Bio Exam 2

1. What does the abbreviation HIV stand for? AIDS?

Human Immunodeficiency Virus Acquired Immunodeficiency Syndrome

HIV

Human Immunodeficiency Virus Virus that affects humans, people that are affected lose their immune system and are unable to fight off infection >95% of people who are infected and are untreated will develop AIDS 1.6 million people die every year

Human affect on nitrogen cycle

Human alterations of the nitrogen cycle have approximately doubled the rate of nitrogen input to the cycle (via the Haber-Bosch process) Fertilizer runoff can cause eutrophication Excess nitrates in drinking water are a health hazard for infants Burning fossil fuels also releases nitrogen oxides which can react with rain to form acid rain (nitric acid)

In the 1940s, biologist Adolph Murie studied survival in Dall sheep in what is now Denali National Park in Alaska. He found that Dall sheep that survive their first year of life have a high probability of surviving until they are around 9 years old; after that, they rapidly become easy prey for wolves and die at a very high rate. This pattern BEST fits a Type _____ survivorship curve.

I

Influences on primary production

In terrestrial systems, linear relationship with annual precipitation Temperatures- Evapotranspiration rate can predict aboveground primary production nutrients(nitrogen and phosphorus) Can be limiting factor Liebig's law of the minimum

masting

Synchronous production of progeny satiate predators and allow some young to survive Seed herbivory Periodical cicadas

The biome of Pittsburgh is best described as

Temperate deciduous forest

Temperate grassland

Temperature about the same as deciduous forest but drier Humans have completely dedicated this to agriculture A lot of grasses a lot of fire not a ton or rainfall Before human settlement, this biome occupied most of the midwestern United States and south central Canada, dominated by blue-stem and buffalo grasses. Disturbance by fire helps to maintain grass populations in this biome. Lack of precipitation also prevents many species of tree from growing, and those trees that grow are usually in low areas with more available moisture. Because of active decomposers, soils accumulate nutrients, providing some of the most productive agricultural lands in the world. Before colonization by humans, temperate grasslands of North America supported abundant and diverse grazers, including bison, pronghorns, horses, and mammoths. Horses and mammoths became extinct 11,000 years ago, and herds of bison and pronghorn dwindled in the nineteenth century. Burrowing grazers such as prairie dogs remain relatively common, although population sizes have fallen; these species support predators such as ferrets, badgers, foxes, and birds of prey.

coding system to describe the interactions between species

(+) = benefit for a species; (-) = the species suffers; 0 = no effect

Interactions among species, such as competition and consumption, have two main outcomes:

(1) They affect the distribution and abundance of the interacting species (in the short term) (2) they are agents of natural selection and thus affect the evolution of the interacting species often causing coevolution (in the long term).

Alveolates

(a) The arrows point to alveoli, flattened vesicles just beneath the surface of the cell that give alveolates their name. (b) Dinoflagellates have cell walls made of interlocking plates of cellulose. (c) A ciliate has many short flagella, or cilia, that line the cell.

Out-of-Africa Hypothesis

(aka, African replacement. H. sapiens evolves in Africa, and then migrates out of Africa to populate the earth) developed in 1987 from another study from Allan Wilson's laboratory, instead suggested that modern humans arose much more recently from Homo ergaster descendants (sometimes called Homo heidelbergensis) in Africa, about 200,000 years ago. This hypothesis implies that there was one evolutionary origin for modern human traits. supported by data from mtDNA correct one

Multiregional Hypothesis

(an ancestor of H. sapiens migrates from Africa, colonizes other regions, and all populations evolve into H. sapiens together via gene flow)suggested that modern humans, Homo sapiens, derive from the Homo ergaster populations that spread around the world starting about 2 million years ago, implying that different Homo ergaster populations throughout the Old World evolved in parallel, with some limited gene flow among them, to each produce modern H. sapiens populations. In short, modern human traits evolved convergently in multiple populations.

What is the per capita growth rate (=r). Be able to perform a simple calculation to derive r.

(△N/△T)/N1 R= positive = growing R= zero = stays same R= negative = shrinking

Mutualism

+/+ Close associations between species in which both species benefit

consumption

+/- herbivory parasitism predation

Desert

30 degree north and south Hot and dry Strong convergent evolution Not a lot of leaves, adapted to store water Desert occurs in continental interiors around the world north and south of the equator from 15° to 35° latitude. Wind patterns prevent this biome from receiving more than a few centimeters of precipitation annually. Deep-rooted plants, like cactus and euphorb plants, are adapted to store water. Primary production is low, and soils are poor in nutrients but may have high surface salt due to evaporation. Given the low rates of primary production, primary consumers tend to be small, and include diverse lizards as well as rodents. Predators include snakes, cat species, coyotes, and birds such as owls, hawks, and eagles

Homo neanderthalensis

300,000 - 30,000 years ago *confused* -Similar to modern humans—muscular, fully erect, dexterous, large brains. Body type adapted to cold weather. -Developed ritualistic burial ceremonies -Hybridized with Homo sapiens? Evolved in some parts of Europe Good for cold weather Bury their dead "death awareness" Cave men Compared to human crania- their brains are bigger

Be able to identify the different biomes discussed in your book based on their physical characteristics.

:)

Australopithecus afarensis

A basic trend in human evolution is increasing brain size and decreasing sexual dimorphism

fighting

Horns and antlers can be used in defense

8. When did humans populate the Americas?

15,000 years ago

Amoebozoa

A superkingdom of eukaryotes with amoeba-like cells that move and gather food by means of pseudopodia.

Competition

-/- detrimental to both of the individuals or species involved because it reduces available resources occurs when niches overlap

Australopithecines

-Appeared 4 million years ago as evidenced by fossils -Walked upright -Larger brains than other apes, but still pretty small. -2 types: gracile, robust

Ardipithicus ramidus

-Appeared 4.4 million years ago as evidenced by fossils. Perhaps as early as 6 million years. -Walked upright -Had unusual feet: seemed to be adapted for both upright walking and climbing. d. only recently described (October, 2009)

Two graduate students are trying to identify new species of bacteria based on the criteria of Ernst Mayr. They are having a lot of trouble with this method, and then suddenly realize that they can't use Mayr's definition of a species for identifying bacteria species. Why not? (Select all that apply.)

-Bacteria do not reproduce sexually and/or do not undergo meiosis. -DNA can be passed between bacteria of different species by means of horizontal gene transfer.

Bacterial cell

-Plasmid DNA -Chromosomal DNA -Cytoplasm -Ribosome -Flagellum -Plasma membrane -Cell wall

Tree of life

-Prokaryotic cell organization -Eukarya(Eukaryotic cell organization)/Archaea -Bacteria

Because energy transfer is not 100% efficient across trophic levels, a maximum of about ____________% of energy and biomass available at one trophic level is available at the next.

10

What specific morphological changes occur in the hominin lineage and in what order do they appear?

-The foramen magnum, the hole in the base of the skull through which the spinal cord extends, is repositioned so that the human skull is balanced directly on top of the vertebral column. -The human spine is approximately S-shaped, ensuring that the weight is directly over the pelvis. -The pelvis is extensively reconfigured for an upright posture, and the internal organs can sit within it as though it were a kind of basin. The legs are longer, enabling long stride length and therefore efficient locomotion. The anatomy of the legs is also altered—the legs are directly under the body. -The human foot is narrower and has a much more developed heel and a larger big toe, features that contribute to a springier foot.

3. What is: -transduction -Transformation -Conjugation? -Why are these important to prokaryotes?

-Transduction: DNA is transferred from a donor to a recipient by a virus -Transformation: DNA released into the environment by dead cells is taken up by a recipient cell -Conjugation: DNA from a donor cell is transferred through a pilus into a recipient cell, the pilus connects the donor and the recipient, "bacterial sex" -these are important to prokaryotes because this is their only way of exchanging genetic material, similar to their reproduction through binary fission

Conjugation process

-bacterial cell synthesizes a thin strand of membrane-bound cytoplasm (pili) that connects to other cells -this process can transfer cells from one cell to another spreading novel genes throughout a population -genes that confer resistance to antibiotics are a well-studied example of horizontal gene transfer by conjugation -direct cell-to-cell transfer of DNA, usually in the form of a plasmid

Bacterial viruses

-bacterial cells are susceptible to infection by a variety of viruses known as bacteriophages -exhibit 2 reproductive cycles: lytic and lysogenic

mitochondria

-closely resemble free-living bacteria in organization and biochemistry -contain DNA that confirms their close phylogenetic relationship to a form of bacteria—in this case proteobacteria -mitochondria originated as endosymbiotic bacteria -small genome -related to alphaproteobacteria

Origin of Eukaryotic cells

-comes from the symbiosis between an archaeon and protobacterium -Two hypotheses for the origin of the eukaryotic cell

The HIV genome

-encodes 9 genes and multiple proteins -10,000 bp long

Viruses

-genetic entities that infect cells -not alive because they cant replicate by themselves -have intercellular and extracellular portion of their lifecycle -come in may different shapes and the genome can vary as well -They can kill the cell they infect, leading to disease or death, or cause the cell to divide uncontrollably, leading to cancer. -The effects of a virus are ever changing because of the mutation rate and recombination found within them. Viruses with segmented genomes can sometimes exchange whole segments and others can evolve rapidly because of the high mutation rate of their genome.

Primates

-grasping hands: precision grip and power grip -Binocular and color vision with overlapping fields of view -Large brain allowing complex social systems -nails instead of claws

3. What is a hominoid? A hominin?

-hominoid- a member of the biological superfamily Hominoidea, including all modern great apes and humans and a number of their extinct ancestors and relatives. -Hominin - the group consisting of modern humans, extinct human species and all our immediate ancestors (including members of the genera Homo, Australopithecus, Paranthropus and Ardipithecus).

Transduction

-horizontal gene transfer by means of viruses -transferred from a donor to a recipient by a virus

Structure of HIV

-its an enveloped retrovirus -RNA -Reverse transcriptase -core protein -matrix protein -lipid bilayer -surface glycoprotein -transmembrane glycoprotein

diversity in eukaryotes

-membrane dynamics -Compartmentalized metabolism -Genome organization -Genetic diversity by means of sex -Life cycles

What are two local effects on basic climate patterns?

-mountains: the higher you go in a mountain the colder it gets, rain shadows when moist air is moving toward a mountain range so it raises in atmospheric, temperature rises and one side of the mountain is wet and the other side is dry -proximity of land to large bodies of water: climate is much more moderate closer to the ocean -ocean currents: warm or cold, cold-productive places where water is bringing nutrients up from the bottom of the ocean, warm-coral reefs

Eukaryotic cell

-nucleus is defining character -much larger than prokaryotes -cytoskeleton -nuclear membrane -nucleus -Endoplasmic reticulum -Mitochondrion -golgi apparatus -cell membrane

21. Know the main eukaryotic "supergroups". Which one includes the plants? The animals?

-opisthokonta: animals -chanoflaellates: sister taxon to animals -amoebozoa -archaeplastids: plants -stramenopiles -alveolates -rhizarians -excavates

Type I

-rate of loss of juveniles low and most individuals lost later in life -most mortality is late in life. Large animals such as humans, elephants and whales curve down

The life cycle of HIV in a human cell

-the virus integrates into the chromosome of a cell -Virus encounters Helper T cell - makes specific molecular contacts with proteins of the surface of the cell- contents are dumped into cell Double stranded copy of the viral genome Integrase inserts it into the chromosome of the cell

Commensualism

0/+ Interaction where one species benefits and the other isn't affected at all Water buffalo eats grass which insects come up from making it easier for the birds to eat the insects no benefit for buffalo

What are the four basic factors that affect the size of a population?

1) Birth Rate-the number of live births 2) Death Rate-the number of deaths 3) Immigration-the number of people moving into a country. 4) Emigration-the number of people leaving a country.

Why anti RT therapies fail

1. Transcriptional errors made by HIV RT lead to mistakes in the sequence of HIV, in particular the RT gene itself. There is variation in the viral sequence population. RT is a very sloppy polymerase. It makes a mistake every 1/10,000 nucleotides it incorporates. This is equivalent to a mistake every time a viral genome is copied. Therefore, every HIV virion in the body is likely to be different. 2. Variation in RT sequences lead to variation in RT polymerase function. 3. Some virions end up replicating better than others because their RT is resistant to nucleotide analogues. Natural Selection takes place for drug resistant virions. 4. These mutations are passed to mutant offspring which replicate better than wild-type viruses. 5. The HIV population in a patient becomes resistant to RT drug treatment. The therapy fails.

Average temperature to annual precipitation: 1. Hot- most precipitation to least 2. Moderately hot-most precipitation to least 3. Cold: most precipitation to least

1. Tropical rain forest (most rain fall), Tropical deciduous forest, tropical grassland, hot desert 2. Temperate rain forest, temperate deciduous forest, temperate grassland, cold desert 3. Taiga, Tundra

HIV United States

1.242 million people 13% undiagnosed Most are black gay men

Homo erectus

1.8 million years ago to 500,000 ya. -Large brain -More socially advanced -Sophisticated stone tools aided in hunting -Used fire -migrated out of Africa as far east as Indonesia -First species to migrate and populate other parts of the world

A single herbivore can affect many species

A community is the set of all populations found in a given place. Populations in a community are tied together by the various interactions that secure their spot in a food web as well as by their physical location. But when we look at the details of where particular species occur, it turns out that almost no two species have exactly the same geographic distributions. This is partly a result of competitive exclusion. Even within a local habitat like a meadow, species have different distributions that may reflect differences in soil moisture or patterns of sunlight exposure.

Stramenopila

A eukaryotic superkingdom including unicellular organisms, giant kelps, algae, protozoa, free-living cells, and parasites; distinguished by a flagellum with two rows of stiff hairs and, usually, a second, smooth flagellum. (most are photosynthetic)

Archaeplastida

A eukaryotic superkingdom of photosynthetic organisms; includes the land plants (photosynthetic) three major phylogenic groups

Alveolata

A eukaryotic superkingdom, defined by the presence of cortical alveoli, small vesicles that, in some species, store calcium ions.

Metapopulations

A group of populations linked by immigrants is a group of independent populations connected by occasional immigrants that travel through corridors. This can be illustrated by populations of White-breasted nuthatches. The White-breasted nuthatches that occupy a particular tree grove contact one another more frequently than they do individuals of other tree groves, and so each group is considered a local population. Occasionally, a few migrants might move from grove to grove, enabling gene flow between local populations

Lytic vs Lysogenic

A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA.

bacteriochlorophyll

A light-harvesting pigment closely related to the chlorophyll found in plants, algae, and cyanobacteria.

Chaparral

A little more water than desert Mediterranean climate Like that of deserts, the distribution of chaparral reflects a narrow range of climate conditions and occurs on the western edge of continents from 32° to 40° latitude north and south of the equator. Precipitation ranges from 30 to 75 cm per year, usually falling in a period of 2 to 4 months. Typical plants are herbs that die and reseed themselves every year, evergreen shrubs, and small trees. Olives, eucalyptus, acacia, and oaks are typical woody species, always drought resistant and often adapted to withstand fire. Limited precipitation means soils are not rich in organic materials

Tropical Rain Forest

A lot of rain Very warm Most productive terrestrial ecosystems on earth Most terrestrial species live here The most diverse of all terrestrial biomes, tropical rain forests extend north and south of the equator from 10° N to 10° S. Annual precipitation is commonly more than 250 cm, and tree diversity alone often exceeds 300 species per hectare. Trees grow tall, and many have buttressed roots for support. Lianas and other epiphytic plants are common. Most leaves are evergreen and leathery and many have long pointed tips that facilitate drainage of excess moisture. Because of the high temperatures and heavy rains, decomposition by fungi and bacteria is rapid, preventing the accumulation of organic materials in clay-rich or sandy soils. There are few large grazers, but smaller mammals such as primates, bats, and rodents are highly diverse, as are birds, snakes, and lizards. Insects are especially abundant and diverse. Ants alone make up as much as 30% of animal biomass in rain forests, and they are the principal grazers on rain forest trees.

chemoautotrophs

A microorganism that obtains energy from chemical compounds, not from sunlight.

cyanobacteria

A monophyletic group of bacteria capable of oxygenic photosynthesis. -the only photosynthetic bacterial lineage

Cranium size increases

A number of trends can be seen when looking over the entire record. Body size increased, as did the size of the cranium (which is inferred to also include the size of the brain).

autotrophs

A organism capable of making nutritive organic molecules from inorganic sources via photosynthesis (involving light energy) or chemosynthesis (involving chemical energy) (inorganic molecules, CO2)

fermentation

A process of breaking down pyruvate through a wide variety of metabolic pathways that extract energy from fuel molecules such as glucose; the partial oxidation of complex carbon molecules to molecules that are less oxidized than carbon dioxide

Opisthokonta

A superkingdom that encompasses animals, fungi, and related protists

Where did Homo sapiens originate?

Africa

Where did humans humans evolve?

Africa

Where do we look for fossil hominins?

Africa

Which human populations have the HIGHEST levels of genetic variation?

African populations

chemoheterotrophs

An organism deriving energy by ingesting intermediates or building blocks that it is incapable of creating on its own (animals, fungi, prokaryotes)

heterotrophs

An organism that is unable to synthesize its own organic carbon-based compounds from inorganic sources, hence, feeds on organic matter produced by, or available in, other organisms. (organic molecules, glucose)

chemotrophs

An organism that obtains energy mainly from carbon dioxide and from other inorganic chemicals through a process called chemosynthesis (chemical compounds)

photoheterotrophs

An organism that uses the energy from sunlight to make ATP and relies on organic molecules obtained from the environment as the source of carbon for growth and other vital functions. (microorganisms)

photoautotrophs

An organism, typically a plant, obtaining energy from sunlight as its source of energy to convert inorganic materials into organic materials for use in cellular functions such as biosynthesis and respiration (plant, algae, cyanobacteria)

phototrophs

An organism, typically a plant, obtaining energy from sunlight as its source of energy to convert inorganic materials into organic materials for use in cellular functions such as biosynthesis and respiration (sun)

Cellular

Antigen activate cytotoxic T cells kill cells

A three-branched tree of life, based on sequence comparisons of the genes for the small subunit of ribosomal RNA

Archaea and Bacteria form distinct branches, although they inherited prokaryotic cell organization from a common ancestor. Some data suggest that eukaryotes arose within the Archaea, making this domain paraphyletic.

Outline the basic pattern of human evolution based on the fossil record. Include in your discussion the following species: Ardipithecus ramidus; the "Gracile" Australopithecines (as a group); the "robust" Australopithecines (as a group); Homo erectus; Homo sapiens. Finally, comment on whether or not you believe sexual selection is at work in Homo sapiens and back up your statement with at least one piece of data.

Ardipithecus ramidus is the oldest known ancestors of humans. They appeared between 4.4 and 6 million years ago and walked upright and were adapted to walking and climbing. The gracile australopithecines had larger brains than previous apes and appeared 4 million years ago and walked upright They had smaller features such as smaller hands, feet, and jaw. The robust australopithecines, which appeared at the same time as the gracile australopithecines, had bigger cheekbones and wider teeth. The robust australopithecines left no living descendants. The Homo erectus lived 1.8 million years ago and began to adapt more human characteristics. For example they had larger brains and were more sophisticated using tools and fire. They were also the first ones to migrate out of africa. Homo sapiens appeared 200,000 years ago and are direct ancestors of modern humans and the largest cranium out of all. Sexual selection promotes traits that increase an individual's access to reproductive opportunities. I believe that humans do have sexual selection because there could be features that attached females to mate with males of that certain feature such as male peacocks with there colorful feathers. Females could have picked males based on physical appearance such as muscle built instead of just random mating.

Plant defenses

Array of unusual and powerful chemicals secondary metabolites mechanical defenses like thorns and spines

Elevation and other local features can affect climate

As air rises over the mountain, it cools, releasing its moisture as rain. Once over the mountain, the air descends, warming and taking up moisture.

4. What are the three domains of life?

Bacteria Archaea Eukarya

What mediates anoxygenic photosynthesis?

Bacteriochlorophyll

You are adding specimens to your insect collection and you net what you think is a wasp. When you examine the specimen more closely in the lab, you discover that it is a moth that looks very similar to a wasp. This is an example of

Batesian mimicry

Did H. sapiens hybridize with H. neanderthalensis?

Because Neanderthal mtDNA does not fall within the human family tree (red), we initially believed that Neanderthals and our ancestors did not interbreed. However, studies of the full Neanderthal genome revealed that there was interbreeding, probably in the Middle East as H. sapiens first emerged from Africa about 60,000 years ago.

Why do we think that male Neanderthals mated with non-African ancestral Homo sapiens?

Because Neanderthal nuclear DNA sequences are present in the human gene pool, and Neanderthal mtDNA sequences are not.

extracellular phase

Before it invades a host cell, a virus is in the 'extracellular state'. An extracellular virus is called a virion (vie-ree-on). In this form, the virus consists of a protein coat (capsid) surrounding nucleic acid. In addition, some viruses have phospholipid envelope surrounding the capsid. This outermost layer provides protection and recognition sites for host cells.

Chemical defense

Bombardier beetle ejects hot spray Aposematic coloration, or warning coloration, which advertises an organism's unpalatable taste Many tropical frogs have bright coloration to advertise their skin's lethality

Fusion of enveloped virus and host cell

Both HIV particles and human immune cells have specialized proteins in their membranes HIV's envelope protein binds to CD4 and a co-receptor The binding event causes the membranes to fuse, allowing the viral capsid to enter the target cells to start an in infection cycle

Eukaryotic Tree of Life

Branches with photosynthetic species (shown in green) are distributed widely. Additional branches, including animals, foraminiferans, radiolarians, and ciliates, contain species that harbor photosynthetic symbionts. Dashed lines indicate a high degree of uncertainty.

The eukaryotic tree of life showing major groups

Branches with photosynthetic species (shown in green) are distributed widely. Additional branches, including animals, foraminiferans, radiolarians, and ciliates, contain species that harbor photosynthetic symbionts. Dashed lines indicate a high degree of uncertainty.

6. What is CD4? What is CCR5? What is delta 32?

CD4- glycoprotein found on the surface of immune cells CCR5- protein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines D32- deletion mutation of a gene, mutant of the CCR5 allele (resistant to HIV)

Cryptic coloration

Camouflage Stick insects mimic branches Sea horses adopt body coloration to mimic habitat

Why is energy lost between trophic levels?

Caterpillar eating a leaf, consuming 1000 J of energy, 500 J are lost to feces Of the energy of it can use, 320 of it go to cellular respiration 180 J for growth Only 18% used for making more caterpillar

10. Where did HIV apparently originate (geographically)? From what species did HIV probably transfer to humans?

Central Africa Chimpanzees

Chain lengths short in most food webs

Chain length refers to the number of links between the trophic levels involved Usually less than 6 levels Based on laws of physics and chemistry

Symbiosis

Close interaction between species that live together, often interdependently.

uniform

Competition may cause this pattern May also result from social interactions [animal behavior]

Where do we look for our closest relatives?

Darwin thought it should be Africa

Herbivores can overcome plant defenses

Detoxify using 2 pathways oxidation conjugation

Atmospheric circulation

Differences in temperature occur due to latitudinal variations in incoming solar radiation In higher latitudes the sun's rays hit the Earth obliquely and are spread out over more of the planet's surface than they are in equatorial areas Generally, temperature increases as the amount of solar radiation increases

age structure

Differences in the age structure of other species can reveal threats from various sources. For example, the age structure of fish populations can be affected by the preferential capture of the largest fish, a recurring problem in commercial fisheries. Because the larger fish produce most of the eggs each year, this pattern can eventually lead to a rapid decrease in the population. The curve representing the growth of a population of long-lived Pacific rockfish that is not exposed to fishing shows many individuals close to and past the age of 10 years, when reproductive ability starts to climb. In fished populations, the curve shows a sharp decline of individuals older than 6 years because mostly older and larger fish are caught. Because these older fish produce most of the eggs and young fish, the annual reproductive effort of fished populations is severely affected by their removal.

The fate of the Neanderthals

Disappeared from Europe around the time of modern humans Modern humans outcompeted them

Drug Treatment for HIV: Why does it fail in the long run?

Drug treatment usually tries to target some vital viral function. Two general types available: anti-reverse transcriptase (RT) and protease inhibitors virus comes back

What Causes Seasonality in Weather?

Earth's tilt

7. Where is the geographic origin for the species Homo sapiens?

East Africa

Site

Ectoparasites Endoparasites

Abiotic enviornment

Energy come from the sun, captured by primary producers stored in carbon bonds, fed upon by consumers When both of these things die recycled by decomposers

Where did HIV come from?

Epidemiological data suggests Central Africa as the source of HIV HIV infecting us came from chimpanzees How this happened: transfer from chimpanzee to human from bushmeat [hunting] Probably happened about 3 separate times, at least

Discuss the evolution of eukaryotes in terms of symbiosis. In your answer, describe what kind of symbioses has taken place. Explain whether or not these events occurred once or many times and what the evidence to support those claims is.

Eukaryotes evolved through symbolism is the close interaction between species that have evolved over long periods of time. The kind of symbiosis that has taken place is the form of endosymbiosis which is a symbiosis in which on organisms lives inside the other. An example of this is the chloroplast and the mitochondria. The chloroplast has structures similar to cyanobacteria in the fact that they have DNA organized in circles and undergo oxygenic photosynthesis. They are said to be like specialized cyanobacteria that can't live on their own. The mitochondria are very similar to proteobacteria, which also has a circular chromosome like mitochondria. Genes on chromosomes in both the mitochondria and the proteobacteria have many genes that seem to match.

Hypothesis 1

Eukaryotic cells evolved from an archaeon-like prokaryote and only later incorporated the proteobacterial cell that became a mitochondiron

Hypothesis 2

Eukaryotic cells evolved from symbiosis between an archaeon and a proteobacterium. The proteobacterium became a mitochodnrion

Compare and contrast the exponential and logistic population growth models. In your discussion make certain that you explain the terms used in the models and how they affect the behavior of each model.

Exponential growth is resources are not limiting the growth so there is a very fast growth rate. Logistic growth is when resources are limited causing limits to growth rate. Exponential growth has a birth rate greater than 0 because they are increasing rapidly. The r in this equation represents the rate of growth per capita, which is births - deaths. If this is positive there is an increase in the population. When this is graphed it has a J shaped curve. When there is a logistical growth graph this means that there is a carrying capacity. This is the more realistic graph because it depicts that there are limited resources. The K in this equation represents the carrying capacity. The carrying capacity is what makes this graph have an S shape to it. At the beginning it has an exponential growth similar to that of a J graph but as it increase it hits equilibrium.

Experimental patches of habitat

Extinction is less of a problem if links are present In general, small populations become extinct more often than large populations. They are more susceptible to random factors that increase mortality, such as weather, natural disasters, or predation. However, as long as not all local populations become extinct at the same time, these populations can recolonize old habitats or find new habitat patches, ensuring survival of the metapopulation. Experiments with patches of moss growing on boulders showed that the size and connectedness of the patches of moss affected the probability that species of arthropods inhabiting the moss would become extinct. Researchers cut large patches of moss into several small fragments and sampled the number of insect species in each patch over time. Isolated patches showed decreases in species diversity, up to 40% in 1 year. Some species became extinct. However, when nearly isolated moss patches were left with a narrow corridor of moss connecting them, the rate of extinction was lower. Even narrow corridors of habitat can allow species to move between patches of habitat and prevent extinction, or serve to reintroduce species that become locally extinct.

What determines what an ecosystem looks like?

Flow of energy through ecosystems Cycling of chemical elements within ecosystems

Succession is the community response to disturbance

Following disturbance or the appearance of a new habitat, a community goes through a series of changes. These changes involve a predictable sequence of species that colonize and then transform the community, in what can appear to be a linear process of maturation. This process of species replacing each other in time is called succession. In new habitats or following disturbance, species colonize and transform the habitat in a predictable sequence that reflects the adaptations of participating species forming a mature assembly commonly called a climax community. A climax community is one in which there is little further change in species composition.

The latitudinal diversity gradient refers to what pattern of species diversity?

For many kinds of organisms, species diversity is greatest near the equator and lowest near the poles.

net primary productivity

GPP-R Amount of energy available to primary consumers Measured in calories

Birth of competitive exclusion principle

Gause worked with 3 protists - Paramecium aurelia, Paramecium bursaria, and Paramecium caudatum Grown separately all 3 grew logistically When P. caudatum and P. aurelia grown together, P. caudatum went extinct When P. caudatum and P. bursaria grown together, neither went extinct Concluded that 2 species with exactly the same requirements cannot live together in the same place and use the same resources, that is, occupy the same niche

Nitrogen cycle

Global but strongly local Limiting nutrient because it is essential component of proteins, nucleic acids, and chlorophyll 78% of Earth's atmosphere is N2

Biome distribution

Globally, the distribution of biomes corresponds closely to climate. This correspondence reflects the need for plants to balance CO2 intake against water loss, a balance commonly struck by means of adaptations in the shape and physiology of leaves, stems, and roots.

agility

Grasshoppers powerful jumping ability

Why are some people resistant to infection with some strains of HIV?

HIV entry into cells requires the presence of the CCR5 co-receptor People who express the Δ32 allele of CCR5 are resistant to infection There are different alles for the chemokine: delta 32 allele - people are resistant to the infection Delta 32: Deletion in sequence that causes them to make a mutant form of the protein which cant bind the protein

2. What kind of virus is HIV? What kind of genome does it have?

HIV is an enveloped retrovirus Ca. genome, 1000bp long

3. What cells does HIV target? How does it target these specific cells?

HIV targets helper T-cells process of replacing virus kills cells

Global patterns of atmospheric circulation and precipitation are influenced by solar energy

Hadley proposed model based on one large convection cell in each hemisphere Based on warmth at equator causing air to rise and flow north and south toward poles Air would cool and fall, flowing back to the equator

Density-independent factors

Happen regardless of how big population is Mortality factor whose influence is not affected by changes in population size or density Generally physical factors - weather, drought, flood, fire

Gibbons and orangutans are from Asia. Gorillas and chimpanzees are from Africa. How was Charles Darwin able to hypothesize that humans evolved in Africa?

He understood that humans and gorillas/chimpanzees are more closely related than humans and orangutans based on anatomical criteria.

5. What are helper T cells? What role do they play in the immune system?

Helper T cells are central to both immune system responses CD4+ and T4 secrete many cytokines that stimulate other immune system cells

Plant/herbivore "arms race"

Herbivory can be lethal to small species Usually not lethal to larger species Generalist herbivores can feed on many plant species Specialist herbivores restricted to 1 or 2 host plants

Primary productivity varies

Highest in tropical rainforests Decreases progressively toward the poles May cause the latitudinal gradient of species richness Greatest marine production occurs on coral reefs where temperature is high and light is not limiting

Homo sapiens

Homo sapiens 200,000 years ago Cro-Magnons evolved 90,000 years ago -Direct ancestors of modern humans -Were artistic and made precision tools

Mutualism and coevolution

Interactions between species do not necessarily pair a gain for one participant with a loss for the other. Some interactions benefit both participants. When the interaction between species drives reciprocal adaptations in both participants, this opens the possibility for long-term coevolution because the descendants of each side will also be associated with each other, just as were past generations. Any mutations that arise can affect both sides of the partnership because neither aphids nor bacteria are found without the other.

Anoxygenic photosynthesis differs from oxygenic photosynthesis in an important way

It employs only a single photosystem

Chloroplasts have an outer and an inner membrane that separate the stroma and thylakoid membrane from the cytoplasm. What is believed to be the origin of the outer membrane of the chloroplast?

It is the remnant of the ancient host cell's plasma membrane following endocytosis of the cyanobacterium.

The oldest plant community in Glacier Bay is hemlock-spruce forest. You would predict that hemlock and spruce trees are ____________-selected species.

K

Logistic growth

K= carrying capacity [maximum stable size of a population] △N/△T= rN (k-N/k) For most species, resources become limiting as populations grow Carrying capacity (K) or upper boundary for population Logistic equation

Ecosystem Engineers as keystone species

Keystone species called ecosystem engineers actively shape the physical environment, creating habitat for others. The classic example is beavers, which produce ponds by damming streams in forests, creating habitat that would not otherwise exist.

Example of mutualism

Leaf-cutting ants and fungus Ants chew up leaves to feed to fungus they care for Fungus produces gongylidia as ant food Ants circumvent chemical defenses of leaves Trophic mutualism - utilize a common resource

Aquatic ecosystem primary productivity

Limited mainly by light and nutrient availability Water absorbs light At 1 m more than half the solar radiation absorbed Limits depth of algal growth Nitrogen and phosphorus occur in very low concentrations Algal blooms result naturally from upwellings

humoral

Macrophages when they detect and antigen they engulf it and break it into little parts which are directed to the Helper T cells Once activated, they divide and interact with B cells and begin to make antibodies and removed from body

Are there any of our current traits or behaviors that can be ascribed to selection? What about culture?

Mate choice (sexual selection) Morning sickness (natural selection) Music/Dance

How much of our behavior is a product of different evolutionary forces? Need to be careful since humans can easily choose to modify our behavior and it is strongly affected by culture.

Mate choice (sexual selection) Morning sickness (natural selection) Music/Dance

size

Microparasites Macroparasites

Red algae

More abundant and diverse is the second major archaeplastida group

Density-dependent factors

More important as population gets big Mortality factor whose influence varies with the density of the population Parasitism, predation, and competition Predators kill few prey when the prey population is low, they kill more prey when the population is higher Detected by plotting mortality against population density and finding positive slope

clumped

Most common Resources tend to be clustered in nature Social behavior may promote this pattern individuals cluster together in a small space. This occurs sometimes when resources are distributed patchily within the range, or the chances of a new individual's surviving are enhanced by the presence of other individuals.

10. What is a microbial mat? How are they organized?

Multi-layered sheet of microorganisms, mainly bacteria and archaea grow at interfaces between different types of material, mostly submerged or moist surfaces, but a few survive in deserts blue green pigment- identifies cyanobacteria, dominate well-lit oxidative surface(oxygenic photosynthesis-producing oxygen, aerobic respiration) purple pigment- light but no oxygen gas (anoxygenic photosynthesis- doesn't release oxygen) black subsurface- anaerobic respiration and fermentation (using something else to burn carbon)support microbial populations

Explain the basic principles involved with viral evolution using HIV-1 as your model. Frame your answer in terms of the basic model of how natural selection works. Be sure to include in your discussion how viral variation is generated, how the virus manages to evade the immune system, why it is so hard to treat the virus with drugs, and why it has been so difficult to prevent viral infection with a vaccine.

Natural selection is survival of the fittest and viral infections are no different than any other organism when it comes to this concept. HIV virus invades the immune system by entering through the blood system. Once in the blood system it can contact the proteins on the surface of the of the helper t cell and binds to the glycoproteins on the outside of the virus. The interaction between the two proteins allows the virus to invade the host cell. Once the virus was inside of the capsid it uncases exposing the RT and Viral RNA. The RT makes a copy of its DNA while at the same time it is making integrates. The dsDNA copies the virus DNA and enters the nucleus of the helper to cell with the help of inter puts it into the chromosomes. The new provirus begins to be translated and transcribed and the products begin to leave the nucleus and are enabled into new viral particle start bud off from the cell. When these cells begin to reproduce there is a huge variation. This is because RT is a sloppy polymerase making a mistake 1/10,000 times. Because each virus only has a genome of 10,000 this means every cell is slightly different. The natural selection occurs whenever some of the viruses end up replicating better than other because their RT is resistant to nucleotide analogues. This is the natural selection taking place for drug resistant virus. Because of all the different viral variations it can be extremely difficult to treat. One way to try to treat this is to make a drug cocktail to attack all the different parts of the virus. These drug cocktails can contain drugs to attack RT, protease, and many other stages.

9. Did humans hybridize with any other hominin? What is the evidence?

Neanderthals: -similar to modern humans muscularly, fully erect, dexterous, large brains body type adapted to cold weather developed ritualistic burial ceremonies studies of neanderthal genomes have revealed that there was interbreeding probably in the Middl East as H. Sapiens first emerged from Africa about 60,000 years ago Homo erectus, Homo neanderthalensis, homo sapiens, homo floresiensis evidence: synapomorphies-shared derived characteristics age of fossils hominin lineages

Which is not a normal part of the nitrogen cycle?

Nitrogen fixation by the Haber-Bosch process

Birth and death rate vary with age and environment

Not all organisms in a population contribute equally to population growth because some reproduce more than others. Therefore, it is also useful to take into account individuals that have differing reproductive capacities, which most often depend on differences in age. The age structure of a population is the number of individuals within each age group of the population studied. A population in which most individuals are past their age of greatest reproduction (because for some reason young are not surviving) or a population mostly composed of individuals younger than this age (because older individuals are not surviving) will not increase as rapidly as one dominated by individuals capable of greatest reproductive output.

anoxygenic

Not producing oxygen; these photosynthetic bacteria do not gain electrons from water and so do not generate oxygen gas.

Do humans practice random mating?

OK, so some individuals are more attractive to us than others What is "attractiveness" and what does it mean? - cues for fitness? - cues for genetic relatedness?

Disturbances modify community composition

Often, dramatic changes in climate or weather Fire, flood, drought, volcanoes, hurricanes, frost Also, biotic changes to communities: human activity, beaver dams

Ape Family Tree

One line of Old World monkeys gave rise to apes, which lack a tail and show more sophisticated behaviors than other monkeys. The apes are split into two groups: the lesser and the great apes. Lesser apes include fourteen species of gibbon, which are all found in Southeast Asia. The great apes include the orangutan, gorilla, chimpanzee, and humans.

choanoflagellate

One of a group of mostly unicellular protists characterized by a ring of microvilli around the cell's single flagellum. (sister taxon to the animals)

superkingdom

One of seven major groups of eukaryotic organisms, classified by molecular sequence comparisons.

Archaea

One of the three domains of life, consisting of single-celled organisms with a single circular chromosome and no true nucleus that divide by binary fission and differ from bacteria in many aspects of their cell and molecular biology -many are extremophiles

Crenarchaeota

One of the three major divisions of Archaea; includes acid-loving microorganisms (Headwaters of the Rio Tinto, southwestern Spain)

Euryarchaeota

One of the three major divisions of Archaea; includes acid-loving, heat-loving, methane-producing, and salt-loving microorganisms

Thaumarchaeota

One of the three major divisions of Archaea; thaumarchaeota are chemotrophs, deriving energy from the oxidation of ammonia. Only group that makes methane

Bacteria

One of the three monophyletic domains of life, consisting of single-celled organisms with a single circular chromosome but no nucleus that divide by binary fission and differ from archaeons in many aspects of their cell and molecular biology

Parasitism

One organism feeds off another, but does not normally kill it outright Predatory organism is termed a parasite and the prey a host

To which superkingdom do humans belong?

Opisthokonta

niche differentiation

Partial niche overlap both species existing using recourses in different ways

Tundra

Permafrost Reindeer Birds Few species Tundra is the coldest biome, and short days in winter limit the growing season. Tundra occurs close to the North Pole, above 65° N. The South Pole is largely surrounded by the ice and seas of Antarctica, and so there is very little area with plants. Precipitation is low, but because rates of evaporation are also low and because drainage is commonly poor, the ground is usually waterlogged and permanent ice occurs below a few centimeters of soil. Primary producers are mostly mosses, lichens, herbs, and low shrubs. Grasses and sedges occur in drier places, as do other flowering plants. Plant diversity is low, and most plants are small. Caribou are conspicuous grazers, but other primary consumers, including rabbits, birds, and insects, occur as well. Wolves and foxes are key predators. Fungi and bacteria decompose organic detritus, but low temperatures and water-logged soils limit rates of respiration.

Interactions

Populations do not exist in isolation. All populations are tightly linked to other populations that share the same habitat

Displays of intimidation

Porcupine fish inflates itself Deceive predator about ease of eating prey

The activities of different populations in a community vary in time.

Predators and prey interact in settings as different as a tropical rain forest or Arctic tundra. In habitats with many different species of predators and prey, identifying the way each species affects others can be challenging. For this reason, much research on how predators and prey influence community structure has been carried out in the Arctic, where communities tend to have relatively few species. One well-studied community is found on Bylot Island in the Canadian territory of Nunavut. There, two species of lemming, the main herbivores in tundra communities, affect the populations of other herbivores and predators. Snow Geese are herbivores that live alongside the lemmings, and both geese and lemmings eat the grasses and other low plants that grow on the island. The main predators of lemmings and snow geese are Arctic foxes and snowy owls. Lemmings, foxes, snowy owls, geese, and plants, then, are linked by a set of mutualisms and antagonisms. Changes in one species can affect all of the others.

Carbon cycle

Present in atmosphere in low concentrations Autotrophs incorporate it into organic matter via photosynthesis Plants remove about 1/7 of the CO2 in the atmosphere Respiration and decomposition of plants recycles a similar amount back into the atmosphere as CO2 Carbon is incorporated into shells of marine organisms eventually forming limestone deposits Volcanoes and hot springs release large amounts Burning fossil fuels is adding CO2 and particulate matter to the atmosphere Direct measurements over the last 50 years has shown a steady rise in atmospheric CO2 Because of its high concentration in the atmosphere, CO2 is the most significant of the greenhouse gases, which are a primary source of global warming largely global

Black smoker

Primary production could be accomplished by anoxygenic photosynthesis, which does not generate oxygen. Oxidation of organic matter to carbon dioxide could be accomplished by anaerobic respiration (and fermentation), which does not use oxygen.

The Δ32 allele is at high frequency in European populations and virtually absent in Asian or African populations. Why?

Probably due to an old selection event. Δ32 also seems to confer resistance to Yersinia pestis, the causative agent of Bubonic Plague Nearly 1/3 of the European population was killed by plague in the 14th century. Those who were resistant were more fit. The allele responsible for that fitness was selected for.

Per capita (per head) value

R=per capita growth rate can compare changes between different populations using rates of change R= per capita growth rate (△N/△T)/N1 R= positive = growing R= zero = stays same R= negative = shrinking

random

Rarest Resources are rarely randomly spaced May occur where resources are common and abundant a new individual has an equal chance of occupying any position within the range, and the location of one individual has no influence on where the next will occur.

Temperate Coniferous Forest

Related to Taiga Same forests but near coast More moisture Redwoods Two broad areas of temperate coniferous forest occur below 50° N in North America, northern Japan, and parts of Europe and continental Asia. Along the Pacific coast of North America, warm summers and mild winters, along with abundant precipitation, permit growth of enormous conifers such as Douglas Fir, Red Cedar, Sitka Spruce, and redwoods. Much of the undergrowth consists of grasses, ferns, and members of the blueberry family. Understory shrubs are uncommon. In the interior of North America, much less precipitation and colder winter temperatures support drought-resistant conifers such as Ponderosa and Lodgepole Pines and Englemann Spruce. Diverse invertebrate species live in the soils, supported by active microbial decomposers. Insect and vertebrate diversity are all higher than in taiga forests.

intracellular phase

Replication form utilizes metabolic pathways of host + viral genome to produce new virions. Intracellular State: Once the virus invades a host cell it is in an 'intracellular state.' In this state, the capsid is removed and the virus exists as only as nucleic acid (genetic material).

mimicry

Resemblance of mimic to another organism (model) Mullerian mimicry - noxious species converge to reinforce warning, black and yellow stripes of bees and wasps Batesian mimicry - palatable mimic resembles unpalatable model, scarlet king snake and coral snake

How do we figure out which hominin is related to which other ones?

Synapomorphies Age of the fossils

What is the species-area equation?

S= cA^x

Proximity of land mass

Sea breezes in coastal areas during the day During the day, land heats up and air rises pulling cooler ocean air in to replace it Offshore breezes at night Land cools quicker than the sea and the pattern reverses Sea moderates coastal and island temperatures

Armor

Shells of turtles provide strong defense Beetle exoskeleton

The first law of thermodynamics states that energy can be transformed from one state to another, but it cannot be created or destroyed. Taking this into consideration, what can be said about the energy transferred between levels in a trophic pyramid?

Some of the energy in a trophic level is converted to heat and is unavailable to the next level.

10. What important archaeological site documenting early N. American humans is close to Pittsburgh?

Some of the oldest evidence for N. American colonization is the Meadocroft Rock Shelter in Washington County, PA

Bacterial and archaeal phylogeny

Some scientists argue that the evolution of prokaryotes should not be viewed as a tree but as a series of branches that diverge and then come back together, representing genes that diverge from one another but then come to reside together in new organisms because of horizontal gene transfer.

Habitat Fragmentation

Species survival depends not only on the health of local populations, but also on the ability of individuals to colonize new habitat patches. As the simple experiment with mosses shows, corridors that connect endangered populations can dramatically increase the probability that a species will survive. The same was shown to occur in larger habitats, like the rainforest. The Biological Dynamics of Forest Fragments Project in Brazil found that fragmentation strongly affects forest biodiversity, providing clues to the design of effective refuges.

Island Size and Species Number

Species-Area relationship: S = cAx At a larger scale, the number of animal species counted on tropical islands generally fits the predictions of island biographic theory. This figure shows not only that larger islands support more species than smaller ones, but also that there is a quantitative relationship between island size and species number. The relationship can be described mathematically as a species-area relationship where S is the number of species at equilibrium, c is a mathematical constant, A is the habitat area, and x is an experimentally determined exponent relating species number to habitat area. In many experiments, x has fallen within the range of 0.1 to 0.4. The best way to conserve species is to retain large amounts of suitable habitat!

Cellular slime molds

Starvation causes amoeboid feeding cells of cellular slime molds to aggregate into a multicellular "slug" that can migrate along surfaces, leaving behind a trail of slime. "Slugs" differentiate to form stalked sporangia that produce spores. spend most of their life cycle as solitary amoeboid cells feeding on bacteria in the soil. Starvation, however, causes these cells to produce the chemical signal cyclic AMP

Tranformation

The conversion of cells from one state to another, as from nonvirulent to virulent, when DNA released to the environment by cell breakdown is taken up by recipient cells. In recombinant DNA technology, the introduction of recombinant DNA into a recipient cell. -DNA released into the environment by dead cells is taken up by a recipient cell

Effect of distance from the mainland

The distance of the island from a source of colonists is another major factor in predicting how many species an island can support. More distant islands have lower rates of colonization, moving equilibrium species diversity toward lower values

Eukarya

The eukaryotes; one of the three domains of life, in which cells have a true nucleus and divide by mitosis.

Steps of virus

The first step for a virus to attack is that it must attach to the host. Here, HIV attaches to proteins on the surface of the cell and fuses with the plasma membrane and enters the cytoplasm of the host by endocytosis. Once inside the cell, the HIV virus releases its viral RNA genome and proteins. The enzyme reverse transcriptase (brought by the virus) copies the virus's RNA to DNA, which is able to enter the host cell's nucleus. Once in the nucleus the virus's double stranded DNA is incorporated into the host cell's DNA by a viral enzyme. The virus uses the host cell's machinery to transcribe and integrated its viral DNA into the mRNA which is translated to protein in the cytoplasm. These proteins then self-assemble on their own releasing new viruses. In the case of HIV, new viruses bud from an intact cell. Other kinds of viruses can burst the cell to exit, while others incorporate their viral genome into that of the host, but are replicated and released at a later time. use the resources of the host to replicate

Phagocytosis

The flexibility of the eukaryotic cytoskeleton and membrane system enables eukaryotic cells to engulf food particles, including other cells.

Compare and contrast the flow of energy through an ecosystem with cycling of nitrogen within an ecosystem. How does each of these phenomena shape the final form of the ecosystem? Use contrasting examples.

The flow of energy in an ecosystem is passed from the abiotic environment(the sun), to the biotic part of the system. The sun is the external energy source and transfers its energy to the primary producers of the ecosystem from there, energy is generally passed to the consumer and then the decomposers. The transfer of energy between trophic levels is inefficient and therefore, at each transfer the available energy units decreases. The lost energy is not gone but rather given off as heat. The cycling of Nitrogen begins with the process of Nitrogen fixation where certain bacteria are able to convert nitrogen to N2 and release ammonium and ammonia. Then with the process of Nitrification, soil bacteria are able to convert that ammonium or ammonia to nitrate (NO3-) to be used by plant life. Then Assimilation occurs when those plants and sometimes animals incorporate the ammonia and ammonium back into the environment. Another way for nitrogen to enter into the soil is Ammonification where organic nitrogen is converted to NH3 and NH4+ by bacteria and fungi. This is the most common way for nitrogen to enter the soil. Last, Denitrification occurs with the reduction of nitrate to gaseous N2 by bacteria and some nitrogen is returned to the atmosphere. There is a major similarity between the cycles by the basic path they follow. Both draw upon a source, either the sun (for energy) or atmospheric nitrogen (for nitrogen cycle). At each step of the process some of that initial source is used and therefore lost from the cycle before it is passed onto the next step or trophic level

biological transport mechanisms

absorption of chemicals by living organisms and their subsequent release back into the environment

Hominin Lineages

The hominin lineage produced many different species in Africa. At times, there were as many as three species living at the same time. All hominins have a common ancestor, but not all of them lead to modern humans, which are called Homo sapiens. Instead, these branches ultimately went extinct. The fossil record indicates that the first hominin lineage to venture out of Africa was Homo egraster (also called Homo erectus), and did so about 2 million years ago. Fossils have been found throughout Eurasia but not in Australia or the Americas. Homo neanderthalensis was a descendent of H. egraster and was closely related to Homo sapiens. Its fossils were found in Europe and the Middle East. Neanderthals were thicker boned than us and had flatter heads with brains about the same size as us. Neanderthals first appeared in the fossil record around 600,000 years ago and disappeared around 30,000 years ago. Homo floresiensis, also popularly known as the Hobbit, was another descendent of H. egraster that became extinct 12,000 years ago,. This species was limited to the Indonesian islands of Flores. Adults were just over 3 feet tall.

HIV infection directly kills off the cells central to the immune response

The host dies from AIDS, or Acquired Immune Deficiency Syndrome, which makes the person extremely susceptible to infections and cancers normally taken care of by the immune system.

How HIV beats the immune system

The immune system, like antiviral drugs, is an agent of selection. The immune system relies on epitopes to detect foreign entities. 1. HIV, with its high error rate, is constantly changing its epitopes so the immune system can miss it or not recognize it as foreign. The same sloppy RT is responsible for generating epitope variation. 2. Worse, HIV kills off the immune system through viral infection and via destruction of Helper T cells by Killer T cells. 3. The high error rate of HIV RT is likely to be an adaption it acquired in its interaction with the immune system. Without it, the immune system might win.

How specifically did humans evolve?

The out-of-Africa theory of human origins suggests that modern-day Homo sapiens evolved from a descendant of Homo ergaster in Africa about 200,000 years ago. Mitochondrial DNA and the Y chromosome do not undergo recombination, so the only genetic variation arises from mutation. By studying the variation of these two types of genetic material from different populations of people throughout the world, scientists were able to calibrate the rate at which mutations occur, build a phylogenetic tree showing the relationships between humans and that they had a common ancestor, and determine the timeline of modern-day Homo sapien occurrence.

2. What is horizontal transfer?

The process of swapping genetic material through no traditional means -transduction -conjugation -transformation

effects of island size

The theory of island biogeography, states that the number of species that can occupy a habitat island depends on two factors. The first is the size of the island. Because of their size, larger islands receive more colonists than smaller ones. Furthermore, larger islands can support more species than smaller ones can, so extinction rate goes down. For these reasons, the equilibrium number of species expected for larger islands will be greater than that for smaller islands. Small islands= higher extinction rate, less immigration

Horizontal Gene Transfer

The transfer of genetic material between organisms that are not parent and offspring. Conjugation Transformation Transduction

What is the trophic structure of an ecosystem?

each level of the feeding chain (food web)

Heterotrophs

eat other organisms

The human microbiome

There are 10X more microbial cells in your microbiome than your own cells (GI tract, mouth, skin, airways) affects your phenotype

Explain the different major kinds of species interactions that we discussed. For each, be sure to use the +/- system to help explain which species gain or lose and what the long-term evolutionary outcome of the interaction is likely to be. Use specific examples of species interactions where appropriate.

There are 4 major species interactions, which are commensalism (0/+), competition (-/-), consumption (-/+), and mutualism (+, +). The first is commensalism while one species gains and the other has no effect. An example of this is the water buffalo buffalo stirring up insects in the ground for birds to eat but the bird has no effect on the buffalo. The next type is competition where both species involved are hurt because it reduces available resources. This occurs when two species niches overlap. Over time natural selection will occur causing for a reduced completion. One example of this is birds living in a tree. There are many birds that live in the same tree and instead of going extinct they each narrow their niche range to a specific part of the tree. The next type of species interaction is consumption competition. This occurs whenever one species gains and one species loses. There are three types of parasitism, predation and herbivoary. Examples of this I an herbivore eating a plant, a parasitism living inside of a host, and a predator killing its prey. In the long run this leads to anti-predator strategies emerging such as chemical defense, cryptic coloration (stick insect mimicking branch), mimicry, agility, and many more. The last example of species interaction is mutualism which is when both species benefit. For example, plants produce seed/fruit for birds to eat and in return the bird disperses the seeds. Another example in how ants live in the hollowed out thorns on trees and in exchange the ants protect it from herbivores.

Primate family tree

There are about 400 species of primates that include prosimians, monkeys( new and old world), and apes

Aquatic productivity

There are vast areas of the ocean where photosynthesis doesn't occur Concentrated mainly around coasts of continents Shallow water and upwelling (water hits coast)

viral proteases

There is evidence of resistance to all 6 currently used protease inhibitor therapies, for the same reasons RT resistance developed.

A high school student in Nepal is accepted to—and eventually attends—college in the United States. His diet changes from one that is rich in vegetables and grains to one that primarily consists of meat and sugars. What will happen to the bacteria living in his intestines?

There will be more Firmicutes inhabiting his intestinal tract.

Kelps

These complex multicellular brown algae can form "forests" tens of meters high in the ocean.

1. Why are bacteria usually small?

They are usually single-celled Prokaryotes- do not have membrane bound structures that occupy space within the cell

18. Where did chloroplasts come from? What is the evidence?

They have structures very similar to that of cyanobacteria -DNA organized in a circle -undergo oxygenic photosynthesis chloroplasts- cyanobacteria

Amoebozoans

This group includes protists with an amoeboid stage in their life cycle.

Opisthokonts

This superkingdom includes animals and fungi, as well as several protistan groups, including choanoflagellates, the closest protistan relatives of animals

Alpine

Tops of mountains Short growing season Cold No permafrost Plants similar to tundra Convergent evolution The Alpine biome is similar to tundra but lacks permanent ice below the soil, and the temperatures vary more widely. Alpine areas occur throughout the world, often at about 10,000 feet (3000 m) at lower latitudes, but always just below the snow line. Because of their altitude, these are windy, cold places. The thin atmosphere provides only limited protection from UV radiation. Many alpine plants are therefore low and slow growing. Grasses are abundant, as are herbs that can provide spectacular wildflower displays during the short growing season. Alpine grazers include mountain goats, llamas, yaks, and marmots, as well as seasonally active insects. Predators include wolves and cats such as the Himalayan snow leopard.

Autotrophs produce carbohydrates by reducing CO2, whereas heterotrophs synthesize carbohydrates by ingesting smaller preformed organic compounds like glucose.

True

If the genes used to generate molecular phylogenies were subject to horizontal gene transfer, then they will not reflect the evolutionary history of the organisms in which they occur.

True

9. Describe the events leading up to the evolution of the first eukaryotes.

Two hypotheses: come from symbiosis of an archaea and a bacteria Endosymbiosis- from prokaryotes to eukaryotes -start with 2 independent bacteria -one engulfs the other, on bacteria now lives within the other -both benefit from the arrangement -internal bacteria are not passed on through the generations Eukaryotes arose from cyanobacterium through endosymbiosis

How is HIV transmitted?

Unprotected sexual intercourse, contact with contaminated blood (sharing of needles, transfusion with contaminated blood, etc.)

Taiga

Vast areas of coniferous forest Evergreens, pines Adapted fro heavy snowfall Relatively dry Not may species Growing season not that long Covers vast parts of the earth These cool, moist forests occur from 50° N to 65° N. The short summer brings rain, and most of the plants are low-growing conifers like spruce, fir, larch, and pine, with an understory dominated by shrubs in the blueberry and rose families. Mosses commonly form an extensive and soggy groundcover. The soils are deep with accumulated organic matter because the low temperatures result in slow decomposition, but they are also acidic and poor in nutrients, helping to explain the limited stature of most plants. Birds, insects, and other invertebrate animals are more abundant and diverse than those of tundra biomes, but mammals are the most conspicuous consumers. Grazers include elk, moose, caribou, porcupines, hares, and a diversity of rodents. Bears, lynx, wolverines, weasels, mink, wolves, and foxes are well-known predators.

Water cycle or hydrological cycle

Water cycle or hydrological cycle Very little of the water that cycles through ecosystems is chemically changed by any of the cycle's components Physical process fueled by the sun's energy Evaporation and precipitation Over land, 90% of the water that reaches the atmosphere is moisture that has passed through plants and exited from the leaves via evapotranspiration Though most organisms consist largely of water, only about 2% of the total volume is held in the bodies of organisms or is held frozen or in the soil Remainder cycles between the oceans, the atmosphere, and the land Deforestation significantly alters cycle - less moisture transpired, diminishes precipitation, and area undergoes drought

Keystone species have outsized roles on a community

While all or nearly all species in a given place have some effect on one another, the integrity of a community may depend on a single species. This situation can occur when one species influences the transfer of a large proportion of biomass and energy from one trophic level to another or when the species modifies its physical environment, as beavers do when they make ponds. Such pivotal populations are called keystone species. Though all species contribute to the structure of a community, a keystone species affects other members of the community in ways that are disproportionate to its abundance or biomass.

Myxobacterium

a bacteria in which cells aggregate to form fruiting bodies

When people are infected with HIV

a certain population of cells are affected Helper T cells

Ecosystem

a community of organisms and the physical environment it occupies

What is an ecosystem?

a community of organisms and the physical environment it occupies; flow of energy through ecosystems; cycling of chemical elements within ecosystems

predation can lead to

a decrease in competition and allow competitors to occupy the same environment

Homo floresiensis

a dwarfed hominin most closely related to Homo erectus was discovered October 2004

What is a metapopulation?

a group of population linked immigrants individual populations can move between each of the other populations through corridors. all of the separate populations together make metapopulation

6. What is an extremeophile? What are some examples?

a microorganism that thrives in extreme conditions, for example, temperature, acidity, chemical concentration, etc. -bacteria living under rocks -many archaea

CCR5 co-receptor

a protein on the surface of white blood cells that is involved in the immune system as it acts as a receptor for chemokines.

Haloquadratum walsbyi

a square archaean that lives in salt ponds

protease

a type of enzyme that functions mainly to help us digest different kinds of proteins

How are different organisms divided into different trophic levels in an ecosystem?

abiotic environment: external energy source, primary producers, consumers, decomposers

a network or membranes (eukaryotic cell)

able to change shape and package molecules and particles for transport within the cell

From the base of plant productivity

about 10% of the biomass of each trophic level is passed on to the next-higher level

The advent of "modern" humans

about 50,000 ya.

Anti-RT drugs

aim to stop viral DNA synthesis by incorporating nucleotide analogues (the drug) to halt reverse transcription, the special viral form of DNA synthesis. This happens because no further nucleotides can be added since the analogues lack a 3' OH.

Movement of air creates

air currents Rising and descending air organizes the atmosphere into a series of cells from the equator to the poles. High temperatures warm air near the equator. Because of its lower density, the warm air rises. As air rises and spreads outward toward the poles, it cools, eventually becoming dense enough to sink back to the surface.

Rank Most productive aquatic areas to least productive

algal beds and coral reefs wetlands estuaries upwelling zones continental shelf lake and stream open ocean

A niche can be defined as

all of the habitat requirements of a particular species

fundamental niche

all resources an organism can use

oxygen

all that we breathe today is a result of photosynthesis originated 2.4 billion years ago as levels increased, new metabolisms evolved expanding possibilities for cellular respiration and chemoautotrophy

population

all the individuals of a given species that live and reproduce in a particular place

19. Where did mitochondria come from? What is the evidence?

also a case of symbiosis very similar to alphaproteobacteria

Bacteriophages

also called phage or bacterial virus , any of a group of viruses that infect bacteria

integrase

an enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell

29. Which two multicellular kingdoms are contained in the Opisthokonta?

animals fungi

predation

another form of antagonism, as the predator benefits at the expense of the prey. We have seen that when species overlap in resource use and their populations increase to the point where they compete for resources, they must be separated in space or time or risk local extinction through competitive exclusion when resources become limited If, however, populations do not rise to densities at which resources are limiting, competition is reduced and species can overlap in niches without excluding one another. Parasites can also limit the population size of their host, keeping numbers well below the carrying capacity of the environment

Chemokine

any of a class of cytokines with functions that include attracting white blood cells to sites of infection.

What is aposematic coloration? What is cryptic coloration?

aposematic coloration is warning coloration which advertises an organism's unpalatable taste -tropical frogs have bright coloration to advertise the skin lethality cryptic coloration: also known as camouflage some insects mimic the look of a stick sea horses change color to fit into environment

2. Understand the basic fossil record of humans. When did upright walking evolve? How do we know?

ardipithecus ramidus appeared 4.4 million years ago as evidenced by fossils (could have been 6 million years ago)

logistic growth curves

are S-shaped because they actually reflect two sets of processes, each related to population size. At first, growth reflects only the rate at which individuals can reproduce themselves, so the curve rises steeply. The second part of the curve, where it starts to level off, reflects the onset of additional factors that become important above a certain population size, such as decreasing availability of food and space.

When (K - N)/K = 0, what does that imply about the birth rate (b) and death rate (d)?

b = d

Fossil Record of Bacteria

back to 3.8-3.5 billion years ago (a) Bacteria that probably metabolized iron in 1.9-billion-year-old rock from the Gunflint Formation in northwest Ontario, Canada. (b) Cyanobacteria preserved in 800-million-year-old silicified marine carbonates from the Draken Formation in Spitsbergen, Norway. (c) A short cyanobacterial filament from silicified tidal flat carbonates of the 1.5-billion-year-old Bilyakh Group in northern Siberia.

5. Which domains are prokaryotic and what does that mean?

bacteria and archaea they do not have nuclei all other organisms are eukarya means they lack a nucleus

An expanded carbon cycle

bacteria and archaea fix carbon and respire in a variety of ways that are unique to them alone -anoxygenic photosynthesis and chemoautrophy are things that eukaryotes dont do

E. coli

bacterial rods

4. When did hominins acquire a large brain?

homo erectus 1.8 million to 500,000 years ago

30. Why are choanoflagellates considered the sister taxon of the animals?

because in early 1841, the close similarity between choanoflagellates and the collared feeding cells of sponges suggested that these minute organisms might be our closest protistan relatives

Conjugation

between cells closely related to each other, pilus links 2 cells pulls cells together and creates a gap circular DNA transfers from one to another -DNA (usually a plasmid) from a donor cell is transferred to an adjacent recipient cell -a pilus tethers the donor to the recipient and brings the cells together -once the cells are closely aligned, the DNA passes through a small opening formed between the cells -the process by which one bacterium transfers genetic material to another through direct contact. During conjugation, one bacterium serves as the donor of the genetic material, and the other serves as the recipient.

Movements of chemicals through ecosystems involve

biological transport mechanisms geological transport mechanisms chemical transport mechanisms

demography

birth rates, death rates, age distributions, and sizes of populations the study of the size, structure, and distribution of populations over time

biomes

broad ecologically uniform areas

Biome localities are determined

by temperature and moisture on land. Those, in turn, depend a lot on atmospheric circulation

adaptive immune system

can target foreign pathogen that enters your body

Who is our closest relative among the apes?

cant tell strictly by morphology Only molecular analysis of human and primate DNA could reveal that our lineage split from the chimpanzee lineage about 5−7 million years ago.

Gross primary production (GPP)

carbon fixed during photosynthesis

oxidation

catalysis of secondary metabolite to corresponding alcohol by mixed-function oxidases (MFOs)

position of helper t cells

center of immune system to cope with infections

Lysogenic cycle

characterized by integration of the bacteriophage nucleic acid into the host bacterium's genome or formations of a circular replicon in the bacterial cytoplasm.

Antipredator strategies

chemical defense cryptic coloration mimicry displays of intimidation fighting agility armor masting

An organism that oxidizes H2S to gain energy and utilizes CO2 as a carbon source (to generate carbohydrates) would be classified as a:

chemoautotroph

13. What kind of organisms fuel the carbon cycle around hydrothermal vents?

chemoautotrophs these environments do not depend at all on photosynthesis

hypothermal vents

chemoautotrophs fuel the carbon cycle in these environments do not depend at all on photosynthesis

1. What animals are the closest living relatives of humans? How do we know this?

chimpanzees because of the primate family tree molecular analysis of human and chimpanzee DNA

bacteria gave rise to

chloroplasts and mitochondria

Dispersion patterns

clumped uniform random

How can populations be distributed in space?

clumped, uniform, random

Plasmodial slime molds

coenocytic structures containing many nuclei. generate sporangia, stalked structures that produce spores for dispersal. haploid cells fuse to form zygotes that subsequently undergo repeated rounds of mitosis but not cell division to form colorful, often lacy structures visible to the naked eye

Grey whales in the pacific ocean often have barnacles attached to their skin. The whales seem unaffected, while the barnacles get a place to live that transports them to areas where food is abundant. This kind of species interaction is best described as

commensualism

Succession

communities change over time Gradual and continuous change in species composition and community structure over time

The competitive exclusion principle

complete competitors cannot coexist

gag

components of capsid -matrix -capsid -nucleocapsid -Vpr-binding protein is the genetic material that codes for the core structural proteins of a retrovirus.

Using the +, -, 0 notation, what kind of interactions are: Parasitism Predation Herbivory Competition Commensualism Mutualism Be able to cite some examples of each kind. Understand what the short term and long term consequences of each is.

consumption: parasitism (+/-) predation (+/-) herbivory (+,-) competition (-,-) commensalism (0,-) mutualism (+,+)

coenocytic

contain many nuclei within one giant cell

16. Why are eukaryotic cells usually larger than prokaryotes?

contain organelles and a nucleus

eukaryotic diversity

continued to rise as oxygen levels increased the radiations of marine animas and later land animals, land plants and fungi

ammonification

conversion of organic nitrogen to NH3 and NH4+ by bacteria and fungi (most common pathway for nitrogen to enter soil)

rain shadow

creates dry areas next to mountains

The most important kind of evolution in humans now may be

cultural

For the first 2 billion years of its history, Earth's atmosphere lacked (or had very little) oxygen. Which of the following organisms produced much of the oxygen that now makes up the present-day atmosphere of Earth?

cyanobacteria

Chloroplasts have structures very similar to that of

cyanobacteria (DNA in a circle, oxygenic photosynthesis)

What is a life table and what does it measure?

data on the number of individuals alive in a particular age class and males are usually not included

The study of the size, structure, and distribution of populations over time is called

demography

A biologist tells you that there are about 50 white tailed deer per square mile in W. PA. What population data has she shared with you?

density

Checks on population growth

density-dependent factors density-independent factors

Describe several density-dependent factors affecting population growth. Describe density-independent factors.

dependent: competition, predation, parasitism, disease independent: unusual weather, natural disasters, seasonal cycles, certain human activities such as damming rivers

How does resource allocation affect life history?

depending on the resources available and the assignment of each resource to each task, the way the earth will evolve can differ

What is competition? Know some examples.

detrimental to both of the individuals or species involved because the available resources are reduced. every species requires a unique niche and competition occurs when the niches overlap -trees w/ overlapping roots competing for water and nutrients -space and habitat such as with barnacles for competitors -large fern overgrowing and shading others from the sun -grizzly bear vs. black bear

Detritivores or decomposers eat

detritus

25. What is the primary characteristic of the Alveolata?

dinoflagellates have cell walls made of interlocking plates of cellulose ciliate has many short flagella or cilia that line the cell alveoli contains a lot of parasites including malaria parasites

chemical transport mechanisms

dissolved matter in rain and snow, atmospheric gases, and dust blown by the wind

What is the age structure of a population? What factors affect age structure?

distribution of males and females based on age in a population survivorship lifespan

26. What is the primary characteristic of the Stramenophila?

diverse and distinctive included unicellular organisms and giant kelps, algae and protozoa most are photosynthesis characterized by hairy flagella

species diversity

diversity reflects both the rate at which new species arrive on the island, and the rate at which species already on the island become extinct. As species arrive on an uninhabited island, the colonization rate is high because there are no predators yet and the small number of colonists means that competition for resources is limited. As more and more species establish themselves on the island, the rate of colonization goes down both because competition and predation increase, making successful colonization more difficult, and because of the diminishing number of species left in the pool of potential colonists. In contrast, extinction rate goes up as newly arrived species compete.

What are community disturbances? What is succession?

dramatic changes in climate or weather -fire, flood, drought, volcanos, hurricanes, frost there are also biotic changes like human activity or beaver dams succession is gradual and continuous change in species composition and community structure over time -primary: succession on a newly exposed site that was not previously occupied soil and vegetation -secondary: succession on a site that has already supported life but that has undergone a disturbance, such as fire, tornado, hurricane and flood

4. Why does drug therapy with a single drug usually fail with HIV?

drug therapy usually tries to target some vital viral function and HIV is constantly changing virus

Why are there not more links in most food chains?

due to the energy lost in each level of the food chain, refers to the number of links between the trophic levels involved

What is an ecological niche? What is a fundamental niche? A realized niche? What is the competitive exclusion principle? What is niche differentiation and what causes it?

ecological niche- a unique niche or set of habitat requirements for a certain species. every species has their own ecological niche -the competitive exclusion principle states that 2 species with the exact same requirements cannot live together in the same place and use the same resources which would be occupying the same niche. also complete competitors cannot coexist with one another

Glacier Bay in Alaska is a fjord whose lowlands were covered by glacial ice until around 230 years ago. As the glacier retreated, glacial till was exposed to plant colonization; remarkably (and fortunately for generations of ecologists), the location of the tip of the retreating glacier has been frequently documented since the late 1700's. This means that scientists have been able to develop a detailed timeline of the changes in the plant community, or ____________ in Glacier Bay over time.

ecological succession

cytoskeleton (eukaryotic cell)

enables cells to change shape by remodeling quickly

8. The cyanobacteria were involved in a horizontal transfer event. What was it?

endosymbiosis (inside living together)

Second law of thermodynamics

energy conversions are not 100% efficient and that, in any transfer process, some energy is lost

Why is energy lost as it is transferred between trophic levels?

energy is used for digestion as well as to maintain body heat of an animal

R=

energy lost in plant cellular respiration

There are two basic models that account for how populations grow

exponential growth and logistic growth

Five species of ants can be found on aspen sunflowers (Helianthella quinquenervis), which live in wet mountain meadows of the Rocky Mountains. The aspen sunflowers provide nectar to the ants in special structures called extrafloral nectaries. The ants, in turn, protect the sunflowers from other insects. The ants, however, are not found solely on the sunflowers—they can be found tending aphids on other flower species and collecting nectar from other species as well. This, then, is an example of a(n):

facultative mutualism.

Layers of Microbial Mats

fairly sharp boundaries -cyanobacteria: the oxygenic photosynthetic bacteria that dominate the well-lit, oxygen-rich mat surface -purple bacteria: anoxygenic photosynthetic bacteria that live where there is light but no oxygen gas -black subsurface: anaerobic respiration and fermentation support microbial populations

Type II

fairly uniform death rate consistent levels of mortality throughout life. Birds and many small mammals linear down

polyphagous

feed on many hosts

monophagous

feed on one or two closely related hosts

22. What is the main characteristic of the Excavata?

flagellated feeding groove oldest flagellated organisms unicellular

secondary production

gain in the biomass of heterotrophs and decomposers

What do bacteria acquire by horizontal gene transfer?

genetic diversity

You are surveying biodiversity on a new island chain. You have counted the number of bird species on one island already. The next island is larger and closer to the mainland than the one you have just surveyed. According to the theory of island biogeography, the total number of its bird species should be _____ than on the current island because the rate of immigration to the new island should be _____ and the rate of extinction should be _____.

greater; higher; lower

27. What is the primary characteristic of the Amoebozoa?

group of eukaryotes with amoeba-like cells that move and gather food by means of pseudopedia

Define the term population.

group of interbreeding occupying the same habitat at the same time

Autotrophs

harvest light or chemical energy and store it in carbon bonds

Microbial Mats

have sharp vertical gradients of light, oxygen and other chemical compounds and so support nearly all the energy metabolisms found in the expanded carbon cycle

Streptomyces

helical bacteria that produce antibiotics

r-selected

high rate of per capita population growth, r, but poor competitive ability (weeds)

Life history

how an individual allocates resources to growth, reproduction, and survival. Not everything can be maximized at the same time! -continuum -r selected -k selected how an individual allocates resources to growth, reproduction, and survival. Not everything can be maximized at the same time! There are tradeoffs to be made

density

how crowded or dispersed the individuals are that make up the population. Population density is defined as a population's size divided by its range. For krill, 800 trillion animals are spread over 19 million square kilometers—a density of 42 million animals per square kilometer.

Categories of consumption can be classified according to

how lethal they are for the prey and the length of association between consumer and the consumed

geographic range

how widely a population is spread and the factors that determine its distribution. For example, the krill population ranges through an area of 19 million square kilometers around Antarctica. The geographic range of any species determines how much variation in climate a population can tolerate and how many other species the population encounters

2 parts of adaptive immune system

humoral and cellular

What is exponential population growth? What is the general equation that describes this kind of growth? What are the parameters?

if a population has a constant birth rate through time and is never limited by food or disease. Equation: N/T = (rmax)N For this type of growth to occur there must be an unlimited amount of space of space and resources (no carrying capacity)

what is a bacterial species?that promote divergence.

in the age of molecular sequence comparisons, bacterial species have sometimes been defined as populations whose small-subunit rRNA sequences are more than 97% identical. It would be useful, however, to conceive of bacterial species in terms of functional processes, much as Ernst Mayr did for eukaryotic organisms. In plants, animals, and single-celled eukaryotes, interbreeding ensures that populations share the same pool of genes, providing a counterforce to mutations and selection pressures that promote divergence.

Green Algae

include a diverse assortment of species (about 10,000 have been described) that live in marine and, especially, freshwater environments. Green algae range from tiny single-celled flagellates to meter-scale seaweeds. They all are united by two features: the presence of chlorophyll a and chlorophyll b in chloroplasts that have two membranes, and a unique attachment for flagella.

over dispersed distribution

individuals are distributed more nearly uniformly than would be predicted by chance. Overdispersal can occur if one individual of a population prevents another from settling nearby, for example if all individuals depend on the same set of resources.

immigration

individuals coming in from somewhere else

preemptive competition

individuals occupy space, preventing access to resources

Humans add a lot of N to this cycle by

industrial processes

What are the basic patterns of air circulation and why do they function the way they do?

influenced by solar energy hadley cell -equator is heated so air rises (moist) and tons of precipitation forms, wet degrees -once the air drops its moisture (dry air), it moves north, cold dry air subsidence zone -biome existence by this air circulations -equator tropical forest much rainfall and high temperatures -just above and below the tropics, major deserts

Biotic interactions

interactions among living things

Abiotic

interactions between organisms and their nonliving environment

food web

interconnections organisms

CD4 receptor

is a glycoprotein found on the surface of immune cells such as T helper cells, monocytes, macrophages, and dendritic cells.

reverse transcriptase

is an enzyme used to generate complementary DNA (cDNA) from an RNA template

resource partitioning

is the process whereby similar species exploit the limited resources in an ecological area without one species driving the others into extinction.

Fore HIV to invade T cell

it must interact with CD4 and CCR5

HIV reverse transcriptase is very "sloppy", meaning that it makes many errors as it copies the viral genome. Why is this enzyme so sloppy?

it needs to generate a lot of variation to avoid the immune system

What are size, range and density?

key features of a population

The intensity of solar radiation varies with

latitude and altitude, as does the amount of annual precipitation and wind. These factors determine the amount of evaporation from Earth's surface to the atmosphere, including the amount transpired by plants. Evapotranspiration is the amount of water evaporated from the Earth's surface, either directly from ponds, rivers, and soils, or as water vapor transpired by plants

Stromatolites

layered mounds, columns, and sheet-like sedimentary rocks. They were originally formed by the growth of layer upon layer of cyanobacteria, a single-celled photosynthesizing microbe that lives today in a wide range of environments ranging from the shallow shelf to lakes, rivers, and even soils -among earliest records of life on Earth

What is life history? What factors affect the life history of an organism?

life history- how an individual allocates resources to growth, reproduction and survival. not everything can be maximized at the same time development, reproductive rate, reproductive age, body size, length of life, competitive ability, survivorship, population size, dispersal ability, habitat type, parental care

Food chain

linear depiction of energy flow Each feeding level in a chain is a tropic level

Macroparasites

live in host but release juvenile stages outside host's body

Endoparasites

live inside the host body (bacteria and tapeworms)

Ectoparasites

live on the outside of the host body (fleas and ticks)

How does the level of genetic variation in humans compare to the level of genetic variation in other species?

lower than other species

Robust Australopithecines

massive cheek teeth, massive cheekbones, saggital crest

eukaryotic origins

may have originated by symbiosis between an archaeon and a proteobacterium began to diversify after oxygen started to accumulate in the atmosphere and surface oceans

14. What is a microbiome? Why is it important?

microbe interaction within communities that respond to their surroundings essentially an environmental niche there are 10x more microbial cels in your microbiome than your own cells your microbiome affects your phenotype

differences in diet are apparent in

microbiota

What is mimicry? What is the difference between Batesian mimicry and Mullerian mimicry?

mimicry- the resemblance or mimic to another organism mullerian- the noxious species converge to reinforce warning (black and yellow striped of bees) batesian- palatable mimic resembles unpalatable model (scarlet king snake and coral snake)

territorial competition

mobile organisms protect a feeding or breeding territory

What biological technique has provided evidence used in establishing the eukaryotic superkingdoms?

molecular sequence comparisons

Host range

monophagous polyphagous

k-selected

more or less stable populations adapted to exist at or near carrying capacity, K Lower reproductive rate but better competitors (trees)

28. What is the primary characteristic of the Opisthokonta?

most diverse eukaryotic superkingdom, closest to humans and animals

7. What are the cyanobacteria? What is their primary claim to fame?

most successful group of microorganisms obtain their energy through photosynthesis, only photosynthesis bacterial lineage genetically diverse, live in many habitats formed early eukaryotes

Global patterns are affected by

mountains

Microparasites

multiply within hosts, usually within cells (bacteria and viruses)

5. What is the multiregional hypothesis? What is the Out of Africa (=African replacement) hypothesis? Which is most strongly supported by the data?

multiregional- an ancestor of H. sapiens migrated from Africa, colonized other regions, and all populations evolve into H. sapiens together via gene flow out of africa- african replacement, H. sapiens evolved in Africa and the migrates out of Africa to populate Earth Out of Africa hypothesis due to mose of the diverse fossils being found in this area

over time, competition can cause

niche differentiation

two key components of fertilizer

nitrogen and phosphorus

You work on a drug and discover that it is very effective against HIV in the laboratory. A drug company buys it from you and sells it to physicians who begin to give it to patients by itself. Should you be happy about this?

no, HIV will evolve resistance to my drug under these conditions

secondary metabolites

not part of primary energy generating metabolic pathway Alkaloids (nicotine in tobacco, morphine in poppies, cocaine in coca, and caffeine in coffee), phenolics (lignin in wood and tannin in leaves), and terpenoids (in peppermint) Over 25,00 compounds

15. What are the defining features of eukaryotic cells?

nucleus- prokaryotes do not have a nucleus size- eukaryotes are larger than prokaryotes, membrane bound organelles make the cell larger

What is logistic population growth? What is the general equation that describes this kind of growth? What are the parameters?

occurs when the growth rate decreases as the population reaches carrying capacity. dN/dt=rN(K-N/K) the parameters in this situation is that there is a carrying capacity

The prevailing winds drive

ocean currents

overgrowth competition

one organism grows over another

chemical competition

one species produces toxins that negatively affect another

nitrogen fixation

only certain bacteria are able convert to N2 and release ammonia (NH3) or ammonium (NH4+)

in eukaryotes, energy metabolism that requires membrane stability is confined to

organelles

consumptive competition

organisms consume the same resources

encounter competition

organisms interfere directly for access to specific resources

How did humans populate the earth?

our species migrate a lot

chemoautotroph

oxidize inorganic compounds

photosynthesis and respiration

oxygenic 6CO2+6H2O - C6H12O6+602

8. Why are some people resistant to HIV infection?

people who express the D32 allele of the CCR5 are resistant to infection

11. Describe the major modes of nutrition among bacteria and archaea (photoautotroph, chemoautotroph, etc..).

photoautotroph: get energy from the sun, carbon from inorganic molecules, CO2 chemoheterotroph: get energy from chemical compounds, carbon from organic molecules, glucose photoheterotrophs: get energy from sun, carbon from organic molecules, glucose chemoautotrophs: get energy from chemical compounds, carbon from inorganic molecules, CO2

23. What are the Archaeplastida?

photosynthesis organisms, including land plants most diverse next to opisthokonts

assimilation

plants and animals incorporate ammonia and NO3-

24. What is a primary plastid? A secondary plastid? How can you tell the difference?

plastid- double membrane bound organelle primary plastid- two membranes secondary plastid- multiple membranes (more than 2 because engulfing primary)

secondary consumers eat

primary consumers carnivores

base of the food chain

primary producers

Primary consumers eat

primary producers herbivores

In a pond, tadpoles eat algae and fish eat the tadpoles. Above the pond, grasshoppers eat grass and, at night, are preyed upon by bats. Other bats eat the fish that eat the tadpoles. In this community, the algae are:

primary producers.

A K-strategist will typically:

produce a few relatively large offspring and provide abundant parental care.

11. What is reverse transcriptase? Why is the RT of HIV so "sloppy"?

protein - RNA - DNA RT: the special viral form of DNA synthesis -‐ transcriptional errors made by HIV RT lead to mistakes in the sequence of HIV, in particular the RT gene itself -‐ there is variation in the viral sequence population -‐ RT is a very sloppy poymerase. It makes mistakes every 1/10,000 nucleotides it incorporates -‐ this is equivalent to a mistake every time a viral genome is copied -‐ this causes every HIV virion in the body to be different.

pol

proteins required for reverse transcriptase and integration into host DNA -Protease -Reverse transcriptase -integrase

In Glacier Bay, one of the first species to colonize a newly exposed area of glacial till is fireweed. You would predict that fireweed is a(n) ____________-selected species.

r

What are r-selected species? What are k-selected species.

r: high rater of per capita population growth, but poor competitive ability k: more or less stable population adapted to exist at or near carrying capacity. lower reproductive rate but better competitors

The most species rich terrestrial biome is

rain forest

The coastal redwood occupies an area 450 miles long and 5-35 miles wide from SW Oregon along the Pacific coast to just south of Monterey, California. What aspect of the population ecology of the coast redwood does this statement describe?

range

Type III

rate of loss for juveniles high and then loss low for survivors high mortality at the earliest stages of the life cycle. Small herbaceous plants, small animals such as mice, insects like the Lime Swallowtail, and other organisms that grow fast and reproduce early down and then straight

survivorship curves

record changes in survival probability over an organism's life span

In the Sierra Nevada Mountains of California there are many populations of the checkerspot butterfly Euphydryas editha. You notice that females of one population lay their eggs near the tip of a plant's stem (population A). Females of another population in the same area lay their eggs at the base of the stem on a different type of plant (population B). The young hatch out as caterpillars; they live on the host plant and eat its leaves.

reduced competition through resource partitioning

denitrification

reduction of nitrate (NO3-) to gaseous nitrogen (N2) by bacteria returns a small amount of nitrogen to the atmosphere

Amoebic Dysentery

responsible for 50,000-100,000 deaths every year.

Competitive exclusion

results when niches completely overlap

nuclear membrane (eukaryotic cell)

separates transcription and translation

niche

set of habitat requirements

17. What promotes genetic diversity in eukaryotes?

sex

6. Can different kinds of selection (what kinds?) be detected in the way we now behave? Give some examples.

sexual selection- mate choice natural selection- morning sickness toxins out of the body

Phylogeny of Archaea

showing the evolution of temperature preference, salt tolerance, acid tolerance, and production of methane within the domain.

How is the earth heated by the sun?

since its a sphere the earth cant be heated equally energy per unit area is different depending where you are on the earth more heat at the equator less at the poles seasons earth is not perpendicular to the sun different hemispheres are tilted at the sun at different times 23.5 degrees ile

majority of eukaryotic diversity

single-celled (protists)

key features of a population

size, range, density

nitrification

soil bacteria convert NH3 or NH4+ into nitrate (NO3-) used by plants

What is Liebig's Law of the Minimum?

species biomass or abundance is limited by the scarcest factor ex: nitrogen is the scarcest factor but once it is added phosphorous is the scarcest factor

Liebig's law of the minimum

species biomass or abundance is limited by the scarcest factor people went to a marsh and measured productivity added phosphorous did nothing so its not limited added nitrogen growth went up so this is the limiting factor

Island biogeography can explain

species diversity on islands Islands represent extremes in habitat patchiness for colonizing species: organisms that live on a mainland must successfully cross a barrier of water to establish a new population on an island. The term "island" includes any habitat patch that is surrounded by inhospitable environment. "Island" can apply to a body of water surrounded by land, an expanse of forest surrounded by grasslands, or a mountaintop alpine field surrounded by forests at lower elevation.

How do species interactions cause coevolution? Give an example.

species interactions are agents of natural selection and thus affect the evolution of the interacting species often causing coevolution -keystone species have outsized roles on a community -ecosystem engineers as keystone species

The antiviral drug AZT works by

stopping viral DNA synthesis

Streptococcus

strings of spheroidal or coccoidal bacteria

Community ecology

studies how groups of species interact and form functional communities

ecology

study of interactions among organisms and their environment

population ecology

study of what factors affect population size and how these factors change over space and time uses the tools of demography

Primary succession

succession on a newly exposed site that was not previously occupied by soil and vegetation

Secondary succession

succession on a site that has already supported life but that has undergone a disturbance, such as a fire, tornado, hurricane, or flood

Env gene

surface proteins -surface glycoprotein -transmembrane glycoprotein encodes a polyprotein which is a protein that later gets cut up

What are survivorship curves? Be able to distinguish between type I, type II, and type III survivorship curves.

survivorship curves plot numbers of surviving individuals at each age type 1- rate of loss of juveniles low and most individuals lost later in life (humans) type 2- fairly uniform death rate type 3-rate of loss for juveniles is high and then loss low for survivors - give birth to a lot of babies at once

Eukaryotic evolutions dominated by

symbioses, especially in the origin of organelles

Savanna

temperate grass land Tall, perennial grasses dominate this biome, which occurs in warm, relatively dry regions of eastern Africa, South America, and Australia. Rain is seasonal and ranges from 75 to 150 cm per year. Scattered trees and shrubs usually drop their leaves in the dry season to conserve moisture. As in temperate grasslands, fire plays a key role in maintaining this biome. Large mammalian grazers are abundant and diverse; these include the migrating antelopes, zebras, and giraffes well known from Africa, but also kangaroos and other marsupials in Australia and large rodents in South America. Predator diversity can also be high, as exemplified by lions and other cat species, hyenas, and wild dogs. Dingos are important predators in Australian savannas, but were introduced only a few thousand years ago from southeastern Asia. Before that, the top carnivores included large, now-extinct lizards, as well as snakes and smaller lizards still present in the biome.

Because energy is lost at each step of the pyramid

the amount of biomass present at any one level is only about 10% to 15% of that at the preceding level.

What is mutualism? Know some examples

the close association between the species in which both species benefit -ants chew up leaves to feed fungus they care for and then the fungus produces gongylidia as ant food

AIDS is caused, ultimately, by

the destruction of helper t-cells

What are some limits to productivity (terrestrial and aquatic)? What are the most productive ecosystems (terrestrial and aquatic)? What are the least productive?

the drier it is the less photosynthetic/the wetter it is the more photosynthesis; the warmer it is the more primary productivity/the colder it is the less; more nitrogen and phosphorous in the soil the more primary productivity; the more water productivity, the more primary productivity; tropical rainforest-most production; hot desert- least production; algal beds and coral reefs-most production, open ocean- least production

7. Why does the immune system fail after HIV infection?

the immune system fails after the HIV infection because the HIV virus directly kills off the cells central to the immune response

What plays a fundamental role in HIV infection

the immune system, it is both the defense against and the target of HIV

Diatoms

the most diverse stramenopiles, and among the most diverse of all protists. Their shapes, outlined by their tiny skeletons made of silica (SiO2), can be (a) like a pill-box, (b) elongated, or (c) twisted around the long axis of the cell. Some diatom species form colonies, like those shown in (d).

Secondary plastids support

the multiple evolution scenario

population size

the number of individuals of all ages alive at a particular time in a particular place. For example, the population of krill around Antarctica is estimated to be 800 trillion. The size of a population may increase, decrease, or stay the same over time, and trends in population size are a key focus of ecological research and its application to conservation biology.

What is carrying capacity?

the number of people, other living organisms, or crops that a region can support without environmental degradation amount of people environment can hold

What are biogeochemical cycles? Be sure to understand how the following cycles work: Water, Carbon, Nitrogen

the physical stuff that makes up energy

What is predation? What are the animal defenses against predation? What are some plant defenses against herbivory?

the preying of one animal on others animals: toxic chemicals, mimicry, camouflage plants: chemicals, tissue toughness, thorns, barbs

Diffusion

the primary limit to bacterial size

What is habitat fragmentation? How can it lead to extinction?

the process by which habitat loss results in the division of large, continuous habitats into smaller more isolated remnants causes organisms to leave their habitats which causes population fragmentation and eventually ecosystem decay and extinction

evapotranspiration

the process by which water is transferred from the land to the atmosphere by evaporation from the soil and other surfaces and by transpiration from plants.

A consequence of how the earth is heated by the sun is that

the region around the equator is warm and wet the areas around 30 degrees north and south latitude tend to be dry sea breezes blow on shore during the day and out sea at night

Community

the set of all populations found in a given place Can occur on a wide variety of scales and can be nested

What is island biogeography? What are the main factors that lead to a stable number of species on any give island?

the study of the species composition and species richness on islands size, distance, resources

What is the ultimate source of energy in most ecosystems?

the sun

12. Why do some scientists look on the tree of life as more of a bush?

the tree of life is more complex and its growing in crazy directions rather than in a straight formation organisms are more complex and have fore lineage, new branches are arising

Prokaryotic diversity

the two great prokaryotic domains, Bacteria and Archaea, originated 4-3.5 billion years ago. They diversified greatly with the rise in oxygen levels in the atmosphere and oceans about 2.4 billion years ago, and again with the diversification of animals during the Cambrian explosion, reflecting coevolution between eukaryotes and prokaryotes

Lytic cycle

the viral DNA directs the production of new viral particles by the host cell until the virus kills the host by lysis In the lytic cycle, the bacteriophage DNA is integrated into the host chromosome. This prophage is replicated along with the host DNA as the bacterium divides. It may persist as a prophage, or enter the lytic cycle and kill the cell.

Which statement is NOT true about robust australopithecines?

they gave rise to the genus Homo.

Some people are resistant to infection with HIV because

they have mutant alleles of helper T-cell surface proteins that cannot bind the virus

9. How is HIV transmitted?

through direct contact with an infected individual through body fluids

vesicles budding off from membranes (eukaryotic cell)

transport materials into the cell in endocytosis and release material from the cell in exocytosis

The lineage that leads from the last common ancestor of chimps and humans to living humans contains all the species in the

tribe Homininae

The hominoidea

tribe hominini all apes This evolutionary tree was derived from the nucleotide sequences of several different genes that are common to humans and apes.

Rank Most productive terrestrial areas to least productive

tropic rain forest tropical deciduous forest temperate deciduous forest savanna Prairie Cultivated land Taiga Tundra Hot desert

Terrestrial productivity

tropical rainforests, a lot of primary productivity Less as you scatter from equator

3 patterns of survivorship curves

type 1 2 and 3

detritus

unconsumed plants, remains of animals, and waste products

conjugation

unites results of oxidation with another molecule to create inactive and readily excreted product

If you were to sequence HIV virions from an infected person over time, the sequence of those viruses would

vary dramatically over time

Gracile australopithecines

vertical posture

What is considered attractive changes over time and culture

w/h=.7 Some aspects of attractiveness are cross cultural. Males of different cultures select the same shaped females as most attractive.

Imagine that you have a garden full of sunflowers in your backyard. Unfortunately, you don't have much time to tend to the garden. You eventually notice that two small birch trees sprout and begin to grow among the sunflowers. The birch trees are slower growers than the sunflowers, but by the fifth summer they start to shade the sunflowers. The birch trees and the sunflowers are in competition for:

water, nutrients, light

If niches do not overlap completely

weaker competitors use nonoverlapping resources

geological transport mechanisms

weathering and erosion of rocks, and elements transported by surface and subsurface drainage

realized niche

what resources the species can actually use

The ratio of evaporation to transpiration effectively tells us

what type of vegetation can be supported in a given region. Deserts, with low annual precipitation, have a high evapotranspiration ratio: Soil moisture evaporates rapidly, and plants must keep transpiration (and therefore photosynthetic rate) to a minimum. At the other extreme, rain forests have low evapotranspiration ratios: High precipitation permits nearly unlimited transpiration (and therefore high photosynthetic rates, leading to luxuriant growth), enabling the development of wet forests with high biomass. Intermediate evapotranspiration ratios occur in the temperate zones that encompass much of the United States, Europe, and parts of eastern Asia, as well as at mid-altitudes, below the highest mountain peaks but well above the coastline. Both latitude and altitude influence evapotranspiration through their effects on temperature and precipitation, and the combined effects of these factors are reflected in the distribution of biomes around the world.

What is commensalism? Know some examples

when one organism benefits off of another with no affect on the other individual -example is a water buffalo kicking up bugs out of the dirt for birds to eat

Deciduous Forest

where we live A moderate climate and dominance of hardwood deciduous trees occur across much of eastern North America, Europe, and Asia. Much of this biome has been subjected to human disturbance for agriculture and urban development. There are usually 15 to 25 tree species, including maples, oaks, poplars, and birches. Springtime sun passes through seasonally leafless trees to reach a diverse understory flora. Soils are rich in nutrients from annual leaf fall, and the moderate temperatures and precipitation promote decomposition, while the cool winters promote accumulation of organic materials. Soils contain a diversity of microbes and fungi, along with the protists and invertebrate animals that feed on them. Insects, birds, and mammals are relatively diverse, joined by snakes, lizards, and amphibians.

The latitudinal difference in incoming solar energy density explains

why Earth's surface is hotter at the equator and cools towards the poles

Can humans detect genetic relatedness by smell?

yeet

20. Are protists a monophyletic taxon? Explain your answer.

yes because it includes all ancestors

Exponential Growth

△N/△T = rN When r>0, population increase is rapid Characteristic J-shaped curve Intrinsic rate of increase, rmax = r at maximum Because population growth depends on the value of N as well as the value of r, the population increase is even greater as time passes This happens in nature sometimes for brief periods, e.g., reintroduction of a population to a habitat, growth of introduced exotic species, and global human population

Exponential growth

△N= N2-N1= (B-D) + (I-E) △N= change in population size △N/△T = rN B= # births D= # deaths I= # immigrants (enter a population) E= # emigrants (leave a population)