central dogma summarizes the flow of information in cells. It states that DNA codes for RNA, which codes for proteins: DNA  RNA  proteins • The sequence of bases in a particular stretch of DNA specifies the sequence of bases in an RNA molecule, which specifies the sequence of amino acids in a protein. In this way, genes ultimately code for proteins.

19. The Roles of Transcription and Translation • DNA is transcribed to messenger RNA by RNA polymerase. • Transcription is the process by which the hereditary information in DNA is copied to RNA. • The mRNA is then translated to protein. • Translation is the process wherein the language of nucleic acids, the order of the nucleotide bases, is converted to the language of proteins, the order of amino acids.

20. Visualizing the Central Dogma DNA (information storage) Transcription mRNA (information carrier) Translation Proteins (active cell machinery)

21. The Central Dogma • According to the central dogma, an organism’s genotype is determined by the sequence of bases in its DNA, while its phenotype is a product of the proteins it produces. • Alleles of the same gene differ in their DNA sequence. Thus, the proteins produced by different alleles of the same gene frequently differ in their amino acid sequence.

25. Exceptions to the Central Dogma • Many genes code for RNA molecules that do not function as mRNAs and are not translated into proteins. • These other RNAs perform important functions in the cell. • Sometimes information flows in the opposite direction—from RNA back to DNA. • For example, some viral genes are composed of RNA and use reverse transcriptase, a viral polymerase, to synthesize a DNA version of the virus’s RNA genes.

26. The Genetic Code • Once the pattern of information flow in a cell was determined, biologists next strove to determine exactly how the sequence of bases in a strand of mRNA codes for the sequence of amino acids in a protein. • The geneticcode contains the rules that specify the relationship between a sequence of nucleotide bases in DNA or RNA and the corresponding sequence of amino acids in a protein.

27. How Long Is a Word in the Genetic Code? • George Gamow predicted that each word in the genetic code contains three bases. • As there are 20 amino acids and only four different RNA bases, a three-base code is the least that could specify enough amino acids—it could code for 4  4  4 = 64 different amino acids. • A three-base code provides more than enough messages to code for all 20 amino acids. A three-base code is known as a triplet code.

29. How Long Is a Word in the Genetic Code? • The triplet code is redundant, with some amino acids being specified by more than one triplet code. • The group of three bases that specifies a particular amino acid is called a codon. • Francis Crick and Sydney Brenner found that the reading frame (sequence of codons) of a gene could be destroyed by mutation but then restored if the total number of deletions or additions were multiples of three.

30. How Did Researchers Crack the Code? • Marshall Nirenberg and Philip Leder devised a system for synthesizing specific codons and were able to decipher the genetic code by determining which of the 64 codons coded for each of the 20 amino acids. • There is one start codon (AUG), which signifies the start of the protein-encoding sequence in mRNA. • There are three stop codons (UGA, UAA, and UAG) in the genetic code that signal the end of the protein-coding sequence.

32. Important Properties of the Code • It is redundant. • All amino acids except two are encoded by more than one codon. • It is unambiguous. • One codon never codes for more than one amino acid. • It is nearly universal. • With a few minor exceptions, all codons specify the same amino acids in all organisms. • It is conservative. • The first two bases are usually identical when multiple codons specify the same amino acid.

33. Using the Code • Biologists can work forwards or backwards in the central dogma to: • Predict the codons and amino acid sequence encoded by a particular DNA sequence. • Approximate the mRNA and DNA sequence that would code for a particular sequence of amino acids.

37. What Is the Molecular Basis of Mutation? • A mutation is any permanent change in an organism’s DNA. It is a modification in a cell’s information archive—a change in its genotype. Mutations create new alleles. • There are different types of mutations. • Point mutations result from a single base change. • Chromosome-level mutations are larger in scale, often resulting from the addition or deletion of chromosomes from the individual’s karyotype.

38. Point Mutations • Point mutations occur when the DNA polymerase inserts the wrong base into the newly synthesized strand of DNA. • Results in a change in the DNA base sequence if the DNA polymerase proofreading and mismatch repair systems fail. • Point mutations may be: • Missense, or replacement mutations. • Result in changes in the amino acid sequence of the encoded protein. • Silent mutations. • Does not change the amino acid sequence of the gene product.

40. Mutations Have Varying Effects on Organisms • Mutations fall into one of three categories: • Beneficial mutations increase the fitness of the organism. • Neutral mutations do not affect an organism’s fitness. ─Silent mutations are usually neutral. • Deleterious mutations decrease the fitness of the organism. • Most mutations are neutral or slightly deleterious.

41. Triplet Nature of the Genetic Code

42. Chromosome-Level Mutations • Chromosome-level mutations may involve changes in chromosome number. • Polyploidy is an increase in the number of each type of chromosome. • Aneuploidy is the addition or deletion of a chromosome. • Chromosome composition can also change. • Inversions occur when sections of a chromosome break and rotate before rejoining the chromosome. • Translocation occurs when a broken section of one chromosome becomes attached to another chromosome. • Chromosome-level mutations can be visualized via the karyotype of a cell.