Exam Review 2 Flashcards
1
Q
What is HIV?
A
- Human Immunodeficiency Virus
- Most cases are present in subsaharan Africa (2/3)
- HIV can lead to AIDS if left untreated
2
Q
How is HIV transmitted?
A
- it is sexually transmitted, but can also be transmitted through blood
- 2/3 cases are common amongst homosexual and bisexual men
3
Q
People who die from HIV don’t die from the virus but…
A
- they die from t he infections that that virus prohibits your body to fight off
- the rates in the U.S are declining
- it takes a very long time (years) to kill you
4
Q
What is the structure of HIV?
A
- it is an enveloped retrovirus
- has an RNA genome
- Reverse transcriptase enzymes
- has surface glycoproteins which allows for its connection to other cells
5
Q
How many genes can HIV encode?
A
- HIV genome can encode 9 genes and multiple proteins
- some of the genes that are encoded that are translated as poly proteins which are attached into individual proteins later by action of a viral protease
6
Q
What is the life cycle of HIV?
A
- ## it has an extracellular and intracellular phase
7
Q
What is the immune system’s role in HIV infection?
A
- to is the defense against HIV but it is also the target of HIV
- the proteins in helper T cells in the immune system are what HIV infection is attracted to
8
Q
What is an adaptive immune system?
A
- its the immune system that responds to infections and remembers them in order to fight them off better next time
- has two parts: humoral and cellular
9
Q
What are Helper T cells?
A
- they are CD4+ or T4 cells that are central to both immune system response
- they are what the HIV virus uses to get into other cells
10
Q
Why is drug treatment ineffective in the long run for HIV?
A
- viruses use your own cells to make copies and replicate
- drug treatment usually only tries to target some vital viral infection
- two types of treatments available: anti-reverse transcriptase (RT) and protease inhibitors
11
Q
What is the Anti-reverse transcriptase (RT)?
A
- targets viral DNA synthesis
- aims to stop synthesis by incorporating nucleotide analogues (the drug) to stop transcription (it adds a chain terminating nucleotide)
12
Q
Why does anti RT therapies fail?
A
- it is a very sloppy polymerase which makes a lot of mistakes resulting in every HIV virion in the body to be different
- the variation in RT sequences lead to variation in RT polymerase function
- Natural selection takes place for drug resistant virions
- mutations are passed to mutant offspring
- then the HIV population in a patient becomes resistant to the RT drug treatments
13
Q
How is HIV treated now?
A
- modern HIV uses cocktails of drugs because of how frequent and quickly the virus mutates
14
Q
How does HIV beat the immune system?
A
- the immune system is an agent of selection and it relies on epitopes to detect foreign entities.
- HIV constantly changes its epitopes so the immune system misses or doesn’t recognize it as foreign
- HIV also kills off the immune system through viral infection and through the destruction of Helper T and Killer T cells
- The high error rate of HIV RT is likely an adaptation acquired by its interaction with he immune system
15
Q
What does HIV require to enter into cells?
A
- the presence of the CCR5 co-receptor
- people express delta 35 allele of CCR5 are RESISTENT to infection but not immune
16
Q
Where did HIV come from?
A
- Epidemiological data suggest Central Africa as the source of HIV
- HIV is thought to be zooiotic meaning it was present in animals and then transferred to humans.
- for example; when chimps were hunted, and their blood was transferred to humans, it could have been infected with the HIV virus and infected the hunters.
17
Q
What is SARS-CoV2?
A
- it is Severe Acute Respiratory Syndrome that was caused from Corona Virus 2 caused by COVID-19
- this disease emerged in December 2019
- it’s transmitted by droplets person to person
18
Q
What does COVID affect?
A
- the respiratory tissues initially, but it can move and spread throughout the body after infection
- this virus can also infect deer, guinea pigs, bats, etc.
19
Q
What is the viral structure of COVID?
A
- it is a positive sense ssRNA virus
- the virus is enveloped like HIV
- the surface proteins include SPIKE glycoprotein
- the genome encode polyproteins that are cleaved by proteases to produce structural and non structural proteins
20
Q
What is the Life Cycle of SARS-CoV2?
A
Stage 1 -
Stage 2 -
Stage 3 -
Stage 4 -
Stage 5 -
21
Q
What is the Diversity in Phylogeny?
A
- variants in the phylogenetic contain novel mutation
- clades are viruses that share various mutations
- major new clades are gives Greek letters (i.e Omicron)
- some clades have gone extinct (we think)
22
Q
Why does Omicron contain many more mutations than previous variants?
A
there are 3 alternative hypotheses
- believed researches simply missed a series of mutations that led to Omicron in places like S. America or Africa
- PREFERRED: variant evolved mutation in one person as part of a long-term infection
- could have emerged in unseen animal hosts
23
Q
What increases the amount of SARS-CoV2 virus variability?
A
- recombination between strains will increase variability
- recombination takes place in a single person infected with more than one strain
- recombination generates more diversity in the virus which is very bad
24
Q
Where do mutations take place in SARS-CoV2?
A
- lots of the mutations take place on the surface which is where the spike protein is encoded
- genes exposed to the surface
25
Where did SARS-CoV2 come from?
- it is a zoonotic virus // moved from animals to humans like HIV
- the closest relative in nature are the coronaviruses in bats
26
What are prevention and treatment plans for SARS-CoV2?
- Masks (N95s)
- Drugs
- Contact tracing, testing, and quarantine
- Vaccines
- Ventilations (opening windows, etc)
27
SARS-CoV2 Vaccines
4 types
- Pfizer & Moderna (new technology involved with mRNA)
- J&J, AstraZeneca, & Sputnik (new technology involving non-replicating adenoviral vector)
- Sinovac, Sinopharm, & Covaxin (injects inactive virus)
- Abdala & Soberana 2 (utilizing protein subunits)
28
What are humans and how are they characterized?
- humans are primates
- primates are characterized by
a. grasping hands -- precision grip (holding a pencil) and power grip
b. binocular and color vision with overlapping fields of view -- aids with depth perception
c. large brain allowing complex social systems
d. nails instead of claws
29
Where did Darwin think we should look for our closest living relatives?
- Africa
- just using morphology, it is hard to tell who our closest relative was among the apes
- we have possible relationships among chimps and gorillas
30
How did scientist connect humans to chimpanzees?
- using Molecular Analysis (DNA-DNA hybridization), relationships were found
31
Where do Humans fall with our lineage? What tribe?
- tribe Hominini
- there is very little genetic diversity between humans compared to other apes
- the Great Apes (gorilla, orangutans, gibbons) are all from the family Hominidae
32
Where do we look for fossil hominins?
- there are fossil sites found in Africa
- Africa is said to be where the oldest fossils are found
- they are usually found in the Riff Valley
33
Did humans evolve from chimpanzees?
- they did not. These species share a common ancestor
34
Homonin Evolution: Ardipithicus ramidus
- they appeared 4.4 mil years ago
- walked upright (their foramen Magnum was rotated already)
- their feet were unusual since they seemed to be adapted to walking upright and climbing
- they have small bodies & brain
- pointy and small canines
- long arms and big hands
- only recently described (2009)
35
Homonin Evolution: Australopithecines (southern apes)
- appeared 4 mil years ago
- walked upright
- they had larger brains than the other apes, but still relatively small
- two distinct branches
36
What are the two branches of Australopithecines?
Africanus
- famous for the Lucy skeleton
- their big toe was rotated towards the front similar to humans
- we can see a basic trend in human evolution which is that the increasing brain size and decreased sexual dimorphism
- compared to H. Sapiens many traits changed together
- since Africanus was smaller, their pelvic bone was smaller and more compact -- human pelvic bones grew in order to compensate their bigger brains
"Robust"
- contain sagittal crest
- massive cheekbones and cheek teeth
- males were bigger than females
- they were a "side branch" of the hominin tree
- they left no living Descendents
37
Genus Homo
- a big brain develops here and there are three types:
Homo erectus
- 1.8 mil years ago
- large brains
- more socially advanced
- had sophisticated stone tools that aided in hunting
- used fire
- migrated out of Africa to places like Indonesia
Homo neanderthalensis
- 300,000 - 30,000 years ago
- similar to modern humans // muscular, fully erect, dexterous, large brains // their body type adapted to colder weather
- developed ritualist burial ceremonies
Homo sapiens
- 200,000 years ago
- developed a chin
- direct ancestors of modern humans
- they were artistic and made precision tools
38
Who are the new hominins we keep finding?
Homo floresiensis
- dwarfed hominin most closely related to H. erectsus (discovered in '04)
Homo nadeli
- found almost complete skeleton
- were they intentionally buried
- discovered in 2015
- very young yet have primitive features on their cranium
39
How do we determine which hominin is related to the other?
- synapomorphies
- age of fossils
40
What are the Origins of Homo sapiens? (Hypotheses)
2 hypotheses
- Multiregional Hypothesis (ancestor migrated from Africa, colonizes other regions, and all populations evolve into H. sapiens together via gene flow -- this accounts for geological differences)
- Out of Africa Hypothesis (aka African Replacement -- H. sapiens evolve in Africa, then migrate our to populate the earth)
41
How do we test the hypotheses and what were the findings?
- using mitochondrial DNA to test hypotheses
- data from the mtDNA supports the out-of-Africa hypothesis // because it demonstrates that the differences seen in people are superficial // most genetic diversity is in Africa -- as you move further out, the less diverse
42
Why are modern humans thought to be interspecies hybrids?
- thought to have hybridized with H. neanderthals at least twice
- African people have no H. neanderthal DNA but European people have 2-3%
43
Natural Selection in Modern Humans
morning sickness (a behavior)
- thought to be an adaptation that evolved to protect the fetus in early development since food is toxic // plants especially
lactose tolerance (a change in physiology)
- human babies are lactose-tolerant
- in majority of humans, this stops by adulthood
- the degree of lactose intolerance in adults varies geographically
- adult humans that are lactose tolerant are mutants
44
What is ecology?
- study of interactions among organisms and their environment
There are 2 types of interactions
- biotic interactions // interactions among living things
- abiotic interactions // interactions between organisms and their nonliving environment
45
What is a population?
- all the individuals of a given species that live and reproduce in a particular place
46
What is population ecology?
- the study of what factors affect population size and how these factors change over space and time
47
What tools does population ecology use?
- uses the tools of demography // birth rates, death rates, age distributions, and sizes of populations
48
What are key features of a population?
- size // how many organisms in a population
- range // where do these populations live
- density // how many organisms per unit area
49
What are dispersion patterns that are related to density?
Clumped - if you encounter one, you'll encounter another close by
- most common
- resources tend to be clustered in nature
- social behavior can promote this pattern
Uniform - if you encounter one, you'll encounter another on equal amount of space away
- competition may cause this pattern
- may also result from social interactions
Random - if you encounter one, you don't know where you'll see another
- rarest pattern
- resources are rarely randomly spaced
- it can occur where resources are common and abundant
50
Name the four factors that affect population size
- birth (positively affects)
- Immigration (positively affects)
- Emigration (negatively affects)
- Mortality (negatively affects)
51
What are the two basic models that account for how populations grow?
- Exponential growth (J) curve // simplest, but unrealistic
- Logistical growth (S) curve // realistic
52
What are the key terms to know for exponential growth?
- N = population size
- change in N = change in population size
- B = number of births
- D = number of deaths
- I = number of immigrants
- E = number of emmigrants
- r = per capita growth rate
Equation:
Change in N = N2 - N1 = (B - D) + (I - E)
Change in N / change in time = population size per capita
53
Exponential Growth
- assumes no limits
- when r > 0, population increase is rapid
- has a J shaped curve
- there's a max growth rate
54
Logistic growth
- more realistic because it incorporates limits on growth
- s shaped curve
- incorporates carrying capacity (K)
55
What is the equation for logistic growth?
- change in N / change in T = rN(K-N/K)
- when the number is low, it grows faster // when the number is bigger it grows slower
56
What are the checks on population growth?
Density-dependent factors
- mortality factor whose influence varies with the density of the population
- parasitism, predation, competition, and disease
- predators kill few prey when the prey population is low, they kill more prey when the prey population is larger
Density independent factors
- predators will kill the same number of prey no matter their population size
- physical factors // weather, drought, flood, fire
57
Population growth based on age structure
- not all organisms in a population contribute equally to population growth
- birth and death rates vary with age and environment
58
What is demography?
- the study of the size, structure, and distribution of populations over time
59
What are survivorship curves?
- curves that record changes in survival probability of an organism's life span
There are 3 patterns of survivorship curves:
- Type I // rate of loss of juveniles is low and most individuals are lossed later in life
- Type II // fairly uniform death rate
- Type III // rate of loss for juveniles is high and the loss is low for survivors
60
What is life history, and its strategies?
life history // how an individual allocates resources for growth, reproduction, and survival
strategies //
- continuum
- r-selected species // high rate of per capital population growth, r, but poor competitive ability (i.e weeds)
- k-selected species // more or less stable populations adapted to exist at or near carry capacity (K) // lower reproductive rater but better competitors (i.e trees)
61
What is a metrapopulation?
- a group of populations linked by immigrants
62
What are the two main outcomes of species interactions and communities?
- interactions such as competition and consumption can
1. 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 co-evolution (in the long term)
63
Interactions among species
- populations do not exist in isolation
- all populations are tightly linked to other populations that share the same habitat
64
What are the 4 types of interactions between species?
- Commensalism (0/+)
- Competition (-/-)
- Consumption (+/-)
- Mutualism (+/+)
65
What is commensalism?
- one species is not affected and the other species benefits
i.e when a buffalo steps on the ground making bugs fly away which allows the birds that follow the buffalo to get food
66
What is competition?
- it is detrimental to both individuals // reduces available resources
- every species has a niche and competition comes when the niches overlap
- competitive exclusion results when niches completely overlap // can drive to extinction (locally)
- niche differentiation (resource partitioning) happens with a partial niche overlap
67
What is the competitive exclusion principle?
- complete competitors cannot coexist
68
What happens when a niche doesn't completely overlap?
- the weaker competitor uses non overlapping resources
69
What happens during resource partitioning?
- natural selection will favor individuals that do not compete // changing its fundamental niche -- niche becomes more specialized reducing its competition
70
What is consumptive competition?
- it is where organisms consume the same sources // competing for H2O and minerals
i.e ) tree roots competing for water and nutrients
71
What is preemptive competition?
- Where individuals occupy space, preventing access to resources // fighting for space -- excluding any other species from their space
72
What is overgrowth competition?
- where one organism grows over another // competing for light -- usually grows faster and bigger
i.e) fern overgrows compared to other individuals and is shading them
73
What is chemical competition?
- where one species produces toxins that negatively affects another one // competition for water -- plants poison other plants to stop them from growing
74
What is territorial competition?
- where mobile organisms protect a feeding or breeding territory // competition for space
i.e) grizzly bears drive off black bears
75
What is encounter competition?
- organisms interfere directly for access to specific resources // competition for food
i.e) hyenas and vultures fighting over a zebra carcass
76
What is consumption?
- one species benefits while the other is harmed
- herbivory (herbivore +, plant -)
- parasitism (parasite +, host - )
- predation (1 animal eats another)
77
What does predation lead to?
- coevolution by prey
78
What are the anti predator strategies?
- Chemical defense
- Cryptic coloration
- Mimicry
- Displays of intimidation
- Fighting
- Agility
- Armor
79
What is the anti predator strategy of chemical defense?
- when animals or plants have a chemical that they can secrete to harm other animals/plants
- aposematic coloration (warning coloration) warn predators
- example would be tropical frogs
80
What is the anti predator strategy of cryptic coloration?
- camouflage
- stick insects blend in with branches, sea horses can adopt a body coloration
81
What is the anti predator strategy of Mimicry?
- resemblance of mimic to another organism
2 types
- Müllerian mimicry // noxious species converge to reinforce warning -- example) black and yellow stripes on bees and wasps
- Batesian mimicry // non toxic species that resembles a toxic species
82
What is the anti predator strategy of displays of intimidation?
- porcupine fish inflates itself
- deceive predator about ease of eating prey
83
What is the anti predator strategy of fighting?
- horns and antlers can be used to defend
84
What is the anti predator strategy of Agility?
- be faster than predator
- grasshoppers powerful jumping ability
85
What is the anti predator strategy of Armor?
- shells of turtles provide strong defense
- beetle exoskeleton
86
What is the 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 are restricted to feeding on 1 or 2 host plants
87
What are plant defenses?
they have an array of unusual and powerful chemicals
- secondary metabolites // not part of the primary energy generating metabolic pathway -- they have alkaloids that taste bitter -- have mechanical defenses like thorns and spines
- plants also make new chemicals which makes herbivores affected until they develop mechanisms to fight off the chemical
plants & herbivores go back and forth like this
88
How can herbivores over come plant defenses?
they detoxify using 2 pathways
- oxidation // catalysis of secondary metabolite
- conjugation // unites results of oxidation with another molecule creating an inactive and readily excreted product
89
What is mutualism?
close associations between species in which both species benefit -- 2 types
- facultative // short term; non-essential mutualism
- obligate // necessary mutualism (cannot live / function without each other)
90
What is a community?
- the set of all populations found in a given place
- can occur on a while variety of scales and can be nested
91
What is community ecology?
- studies how groups of species interact and form functional communities
- if they interact for a long time, they'll become adaptive to one another (co-evolution)
92
What is a keystone species?
- species that have outsized roles on a community
i.e) sea kelp are key to the health of otters -- it keeps them safe and protected
93
What modifies community composition?
- disturbances such as dramatic changes in climate or weather
- fire, flood, drought, volcanoes, hurricanes, frost, etc
- biotic changes to a community as well such as human activity or beaver dams
94
What is succession?
where communities change over time // the community's response to disturbance
- gradual and continuous change in species composition and community over time
- primary succession // begins on bare rock
- secondary succession // succession on a site that already supported life but was disturbed by fire, tornado, etc.
95
What is island biogeography?
- balance of immigration of new species & extinction of old ones
96
What is the effect of immigration / extinction on island size?
- larger islands have higher immigration rates than smaller ones bc they have more space for them to inhabit
- the larger islands have lower extinction rates than small islands bc they have more resources to keep them alive
97
What is the effect of immigration and extinction of distance of an island?
- its easier to migrate to an island closer than farther away
- extinction rates are not influences by distance
98
What is an ecosystem?
- a community of organisms and the physical environment it occupies
99
What features determine a biome (what they look like?
- flow of energy
- cycling of chemical elements within the ecosystem
100
What is a food chain?
linear depiction of energy flow
- each feeding level is a trophic level
- comply models turn into food webs
101
Explain abiotic environmental food chain
- primary producers collect energy from sun
- consumers come and eat the primary producers
- when consumers die, decomposers come in to recycle their nutrients back
102
What are autotrophs?
- organisms that harvest life or chemical energy
- primary producers are autotrophs
Chemotrophs
- oxidize inorganic cmpds
103
What are heterotrophs?
they eat other organisms
- primary consumers eat primary producers (herbivores)
- secondary consumers eat primary consumers (carnivorous)
104
What does a trophic pyramid tell us?
- biomass amounts decrease as you go up trophic levels
105
Why are chain lengths small in most food webs?
- because the second law of thermodynamics says that energy conversions are not 100% so some energy is lost in every transfer process
106
what are Biological transport mechanisms?
- absorption of chemicals by living organisms and their subsequent release back into the environment
107
What are Geological transport mechanisms?
- weathering and erosion of rocks, and elements transported by surface and subsurface drainage
108
What are chemicals transport mechanisms?
- dissolved matter in rain and snow, atmospheric gases, and dust blown by wind
109
What do movements of chemicals through ecosystems evolve?
- Biological transport mechanisms
- Geological transport mechanisms
- Chemical transport mechanisms
110
What is the Nitrogen cycle?
1. Nitrogen fixation - only certain bacteria are able to convert to N2 and ammonia/ammonium
2. Nitrification - soil bacteria converts ammonia/ammonium to Nitrate used by plants
3. Assimilation - plants and animals incorporate ammonia and Nitate
4. Ammonification - conversion of organic N to ammonia/ammonium // most common pathway for N to enter soil
5. Dentrification - reduction of nitrate to gaseous N2 by bacteria // returns small amount of N to the atmosphere
111
What causes eutrophication?
- fertilizer runoff
112
What are biomes?
- they're broad ecologically uniform areas
- biome location is dependent on climate
- dependent on atmospheric circulation as well
113
What is atmospheric circulation?
- differences in temperature that occur due to lat. variation
- because it is on a tilt the earth is not heated uniformly
114
What are global patterns of atmospheric circulation and precipitiation influenced by?
- by solar energy
- based on warmth at equator causing air to rise and flow north and south toward poles
- air cools and falls, flowing back to the equator
115
Rain fall patterns
- 0 degrees is a wet band (rain forests)
- 30 degrees is a dry band (deserts)
- rising air cools, generating rainfall
116
What affects climate?
- elevation and other local features
117
What are rain shadows?
prevailing winds hit mountain air goes up, cools down, and dries -- can lead to desserts on sides of mountains
118
What is proximity of land mass to H2O?
- sea moderates coastal and island temperatures
119
What is plant convergence?
- plants ability to adapt to biomes
120
Tundra
- cold, little rain fall
- highest latitudes
- plants with shorter growing seasons
- lots of migration in summer
121
Alpine
- tops of highest mountains
- cold, little moisture
- plants have short growing seasons
122
Taiga
- slightly warmers, more moisture
- adapted for snowfall
- evergreen trees
- bear, tiger, reindeer
- decomposition is slow here
- soil is acidic
123
Temperate coniferous forest
- more coastal
- warmer
- home to largest organisms on Earth
124
Deciduous forest
- increased rainfall
- eastern North America
- we live here
- plants go dormant
125
Temperate grasslands
- mid west
- dryer conditions
- turned over for agriculture
- characterized by fire and plants have adapted here
- cannot support trees
126
Dessert
- extremely dry
- very little rainfall
127
Chaparral
- coastal Mediterranean
- have shrubby bushes
- where olives grow
128
Savanna
- tropical grasslands
- seasonal rains
- warm and dry
- lots of fire
- support large animals
- majority in Africa
129
Tropical rain forest
- lots of rain
- almost always warm
- home to most species
- large human population
130
What are the influences on primary production?
- in terrestrial systems, linear relationship with annual precipitation
- temerpatures
- Nutrients (N and P) // species biomass or abundance is limited by the scarcest factor
131
What are two key. components of fertilizer?
- Nitrogen and Phosphorus
132
Aquatic ecosystem primary productivity
- limited by light and nutrient availability
- water absorbs light (photosynthesis happens at surface)
- Nitrogen and Phosphorus occur in very low concentrations
133
How does primary productivity vary?
- highest in tropical rainforests
- decreases progressively toward poles
134
What are the patterns of Primary Productivity on Land vs Oceans?
- higher at the equator
- decreases at the poles
- higher at coasts near mountains
