Biology Exam #4

Describe the environment preferred by each type of archaea: methanogens

Anaerobic environments - produce methane; live in the digestive tracts of vertebrates

Name some human and non-human animal diseases caused by viruses.

Animal: - Hog cholera - Foot (or hoof)-and-mouth disease - Canine distemper - Feline Leukemia Humans: - ebola - chicken pox - mumps - measels - influenza - Aids - monoculeosis

Give examples of complexity in molecular biology.

- ATP synthase - DNA replication, transcription, and translation - Packaging of DNA in a cell - Cell division, kinetochores - Nuclear pore transport.

What are antibiotics and probiotics?

- Antibiotics are medicines that fight bacterial infections in people and animals. - Conversely, probiotics are live bacteria and yeasts that are good for you, especially in your digestive system

Explain: bacteriophage, membrane fusion, and endocytosis.

- Bacteriophages infect bacteria. - Enveloped viruses infect by membrane fusion or endocytosis.

Describe the contributions that Louis Pasteur made to microbiology, public health, and medicine.

- He is considered the "Father of Microbiology" - Disproved "spontaneous generation" - Developed vaccines against rabies and anthrax - Invented pasteurization (milk and wine) - Encouraged hand washing and other sanitary measures in hospitals

Describe the important discovery of Anton van Leeuwenhoek in 1674.

- He was a Dutch microbiologist - Discovered bacteria in 1674 by looking at drops of lake water using a glass lens.

Describe the viral structures: helical, icosahedral(polyhedral), enveloped, and helical-icosahedral (complex).

- Helical: viral nucleic acid coils into a helical shape and the capsid proteins wind around the inside or outside of the nucleic acid, forming a long tube or rod-like structure. Ex. Tobacco mosaic virus. - Icosahedral (polyhedral): Polyhedral viruses have nucleic acid encased in a polyhedral (many-sided) shell or capsid, which is commonly shaped like an icosahedron. Adenoviruses are one example of this. - Enveloped (spherical): These viruses appear spherical in shape, but a closer look actually reveals they are icosahedral. Example: influenza virus. - Complex: viruses with asymmetrical structures are referred to as "complex. " These viruses possess a capsid that is neither purely helical nor purely icosahedral, and may possess extra structures such as protein tails or a complex outer walls. Example: Bacteriophage.

Describe the scientific data that support Creation and contradict macroevolution.

- Origin of life - Fossil record: Sudden appearance of all existing phyla (Cambrian "explosion") - General absence of transitional fossils - Sedimentation and catastrophic: (Evidence for rapid sedimentation and catastrophic death events can be observed in geology and paleontology). - The complexity of molecular biology

Name and describe three types of evidence that are often cited in support of macroevolution.

- Radiometric dating of rocks (assumes rates of decay are constant) - Other dating methods: ice cores, corals, and paleomagnetism. - Fossil Record: orderly fossil record and the hominin record.

Describe the scientific data that support macroevolution and contradict Creation.

- Similarities in embryos - Homology: Similar bones, similar proteins, similar genes - Fossil: Orderly progression. Not randomly distributed. Some apparent sequences of evolutionary intermediates (whales, fish-to-amphibian transition) - Biogeography: the study of the past and present geographic distribution of organisms

Explain why Creation is important to Christians today.

- Verses referring to Creation - Entire Bible testifies to Creation - References to Jesus believing in Creation and the Flood

Describe viruses.

- Very small infective agents (20-300nm) - Have a core of nucleic acids (Both RNA, DNA, single/double-stranded) - Are nonliving particles and are obligate intracelluar parasites. - Take over living cells to produce more viral particles.

Name and describe the characteristics of the pelvis that are used to describe hominoid species.

1. Bowl-like pelvis (hip bone) supports organs. (Ape has longer pelvis to support back. 2. Angle of femur insertion. Results in longer stride when upright

Name and describe the characteristics of the scapula that are used to describe hominoid species.

1. In apes, adapted for arboreality (living in trees) or knuckle-walking (quadrupeds).

Name and describe the characteristics of the mandible that are used to describe hominoid species.

1. Lower Jaw. Transvers torus (simian shelf) is absent only in modern humans. 2. Mental eminence (chin). Present only in modern humans.

Name and describe forces that drive microevolution.

1. Mutation: source of genetic variation (new alleles) 2. Genetic drift: random events changing allele frequencies; bottleneck (large die-off) and founder effect (migration) 3. Gene flow: migration & mixing of populations 4. Natural selection: differential success of organisms resulting from their environmental interactions All these forces change allele frequencies in populations.

Name and describe the characteristics of the skull that are used to describe hominoid species.

1. Reduction of brow ridge (supraorbital sulcus) 2. Loss of protruding mouth (prognathism) 3. Changes in the shape of back of skull (occipital bun)

What is the main difference in the structure of bacteria and archaea?

Archaea: - lack peptidoglycan in cell walls - lives n extreme environments

Explain: Spirilla and Vibrio

Are both rigid in shape Vibrio is more curved in shape.

Explain: spirochete

Are flexible - Cause Lyme disease

What is an important concern about overusing antibiotics?

Bacteria mutate frequently and can reproduce rapidly. - mutations can lead to antibiotic resistant genes known as R factors - resistant bacteria can multiply and produce a resistant population after an antibiotic treatment. Overuse of antibiotics has led to the rise of resistant bacterial strains. Forms of overuse: - Taking antibiotics when you don't need them. - Taking the wrong antibiotic - Not taking antibiotics as directed

Draw a diagram illustrating the basic anatomy of a bacterium.

Bacterial Structures include: - Fimbriae - Plasma membrane - nucleoid - flagella - outer membrane - cell wall - plasmid - ribosome - cytoplasm

Describe the structure of the bacterial flagellum.

Bacterial flagellum are used for movement. - Different from eukaryotic flagellum and made of the protein flagellin rather than tubulin. Has three parts: - Basal body is the motor (rotates filament counterclockwise and powered by a proton pump. - The Hook attaches the basal body to the long filament.

Describe binomial system of nomenclature designed by Carolus Linnaeus.

Binomial system (Genus species) developed by Carolus Linnaeus in 1700s. Scientific names are often: - Descriptive of the species - Based on where the species lives - Named after the person who found it or someone famous - Always italicized

Name the different ways in which prokaryotes get their energy and their carbon.

Carbon source - Autotroph: use inorganic carbon to make their own organic molecules. (Organism that makes its own food using inorganic substances) - Heterotroph: obtain carbon from organic compounds from other organisms Energy source: - Chemotroph: obtain energy from chemical compounds - Phototroph: obtain energy from light.

Explain: chemotaxis exotoxin, endotoxin

Chemotaxis determines movement patterns. (Movement toward or away from specific chemicals) Exotoxin: potent poisons that are secreted or leak out when a cell is destroyed. Release by bacteria when they have been injured by the immune system. Endotoxin: lipopolysaccharides of the cell wall; only released from dead bacteria. Can cause fever and aches. Found only in gram negative bacteria. Can cause fevers.

Explain our current understanding of the relationship between Neanderthals and humans.

DNA extracted from fossil bones - Sequence published in 2013 - Compared to genome of modern humans - Evidence of gene flow (interbreeding) - Eurasians: 1-4% genes shared with Neanderthals - Africans: no shared genes

Explain what a biofilm is and explain its importance in medicine.

Definition: an ecosystem consisting of many microbes living together in a slimy film of clay glycoproteins - Are used for protection. - Some biofilms are resistant to immune system and antibiotics Ex. Dental plaque and soap scum.

Explain the contributions of Ivanovsky and Beijerinck to the field of virology.

Dmitri Ivanovsky: - Studied tobacco mosaic disease (TMD) that stunts the growth of the tobacco plant. - He looked for a bacterial cause but found the causative agent filtered through porcelain. - He concluded that the cause of the disease had to me smaller than bacteria. Martinus Beijerinck: - Also studied TMD. He found that the microbe causing the disease could only reproduce in the presence of living plant cells - He first named the causative agent "virus" which is latin for poison.

Name the taxonomic levels in order (DKPCOFGS).

Domain Kingdom Phylum Class Order Family Genus Species

Describe the environment preferred by each type of archaea: acidophile

Extreme pH levels

Place the following in order of gradual morphological (shape) changes: Australopithecines, Homo habilis, Homo erectus, Neanderthals, modern man

Fossils in order of gradual changes: - Australopithecus sp. - Paranthropus sp. - Homo habilis - Homo erectus - Neanderthals - "Modern man"

Explain: bacilli

Generally rod-shaped with variations Cause food poisoning

Explain: cocci

Generally spherical and round - common in skin and wound infections

Contrast the cell wall structure of gram-positive and gram-negative bacteria.

Gram positive bacteria retain a stain after being rinsed. - they have a thick peptidoglycan cell wall - made of peptidoglycan - thick cell wall - retains initial stain Gram negative bacteria lose stain after being rinsed. - they have an outer membrane - made of lipopolysacharides. - made of peptidoglycan but less than gram-positive - thin cell wall - loses initial stain when rinsed with alcohol

Name the two kinds of animals included as Hominoids.

Hominoidea: Family of primates that includes apes and humans

Explain each of the three methods of horizontal gene transfer in bacteria.

Horizontal Gene transfer involves the transfer of genetic material to another organism that is not its offspring. Nothing sexual occurs. Transformation - Occurs when a bacterial cell dies. - Released DNA is picked up by other living bacteria and incorporated into their own genome. - Results in genetic variation. Transduction - Phage infects on bacterium (or virus infected bacteria) - Picks up bacterial DNA - Infects a different bacterium - DNA recombines in a new host (Virus is like the middle man) Conjugation - Direct transfer of plasmid DNA - Resembles sexual reproduction but is NOT - Sex pilus physically connects both cells. - F genes (usually found in the plasmid of DNA of F+ cells (donor)) encodes for the sex pilus. - Recipient (F-) cell usually receives some benefit such as antibiotic resistance and can not be a donor. F factors refer to mating types.

Describe the amount of fossil evidence that exists for the period in which molecular biology would have had to evolve.

Irreducible complexity (IC) is the argument that certain biological systems cannot have evolved by successive small modifications to pre-existing functional systems through natural selection, because no less complex system would function.

Describe the environment preferred by each type of archaea: thermophile

Live in extremely hot or cold environments; optimum growth. > 100 C or < 2 C

What is lysogenic conversion?

Lysogenic Conversion: Bacteria acquire new trait from temperate phage (permanent and passed to progeny cells)

Describe the lysogenic cycle.

Lysogenic Cycle: 1. Attachment: phage attaches to cell surface of bacterium. 2. Penetration: phage DNA enters bacterial cell. 3. Integration: Phage DNA integrates into bacterial DNA. 4. Replication: integrated prophase replicates when bacterial DNA replicates. • Lysogenic viruses are known as temperate—don't destroy host cell. ◦May become Lytic spontaneously ◦Integrated virus known as a prophage or provirus. • Lysogenic viruses usually acquire new characteristics/abilities.

Describe the lytic cycle

Lytic Cycle: • In a Lytic cycle, the viruses destroys the host cell. ◦Virulent phages (causes disease and infection) Steps of Lytic Cycle: 1. Attachment: phage attaches to a cell surface of bacterium. 2. Penetration: phage DNA enters bacterial cell. 3. Replication and Synthesis: phage DNA is replicated. Phage proteins are synthesized. 4. Assembly: phage components are assembled into new viruses. 5. Release: bacterial cell lyses and releases many phages that can then infect other cells.

Explain the evidence of change in nature (since Creation) that is found in the Bible. (See Gen. 3)

Microevolution - Small changes caused by changes in allele frequencies of populations - "Adaptation" or "speciation" resulting in similar organisms - Not inconsistent with Biblical Creation story

Explain the difference between microevolution and macroevolution. Explain which theory is consistent with a literal reading of the Biblical Creation story.

Microevolution is consistent with the Biblical Creation story. - Macroevolution: large changes over long periods of time. Results in new groups of organisms. - Microevolution: Small changes caused by changes in allele frequencies of populations. Results in adaptation or speciation or similar organisms.

Although apparent transitions exist in the hominin fossil record, explain why scientists cannot say for sure how these species are related to one another.

No known species with all the right character states in the right order. There is an assumption that everyone is related by a common ancestor. - We have an incomplete picture of these fossils. We don't have everything or all the knowledge. - There are no distinct transitions between ape-like creatures and humans.

Describe the principle of parsimony.

Parsimony: the simplest explanation is probably the best. - Fewest events necessary to arrive at a result - Based on maximum likelihood models

Explain why prokaryotes are important ecologically and economically.

Prokaryotes are ecologically important: - Decomposers: recycle nutrients (nitrogen, oxygen, carbon, etc...). - Bioremediation: detoxify or remove pollutants - Fix Nitrogen for plant roots: plants need nitrogen but can't use all forms of Nitrogen. Bacteria can get nutrients from plants and turns the nitrogen from an unusable form to a usable form that can be used by the plant. Ex. Rhizobia in legumes. This is a mutualistic relationship. - Produce O2 and fixes CO2: like cyanobacteria and produce O2 and remove CO2 from the atmosphere. Similar to plants.

Describe the environment preferred by each type of archaea: halophile

Require high-sodium environments. Ex. Dead Sea; salt ponds (harvest salt)

Explain what is unique about retroviruses.

Retroviruses use the reverse transcriptase enzyme to create double-stranded DNA from single stranded RNA. - They reverse the RNA to DNA - Incorporate their genes into the host's genome.

Name and describe the different types of subviral agents.

Satellites: - Indistinguishable from ordinary virus particles - Depend on another virus, a host or helper virus, for propagation. - Often called "a parasite of a parasite" Viroids: - Naked rings of RNA only that are replicated by host RNA polymerase - Silence expression of critical genes in plants - Hardy; resistant to UV Prions: - Transmissible, misfolded proteins. - No nucleic acids - Can induce other proteins to misfold and act incorrectly - Tend to aggregate which can lead to tissue necrosis - Several brain diseases like Alzheimer's and Parkinson's disease.

Explain how phylogenic trees or cladograms are created.

Sort organisms by shared characteristics - Arrange in order by stepwise differences Make a dichotomous (branching) tree - Yes, this organism has this character, or - No, this organism does not

Explain: taxonomy, systematics, and classification.

Systematics is the study of the diversity of organisms & evolutionary relationships. Taxonomy is a part of systematics. Involves naming, describing, and classifying. Classification is assigning organisms into groups based on similarities or supposed relationships.

Name the first virus discovered.

The Tobacco mosaic virus

Explain why issues of origins are ultimately outside the realm of science.

The origins of life lie outside the realm of science and belong in the realm of philosophy and religion. The origin of the diversity of life cannot be observed. - data collected on natural history is forensic (not experimental). Creation was an unrepeatable historical event.

Explain how evidence can be used to help determine which of two competing theories is likely correct.

There are two types of data: - Data that support one theory only (and contradict the other) - Data compatible with both theories.

Explain how viruses generally only infect specific species and tissues.

Viruses are specific to the organism to live off on. - Most viruses must be transmitted rapidly - Attachment is very specific - Viruses must bind to receptors located on host - Specific to host species - Specific to cell type Ex. Flu virus infects cells of respiratory tract.

List the kinds of organisms that can be infected by viruses.

Viruses can infect a variety of living organisms, including bacteria, plants, animals and humans.

Explain: endospore

When the environment becomes too dry or there are not enough nutrients for survival, some bacteria form endoscopes. - Occurs when mature gram positive bacteria produce a dormant, dehydrated cell that is resistant to extreme weather. - 1 bacterium produces 1 spore - Endospores are NOT spores since they aren't used for reproduction Endoscopes germinate when conditions become a favorable again.

What issues are at stake when we discuss the idea of human evolution? What is the big religious/philosophical dilemma?

Your faith is at stake. The idea of human evolution contradicts the existence of a Creator God which clashes with religion.