Biology 211 Exam 1 - Iowa State University

What trait distinguishes Alveolatans? Compare and contrast Ciliates, Dinoflagellates, and Apicomplexans.

-Alveolatans have mitochondria with tubular cristae and their flagellae or cilia have a distinct structure. -Ciliates: Single celled animal of a phylum distinguished by the possession of cilia or ciliary structures. -Dinoflagellates: Unicellular organisms with 2 whip like tails called flagella -Apicomplexans: Posses a unique for of organelle that comprises a type of plastid called an apicoplast and an apical complex structure.

How do ancestral traits differ from derived traits? What is an example of an ancestral trait when comparing cats and dogs? What is a derived trait in cats?

-Ancestral traits are a character trait that existed in an ancestor. Derived traits are those that is a modified form of the ancestral trait, found in a descendant. -An ancestral trait that cats and dogs share is the Dormaalocyon's ankle bones. -A derived trait in cats is hair.

Compare and contrast conjugation, transduction, and transformation. Is conjugation in bacteria a form of sexual reproduction? Why or why not?

-Conjugation: When genetic information is transferred by direct cell to cell contact -Transduction: When viruses pock up DNA from one prokaryotic cell and transfer it to another -Transformation: When bacteria and archaea naturally take up DNA from the environment that has been released by cell lysis or secreted -Conjugation is a form of sexual reproduction because of the swapping of DNA between the two organisms.

Compare and contrast the protective structures found in diatoms, dinoflagellates and foraminiferans. Why are these protists used to study fossils (forams) and dead bodies (diatoms)?

-Diatoms: Surrounded by cell wall made of silica (hydrated silicon dioxide) -Dinoflagellates: Surrounded by cell wall made of cellulose. -Foraminiferans: Cell wall is made of shells that are commonly divided into chambers that are added during growth. These are extremely useful in age-dating, correlation and paleoenvironmental reconstruction.

What are the 5 fundamental traits of life? With these traits in mind, are viruses alive? What evidence supports your conclusion?

-Energy Use and Metabolism -Cell Theory -Information, Genetics -Replication or reproduction -Biological Evolution -No, viruses are not alive because they do not have cells.

What colors do Gram negative and Gram positive stain? How does the Gram negative cell wall differ from the Gram positive cell wall?

-Gram Negative: Pink, thin peptidoglycan layer -Gram Positive: Purple, thick peptidoglycan layer

Define haploid and diploid. Which is 2n and which is 1n? What does n mean in this context?

-Haploid: A cell that contains a single set of chromosomes; 1n -Diploid: Having paired sets of chromosomes in a cell or cell nucleus; 2n N refers to the ploidy level of the organisms. The ploidy level is the number of sets of chromosomes.

Draw a bacterial cell and label the nucleoid region, cytoplasm, flagella, fimbriae, plasmids, cell wall, plasma membrane, and ribosomes. What is the function of each of these structures?

-Nucleoid Region: location of bacterial chromosome - Cytoplasm: Where the functions for cell growth, metabolism, and replication are carried out. - Flagella: locomotion - Fimbriae: (pili) adherence of bacteria to surfaces, substrates, and other cells or tissues in nature. - Plasmids: Small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA. Often, the genes carried in plasmids provide bacteria with genetic advantages, such as antibiotic resistance. -Cell Wall: Provide rigidity, tensile strength, structural support, protection against mechanical stress and infection. -Plasma Membrane: Permeability barrier for most molecules and serving as the location for the transport of molecules into the cell -Ribosomes: Workbench for protein synthesis where they receive and translate genetic instructions for the formation of specific proteins.

What are three different types of photosynthesis that bacteria are capable of completing? How does oxygenic photosynthesis differ from anoxygenic photosynthesis?

-Photophosphorylation, oxygenic photosynthesis, and anoxygenic photosynthesis. The main difference between oxygenic and anoxygenic photosynthesis is that oxygenic photosynthesis produces oxygen as a byproduct wheras anoxygenic photosynthesis does not produce oxygen as a byproduct.

How is energy generated in an electron transport chain? Why is a membrane required to generate ATP? What do we mean by "bacteria have a diversity of electron donors and acceptors" (refer to table 26.3)

1. As electrons pass from complex to complex they power the movement of hydrogen atoms into the intermembrane space. The number of hydrogen atoms will build up and flow back to the matrix simultaneously powering the production of ATP. At the end of the chain, the electrons are taken up by oxygen molecules to make water. The membranes are required because only certain molecules are allowed inside, making the process very important.

Give examples of different characters that could be used to construct the data matrix that is used to build a phylogenetic tree.

1. Cladistic approach: shared derived characteristics 2. Parsimony: least amount of change

Compare and contrast prokaryotic and eukaryotic cells. What are 3 key differences between the 2 cell types?

1. Eukaryotic chromosomes are inside a nucleus and linear. 2. Eukaryotic cells are much larger. 3. Eukaryotic cells contain extensive amounts of internal membrane. Eukaryotic cells feature a complicated cytoskeleton.

What are the 4 macromolecules that make up a cell and what is the general function of each class of macromolecule?

1. Nucleic acid: genetic function/information 2. Proteins: enzymes break things down and build things up 3. Lipids: Store energy 4. Carbohydrates: short term energy

Describe three distinct methods used by protists to obtain carbon (food). Can protists with a cell wall feed by phagocytosis? How does absorptive feeding differ from phagocytosis? Which type of organism feeds on detritus?

1. Protozoa: Heterotrophic 2. Algae: Photosynthetic 3. Fungus-like: Endocytosis (Wrap around it's prey and takes it in through it's membrane.) No, protists with a cell wall cannot feed by phagocytosis. Bacteria and fungi feed on detritus.

What are control groups and why are they important?

A control group is the group in an experiment or study that does not receive treatment by researchers and is then used as a benchmark to measure how the other tested subjects do.

How do hypotheses and theories differ? What do scientists mean by "theory" and does this mean the same thing as "in theory" that non-scientists may say in conversation? Explain.

A hypothesis is a constructed idea before any applicable research has been done. A theory is an idea supported by evidence. When scientists say theory, they mean something that is true and supported by evidence. When it is used in everyday conversations, it is simply an idea that hasn't been proven, aka a hypothesis.

Draw an algal life cycle that has alternation of generations. Label the gameophyte, sporophyte, zygote, gamete and spore stages. Indicate where mitosis, meiosis, and fertilization occur. Label each stage as either haploid or diploid.

A multicellular gametophyte, which is a haploid with n chromosomes, alternates with a multicellular sporophyte, which is diploid with 2n chromosomes.

What is the smallest unit that can evolve? Do individuals evolve?

A population is the smallest unit that can evolve. Individuals do not evolve.

What is the relationship between synamorphies and monophyletic groups?

A synamorphy allows the recognition of monophyletic groups.

What two things do ALL organisms need, metabolically? Compare and contrast phototrophs, chemoorganotrophs, chemolithotrophs, autotrophs and heterotrophs.

All organisms need energy and carbon. - Phototrophs: from sunlight - Chemolithotrophs: from organic molecules - Chemolithotrophs: from inorganic molecules - Autotrophs: self synthesized from simple molecules - Hetertrophs: from molecules produced by other organisms.

What were the 2 claims made by Wallace and Darwin as they described the process of evolution?

All species are related by common ancestry and characteristics of species can be modified from generation to generation because of natural selection.

What discoveries did Dr. Woese and his group make about: 1. Archaea and Bacteria 2. Fungus, Animals, and Plants

Although Archaea and Bacteria are very similar in structure, Archaea are more closely related to Eukaryotes than Bacteria. Fungi are more closely related to Animals than to Plants.

Looking at a simple phylogenetic tree of the 3 domains, which domain shares the most common ancestry with Domain Eukarya - Bacteria or Archaea?

Archaea

How are Archaea and Bacteria related to each other? Are Archaea more closely related to Bacteria or to Eukarya?

Archaea and Bacteria are related to each other through LUCA/ They are very similar in their structure but Archaea are more closely related to Eukarya.

Using the data in Figure 1.7, compare the diameter of the prokaryotic cell to that of the eukaryotic cell. How much bigger is the eukaryotic cell when compared to the prokaryotic cell?

At 0.1-5.0 ocular units, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10-100 ocular units.

Which domain(s) have/has peptidoglycan? What is its function?

Bacteria and Archaea, it makes up the cell walls.

What are the 3 domains that scientists use to organize living organisms? Which are prokaryotes and which are eukaryotes?

Bacteria, Archaea, and Eukarya.

How do biologists correctly write an organism's genus and species?

Capital lowercase (Italics)

Write the Cell Theory in your own words. Did the Cell Theory challenge or support the concept of spontaneous generation? Explain.

Cell Theory: All cells come from pre-existing cells. The Cell Theory challenged Spontaneous Generation and tested against it through the Pasteur Flask Experiments.

What synapormorphy defines ALL Eukaryotes (and is unique to Eukaryotes)?

Compartmentalized organelles

What is convergent evolution and why does it occur? Give 2 specific examples of convergent evolution.

Convergent Evolution: When natural selection favors similar solutions to different species. 2 examples of this are (1)winged flight in insects and birds and (2)fish-like characteristics in dolphins, sharks and whales.

What protist is responsible for algal blooms (aka "Red Tides")? How do these blooms affect humans?

Dinoflagelletes, can be lethal to humans.

Are energy sources electron donors or acceptors? In aerobic respiration, is oxygen the electron donor or acceptor. Explain.

Energy sources are electron acceptors. Anaerobic respiration is the formation of ATP without oxygen, which is the donor instead of the acceptor.

How are taxonomy and phylogeny related? Which is larger - a domain or a phylum?

Evolutionary relationships of a species can be used to build taxonomic groups. The evolutionary history of a species is a phylogeny. Domains are larger than phylums.

Why do researchers study extremophiles and how is this related to astrobiology?

Extremophiles live in very harsh conditions and astrobiologists want to use them to see if and how life survives on other planets.

Distinguish between fitness and adaptation? What organism are the most evolutionarily fit?

Fitness is how well you produce offspring and how well they produce offspring. Adaptation is a trait that increases the fitness of an individual in a certain environment.

Why do giraffes have long necks? What are the different hypotheses used to explain a giraffe's long neck? If the "food availability" hypothesis is correct, then the feeding height would be (higher or lower) when compared to the population's average height? Looking at Figure 1.8, does the data support the "food availability" hypothesis? What data supports the "sexual selection" hypothesis?

Giraffes have long necks because of natural selection. Two hypotheses of why is because they use it to reach food and fight for a mate. If the food hypothesis is correct, the feeding height would be much higher than the average height that has been recorded. The data that supports the sexual selection hypothesis is that giraffes use their necks to swing their heads at an opponent during mating season. The giraffes with longer necks win because the force is much greater.

What are the 2 conditions required for natural selection to occur? Would a trait that increases the lifespan of each individual in the population but decreases overall fertility lead to greater or lesser fitness of the affected individuals?

Individuals must vary in characteristics that are heritable and in a certain environment, certain versions of these traits can help individuals reproduce more than other versions. A trait that increases lifespans but decreases overall fertility would lead to lesser fitness in the affected individuals.

What is meta genomics and how is it done? What % of the total number of bacteria in a sample can actually be grown in lab?

Meta genomics is used to catalog all the genes in a mixed community of prokaryotes. It is done by extracting DNA from an environmental sample and then compared to known DNA sequences.

What evidence is there for the endosymbiosis theory? When sequenced, does the DNA from a mitochondrion more closely match the DNA from its cell's nucleus or a bacterial species? Explain. What do the ribosomes of mitochondria and chloroplasts resemble - prokaryote or eukaryote ribosomes? What evidence is there that chloroplasts are closely related to cyanobacteria?

Mitochondria are more closely related to bacteria than eukarya, proving the endosymbiosis theory. Mitochondria ribosomes resemble a prokaryotes ribosomes more than a eukaryotes ribosomes.

Draw the endosymbiosis theory of mitochondrial origins. What do mitochondria provide the "host" cell? What do the host cells provide for the mitochondria? How did chloroplasts originate?

Mitochondria provide the host cell with ATP and the host cell provides the mitochondria with protection. Chloroplasts originated from cyanobacteria through endosymbiosis-when a eukaryotic cell engulfed a photosynthesizing cyanobacterium that became a permanent resident in the cell.

Diagram the central dogma of genetics. Label the 3 steps in order, from DNA to protein.

Molecular machinery makes copies of DNA in a closely related molecule known as RNA, which is translated into protein.

If a phylogenetic tree lacks a scale bar, can you make inferences about how long ago two species diverged based on the length of each branch?

No, different branch lengths mean different things.

Do most bacteria cause disease? Diagram Koch's postulates and be able to explain how this process is used. Why are some bacteria pathogenic? Why is antibiotic resistance a growing concern?

No, only a small percentage of bacteria are pathogenic. To establish a causative link between sickness and a certain type of organism, the four criteria must be met. (1.) The microbe must be present in the sick individual and absent in the healthy one. (2.) The organism must be isolated and grown in a pure culture. (3.) The organism from the pure culture must be injected into a healthy animal to see if the symptoms return. (4.) The organism should be isolated from the diseased animal and cultured again to see if it's the same. Toxins are proteins that are in some bacteria that cause humans to get sick while endospores are released from the bacteria that also make us sick. Both are only present in some bacteria. Toxins are proteins that are in some bacteria that cause humans to get sick while endospores are released from the bacteria that also make us sick. Both are only present in some bacteria. Antibiotic resistance is a growing concern because the pathogenic bacteria is becoming immune to the medicine, meaning that soon it won't work at all.

Are science and religion in conflict with one another? What types of questions are answered by each?

No, they are able to explain things to people when one fails to do so.

If you have a node with 2 branches, does it matter which branch you write on top and which you write on the bottom (or left/right if it is going vertically)? Why is this an important detail to consider as you evaluate phylogenetic trees?

No, they are so closely related that they can be interchanged. This is important because you need to know that all of the nodes can be rotated, there's no true order, as long as they stay on that node.

What three features do all eukaryotes alive today share?

Nucleus, DNA inside the nucleus, and compartmentalized organelles.

On a phylogenetic tree, are the taxa at the nodes, roots, or tips of the tree? Why is that important?

On a phylogenetic tree, taxa are at the tips to show the most recent organisms. This shows which species are related to one another and how closely they are related to one another.

What is an outgroup and why is it important to include when evaluating several species and starting the process of drawing a phylogenetic tree?

Outgroups are used to establish the relative timing of evolution of each character. It is important to include because it is can tell where character traits ceased and where the evolution of a trait began.

Outline Pasteur's swan-necked flask experiment. What was the one variable that differed between the test and experimental groups? Why is it important to test one variable at a time?

Pasteur was comparing the ideas of spontaneous generation and cell theory against each other. To do this, he first set up an experiment where he had a straight neck flask filled with broth. He boiled all of the bacteria out of the broth and left it to sit. After a couple of days, there were bacterial cells. He then took a straight necked flask and bent it into a swan necked flask. He then performed the same experiment, boiling broth in both flasks and leaving them. After a couple of weeks, the straight necked flask had bacterial cells in it again, but the swan neck did not. Instead, the cells clumped inside the bend in the neck. It's important to test one variable at a time so that the experiment isn't overwhelmed and you can keep track of each variable that you're testing.

Internal membranes are needed for a cell to complete which process?

Photosynthesis

What are the 2 groups of cells named (based on presence or absence of a nucleus)?

Prokaryotes and Eukaryotes

How long have Prokaryotes been on Earth compared to Eukaryotes?

Prokaryotes have existed on Earth since at least 3.8 billion years ago. The earliest evidence of eukaryotes is from 2.7 billion years ago.

Do protists make up a monophyletic or paraphyletic group? Explain. Is there a synapormorphy that defines protists?

Protists are not a monophyletic and there are not synapomorphies that define protists.

Draw an aquatic food chain, describing how protists influence the carbon cycle. Why would researchers want to add iron to the open ocean? What are some concerns with this plan?

Researchers want to add iron to the ocean to slow global warming by having the protists produce more oxygen. The concern is that too much iron can cause an algal bloom and everything else will die.

Describe two different methods scientists use in bioremediation.

Scientists fertilize contaminated sites to encourage the growth of prokaryotes that degrade toxic compounds, and they add specific prokaryotes to the ground to help as well.

Compare and contrast sexual and asexual reproduction. What are the advantages and disadvantages of each mode of reproduction? What is the relationship between reproductive mode and environmental stress? Does a stressful environment favor sexual or asexual reproduction? Explain.

Sexual: Production of new living organisms by combining genetic information from 2 individuals of different types. Advantage: More variation to assist with survival. Disadvantage: Requires 2 parents. Asexual: Offspring arise from a single organism and inherit the genes of that parent only. Advantage: Allows plants to reproduce quickly Disadvantage: No variations The more environmental stress there is, the more likely that there will be more sexual reproduction and vice versa with asexual reproduction. A stressful environment favors sexual reproduction because more variation gives the new organism the chance to survive.

If several taxa are extinct on a phylogenetic tree, does that indicate those taxa are the ancestors of modern taxa?

Sometimes, not always.

What traits distinguish Ameobozoans as a group? How do these organisms "eat" and move?

Species of Ameobozoa may be either shelled or naked, and cells may possess flagella. Free living species are common in both salt water and freshwater as well as soil, moss, and lead litter. These organisms have thick pseudopods, bulges in the cell that helps them move and eat.

Describe the DNA found in a bacterial cell? (Is it single or double stranded? Is it circular or linear? Where is it found?) How does a plasmid differ from a chromosome? Would you expect the genes for a plasma membrane to be on the chromosome or plasmid? Why?

The DNA is a double helix that is coiled in on itself to fit into the tiny space within the nucleoid. Plasmids contain genes but are physically independent of the cellular chromosomes.

Why is the Germ Theory of disease considered the foundation of modern medical care? What are the 3 main ways infectious diseases can spread?

The Germ Theory of disease laid the foundation of modern medical care mainly by promoting sanitation. Infectious disease can be spread person to person, from the bite of an insect or animal, and by drinking contaminated water or eating contaminated food.

What is nitrogen fixation and where does it happen in terrestrial environments?

The chemical processes by which atmospheric nitrogen is assimilated into organic compounds, especially by certain microorganisms as part of the nitrogen cycle. It happens within the soil, when atmospheric nitrogen is converted to ammonia by an enzyme called a nitrogenase.

What is the goal of an enrichment culture?

The goal of an enrichment culture is to find out what organisms live in extreme environments that scientists cannot get to.

What is the oxygen revolution? Why is aerobic respiration more efficient than anaerobic respiration? Where do scientists think that the first free oxygen came from on Earth?

The oxygen revolution happened about 2.5 billion years ago. Oxygen was produced by photosynthetic organisms, mostly cyanobacterium. Aerobic respiration produces more ATP than anaerobic respiration.

Diagram the life cycle of Plasmodium. Indicate the sexual and asexual stages of this life cycle. Which stage (sexual or asexual) increases the diversity of the offspring produced? Which stage greatly increases the total number of offspring produced? What disease does Plasmodium cause? What is the global impact of this disease?

The sexual stage increases the diversity of the offspring produced. The asexual stage increases the total number of offspring produced. Plasmodium causes malaria. In 2016, an estimated 445,600 people died of malaria.

Microscopy has allowed researchers to group brown algae and water molds (e.g. causative agent of the Irish potato famine) in the same group (Stramenopilans) because they have similar _____.

They have a similar type of flagellum.

Why are endospores and toxins associated with pathogenic bacteria?

Toxins are proteins that are in some bacteria that cause humans to get sick while endospores are released from the bacteria that also makes us sick.

Compare and contrast Unikonta and Bikonta. Which structural feature distinguishes these two groups?

Unikonta are formed by amoebozoa and the opishokonta (fungi and animals) - form a monophyletic group. The other 5 major lineages form a monophyletic group called bikonta.

What is a nitrate pollution and how does it lead to large dead zones in the Gulf of Mexico?

Water contamination caused by the presence of excessive amounts of nitrates washed out from inorganic fertilizers. Rain washes nitrogen and phosphorous nutrients from the fertilizer into nearby streams and rivers, which eventually feeds into the Gulf of Mexico.

Why did Carl Woese and his colleagues compare ribosomal RNA to build their phylogenetic trees? Could they have used the gene for a protein like keratin or pilin? Why or why not?

Woese and his colleagues compared ribosomal RNA to build their phylogenetic trees because it is very simple and every organism uses ribosomes to make proteins. They couldn't have used the gene for proteins like keratin and pilin because not every organism produces those. However, all of them have some sort of ribosomal RNA.

If you continuously bred large-pod peas to other large-pod peas, would you expect the average pod size to get smaller or larger? Why? What is this process called?

You would expect the average pod size to get larger because it is a desirable heritable trait due to natural selection.