AP Biology Notes Outline Enduring Understanding 3.C

L. Carnes

Big Idea 3: Living systems store, retrieve, transmit and respond to information essential to life processes.

Enduring Understanding 3.C:

The processing of genetic information is imperfect and is a source of genetic variation.

Learning Objectives: Essential Knowledge 3.C.1: Changes in genotype can result in changes in phenotype.

– (3.24) The student is able to predict how a change in genotype, when expressed as a phenotype, provides a variation that can be subject to natural selection.

– (3.25) The student is able to create a visual representation to illustrate how changes in a DNA nucleotide sequence can result in a change in the polypeptide produced.

– (3.26) The student is able to explain the connection between genetic variations in organisms and phenotype variations in populations. Essential Knowledge 3.C.2: Biological systems have multiple processes that increase genetic variation.

– (3.27) The student is able to compare and contrast processes by which genetic variation is produced and maintained in organisms from multiple domains. – (3.28) The student is able to construct an explanation of the multiple processes that increase variation within a population.

Essential Knowledge 3.C.3: Viral replication results in genetic variation, and viral infection can introduce genetic variation into the hosts.. – (3.29) The student is able to construct an explanation of how viruses introduce genetic variation in host organisms. – (3.30) The student is able to use representations and models to describe how viral replication introduces genetic variation in the viral population.

Bozeman Instruction Videos: http://www.bozemanscience.com/ap-biology/ 3.C.1 - #033: Genotypes and Phenotypes 3.C.2 - #034: Increasing Genetic Variation 3.C.3 - #035: Viral Replication

Animated Content Review Videos:

Types of Mutations: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_4.html

Nondisjunction in Meiosis: http://glencoe.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::550::400::/sites/dl/free/0078695104/383925/Chapter11_NGS_VisualizingNondisjunction_10_10_06.swf::Visualizing+Nondisjunction

Alterations of Chromosome Number: http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter15/changes_in_chromosome_structure.html

Bacterial Transformation: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_1.html

Bacterial Transduction: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_2.html

Conjugation of the F Plasmid in Bacteria: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_3.html

General Conjugation in Bacteria: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_4.html

Transposons: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_5.html

Transposons: http://www.youtube.com/watch?v=6vWrxt1ZCUY

Rolling Circle Replication in Bacteria: http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_6.html

Lytic & Lysogenic Viral Cycles: http://highered.mheducation.com/sites/0072556781/student_view0/chapter17/animation_quiz_2.html

Reproduction in HIV: https://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter24/animation__hiv_replication.html

Required Readings: 3.C.1 – Ch. 17 (pp. 344-347); Ch. 15 (pp. 297-300); Ch. 23 (pp. 470-471) 3.C.2 – Ch. 16 (pp. 316-318); Ch. 27 (pp. 561-564); Ch. 21 (pp. 435-436) 3.C.2 – Article: Barbara McClintock & Mobile Genetic Elements 3.C.3 – Ch. 19

Practicing Biology Homework Questions: Questions #34-39

Essential Knowledge 3.C.1: Changes in genotype can result in changes in phenotype.

Genetic information is a set of instructions necessary for the survival, growth and reproduction of an organism. In order for the information to be useful, it needs to be processed by the cell. Processing includes replication, decoding and transfer of the information. When genetic information changes, either through natural processes or genetic engineering, the results may be observable changes in the organism. At the molecular level, these changes may be the result of mutations in the genetic material, the effects of which may be seen when the information is processed to yield a nucleic acid or a polypeptide. The processes of transcription, mRNA processing and translation are imperfect, and errors can occur and may, in certain cases, alter phenotypes. However, these errors are random and are not heritable except in the case of RNA viruses where the random errors change the genetic information of the virus. External factors in the environment can affect the degree of, or the potential for increased probability for, errors in the information and processing. Cellular mechanisms that usually correct errors have evolved. Genetic variations at the genome level, when expressed as phenotypes, are subject to natural selection. Alterations in a DNA sequence can lead to changes in the type of amount of the protein produced and the consequent phenotype. A mutation is any change in the genetic information of a cell (or virus). Mutations are the primary source of genetic variation. Mutations may involve large portions of a chromosome or affect just one base pair of nucleotides. DNA mutations can be positive, negative or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein. If the mutation is in a cell that gives rise to a gamete, it may be passed on to offspring. Types of DNA Mutations Point mutations can are chemical changes in just one base pair of a gene. The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein. Sickle-cell disease is the most common inherited disease among African Americans. Due to a single amino acid substitution in the hemoglobin protein, red blood cells deform into a sickle shape when blood oxygen concentration is low, triggering blood clumping and other detrimental effects.

http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_4.html

Point mutations within a gene can be divided into two general categories: (1) base-pair substitutions; and (2) ase-pair insertions or deletions.

1. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides.

2. Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code.

3. Missense mutations still code for an amino acid, but not necessarily the right amino acid.

4. Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein.

5. Insertions and deletions are additions or losses of nucleotide pairs in a gene. These mutations have a disastrous effect on the resulting protein more often than substitutions.

6. Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation.

Errors in DNA replication or repair mechanisms and external factors can cause random changes (mutations) in the DNA. Mutations can occur in a number of ways. Spontaneous mutations include base-pair substitutions, insertions, deletions and longer mutations that occur during DNA replication, repair, or recombination. Physical agents, such as X-rays and UV light, and various chemical agents that cause mutations are called mutagens. Whether or not a mutation is detrimental, beneficial or neutral depends on the environmental context.

Errors in mitosis or meiosis can result in changes in phenotype. Nondisjunction occurs when a pair of homologous chromosomes does not separate properly in meiosis I or sister chromatids do not separate in meiosis II. As a result, a gamete receives either two or no copies of that chromosome. A zygote formed with one of these aberrant gametes has a chromosomal alteration known as aneuploidy, a non-typical number of a particular chromosome. This can include trisomy (2n+1) or monosomy (2n-1).

• Changes in chromosome number often result in new phenotypes, including sterility caused by triploidy and increased vigor of other polyploids.

• Changes in chromosome number often result in human disorders with developmental limitations, including Trisomy 21 (Down syndrome) and XO (Turner syndrome).

http://glencoe.mcgraw-hill.com/olcweb/cgi/pluginpop.cgi?it=swf::550::400::/sites/dl/free/0078695104/383925/Chapter11_NGS_VisualizingNondisjunction_10_10_06.swf::Visualizing+Nondisjunction Alterations of Chromosome Number Polyploidy is a condition in which an organism has more than two complete sets of chromosomes. It is common in plants, but not in animals.

• Triploidy (3n) is three sets of chromosomes • Tetraploidy (4n) is four sets of chromosomes

New Phenotypes Can Arise from Changes in Chromosome Number Sterility can be caused by triploidy:

– An extra X chromosome in a male (XXY) produces a disorder known as Klinefelter. These individuals have male sex organs, but the testes are abnormally small and the man is sterile.

Increased vigor can be seen in some polyploids:

– A common example in plants is the observation of hybrid vigor whereby the polyploid offspring of two diploid individuals is more vigorous and healthy than either of the two diploid parents.

Human Disorders Due to Chromosomal Alterations Alterations of chromosome number and structure are associated with some serious disorders. Some types of aneuploidy appear to upset the genetic balance less than others, resulting in individuals surviving to birth and beyond. These surviving individuals have a set of symptoms, or syndrome, characteristic of the type of aneuploidy (i.e. trisomy 21, or Down syndrome). Nondisjunction of sex chromosomes produces a variety of aneuploid conditions:

• Klinefelter syndrome is the result of an extra chromosome in a male, producing XXY individuals. • Monosomy X, called Turner syndrome, produces X0 females, who are sterile; it is the only known viable monosomy in

humans.

Alterations of Chromosome Structure http://highered.mcgraw-hill.com/sites/9834092339/student_view0/chapter15/changes_in_chromosome_structure.html Breakage of a chromosome can lead to four types of changes in chromosome structure: • The syndrome cri du chat (“cry of the cat”), results from

a specific deletion in chromosome 5. A child born with this syndrome is mentally retarded and has a catlike cry; individuals usually die in infancy or early childhood.

• Certain cancers, including chronic myelogenous leukemia (CML), are caused by translocations of chromosomes.

Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected by environmental conditions. Selection results in evolutionary change.

• Illustrative examples include: – Antibiotic Resistance Mutations – KNOW IT! – Pesticide Resistance Mutations – KNOW IT! – Sickle Cell Disorder and Heterozygous Advantage – KNOW IT BIG TIME!

Essential Knowledge 3.C.2: Biological systems have multiple processes that increase genetic variation.

Since all organisms, as well as viruses, exist in a dynamic environment, mechanisms that increase genetic variation are vital for a species’ ability to adapt to a changing environment. In a meiotic organism, the transfer process, whereby each gamete receives one set of chromosomes, ensures that this set is unique and different from that of the parent. Random processes such as the transposition of DNA regions (“jumping genes”) occur in all biological domains. Bacteria divide by binary fission and do not have random assortment processes that occur in eukaryotic organisms. Nonetheless, mechanisms have evolved in bacteria that ensure genetic variation beyond the variation that is introduced through normal DNA metabolism (i.e. replication, repair and recombination). Bacterial genetic information can be transmitted or exchanged laterally through a variety of processes, including conjugation, transduction and transformation. This type of exchange yields rapid dissemination of new phenotypes within and between bacterial populations, allowing for rapid evolution. The imperfect nature of DNA replication and repair increases variation. Initial pairing errors in nucleotide placement may occur as often as 1 per 100,000 base pairs. The amazing accuracy of DNA replication (one error in ten billion nucleotides) is achieved as DNA polymerases check each newly added nucleotide against its template and remove incorrect nucleotides.

• While the DNA proofreading and repair mechanisms are highly accurate, sometimes errors in DNA replication are not detected. These errors (mutations) can increase variation among individuals of the same species and, in some cases, can be selected for among individuals in a population.

• In Darwin’s theory of evolution by natural selection, genetic variations present in a population result in adaptation as the individuals with the variations best suited to an environment produce the most offspring.

The methods of horizontal acquisition of genetic information in prokaryotes increase variation. http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_1.html http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_2.html http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_3.html http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_4.html http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_5.html http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter13/animation_quiz_6.html

1. Transformation (the uptake of foreign DNA from the surrounding environment). 2. Conjugation (the direct transfer of genes from one prokaryote to another). 3. Transduction (the transfer of genes from one prokaryote to another via a viral vector). 4. Transposition (movement of DNA segments within and between DNA molecules).

In transformation, the genotype and possibly the phenotype of a prokaryotic cell are altered by uptake of foreign DNA from its surroundings. Example, bacteria from a harmless strain of Streptococcus pneumoniae can be transformed into pneumonia-causing cells if they are placed into a medium containing dead, broken-open cells of the pathogenic strain (Griffith’s experiment). The foreign allele is then incorporated into the cell’s chromosome, replacing the existing nonpathogenic allele. Transduction is the movement of genes between bacteria by bacteriophages (viruses that infect bacteria). Recombination may cause the transferred DNA to be incorporated into the genome of the recipient. The recipient cell now has new genetic properties and will pass on these properties as it divides by binary fission. Conjugation is the process where genetic material is transferred between bacterial cells. Sex pili allow cells to connect and pull together for DNA transfer. A piece of DNA called the F factor is required for the production of sex pili. The F factor can exist as a separate plasmid or as DNA within the bacterial chromosome.

R Plasmids and Antibiotic Resistance R plasmids carry genes for antibiotic resistance. Antibiotics select for bacteria with genes that are resistant to the antibiotics. Antibiotic resistant strains of bacteria are becoming more common. Exposing a bacterial population to a specific antibiotic will kill antibiotic-sensitive bacteria but not those that happen to have R plasmids with genes that confer antibiotic resistance. Humans impact variation in other species and the overuse of antibiotics is an example of how natural selection can play a major role in the evolution of a species. Under these circumstances, the fraction of the bacterial population carrying genes for antibiotic resistance will increase. Following this, the medical consequences are predictable: resistant strains of pathogens are becoming more common, making the treatment of certain bacterial infections more difficult.

Transposons Stretches of DNA that can move about within a genome through a process called transposition are called transposable genetic elements, or transposable elements. Transposons move about a genome as a DNA intermediate, either by a “cut-and-paste” or a “copy-and-paste” mechanism.

• Read Article: Barbara McClintock & Mobile Genetic Elements • Watch Video: http://www.youtube.com/watch?v=6vWrxt1ZCUY

Sexual reproduction mechanisms involving gamete formation in eukaryotes serve to increase genetic variation. Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms. These processes include:

• Crossing over during meiosis • Random assortment of chromosomes during meiosis. • Fertilization • REMEMBER WHAT YOU HAVE ALREADY BEEN TAUGHT!!!

Essential Knowledge 3.C.3: Viral replication results in genetic variation; and viral infection can introduce genetic variation into the hosts.

The basic structure of viruses includes a protein capsid that surrounds and protects the genetic information (genome) that can be either DNA or RNA. Viruses have a mechanism of replication that is dependent on the host metabolic machinery to produce necessary viral components and viral genetic material. Some classes of viruses use RNA without a DNA intermediate; however, retroviruses, such as HIV, use a DNA intermediate for replication of their genetic material. Some viruses introduce variation into the host genetic material. When the host is bacterial, it is referred to as lysogenesis; whereas in eukaryotic cells, this is referred to as transformation. Since viruses use the host metabolic pathways, they experience the same potential as the host for genetic variation that results from DNA metabolism. The basic structure of viruses includes a protein capsid that surrounds and protects the genetic information (DNA or RNA). Viruses are not cells. Viruses are very small infectious particles consisting of nucleic acid enclosed in a protein coat and, in some cases, a membranous envelope. Viral genomes may consist of either (1) double or single stranded DNA; or (2) double or single-stranded RNA. Depending on its type of nucleic acid, a virus is called a DNA virus or an RNA virus.

• IMPORTANT: Viruses have a mechanism of replication that is dependent on the host metabolic machinery to produce necessary viral components and viral genetic material.

• Bacteriophages, also called phages, are viruses that infect bacteria. •

Viral replication differs from other reproductive strategies and generates variation via various mechanisms. Viruses have highly efficient replicative capabilities that allow for rapid evolution and acquisition of new phenotypes:

• They replicate via a component assembly model allowing one virus to produce many progeny (lytic cycle). • Viral replication allows for mutations to occur through usual host pathways. • Some viruses lack replication error-checking mechanisms, and thus have higher rates of mutation. • Related viruses can combine/recombine if they infect the same host cell. • Some viruses can integrate into host DNA and establish latent (lysogenic) infection – can result in new properties for host

cell. Figure 19.4: The reproductive cycles of viruses facilitate transfer of genetic information because viruses transmit DNA or RNA when they infect a host cell. Viruses are obligate intracellular parasites, which means they can reproduce only within a host cell. Each virus has a host range, a limited number of host cells that it can infect. Once a viral genome has entered a cell, the proteins it encodes can command the host cell and reprogram it to copy the viral nucleic acid such that the host cell begins to manufacture viral proteins. The virus makes use of host enzymes, ribosomes, tRNAs, amino acids, ATP, and other molecules. Viral nucleic acid molecules and capsomeres spontaneously self-assemble into new viruses.The viral cycle ends with the exit of thousands of viruses – often damaging the host cell. The viral progeny have the potential to infect additional cells, spreading the viral infection. This is a highly efficient replicative capability that allows for rapid evolution and acquisition of new phenotypes.

Phages (viruses that infect bacteria) are the best understood of all viruses – they have two reproductive mechanisms: the lytic and the lysogenic cycle.

Figure 19.5: The lytic cycle of phage T4, a virulent phage The lytic cycle is a phage reproductive cycle that culminates in the death of the host cell. This is a component assembly model that allows one virus to produce MANY progeny simultaneously. The lytic cycle produces new phages and digests the host’s cell wall, releasing the progeny viruses. A phage that reproduces only by the lytic cycle is called a virulent phage. Bacteria have defenses against phages, including restriction enzymes that recognize and cut up certain phage DNA.

Figure 19.6: Some viruses are able to integrate into the host DNA and establish a latent (lysogenic) infection. The lysogenic cycle replicates the phage genome without destroying the host. The viral DNA molecule is incorporated into the host cell’s chromosome.

This integrated viral DNA is known as a prophage – one prophage gene codes for a protein that prevents transcription of the other prophage genes, thus the phage genome is mostly silent within the bacterium.

Every time the host divides, it copies the phage DNA and passes the copies to daughter cells

An environmental signal can trigger the virus genome to exit the bacterial chromosome and switch to the lytic mode

Phages that use both the lytic and lysogenic cycles are called temperate phages.

The reproductive cycles of viruses facilitate transfer of genetic information. During infection, some viruses introduce variation into the host genome in the form of DNA or RNA.

• When the host cell is bacterial, it is referred to as lysogenesis; whereas in eukaryotic cells, this is referred to as transformation.

• Since viruses use the host metabolic pathways, they experience the same potential as the host for genetic variation that results from DNA metabolism. Illustrative examples include:

– Transduction in Bacteria – Transposons present in incoming DNA

Generating Genetic Variation via Lysogenic Infections Viral replication often allows for mutations to occur through usual host mechanisms. While many prophage genes are silenced as a viral genome “hides” in the host cell during a latent infection, other prophage genes may be expressed during lysogeny. Expression of these genes may alter the host’s phenotype.

• Example: the three species of bacterial that cause diphtheria, botulism, and scarlet fever would not be so harmful to humans without certain prophage genes that cause the host bacteria to make toxins.

• Example: The difference between the E. coli strain that resides in our intestines and the strain that has caused several deaths by food poisoning appears to be the presence of prophages in the harmful strain.

RNA Viruses

• Often times, the viruses that infect animals are RNA viruses (retroviruses). Retroviruses are RNA viruses that are equipped

with an enzyme called reverse transcriptase, which transcribes an RNA template into DNA, providing an RNADNA information flow, the opposite of the usual direction. RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation.

• HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome). HIV is a

well-studied system where the rapid evolution of a virus within the host contributes to the pathogenicity of viral infection.

Figure 19.8 The reproductive cycle of HIV, the retrovirus that causes AIDS https://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter24/animation__hiv_replication.html In the complicated reproductive cycle of retroviruses such as HIV, the viral genome is transcribed into double-stranded DNA by a viral enzyme called reverse transcriptase. The viral DNA is then integrated into a chromosome, where it is transcribed by the host cell into viral RNA, which acts both as new viral genome and as mRNA for viral proteins. HIV (human immunodeficiency virus) is the retrovirus that causes AIDS (acquired immunodeficiency syndrome). The integrated viral DNA remains as a provirus within the host cell DNA. New viruses, assembled with two copies of both the RNA genome and reverse transcriptase within a capsid, bud off covered in host cell plasma membrane studded with viral glycoproteins. Emerging Viruses Emerging viruses are those that appear suddenly or suddenly come to the attention of scientists. Severe acute respiratory syndrome (SARS) recently appeared in China. Outbreaks of “new” viral diseases in humans are usually caused by existing viruses that expand their host territory

• Flu epidemics are caused by new strains of influenza virus to which people have little immunity • Viral diseases in a small isolated population can emerge and become global • New viral diseases can emerge when viruses spread from animals to humans • Viral strains that jump species can exchange genetic information with other viruses to which humans have no immunity • These strains can cause pandemics, global epidemics • The “avian flu” is a virus that recently appeared in humans and originated in wild birds

RNA viruses lack replication error-checking mechanisms, and thus have higher rates of mutation. This often leads to emerging viruses and epidemics within populations. An error in replicating the genome of an RNA virus is not corrected by proofreading. Some mutations change existing viruses into new genetic varieties that can cause disease. Influenza is an example of an emerging virus.

Emerging viruses can also occur when an organism is infected with more than one strain of a virus. Often times, the different strains can undergo genetic recombination if the RNA molecules making up their genomes mix and match during viral assembly. Coupled with mutations, these changes can lead to the emergence of a viral strain capable of infecting new host organisms. Important: it is important to note that emerging viruses are generally not new; rather, they are existing viruses that mutate, disseminate more widely in current host species, or spread to new host species. Changes in host behavior or environmental changes can increase the viral traffic responsible for emerging diseases.