Discover Biology Chapter 11: DNA and Genes PDF

Anu Singh-Cundy Gary Shin Discover Biology SIXTH EDITION CHAPTER 11 DNA and Genes © 2015 W. W. Norton & Company, Inc.  An Overview of DNA and Genes Genes code for genetic traits and are located on chromosomes. DNA is the genetic material that make...

Anu Singh-Cundy Gary Shin Discover Biology SIXTH EDITION CHAPTER 11 DNA and Genes © 2015 W. W. Norton & Company, Inc.  An Overview of DNA and Genes Genes code for genetic traits and are located on chromosomes. DNA is the genetic material that makes up genes. In the early part of the 1900s, scientists were unsure if the genetic material contained in genes was the protein or the DNA. By 1952, through a series of experiments with bacteria, biologists determined that the genetic material was DNA.  DNA Stores Genetic Information as a Sequence of Nucleotides DNA is a nucleic acid composed of two strands of polynucleotides twisted to form a double helix. Four different nucleotides make up polynucleotides and can be found in the DNA of all cells.  Generally, Complex Organisms Have a Larger Genome and a Larger Number of Genes TYPE OF GENOME SIZE (BP)* NUMBER OF VIRUS/ORGANISM GENES" Porcine circo virus Smallest eukaryotic virus; causes wasting 1,759 3 type 1 disease in pigs Mycoplasma Smallest bacterium 580,073 517 genitalium Mimivirus Largest known virus; infects Amoeba 1,181,404 1,262 Escherichia coli Most widely used lab bacterium 4,639,221 4,377 K-12 Saccharomyces Yeast (fungus) species used in baking and 12,110,000 5,770 cerevisiae brewing Drosophila Fruit fly used in genetics and other types 130,000,000 17,000 melanogaster of research Arabidopsis Thale-cress, a model plant used in 157,000,000 27,407 thaliana agricultural and other types of plant research Homo sapiens Humans 3,200,000,000 21,000 Oryza sativa Rice plant 4,311,000,000 56,000 Among eukaryotes, however, no strict relationship exists between genome size and the structural and behavioral complexity of species.  Most Genes Code for Proteins, Which Generate Phenotypes RNA is a single-stranded nucleic acid similar to DNA. Messenger RNA (mRNA) delivers the genetic information, or instructions, from DNA to the ribosomes, where proteins are made. The conversion of a DNA-based sequence of nucleotides in a gene to an RNA-based sequence is called transcription. The process by which ribosomes convert the genetic information in Each protein has a unique amino acid sequence, mRNA into proteins is known as which gives it a unique function; protein function translation. produces the phenotype, the particular version of a genetic trait in the individual organism.  A Unique Set of Genes Is Expressed in Each Specialized Cell Type Gene expression is the manifestation of the information encoded in a gene as a specific phenotype. All cells in a multicellular individual have essentially the same DNA-based information; however, not all cells express all the genes present in the genome. Gene promoters are sections of a gene that function as an on/off switch for transcription. The expression of developmentally regulated genes changes as an organism develops. Structure  The Three-Dime nsional Structure of DNA James Watson and Francis Crick deciphered the physical structure of DNA in 1953. Watson and Crick won the Nobel Prize for discovering that DNA is built from two helically wound polynucleotides (the double helix).  DNA’s Structure Explains Its Function Base pair is the term for two nitrogenous bases held together by hydrogen bonds in a DNA molecule. Base-pairing rules, first proposed by Watson and Crick, state that a base on one strand of DNA pairs exclusively with a corresponding base on the other strand, resulting in two complementary stands of DNA.  DNA Stores Information in the Order of the Bases in the Polynucleotide Chain Differences in DNA sequences account for genetic variation. One gene is different from another gene because the two have a different DNA sequence. The same gene may have a slightly different sequence between two individuals of the same species, and is likely to be yet more variable between different species. Replication  DNA Replication Is Semiconservative DNA replication involves unwinding a DNA double helix and using each strand as a template for a new, complementary strand. The replication is semiconservative because one “old” strand (the template strand) is retained, or conserved, in each new double helix. 5’ -> 3’  Few Mistakes Are Made in DNA Replication DNA polymerase is the enzyme that connects nucleotides to make the new strand, using the old strand as the template. DNA polymerase proofreads as it links nucleotides; mismatches are detected, removed, and replaced with a 1 in 11 million error rate. Cells contain special DNA repair proteins that correct 99 percent of any base pair mismatches not caught by DNA polymerase.  DNA Replication DNA replication starts at the origin of replication (ori). An AT rich region of nucleotides. One strand serves as a template for the production of a second strand Topoisomerase (gyrase) relax the strands Helicase separates the strands A replication fork is created (or replication bubble)  DNA Replication DNA polymerase adds nucleotides to the growing DNA strand – In the 5‘ 3' direction – Initiated by an RNA primer – Leading strand is synthesized continuously – Lagging strand is synthesized discontinuously, creating Okazaki fragments – DNA polymerase removes RNA primers; Okazaki fragments are joined by the DNA polymerase and DNA ligase Table 8.1 Important Enzymes in DNA Replication, Expression, and Repair https://www.youtube.com/watch?v=TNK WgcFPHqw Figure 8.5 A Summary of Events at the DNA Replication Fork REPLICATION Proteins stabilize the The leading strand is unwound parental DNA. synthesized continuously by DNA polymerase. 3' DNA polymerase 5' Enzymes unwind and unzip the parental double helix. Replication fork RNA primer Primase 5' DNA polymerase 3' Okazaki fragment DNA ligase Parental 3' DNA strand polymerase 5' The lagging strand is DNA polymerase DNA ligase joins synthesized discontinuously. digests RNA primer the discontinuous Primase, an RNA polymerase, and replaces it with DNA. fragments of the synthesizes a short RNA primer, lagging strand. which is then extended by DNA polymerase.  DNA Replication Energy Needs – Energy for replication is supplied by nucleotides – Hydrolysis of two phosphate groups on ATP provides energy Most bacterial DNA replication is bidirectional Each offspring cell receives one copy of the DNA molecule Replication is highly accurate due to the proofreading capability of DNA polymerase  Figure 8.4 Adding a Nucleotide to DNA New Template Strand Strand Sugar Phosphate When a nucleoside triphosphate Hydrolysis of the phosphate bonds bonds to the sugar, it loses provides the energy for the two phosphates. reaction. Organization  A Closer Look at Genome Organization PROKARYOTES EUKARYOTES Size and organization of Several million base pairs in a single Hundreds of millions to billions of base pairs the genome chromosome. distributed among two to many chromosomes. Noncoding DNA Very little; most DNA codes for Large amount, found both within genes and proteins. between genes. Organization of genes Commonly organized by function; Genes with related functions may be found genes for a particular pathway tend distant from one another, even on other to be clustered together. chromosomes. A bacterium contains one circular chromosome made up of several million base pairs of DNA. Prokaryotic genes tend to be organized by function. Eukaryotes in general are structurally and behaviorally more complex than prokaryotes and have larger genomes. Eukaryote DNA contains large amounts of noncoding DNA; prokaryotes rarely contain noncoding DNA.  Genes Constitute Only a Small Percentage of the DNA in Most Eukaryotes Noncoding DNA is DNA that does not code for any kind of functional RNA. Noncoding DNA that separates one gene from another is called spacer DNA. Transposons are sequences that can move from one position on a chromosome to another, or even from one chromosome to another, and may disrupt a gene’s function in the process. Introns are noncoding sections interspersed with the coding regions of a gene or exons.  Eukaryotic DNA Is Highly Compacted Eukaryotic cells must use packaging proteins to compress a large amount of genetic information into each chromosome. Short lengths of DNA are wound around histone proteins to create a bead-on-a-string structure that is further compressed into a looped, 30-nanometer fiber. During cell division, DNA condenses into shorter, thicker chromosomes, the highest level of packing a chromosome can acquire. Class Quiz, Part 2 What is the percentage of adenines (A) in a DNA double helix in which 30 percent of the nitrogenous bases are guanine (G)? A. 20 percent B. 23.3 percent C. 30 percent D. 40 percent E. 70 percent  Class Quiz, Part 3 In about 5 minutes, 23 students at Medaille College squeezed themselves into this Volkswagen Beetle, during their annual “Stuff the Bug” event. Each student’s genome achieves an equally impressive feat. Which of the statements below is TRUE? A. The eukaryotic genome has more noncoding DNA than does the prokaryotic genome. B. The prokaryotic genome is larger, on average, than the eukaryotic genome. C. Prokaryotes have more genes on average than single-celled eukaryotes. D. Humans have the largest genomes because humans are the most complex species. Class Quiz, Part 4 DNA repair is A. important only during replication. B. found in eukaryotes but not in prokaryotes. C. vital to maintaining DNA’s integrity. D. an inherited disorder.  11.1 Concept Check, Part 1 1. What is gene expression? ANSWER: Gene expression consists of the processes by which a gene produces a phenotype. For protein-coding genes the gene’s DNA is transcribed into mRNA, mRNA is translated into protein, and protein function produces a phenotype.  11.1 Concept Check, Part 2 2. Is the genome of your neurons (nerve cells) identical to that of your liver cells? ANSWER: Yes. All cells in the body have essentially the same DNA-based information, or genome.  11.1 Concept Check, Part 3 3. We have at least 21,000 protein-coding genes. Are all of these genes expressed in each of your neurons (nerve cells)? ANSWER: No. A unique subset of the approximately 21,000 protein-coding genes is expressed in each cell type.  11.2 Concept Check, Part 1 1. If one strand of a DNA molecule has the sequence ATATCTAT, what is the sequence of its complementary strand? ANSWER: A bonds with T, and C bonds with G. Therefore, the sequence of the complementary strand is TATAGATA.  11.2 Concept Check, Part 2 2. What is the percentage of thymine (T) in a DNA double helix in which 20 percent of the nitrogenous bases are guanine (G)? ANSWER: 30 percent (if G = 20 percent, C = 20 percent. When G + C = 40 percent, then A + T = 60 percent; therefore T = 30 percent)  11.2 Concept Check, Part 3 3. If all genes are composed of just four nucleotides, how can different genes carry different information? ANSWER: The information encoded by a gene is determined by the precise sequence in which the four nucleotides are arranged; changing the nucleotide sequence changes the information. Because genes can differ in the total number of nucleotides, they can vary in length as well.  11.3 Concept Check, Part 1 1. What key function is performed by DNA polymerase? Where is this enzyme found in eukaryotic cells? ANSWER: DNA polymerase catalyzes the formation of a polynucleotide strand complementary to a template DNA strand. It is localized in the nucleus in eukaryotic cells.  11.3 Concept Check, Part 2 2. What is meant by the “semi” in semiconservative replication? ANSWER: “Semi” means that one strand (or half) of each newly synthesized DNA double helix comes from the original parent DNA.  11.4 Concept Check, Part 1 1. What mechanisms reduce the chance of DNA mutation? Are these mechanisms 100 percent effective? ANSWER: Proofreading by DNA polymerase and the DNA repair system reduce the chance of mutation. Neither mechanism is 100 percent effective.  11.4 Concept Check, Part 2 2. What are the key steps in DNA repair? ANSWER: There are three key steps: (1) recognition of the damaged strand, (2) removal of the damaged DNA, and (3) replacement of the removed DNA with a newly synthesized segment.  11.5 Concept Check, Part 1 1. Each human cell contains over a thousand times as much DNA as an E. coli bacterium has. Do we have over a thousand times as many genes as E. coli has? Explain. ANSWER: No. Humans have only about 5.6 times as many genes as E. coli has. We have more DNA because we have a large amount of noncoding DNA.  11.5 Concept Check, Part 2 2. Is all noncoding DNA useless “junk DNA”? ANSWER: No. Noncoding DNA can regulate gene expression, have structural functions, and serve as a connector (intron) between segments in a single gene. However, the function of most noncoding DNA is unknown.  11.6 Concept Check, Part 1 1. Which is a more compact form of DNA: the beads-on-a-string configuration or the 30-nanometer fiber? ANSWER: The 30-nanometer fiber  11.6 Concept Check, Part 2 2. What is the functional value of the roughly twofold greater condensation that chromosomes undergo during prophase of mitosis or meiosis? ANSWER: The increased condensation reduces the chance that the chromosomes will become entangled and break while being separated into different daughter cells.  11.7 Concept Check, Part 1 1. What is the adaptive value of gene regulation? ANSWER: Gene regulation ensures that genes are expressed only when and where they are needed, preventing waste of resources. It also enables organisms to turn genes on or off to better cope with a changing environment.  11.7 Concept Check, Part 2 2. How are housekeeping genes different from regulated genes? ANSWER: Unlike regulated genes, housekeeping genes provide essential functions and are therefore kept on all of the time in almost all cell types.