EXAM #1 STUDY GUIDE

Mechanisms of Evolution (Chapter 22/23)I. TERMS

Evolution – Evolution is descent with modification / change in the genetic composition of a population from generation to generation.

Natural selection – Heritable traits prevail in environment if they make the organism more favorable in terms of survival and reproduction. Elements of natural selection are: more offspring produced than can survive/exhibit variation/competition for access to resources/variation leads to differential survival and reproduction.

Adaptation – Inherited characteristics of organisms that enhance their survival and reproduction in specific environments (increase fitness).

Theory – Coherent body of evidence / general laws, principles, or causes of observed phenomena (have been tested many times).

Population – All individuals of the same species who live in the same geographic area that interbreed.

Microevolution - Change in allele frequencies (traits) in a population over generations.

Gene pool – All alleles at each locus in a population.

Hardy-Weinberg Equation – Allele frequency (p+q=1) / Genotype frequency (p^2+2pq+q^2=1)

Genetic drift – Change in allele frequency in a population caused by chance – usually in small populations, results in loss of genetic variation.

Bottleneck – Population undergoes sudden and dramatic reduction in size due to environmental change. The gene pool is no longer the same of the original population.

Founder effect – Few individuals become isolated from a larger population and establish a new population. Allele frequencies in small founder population can be different from those in the larger parent population.

II. CONCEPTS1. Observations of Darwin’s time that supported his theory of evolution: Offspring

exhibit variation in which some are heritable / more offspring are produced than can survive. Evidence: embryology/artificial selection/biogeography/paleontological record/vestigial structures/comparative anatomy and homology.

a. Ideas which ran counter-concurrent to his theory: Idea of “use-disuse” by Jean Baptiste de Lamarck / religious teachings / Georges Cuvier – opposed idea of evolution and suggested mass extinction events caused species disappearing, etc.

2. Two principles of Jean Baptiste de Lamarck’s mechanism of evolution and problems with it: 1. Idea of use and disuse (used parts become stronger and unused parts

deteriorate). 2. Organisms can pass new modifications to their offspring. Problem: Organisms do not evolve individually.

3. Main points/central elements of Darwin in his book “Origin of Species”: 1. Unity of life – descent of all organisms from a common ancestor in the remote past. 2. Descent with modification – As organisms live in diverse habitats, they adapted to the environment. 3. Natural selection – mechanism of evolution.

4. Darwin’s two observations and inferences: O1: Offspring exhibit variation in which some are heritable. I1: Individuals whose inherited traits give them a higher probability of surviving and reproducing in an environment tend to have more offspring. O2: More offspring are produced that can survive. I2: Differential ability to survive and reproduce will lead to accumulation of favorable traits in a population over time.

5. Two examples which support theory of evolution: See answer for question 1. Also, Darwin’s finches (beak depth), Hopi Hoekstra’s Beach Mice (white mice on white sand).

6. Three key points of evolution: Populations evolve, individuals do not. Only traits coded by genes may be passed onto offspring. Evolution does not perfect traits but adapts to certain environmental conditions which vary from one place to another (existing traits only/traits can have a cost vs. benefit/chance events can alter the types of traits in a population/environmental conditions can change).

7. Genetic variation and what two forms is it found as: Genetic variation are traits (physical and molecular) which vary in a population due to differences in genes responsible for that trait.

8. Two sources of genetic variation - 1) Mutation – Change in DNA sequence can lead to variation of traits. 2) Sexual reproduction – Generates unique arrangements of traits within offspring from two parents.

9. Hardy-Weinberg Formula – See TERMS. Hardy-Weinberg can help us recognize if adaptation/natural selection is occurring.

10. Requirements for Hardy-Weinberg: Hardy-Weinberg Equilibrium – 1) No mutations. 2) Random mating. 3) No natural selection. 4) Large population. 5) No gene flow.

11. Compare/contrast genetic drift, gene flow, and natural selection: Genetic Drift - Change in allele frequency in a population caused by chance – usually in small populations, results in loss of genetic variation. Gene flow – Transfer of alleles WITHIN a population. Natural selection: Heritable traits prevail in environment if they make the organism more favorable in terms of survival and reproduction.

12. Different types of genetic drift and natural selection: Genetic drift – bottleneck / founder effect. Natural selection – Directional selection (when conditions favor individuals exhibiting ONE extreme of phenotypic range) / Disruptive selection (conditions that favor individuals exhibiting BOTH extremes of phenotypic range) / Stabilizing selection (Acts against both extremes and favors the intermediate).

13. Prevailing world view up to Darwin’s theory – Aristotle: species were fixed and unchanging / Religious: Organisms are as God initially made them / Jean Baptiste de Lamarck’s “use and disuse”.

14. Evidence available to Darwin which supported his idea: 1. Artificial selection: breeding of livestock and dogs (small/large). 2. Embryology: Descent from common ancestor (evolution tweaks development leading to different adult forms – tails, etc.) 3. Homology: similarity of structure due to common ancestors despite differences in function (wings/fins/arms/legs). 4. Biogeography: species colonized new habitats and divided by geographic barriers, took on distributions they have today. 5. Fossils: Fossils showed transitional forms and Darwin hypothesized that modern day animals evolved from land dwelling ancestors.

15. Two sources of genetic variation: See answer for question 7.

Origin of Species (Chapter 23/24)I. TERMS

Variation – Difference between cells, individuals, or groups of species caused by genetic differences (genotypic variation) or by expression of genetic potentials (phenotypic variation). Mutation is the ultimate source of variation (appears at the allele level). If mutation confers advantage, allele increases in frequency.

Reproductive Isolation – Existence of biological factors that impedes members of two species from interbreeding and producing viable/fertile offspring. Blocks gene flow between two species and limits the formation of hybrids. Prezygotic barriers: Habitat isolation, temporal isolation, behavioral isolation, mechanical isolation, gametic isolation. Postzygotic barriers: Reduced hybrid viability, reduced hybrid fertility, hybrid breakdown (1st generation viable but following offspring not).

Species – Species is the fundamental evolutionary unit. Species is a group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring – but do not produce viable, fertile offspring with members of other such groups.

Speciation – The process of a species splitting into two or more species (focal point of evolutionary theory).

Macroevolution – Broad patterns of evolution change above the species level.

Reproductive Barriers – Prezygotic and postzygotic barriers. (See definition for “reproductive isolation”.)

Prezygotic/Postzygotic – See definition for “reproductive isolation”.

Allopatric speciation – Gene flow is interrupted when population is divided by geography into an isolated subpopulation. Different mutations arise and natural selection/genetic drift may alter allele frequencies.

Sympatric speciation – Speciation occurs in populations that live in the same geographic area. Occurs if gene flow is reduced by polyploidy (accident in cell division that results in extra sets of chromosomes), habitat differentiation (new food source or protective location), or sexual selection (mate choice based on color, physical traits, or behavior).

Adaptive radiation – The evolution of many species from a single common ancestor (Example: Galapagos Islands due to relative isolation).

Punctuated equilibrium – Periods of stasis punctuated by sudden change (seen in fossil record).

II. CONCEPTS1. What are species? See definition for “species”.2. Biological Species Concept (BSC): Two individuals who can create offspring and the

offspring are fertile (Problems are interpretation of fossil record, asexual reproduction, and species who appear different from one another who can mate and produce viable

offspring). Morphological Species Concept: Species are classified based on appearance. Can be applied to asexual organisms and fossil records. (Problems are that it relies on subjective criteria and does not always match DNA sequences). Ecological Species Concept: Classified based on food source and habitat. (Problems: Organisms can occupy similar ecological niches and not produce viable offspring). Phylogenic Species Concept: Classified as the smallest group of organisms which share a common ancestor. Compare appearance, DNA sequences, and metabolism pathways (Problems: How many differences define a different species?). Mate Recognition Species Concept: Recognition of mates (Problems: Cannot apply to fossil record).

3. Reproductive isolation is the key to the BSC. Prezygotic barriers: Habitat isolation (geography separates them – Ex. Snakes who live in water/land), temporal isolation (different breeding times – Ex. Two types of skunks who breed in late winter/late summer), behavioral isolation (courtship rituals – Ex. Blue foot boobies who do a high step to show off their blue feet), mechanical isolation (morphological differences prevent successful completion of mating – Ex. Snails with opposite genital opening direction), gametic isolation (Sperm cannot fertilize eggs of another species – Ex. Sea urchins, proteins on surfaces of sperm eggs make them bind poorly in difference species). Postzygotic barriers: Reduced hybrid viability (impair hybrid development or survival – Ex. Frail hybrid salamanders), reduced hybrid fertility (hybrids who are sterile – Ex. Male donkey/female horse = mule), hybrid breakdown (1st generation viable but following offspring not – Ex. Strains of cultivated rice).

4. BSC is more useful in theory than in practice. Problems are interpretation of fossil record, asexual reproduction, and species who appear different from one another but can mate and produce viable offspring.

5. BSC does not apply to asexual or extinct organisms.6. Hybridization complicates the BSC. Example are female horses who can mate with male

donkeys and produce mules. Another example are ligers and tigons (between lions and tigers).

7. Prezygotic barriers: Habitat isolation (geography separates them – Ex. Snakes who live in water/land), temporal isolation (different breeding times – Ex. Two types of skunks who breed in late winter/late summer), behavioral isolation (courtship rituals – Ex. Blue foot boobies who do a high step to show off their blue feet), mechanical isolation (morphological differences prevent successful completion of mating – Ex. Snails with opposite genital opening direction), gametic isolation (Sperm cannot fertilize eggs of another species – Ex. Sea urchins, proteins on surfaces of sperm eggs make them bind poorly in difference species).

8. Postzygotic barriers: Reduced hybrid viability (impair hybrid development or survival – Ex. Frail hybrid salamanders), reduced hybrid fertility (hybrids who are sterile – Ex. Male donkey/female horse = mule), hybrid breakdown (1st generation viable but following offspring not – Ex. Strains of cultivated rice).

9. Reproductive barriers: See definition for “reproductive barriers”. 10. Mechanisms responsible for speciation: See definitions for “allopatric and sympatric”

speciation.

11. How can speciation occur with or without natural selection: Mutations, hybridization, allopatric speciation, and sympatric speciation.

12. How can natural selection enhance reproductive isolation? Through genetic variation, this can prevent gene flow between species due to variation in the gene pool.

History of Life (Chapter 25)I. TERMS

Macroevolution - Broad patterns of evolution change above the species level.

Radiometric dating – In order to obtain the relative ages of substances, radiometric dating is used (based on decay of radioactive isotopes). Half-like: Time required for 50% of parent isotope to decay. Radioactive “parent” isotope decays to “daughter” isotope at a characteristic rate. Carbon in fossils from when it ingested it as a living organism is used for radiometric dating. If the fossil is too old, radiometric can be used on the rock around the fossil, allowing them to assign a relative age.

Geologic Record – Standard time scale that divides the Earth’s history. Four Eons: Hadean/Archaean/Proterozoic/Phanerozoic. Phanerozoic: (Paleozoic/Mesozoic/Cenozoic – now).

Fossil Record – Fossil record captures the history of life on Earth in the form of mineralized bones, organisms trapped in amber/ice, and preserved impressions as a mold or cast (trace fossil). Usually found in sedimentary rock layers. It is an incomplete record because some fossils are destroyed, few individuals are fossilized, few fossils are discovered, and only shows abundant/long lived/widespread/had hard body parts/lived and died in certain environments. Successions of fossils revealed when geological strata are exposed. Strata can be used for relative dating.

Endosymbiotic Theory – Within early Earth, in the process of becoming independent, the host and endosymbionts would have become a single organism. Mitochondria/plastids (chloroplasts and organelles) were former prokaryotes living within larger host cells. Hosts were anaerobic and could have benefitted from endosymbionts who can utilize oxygen.

Continental Drift / Plate Tectonics – Continents are part of great plates (part of the crust) which are floating on hot mantle. Continents used to be only one large land mass but separated over long periods of time. Continental drift led to allopatric speciation. Plates either collide, slide, or separate. (Ex. Created the African rift / Africa looks like it can fit into between North and South America)

Adaptive Radiation – From extinction events (less competition), evolution of new character that is novel (super competitive), and migration into new environments. Adaptive radiation is evolution of many species from a single common ancestor.

Cenozoic Era – The current era (65 million years ago to present). The start of the Cenozoic was the KT extinction event at the end of the Mesozoic Era (cretaceous extinction due to meteor followed by adaptive radiations).

II. CONCEPTS1. Features of Earth which made it favorable for life on earth: Sun of moderate size / orbital

distance from the Sun provided for moderately stable climate / mix of atomic elements (carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur, liquid water) / iron core

(magnetic shield protection from solar and cosmic radiation. Later on the ozone layer emerged from free oxygen produced by living organisms.

2. Four sequential stages of the origin of life from non-living matter: 1. Synthesis of small organic molecules (amino acids/nucleotides) by non-living processes – organic molecules created from lightning and UV radiation / deep sea alkaline vents with high pH, warmth, and amino acids with ammonia / volcanos produced sponge-like minerals (zeolites) organic compounds / meteorites contained amino acids, lipids, simple sugars, and uracil. 2. Joining organic molecules into polymers (proteins and nucleic acids) such as heated monomers will form cross-linked polymers on hot sand, clay, and rock. 3. Packaging molecules into protocells with lipid membranes (can absorb molecules and replicate – metabolism and replication are key properties of life). 4. Origin of self-replicating molecules required for inheritance (short RNA molecules can form from monomers and a complementary strand can give rise to double stranded RNA – gave template to more stable DNA).

3. How rock and fossil records can be analyzed in order to decipher evolutionary time and evolutionary events: Succession of fossils through strata / radiometric dating can be used.

4. Limitation of using fossil record: It is an incomplete record because some fossils are destroyed, few individuals are fossilized, few fossils are discovered, and only shows abundant/long lived/widespread/had hard body parts/lived and died in certain environments.

5. Evidence to support endosymbiotic theory: 1. Plasma membrane of prokaryotes similar to inner membranes of chloroplasts and mitochondria. Eukaryotes have organelles that seem to have an independent origin of life. 2. Mitochondria, chloroplasts, and prokaryotes replicate by binary fission, have circular DNA, can transcribe mRNA and translate protein, and they have similar ribosome size/sequence.

6. Major events in Earth’s history which lead to changes in life on Earth: Explosion of animals occurs during Cambrian explosion (first predators appear). Colonization of land started with plants and fungi. Mass extinctions: Permian Extinction (possibly by volcanic activity), Cretaceous Extinction: (meteor). Adaptive radiation followed mass extinction allowed for new habitats to be exploited by survivors and the potential for rapid speciation.

7. Continental drift and mass extinctions stimulated speciation: allopatric speciation / adaptive radiation. Different environments / different level of competition / exploitation of new habitats / adaptation to new environments / natural selection.

8. Three scenarios in which adaptive radiation likely to occur: 1. Extinction events (less competition / exploitation of new environments by survivors / adaptation). 2. Evolution of new character which is novel (super competitive). Natural selection can increase frequency of the trait. 3. Migration into a new environment.

9. Process of speciation is not goal directed, can reverse itself, and is not a straight line but a branching tree.

Phylogeny and the Tree of Life (Chapter 26)I. TERMS

Phylogenic Tree – Evolutionary history of a group of organisms in a branching diagram (phylogenic trees are hypotheses). The purpose is to interpret the relationship between species or groups through common ancestors.

Homology / Homoplasy – Homologies are phenotypic/genetic similarities due to a shared ancestry. Homoplasy is an analogous structure that arose independently (similar feature except the similar resulted from independent origins.

Derived Trait – de novo (new) in the group in question.

Primitive Trait – Evolved in a more distant ancestor of group – not new at the level of the group in question.

Synapomorphy – Shared derived trait. Synapomorphies are homologous.

Monophyletic Group – Common ancestor and ALL of its descendants. (Aka clade)

Paraphyletic Group – Consists of an ancestral species and SOME of its descendants.

Polyphyletic Group – There is a common ancestor somewhere but its members are not part of the group.

Root – Most recent ancestor of ALL taxa on the tree.

Node – Nodes represent common ancestors (branching point).

Terminal – At the topmost part of each branch – labeled by the taxa of the population represented by that branch.

Genus Epithet – Before “species” (Domains->Kingdoms->Phyla->Class->Order->Family->Genus->Species). The genus epithet is listed first and is capitalized. (Ex. Staphylococcus aureus) “Staphylococcus” is the genus epithet.

Species Epithet – Species is lower case. Together with the genus epithet, it is italicized or underlined. (Ex. Staphylococcus aureus) “Aureus” is the species epithet.

II. CONCEPTS1. The goal of phylogenetic(s) is to hypothesize about the relationship between species or

groups of species by the interpretation of common ancestors. 2. Darwinian notion of descent with modification aligns with the construction of a

phylogenetic tree because it supports Darwin’s idea of unity of life (common ancestors) and that species are related to each other.

3. Phylogenetic tree is a reasoned hypothesis of evolutionary relationships among organism.4. The root is the branch point within a tree that represents the most common ancestor of

ALL taxa on the tree.5. Members of a sister group are more closely related to one another than they are to

members of any other group.

6. A node is a branching point on a tree and can be rotated without changing evolutionary relationships.

7. A tree is built on the basis of shared derived characteristics rather than primitive traits because nodes (branching) can be created based on derived traits and compared to other species who may or may not have the derived trait. Therefore, we have more data to hypothesize the relationships of species/groups.

8. Only shared derived (synapomorphic) characters are useful in constructing a phylogenetic tree.

9. Morphological and molecular data provide a wealth of characters for tree building.10. The concept of parsimony in tree building is the concept in which trees require the fewest

evolutionary events invoked to explain traits in the studied groups. This affects tree building because it minimizes the number of independent origins of that character state (makes it less complicated).

III. SCENARIOS1. Human-Chimpanzee-Bonobo-Gorilla phylogeny – Humans form a sister group with the

chimp/bonobo group (are more closely related to each other than either is to the gorilla). However, chimps and bonobos look more similar to gorillas. However, chimp/bonobo molecular data is more similar to humans.

Micro-Organisms: Bacteria, Archaea, Protists, and VirusesI. TERMS

Domains (Tree of Life) – Domain Eukarya / Domain Archaea / Domain Bacteria

Prokaryote – Single celled organism that lacks a membrane bound nucleus, mitochondria, or any other membrane bound organelle. Some of the earliest forms of life on Earth are bacteria and archaea.

Bacteria – Large group of unicellular microorganisms that have cell walls but lack organelles and an organized nucleus, including some that can cause disease.

Archaea – Microorganisms that are similar to bacteria in size and simplicity of structure but are radically different in molecular organization.

Binary Fission – Single prokaryotic cell divides into two (asexual reproduction).

Horizontal Gene Transfer – Process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and fusions of organisms (endosymbiosis).

Conjugation - DNA transferred between two prokaryotic cells that are temporarily joined. Pilus from donor cell attaches to recipient and retracts, bringing them together. Then DNA is transferred. F factor DNA allows for formation of pili and donation of DNA during conjugation.

Transformation - Genotype and possibly phenotype of prokaryotic cell altered by uptake of foreign DNA from its surroundings. Cell is now recombinant.

Transduction - Bacteriophages (viruses that infect bacteria) carry prokaryotic genes from one host cell to another. Mostly occurs from accidents during phage replicative cycle but phages can also inject DNA (if incorporated into recipient cell by crossing over, then recombinant cell is formed). Can be used to introduce novel genes into bacteria for medical research.

Obligate Anaerobe – Cells that are poisoned by O2 (live by fermentation).

Obligate Aerobe - Cells that must use O2 for cellular respiration.

Facultative Anaerobes – Cells that use O2 if present but also carry out fermentation or anaerobic respiration in an anaerobic environment.

Extremophile - “Lovers” of extreme conditions (Extreme Halophiles – live in highly saline “salty” environments / Extreme thermophiles – thrive in hot environments).

Protist – Eukaryotic microorganisms. Most are aquatic and form symbiotic relationships with other species (some are parasitic). Protists are unicellular eukaryotes (membrane bound organelles, nucleus). Most diverse group of eukaryotes. Can be photoautotrophs, heterotrophs, or both (mixotrophs). Can reproduce sexually or asexually.

Virus – Lacking the structures and metabolic machinery found in a cell, a virus is an infectious particle consisting of little more than genes packaged in a protein coat. They may contain either DNA or RNA.

Viron – Complete, fully developed, infectious viral particle with a nucleic acid surrounded by a protein coat. Viruses are classified by differences in the structure of the protein coat.

Capsid – The protein shell enclosing the virus genome. The capsid may be rod-shaped, polyhedral, or more complex in shape.

Virus morphology – Virus morphology is a way to classify viruses based on their capsid structure. 1. Helical: Resemble long helical rods with the nucleic acid in the hollow center (Ebola, rabies viruses). 2. Polyhedral: Many sided virus with each face forming an equilateral triangle (Polio virus). 3. Enveloped: Capsid (helical or polyhedral) covered by a roughly spherical envelope (Influenza, herpes simplex viruses). 4. Complex: Have capsids with additional structures attached (bacteriophages).

Host Range – The spectrum of host cells the virus can infect. Determined by the viruses specific attachment to the surface of the host cell. This could be the cell wall, fimbriae, or flagella in bacteria or plasma membrane in animal cells. The host range can be broad or narrow.

Bacteriophages – Viruses which infect bacteria (also called “phages”).

Lytic Cycle – One of the mechanisms of bacteriophage multiplication. The phage attaches to a host cell and injects DNA and the phage DNA circularizes. Then either lytic cycle induced or lysogenic cycle entered. If lytic cycle induced, new phage DNA and proteins are synthesized and self-assemble into phages. Then, the cell lyses and the phages are released. The lytic cycle culminates in the death of the host cell. A virulent phage only uses the lytic cycle for replication.

Lysogenic Cycle – If lysogenic cycle is entered, phage DNA integrates into the bacterial chromosome, becoming a prophage. The bacterium reproduces normally, copying the prophage and transmitting it to daughter cells. Many cell divisions produce a large population of bacteria infected with the prophage (prophage is viral DNA through the lysogenic cycle). Occasionally, the prophage exits the bacterial chromosome and initiates a lytic cycle.

Vaccine – A harmless form, derivative, or segment of pathogen which stimulates the immune system to acquire long term defenses against the harmful pathogen. Some viruses which pose greater health risks can be prevented through the use of vaccines.

Emerging Virus – Viruses which suddenly become important to human public health. Viruses emerge through: 1. High mutation rate of replicating virus. 2. Increase in human contact due to travel, blood transfusions, etc. 3. Increase transmission from animals (act as a reservoir for virus).

II. CONCEPTS

1. Unique characteristics of prokaryotes - Cell wall: made of peptidoglycan – structure of the cell wall can be identified by gram stain (gram positive have simpler walls with large amount of peptidoglycan / gram negative have less peptidoglycan and more complex with outer membrane that contains lipopolysaccharides). Endospore: original cell produces copy of its chromosome and surrounds it with tough multilayered structure. Water is removed and original cell lyses, releasing the endospore. Therefore, it can withstand harsh environments. Capsule: Cell wall surrounded by capsule (sticky layer of polysaccharide or protein – protects against dehydration and attacks from immune system / helps them adhere to substrates or colonies). Fimbriae: Hair-like appendages used to stick to substrate or one another (shorter and more numerous than pili). DNA: Have circular chromosomes associated with fewer proteins than in eukaryotes. They do not have a nucleus. Prokaryotes have a nucleoid which is a region of cytoplasm not enclosed in membrane where DNA is located. Prokaryotes also have plasmids (smaller rings of independently replicating DNA molecules – rings). Size and Shape: Diameters ranging from 0.5 to 5 micrometers. They have a variety of shapes, including spherical (cocci), rod-shaped (bacilli), and spiral (spirilla).

2. Mechanisms of prokaryotes that contribute to their variation and diversity: Rapid reproduction by binary fission / horizontal gene transfer / transformation / transduction / conjugation / mutations.

3. Energy source and carbon source – Energy source for metabolism: phototrophs (use light energy) / chemotrophs (use chemical energy). Carbon source (needed for protein building): autotrophs (need CO2 for carbon) / heterotrophs (need organic compounds for carbon).

4. Characteristics of viruses: see virus morphology, lytic cycle, lysogenic cycle, and definitions for virus.

5. Structural components of viruses - Nucleic acid: DNA or RNA can either be single or double stranded. Nucleic acid can be linear of circular. Can have 3-1000 genes. Capsids: Genome protected by protein shell called capsid made up of subunits called capsomeres (helical, polyhedral, enveloped, or complex). Envelope contains lipids and proteins from host along with viral protein-carbohydrate spikes which are used to attach to host ells.

6. Lytic and lysogenic cycle - Lytic Cycle: 1. Attachment 2. Entry of phage DNA and degradation of host DNA 3. Synthesis of viral genomes and proteins 4. Self-assembly 5. Release. Lysogenic Cycle: See definition.

7. Main structural feature of animal viruses which make them different from phages and how are they used during the replication cycle? Nearly all animal viruses with RNA genome have an envelope as do some with DNA genomes. It uses the envelope to enter the host cell. There are viral glycoproteins that protrude from the envelope that bind to specific receptor molecules on the surface of the host cell. In this cycle, the digestion of the capsid by cellular enzymes releases the viral genome. Complementary strands are made of RNA and new copies of viral genome RNA are made using the complementary strands as template. Complementary RNA also function as mRNA, which is translated into both capsid proteins and glycoproteins for the viral envelope. Vesicles transport envelope glycoproteins to the plasma membrane. A capsid assembles around each viral genome molecule. Each new virus (capsid) buds from the cell wrapped in membrane and

its envelope is studded with viral glycoproteins embedded in membrane derived from the host cell.

8. Emerging Viruses – Emerging viruses are viruses which suddenly become important to human public health. These viruses emerge from 1. High mutation rate of replicating virus RNA/DNA. 2. Increase in human contact due to travel, blood transfusions, etc. 3. Increase transmission from animals who act as a reservoir for virus. Epidemic: widespread outbreak. Pandemic: Global widespread outbreak.

III. THOUGHT QUESTIONS1. Features of prokaryotes which enable them to survive environments that are too harsh for

humans: Their ability to rapidly reproduce combined with mutation allowed them to adapt to different environments. Their different sources of nutrition and different modes of metabolism (also their ability to colonize and form symbiotic relationships).

2. Is virus a living organism? They have genetic information (DNA or RNA) and have protein coat that surround the nucleic acid. They have the ability to replicate through cell machinery. They synthesis specialized structures that can transfer viral nucleic acid to other cells (sophisticated adaptations).

3. What viral traits suggest they are not living? No modes of metabolism. They lack enzymes for protein synthesis and ATP generation.

4. What features suggest viruses are simple organism? They are simply composed simply of nucleic acid surrounded by protein coat.

5. What features of viruses suggest they are complex? Their capsid structure (helical, polyhedral, enveloped, and complex). Their modes of replication (lytic and lysogenic cycles / replication of animal viruses).

6. In what ways are bacteria and viruses alike? How do they differ? They are both pathogenic (bacteria releases exotoxins – poison / endotoxins – released when bacteria die and cell wall breaks down….. viruses use cells as hosts for replication and can destroy the cell). They both have genetic material that is not organized in a nucleus. They differ because bacteria have modes of metabolism and viruses do not. Bacteria can also self-replicate through binary fission while viruses need a host cell to replicate.

7. Scientists know less about archaea organism because they can live in very extreme environments (I.e. Hypothermal vents underwater, under ice, etc.)

8. What aspects of bacteria and archaea biology lead to rapid evolution? Rapid reproduction by binary fission / horizontal gene transfer / transformation / transduction / conjugation / mutations.