Unit 8: Flashcards

Question

What are complimentary base pair How many h bonds

Answer 1

DNA: - adenine (A) and thymine (T) are complementary base pairs, - cytosine (C) and guanine (G) are also complementary base pairs, adenine and thymine form two hydrogen bonds between them, cytosine and guanine form three hydrogen bonds between them.

Answer 2

high temperatures or certain chemicals can break the hydrogen bonds between complementary bases in dna, thus separating the strands into two separate single strands of DNA (single-stranded DNA [ssDNA]). is analogous to protein denaturation, as described in Proteins. The ssDNA strands can be put back together as double-stranded DNA (dsDNA), by cooling or removing the chemical denaturants, allowing these hydrogen bonds to reform. high GC content is more difficult to denature than DNA with a lower GC content because of the three bonds

Answer 3

Vertical: - transmission of this information (DNA) from mother to daughter cells is called vertical gene transfer - it occurs via DNA replication. DNA can also be enzymatically degraded and used as a source of nucleosides and nucleotides for the cell. Unlike other macromolecules, DNA does not serve a structural role in cells.

Answer 4

Historically, women have been underrepresented in the sciences and in medicine, For example, although Rosalind Franklin performed the X-ray diffraction studies demonstrating the double helical structure of DNA, Watson and Crick became famous for this discovery, building on her data. Similarly, Barbara McClintock did pioneering work in maize (corn) genetics from the 1930s through 1950s, discovering transposons (jumping genes), but she was not recognized until much later, receiving a Nobel Prize in Physiology or Medicine in 1983 (Figure 10.19). Today, While more than half of the undergraduate degrees in science are awarded to women, only 46% of doctoral degrees in science are awarded to women. In academia, the number of women at each level of career advancement continues to decrease, with women holding less than one-third of the positions of Ph.D.-level scientists in tenure-track positions, and less than one-quarter of the full professorships at 4-year colleges and universities. Even in the health professions women are underrepresented in many medical careers and earn significantly less than their male counterparts, as shown in a 2013 study published by the Journal of the American Medica! Association. Why do such disparities continue to exist and how do we break these cycles? The situation is complex and likely results from the combination of various factors: - including how society conditions the behaviors of girls from a young age and supports their interests, both professionally and personally. Some have suggested that women do not belong in the laboratory, including Nobel Prize winner Tim Hunt, whose 2015 public comments suggesting that women are too emotional for science were met with widespread condemnation. Perhaps girls should be supported more from a young age in the areas of science and math Science, technology, engineering, and mathematics (STEM) programs sponsored by the American Association of University Women (AAUW)24 and National Aeronautics and Space Administration (NASA) are excellent examples of programs that offer such support. Contributions by women in science should be made known more widely to the public, and marketing targeted to young girls should include more images of historically and professionally successful female scientists and medical professionals, encouraging all bright young minds, including girls and women, to pursue careers in science and medicine.

Answer 5

Based on his symptoms, Alex's physician suspects that he is suffering from a foodborne illness that he acquired during his travels. Possibilities include: - bacterial infection (e.g., enterotoxigenic E. coli, Vibrio cholerae, Campylobacter jejuni, Salmonella) - viral infection (rotavirus or norovirus), - protozoan infection (Giardia lamblia, Cryptosporidium parvum, or Entamoeba histolytica). His physician orders a stool sample to identify possible causative agents (e.g., bacteria, cysts) and to look for the presence of blood because certain types of infectious agents (like C. jejuni, Salmonella, and E. histolytica) are associated with the production of bloody stools. Alex's stool sample showed neither blood nor cysts. The hospital physician suspected that Alex was suffering from traveler's diarrhea caused by enterotoxigenic E. coli (ETEC), the causative agent of most traveler's diarrhea. To verify the diagnosis and rule out other possibilities, Alex's physician ordered a diagnostic lab test of his stool sample to look for DNA sequences encoding specific virulence factors of ETEC. The physician instructed Alex to drink lots of fluids to replace what he was losing and discharged him from the hospital. ETEC produces several plasmid-encoded virulence factors that make it pathogenic compared with typical E. coli. These include the secreted toxins heat-labile enterotoxin (LT) and heat-stabile enterotoxin (ST), as well as colonization factor (CF). Both LT and ST cause the excretion of chloride ions from intestinal cells to the intestinal lumen, causing a consequent loss of water from intestinal cells, resulting in diarrhea. CF encodes a bacterial protein that aids in allowing the bacterium to adhere to the lining of the small intestine. • Why did Alex's physician use genetic analysis instead of either isolation of bacteria from the stool sample or direct Gram stain of the stool sample alone?

Answer 6

RNA is single stranded and made of ribonucleotides that are linked by phosphodiester bonds. ribonucleotide: - contains ribose (the pentose sugar), one of the four nitrogenous bases (A, U, G, and C), and a phosphate group. DNA is more stable, making it more suitable for storage of genetic information the instability of RNA makes it more suitable for its more short-term functions. uracil forms a complementary base pair with adenine and is used instead of the thymine. Even though RNA is single stranded: - most types of RNA have intramolecular base pairing between complementary sequences within the RNA strand - creating a three-dimensional structure essential for their function

Answer 7

Used for the synthesis of proteins via translation. The three main types of RNA: - messenger RNA (mRNA) - ribosomal RNA (rRNA) - transfer RNA (tRNA). mRNA: - carries the message from the DNA, which controls all of the cellular activities in a cell. - If a cell requires a certain protein to be synthesized, the gene for this product is "turned on" and the mRNA is synthesized through transcription - The mRNA then interacts with ribosomes and other cellular machinery to direct the synthesis of the protein it encodes during translation mRNA is unstable and short-lived in the cell, especially in prokaryotic cells, ensuring that proteins are only made when needed.

Answer 8

In 1961, French scientists François Jacob and Jacques Monod: - hypothesized the existence of an intermediary between DNA and its protein products, which they called messenger RNA.

Answer 9

rRNA and tRNA: - are stable types of RNA. - In prokaryotes and eukaryotes, tRNA and rRNA are encoded in the DNA, then transcribed into long RNA molecules that are cut to release fragments that are the individual mature RNA species. synthesis, cutting, and assembly rRNA into ribosomes: - In eukaryotes, takes place in the nucleolus of the nucleus, - in prokaryotes, takes place in the cytoplasm. Neither rRNA or tRNA carries instructions to direct the synthesis of a polypeptide, but they play other important roles in protein synthesis.

Answer 10

Ribosomes: - composed of rRNA and protein. - rRNA makes up to about 60% of the ribosome by mass and provides the location where the mRNA binds. - rRNA ensures the proper alignment of the mRNA, tRNA, and the ribosomes; - rRNA of the ribosome also has enzymatic activity (peptidyl transferase) and catalyzes the formation of the peptide bonds between two aligned amino acids during protein synthesis. Transfer RNA: - small, only 70-90 nucleotides long. - It carries the correct amino acid to the site of protein synthesis in the ribosome. - contains an amino acid binding site and an mRNA binding site - It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain being synthesized Any mutations in the tRNA or rRNA can result in global problems for the cell because both are necessary for proper protein synthesis

Answer 11

Scientists in the laboratories of Thomas Steitz (1940-) and Peter Moore (1939-) : - crystallized the ribosome structure from Haloarcula marismortui, a halophilic archaeon isolated from the Dead Sea. - Because of the importance of this work, Steitz shared the 2009 Nobel Prize in Chemistry with other scientists who made significant contributions to the understanding of ribosome structure. - Although rRNA had long been thought to serve primarily a structural role, its catalytic role within the ribosome was proven in 2000

Answer 12

Does have the additional capacity to serve as genetic information In viruses that do not contain DNA. RNA is typically single stranded within cells but there is diversity in viruses: - Rhinoviruses which cause the cold; influenza viruses; and the Ebola virus and are single-stranded RNA viruses. - Rotaviruses, which cause severe gastroenteritis in children, have double-stranded RNA. Because double-stranded RNA is uncommon in eukaryotic cells, its presence serves as an indicator of viral infection.

Answer 13

Genes: - Segments of DNA molecules - individual genes contain the instructional code necessary for synthesizing various proteins, enzymes, or stable RNA molecules. Genotype: - The full collection of genes that a cell contains within its genome - a cell does not express all of its genes simultaneously. Instead, it turns on (expresses) or turns off certain genes when necessary. Phenotype: - The set of genes being expressed at any given point in time determines the cell's activities and its observable characteristics, Constitutive genes: - Genes that are always expressed - some constitutive genes are known as housekeeping genes because they are necessary for the basic functions of the cell.

Answer 14

the genotype of a cell remains constant the phenotype may change in response to environmental signals (e.g., changes in temperature or nutrient availability) that affect which nonconstitutive genes are expressed. example: - the oral bacterium Streptococcus mutans produces a sticky slime layer that allows it to adhere to teeth, forming dental plaque - however, the genes that control the production of the slime layer are only expressed in the presence of sucrose (table sugar). - Thus, while the genotype of S. mutans is constant, its phenotype changes depending on the presence and absence of sugar in its environment. Temperature: - can also regulate gene expression. - example: the gram-negative bacterium Serratia marcescens, a pathogen associated with hospital-acquired infections, produces a red pigment at 28 °C but not at 37 °C, the normal internal temperature of the human body

Answer 15

The majority of an organism's genome is organized into the cell's chromosomes: - chromosomes are discrete DNA structures within cells that control cellular activity. Chromsomes - eukaryotic chromosomes are housed in the membrane-bound nucleus - prokaryotes contain a single, circular chromosome that is found in the cytoplasm, specifically the nucleoid - A chromosome may contain several thousand genes.

Answer 16

Eukaryotic chromosomes: - typically linear - cells contain multiple distinct chromosomes. - eukaryotic cells contain two copies of each chromosome and, therefore, are diploid. Length: - length of their chromosome exceeds the length of the cell, it’s packaged into a very small space to fit within the cell. During DNA packaging: - histones do DNA wrapping and attachment to scaffolding proteins. - The combination of DNA with histones is referred to as chromatin. In eukaryotes, the packaging of DNA by histones may be influenced by environmental factors that affect the presence of methyl groups on certain cytosine nucleotides of DNA. The influence of environmental factors on DNA packaging is called epigenetics. Epigenetics is another mechanism for regulating gene expression without altering the sequence of nucleotides. Epigenetic changes can be maintained through multiple rounds of cell division and, therefore, can be heritable.

Answer 17

DNA supercoiling refers to the process by which DNA is twisted to fit inside the cell. - Supercoiling may result in DNA that is either underwound (less than one turn of the helix per 10 base pairs) or overwound (more than one turn per 10 base pairs) from its normal relaxed state. Proteins involved in supercoiling include topoisomerases: - these enzymes help maintain the structure of supercoiled chromosomes, preventing overwinding of DNA during certain cellular processes like DNA replication

Answer 18

Chromosomes in bacteria and archaea are usually circular a prokaryotic cell typically contains only a single chromosome within the nucleoid. Because the chromosome contains only one copy of each gene, prokaryotes are haploid. Packaging: As in eukaryotic cells, DNA supercoiling is necessary for the genome to fit within the prokaryotic cell. The DNA in the bacterial chromosome is arranged in several supercoiled domains. As with eukaryotes, topoisomerases are involved in supercoiling DNA. DNA gyrase is a type of topoisomerase, found in bacteria and some archaea, that helps prevent the overwinding of DNA. (Some antibiotics kill bacteria by targeting DNA gyrase.) In addition, histone-like proteins bind DNA and aid in DNA packaging. Other proteins bind to the origin of replication. Because different regions of DNA are packaged differently, some regions of chromosomal DNA are more accessible to enzymes and thus may be used more readily as templates for gene expression. , several bacteria, including Helicobacter pylori and Shigella flexeri, have been shown to induce epigenetic changes in their hosts upon infection, leading to chromatin remodeling that may cause long-term effects on host immunity.

Answer 19

noncoding DNA do not encode proteins or stable RNA products. Noncoding DNA is commonly found in areas prior to the start of coding sequences of genes as well as in intergenic regions (i.e., DNA sequences located between genes) noncoding DNA regions were once referred to as "junk DNA"; , this terminology is no longer accepted because scientists have found roles for some of these regions, many of which contribute to the regulation of transcription or translation through the production of small noncoding RNA molecules, DNA packaging, and chromosomal stability. Although scientists may not fully understand the roles of all noncoding regions of DNA, it is generally believed that they do have purposes within the cell.

Answer 20

only an average of 12% of the genome is taken up by noncoding sequences. noncoding DNA can represent about 98% of the genome in eukaryotes, as seen in humans, but the percentage of noncoding DNA varies between species.

Answer 21

additional molecules of DNA outside the chromosomes that are also part of the cells genome. The genomes of eukaryotic cells also include the chromosomes from organelles such as mitochondria and/or chloroplasts that these cells maintain: - The maintenance of circular chromosomes in these organelles is a supports the endosymbiotic theory genomes of certain DNA viruses can also be maintained independently in host cells during latent viral infection. In these cases, these viruses are another form of extrachromosomal DNA: - For example, the human papillomavirus (HPV) may be maintained in infected cells in this way.

Answer 22

Besides chromosomes, some prokaryotes have smaller loops of DNA called plasmids: - they may contain one or a few genes not essential for normal growth - Bacteria can exchange these plasmids with other bacteria via horizontal gene transfer (HGT). - this transfer sometimes provides microbes with new genes beneficial for growth and survival under special conditions. genes obtained from plasmids may have clinical implications: - they encode virulence factors that give a microbe the ability to cause disease or make a microbe resistant to certain antibiotics. - Plasmids are also used heavily in genetic engineering and biotechnology as a way to move genes from one cell to another.

Answer 23

Maria, recently became ill in the African nation of Botswana Maria's research was focused on traditional African methods of tanning hides for the production of leather. She visited a tannery daily for several hours. after returning from the tannery, Maria developed a fever, chills, and a headache, along with chest pain, muscle aches, nausea, and other flu-like symptoms. her fever spiked and she began to cough up blood After learning about her recent work at the tannery, the physician suspected that Maria had been exposed to anthrax. He ordered a chest X-ray, a blood sample, and a spinal tap, and immediately started her on a course of intravenous penicillin. , lab tests confirmed the physician's presumptive diagnosis. Maria's chest X-ray exhibited pleural effusion, the accumulation of fluid in the space between the pleural membranes, and a Gram stain of her blood revealed the presence of gram-positive, rod-shaped bacteria in short chains, consistent with Bacillus anthracis. Blood and bacteria were also shown to be present in her cerebrospinal fluid, indicating that the infection had progressed to meningitis. Despite supportive treatment and aggressive antibiotic therapy, Maria slipped into an unresponsive state and died three days later. Anthrax is a disease caused by the introduction of endospores from the gram-positive bacterium B. anthracis into the body. Once infected, patients typically develop meningitis, often with fatal results. In Maria's case, she inhaled the endospores while handling the hides of animals that had been infected. The genome of B. anthracis illustrates how small structural differences can lead to major differences in virulence. In 2003, the genomes of B. anthracis and Bacillus cereus, a similar but less pathogenic bacterium of the same genus, were sequenced and compared. Researchers discovered that the 16s rRNA gene sequences of these bacteria are more than 99% identical, meaning that they are actually members of the same species despite their traditional classification as separate species. Although their chromosomal sequences also revealed a great deal of similarity, several virulence factors of B. anthracis were found to be encoded on two large plasmids not found in B. cereus. The plasmid pX01 encodes a three-part toxin that suppresses the host immune system, whereas the plasmid pX02 encodes a capsular polysaccharide that further protects the bacterium from the host immune system Since B. cereus lacks these plasmids, it does not produce these virulence factors, and although it is still pathogenic, it is typically associated with mild cases of diarrhea from which the body can quickly recover. Unfortunately for Maria, the presence of these toxin-encoding plasmids in B. anthracis gives it its lethal virulence.

Answer 24

The results of the diagnostic test analysis of Alex's stool sample revealed that it was positive for heat-labile enterotoxin (LT), heat-stabile enterotoxin (ST), and colonization factor (CF), confirming the hospital physician's suspicion of ETEC. physician noted that Alex's symptoms were not resolving quickly and he was experiencing discomfort that was preventing him from returning to classes. The family physician prescribed Alex a course of ciprofloxacin to resolve his symptoms. , the ciprofloxacin resolved Alex's symptoms within a few days. Alex likely got his infection from ingesting contaminated food or water. Emerging industrialized countries like Mexico are still developing sanitation practices that prevent the contamination of water with fecal material. Travellers in such countries should avoid the ingestion of undercooked foods, especially meats, seafood, vegetables, and unpasteurized dairy products. They should also avoid use of water that has not been treated; this includes drinking water, ice cubes, and even water used for brushing teeth. Using bottled water for these purposes is a good alternative. Good hygiene (handwashing) can also aid the prevention of an ETEC infection. Alex had not been careful about his food or water consumption, which led to his illness. Alex's symptoms were very similar to those of cholera, caused by the gram-negative bacterium Vibrio cholerae, which also produces a toxin similar to ST and LT. At some point in the evolutionary history of ETEC, a nonpathogenic strain of E. coli similar to those typically found in the gut may have acquired the genes encoding the ST and LT toxins from V. cholerae. The fact that the genes encoding those toxins are encoded on extrachromosomal plasmids in ETEC supports the idea that these genes were acquired by E. coli and are likely maintained in bacterial populations through horizontal gene transfer.

Answer 25

Viral genomes has significant diversity in structure. Some viruses have genomes that consist of DNA as their genetic material: - This DNA may be single stranded, like human parvoviruses, or double stranded, like herpesviruses and poxviruses. - also, although all cellular life uses DNA as its genetic material, some viral genomes are made of either single-stranded or double-stranded RNA molecules, Viral genomes are smaller than most bacterial genomes, encoding only a few genes, because they rely on their hosts to carry out many of the functions required for their replication.

Answer 26

Mark is 60-year-old software engineer who suffers from type II diabetes, which he keeps under control through diet and exercise. he scraped his lower leg while walking through blackberry brambles. did not bother to clean the wound and treat it with antibiotic ointment until later that evening. For the next 2 days, his leg became increasingly red, swollen, and warm to the touch. It was sore not only on the surface, but deep in the muscle. After 24 hours, Mark developed a fever and stiffness in the affected leg. Feeling increasingly weak, he called a neighbor, who drove him to the emergency department. • Did Mark wait too long to seek medical attention? At what point do his signs and symptoms warrant seeking medical attention? • What types of infections or other conditions might be responsible for Mark's symptoms?

Answer 27

serves two essential functionss: -is the genetic material responsible for inheritance and is passed from parent to offspring for all life on earth. - directs and regulates construction of the proteins necessary to a cell for growth and reproduction in a particular cellular environment. Genetic material: - To preserve the integrity of this genetic information, DNA must be replicated with great accuracy, with minimal errors that introduce changes to the DNA sequence. Genome: - A genome has the full complement of DNA within a cell and is organized into smaller units called genes that are arranged on chromosomes and plasmids. Gene: - A gene is composed of DNA that is transcribed to produce an RNA molecule during transcription. - messenger RNA (mRNA), provides the information for the ribosome to catalyze protein synthesis in a process called translation. Gene expression: - The processes of transcription and translation are collectively referred to as gene expression. - the synthesis of a specific protein with a sequence of amino acids that is encoded in the gene. Central dogma: - flow of genetic information from DNA to RNA to protein - This central dogma of molecular biology further elucidates the mechanism behind Beadle and Tatum's "one gene-one enzyme" hypothesis Each of the processes of replication, transcription, and translation includes the stages of 1) initiation, 2) elongation (polymerization), and 3) termination.

Answer 28

phenotype : - the product of the array of proteins being produced by the cell at a given time, which is influenced by the cell's genotype as well as interactions with the cell's environment. - Production of a specific protein encoded by an individual gene results in a distinct phenotype for the cell compared with the phenotype without that protein. Genotype: - Although a cell's genotype remains constant, not all genes are used to direct the production of their proteins simultaneously. - Cells carefully regulate expression of their genes, only using genes to make specific proteins when those proteins are needed

Answer 29

semiconservative replication: - the two strands of the double helix separate during DNA replication -each strand serves as a template from which the new complementary strand is copied; after replication, each double-stranded DNA includes one parental or "old" strand and one "new" strand. conservative: - parental DNA strands (blue) remained associated in one DNA molecule while new daughter strands (red) remained associated in newly formed DNA molecules. - old stay with old, new with new dispersive: - all resulting DNA strands have regions of double-stranded parental DNA and regions of double-stranded daughter DNA.

Answer 30

In 1958 Matthew Meselson (1930-) and Franklin Stahl (1929-): - tested which model correctly represents DNA replication Procedure: - had ecoli in medium with a "heavy" isotope of nitrogen (15N) that was incorporated into nitrogenous bases and, eventually, into the DNA. - This labeled the parental DNA. - The E. coli culture was then shifted into a medium containing 14N and allowed to grow for one generation. - The cells were harvested and the DNA was isolated. - The DNA was separated by ultracentrifugation, during which the DNA formed bands according to its density. - DNA grown in 15N would form a band at a higher density position than that grown in 14N. - After one generation of growth in 14N, the single band was in between 15N or 14N. This suggested either a semiconservative or dispersive mode of replication. Some cells were allowed to grow for one more generation in 14N and spun again: - DNA harvested from cells grown for two generations in 14N formed two bands: one DNA band was at the intermediate position between 15N and 14N, and the other corresponded to the band of 14N DNA. - These results could only be explained if DNA replicates in a semiconservative manner. - If DNA replication was dispersive, a single purple band positioned closer to the red (14N) would have been observed, as more 14N was added in a dispersive manner to replace 15N. - Therefore, the other two models were ruled out. Because of this we know that DNA replication, is semiconservative. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.

Answer 31

The process is rapid and occurs with few errors. enzyme DNA polymerase: - In bacteria, three main types of DNA polymerases are known: DNA pol I, DNA pol II, and DNA pol III. - dna pol I AND II are primarily required for repair. - DNA pol III is the enzyme required for DNA synthesis; The addition of nucleotides by dna pol III requires energy which comes from the bonds of three phosphate groups attached to each nucleotide (a triphosphate nucleotide), similar to how energy is stored in the phosphate bonds of adenosine triphosphate (ATP) When the bond between the phosphates is broken and diphosphate is released, the energy released allows for the formation of a covalent phosphodiester bond by dehydration synthesis between the incoming nucleotide and the free 3'-OH group on the growing DNA strand.

Answer 32

Origin of replication: - initiation of replication occurs at the origin of replication, where proteins bind to begin the replication process. - E. coli has a single origin of replication (as do most prokaryotes), called oriC, on its one chromosome. - The origin of replication is 245 base pairs long and is rich in adenine-thymine (AT) sequences. Protiens bind to the origin to separate DNA: - Chromosomal DNA is typically wrapped around histones (in eukaryotes and archaea) or histone-like proteins (in bacteria), and is supercoiled and twisted on itself. - topoisomerase II ( DNA gyrase ) changes the shape and supercoiling of the chromosome to relax it . - helicase separates the DNA strands by breaking the hydrogen bonds between the nitrogenous base pairs. - These enzymes require ATP hydrolysis. - As the DNA opens up, two replication forks are formed at the origin of replication, allowing for bidirectional replication and formation of a replication bubble - The DNA near each replication fork is coated with single-stranded binding proteins to prevent the single-stranded DNA from rewinding into a double helix. - Once single-stranded DNA is accessible at the origin of replication, DNA replication can begin. RNA Primer: - DNA polymerase requires a free 3'-OH group to add nucleotides by forming a phosphodiester bond between the 3'-OH end and the 5' phosphate of the next nucleotide. - single strand of DNA doesn’t have the 3’ OH - primer RNA provides the free 3'-OH end. - The primer is five to 10 nucleotides long and complementary to the template DNA. - synthesized by RNA primase, which is an RNA polymerase. RNA polymerases: - Unlike DNA polymerases, RNA polymerases do not need a free 3'-OH group to synthesize an RNA molecule.

Answer 33

Elongation: - addition of nucleotides occurs at its maximal rate of 1000 nucleotides per second. Okazaki fragments: - DNA polymerase III can only extend in the 5' to 3' direction - The DNA double helix has one strand is oriented in the 5' to 3' direction and the other is oriented in the 3' to 5' direction -leading strand (complimentary to the 3’ to 5’ template dna) is made continuously - lagging strand (complementary to the 5' to 3' parental DNA), grows away from the replication fork, its synthesis is said to be discontinuous. - so the polymerase must move back toward the replication fork to begin adding bases to a new primer, again in the direction away from the replication fork. - It does so until it bumps into the previously synthesized strand and then it moves back again - this makes small DNA fragments called Okazaki fragments, each separated by RNA primer. - The overall direction of the lagging strand will be 3' to 5', and that of the leading strand 5' to 3'. Sliding clamp: - it is a ring-shaped protein that binds to the DNA and holds the polymerase in place as it continues to add nucleotides. Topoisomerase: - topoisomerase also prevents the overwinding of the DNA double helix ahead of the replication fork as the DNA is opening up - does so by causing temporary nicks in the DNA helix and then resealing it. - As synthesis proceeds, the RNA primers are replaced by DNA. Primer removal: - primers are removed by the exonuclease activity of DNA polymerase I, and the gaps are filled in. - The nicks that remain between the DNA that replaced the RNA primer and the previously synthesized DNA are sealed by DNA ligase

Answer 34

less is known about the termination process. Following replication, the complete circular genomes of prokaryotes are concatenated ( the circular DNA chromosomes are interlocked and must be separated from each other) Topoisomerase IV: - bacterial topoisomerase IV introduces double-stranded breaks into DNA molecules, allowing them to separate from each other - the enzyme then reseals the circular chromosomes. resolution of concatemers is unique to prokaryotic DNA replication because of their circular chromosomes. Because both bacterial DNA gyrase and topoisomerase IV are distinct from their eukaryotic counterparts, these enzymes are used as targets for a class of antimicrobial drugs called quinolones.

Answer 35

Larger and more complex that prokaryotes Has multiple origins of replication on each eukaryotic chromosome The rate of replication is approximately 100 nucleotides per second, 10 times slower than prokaryotic replication.

Answer 36

essential steps of replication in eukaryotes are the same as in prokaryotes. Initiation: - Before replication can start, the DNA has to be made available as a template. - Eukaryotic DNA is highly supercoiled and packaged due to histones - At the origin of replication, a prereplication complex with helicase recruits other enzymes involved in the initiation of replication, including topoisomerase to relax supercoiling, single-stranded binding protein, RNA primase, and DNA polymerase. Elongation: - elongation is facilitated by eukaryotic DNA polymerases. - The leading strand is continuously synthesized by the eukaryotic polymerase enzyme pol deta while the lagging strand is synthesized by pol epsilon - A sliding clamp protein holds the DNA polymerase in place so that it does not fall off the DNA. Primer removal: - ribonuclease H (RNase H), instead of a DNA polymerase as in bacteria, removes the RNA primer, which is then replaced with DNA nucleotides. - The gaps that remain are sealed by DNA ligase.

Answer 37

Issue:: - leading and lagging strand are still present in the eukaryotic dna - because its linear, when the replication fork reaches the end of the chromosome, there is no place to make a primer for the DNA fragment to be copied at the end of the chromosome. - These ends remain unpaired and, over time, they may get progressively shorter as cells continue to divide. Telomeres: - ends of the linear chromosomes are known as telomeres and consist of noncoding repetitive sequences. - The telomeres protect coding sequences from being lost as cells continue to divide. - In humans, a six base-pair sequence, TTAGGG, is repeated 100 to 1000 times to form the telomere. Telomerase: - Telomerase contains a catalytic part and a built-in RNA template. - It attaches to the end of the chromosome, and complementary bases to the RNA template are added on the 3' end of the DNA strand. - Once the 3' end of the lagging strand template is sufficiently elongated, DNA polymerase can add the nucleotides complementary to the ends of the chromosomes. - In this way, the ends of the chromosomes are replicated. - In humans, telomerase is typically active in germ cells and adult stem cells; it is not active in adult somatic cells and may be associated with the aging of these cells. - Eukaryotic microbes including fungi and protozoans also produce telomerase to maintain chromosomal integrity. - For her discovery of telomerase and its action, Elizabeth Blackburn (1948-) received the Nobel Prize for Medicine or Physiology in 2009.e

Answer 38

many bacterial plasmids replicate similarrly the bacterial chromosome, But other plasmids, several bacteriophages, and some viruses of eukaryotes use rolling circle replication Rolling circle replication: - begins with the nicking of one strand of the double-stranded circular dna at the double-stranded origin (dso) site. - In bacteria, DNA polymerase III binds to the 3'-OH group of the nicked strand and begins to unidirectionally replicate the DNA using the un-nicked strand as a template, displacing the nicked strand as it does so. - Completion of DNA replication results in full displacement of the nicked strand, which may then recircularize into a single-stranded DNA molecule. RNA primase then synthesizes a primer to initiate DNA replication at the single-stranded origin (sso) site of the single-stranded DNA (ssDNA) molecute, resulting in a double-stranded DNA (dsDNA) molecule identical to the other circular DNA molecule.

Answer 39

Transcription in prokaryotes and in eukaryotes requires the DNA double helix to partially unwind in the region of RNA synthesis. The unwound region is called a transcription bubble. Transcription of a gene always proceeds from one of the two DNA strands: - antisense: the one that acts as a template, the 3-5 strand - The RNA product is complementary to the template strand of DNA and is almost identical to the nontemplate DNA strand (sense strand) - The only difference is that in RNA, all of the T nucleotides are replaced with U nucleotides; during RNA synthesis, U is incorporated when there is an A in the complementary antisense strand.

Answer 40

Bacteria use the same RNA polymerase to transcribe all of their genes DNA polymerase requires such a 3'-OH group, thus necessitating a primer, whereas RNA polymerase does not. In E. coli: - RNA polymerase is made of six polypeptide subunits, five of which compose the polymerase core enzyme responsible for adding RNA nucleotides to a growing strand. - The sixth subunit is known as sigma . - The sigma factor enables RNA polymerase to bind to a specific promoter, thus allowing for the transcription of various genes. There are various sigma factors that allow for transcription of various genes.

Answer 41

initiation: - begins at a promoter, a DNA sequence onto which the transcription machinery binds and initiates transcription. - the intitation site: The nucleotide pair in the DNA double helix that corresponds to the site from which the first 5' RNA nucleotide is transcribed - Nucleotides before the initiation site are “upstream," nucleotides following the initiation site are "downstream" Promoter: - promoters are located just upstream of the genes they regulate. - At the -10 and -35 positions within the DNA prior to the initiation site (designated +1), there are two promoter consensus sequences, or regions that are similar across all promoters and across various bacterial species. - The -10 consensus sequence, called the TATA box, is TATAAT. - The -35 sequence is recognized and bound by sigma factor Elongation: - begins when the sigma subunit dissociates from the polymerase, allowing the core rna polymerase enzyme to synthesize RNA - his happens at a rate of 40 nucleotides per second. - As elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it Termination: - Once a gene is transcribed, the bacterial polymerase must dissociate from the DNA template and liberate the newly made RNA. - The DNA template includes repeated nucleotide sequences that act as termination signals, causing RNA polymerase to stall and release from the DNA template, freeing the RNA transcript.

Answer 42

Eukaryotes: - use three different polymerases, RNA polymerases I, II, and III, all structurally distinct from the bacterial RNA polymerase. - Each transcribes a different subset of genes. - Interestingly, archaea contain a single RNA polymerase that is more closely related to eukaryotic RNA polymerase II than to its bacterial counterpart. - Eukaryotic mRNAs are also monocistronic, meaning that they each encode only a single polypeptide, - prokaryotic mRNAs of bacteria and archaea are polycistronic, meaning that they encode multiple polypeptides, or monocistronic. eukaryotes have membrane-bound nucleus: - With the genes bound in a nucleus, the eukaryotic cell must transport protein-encoding RNA molecules to the cytoplasm to be translated. - Protein-encoding primary transcripts, the RNA molecules directly synthesized by RNA polymerase, must undergo several processing steps to protect these RNA molecules from degradation when they are transferred from the nucleus to the cytoplasm and translated into a protein. - For example, eukaryotic mRNAs may last for several hours, whereas the typical prokaryotic mRNA lasts no more than 5 seconds.

Answer 43

primary transcript (also called pre-mRNA): - is first coated with RNA-stabilizing proteins to protect it from degradation while it is processed and exported out of the nucleus. 5’cap: - happens while the primary transcript is still being made - 7-methylguanosine nucleotide, called the 5' cap, is added to the 5' end of the growing transcript. - In addition to preventing degradation, the cap is recognized by factors involved in subsequent protein synthesis, which helps initiate translation by ribosomes. Poly A tail: - Once elongation is complete, another processing enzyme adds a string of approximately 200 adenine nucleotides to the 3' end, called the poly-A tail. - This modification further protects the pre-mRNA from degradation and signals to cellular factors that the transcript needs to be exported to the cytoplasm. Exons and introns - Eukaryotic genes are composed of coding sequences called exons (ex-on signifies that they are expressed) and intervening sequences called introns (int-ron denotes their intervening role). - introns do not encode regions of the functional polypeptide and are removed from the pre-mRNA during processing. - all of the intron-encoded RNA sequences must be completely and precisely removed from a pre-mRNA before protein synthesis so that the exon-encoded RNA sequences are properly joined together to code for a functional polypeptide. - If the process errs by even a single nucleotide, the sequences of the rejoined exons would be shifted, and the resulting polypeptide would be nonfunctional. - introns are remove while rna is in the nucleus snRNP: - do rna splicing: remove intron-encoded RNA sequences and reconnect those encoded by exons - spliceosome containing small nuclear ribonucleo proteins (snRNPs).

Answer 44

Although they are not translated, introns can do gene regulation and mRNA transport. Alternative splicing: - Introns can be spliced out differently, resulting in various exons being included or excluded from the final mRNA product. - The advantage of alternative splicing is that different types of mRNA transcripts can be generated, all derived from the same DNA sequence. In recent years, it has been shown that some archaea also have the ability to splice their pre-mRNA.

Answer 45

Mark's symptoms had progressed, with the area of skin affected and the amount of swelling increasing. Within the affected area, a rash had begun, blistering and small gas pockets underneath the outermost layer of skin had formed, and some of the skin was becoming gray. Based on the putrid smell of the pus draining from one of the blisters, the rapid progression of the infection, and the visual appearance of the affected skin, the physician immediately began treatment for necrotizing fasciitis. Mark's physician ordered a culture of the fluid draining from the blister and also ordered blood work, including a white blood cell count. Mark was admitted to the intensive care unit and began intravenous administration of a broad-spectrum antibiotic to try to minimize further spread of the infection. Despite antibiotic therapy, Mark's condition deteriorated quickly. Mark became confused and dizzy. Within a few hours of his hospital admission, his blood pressure dropped significantly and his breathing became shallower and more rapid. Additionally, blistering increased, with the blisters intensifying in color to purplish black, and the wound itself seemed to be progressing rapidly up Mark's leg. • What are possible causative agents of Mark's necrotizing fasciitis? • What are some possible explanations for why the antibiotic treatment does not seem to be working?

Answer 46

Translation: - translation of mRNA template converts nucleotide-based genetic information into the "language" of amino acids to create a protein product. protein sequence: - consists of 20 commonly occurring amino acids. - Each amino acid is defined within the mRNA by a triplet of nucleotides called a codon. Genetic code - The relationship between an mRNA codon and its corresponding amino acid is called the genetic code. - The three-nucleotide code means that there is a total of 64 possible combinations (4^3, with four different nucleotides possible at each of the three different positions within the codon). - This number is greater than the number of amino acids and a given amino acid is encoded by more than one codon - This redundancy in the genetic code is called degeneracy. Wobble: - the first two positions in a codon are important for determining which amino acid will be incorporated into a growing polypeptide, - In some cases, if the nucleotide in the third position is changed, the same amino acid is still incorporated. Third postion is less important Stop codon: - three of the 64 codons do not code for an amino acid - they terminate protein synthesis, releasing the polypeptide from the translation machinery. - These are called stop codons or nonsense codons. Start: - AUG, - In addition to specifying the amino acid methionine, it also serves as the start codon to initiate translation. reading frame: - the way nucleotides in mRNA are grouped into codons, - for translation it is set by the AUG start codon near the 5' end of the mRNA. - Each set of three nucleotides following this start codon is a codon in the mRNA message. unusual amino acids: - most amino acid are conserved across all organisms - but others called selenocysteine and pyrolysine have been observed in archaea and bacteria. - for selenocysteine, the codon used is UGA (normally a stop codon). However, UGA can encode for selenocysteine using a stem-loop structure (known as the selenocysteine insertion sequence, or SECIS element) which is found at the 3' untranslated region of the mRNA. - Pyrolysine uses a different stop codon, UAG. The incorporation of pyrolysine requires the pylS gene and a unique transfer RNA (tRNA) with a CUA anticodon.

Answer 47

ribosome: - composed of catalytic rRNAs (called ribozymes) and structural rRNAs, and distinct polypeptides. - Mature rRNAs make up 50% of each ribosome. - Prokaryotes have 70S ribosomes, - eukaryotes have 80S ribosomes in the cytoplasm and rough endoplasmic reticulum, and 70S ribosomes in mitochondria and chloroplasts. - In E. coli, the small subunit is 30S (which contains the 16S RNA subunit), and the large subunit is 50S (which contains the 5S and 23S RNA subunits), for a total of 70S (Svedberg units are not additive). Eukaryote ribosomes have a small 40s subunit (which contains the 18S RNA subunit) and a large 60S subunit (which contains the 5S, 5.8S and 28S RNA subunits), for a total of 80S. small subunit: - binds the mRNA template - large subunit binds tRNAs mRNA is read 5' to 3' and synthesizing the polypeptide from the N terminus to the C terminus. Polyribosome: - The complete structure containing an mRNA with multiple associated ribosomes is called a polyribosome (or polysome). In both bacteria and archaea: - each protein-encoding transcript is already being used to begin synthesis polypeptides because the processes of transcription and translation can occur concurrently - this forms polyribosomes - The reason why transcription and translation can occur simultaneously is because both of these processes occur in the same 5' to 3’ direction, they both occur in the cytoplasm of the cell, and because the RNA transcript is not processed once it is transcribed. - This allows a prokaryotic cell to respond to an environmental signal requiring new proteins very quickly. In contrast, in eukaryotic cells, simultaneous transcription and translation is not possible. Although polyribosomes also form in eukaryotes, they cannot do so until RNA synthesis is complete and the RNA molecule has been modified and transported out of the nucleus.

Answer 48

Transfer RNAS (tRNAs) : - structural RNA molecules, many different types of tRNAs exist in the cytoplasm. - Bacterial species typically have between 60 and 90 types. - each tRNA type binds to a specific codon on the mRNA template and adds the corresponding amino acid to the polypeptide chain. - so, tRNAs are the molecules that actually "translate" the language of RNA into the language of proteins. The tRNA molecule interacts with three factors: aminoacyl tRNA synthetases, ribosomes, and mRNA. Mature tRNAs take on a three-dimensional structure when complementary bases exposed in the single-stranded RNA molecules hydrogen bond with each other This shape positions the CCA amino-acid binding site, which is a cytosine-cytosine-adenine sequence at the 3' end of the tRNA, and the anticodon at the other end. The anticodon is a three-nucleotide sequence that bonds with an mRNA codon through complementary base pairing. Charging: - An amino acid is added to the end of a tRNA molecule through the process of tRNA "charging," during which each tRNA molecule is linked to its correct amino acid by aminoacyl tRNA Synthetases. At least one type of aminoacyl tRNA synthetase exists for each of the 20 amino acids. During this process, the amino acid is first activated by the addition of adenosine monophosphate (AMP) and then transferred to the tRNA, making it a charged tRNA, and AMP is released.

Answer 49

formation of an initiation complex: - In E. coli, this complex has the small 30S ribosome, the mRNA template, three initiation factors that help the ribosome assemble correctly, guanosine triphosphate (GTP) as an energy source, and a special initiator tRNA carrying N-formyl-methionine (Met-tRNA^fmet) - initiator tRNA interacts with the start codon AUG of the mRNA and carries a formylated methionine (fMet). - Because of its involvement in initiation, fMet is inserted at the beginning (N terminus) of every polypeptide chain synthesized by E. coli. - In E. coli mRNA, upstream of the first AUG codon, the Shine-Dalgarno sequence (also known as the ribosomal binding site AGGAGG), interacts with the rRNA in the ribosome via complementary base pairing - This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. - then the 505 ribosomal subunit binds to the initiation complex, forming an intact ribosome. In eukaryotes,have the following differences: • The initiator tRNA is a different specialized tRNA carrying methionine, called Met-tRNAi • Instead of binding to the mRNA at the Shine-Dalgarno sequence, the eukaryotic initiation complex recognizes the 5' cap of the eukaryotic mRNA, then tracks along the mRNA in the 5' to 3' direction until the AUG start codon is recognized. - At this point, the 60S subunit binds to the complex of Met-tRNAi, mRNA, and the 40S subunit.

Answer 50

In E. coll, the intact ribosome forms three ribosomal sites: - The A (aminoacyl) site binds incoming charged aminoacyl tRNAs. - The P (peptidyl) site binds charged tRNAs carrying amino acids that have formed peptide bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. - The E (exit) site releases dissociated tRNAs so that they can be recharged with free amino acids. exception to this assembly line of tRNAs: - During initiation complex formation, bacterial Met-tRN^fMet or eukaryotic Met-tRNAi enters the P site directly without first entering the A site, providing a free A site ready to accept the tRNA corresponding to the first codon aftor the AUG. - Elongation proceeds with single-codon movements of the ribosome oach called a translocation event. During each translocation event, the charged tRNAs onter at the A site, then shift to the P site, and then finally to the E site for removal. Ribosomal movements, or steps, are induced by conformational changes that advance the ribosome by three bases in the 3' direction. Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA. The formation of each peptide bond is catalyzed by peptidyl transferase, an RNA-based ribozyme that is integrated into the 50S ribosomal subunit. The amino acid bound to the P-site tRNA is also linked to the growing polypeptide chain. As the ribosome steps across the mRNA, the former P-site tRNA enters the E site, detaches from the amino acid, and is expelled. Several of the stops during elongation, including binding of a charged aminoacyl tRNA to the A site and translocation, require energy derived from GTP hydrolysis, which is catalyzed by specific elongation factors. , the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a 200 amino-acid protein can be translated in just 10 seconds.

Answer 51

occurs when a nonsense codon (UAA, UAG, or UGA) is encountered for which there is no complementary tRNA. When in the A site, these nonsense codons are recognized by release factors in prokaryotes and eukaryotes This results in the P-site amino acid detaching from its tRNA, releasing the newly made polypeptide. The small and large ribosomal subunits dissociate from the mRNA and from each other; they are recruited almost immediately into another translation initiation complex.

Answer 52

Eukaryotes have met prokaryotes have fmet

Answer 53

To be biologically active. Post-translational modifications include: removal of translated signal sequences: - short tails of amino acids direct a protein to a specific cellular compartment proper "folding" of the polypeptide and association of multiple polypeptide subunits: - often done by chaperone proteins, into a distinct three-dimensional structure proteolytic processing of an inactive polypeptide: - to release an active protein component, and various chemical modifications (e.g., phosphorylation, methylation, or glycosylation) of individual amino acids.

Answer 54

a heritable change in the DNA sequence of an organism. The resulting mutant, may have a recognizable change in phenotype compared to the wild type A change in the DNA sequence is conferred to mRNA through transcription, and may lead to an altered amino acid sequence in a protein on translation. Because proteins carry out the vast majority of cellular functions, a change in amino acid sequence in a protein may lead to an altered phenotype for the cell and organism.

Answer 55

point mutation: - affects a single base and most commonly occurs when one base is substituted or replaced by another. - silent mutation: because of the degeneracy of the genetic code, point mutation will result in the same amino acid being incorporated into the resulting polypeptide despite the sequence change. This change would have no effect on the protein's structure - also includes missense mutations and nonsense mutations Insertion: - addition of one or more bases, Deletion: - the removal of one or more bases Deletions and insertions can cause Framshift

Answer 56

A missense mutation: - results in a different amino acid being incorporated into the resulting polypeptide. - effect of a missense mutation depends on how chemically different the new amino acid is from the wild-type amino acid. - The location of the changed amino acid within the protein also is important. - For example, if the changed amino acid is part of the enzyme's active site, then the effect of the missense mutation may be significant. - Sometimes the effects of missense mutations may be only apparent under certain environmental conditions; such missense mutations are called conditional mutations. - Under the right environmental conditions, this type of mutation may give the organism that harbors it a selective advantage. Nonsense mutation: - converts a codon encoding an amino acid (a sense codon) into a stop codon (a nonsense codon). - Nonsense mutations result in the synthesis of proteins that are shorter than the wild type and not functional.

Answer 57

Because codons are triplets of nucleotides, insertions or deletions in groups of three nucleotides may lead to the insertion or deletion of one or more amino acids and may not cause significant effects on the resulting protein's functionality. However, frameshift mutations, caused by frameshift mutations can change every amino acid after the point of the mutation. The new reading frame may also include a stop codon before the end of the coding sequence. Consequently, proteins made from genes containing frameshift mutations are nearly always nonfunctional.

Answer 58

Mistakes in the process of DNA replication can cause spontaneous mutations to occur. The error rate of DNA polymerase is one incorrect base per billion base pairs replicated. Exposure to mutagens cause induced mutations, which are various types of chemical agents or radiation: - Exposure to a mutagen can increase the rate of mutation more than 1000-fold. - Mutagens are often also carcinogens, agents that cause cancer. - However, whereas nearly all carcinogens are mutagenic, not all mutagens are necessarily carcinogens.

Answer 59

chemical mutagens interact directly with DNA either by acting as nucleoside analogs or by modifying nucleotide bases. nucleoside analogs: - are structurally similar to normal nucleotide bases and can be incorporated into DNA during replication - These base analogs induce mutations because they have different base-pairing rules than the bases they replace. nitrous acid: - deaminates cytosine, converting it to uracil. - Uracil pairs with adenine in a subsequent round of replication, resulting in the conversion of a GC base pair to an AT base pair. - Nitrous acid also deaminates adenine to hypoxanthine, which base pairs with cytosine instead of thymine, resulting in the conversion of a TA base pair to a CG base pair. intercalating agents: - slide between the stacked nitrogenous bases of the DNA double helix, distorting the molecule and creating atypical spacing between nucleotide base pairs - As a result, during DNA replication, DNA polymerase may either skip replicating several nucleotides (creating a deletion) or insert extra nucleotides (creating an insertion). - Either outcome may lead to a frameshift mutation. Combustion products: - like polycyclic aromatic hydrocarbons - are dangerous intercalating agents that can lead to mutation-caused cancers. - The intercalating agents ethidium bromide and acridine orange are commonly used in the laboratory to stain DNA for visualization and are potential mutagens.

Answer 60

Exposure to either ionizing or nonionizing radiation can each induce mutations in DNA, although by different mechanisms. Strong ionizing radiation : - like X-rays and gamma rays can cause single- and double-stranded breaks in the DNA backbone through the formation of hydroxyl radicals on radiation exposure - Ionizing radiation can also modify bases; for example, the deamination of cytosine to uracil, analogous to the action of nitrous acid. - Ionizing radiation exposure is used to kill microbes to sterilize medical devices and foods, because of its dramatic nonspecific effect in damaging DNA, proteins, and other cellular components Nonionizing radiation: - like ultraviolet light, is not energetic enough to initiate these types of chemical changes. - However, nonionizing radiation can induce dimer formation between two adjacent pyrimidine bases, commonly two thymines, within a nucleotide strand. - During thymine dimer formation, the two adjacent thymines become covalently linked and, if left unrepaired, both DNA replication and transcription are stalled at this point. - DNA polymerase may proceed and replicate the dimer incorrectly, potentially leading to frameshift or point mutations.

Answer 61

mistakes in dna replication can occur spontaneously or be induced by mutagens. Proofreading: - solves most of the mistakes introduced during DNA replication - In proofreading, the DNA polymerase reads the newly added base, ensuring that it is complementary to the corresponding base in the template strand before adding the next one. - If an incorrect base has been added, the enzyme makes a cut to release the wrong nucleotide and a new base is added.

Answer 62

errors introduced during replication are corrected shortly after the replication machinery has moved. The enzymes recognize the incorrectly added nucleotide, excise it, and replace it with the correct base. example: - the methyl-directed mismatch repair in E coli. - DNA is hemimethylated (parental strand is methylated while the newly synthesized daughter strand is not). - It takes several minutes before the new strand is methylated, - MutS, MutL, and MutH bind to the hemimethylated site where the incorrect nucleotide is found. - MutH cuts the nonmethylated strand (the new strand), - An exonuclease removes a portion of the strand (including the incorrect nucleotide). The gap formed is then filled in by DNA pol IlI and ligase,

Answer 63

production of thymine dimers is common (many organisms cannot avoid ultraviolet light), Via nucleotide excision repair (alse called dark repair): - enzymes remove the pyrimidine dimer and replace it with the correct nucleotides - In E, coli, the DNA is scanned by an enzyme complex. If a distortion in the double helix is found that was introduced by the pyrimidine dimer, the enzyme complex cuts the sugar-phosphate backbene several bases upstream and dewnstream of the dimer, and the segment of DNA between these twe cuts is then enzymatically removed - DNA pol I replaces the missing nucleotides with the correct ones and DNA ligase seals the gap in the sugar-phesphate backbone. Via The direct repair (also called light repair): - occurs through the process of phetereactivation in the presence of visible light. - photolyase recognizes the distertion in the DNA helix caused by the thymine dimer and binds to the dimer, - Then, in the presence of visible light, the photolyase enzyme changes conformation and breaks apart the thymine dimer, allewing the thymines te again correctly base paif with the adenines on the complementary strand. - Phetoreactivation is present in all organisms, with the exception of placental mammals, including humans, Phetereactivation is particularly impertant fer organisms chronically exposed to ultraviolet radiation, like plants, phetosynthetie bacteria, algae, and cerals, te prevent the accumulation of mutations caused by thymine dimer farmation.s

Answer 64

replica plating: - used to detect nutritional mutants, called auxotrophs, which have a mutation in a gene for an enzyme in the biosynthesis pathway of a specific nutrient, such as an amino acid. - wild-type cells retain the ability to grow normally on a medium lacking the specific nutrient, auxotrophs are unable to grow on such a medium. Procedure: - a population of bacterial cells is mutagenized and then plated on a complex nutritionally complete plate and allowed to grow into colonies. - Cells from these colonies are removed from this master plate using sterile velvet. - This velvet with the cells, is pressed in the same orientation onto plates of various media. At least one plate should also be nutritionally complete to ensure that cells are being properly transferred between the plates. - The other plates lack specific nutrients, allowing discovery of various auxotrophic mutants unable to produce specific nutrients. - Cells from the corresponding colony on the nutritionally complete plate can be used to recover the mutant for further study.

Answer 65

developed by Bruce Ames (1928-) in the 1970s uses bacteria to screen for rapid screening of the carcinogenic potential of new chemical compounds. The test measures the mutation rate associated with exposure to the compound, which, if elevated, may indicate that exposure to this compound causes greater cancer risk test organism: - a strain of Salmonella typhimurium that is a histidine auxotroph, unable to synthesize its own histidine - After exposure to a potential mutagen, these bacteria are plated onto a medium lacking histidine, and the number of mutants regaining the ability to synthesize histidine is recorded and compared with the number of mutants that arise in the absence of the potential mutagen - Chemicals that are more mutagenic will bring about more mutants with restored histidine synthesis in the Ames test. - Because many chemicals are not directly mutagenic but are metabolized to mutagenic forms by liver enzymes, rat liver extract is commonly included at the start of this experiment to mimic liver metabolism. - After the Ames test is conducted, compounds identified as mutagenic are further tested for their potential carcinogenic properties by using other models, including animal models like mice and rats.

Unit 8: Flashcards

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