Bio 121 | | Lectures 1-29 | Final Exam
T/F O is the least common phenotype.
F It is fairly frequent, even though it is homozygous recessive. [Big Picture: Whether it is dom or res does not affect how common or valuable the trait is → dom ≠ superior, res ≠ inferior]
T/F Almost 35% of all species are parasites.
F More than *50%* of all species are parasites.
discrete exponential growth
Exponential growth that happens at specific intervals (ex. a certain species only breeds during one particular season) --- only for *non-overlapping breeders* N = population N₀ = population (initial) R₀ = net reproduction rate t = time
Humans have __________ base pairs in a *haploid* genome which contains ____________ protein-coding genes.
3x10^9 (3 billion) 21,000
stribild
4 drugs to combat AIDS in a 1-a-day pill --- $38,000/year
how many possible codon combinations are there? how many amino acids are there?
4 nucleotides 3 base pairs = 4³ = 64 bp Only 20 amino acids --- several amino acids can have more than one codon combinations ~ *degenerate* ----- ex. Proline = CCC/CCU/CCA
amino acid structure
5 Parts: --- carbon --- hydrogen --- carboxyl group --- amino --- R group
nucleotides are made of
5 carbon sugar, phosphate group, nitrogenous base
RuBP
5c NOT DUN
Escherichia coli (aka E. Coli) has a between ______ - ______ total proteins
600 800
P680
680 implies that the chlorophyll α works best at that wavelength
1 mol of glucose = __________ kcal E
686
T/F Most growth will occur in developed nations.
F Most growth will occur in developing nations --- By 2050: 8.4 bil in developing nations, 1.4 bil in developed
T/F Mutations have a large effect on evolution.
F Mutations are the ultimate source of GV, but have little effect on evolution
T/F 80% of the energy autotrophs obtain from the sun is used for photosynthesis.
F Only 1-3%
T/F Parasites are found only in Protista, Archaea, Bacteria.
F Parasitic organisms are in all 6 kingdoms.
T/F HIV kills its host by destroying T helper cells which suppresses the immune system.
F Rather, because the immune system is suppressed, other *opportunistic infectors* are no longer help back from laying havoc in our bodies. HIV does not kill directly, it is indirectly involved.
T/F Sex will change allele frequency.
F Sex will change GENOTYPE frequencies, but will not change allele frequencies (only jumbles them around)
T/F There is only one sure-fire way to cure AIDS.
F There are *NO* cures to AIDS currently, only delaying the effects
T/F C₄ and CAM plants do not go through the Calvin Cycle.
F They still go through it, just with an extra step
Reproductive Differences Between Males and Females
Female → produce fewer/larger gametes and tend to invest more in reproduction Male → produce more/smaller gametes and invest less in reproduction
homogametic
Females (XX)
Using the Logistic Growth Equation
Find the logistic growth rate for N = 100, 500, 700 and explain your results K = 1000 r = 0.3/wk ∆N/∆t = rN*(K-N)/K N = 100 → ∆N/∆t = 27 N = 500 → ∆N/∆t = 75 N = 900 → ∆N/∆t = 27 The graph of this population follows a standard logistic curve. It rises from the bottom, reaches its highest rate at N=500 (since point of max growth = K/2), then the rate mellows out as it aproaces K.
NPP explained through thermodynamic
First Law of Themoodynamics - energy is conserved → energy input is either used to do work or is stored --- GPP is either stored (NPP) or used to do work (RSP) Second Law of Thermodynamics - the amount of energy free energy in an isolated system declines due to an increase in disorder (entropy) --- Ecosystems are NOT isolated systems since they are constantly getting energy from the sun --- RSP is the energy cost for maintaining order
Ubiquinone
First major protein complex in the ETC --- contains NADH-Q REductase and Succinate Dehydrogenase
Glycolysis
First step of aerobic AND anaerobic respiration because it *does not require oxygen* Occurs in the *cytosol* (the aqueous component of the cytoplasm of a cell) Starts with *Glucose (6c)*; Ends with *2 Pyruvate (3c)* + net *2 ATP *and *2 NADre* --- 10 total steps (although we just look at the big picture) *Steps:* a) Activate Glucose (6c) (needs E to start reacting) → *cost 2 ATP* b) Form 2 PGALs (3c) [phosphoglyceraldehyde] c) Create 4 ATP (not 2) and 2 NADre d) Form 2 Pyruvate (3c)
Tribolium
Flour Beetle experimented on by Park 2 species in container - winner determined by environment T. castaneon --> wins when hot/moist T confusum --> wins when cool/dry *Either species wins depending on environmental conditions*
Why are most of the energy humans could consume from grain wasted? (this is a poorly phrased question I don't know how else to word it)
70% of grain is used to feed livestock (which means we lose 90% of the energy that we could have consumed)
Nitrogen-fixing bacteria
79% air is nitrogen, but plants can't get is since N2 is triple bonded Certain bacteria can fix atmospheric nitrogen into useable organic nitrogen --- uses enzyme nitrogenase --- N2 +8H2 --> 2NH3 + H2 --- requires 16 ATP (quite a lot) Rhizobium, a nitrogen-fixing bacteria, invades roots of legume tree where it can fix nitrogen and release extra nitrogen into the soil (SYMBIOTIC) *Mutualism* --- Rhiz supplies Nitrogen --- tree supplies sugar from PHS and provides anaerobic environment
Chimps and humans are ____% genetically similar
98
DNA between humans is ________% identical
99.5
Any two unrelated individuals are _____% identical
99.5 --- simply b/c human haven't been around long enough
Cholesteral
A type of lipid made from *saturated (fatty) acids* used in the building of cell membranes and sex hormones (testosterone and estrogen) Transported throughout the body by *lipoprotein*
*Generalized *photosynthesis equation (i don't think we'll need this particular version of the equation but he included it in his lecture)
CO₂ + H₂O + light energy → CH₂O + O₂
Cryptic Coloration
Camouflage; makes an organism difficult to spot. --- ex. peppered moth
Advantage of rapid reproduction
Can recover from hardship relatively easily *Ex.* Haddock (r-selected) recovered from over-fishing; Blue whales (k-selected) were hunted to near extinction and reproduce rarely so the population did not recover
tumor angiogenesis
Cancer cells have the capacity to get their own blood supply to provide nutrients and resources --- growth of blood vessels by energy-hungry tumors
Henrietta Lacks
Cancer cells taken without her knowledge, became HeLa cell line.
Polysaccharides
Carbohydrates that are made up of more than two monosaccharides Ex. --- starch → bunch of glucose monomers (*branched*) --- cellulose → also glucose monomers but *UNBRANCHED* --- chitin → bunch of glucose w/ amino amino sugar
Founded the 3 Domain System
Carl Woese
macrophages
Cells used by the immune system to break down parasites --- defensive molecules that are supposed to destroy pathogens
Why are certain newly-introduced species so successul to the point of becoming invasive?
Certain newly-introduced species can increase population rapidly since their old predators, competition, pathogens, etc. are no longer present ex. Zebra Mussel introduced into North America in Lake St. Clair by European cargo ships Increased exponentially in 2 years b/c no density-dependent agents present in new environment
blood genotypes
Controlled by 3 alleles: I^(A), I^(B), i (cursive) I^(A) and I^(B) are dom over i I^(A) and I^(B) are *co-dominant*
Photosynthesis
Conversion of light energy from a light source into chemical energy
redox reactions (oxidation-reduction reactions)
Coupled reactions that involves the gain or loss of an electron
Rate of Increase in Human Population Calculate the theoretical population in 2019 from a 1999 standpoint (initial population: 6 bil)
Currently 7.6 billion people 83 million new people per year (almost the population of Germany) Every minute 250 born, 100 die --> net 150 new people World Birth Rate: .02 people per year World Death Rate: .008 people per year r = .02 - .008 = 0.012 peopleper year (aka population increases by 1.2% each year) Human Population increases exponentially 1999 pop = 6x10^9 2019 pop = (6x10^9)*e^(0.012x20) = 7.6 billion (fairly accurate to actual population)
Exceptions to Standard Photosynthesis
C₄ and CAM plants Have an *extra step* between the *fixation of CO₂* and *making of the sugar*
Central Dogma
DNA -(transcription)→ RNA -(translation)→Protein
What biological molecule can scientist use to distinguish evolutionarily similar species and why?
DNA nucleotides b/c they change much more rapidly than other biological particles (ex. Cytochrome C) so they may contain sequences unique to an individual species
Transcription
DNA template recorded onto *mRNA* using *RNA Polymerase* --- copy mRNA uses U the making of mRNA off the master strand of DNA using RNA nucleotides from the nucleolus and the enzyme RNA polymerase. The DNA unzips and untwists at the hydrogen bonds using DNA helicase.
Chromosomes
DNA tightly coiled around histones and other proteins in long strands
DNA Replication
DNA unzips into two parts and splits with the cell. In it's new home each side of the DNA strand attack to matching nucleotides to create 2 exact copies --- sequence of one strand specifies the other
presymptomatic testing
DNA-based technique for distinguishing whether a person who is 'at risk' but who shows no clinical signs has inherited the allele(s) that is the cause of a particular genetic disease; also known as predictive testing --- typically occurs immediately after birth to test for diseases --- only needs blood All states require screening of *32* "core panel" of conditions, IN requires *53* Able to find diseasse, but not certain it can be cured
continuous exponential growth
Exponential growth with a species that breeds repeatedly (does not have a designated breeding season) --- overlapping generations Two Formulas: To find the rate of population growth ∆N/∆t = rN To find the # of the population over time N = N₀e^(rt)
Hygene Hypothesis
Exposure to bacteria at a young age is critical for dealing with pathogens when we are older
T/F Inbreeding will change allele frequency
F (Same as sex) Inbreeding will change GENOTYPE frequencies (more towards *homozygosity*), but will not change allele frequencies (only jumbles them around)
T/F 25% of plant are polyploidy.
F Almost half of all plants
Darwin
English natural scientist who formulated a theory of evolution by natural selection (1809-1882) --- voyaged on *SS Beagle* Unwilling to publish research for 20 years b/x it would shock society 1858, gets a letter from Wallace who had the same ideas as Darwin and wants Darwin to look over it before he publishes it. Agree to announce it together Darwin publishes *On the Origin of Species by Means of Natural Selection*
DNA Polymerase
Enzyme involved in DNA replication that joins individual nucleotides to produce a DNA molecule
Rubisco
Enzyme responsible for the fixation of carbon (1st step in the carbon cycle) --- famously inefficient, plant scientist are always trying to get it to work better
Nondisjunction
Error in meiosis in which homologous chromosomes fail to separate. --- ex. trisomy
Total Species Density
Estimate of the actual total number of species in existence Roughly *8.7 million*
Blue Gill Study
Experiment to see if predators actually optimize their foraging Blue gills are a fish that eat Daphnia (available in small, medium, and large sizes) *Prediction* --- At low prey density, bluegills would eat any size daphnia --- At high prey density, bluegills would only eat large daphnia (since they have the highest net benefit) *Observed* --- At low prey density, bluegills would eat any size daphnia [Matches Prediction] --- At high prey density, bluegills ate primarily large daphnia but still had several medium and some small daphnia [similar to prediction but not a match] Researchers suggested that this may be due to the fact that bluegills might not be able to accurately differentiate prey by size
lx survivorship
proportion of original cohort (group of individuals produced at the same time) surviving to age X if lx_1 = 0.1, that means that 10% of the cohort is alive --- lx_2 = (0.1)(0.1) --- lx_3 = (0.1)(0.1)(0.1)
Age Structure
proportion of population in different age classes Sweden: stable Mexico: growing US: mid
Lipoproteins
protein and fat clusters that transport cholesterol in the blood --- LDL --- HDL
tetrad
protein complex that hold the 2 homologous chromosomes (4 chromatids) during meiosis
Enzyme
protein that acts as a biological catalyst Enzymes *change the rate of a reaction*, does not impact whether the reaction takes place in the first place --- it will happen with or without the enzyme, only will take much longer Enzyme features: a) useful in small amounts (don't need a lot) b) catalyst c) *lowers* Energy of Activation (E∨a) d) *does NOT change free energy change (∆G)*
ATP Synthase
protein that uses energy from proton gradient to generate ATP ---adds Pi to ADP
Over 50% of the dry weight in our cell consists of ______________
proteins (proteins are the most abundant biological molecules in our cells)
Life History Spectrum
r-selected (opportunistic) → k-selected (N.B. like political spectrum)
Ecological Niche
range of conditions where an organism can survive and reproduce --- set of tolerance curve
How many new point mutations are in a zygote?
rate of point mutation: 10^(-9)/bp base pairs per gamete: 3*10^9 bp On avg, each gamete has 3 new point mutation; each zygote has 6
Phosphorylation
reaction involving the addition of a phosphate group --- ex. regeneration of ATP
Meiosis
reduction cell division a type of cell division that results in four daughter cells each with half the number of chromosomes of the parent cell --- only in diploid species Meiosis only occurs in reproductive tissue
consanguineous
related by blood; share a common ancestor --- family, cousins, can also be distantly-relatives, etc...
Stimulus leads to a
response
regeneration of ATP
reverse of standard ATP reaction --- type of phosphorylation reaction ADP + P + energy → ATP + H₂O
S Phase
second part of interphase, stands for synthesis because the DNA is replicated --- goes from 1 to 2 chromatids
Test Cross
the crossing of an individual of unknown genotype with a homozygous recessive individual (*rr*) to determine the unknown genotype --- used to distinguish RR and Rr
Spatial Learning
the establishment of a memory that reflects the environment's spatial structure --- store information for later use --- ex. wasp recognize area around home location; when researcher changed the area the wasps became confused
Interphase
the period between cell divisions --- DNA is copied and formed into sister chromatids that are joined at the centromere --- Chromosomes are prepared for cell division + sister chromatid at the centromere
You don't actually inherit a trait, you inherit....
the potential to express a trait
Imprinting
the process by which species form attachments during a critical period very early in life --- response to a stimulus at a particular age *w/out reward or punishment*
Mitosis
the process in which eukarytoic cells divide to make two daughter cells with the same genomic complement as the parent
Translation
the process whereby genetic information coded in messenger RNA directs the formation of a specific protein at a ribosome in the cytoplasm the ribosome moves along mRNA and specific amino acids are brought in by *tRNA*
primary productivity
the rate that light energy gets converted to chemical energy
Demography
the science of population changes --- examining the statistics that affect population growth/size
Phenotype
the set of observable characteristics of an individual resulting from the interaction of its genotype with the environment
complement strand
the strand that is not copied during transcription --- the mRNA sequence is identical to this except it has U instead of T
Competition
the struggle between organisms to survive in a habitat with limited resources --- mutually negative effect Types --- interspecific --- intraspecific --- exploitation --- interference
epigenetics
the study of environmental influences on gene expression that occur without a DNA change
Assortative Mating (RECHECK)
the type of selectivemating that occurs when an organism selects a mating partner that resembles itself (share phenotypes) --- ex. both tall In humans, can be because social, ethnic, religion --- leads to reproductive isolation --- ex. sickle cell in West Africans, Tay-Sachs is Eastern European Jews, Albinism in Hopi AZ/Zuni NM
life history trade offs (i don't get theses)
trades quantity of offspring for quality of offspring??? negative relationships among growth, reproduction, and survival Ex. Can't reproduce forever Reproducing more often makes an organism more likely to die Can't have unlimited offspring
Polygenic
trait controlled by two or more genes --- characters that are polygenic have vary wildly in a population ex. height, IQ, behavior, pigmentation --- Unlike Mendel's peas, people do not all fall into two categories: short or tall Standard example: melanin in skin is controlled by *3 genes"; but also determined by environmental factors (exposure to sun, nutrition)
Horizontal Gene Transfer
transfer of genes between cells of the same generation --- common in bacteria
Disaccharide
two monomers linked by dehydration synthesis Ex. --- sucrose → glucose + fructose --- maltose → glucose + glucose
alpha helix and beta pleated sheet
two of the most common type of secondary protein structures
homologous chromosomes
two pieces of DNA which carry the same genes, one from each parental source.
Nucleic Acids
Polymers of nucleotides --- Composed of C, H, O, P, N (CHOP'N) --- Their structural unit, the nucleotide, is composed of N-containing base, a pentose sugar, and a phosphate group --- 5c nitrogen bases contribute to nucleotide structure * Adenine, Guanine, Cytosine, Thymine, and Uracil* - --Two major classes --> DNA & RNA *Functions:* A) info transfer/store genetic info B) synthesis of proteins (mRNA) C) Transfer of chemical E (Adenosine Triphosphate [ATP]) D) RNA → can act as an* enzyme* or regulate elements (like a switch)
How is polyploidy a form of sympatric speciation?
Polyploidy individuals cannot mate with members of the of population b/c since they have a different number of sets, the chromosomes can't line up properly during meiosis creating gametes with wildly different number of chromosomes --- when a group of organisms has 4 sets of chromosomes in a population with 2 sets, they cannot breed with the og population --- leads to *instantaneous speciation* b/c it creates a barrier to gene flow
Realized Niche
Portion of the fundamental niche that an organism actually uses (restricted); limited by competition
PrEP
Pre Exposure Prophylaxis For people who are HIV*-* but are at high risk of being exposed --- medication taken every day to prevent HIV
G2 phase
Prepares cell for mitosis
Escape in space or time [Prey Avoidance Adaptations]
Prey's behavior or activity is unpredictable and sporadic; can't rely on them as a food source [predator won't evolve to be better at catching them as opposed to species that can track easily] *Ex.* 17-year cicada only comes out once every (you guessed it) 17 years. No predator is going to specialize in catching something that comes out so infrequently.
Transformation
Process by which bacteria pick up genetic material from the *environment* --- commonly used in lab settings
Fermentation
Process by which cells release energy in the absence of oxygen --- takes the 2 NADre from glycolysis, coverts to NADox to be used to create energy *In Fungi:* 2 Pyruvate + 2 NADre (both from glycolysis) → ethanol + 2NADox (aka energy used up) + 2 CO₂ --- the CO₂ is why champagne foams *In Animals* 2 Pyruvate + 2 NADre (both from glycolysis) → * 2 lactic acid* + 2 NADox
Crossing Over
Process in which homologous chromosomes exchange portions of their chromatids during meiosis. --- occus during *Prophase I*
low-density lipoprotein (LDL)
Protein that transports cholesterol to organs and tissues; excess amounts result in the accumulation of fatty deposits on artery walls --- aka *delivery trucks *for cholesterol
Meselson and Stahl
Proved that DNA replicates in a semiconservative fashion, confirming Watson and Crick's hypothesis. Cultured bacteria in a medium containing heavy nitrogen (N¹⁵) and then a medium containing light nitrogen (N¹⁴); after extracting the DNA, they demonstrated that the replicated DNA consisted of one heavy strand and one light strand
Largest Organism in Existence
Quaking Aspen --- system of *vegetative reproduction* that consists of 47,000 genetically identical trees
In a general amino acid structure, the _________________ determines which amino acid the structure is?
R group
NADox/NADre reaction (get pic)
REdox reaction involving NAD --- NADox = oxidized NAD --- NADre = reduced NAD
peptide bond
The bond that forms between* amino acids* --- forms between the carboxyl group of one amino acid and the amino group of another amino acid --- *dehydration reaction*
Systematics
The branch of biology concerning evolutionary and genetic relationships b/w organisms --- an attempt to form a "tree of life" --- includes taxonomy
HeLa cells
The cancer cells from Henrietta Lacks that multiply at an extremely fast rate even after her death and are considered "immortal" because of this. They have been used to over 60,000 scientific papers and studies for cancer, AIDS, and polio
Anaphase II
The centromere divides. The chromatids seperate and move to opposite ends of the cell. Each chromatid is now an individual chromosome (b/c they have their own centromere.)
inclusive fitness
The total effect an individual has on proliferating its genes by producing its own offspring and by providing aid that enables other close relatives to increase the production of their offspring
Behavior
The way an organism reacts to changes in its internal condition or external environment Most behavior is *adaptive* and *shaped by natural selection*
Why is Photosystem I after Photospsytem II?
They discovered I first
What did they know about photosynthesis in the 1850's?
They knew... 1) An increase in carbon in plants was due to CO₂ 2) The nitrogen in plants came from the *soil*, not the air 3) Plants use both *light* and *chlorophyll* to grow 4) Plants give off *O₂ in the day*, and release *CO₂ at night* 5) Plants do *respiration 24/7* and *photosynthesis at night* --- 5 explains 4 6) Plants *split CO₂ to get O₂* and the *remaining C joined with H₂O to form CH₂O *(a carbohydrate [energy]) --- this ended up being *WRONG* 5/6 is not bad
How are cancer cells essentially immortal?
They will keep on replicating until they run out of resources/break down
Since he mentioned David Attenborough
This seems like a good time to use this photo of him with the second greatest animal of all time also im bored and its like 3 am sue me
Why does life adapt?
To protect against *abiotic *and* biotic* enemies
Retinoblastoma
Tumor that is caused by dominant allele In a cross b/w Aa x aa, expected 0.5 offspring to show it BUT it has low penetrance (~20%) 0.2*0.5 = 0.1 Only 10% will show it
universal acceptor
Type AB --- contains no AB antibodies
universal donor
Type O --- contains no antigens
AIDS (acquired immune deficiency syndrome)
a life-threatening, sexually transmitted infection caused by the human immunodeficiency virus (HIV). AIDS depletes the immune system, leaving the person vulnerable to infections.
Typical cause of cancer
abnormal cell division (pathological mitosis) --- uncontrolled growth of cells --- growth checkpoints improperly function One wrong vell is enough for it to happen
interference competition
actively prevent competitors from getting resources (direct competition) --- * territory* is an example of int comp
ATP Structure
adenine + ribose (5c sugar) + 3 phosphate (the reaction only deal with the terminal phosphate)
ATP stands for
adenosine triphosphate
ATP
adenosine triphosphate the main source for chemical energy in cells --- 7.5 kcals of Energy *Structure:* adenine + ribose (5c sugar) + 3 phosphate (the reaction only deal with the terminal phosphate)
vectors
agents that transmit disease from one carrier to another (but does not get infected themselves) --- ex. mosquitos for zika virus
PGA
aka 3PG NOT DUN
Triose Example?
aka 3c 3 carbon monosaccharide Ex. *glyceraldehyde* C₃H₆O₃ --- very important molecule
Pentose Example?
aka 5c 5 carbon monosaccharide Ex. --- ribose C₅H₁₀O₅ --- deoxyribose C₅H₁₀O₄ ("deoxy" implies losing oxygen)
Hexose Example?
aka 6c 6 carbon monosaccharide Ex. glucose C₆H₁₂O₆
T helper cells
aka CD4 cells help make antibodies (though they do not make antibodies themselves) target of HIV --- when these get infected by HIV, the *immune system is crippled*
Sex-linked disorders
aka X-linked An inheritance pattern in which traits are controlled by genes located on the X chromosome. Ex. Duchenne muscular dystrophy, severe combined immune deficiency diseases (boy in bubble movie), red/green colorblindness, *hemophilia* *Characteristics* a) incidents are higher in males b) phenotypes *NEVER* transmitted from father to sons (b/c father gives Y chromosome)
PKU and HW Equilibrium
autosomal recessive 1 out of 10,000 babies affected in US = qq = .0001 sqrt(qq) = .01 = q p = 1-0.1 = 0.99 to get genotype frequency, insert p and q values into equation
Detritivore
heterotrophs that obtain nutrients by utilizing waste products --- ex fungi, worms, etc...
Succinate Dehydrogenase
large protein complex in the electron transfer train that collect the electrons from FADre Combines with NADH-Q Reductase to form Ubiquinone
NADH-Q reductase
large protein complex in the electron transfer train that collect the electrons from NADre Joins with Succinate Dehydrogenase to form Ubiquinone
Telophase I
new *haploid* nuclei form each cell has 1/2 chromosomes, but still 2 chromatids
Problem with Non-Adaptive Groups
non-adaptive groups can have localized resources --- *Ex* seals want to breed on beaches to avoid sea predators and on cliffs to avoid land predators. There are not many places that share both qualities so many seals will breed in the same place not because it is good for them but because it's their only option --- *NOT an advantage to join a group, just no other option*
abiotic factors
nonliving parts of an ecosystem
abiotic factors
nonliving parts of an ecosystem --- ex. environment, weather
Tumor Supressing Genes
normally inhibit cell division mutation can prevent them from functioning --- "defective brakes"
Fidelity
nucleotides are coded at around *1,000 nucleotides/second* DNA miscopies *1 *out of every *10⁶ bps* *Proofreading enzymes* lowers this to *1* out of every 10¹⁰ bps
Ants and Acacia Trees
obligate mutualism where the ant receives vital nutrients and shelter from the tree, while the tree is provided with a defense mechanism against other herbivores. neither would survive without each other *Mutualism* --- Acacia's hollow thorns are nest for ants; provide food in nectaries year-round *24/7* --- Ants protect plants from other insects, active *24/7* --- Both ants and acacia trees are not typically active 24/7, but evolutionary changes have occurred in both species that promote mutualism
phototrophs
obtain energy from light --- CO2 + light → energy
exploitation competition
obtain resources before competitors (indirect competition)
bottleneck population
occurs when a population falls to just a few individuals, results in a massive change in allele frequencies --- type of genetic drift
Phototrophic organisms
organisms (commonly plants) that carry out photosynthesis to acquire energy
Eubacteria (kingdom) is under what domain?
Bacteria
3 Domains
Bacteria Archaea Eukarya
Homozygous
having two identical alleles for a trait (RR, rr)
Mutation
heritable change in DNA
Biological Species Concept
"Defines species as a population or group of populations whose members have the potential to interbreed in nature and produce viable, fertile offspring, but are not able to produce viable, fertile offspring with members of other populations." --- main criteria for living species is "actual or potential gene flow* How scientist determine species: A genetically distinct group of a natural population that share a common gene pool (aka they interbreed) and reproductively isolated from others under natural conditions 1) genetically distinct from other pop 2) interbreed among themselves 3) occurs under natural conditions (ex. ligers)
Speciation
"Formation of new species" Process of splitting 1 interpbreeding population into two
discontinuous traits
"either-or" phenotypic differences between alternative alleles --- ex. purple or white, wrinkled or round
Symbiosis
"living together" A relationship in which two different organisms live in close association with each other
Allopatric Speciation
"other homeland" The formation of new species in populations that are *geographically isolated *from the source population --- depends on the animal; pollen can travel great distances, but snails are greatly impacted by physical barriers splinter group separated (allopatric), then it changes genetically - *but does not often lead to new species*
Heterotrophy
"other-feeding" an organism that cannot synthesize its own food and is dependent on complex organic substances for nutrition --- energy from organic sources
genetic screening
"personalize medicine" process of testing DNA to determine the chance a person has, or might pass on, a genetic disorder Over 2000 genetic screenings avaliable
Autotrophy
"self-feeder" synthesize organic-rich components from inorganic sources 2 Types: --- Phototrophs --- Chemotrophs
Escape in numbers [Prey Avoidance Adaptations]
"they can't get us all" mentality *Ex.* 17-year cicadas all come to the surface at the same time; predators can only eat so many
Sympatric Speciation
"together homeland" Population becomes a new species in the midst of the parent population --- no geographical difference (population ranges overlap) --- often due to *genetics* - ex. POLYPLOIDY
Penetrance
% of individuals carrying a gene that show the expected phenotype
If you have 100 amino acids to make a protein, how many different protein variations could you produce? (N.B. there are 20 different types of amino acids)
(20)¹⁰⁰ different combinations [Big Picture: each molecules uses the same monomers, but the order in which the monomers are linked together to form a polymer determines structure and function]
Carbohydrates standard ration
(CH₂O)ₙ
Relative Fitness
(W with a bar over it) the contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals Compare a given phenotype to the best phenotype in a particular environment
Cholesterol Ratio
(Your total cholesterol count) / (Total HDL count) Men avg - *5* Women avg - *4*
Photosynthesis Equation
(essentially the reverse of aerobic respiration equation)
Annual Carbon Cycle
(get image) During winter when plants are not doing photosynthesis, there is more CO₂ in the air, once summer happens it gpes back up again
Five Kindgoms
(outdated) ○ Monera ○ Protista ○ Plantae ○ Fungi ○ Animalia
2 Domains
(outdated) ○ Prokaryotes ○ Eukaryotes
Selection Coefficient
(s) a measure of the strength of natural selection for or against a specific phenotype or genotype --- s= 1 - [Relative Fitness] --- measures selection against an inferior genotype --- the worse the allele, the higher the selection coefficient --- 0 --> 1; 1 is lethal
Meselson-Stahl Experiment
(see notes)
4 Classes of Biomolecules
*1) *Carbohydrates *2)* Lipids *3)* Proteins *4)* Nucleic Acid
Overview of Respiration (ALL eukaryotes and most bacteria do these 4 steps)
*1) *Glycolysis *2) *Oxidation of pyruvic acid *3) *Krebs citric acid cycle *4)* Respiratory electron transport chain A very limited amount of ATP is made in steps 1-3. Instead, a bunch of NADre and FADre are produced to be cashed in in step 4
Types of Lipids Structure?
*1) *Triglycerides --- glyceral + 3 fatty acids *2) *Phospholipids --- glyceral + 2 fatty acids + phosphate group *3) *Steroids --- 4 fused carbon rings
biological particles commonly associated with molecular phylogeny
*1) *amino acids (protein formation) → count # of amino acid differences/similarities "tape measure of evolution" *2)* nucleic acid (gene formation) → changes relitvely fast *3[later addition]) *ribosomal RNA
Influence of competition on predation
*1) *competitive forces --> one predator might force another predator into a more dangerous place *2)* A predator prefers eating the dominant competitor, and since the dominant competitors' population is kept in check the lesser competitors are able to survive in that environment (in this case, the predator is called a *keystone predator*) [this makes more sense after looking at the sea star study]
7 Challenges to Human Survival
*1) Agricultural Productivity* --- can't keep pace with growing population --- food not distributed evenly *2) Non-reusable energy* --- harms atmosphere *3) Loss of biodiversity* *4) Accumulation of pollutants* --- 9 million premature deaths due to pollutants *5) Water stress* --- 1.2 bil experience water scarcity *6) Desertification* --- losing good soil (topsoil) at a fast rate, taken over by desert --- 40% of Earth is dry land *7) Climate Change* --- CO2 emissions of developed nations --- increased infectious diseases
Problems with HIV testing
*1) Delayed development of antibodies* --- HIV tests look for the presence of HIV antibodies which require at least 3 months to reach a detectable level --- could give a false positive *2) Discrimination* --- people are scared to work with someone who has AIDS
Mitosis (overview)
*1) Interphase* - period between divisions --- DNA is copied and formed into sister chromatids that are joined at the centromere --- Chromosomes are prepared for cell division + sister chromatid at the centromere *2) Prophase* --- spindle fibers appear --- nuclear membrane starts to disappear *3) Metaphase* --- Chromosomes arranged linearly on the *equatorial plane* --- Spindle Fibers attach to centromere (N.B. Each chromosome behaves independently) *4) Anaphase* --- Chromatids separated and brought to different poles *5) Telophase* --- spindle fibers go away, nuclear membrane reappears --- *Cytokinesis* - division of cytoplasm and organelles
Group as Anti-predator Mechanism
*1) Passive Defense* --- less likely predator will target you know that you are surrounded by equally viable targets; "you might not get it but the other guy might" --- "safest place is the center" --- typically uniform in color, size, etc... b/c anything out of the ordinary will attract predators --- ex. flocks, schools *2) Improved Predator Detection* --- more eyes, ears, noses etc... on the lookout for predators --- ex. study found that hawk success rate decreased as pigeon flock size increased --- increased overall vigilance while decreased individual vigilance (since each individual no longer needs to be on the constant lookout for predators) ---- ex. prairie dogs/groundhogs have alarm calls to warn other members of the group *3) Random Dispersal* --- immediate response of some prey to predators is to run in random directions --- crisscrossing prey confuses predators --- ex. antelope move in zig-zags to avoid lions. Also used to protect rhino since antelopes and rhinos usually graze together, so by tracking when the antelopes zig-zag game wardens can figure out when poachers are hunting the rhinos *4) Active Defense* --- some groups can physically hold back predators --- ex. musk ox form a defensive circle around their young ("circle the wagon")
Why study population growth?
*1) Predict Growth Trends* --- ex. endangered species; how many fish can be harvested without destroying the population *2) Indicator of Ecological Conditions* --- ex. rate of algae growth corresponds to pollution present in the ecosystem *3) Interaction with abiotic/biotic factors*
Why Conserve Biological Diversity?
*1) greed/self-interest * --- a valuable resource for humans --- "the cure for cancer might be in there!" *2) free-market environmentalism* --- the cost of a resource reflects the cost to society (the cost to society would be in the form of pollution, toxins, etc..) --- the idea that a free-market is the best way to preserve the environment --- straight from Wikipedia: "Free-market environmentalists, therefore, argue that the best way to protect the environment is to clarify and protect property rights. This allows parties to negotiate improvements in environmental quality. It also allows them to use torts to stop environmental harm. If affected parties can compel polluters to compensate them they will reduce or eliminate the externality." --- kinda ironic since businesses are the reason environment action needs to be taken in the first place, yet FMEs expect business to limit their resource intake without government pressure *3) moral ethics* --- we are not the masters of this planet, only its inhabitants --- *E.O. Wilson *claims that we need to keep half of the earth's resources intact in order to thrive as a species
Survivorship varies
*1)* among species *2)* among sexes --- ex. females live longer in humans *3)* different environmental conditions --- ex. developed vs undeveloped countries
Why do we need energy?
*1)* order out of chaos *2)* active transport *3)* maintain membrane *4)* movement *5)* build complex molecules *6)* degrade molecules in order to extract energy --- "need money to make money"
What year did Mendel first propose his theory for genetic transfer? What was the response from the scientific community?
*1865* Scientist at the time did not believe his theory. It only became accepted *30 years* after the initial discovery.
Net ATP from Fermentation
*2 ATP* Since 1 ATP ~ 7.5 kcal, 2 ATP is approximately 15 kcal Glucose has a total of 686 kcal 15/686 ~ *2% efficiency*
Diploid
*2N* a cell with two copies of the genomes (two of each chromosome)
Model of Host Parasite Dynamics
*3 Types of Host* --- Susceptible Host (N) --- Infected Host (Y) --- Immune Host (Z) β = transmission efficiency V = recovery rate from infection (immunity) d + α = infected host death (b/c they live shorter lives)
Supposedly, ____% of all species live in ___________________ (approximately _____% of the world's surface)
*50* *rainforests* *6 *(but shrinking considerably)
Most taxonomy that is done today is done with ____ Kingdoms and ____ Domains
*6* *3*
Outcomes of Predation
*A) *Predator population size fluctuates, though a lot less than prey population *B)* Cycles in and out of phase [this makes more sense after looking at the example] *Ex.* Hare and Lynx in Canada - populations oscillate every 10 years --- Step 1) Hare population will go up --- Step 2) Since there are so many hares, the lynx population will also increase --- Step 3) Overpredation by lynx causes hare population to decrease --- Step 4) Fewer hares means the lynx population will also go down --- Step 5) Fewer lynx means the hare population will go up and the cycle continues (The 10-year oscillation is most likely caused by predation, but vegetation may also play a role since the food supply for the hares follow a similar oscillation)
Common Solutions Against Abiotic/Biotic Factors for Living Organisms
*A) *Replicate DNA *B) *Metabolic Pathways - ex. glycolysis (common to every organism) *C)* genetic code
Why do developing countries have high birth rates and low death rates?
*A) Historical view* --- in undeveloped countries, people would have lots of children in the hopes that some of them will survive. Now that the country is developing, most of the children will survive; but, due to a lack of education and awareness, the population will not initially notice the trend *B) Children are free labor* *C) Desire to increase your "group" compared to other groups* *D) children = prestige* --- some culture keep on having children until they have a son --- selective female abortion *E) Birth control is limited*
Levels of Protein Structure
*A) Primary Structure* --- linear sequence of amino acids --- determined by genetic info --- called *polypeptide* *B) Secondary* --- twisting/folding --- caused by *hydrogen bonds *interacting --- forms 3-D structure *C) Tertiary* --- additional folding due to *interactions b/w R groups* (when the R groups get close enough to each other, they can bond) --- disulfide bond *D) Quaternary* --- number and arrangement of the protein subunits --- several polypeptide chains
Evidence for a Strong Learning Component to Behavior
*A) White-crowned sparrows* If a male is isolated from sound, he will not develop a normal song, BUT if he hears a song *one time* when between 10-30 days old (critical period) he will develop a normal song. This learned behavior is *selective*. He will only learn the song if it is from the same bird species. *B) fruit flies* Fruit flies were electrically shocked while in a system filled with Chemical O. Fruit flies were NOT shocked in a system filled with Chemical M. When given the choice of environment, 90% of the flies went to the side with M.
Evidence for a Strong Genetic Component to Behavior
*A) maze-running rats* Certain rats completed a rat maze with fewer mistakes than other rats. The "bright" rats were bred together for seven generation, and the "dull" rats went through a similar process. The researchers found that the bright rats produced bright offspring, and dull rats produced dull offspring - displaying a clear genetic component to maze-running. --- disruptive selection --- does not indicate that the bright rats are superior to the dull rats, only that they preformed better at maze-running [selected for only a single trait] *B) crossing honey bees and killer bees* Italian honey bees: friendly, but not productive Killer bees: aggressive but productive --- came from Africa, moved to Brazil (1956), crossed US/Mexico border (1990), entered East US (1999) --- will chase you for 1/2 a mile --- when they sting you and die, they release a pheromone telling the other bees to sting you --- 800 stings to kill a human Researchers found a genetic component for aggression. One of the "defensive" genes was a dominant allele, so the hybrids were also aggressive.
Advantages/Disadvantages of Innate (Instinct) Behavior
*Advantages* a) no past experiences necessary; 'perfect' response every time b) pre-packaged response to predictable events *Disadvantages* a) response can be given to the wrong stimulus --- goose rolling the wring object instead of its egg --- motion is caused by a sensory mismatch b/w the eyes (thinks no motion) and inner (thinks motion), so the brain perceives that it's poisoned and induces nausea
Advantages/Disadvantages of Learning Behavior
*Advantages* a) permits response to unpredictable stimulus b) changes as a result of experience *Disadvantages* a) requires more complex nervous system b) more time/energy c) ample room for mistakes (since it's not the same response each time)
Organic molecules always consist of what elements? What other elements are often present?
*Always: *C, H, O *Partially:* N and P (also S but he didn't mention it in the lecture???)
Monera split into ________________ and ________________
*Archaebacteria* *Eubacteria*
Cost/Benefit of Behavior through Natural Selection
*Cost* --- energy --- risk of predation --- opportunity cost *Benefit* --- increased survivability --- reproductive success (fitness) benefits must outweigh for the cost for it to be selected through natural selection --- "life history has trade-offs"
Mutations in what gene causes Cystic Fibrosis
*Cystic Fibrosis Transmembrane Regulator (CFTR)* gene --- most common error is one missing nucleotide in position 508
DNA vs RNA
*DNA* --- *sugar:* deoxyribose --- *bases:* A, G, C, T --- *strands: double stranded *RNA* --- *sugar:* ribose --- *bases:* A, G, C, U --- *strands: single stranded
How to increase reproductive success?
*Depends on sex* Principle constraint for females → access to resources to raise offspring Principle constraint for males → number of females to mate with So natural selection favors different aspects depending on sex --- females look for *quality of mating* --- males look for *number of matings*
Purines
*Double ring structures* Adenine and Guanine
T/F Natural Selection is done for the good of the species.
*F* NS benefits the individuals, not the group --- beneficial to have less reproduction to have more resources (we deem which individual is more "environmentally fit" by how many offsprings it has)
G.I.N.A
*Genetic Information Nondiscrimination Act of 2008* makes it illegal to discriminate against employees because of genetic information including genetic tests, family genetic tests, info about disease, disorder, or condition of an individual's family members with 15 or more employees --- genetic tests for 2000 conditions --- fear of misuse of genetic information --- insurance companies cannot discriminate based on genetic predisposition --- key-step to individualized gene-based medicine
Energy Total from Aerobic Respiration What is the efficiency rate?
*Glycolysis* 2 ATP 2 NADre(x1.5) → 3 ATP *Total: 5* *Pyr → A-CoA* 2 NADre(x2.5) →5 *Total: 5* *Kreb* 2 ATP 6 NADre(x2.5) →15 2 FADre(x1.5) → 3 *Total ATP: 30* 30 ATP 30* 7.3 kcal = 219 kcal Glucose has 686 kcal 219/686 kcal = *32% efficiency*
Types of Age Distribution Graph
*Growing* --- more young people than old people *Stable* --- population growth stays the same *Declining* ___ decrease in young people the difference in growth rate is due to the relative abundance of *reproductive individuals* (middle of graphs) to* non-reproducing individuals* (top of graphs)
Fermentation in Animals
*In Animals* 2 Pyruvate + 2 NADre (both from glycolysis) → * 2 lactic acid* + 2 NADox Occurs in human muscles cells when oxygen is cannot be delivered fast enough -- lactic acid build-up is what makes you feel pain while exercising
Meoisis I (overview)
*Interphase I* --- replicates DNA *Prophase I* --- chromosomes condense --- *homologous chromosomes *find each other and *pair up* --- when they find their pair, they form a protein complex that holds the chromosomes together called a *tetrad* (N.B. 2 chromosomes = 4 chromatids) --- in humans that would be 23 tetrads ---- *Crossing Over* - homologous chromatids exchange pieces; leads to genetic variation *Metaphase I* --- tetrads line up on equatorial plate --- spindle fibers attach to each chromosome *Anaphase I* --- homologous chromosome seperate *Telophase I* --- new *haploid* nuclei form --- each cell has 1/2 chromosomes, but still 2 chromatids
1 out of 3 AIDS-related deaths is caused by _________
*LTBI *(latent tuberculosis) [opportunistic infection]
Haploid
*N* Containing only one copy of each chromosome. Ex: Germ cells
Conclusion from Observations from On the Origin of Species
*Natural Selection* 1) Differential survival and reproduction within a species --- not all sperm/egg become zygote; not all zygotes become adults; not all adults live long enough to reproduce 2) Individuals with *favorable* (better adpated to CURRENT environment) variation will survive in greater numbers and produce more kids
How did Mendel set up his pea experiments?
*P Generation:* --- took *pollen* from one plant and hand-placed it in the *stigma* of another plant --- prevent self-pollination by removing *stamens* (guy parts) *F Generations:* --- allowed to *self-pollinate*
Sea Star Study
*Paine* conducted a study on starfish in the Pascific Coast of NA Sea stars can feast on the 15 species of invertebrates on the rocks but prefer to eat mussels Paine removed the starfish from the environment and observed the results --- The mussel population increased --- The 15 species of invertebrates had reduced to 8 since the mussel had taken over their habitat on the rocks --- Eventually, only the mussels remained In an undisturbed environment, the starfish prefer to eat mussels. Starfish kept the mussel at low-density (which reduced competition for the 15 invertebrates since mussels were the dominant competitors on the rocks and, when left unchecked, would take over the entire habitat till only the mussel are left), which made space for the lesser competitor. The starfishes presence was responsible for the increased diversity --> sea stars are the *keystone predator*
Calvin Cycle or Light-Independent Reaction
*Part 1:* Fixation of Carbon (aka the plant takes in CO₂) 6CO₂ + 6 RuBP(5c) [ribulose biphosphate]→ 12 PGA [phospglycerate] --- enzyme that makes this happen is *Rubisco* *Part 2:* Reduction 12 ATP and 12 NADPre are used to reduce PGA to PGAL which will be used to make glucose --- Forms net 2 PGAL (12 total , but 10 are used up in step 3) *Part 3:* Regeneration The process of restoring RuBP from *RuMP* [ribulose monophosphate] (RuMP is RuBP without one phosphate [lost its phospate in part 1 in order to form PGA]) --- *6RuMP + 6ATP → 6RuBP* 2 PGALs come together to form glucose, glucose comes together to form starches Total energy consumed to make 2 PGAL: 18 ATP and 12 NADre (quite a bit of energy, 3/4 of the energy cost are used up in the calvin cycle)
Huntington's disease test
*Pre-symptomatic diagnostic test* --- linker marker (DNA near target sequence that can be tracked) on *chromosome 4* --- DNA region cut with *restriction enzymes* *Outcome of HD test* 1) neg 2) pos 3) not the father (2-3% babies born out of wedlock) *Only 25% of people take the test* *Advantages of test* --- risk free children --- can plan life *Disadvantages of test* --- know how you're going to die --- *insurance companies* refuse service --- suicide rate increases
Prokaryotes vs. Eukaryotes
*Prokaryotes* --- asexual --- none/few organelles --- circular chromosomes --- fission *Eukaryotes* --- sexual/asexual --- lots of organelles (chloroplast, mitochondria...) --- linear chromosomes --- mitosis/meiosis
Nitrogenous Bases
*Pyrimidines (1 C ring):* --- cytosine --- thymine --- uracil (RNA only) *Purines (2 C rings):* --- adenine --- guanine
Predator foraging strategies
*Searching *--> look around and if they find something edible they eat it *Pursuing* --> look for prey that are easy to capture since that will increase your net benefit (old, sick, young prey)
Pyrimidines
*Single ring structures* Cytosine and Thymine
Protein Functions
*a) *support *b)* transport *c)* movement *d)* defense *e)* enzymes (regulate chemical reactions)
Plants have __________ cell walls, Fungi have __________ cell walls, Animalia has __________ cell walls
*cellulose* *chitin* *no*
structure of retrovirus
*envelope protein* surrounding *2 identical RNA single-strands*
How can someone affect their LDL and HDL levels (so they can prevent heart attacks)?
*exercise lowers *LDL, raises HDL *smoking reduces* HDL levels *intake of saturated fat increases* LDL levels
SNPs
*single nucleotide polymorphisms* single base differences in DNA that vary among individuals Humans share 99.5% of nucleotides with each other, but there are still *3 million bps* where there is variation (SNPs)
Humans have ____ pairs of chromosomes
23
Light Reaction Equation (RECHECK)
2H₂O + light → O₂ + 4[H⁺] + 4e⁻
Number of possible combinations that can occur from Independent Assortment
2ⁿ n = haploid number In humans: 2²³ ~ 8 million
Wildlife concerns caused by parasites
- population decline - conservation concerns - zoonosis
Test of Cystic Fibrosis
1) *sweat test* (CF patients release excessively salty sweat since they can't handle chlorine) 2) *Prenatal test* can test if an embryo has CF, put to parents if they want to abort --- can also test for carrier status
Types of RIMs
1) Pre-zygotic RIMs 2) Post-zygotic RIMs
Estimate K (carrying capacity) of Earth with US standard of living
3 billion
Cost of Sex
1) Reduces reproduction rate by half (offspring is only 0.5 of your perfect genes) 2) Time/energy in finding a mate 3) Might lose a really good gene combination
base pairs per gamete
3*10^9 bp
Parasitism in Humans
--- 4.5 billion people have worms --- Around 20% of the population has Ascaris (a type of roundworm) [1.5 billion people] --- 1.3 billion people have hookworm --- 665,000 people die from malaria each year --- Schistosomiasis, caused by trematodes (flatworm), affects 200 million people --- Parasitism + malnutrition are responsible for 12 million deaths per year.
Metaphase
--- Chromosomes arranged linearly on the *equatorial plane* --- Spindle Fibers attach to centromere
How can gene flow decrease genetic variation?
--- constrains evolution by homogenizing gene pool --- prevent local adaption --- ex. imagine two pops with very different allele frequencies; when they come together, eventually the allele frequencies will start to match basically, yall get more similar --- homogenizes population
Factors that complicate the patterns of inheritance in humans
--- generation spans ~ 20 years --- few offspring's --- some diseases cannot be identified until the F generations --- unethical to test
Prophase
--- spindle fibers appear --- nuclear membrane starts to disappear
In E. coli, how much ATP in required to make a polysacchride ~ protein ~ new strand of DNA ~
. . 2000 ATP 1500 ATP 120,000,000 ATP (Big Picture: millions of ATP are needed per second to make the bacteria function, the cell can only produce enough ATP to last about 30 seconds at one time, so *constant regeneration* of ATP is required)
It is estimated that the ration of bacteria in your body to humans cells is ____:1.
1
Pyrimidines
1 carbon ring C, T, and U
Pleiotrophy
1 gene has many phenotype effects --- opposite of polygenic kinda --- "sickle-cell anemia" --- albino tigers are all cross-eyed --- white cats w/ blue eyes = deaf
Epistasis
1 gene masks the effect of another -- 1 gene has *veto powers Stadard ex: yellow labs (aa) overrule all other o coloration phenotype of a gene is controlled by many other genes during the pathway of expressing different effects of the gene.
Outcomes of Competition
1) *Competitive Exclusion* - one species becomes locally extinct 2) *Either species wins depending on environmental conditions* --- in one condition one species wins, in dif condition the other does --- competitive abilities are relative 3) *Stable Coexistence* --- 2 Ways: *resource partitioning* and *character displacement*
2 ways to be classified as AIDS
1) *HIV+* and *OI+* (several options) → AIDS 2) *HIV+* and *low CD4 (helper T) count* → AIDS --- around 200 cells/mm3 (normal is 500-1500) [Not enough to just be HIV+, but also have something else]
Stage of Photosynthesis
1) *Light Reaction* → requires light, produces oxygen 2) *Dark (light-independent) Reaction* → does not require direct light, CO₂ from the air gets chemically transformed into carbohydrates
Requirements for Life
1) *Metabolism* - storage and use of chemical energy 2)* Reproduction* - continuation over time 3)* Genetics *- passage of information 4)* Evolution *- ability to change 5)* Growth* - population 6)* Adaption* - against abiotic and biotic enemies * GEM RAG*
All states require screening of *_____* "core panel" of conditions, IN requires *_____*
32 53
Characteristics of Biological Particles That Make Them Useful for Molecular Phylogeny
1) *universally distributed* among organisms (everyone's got it) 2) *functionally similar* (molecule does the same thing in each organism 3) *homologous parts* (if the particle looked the same across different species) 4) *molecules change at a rate that is representative of evolutionary distance* --- broader distance → slower rate (aka it can't change really fast) *FUHC* (*F*unction *U*niversal *H*omogous *C*hange)
HIV Prevention
1) Abstinence 2) Mutually monogamous relationship 3) Condoms --- know partner --- "condom" sense *emotions are no substitute for common sense*
5 Characteristics of Cancer
1) Activation of Oncogenes --- "jammed accelerators" 2) Tumor Suppressor Gene Mutations --- "defective brakes" 3) Limitless reproductive potential (technically immortal) 4)Tumor angiogenesis 5) Metastasis *MALOS*
types of polyploidy
1) Autopolyploidy 2) Allopoluploidy
Different Forms of Gaining Nutrition
1) Autotrophy 2) Heterotrophy 3) Mixotrophy *HAM*
Types of Asexual Reproduction
1) Binary Fission 2) Budding 3) Fragmentation 4) Vegetative Reproduction 5) Parthenogenesis (binary fission is done by prokaryotes and *does not involve mitosis*)
What does the Dark Reaction need in order to occur?
1) CO2 (provided through stomata) 2) energy (provided by the Light Reaction)
Ecological Interaction
1) Competition [mutually destructive] 2) Predation (incl. herbivory) [benefits one species, harms other] 3) Parasitism [benefits one species, harms other] 4) Mutualism [mutually beneficial] 5) Commensalism [benefits one species, does not affect other] 6) Amensalism [harms one species, does not affect other] Species interactions are dynamic and *asymmetrical* (results in evolutionary change) --- not just one or the other; ex. birds and praying mantis eat the same food but birds also eat praying mantis ---> both predation and competition
Interactions between genes
1) Complementation 2) Epistasis 3) Modifier genes 4) Polygenic 5) Pleotrophy
3 classifications of viruses
1) DNA virus 2) RNA virus (single or double stranded) --- ex. zika 3) Retrovirus --- ex. HIV
Ways in which genetic information is transferred
1) DNA → mRNA → proteins 2) duplicated and allocated during cell division
Why is energy lost between trophic levels?
1) Energy is lost through respiration 2) Not everything can be metabolized by a consumer --- ex. we can't break down cellulose (like corn)
Parasite Transmission Adaptations
1) Enormous reproductive output 2) Use of vectors 3) Resting stages 4) Behavioral Modification 5) Timing of Infective Stages 6) Latency/reduced virulence
Interactions b/w Allels
1) Fully dominant, Fully recessive (Mendelian) 2) *Incomplete Dominance* 3) *Multiple alleles*
Advantages of Sex
1) Genetically diverse offspring --- more likely to survive adverse conditions
Types of Sexual Reproduction
1) Hermaphroditism 2) Dioecious (Biparental Reproduction) 3) More than 2! --- man-made
Forming Groups to Improve Foraging
1) If prey is larger than the predator, predators will want to form a group --- ex. wolves hunting deer --- we know that for a group to form the benefit to each individual must be greater than if they were on their own, therefore the amount of prey captured PER INDIVIDUAL must be greater than when they are on their own 2) Information Center --- if prey is scattered/unpredictable/too large for one --- bats, vultures, osprey --- ex. roadkill occurs unpredictably, but scavengers alert others of their presensce
Genetic Variation in Sexual Reproduction
1) Independent Assortment --- Metaphase I (this is what he said in the lecture but according to the practice test it occurs in Anaphase I???) 2) Crossing Over --- Prophase I 3) Random Fertilization
Types of Behavior
1) Innate 2) Learned
types of altruism
1) Kin selection 2) Eusociality
5 assumptions of Hardy-Weinberg
1) Large Population (so allele frequency doesn't change much) 2) No mutation 3) No migration (no genes enter or leave a population) 4) Random Mating 5) All genotypes have equal reproductive success ( each genotype has same survival rate and same number of offspring) --> NO NATURAL SELECTION (Remember, HW operates under the idea that the population is at genetic equilibrium, so the frequency of alleles remains the same)
types of lipoproteins
1) Low Density Lipoprotein (LDLs) --- cholesterol delivery trucks 2) High Density Lipoprotein (HDLs) --- cholesterol garbage trucks
2 processes consistent in all forms of sexual reproduction
1) Meiosis 2) Sygnomy (aka fertilization)
Limitations of Biological Species Concept
1) Only applies to *sexual organisms* (ex. bacteria can discard and add genes all the time through horizontal gene transfer) 2) Does not work well with *fossils* (so we rely on morphological differences) 3) species that interbreed in a lab, does not occur in nature (only works under natural conditions) --- ex. lions and tigers are not the same species, but they can still breed and form ligers and tions
HIV at-home tests
1) Ora-Quick - salvia test 2) Home Access Express - blood test
OVerall, Expression of a gene depends on
1) Overall genetic makeup (between allels, among genes) 2) environment
Nucleotide Structure
1) Phosphate Group 2) Nitrogenous Base 3) Pentose (5c) Sugar (ribose or deoxyribose)
Favorable conditions for allopatric speciation (aka will be likely to produce a new species through allopatric speciation [since it doesn't always lead to new species])
1) Population on frige of species range (pop already a little different than the rest of population; ex. extreme phenotype) 2) Small population ---> Founder's Effect 3) genetic drift (certain alleles may only be in small quantities in this pop and will eventually/possibly go away) 4) Natural selection ---> exposed to different environments
Ways to measure fitness
1) Relative Fitness (W with a bar over it) --- compare a given phenotype to the best phenotype in a particular environment 2) Selection Coefficient (s) --- s= 1 - [Relative Fitness] --- measures selection against an inferior genotype --- the worse the allele, the higher the selection coefficient --- 0 --> 1; 1 is lethal
Why is fixation not 100% with dom alleles Why is it slower than fixation with recessive alleles?
1) Relative Fitness of MM = Relative Fitness of Mm --- both show the same phenotype, so they will have the same fitness; this will retain the recessive allele --- disadvantageous recessive alleles hide in heterozygotes (Mm) 2) mutation at low rate M-->m
Fixation depends on...
1) Strength of selection 2) whether the favored allele is dom or recessive
Two Main Concerns for Parasites
1) Transmission into new host 2) Establishment in new host
3 Ecological Hypotheses for the maintenance of sex
1) Unpredictable environments between generations 2) Resource competition with species (intra species interaction) 3) Rare phenotype (one that is useful against parasites/predators)
Ways that cancer can happen
1) Virus-associated Cancer --- ex. Human Papillomavirus (HPV) -- *85%* or cervical cancer B) Hereditary Predisposition ---- ex. BRCA-1 C) Carcinogens --- primarily air and water related --- cigarettes
4 Observations from On the Origin of Species
1) Without environmental pressures, each species tends to multiply exponentially 2) Yet under field condition (how they would be observed in the field), populations sizes are relatively constant 3) A large amount of variation exists with in species 4) Variations are largely heritable
Ways to identify Trisomy
1) amniocentesis --- draw out amniotic fluids to make a karyotype 2) Noninvasive Prenatal Testing (NIPT) --- looks at fetal DNA in mother's blood (must be al least 10 weeks) --- only test for common trisomies
How can a population level be maintained?
1) birth rate = death rate (aka r = 0) *AND* 2) stable age distribution [need both, watch out for this]
Basis for 5 Kingdom structure
1) cellular structure 2) mode of nutrition
Outside factors that will cause proteins to unravel
1) change in pH 2) change in temp
Types of Exponential Growth
1) discrete 2) continuous
Emergent Properties of Ecosystems
1) energy flow 2) nutrient cycling
Carbohydrates function
1) energy source 2) stored energy 3) structural component --- ex. cellulose in plants, chitin in fungi
Causes of mutation
1) errors in DNA relpication 2) *mutagens* - phys/chem agent 3) *transposable element* - "mobile element" of DNA that can land in the middle of a gene
Evolution is a consequence of of 3 observable factors
1) life forms have offspring (replication) 2) offspring are not identical (variation) 3) some offspring pass more genes than other (selection)
outcome of natural selection depends on what two factors
1) mode of selection 2) strength of selection
Treatment for Cystic Fibrosis
1) most common drug --> *Kalydeco* - only works for about 20% CF patients (must have specific mutation), cost *$30,000* per year 2) *Prenatal test* can test if an embryo has CF, put to parents if they want to abort --- can also test for carrier status
Why is fixation not 100% with recessive alleles Why is it faster than dom alleles?
1) mutation at low rate m-->M It is faster b/c there is only one allele combo (mm) instead of hiding an unfavorable allele like in heterozygotes (Mm)
Types of Autotrophs
1) phototrophs 2) chemotrophs
Types of mutation
1) point mutation 2) frameshift mutation
2 Types of fatty acids
1) saturated 2) unsaturated
Types of Genetic Diseases
1) single gene (can be on on autosomal or sex, can be dom or rec) 2) chromosomal disorder (ex. down syndrome) 3) multifactorial diseases
Human Growth Patterns between Developed and Developing Countries
1) world r>0 (birth rate is greater than death rate) --> human population is increasing 2) Developed nations r is decreasing --- ex. Italy will have 25% fewer in 2050 3) Developing nations r is increasing --- In Africa, r is still high --- By 2050, 26 African nation will have doubled in population --- exception: Asia, r is going down; 60% of pop is Asian so this has a big impact (1.4 bil are Chinese [one child policy till 2015], 1.3 bil are Indian) 4) 80% of people live in developing regions ---> 98% of growth happens there
Options for those with BRCA1 mutations
1)* frequent screenings* for cancer 2) *tamoxofin* - a drug that prevents cells from getting *estrogen* 3)* prophylactic vasectomy *- remove breast and ovaries
Pyruvate
3c end product of glycolysis
Types of Horizontal Gene Transfer
1. Transformation 2. Transduction 3. Conjugation
1 FADre produces _______ ATP
1.5
How many species have been identified (so far?)
1.9 million → primarily insects (~1 mil)
Only ~____ percent of the energy stored in an organism can be passed on to the next trophic level
10 (10,000 J → 1000 J → 100 J [energy gets depleted rather quickly])
Overview of Human Population Growth
10,000 years ago human had a growth surge due to agricultural success By the BC/AD boundary - 250 mil 1650 - 500 mil --- another growth surge occurs due to scientific/industrial advancements leading to a significant decrease in the death rate 1804 - 1 bil 1930 - 2 bil 1960 - 3 bil 1975 - 4 bil 1987 - 5 bil 1996 - 6 bil *October 1st, 2011 - 7 bil* Type of Growth Curve: *Exponential Growth* (which can't continue forever due to resource limits)
What temperature level is considered fatal for humans?
107 F
rate of point mutation
10^(-9)/bp
Humans need about __________ ATP per day
10²⁵
Vertebrate immune system
10¹⁴ unique receptors → very good at catching foreign intruders BUT parasites have counter adaptations against our immune system (evolutionary arms race)
Indiana HIV Statistics
11,600 AIDS, 7125 died 187 HIV+ in Tippecanoe County 6557 living with HIV but not AIDS in Indiana Two local testing sites: Planned Parenthood and TCHD
Dirty Dozen
12 chemicals identified by the Stockholm Convention in 2000 linked to cancer or persist in the environment US and several other countries go together and banned all of them with the exception of DDT since several African nations had insect-related diseases and it was a very effective insecticide
Avg. US citizen consumes _________ lb food per year
1500
Industrial Melanism - peppered moth mode? strength? outcome?
1848: light 99.5% 1895: dark 95% Phenotype: --- light = mm --- dark = Mm or MM Estimated Allele frquency (1848) --- m = .995 --- M = .005 Estimated Allele frquency (1895) --- m = .22 (q^2 = 0.5; sqrt(0.5) = .22) --- M = .78 Recovery Experiment: Polluted woods Dark --- Recapture Rate: 27.5% --- Relative Fitness 27.5/27.5 = 1 --- Selective Coefficient: 0 Light --- Recapture Rate: 13.1% --- Relative Fitness 13.1/27.5 =.48 --- Selective Coefficient: .52 Non-polluted woods Dark --- Recapture Rate: 6.3% --- Relative Fitness 6.3/13.2 = .48 --- Selective Coefficient: .52 Light --- Recapture Rate: 13.2% --- Relative Fitness 13.2/13.2 = 1 --- Selective Coefficient: 0 Directional Selection Predicted outcome - Polluted woods --- Allele M and gentoype MM/Mm approach* fixation* (but never hit 100%) PRedicted outcome - Nonpolluted woods --- Allele mm and genotype mm approach fixation *faster" since it is the recessive allele
Coevolution in European rabbits and Myxomatosis
1959 - some guy introduces 24 European rabbits to his Aussie farm so he can hunt them --- rabbits breed rapidly, have no natural predators, destroyed farmlands ---> turned the area into a desert The government decides to introduce rabbit-specific *Myxoma virus* (causes fibrous cancer in skins) which is transferred by *mosquitos* --- specifically, myxomatosis virus IIIa 1950 - release virus Initially, 99.8% mortality → 90% → 75% → 40% → ... till it barely had an effect *Coevolution in action:* 2 selections occurred *Rabbit*: selected for virus resistance *Virus:* selected for intermediate virulence (pathogenicity) --- virus with high virulence killed its host way to quickly; rabbit died before mosquito had the change to feed on it --- low virulence also had low transmission since those rabbits lacked open sores so mosquitos weren't attracted to them --- thus intermediates had the highest transmissions Since the myxoma virus was no longer effective, the Australian government decided to introduce *European rabbit fleas* in 1957 and *Spanish rabbit flies* in 1993 in an attempt to boost transmission of the virus. Neither worked. --- estimated 17 rabbits per Australian 1996 - Govt. introduced *Rabbit calicivirus* (rabbit hemorrhage disease) Initially 95% successfully, but then coevolution occurred and the same thing happened again
For every 1 molecule of glucose _____ molecules of Acetyl-CoA is/are produced
2
Fermentation in Fungi
2 Pyruvate + 2NADre (both from glycolysis) → ethanol + 2NADox (aka energy used up) + 2CO₂ --- the CO₂ is why champagne foams
Purines
2 fused carbon rings A and G
Mutualism
2 organisms that live together with no negative effect on each other
1 NADre produces _______ ATP
2.5* *glycolysis ATP only has a net 1.5 ATP
How many amino acids are there?
20
____% of new HIV infections are from the 13-24 age range
20
Punnet Square
A chart that shows all the possible combinations of alleles that can result from a genetic cross
Krebs (citric acid) Cycle
A chemical cycle involving eight steps that *completes the metabolic breakdown of glucose* molecules to carbon dioxide; occurs within the mitochondrion --- 1 glucose will produce 2 Acetyl-CoA, so the citric acid cycle will occur twice for one glucose molecule a) Each *Acetyl-CoA (2c)* combines with *oxaloacetic acid* (4c) to *produce citric acid (6c)* --- Acetyl-CoA (2c) + oxaloacetic acid* (4c) → citric acid (6c)* b) 8 steps occur, the end results of which are: --- 4 CO₂ --- 2 ATP --- 6 NADre --- 2 FADre
dehydration reaction
A chemical reaction in which molecules combine and *release water*
Ecosystem
A community of organisms and their abiotic environment (*community + abiotic factors*) --- broadest ecological category --- relatively self-sufficient (some exceptions ex. sunlight) *Ex* forest, lake, desert, etc..
dihybrid cross
A cross between two individuals, concentrating on two definable traits --- can be found using either punnet square or probability ex. mendel crossed round, yellow x wrinkled, green
Pedigree
A diagram that shows the occurrence of a genetic trait in several generations of a family.
Binary Fission
A form of asexual reproduction in single-celled organisms by which one cell divides into two cells of the same size --- only*prokaryotes* --- *no mitosis* --- duplicates chromosomes and splits in half
Vegetative Reproduction
A form of asexual reproduction in which offspring grow from a part of a parent plant --- runners take root and become daughter plants --- ex. strawberries
sexual selection
A form of natural selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates --- differences in sex characteristics increase the chance of male mating but *decreases the chance of male survival* --- proposed by Darwin *Two Components* 1) Mate Competition (intrasexual selection) 2) Mate Selection (intersexual selection)
Mixotrophy
A form of nutriton in which both autotrophy and heterotrophy may be utilized --- ex. carnivorous plants, microalgae (toxic algae bloom [eats alga e/small animals/fish])
Trisomy
A gamete might have 2 copies of a chromosome. When that gamete comes together with a normal gamete, the resulting cell will have *3 copies of that chromosome* --- most trisomies result in spontaneous abortion ex. trisomy 21 -- down syndrome
Characters
A heritable feature that varies among individuals --- ex. flower color heritable characterisitcs
polymer
A long molecule consisting of many similar or identical monomers linked together. --- variation in the linkage of monomers can cause external and internal differences
Fragmentation
A means of asexual reproduction whereby a single parent breaks into parts that regenerate into whole new individuals. --- pieces of the body develop into new individuals --- ex. algae, starfish
Biomass
A measure of the total dry mass of organisms (aka not including water) within a particular region --- forms a *pyramid* → less biomass as moving along trophic levels
Moth population after breeding example
A moth species breeds once in a specific season the dies. Find the population size after 2 and 5 years given the following information. --- starting population: 600 --- net reproduction rate = 1.9 Since the population breeds only during a specific season, it is *non-overlapping*. This means we use the *discrete exponential growth formula*. *After 2 years* N = 600(1.9)² = 2166 moths *After 5 years* N = 600(1.9)⁵ = 14,856 moths
silent mutation
A mutation that changes a single nucleotide, but does not change the amino acid created. --- has no effect - *degeneracy*
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein. --- AUG
Endoparasite
A parasite that lives within a host --- ex. tapeworm, hookworm, plasmodium
Chlorophyll α
A photosynthetic pigment that participates directly in the light reactions --- absorbs blue and reddish-orange areas of the absorption spectra
missense mutation
A point mutation in which a codon that specifies an amino acid is mutated into a codon that specifies a different amino acid. --- amino acid changes --- could be insignificant (not in coding region, could also have massive effect ex. sickle cell
In Vitro Fertilization
A procedure in which gametes are fertilized in a dish in the laboratory and the resulting zygote is implanted in the uterus for development --- a woman's eggs are removed and either frozen or implanted into uterus --- "test tube babies" , over 1 mil so far --- 25% success rate; increases when more than one embryo is used --- better chances with women under 35 --- $12,000-15,000 --- some people born through this process end up infertile
natural selection
A process in which individuals that have certain inherited traits tend to survive and reproduce at higher rates than other individuals because of those traits. --- bad genes gradually go away --- acts on heritable variation expressed in *phenotype* (NS only looks at what is there, not the cod behind it [genotype])
action spectrum
A profile of the relative performance of the different wavelengths in photosynthesis --- which wavelengths give the highest level of photosynthesis Agreement b/w this and the absorption spectrum of photosynthesis, meaning that what is taken up is actually used
Commensalism
A relationship between two organisms in which one organism benefits and the other is unaffected
Mutualism
A relationship between two species in which both species benefit
Asexual Reproduction
A reproductive process that involves only one parent and produces offspring that are genetically identical to the parent
Sexual Reproduction
A reproductive process that involves two parents that combine their genetic material to produce a new organism, which differs from both parents
Rule of Multiplication
A rule stating that the probability of a compound event is the product of the separate probabilities of the independent events.
Rule of Addition
A rule stating that the probability that an event can occur in two or more alternative ways is the sum of the separate probabilities of the different ways.
Complex Interactions
A series of events must occur in a particular sequence to produce a behavioral response --- as opposed to sign stimulus *Ex* courtship displays --- specificity *prevents interspecies mating* between closely-related species
Food Chain
A series of steps in which organisms transfer energy by eating and being eaten --- all food chains begin with an autotrophic organism (light energy → chemical energy) called *producers* --- Producers are eaten by *consumers* Chain: --- 1) producers (plants) --- 2) primary consumers (herbivores) --- 3) secondary consumers (predators) --- 4) tertiary consumers (predators that eat predators) --- ... --- n) All food chains end with *detrivores* (decomposers)
Interkinesis
A short rest period between meiosis I and meiosis II *DNA is not replicated*
codon
A specific sequence of three adjacent bases on a strand of DNA or RNA that provides genetic code information for a particular amino acid
CD4 protein
A surface protein that is known to be the receptor for HIV. It is characteristic to *helper T-cells*.
Phospolipid
A type of lipid and a major component of the cell membrane --- one side is hydrophilic (water-loving) and the other is hydrophobic (water-fearing) *:* glyceral +2 fatty acids + phosphate group
Steroid
A type of lipid characterized by a carbon skeleton consisting of four rings with various functional groups attached --- some hormones are steroids (ex. testosterone) Structure: 4 fused carbon rings
Batesian Mimicry
A type of mimicry in which a harmless species looks like a species that is poisonous or otherwise harmful to predators. *Is only effective if the predators recognize the species that is being mimicked* --- so only works the species and the mimicked species live in the same environment *Ex.* king snakes appear visually like the INCREDIBLY deadly coral snake. Remember "Red and black - friend of Jack [king snake]//Red and Yellow - kill a fellow [coral snake]" *Ex.* Baby cheetah have tufts that look like a honey badger since NOBODY MESSES WITH HONEY BADGERS
provirus
A viral genome that is permanently inserted into a host genome. --- host has virus DNA in its nucleus
Surrogate Mother
A woman who agrees to bear a child for another couple. The husband's sperm is implanted into the woman's uterus. --- carrier who gives birth to another couple's child
What factors affect population size?
A) *Density-independent factors* - not influenced by population size (typically *abiotic*) --- weather, fire, floods, etc... B) *Density-dependent factors* - effect depends on population size (typically *biotic*) ___ predation, disease, competition, crowding, stress
Why is women's education crucial to sustainable development?
A) As female literacy increases, mortality of children under 5 decreases B) Decreased fertility --> greater decision-making capabilities allowed for women (no longer viewed as just baby machines) --- used to be 5 children per women, down to 2.7 In 1970's, women 18-44 only went to school for 2 years
Not-so-common Solutions for Living Organisms When the Climate Is Stressful
A) Bacteria/Fungi → spores B) Plants → dormant periods C) Animalia → hibernate, migrate, etc... D) Protist → form *cysts*
Types of Heterotrophs
A) Predator B) Parasite C) Detritivore
Signs of Increased Death Rate in Human Populations (factors preventing exponential human growth)
A) Starvation --- food production decline in Africa --- 900 mil people (12% of population) are chronically undernourished --- avg # of children per woman (aka fecundity) is increasing in sub-Saharan Africa [more mouths to feed] B) 1/2 of all human deaths in the world are African children under 5 --- malnutrition --- disease (malaria/AIDS/TB) --- average life expectancy in Africa --> 40 years C) 47 cities with 10 mil+ population (megacities) --- cities are mixing pots for human/animal disease hybrids leading to new infection diseases (H1N1/SARS) --- 3.9 bil people already live in cities --- expected 6.3 bil people in 2050
Nucleic Acids Functions
A) info transfer/store genetic info B) synthesis of proteins (mRNA) C) Transfer of chemical E (Adenosine Triphosphate [ATP]) D) RNA → can act as an *enzyme* or *regulate elements (like a switch)*
In what ways can homotherms maintain body heat?
A) insulation --- fat/hair/feathers B) Speed up heat production --- shivering Furnaces, not refrigerators (good at raising temperatures, not so good at lowering them) --- hypothermia
Early Detection [Prey Avoidance Adaptations]
Avoid predators by sensing their presence *Ex.* certain moths are tuned to bat frequencies and dive when they sense them coming
ATP energy producing reaction
ATP + H₂O → ADP + P + *7.3 kcal/mol* this reaction is *reversible*
start codon
AUG (it's on the copied strand, not the template)
Using probability to solve trihybird cross HOw do we find a specific cross How do we solve for all combinations expressing the dominat trait
AaBbCc x AaBbCc solve for aabbcc Solve three monosquares --- Aa x Aa; prob of aa = 1/4 --- Bb x Bb; prob of bb = 1/4 --- Cc x Cc; prob of cc = 1/4 1/4×1/4×1/4 = 1/64
Mimicry
Ability of an animal to look like another more harmful animal *2 Types* 1) Batesian 2) Mullerian
Acetyl-CoA
Acetyl coenzyme A; the entry compound for the (Krebscitric acid cycle in cellular respiration, formed from a fragment of pyruvate
Parasite Establishment Adaptations
Adaptations that improve establishment in a new host 1) Mimicry 2) "Hit and Rin" 3) Live in immune System 4) Antigenic Variation
What process produces the most ATP?
Aerobic Respiration
Alcoholism and genetics
Alcoholism has a genetic component but is also impacted by culture --- presence of alcoholism in family likely increase chances of alcoholism in children --- there is no alcoholism gene, but genetics plays a role --- 930 genes involved in alcoholism in rats Bottom line: gene expression is influence by environmental experiences
Types of Sexual Reproduction involving more than 2 partners
All Human-created 1) ART 2) In Vitro Fertilization (IVF) 3) Surrogate Mothering
What forms of life cannot go through fermentation?
All life can do fermentation
What types of organisms cannot preform glycolysis?
All organisms can do glycolysis
biotic factors
All the living organisms that inhabit an environment (*bio*tic)
Fundamental Niche
All the resources that could theoretically be used by a species in the absence of other species
Life History
All the traits that affect an organism's reproduction and survival --- adaptions that allow an individual to survive in a particular environment --- not about how often you reproduce, but how many of your traits get passed to the next generation Life history has tradeoffs???
Why is it so hard to treat AIDS?
B/c there is a huge amount of variation in HIV (heterogeneity of virus protein) → results b/c the viral *reverse transcriptase is not very accurate *in transcribing DNA --- can be helpful to virus since the immune system won't be able to focus on a specific form of the virus --- 3000-5000 replications in 10 years → 1-10 trillion viruses (excessive genetic diversity) Also bc the virus can be latent as a provirus
Efficiency-wise, what should we be consuming to get the most energy out of our meals?
BUGS
Eusociality
Altruism in social groups that have sterile individuals Social system used by bees, ants, termites, etc... in which there is a) division of labor b) cooperative care of young c) most individuals are sterile In bees, females are diploid and come from fertilized eggs while males are haploid and come from unfertilized eggs. If 1 male mates with the queen, all the daughters are 50% identical to the queen and 100% identical to the male (since the male is haploid and can only pass one set of genes.) Therefore the daughters are 3/4 identical. It is selectively advantageous to produce sisters than have their own kids b/c then the next generation will contain 3/4 of their genes as opposed to only 1/2.
tRNA
An RNA molecule that functions as an interpreter between nucleic acid and protein language by picking up specific amino acids and recognizing the appropriate codons in the mRNA --- contains *anti-codon*
Hemophilia
An X-linked (sex-linked) recessive disorder in which blood fails to clot properly, leading to excessive bleeding if injured Cause by insufficient *factor VIII* which is used in blood clottting Common in royal families across europe b/c formal arranged marraiges across nations
reverse transcriptase
An enzyme encoded by some certain viruses (retroviruses) that uses RNA as a template for DNA synthesis. --- reverse of central dogma
HIV protease
An enzyme that cuts HIV proteins into a usable state
DNA helicase
An enzyme that unwinds the DNA double helix during DNA replication
Tuberculosis
An infectious disease that may affect almost all tissues of the body, especially the lungs --- caused by mycobacterium tuberculosis 90% latent, no TB b/c immune system 10 mil active TB (1.6 mil die) ---5% of them have MDR-TB (multi-drg resistant TB) or EDR-TB (extremely-drug resistant TB) and will resist Rifampin
sessile
An organism that does not move. It remains attached to one place.
Heterozygous
An organism that has two different alleles for a trait (Rr)
blending theory
An outdated, disrepute theory that the phenotype of an offspring was a uniform blend of the parent's phenotypes --- formed intermediates between parents
Erwin Chargaff
Analyzed the base content of DNA in several species and found that the amount of adenine equaled and amount of thymine and the amount of guanine equals the amount of cytosine. --- *Chargaff's Rule*
Autosomes
Any chromosome that is not a sex chromosome --- humans have *22*
Archaebacteria (kingdom) is under what domain
Archaea
Demographic Transition
As a country becomes more and more developed, the birth rate stays high and the death rate drops right away --- model explores relationship between growth and development --- top line is birth rate; bottom line is death rate --- *distance between two lines is r* *Undeveloped* (left side of graph) --- high birth rate --- high death rate *DevelopING* (mid of graph) --- high birth rate --- low death rate *Developed* (right side of graph) --- low birth rate --- low death rate
Why change to 6 Kingdoms?
As new technology emerged, scientist gained the capability to sequence *ribosomal RNA*. Insights from this discovery led to noticeable differences between the various bacteria in Kingdom Monera. As a result, that classification split into *Archaebacteria* and *Eubacteria*.
HIV US Statistics
As of Dec 2017 1,281,787 AIDS cases in US; 700,781 deaths (50%) Rose rapidly in 80's, peaked in 90's, then slowed down US 15,807 deaths in 2016 Deaths have gone down but prevalence has gone up since people are living longer 80% of people with AIDS in US are male homosexuals, IV drug users, or both Heterosexual transmission is increasing; women make up 20% of new cases Used to be 50,000 new infections per year Now 38,739 as of 2017 Overrepresentation in minorities; one of the leading causes of death in women of color in a child-bearing age 1.1 million people in US are HIV+ (appear fine) 1 in 7 don't know
genetic differentiation
As two populations diverge, they accumulate more differences (genetic drift)
Types of Reproduction
Asexual Sexual
Budding
Asexual reproduction in which a part of the parent organism pinches off and forms a new organism --- ex. hydra
Parthenogenesis
Asexual reproduction in which females produce offspring from unfertilized eggs --- found in invertebrates and some reptiles
Gregor Mendel
Augustinian monk and botanist whose experiments in breeding garden peas led to his eventual recognition as founder of the science of genetics --- first to quantitatively observe and propose a mechanism for genetic inheritance
Huntington's Disease is what type of genetic disorder?
Autosomal Dominant
TB and NAtural Selection
Bacteria resistant to Rifampin have a point mutation of gene *rpB* that changes the 3D shape of RNA Polymerase which prevents the drug from binding to the polymerase THE BACTERIA DID NOT DEVELOP A WAY TO DEAL WITH THE DRUG, INSTEAD the mutation was already present beforehand in low frequency, but it wasn't favorable for the bacteria b/c the RNA Polymerase worked slowly However, in an enviornement w/ Rifampin, mutant bacteria has an advantage --- by NS, it increases
Why is inbreeding bad?
Bad reccessive allele are way more likely to be brought together --- probability that you have the same harmful allele as a random person is pretty low, but the probability that you have the same bad recessive allele as your sibling is pretty high more individuals are homozygous for recessive alleles with harmful effects
Barnacles
Barnacle experiment by Joe Connell adult barnacles attach to rock --- Chthamalus - attaches to top of rock --- Semibalanus - attaches to bottom of rock Removes Semi --> Ch takes over entire rock --- Ch's Realized Niche is top of rock and Fundamental Niche is the entire rock Removes Ch --> Semi has no change in distribution --- Semi has a built-in physiological limitation -- Realized and Full Niche are same for semi example of *character displacement*
Altruism
Behavior that reduces an individual's fitness while increasing the fitness of another individual --- seems to cost the individual --- not a selfless act, usually done to indirectly increase the number of their genes passed on to the next generation
How do scientist determine species?
Biological Species Concept
Egg shell removal by black-headed gull
Black-headed gulls instinctively remove egg shells from their nest once their chicks hatch --- looking at the data, the closer the egg shells are to nest, the greater percentage of chicks get taken by predators (greater the distance ---> lower the probability of predation) *Benefits* --- advantageous for gull parents to remove egg shells in order to not attract predators to the nest *Cost* --- when egg shells are removed, the other gulls in the colony recognize the behavior and eat the chicks Through adaption/NS, gulls have learned to wait an hour before removing the egg shells because in that hour the chick dry up and become fluffy making it difficult for the other gulls to swallow --- *trade-off through natural selection*
Oil vs Fat
Both are Triglyceride Called fat if *solid* at room temp (20C) Called oil if *liquid* at room temp (20C)
R₀ vs r
Both are used to relay how populations grow, but have different relevance --- R₀ = (# of females produced)/(# of females currently) --- r = avg birth rate -avg death rate When the population size is *decreasing*, R₀ is *less than 1* [each woman is statistically producing less than one daughter] When the population size is *decreasing*, r is *negative* When the population size is *increasing*, R₀ is *more than 1* When the population size is *increasing*, r is *positive* When the population size is *constant*, R₀ is *1* When the population size is *constant*, r is *0*
Why does respiration require several smaller steps? Why not burn glucose in one step?
Burning glucose in one step would release so much heat that it would kill the living system, so glucose is burned/oxidized in several smaller steps By breaking it down into smaller steps, the energy is conserved in small units → ATP
Lipids
C, H, O but NOT in a 2:1 ratio like carbohydrates NOT polymers Only grouped together because they share the same property of being *insoluble in water* (structurally they can be fairly different)
carboxyl group
COOH C==O found in amino acids
Dark Reaction Equation (RECHECK)
CO₂ + 4[H⁺] + 4e⁻ → CH₂O + H₂O (take carbon from carbon dioxide in the air and stuffs it into a carbohydrate)
Timing of Infected Stages [parasite transmission]
Certain parasite intentionally wait for the ideal times to start infecting *Ex. Schistosomes* (see "Enormous reproductive output") release cercariae from freshwater snails at mid-day b/c that when humans are in the water. In certain schistosomes that want to infect rats, the cercariae are released at night. *Ex. Rabbit Fleas* only reproduce if they feed on the blood of an infected rabbit (b/c then they are certain that there will soon be several bunnies to feed on -- timing is important!) --- no reproduction ever on male rabbits
Mimicry [parasite establishment]
Certain parasite will mask themselves to look like part of the host system --- the immune system doesn't see recognize the parasite as foreign *Ex. Schistosomes* (adult worm versions) that are in human blood will mask themselves by taking on the host's blood antigens (A, B, and/or O) which fools the immune system
Use of vectors [parasite transmission]
Certain parasites use vectors to transfer from one host to a new host *Ex.* Tsetse flies transmit *Trypanosoma* which causes African sleeping disease --- tsetse flies typically don't go for humans since they're only active for 5 min a day and they don't live in urban environments. If a person gets bitten by one, it is most likely because he went out to a place where the flies live.
"Hit and Run" [parasite establishment]
Certain parasites will stimulate the immune system in one part of the body then immediately move where the immune system can't get them (in humans, this is the gut since there is already so many foreign objects in there) *Ex. Ascaris* migrate inside your body The eggs start in the intestines, move to the liver, then the right side of the heart, then lungs. When you do that light-cough-then-swallow thing, they move from the lungs to the small intestines. --- the immune system does see the movement (especially in the liver and heart), but the parasite moves too quickly for the immune system to catch it
Latency/reduced virulence [parasite transmission]
Certain parasites, while they could have high virulence (pathogenic effect), choose to have a moderate or low effect because it improves the probability of transmission into a new host *Ex. myxoma virus* (see "Coevolution in European rabbits and Myxomatosis") --- myxoma virus selected against high and low virulence since the intermediate was the best for transmission
Antigenic Variation [parasite establishment]
Certain pathogens can change their surface antigens at different intervals --- they express different genes at different times in order to get ahead of the immune system --- pathogens alter their surface antigens (and antibodies are rendered ineffective) *Ex. Trypanosomes (blood protozoans)* change their VSG --- *VSG = variant surface glycoprotein*; covers the cell and used by the immune system to identify the pathogen VSG1 is the typical version. As soon as the immune system recognizes the parasite, it creates an antibody to wipe out all cells with VSG1. Some of the parasite cells die, but other parasite cells recognize what is happening and switch to VSG2. Once the immune system recognizes VSG2, the surviving cells switch to VSG3, and so on.
Genetic Drift
Change in allele frequency due to *random chance* --- important for *small populations* (~100 inds) ex. q = 0.2 for allele X In a population of 1 million, that would still be 40,000 copies of X BUT In a pop of 50, there are only two copies And if those individuals happen to die/not reproduce, then allele X would be eliminated Small pop can have random fluctuation in allele frequency that can lead to a loss of a superior allele by chance aka* chance evolution*
character displacement
Change in species traits depends on whether competing or not --- divergence of niche when sympatric (living together), but when allopatric (apart from each other) they are morphologically similar --- The tendency for characteristics to be more divergent in sympatric populations of two species than in allopatric populations of the same two species
Who proposed species *(1) evolved from ancestral forms* (which was already know) through *(2) Natural Selection* (a new mechanism)?
Charles Darwin AND Alfred Russell Wallace
Binomial Nomenclature
Classification system in which each species is assigned a two-part scientific name (genus + species)
Aposematic Coloration
Coloration or markings of an animal serving to warn off predators --- warning colors Ex. Poison Dart Frogs
gene pool
Combined genetic information of all the members of a particular population
disulfide bond
Common bond during the tertiary stage of protein formation (between R groups
How does 23 and Me work?
Companies will compare your SNPs against poeple with a certain disease and assess your *probabilty* (not 100% certain) of getting hundreds of diseases --- not very useful yet since we don't know the specific roles of SNPs --- does not include environment
cDNA
Complementary DNA DNA produced synthetically by reverse transcribing RNA
Food Web
Complete set of food inks in an ecosystem --- differs from food chain in that it is *not linear* and has branching, non-sequential paths
Why do individuals form groups?
Darwinism tells us that we do everything not for the good of the group for the *good of the individual* --- for the individual, the benefit of forming a group outweighs the cost *Cost* *2 Automatic Cost* a) competition for food, mates, etc... b) increased risk of disease *2 Possible Cost* a) risk of exploitation of parental care (using resources for the care of other group members' children) --- *Ex.* In elephant seal society, the strongest males control the territory, so there is a selection for larger males. Females only have one pup per year which grows from 85 to 525 lbs in just four weeks. In order to outcompete the other male pups, males will suckle milk from other mothers than their own. b) Risk of conspecifics killing the offspring of other members of the group --- see" black-headed gull" term *Benefits* a) predator defense b) improved foraging efficiency c) improved defense of resources d) improved care of young
Heterogeneity influences stability in a predator-prey environment
Determined using experiments preformed by Gause and Huffaker *Gause Experiment* --- Placed Paramecium candatum (prey) and Didinium masatum (predator) in a jar --- Initially both go extinct after 4-5 days (predators eat all the prey before the prey have time to replenish their population, and the predators dies soon after since they have nothing to eat) → No stable cycle when in a simple system - *homogeneity* --- Gause added a refuge for the prey and they cycled a bit *Huffaker Experiment* --- similar to Gause but used mites -- 1 prey mite and 1 predator mite (N.B. the prey mite eats oranges) - *40 Orange Universes* (aka ran 40 experiments with oranges for the prey mite to eat) --- like in Gause's experiment, predators overfed and eventually both populations died out → no stable cycle --- tried increasing distances between oranges but did not change results - *120 Orange Universes* --- created an environment with Vaseline barriers, popsicle sticks for climbing, and a fan running above the environment --- Vaseline barriers prevented predators from directly chasing prey since they had to maneuver around barrier --- prey could climb popsticle sticks and use the fan to blow them to a different part of the enclosure --- Huffaker got a cycle going for 8 months since he had a *complex patchy environment* (heterogeneous environment) *Big Picture:* Environmental heterogeneity increases stability (prey needs places/opportunities to hide from predators)
G1 Restriction Checkpoint
Determines whether the cell will proceed with mitosis Looks at: --- cell size --- nutrients --- DNA damage --- growth factors IF it decides not to divide, the cell will proceed to G0
Watson and Crick
Developed the *double helix model* of DNA using research from *Rosalind Franklin*
Cytokinesis
Division of the cytoplasm during cell division after telophase
unsaturated fat
Does *NOT have the max # of H* → has DOUBLE BONDS -- not as tightly packed --- kinked b/c double bond ex. *plant oils*
Bacteria
Domain of unicellular prokaryotes that have cell walls containing peptidoglycan
Pennies example (discrete exponential growth)
Dr. M gives his kid one penny. The next day, his kid asks for two. The day after he asks for four. If this continues for a month, how much money would his kid accrue? N = ??? N₀ = 0.01 R₀ = 2 t = 30 N = 0.01(2)³⁰ = $1,732,418.24
Competitive Exclusion Principle
Ecological rule that states that no two species can occupy the *same exact niche* in the same habitat at the same time --- developed by Gause --- limit to niche overlap
Twin Types
Either 1) Monozygotic (idnetical) ---> 100% identical (came from the same zygote that split early in development) 2)Dizygote (fraternal) ---> 50% identical (born at the same time but came from different zygotes)
Lamarck
French naturalist who proposed that evolution resulted from the inheritance of acquired characteristics in 1809 (pre-Darwin) Proposed: *1) Use and Disuse of Parts* --- organs have a built-in drive for perfection --- structures that are used a lot will be developed further, while structures that are not used will degenerate *2) Inheritance of acquired characteristics* --- modifications made during a lifetime would be inherited by the next generation --- if a giraffe stretched its neck to reach a tree, the offspring will have a longer neck --- if this were true, then incredibly muscular people would have incredibly muscular children *What he was right about:* 1) Earth is old (~4.5 billion years) 2) Evolution is gradual/adaption is important
What happens to a population with no environmental pressures?
Fruit Fly Pop with 60% DD 40% dd --- both evenly split b/w male and female G1 Results: DO weird punnet square: .60Dx.40d (see example in notes; know how to do this) Results ijust see notes for this G2 results same as F group --- Genetic Equilibrium
Phases of Interphase
G1 S G2 (also G0 on a technical sense)
Paramesium
Gause looked at 2 species --- P. aurelia --- P. caudatum Initially grown separately --> both reached carrying capacity When grown together, they compete for the same resources negatively affects both Eventually, P. caudatum brought to local extinction example of *competitive exclusion* (local extinction)
Oncogenes
Genes that code for proteins used during cell division Typically turned off, only used for cell divisions Cancer cells have these always activated --- "jammed accelerators"
Founder Effect
Genetic drift that occurs when a few individuals become isolated from a larger population and form a new population whose gene pool composition is not reflective of that of the original population. New population would have a *decrease in Genetic Variation* than the source and usually an *increase in frequency of rare alleles* Ex. amish in Lanchester, PA frounded by 3 couples 61 cases of Ellis vaGrevald Syndrome (dwarfism/extra toes) Very few cases in rest of world, but so many in this one population --- 13% were found to be carriers 1 of the 6 founders was a carrier
Survivorship curves
Graph of the proportion of a cohort still alive at each age. log of survivorship against time *3 Types* --- Type 1 --- Type 2 --- Type 3 (totally needed to waste 3 lines to write that)
What determines whether a group will form?
Groups form in proportion to predator risk --- so if there are no predators, groups are less likely to form
Logistic Growth
Growth pattern in which a population's growth rate slows or stops following a period of exponential growth --- restricted growth; rate slows steadily as the population approaches maximum size (called *carrying capacity* or *K*) --- formed as a result of *limited resources* and *biotic interactions*
amino
H-N-H found in amino acids
How is HIV transmitted from person to person?
HIV is in a concentration sufficient to transmit in semen, blood, and cervical secretions --- not sufficient in saliva, tears, sweat, urine, etc... 1) Unprotected Sex 2) Exposure to Blood 3) Birth --- HIV+ women could transmit to fetus; mothers can take NRTI's to reduce the likelihood of transmission
HIV vs AIDS
HIV is the virus responsible for AIDS (however, AIDS requires more than just the presence of HIV)
saturated fatty acid
Has *max # of H* → NO DOUBLE BONDS --- packed tightly --- straight ex. *animal fat*
Dioecious
Having male and female reproductive organs in separate plants or animals --- standard sexual reproduction --- what humans go through
Mendel's First Genetics Experiment
He aimed to great a honeybee that was both a *good pollinator* and *non-aggressive* He crossed a *German bee* (hard-working) x *Italian* bee (friendly) Resulting species did very little work and was highly aggressive Switched to peas
In the 70's, world r=0.02 (population increased by 2%) and Doubling Time was 35 years
He said this in the lecture Idk how to incorporate it into a term
Head lice example
Head lice are continuous breeders. Find (1) the rate of growth and (2) the new population after 5 days given that r = .028 lice/day N₀ = 1000 They are *continuous* breeders so we use the continuous exponential growth equations *Gowth Rate* rate = rN = 0.028∙1000 = 28 lice/day *New Population* N = N₀e^(rt) = 1000∙e^(0.028*5) = 1150 lice
incomplete dominance
Heterozygote expresses a phenotype that is intermediate between two homozygous genotypes --- standard sample: crossing red (RR) and white (rr) snap dragons gets all-pink F₁. F₂ will have 1:2:1 ratio of red, pink and white *NOT BLENDING* --- blending implies the red and white traits would be gone in the subsequent generation, but, as we see, they can come back in future generations
Explain how cholesterol management is vital for preventing heart attacks?
High intake of cholesterol will throw the liver off balance since the organ can't cope with so much excess cholesterol needing to be degraded. What happens then is these LDLs are in excess in the blood, so the cells take the LDLs in the form of plaque, clog arteries, and can block blood flow which can lead to heart attacks.
Example of enviromental effect on gene expression
Himalayan Rabbits IF raised in 5C ---> all black 35C ---> all white Why is that? Turns out the enzyme that result in the darkening of pigment is not active at high temperatures (b/c of its shape)
Anaphase I
Homologous chromosomes are pulled to opposite ends of the cell. Note that chromatids do not separate - each duplicated chromosome still has two chromatids. --- *INDEPENDENT ASSORTMENT*
Alternate names for "warm-blooded"
Homothermic *Endo*thermic
HIV
Human Immunodeficiency Virus the retrovirus that causes AIDS --- first identified 1981
Humans as groups
Humans form groups as an anti-predator measure (though in this case, the other predators are almost always other humans) --- we see an increase in nationalism when the treat increases (ex. 9/11) [response to common threat]
"Law of Peas"
Hypothesis of Inheritance Mendel's proposed theories to explain his pea crosses 1) alternate forms (genes) that carry heritable characteristics --- today referred to as *alleles* 2) Diploid → 2 alleles/1 inherited from each parent 3) pollen/eggs → only carry 1 allele for each characteristic ---- allele pairs *segregate* during the production of gametes (huge assumption since meiosis had not been discovered) ---- paired condition restored during random fusion of gametes 4) If two alleles are different, one is fully expressed while the other is masked
How would you remove a population of rats at carrying capacity?
If you tried removing half the rats, you would be at the point of max growth and they would reproduce at the fastest rate. The best way would be to *decrease the carrying capacity (K)*, which can be accomplished by limiting resources (ex. garbage) or introducing predators
Resting stage [parasite transmission]
Improves probability of transmission b/c it allows parasites to withstand hostile environments *Ex.* *Ascaris* eggs last for 10 years
Hardy-Weinberg Equilibrium
In a sexually reproducing population, a single generation of random mating will produce stable frequencies of alleles and genotypes under certain conditions condition that occurs when the frequency of alleles in a particular gene pool remain constant over time
Conjugation
In bacteria, the direct transfer of DNA between two cells that are temporarily joined
Logistic Growth Equation
In notes he says ∆N/∆t instead of dN/dt --> it is the same thing N = current population size K = carrying capacity r = intrinsic growth rate)
Genetic Variation in Asexual Reproduction
In principle, there should be no genetic variation Variation can still occur through *mutation* (low rate though) Bacteria also have a number of processes to transfer genetic material between cells of the same generation (horizontal gene transfer)
World HIV Statistics
In the world, heterosexual transmission is the most common (equal distribution b/w males and females) 1.7 mil acquired HIV in 2018 38 million living with HIV/AIDS currently, w/ 77,000 deaths Sub-Saharan Africa; 15-20% of adults are HIV+ 23 million people are undergoing CART
What would be the result on the age structure of India of you made r instantaneously 0?
Indian's current age structure is growing by a lot (soon to be the largest country), so with so many young people, the population would still be growing for the next 30 years before approaching stable distribution --- currently, 1 out of 5 births are from India
fitness
Individual's reproduction contribution to the gene pool --- how well an organism can *survive *AND *reproduce* in its environment
Behavioral Modifications [parasite transmission]
Infectors can modify host behavior in ways to increase transmission of parasite --- usually it increases chances of predation ------ next host will eat the current host *Ex.* *Dicrocoelium denriticum* Parasite that lives in sheep liver - Sheep defecates DD eggs - Snails eat sheep feces, DD gets inside snail and produces *cercariae* (like in schistosomes) - Snail coughs up cercariae in what is scientifically called a *slime ball* - Ants absolutely love slime balls; parasite ingested by ants *Parasite enters brain of the ant and changes its behavior. Instead of going down the anthill it will climb to the top of a grass blade and just wait there.* -Sheep eats the grass, including the parasite-infested ant, and the cycle continues *Ex. Toxoplasma* - lives in cats Initial host is rats, but parasite want to get inside a cat. Parasite causes infected rats to lose their aversion to cat urine, and instead becomes attracted to cats. Rat gets eaten. sad
Initial Exposure/Effects of HIV
Initially, only mild mono-like symptoms that disappear in days/weeks Virus then is *latent* for *8-10 years* (appear normal) [at this point, you are considered *HIV+*] Once you start showing symptoms, you go from HIV+ to *AIDS*
Population
Interbreeding group of organisms of the same species and from the same area
Phase between Meiosis I and II
Interkinesis
Why is cyanide dangerous?
It bind to cytochrome C which halt the entire ETC
How does polyploidy result in the instant creation of a new species?
It creates an instant species b/c they cannot mate with any other member of the og population --- in most cases, it needs to be able to *self-fertilize* since they can't mate with the rest of the population --- typically found in flowering plants/certain animals (flatworms, snails, earthworms)
Relationship b/w Penetrance and Expressivity
Just because an individual has a dominant allele does not mean it shows it to the fullest degree
Protista
Kingdom sub-group --- *eukaryotes* --- *unicellular* (a few exceptions) --- protozoa --- essentially, all *the "other" eukaryotes* (does not fit into the category of plant, animal, or fungus)
Plantae
Kingdom sub-group --- autotrophs → *PHOTOSYNTHESIS* --- *cellulose* cell wall
Fungi
Kingdom sub-group --- decomposers (mostly) --- *chitin* cell wall
Animalia
Kingdom sub-group --- ingest particulate food --- no cell wall
Monera
Kingdom sub-group (outdated) --- contains *all bacteria*, cyanobacteria (blue/green algae) --- *prokaryotes* --- *unicellular* --- various modes of nutrition
Carrying Capacity (K)
Largest number of individuals of a population that a environment can support
Legal issues with Multiple Parent Technologies
Laws are yet to be made on this technology, so courts are operating on a case-by-case basis
Consequence of limited energy transfer through consumption
Limits the amount of trophic levels --- ex. there are not that many top predators since the food they consume has *limited energy* and are too *widely scattered* Food chain length limited by inefficiently of energy transfer
type 1 survivorship curve
Low mortality until old age --- juvenile mortality relatively low --- these organisms typically have few (well-supervised) organisms ex. humans *k selected*
heterogametic
Males (XY)
Archaebacteria
Many live in *challenging environments* (*Archer* in hard environment)
Inbreeding
Mating between individuals that share genes that are identical by descent (see example thing here) Inbreeding leads to an increase in homozygotes and a decrease in heterozygotes relative to HW expected values
sex chromosomes
One of the 23 pairs of chromosomes in the human, contains genes that will determine the sex of the individual.
Why consume meat if we can get more calories (energy) from eating the producers?
Meat is an inefficient way to obtain calories (since energy is lost at each trophic level), BUT... 1) There are 9 Essential Amino Acids that can't be made in the body but is found in meat, milk, corn, beans, etc... 2) Low-quality pastures are not suitable for human consumption but are perfect for raising cattle ---- (this confuses me b/c Dr.M made it sound like the reason why this was a point was that we can't consume the grass on low-quality pastures - implying that we CAN consume grass on high-quality pastures???)
Mechanisms for Speciation
Mechanisms --> barriers to *gene flow* 1) Allopatric Speciation 2) Sympatric Speciation
Mendel vs. Population Genetics
Mendel focuses on the genotype of the kids of a single pair Population genetics emphasizes the frequency of alleles and genotypes in a population (gene pool)
Who figured out how DNA replicates?
Meselson and Stahl
Prey Avoidance Adaptations
Methods used by prey to avoid predation --- VERY strong selection pressure (since those not selectively fit get eaten) *Types:* a) Poison b) Aposematic Coloration c) Mimicry ---- Batesian ---- Mullerian d) Cryptic Coloration e) Escape in Space or Time f) Escape in Numbers g) Escape in Size h) Early Detection i) Inducible Defense
Point of max growth
N = K/2 When the growth rate is greatest in a logistic gaph
Population Size with Continuous Exponential Growth
N = size of population after time t N₀ = initial population r = intrinsic rate of increase (avg birth rate - avg death rate) t = time
Factors that Affect Future Populations (equation form)
N(future) = N₀ + B - D + I - E *Future populations are affected by 5 factors:* Current Population (N₀) Birth Rate (B) Death Rate (D) Immigration Rate (I) Immigration Rate (E)
Why are so many Americans obese?
N.B. *40%* of Americans are obese Humans are ill-adept for an environment of plenty and we struggle to limit ourselves from sugars, starches, and fats.
Does NAtural Selction lead to perfection
NO "better than" adaptions are often compromises since new genes do not arrive on demand; only works with available variation
If 5 assumptions of HW hold, what results
NO EVOLUTION (which would never happens in reality)
Modern theory of evolution
Natural selection acts on the variations in the population caused by mutations and sexual reproduction
Directional Selection
Natural selection in which individuals at one end of the phenotypic range survive or reproduce more successfully than do other individuals. --- one extreme phenotype is favored --- shifts distribution of next gen in one direction --- could lead to the disappearance of other alleles
Stabilizing Selection
Natural selection that favors *intermediate* variants by acting against extreme phenotypes ---intermediate forms are favored --- increases frequency of average phenotype --- *decreases GV* --- ex. human babies; overweight and underweight not favored
Kin Selection
Natural selection that favors altruistic behaviors by enhancing reproductive success of relatives --- not only concerned with offsprings but with how many copies of your genes get to the next generation --- popularized by W.D. Hamilton --- inclusive fitness Focuses on the passage of genes 1) directly by producing offspring → individual fitness 2) indirectly by helping relatives
NAD
Nicotinamide adenine dinucleotide Readily accepts electrons from various donors NAD is a *dump truck for energy* → simply moves energy from one place to the other
Would this donation work? Type O patient + Type A donor
No
Is a parent supporting their child a form of altruism?
No b/c by having successful children an individual increases their reproductive fitness making it a selfish act
AIDS Treatment
No cure, but can be delayed *Vaccine* Aimed at developing an antibody to envelop viral binding protein (prevents virus from binding to receptor) --- problems arise b/c there are so many variations of HIV such that one type of antibody may only work on a select few viruses *Drugs* 50 FDA approved drugs; block different steps in HIV life cycle *4 Types of Drugs* --- Nucleoside RT Inhibitors (NRTI) --- Protease Inhibitors --- Fusion Inhibitors --- Integrase Inhibitors Similar to vaccines, problems arise since there are so many new mutant HIV which means there can't be a "holy grail" drug for all cases. Instead, we resort to *combination therapy*, or using multiple drugs.
Can you have unlimited offspring?
No, b/c life history has trade-offs Ex. Experiment ran on birds that typically have 3 eggs per nest to test for average fledgling survivorship (how many chicks made it to adulthood). Eggs were removed an added from 30 nest such that some next has 1 egg, some had 2 eggs, some had 3, and some had 4. They found that the next with one egg had poor survivorship, nest with 2 eggs has alright survivorship, nest with 3 eggs had the best survivorship, and nest with 4 eggs had a lower survivorship than nest with 3 eggs. *When brood size was artificially increased, fewer fledglings survived.* In short, this shows how adding more offspring does not increase the likelihood they will survive to adulthood. I don't understand how this is meant to be applied to other species but whatever???
Can you reproduce forever?
No, b/c life history has trade-offs Ex. in rotifin, scientist found a negative correlation b/w current fecundity and the probability of future survivorship (aka lower their fertility, the more likely they were to die) Ex. male fruit flies that mated frequently died a lot earlier than male fruit flies that never mated --- clear tradeoff between current reproduction and survivorship I don't fully understand this one???
IF limited to 2 kids per couple will population growth stop right away?
No, depends on the age structure??? (I don't get this)
DR M STARTED WITH PEARLS BEFORE SWINE
Not important, it just made me happy
Sidenote
Not part of the notes but everyone should know *Poison vs Venom* *Poison* is consumed *Venom* in injected If it bites you and you die, it's venomous. If you bite it and you die, it's poisonous.
When it the rate of population growth the greatest in a logistic model?
Occurs at the point of max growth typically found in the middle of the graph Determined to be when N = K/2
How did scientist figure out that H₂O splits during photosynthesis?
One scientist noticed that this reaction occurred in his bacteria: CO₂ + 2H₂S → CH₂O + 2S He hypothesized that if bacteria could split hydrogen sulfide (H₂S) into energy, then plants could similarly split H₂O to get energy, rather than splitting CO₂ fo energy as was commonly accepted at the time (see #6 on the term above) --- plants split H₂O (energy) → O₂ Twenty years later scientists proved his hypothesis with the following experiment: 2 Stages - Exp 1: CO₂ + 2H₂*O* → CH₂O + H₂O + *O₂* --- *O* is radioactive so it can be traced --- they found that the radioactive O did not go into the carbohydrate or water, but into the oxygen Exp 2: C*O₂* + 2H₂O → CH₂*O* + H₂*O* + O₂ --- the radioactive O is placed in the CO₂ and traced --- found to NOT be in the oxgen
sign stimulus
Only a portion of a stimulus is used by the individual leading to a *fixed action pattern* --- aka looking for only a single stimulus (as opposed to multiple) before producing a response; instinctual *Ex Stickleback males* have red bellies. Whenever a male approaches another male's territory, the defending stickleback instinctively fights the foreigner. Scientists found that the only sensory stimulus the males used to recognize each other were their *red bellies*. Male sticklebacks will attack everything with a red belly, even if it doesn't resemble a fish. Moreover, they wouldn't attack an object that looks like a stickleback as long as it didn't have a red belly. *Ex Ground-nesting birds* instinctively rotate the eggs in their nest. If an egg rolls out of the nest, the mother will come after it and roll it back. Turns out, these birds don't actually recognize their eggs - *only the shape* - so they will roll back whatever ovular object they see first. *Ex* Chicks respond differently to the same shape flown in different directions (see pic.) If it looks like a goose pattern, the chicks are unbothered. If it looks like a hawk, they go into a defensive position. They are not actually seeing a goose or a hawk, they only react to the shape (only a portion of the stimuli is used.)
Mendelian Generations
P (parental) F₁ (filial #1) F₂ (filial #2)
RR x rr Phenotypic ratio? Genotypic ratio?
P) RR x rr F₁) Rr * 4 F₂) RR, Rr, Rr, rr *Phenotypic ratio:* 3:1 *Genotypic ratio:* 1:2:1
Mendel's initial pea plant experiments
P) White flowers x Purple flowers F₁) All purple F₂) 3:1 purple:white same results with round vs wringled seeds
Ectoparasites
Parasites that feed on external surface of host --- ex. mosquitos. lice, louse
Symbiosis [NOT Symbiotic] Ecological Interactions
Parasitism Mutualism Commensalism Amensalism
What is the original source of energy for all species in an ecosystem?
Photosynthesis (all consumers get their energy directly or indirectly from photosynthesis)
C₄ Plants
Plants that separate processes of carbon fixation and the formation of a carbohydrate *in space* aka *structural separation of fixation of CO₂ and making sugar* (all one step in a typical Calvin Cycle) Instead... *PEP* (Phosphoenol pyruvate[3c]) grabs CO₂ and releases it to RuBP (and them the Calvin Cycle can start) --- essentially adding an extra step b/c there is a physical barrier in place (which takes up extra energy) *Why go through this extra step if it takes more energy?* When the temperature is high and light is intense, the *stomata are nearly closed*. This leads to a *low amount of CO₂* and *high amounts of O₂ *. Because of this, the *O₂ outcompete CO₂* for rubisco (the enzyme used in pt 1 of the Calvin cycle) When O₂ combines with RuBP, *photorespiration* occurs (process that breaks down carbon molecules [wasteful of necessary carbon and produces NO ATP]) aka *NOT GOOD FOR THE PLANT* So when it is hot and dry and the stomata are closed, the rate of photosynthesis goes WAY down --- "like RuBP chose the wrong dance partner" *Why is the extra step good?* *PEP *loves CO₂ and so in a mix of CO₂ and O₂ it will *latch onto the CO₂*, then PEP pumps CO₂ directly to the rubisco *Improves photosynthesis when it is hot an dry* ex. sugarcane, corn
CAM Plants
Plants that separate the processes of carbon fixation and the formation of a carbohydrate *in time* *Stomata open up at night* and *fix CO₂ into a 4c organic acid* (essentially saving it for later) *No PHS occurs at night* Stomata close during the day (opposite of most plants) During the day, the 4c organic acid brings CO₂ to RuBP and the Calvin Cycle can begin *Why close stomata during the day?* Save water ex. cactus, pineapple
Alternate names for "cold-blooded"
Poikilothermic *Ecto*thermic (ECTOpuses are cold-blooded)
Post-zygotic RIMs
RIMs that prevent species formation *after fertilizations* *Types* A) *Developmental isolation* - embryo dies/low zygote viability B) *Hybrid inviability* → adult hybrid dies before they can reproduce C) *Hybrid Sterility* - hybrids are incapable of producing offsprings --- ex. mules/ligers are sterile
Pre-zygotic RIMs
RIMs that prevent species formations *before fertilizations* occurs --- reduce probability of forming zygotes *Types* A) *Habitat isolation* → populations live in different habitats --- don't ever meet B) *Temporal isolation* → mating occurs at different seasons/days C) * Behavioral isolation* → little sexual attraction b/w males and females --- pheromones --- communication - ex. blinking light of fireflies to signal mates D) *Mechanical isolation* → structural distinctions b/w genitalia and parts E) *Genetic isolation* → gametes fail to attract --- ex. sperm gets destroyed before ever reaching egg; reproductive track destroys sperm of other species *H*o*T B*a*GM*an
Types of mating
Random Mating Assortative Mating Inbreeding
Random Fertilization
Random fertilization adds to genetic variation because any sperm can fuse with any ovum (unfertilized egg) The ovum has *8 million possible* chromosome combinations, so does the sperm cell. 8 million x 8 million = *64 trillion possible diploid combinations* in EACH AND EVERY zygote!
Iteroparous
Repeated reproduction throughout lifetime
How do you maintain seperate gene pools
Reproductive Isolating Mechanisms (RIMs)
Why change to 3 Domains?
Research done by *Carl Woese* sequencing Ribosomal RNA (same as last thing!) found that differing properties in rRNA fulfilled all 4 requirements ---universally distributed --- makes protein --- homologous parts --- changes slowly Woese determined that there were not 2 but 3 main lines of descent Created a new taxon - Domain
Anaerobic Respiration (overview)
Respiration in the absence of oxygen *1) Glycolysis* Starts with *Glucose (6c)*; Ends with *2 Pyruvate (3c)* + net *2 ATP *and *2 NADre* *Steps:* a) Activate Glucose (6c) (needs E to start reacting) → *cost 2 ATP* b) Form 2 PGALs (3c) [phosphoglyceraldehyde] c) Create 4 ATP (not 2) and 2 NADre d) Form 2 Pyruvate (3c) *2a) Fermentation in Fungi* 2 Pyruvate + 2NADre (both from glycolysis) → ethanol + 2NADox (aka energy used up) + 2CO₂ --- the CO₂ is why champagne foams *2a) Fermentation in Animals* 2 Pyruvate + 2NADre (both from glycolysis) → * 2 lactic acid* + 2NADox Net ATP from Fermentation: *2 ATP* --- Since 1 ATP ~ 7.5 kcal, 2 ATP is approximately 15 kcal --- Glucose has a total of 686 kcal --- 15/686 ~ *2% efficiency*
Aerobic Respiration (overview)
Respiration in the presence of oxygen *1) Glycolysis* Starts with *Glucose (6c)*; Ends with *2 Pyruvate (3c)* + net *2 ATP *and *2 NADre* *Steps:* a) Activate Glucose (6c) (needs E to start reacting) → *cost 2 ATP* b) Form 2 PGALs (3c) [phosphoglyceraldehyde] c) Create net 2 ATP (4 total) and 2 NADre d) Form 2 Pyruvate (3c) *2) Formation of Acetyl-CoA* Starts with 2 pyruvates (3c); End with *2 Acetyl-CoA (2c)* + 2*NADre* + *2CO₂* *Steps:* a) the 2 pyruvates (3c) from glycolysis cross into the *mitochondria matrix* b) *Pyruvate Oxidation* occurs → ends up with *2 Acetyl-CoA (2c)* + 2*NADre* + *2CO₂* *3) Krebs (citric acid) Cycle* --- 1 glucose will produce 2 Acetyl-CoA, so the citric acid cycle will occur twice for one glucose molecule a) Each *Acetyl-CoA (2c)* combines with *oxaloacetic acid* (4c) to *produce citric acid (6c)* --- Acetyl-CoA (2c) + oxaloacetic acid* (4c) → citric acid (6c)* --- b) 8 steps occur (twice b/c there are 2 A-CoAs), the end results of which are: --- 4 CO₂ --- 2 ATP --- 6 NADre --- 2 FADre *After the first 3 stages* of aerobic respiration, only *4 ATP* produced *4) Electron Transport Chain --- series of electron carrier proteins that shuttle high-energy electrons during ATP-generating reactions *Steps:* a) NADre has electrons → gives electrons to *NADH-Q reductase* (large protein complex); FADre does the same with *Succinate Dehydrogenase*. (NAD-Q and Succinate Dehydrogenase combine to form Ubiquinone.) b) At the ends of Ubiquinone is *O₂*. O₂ is an *electron grabber* and it pulls the elections down the rest of the chain, where it will form *H₂O* c) Energy from the channeled electrons is used to pump H⁺ protons across the matrix membrane, creating a *chemiosmotic gradient* --- lot's of H⁺ on one side of the membrane creates an imbalance in charge and protons --- makes them desire to move to the opposite side of the membrane d) *F₁ portion* of *ATP synthase* allows H⁺ to cross the membrane e) The energy created by this action is used to create *ATP*
Suggested music for Lecture 2 (possible E.C.???)
Rock And Roll by The Velvet Underground
Probability Eq
Rule of Multiplication Rule of Addition
How to calculate R₀
R₀ = ∑lxmx =l₁m₁+l₂m₂+l₃m₃ N.B. lx = percent survivorship mx = age-specific fecundity (Both these values can be found on a life table)
Why use HW if it never actually happens
Scientist use it as a baseline to compare actual population --- if there are departures from what is expected from HW equilibrium, then one of the 5 evolutionary forces are making changes
Coevolution
Sequence of evolutionary events in which two interacting species modify their interaction --- occurs with predation, competition, mutualism, and parasitism (doesn't happen with commensalism and amensalism since one of the species is neutral)
Electron Transport Chain (ETC)
Series of electron carrier proteins that shuttle high-energy electrons during ATP-generating reactions Energy from the electrons stored in NADre and FADre are used to pump protons (H⁺) across the membrane *Steps:* a) NADre has electrons → gives electrons to *NADH-Q reductase* (large protein complex); FADre does the same with *Succinate Dehydrogenase* b) At the ends of NADH-Q reductase and Succ. D is *O₂*. O₂ is an *electron grabber* and it pulls the elections down the rest of the chain, where it will form *H₂O* c) Energy from the channeled electrons is used to pump H⁺ protons across the matrix membrane, creating a *chemiosmotic gradient* --- lot's of H⁺ on one side of the membrane creates an imbalance in charge and protons --- makes them desire to move to the opposite side of the membrane d) *F₁ portion* of *ATP synthase* allows H⁺ to cross the membrane e) The energy created by this action is used to create ATP
Semelparous
Single reproductive effort followed by death
Chlamydomonas
Single-celled algae *protist* capable of asexual and sexual reproduction --- adults are haploid --- instead of male and female, there are *+* and *-* --- when + and - fuse, they form a diploid, which goes through meiosis forming 4 haploids Has a FLAGELLUM!!! (unimportant, flagella are just cool)
Escape in size [Prey Avoidance Adaptations]
Some animals are just way to big to be predated on by the predators in their environment --- elephant, hippos
Enormous reproductive output [parasite transmission]
Some parasites resort to producing an enormous amount of offspring to increase the chance that at least some of them will infect a host *Ex.* schistosoma mansoni (aka schistosomes) - flatworm; blood parasite of humans that spend their initial stages in freshwater snails *Life Cycle:* --- male/female produce 400 eggs per day for 6 years = 1 million eggs --- each egg hatches into a *miracidium* which goes into a snail --- once inside the snail, it undergoes asexual reproduction and produces 2000 *cercariae *per day 30 days = 60,000 infecting forms (cercariae) --- That's around *60 billion cercariae per mating pair*, and only 2 are needed to infect a host and start the cycle again *schistosomes are designed for effective but not efficient transmission*
Consequences that *MAY* occur as a result of overshooting the carrying capacity
Sometimes exceeding K could inadvertently lead to a lowering of K for future generations as a result of irreparable damage to the system/resource availability --- BIG PICTURE: K changes when the environment changes Ex. Cattle were introduced to a grassland Population increased rapidly but ended up destroying the grassland in the process Now K is lowered since there is no longer enough food to uphold such a large population Led to a large decrease in cattle population Ex. Reindeer on St. Paul's Island (Alaska) In 1910, 4 male and 22 female 3 years late, 2000 reindeer Overgrazing/destroyed vegetation led to a rapid crash in reindeer population Only 8 deer left
ART
assisted reproductive technology Describes techniques used to aid an infertile couple in achieving a viable pregnancy
Photophosphorylation aka Light-Dependent Reaction (non-cyclic one ONLY)
Step 1: Light hits P680 (collection of Chlorophyll α) Step 2: The excited high-energy electrons go to a primary electron acceptor called *Pheophtin* Step 3: Now chlorophyll α is short of those electrons, so *water is split* to replace electrons → IMPORTANT BY-PRODUCT *O₂* Step 4: Electrons go down *Photosystem II* and through an ETC with ATP synthase generate *ATP* Step 5: Photon hits *P700*, electron gain energy and go to primary electron acceptor *ferredoxin*, --- the other electron coming from Photosystem II take their place so no need to split H₂O Step 6: Electrons go down *Photosystem 1* reduce NADPox → NADPre using NADP⁺ REductase
Competitive exclusion
Strong competition can lead to local elimination of one of the species ex. European starlings eliminates blue birds (sidenote I LOVE starlings but they are f ucking violent birds)
population genetics
Study of evolutionary changes in allele and genotype frequencies in response to environmental pressures --- the study of how populations change genetically over time
Symbiosis vs. Symbiotic
Symbiosis is a close relationship between two species in which at least one species benefits. Mutualism is a symbiotic relationship in which both species benefit
T/F Each American cause 20-100 times more environmental damage comparatively.
T
T/F Except for humans, most behavior is not conscious.
T
T/F Parasites don't always carry diseases.
T
T/F Sex and nonrandom mating can change genotype frequency, but not allele frequency
T
T/F six fingers is a dom trait.
T
fixation is faster with recessive alleles
T
T/F Selection works faster to eliminate a "bad" dominant allele
T (happens b/c fixation is faster if recessive is preferred)
What type of cells does HIV target and why?
T-helper cells because they have a receptor (*CD4 protein*) that the virus' glycoprotein gp120 can attach to
combination therapy
The administration of two or more antimicrobial medications simultaneously to prevent the growth of mutants that might be resistant to one of the antimicrobials --- used in the treatment of HIV *Why do this?* Say the chance of resistance to Drug A is 1 in 100,000; and resistance to Drug B is 1 in 100,000. The probability that resistance to both drugs in the same strand of RNA is 1 in 10 billion - much better odds!
Basic Reproductive Rate [parasitism]
The average number of infected offspring that an infected host gives rise to in a population of susceptible host *R = 1* → transition threshold *R > 1* → virus is spreading in population *R < 1* → virus is disappearing in population *[numerator]* = [βN] = [rate of infection appearance] *[denominator]* = [d + α + V] = [rate of infection disappearance] β = transmission efficiency V = recovery rate from infection (immunity) d + α = infected host death (b/c they live shorter lives)
Prophase I
The chromosomes condense, and the nuclear envelope breaks down. crossing-over occurs. --- chromosomes condense --- *homologous chromosomes *find each other and *pair up* --- when they find their pair, they form a protein complex that holds the chromosomes together called a *tetrad* (N.B. 2 chromosomes = 4 chromatids) --- in humans that would be 23 tetrads ---- *Crossing Over* - homologous chromatids exchange pieces; leads to genetic variation
Prophase II
The duplicated chromosomes and spindle fibers reappear in each new cell.
Metaphase II
The duplicated chromosomes move to the centre of the cell. Each centromere attaches to two spindle fibres instead of one.
Which came first, the chicken or the egg?
The egg, because the amniotic egg evolved well before the first bird.
net primary productivity (NPP)
The energy available to consumers through the consumption of producers (takes into account that some of the energy has been lost through the plant's respiration) *Equation* NPP = GPP - RSP --- NPP = net primary prodctivity --- GPP = gross primary productivity --- RSP = plant's respiration
energy of activation (Ea)
The energy that must be provided to compounds to result in a chemical reaction Enzymes supplant some of the energy that would be needed to complete the reaction
Syngamy
The fusion of two gametes in fertilization --- fertilization
Red Queen Hypothesis
The idea that all life is in an evolutionary "arms race" trying to out-preform the others by rapidly changing their genetics. Since life evolves to adapt to the threat posed by other creatures, they ultimately end up "in the same place." --- name comes from Alice in Wonderland
Live in Immune System [parasite establishment]
The immune system is supposed to stop pathogens, but some parasites figure out how to live inside immune system cells *Ex. Toxoplasma* managed to live inside macrophages (cells meant to destroy parasites) *Ex. Mycobacterium Tuberculosis, the bacteria that causes TB, is supposed to be destroyed by macrophages BUT the pathogen has managed to prevent the defense mechanisms from destroying the bacteria HOWEVER, the host is able to prevent the TB bacteria from reproducing → causes *latent TB Infection (LTBI)* --- approximately 2 billion people with LTBI --- in 2017, there were 10 million cases of TB; 1.6 million died
Relationship b/w light and dark reaction in photosynthesis
The light reaction supplies energy so the dark reaction can go So if the plant is placed in the dark for a while, it will stop doing photosynthesis
Doubling Time (for exponential growth)
The number of years needed to double a population, assuming a constant rate of natural increase (exponential growth) *doubling time = ln(2)/r* [similar to first order rate law] derivation included in pic cause I'm lazy
Carbon Cycle
The organic circulation of carbon from the atmosphere into organisms and back again The constant cycle of Respiration and Photosynthesis kept the cycle fairly balanced over the last 10,000 years However, since the *1850's*, CO₂ in the atmosphere and avg temperature have been increasing exponentially
Metaphase I
The pairs of homologous chromosomes line up in the center of the cell. The centromere of each chromatid pair attaches to one spindle fibre.
Energy Flow
The passage of energy through the components of an ecosystem
absorption spectrum
The range of a pigment's ability to absorb various wavelengths of light.
Telophase II
The spindle fibers disappear, and a nuclear membrane forms around each set of chromosomes. *4 haploid cell formed* (2 pairs of identical cells)
metastasis
The spread of cancer cells beyond their original site
reducing agent
The substance that is oxidized in a redox equation
oxidizing agent
The substance that is reduced in a redox equation
character displacement
The tendency for characteristics to be more divergent in *sympatric* populations of two species than in allopatric populations of the same two species. --- happens in order to reduce hybridization (so they don't wwaste resources
Gross Primary Productivity (GPP)
The total amount of solar energy that producers in an ecosystem capture via photosynthesis over a given amount of time --- not representative of energy available to consumers since some of the energy is lost through *respiration*
Huntington's Disease
Type of *autosomal dominant* disorder incurable disease of the nervous system (brain cells deteriorate) caused by lethal dominant allele --- 1 out of 10,000 people --- not expressed until 30-45 year age range (already had time to reproduce) [see frequency of onset vs age graph in notes] A human genetic disease caused by a dominant allele; characterized by uncontrollable body movements and degeneration of the nervous system; usually fatal 10 to 20 years after the onset of symptoms. Caused by *Trinucleotide Repeat* of *CAG* sequence --- 9-35 copies --> normal --- 40-180 copies ---> Huntington's (more repeats, quicker the onset of the disease) *Pre-symptomatic diagnostic test* --- linker marker (DNA near target sequence that can be tracked) on *chromosome 4* --- DNA region cut with *restriction enzymes* *Outcome of HD test* 1) neg 2) pos 3) not the father (2-3% babies born out of wedlock) *Only 25% of people take the test* *Advantages of test* --- risk free children --- can plan life *Disadvantages of test* --- know how you're going to die --- *insurance companies* refuse service --- suicide rate increases
Cystic FIbrosis
Type of *autosomal recessive* A genetic disorder that occurs in people with two copies of a certain recessive allele; characterized by an excessive secretion of mucus and consequent vulnerability to infection; fatal if untreated. --- affects *1 out of 3000 whites* --- *1 out of 29 whites* are carriers Caused by a mutation on *Cystic Fibrosis Transmembrane Regulator (CFTR)* gene --- most common error is one missing nucleotide in position 508 mutant protein makes body unable to deal with *chlorine* --> creates thick, sticky mucus that can block airways and raise bacteria levels If untreated, patients usually die by 5 With treatment, can live to 40-50 *Treatment* --- most common drug --> Kalydeco - only works for about 20% CF patients (must have specific mutation), cost *$30,000* per year *Tests* --- Can be detected using *sweat test* (CF patients release excessively salty sweat since they can't handle chlorine) --- *Prenatal test* can test if an embryo has CF, up to parents if they want to abort --------- can also test for carrier status
stop codon
UAA, UAG, UGA (it's on the copied strand, not the template
chemotrophs
Use CO2 or S in order to obtain energy by *breaking H2 bonds* --- S + H2 → H2S + energy --- CO2 + 4H2 → CH4 + 2H2O + energy
Survivorship
Used to assess population dynamics --- the percentage of members of a group that are likely to survive to any given age
Carbohydrates (overview)
Usually come in form *(CH₂O)ₙ* *Functions:* 1) energy source 2) stored energy 3) structural component --- ex. cellulose in plants, chitin in fungi *Classifying:* a) monosaccharides --- 3c: Triose (ex. glyceraldehyde C₃H₆O₃) --- 5c: Pentose (ex. ribose C₅H₁₀O₅ & deoxyribose C₅H₁₀O₄_ --- 6c: Hexose (ex. glucose C₆H₁₂O₆) b) disaccharides (ex. sucrose → glucose+fructose; maltose → glucose+glucose) c) polysaccharides (xx. starch, cellulose, chitin)
Lake Maracaibo, Venezuela
Village in Venezuela where a spanish sailor lived and procreated. HAs 7,000 descentendant which have *Huntington's disease*
Retrovirus transmission
Virus attaches to cell and passes its 2 RNA. The virus has an enzyme called *reverse transcriptase (RT)* which it uses to make DNA out of the RNA strands (opposite of central dogma) called *cDNA* (complementary DNA.) cDNA moves into the nucleus of the cell. At this point, the cell is called a *provirus*. The host essentially becomes a virus factory and produces virus proteins. Virus *protease* cuts the protein into the right shapes for use. Finally, new viruses bud off the cell.
Transduction
Virus infecting a bacteria and transferring genetic material from another bacteria
Why do we like spices?
We aren't consuming them for calories or nutritional purposes It is possible that they could help us heal from microbe activity
"If we evolve from apes, why are apes still around"
We only share a common ancestor Tree of life monkeys --> cousins humans ---> you African Apes ---> siblings
What can Chlamydomonas tells us about why sexual reproduction is preferred?
When the environment is stable, Chlamy will reproduce asexually. Only when in unfavorable conditions will sexual reproduction occur. This increases the likelihood that at least some of the offspring will be able to survive the current condition ensuring the survival of the species.
Cystic Fibrosis is a what type of inheritable disease?
autosomal recessive
Outcomes of Secondary Contact
When two population that have been separated for a while come into contact, five things can happen: 1) They could *fuse* back into one population [they were different, but not different enough] 2) *Reinforcement* -->they continue to diverge due to prezygotic mechanism 3) Form *hybrid* zone --- ex. polar bear and grizzly territories cross paths; create hybrids 4) *Extinction* of one population 5) The hybrids become abundant enough that they constitute a *third species*; reach the point where they could no longer mate back with original two species
Atrazine
Widely used herbicide linked to male frogs becoming hermaphrodites (you know, the alex jones one)
DDT
Wildly used pesticide in post-WWII America that was intended to eliminate insects but ended up having a devastating result on fish-eating bird (ex. bald eagle) populations due to *biological magnification*. --- caused a depletion of calcium in egg shells resulting in thin, weak eggs 1963 - only 417 nesting pairs of bald eagles left 1992 - US banned DDT 1974 - 791 nesting pairs 1984 - 1757 nesting pairs 1992 - 3747 nesting pairs 1999 - 5800, taken off endangered species list 2007 - removed from threatened list today - common
Would this donation work? Type AB patient + Type B donor
Yes
Should social behaviors evolve if we can just form groups?
Yes 1) Enhance the original advantage of forming a group --- ex. alarm calls, cooperative hunting came around after groups formed 2) Effect of reproductive competition --- dominant/submissive arises b/c competition within a group
If you are HIV+ but don't have AIDS, should you be taking these drugs?
Yes, b/c it slows prevention
Carbohydrates are made out of what atoms? Lipids are made out of what atoms? Proteins are made out of what atoms? Nucleic acids are made out of what atoms?
[carbs] C, H, O (1:2:1 ratio) [lipids] C, H, O (NOT 2:1 ratio) [proteins] C, H, O, N (sometimes P, S, Mg, Fe) [nucleic acid] C, H, O, P, N
trihybrid cross
a cross involving three traits
zygote
a diploid cell resulting from the fusion of two haploid gametes; a fertilized egg
locus
a gene's specific location along the length of a chromosome (different versions of a gene may be found on maternal and paternal chromosomes)
gametes
a mature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote.
monomer
a molecule that can be bonded to other identical molecules to form a polymer --- ex. amino acids are the monomers for proteins
How can gene flow increase genetic variation?
a new individual can bring in new genes
keystone predator
a predator species that reduces the density of the strongest competitors in a community, thereby helping maintain species diversity
mutations
a random error in gene replication that leads to a change
Amensalism
a relationship in which one organism is harmed and the other is unaffected --- ex. elephant going through forest (does not affect elephant, but trees are destroyed)
Multiple alleles
a situation in which there are more than two allelic forms of a gene; i.e. the *blood types* A, B, AB, and O (as opposed the Mendelian peas being either round or wrinkled)
Poison
a substance that causes illness, injury or death if taken into the body or produced within the body Ex. monarch butterflies produce poison (results from eating milkweed) The first time a predator eats a MB they throw up → learn to avoid eating MB Ex. Certain plants use poisons like nicotine or morphine to deter predators. Had an unintended side-effect.
endosymbiotic theory
a theory that states that certain kinds of prokaryotes began living inside of larger cells and evolved into the organelles of modern-day eukaryotes --- origin of mitochondria and chloroplast early prokaryote engulfed by other prokaryotes Horizontal gene transfer occurs Evolved into mitochondria/chloroplast Theory initially proposed by Margulis, 1970 Initially not supported by the general science population Sequencing of rRNA favors this theory
classical conditioning
a type of learning in which one learns to link two or more stimuli and anticipate events --- rewards and punishments --- ex. Pavlov's dogs
Mullerian Mimicry
a type of mimicry in which two (or more) harmful species resemble each other *Ex.* viceroy butterflies and monarch butterflies are both toxic and resemble each other
Which type(s) of asexual reproduction is/are done by prokaryotes? Which involves mitosis?
a) Binary Fission b) All of them except binary fission
Types of Learning
a) Imprinting b) Habituation c) Classical Conditioning d) Trial & Error e) Spatial Learning f) Insight Learning
Typical Characteristic of Autosomal Dominant
a) affected individuals typically have 1/2 normal, 1/2 affected offspring b) normal children of affected individuals only have normal children c) males = female (affected in similar proportions) d) each sex equally likely to transmit diseases
Consequences of NS
a) certain phenotypes produce more offspring (in a given environment) b) best-adapted individuals contribute more genes to the gene pool c) evolution
Typical characteristics of sex-linked disorders
a) incidents are higher in males b) phenotypes *NEVER* transmitted from father to sons (b/c father gives Y chromosome)
Lipid Funtions
a) membrane structure (phospholipid) b) energy storage c) structural basis for hormones
Types of Carbohydrates
a) monosaccharides b) disaccharides c) polysaccharides
Evolutionary forces that increase GV
a) mutation b) sexual reproduction --- changes genotype frequency, does NOT change allele frequency c) gene flow (immigration) --- new individuals can bring in novel genes
Typical Characteristic of Autosomal Recessive
a) parents clinically normal b) siblings only affected in family c) males = female (affected in similar proportions) d) parents may be consanguineous
a) What would happen if DNA is copied badly? b) What would happen if DNA is copied perfectly?
a) rate of cancer would increase b) no room for adaptation (Evolution)
Evolutionary forces that decrease GV
a) stabilizing selection b) directional selection c) genetic drift --- randomly loses alleles d) inbreeding --- increases hemizygosity, does NOT change allele frequency e) gene flow (emigration) --- homogenizes population
Enzyme features
a) useful in small amounts (don't need a lot) b) catalyst c) *lowers* Energy of Activation (E∨a) d) *does NOT change free energy change (∆G)*
virulence
ability to produce pathogenic effects
intraspecific competition
competition between members of the same species
Biological Magnification
aka bioaccumulation increasing concentration of a harmful substance in organisms at higher trophic levels in a food chain or food web --- certain toxic compounds can't be degraded so they end up persisting in the environment and get passed along to each trophic level --- substances that are retained become more concentrated at each subsequent trophic level because there is less biomass at higher levels but the same amount of pollutants - leading to a higher concentration
Poikilothermic
aka cold-blooded aka ectothermic maintaining the body at the same temperature as the environment --- lose energy to their environment
Mate Competition
aka intrasexual selection Selection in which one sex competes with other members of the same sex for access to the other sex for reproduction --- males fight for territory which dictate the right to copulate with females --- ex. elephant seals
Female Mate Choice
aka mate selection aka intersexual selection Preference by females for certain traits in males --- no male fighting, focused on display Females look for signals of high-quality males --- ex. male zebrafish are selected based on the brightness of their coloration --- ex. damselflies selected for males with higher temperatures b/c that implied they lived in territories in the sun which are better for raising children Females improve reproductive success by going for quality males ("choosier") Looking for a) direct benefits → food/territory b) indirect benefits → "good genes
Resource Partioning
aka niche differentiation When species divide a niche to avoid competition for resources ex. Warbles research by MacArthur 5 species found to be sympatric (all 5 species in same place) MacArthur first assumed that Gause's theory must be wrong if all 5 species coexisted Then notices that their feeding habits were different --- each species feeds on different parts of the trees; reduces interspecies competition (forming 5 *guilds*)
insight learning
aka reasoning The process of learning how to solve a problem or do something new by applying what is already known --- adapting past experiences to new situations --- very few animals can do this
Homothermic
aka warm-blooded aka endothermic Able to maintain a constant body temperature --- birds, mammals
complex traits
ala multifactorial --- ex. smoking behavior traits controlled by multiple genes, the interaction of genes with each other, and with environmental factors where the contributions of genes and environment are undefined --- hard to study b/c so many facotrs involved --- one way to study ---> *TWIN STUDIES*
"tape measure of evolution"
amino acids (b/c the length or the amino acid chains can be used to identify evolutionary distance)
Life Table
an age-specific summary of the survival pattern of a population --- can be used to calculate R₀ x = age group (aka generations) lx = percent survivorship mx = age-specific fecundity lxmx = add all these values to get R₀ (typically not on life table, must be calculated yourself) In this case R₀ is greater than 1, so the population has grown
Fixation
an allele frequency approaching 100% (but never fully achieving it)
Triglycerides
an energy-rich compound made up of a single molecule of glycerol and three molecules of fatty acid --- formed through *dehydration reaction* Called *fat* if solid at room temp; called* oil *if liquid at room temp
lactase
an enzyme that catalyzes the hydrolysis of lactose to glucose and galactose --- lactose intolerant people lack this protein and are unable to breakdown lactose
Autopolyploidy (RECHECK)
an individual that has more than two chromosome sets that are all derived from a single species, usually due to nondisjunction
MRSA (methicillin-resistant Staphylococcus aureus)
an infection caused by specific bacteria that has become resistant to many antibiotics
opportunistic infection (OI)
an infection that causes disease when the immune system is compromised for other reasons --- pathogens that are normally held back by the immune system take over when the immune system is compromised
Hermaphrodite
an organism that has both male and female reproductive organs --- both gametes in a single individual --- most invertebrates, some plants --- can still *mate with members of the same species* Advantageous for *sessile* organisms
Parasite
an organism that obtains nutrients from a host --- antagonistic relationship (+/-) --- host is harmed but usually not immediately killed
chemoheterotroph
an organism that requires organic molecules for both energy and carbon
Habituation
an organism's decreasing response to a stimulus with repeated exposure to it; declined response to an insignificant stimuli --- ignoring a persistent stimuli --- "boy who cried wolf" effect --- not associated w/ punishment or reward ~~~~~~~~~~~~~ "For years this rule has kept me out of hopeless despair You simply do not feel what is always there I ask my brain to entertain that pain is the same That if I feel it all the time, can you really call it pain?" [I will take every possible opportunity to quote Hank Green] but seriously listen to the song cause it's fantastic https://www.youtube.com/watch?v=Ek_wCaBZTCg
Aerobic Respiration formula
analogy: glucose is like a $20 dollar bill - it must be broken down into smaller parts in order to be used in certain functions
Optimal Foraging (predators)
animals maximize their feeding efficiency We expect that predator would maximize the net benefit (benefit - cost) when it comes to finding food --- as a predator, you wouldn't take anything lower than a or greater than b b/c then the cost is greater than the benefits --- in real-life examples though, sometimes predators choose not to optimize the benefits [ex. blue gill study]
Rifampin
antibiotic against TB --- targets RNA Polymerase of bacteria
Reproductive Isolating Mechanisms (RIMs)
any factor - behavioral, ecological, or anatomical - that prevents a male and female of two different species from hybridizing Factors that prevent two species from mating --- prevent gene flow 2 Types: 1) Pre-zygotic RIMs 2) Post-zygotic RIMs
Sickle Cell
autosomal recessive mutation in hemoglobin (carry O) RBC - 300 million copies of hemoglobin --- consist of 4 protein complexes (quaternary structure) single base pair change; sub A for T changes GAG to GUG in mRNA RBC becomes crescent (C-shaped) anemic/clogs blood vessels 100,000 in US currently no cure Hb^+ normal Hb^s sickle cell Genotype: Hb^+Hb^+ = normal/ survivability 100% Hb^+Hb^s = mild anemic/survivability ~100% Hb^sHb^s = anemic/suvivablity 20% Afrcia: sickle cell = 4% = p^2 carrier = 32% = 2pq normal = 64% = q^2 p = .2; q = .8 Why is the amount of carriers so high? ---> Malaria Malaria caused by protist Plasmodium - lives in RBC transferred by Anopleles Mosquito; 200 mil cases worldwide #1 parasitic disease; most affects young 445,000 juvenile death in africa mostly eliminated in US *Hb^s allele makes you more resistant to malaria --- deforming RBC prevent parasite from entering Genotype (taking malaria into account) Hb^+Hb^+ = normal/NOT-resistant/survivability~75% Hb^+Hb^s = mild-anemic/moreresistant/survivability~100% Hb^sHb^s = anemic/resistant/suvivablity 20% (still aneminic) *Heterozygote Advantage* Relative Fitness (W with bar) in malaria region Hb^+Hb^+ = .75 Hb^+Hb^s = 1 Hb^sHb^s = .2 Relative Fitness (W with bar) in NONmalaria region Hb^+Hb^+ = 1 Hb^+Hb^s = 1 Hb^sHb^s = .2 Malaria region - *stabilizing selection* due to heterozygote advantage Nonmalaria region - directional selection favoring Hb^+ --- Hb^s allele decreasing slowly b/c masked by heterozygote What if people moved from Africa to US (done by slave trade) Africa Hb^+ = .8 Hb^s = .2 African Americans Hb^+ = .95 Hb^s = .05 *sickle cell DECREASES* since no longer in malaraia-prevelant environment NB sickle cell is not a "black disease", rather it parallels distributions of malaria
I'm bored
baby cheetah
Mycobacterium tuberculosis
bacteria that caises tuberculosis
MCR1
bacterial gene for resistance to collistan (our last resort antibody) Stored in plasmid HGT that can be transferred to other bacteria
High-density lipoprotein (HDL)
blood fat that helps transport cholesterol out of the arteries, thereby protecting against heart disease --- aka *garbage trucks* for cholesterol Takes excess cholesterol to the *liver* to be degraded
Aerobic Respiration
breakdown of *glucose* in the presence of oxygen order to create chemical energy
BRCA1
breast cancer gene 1 that codes for DNA repair Mutations in this gene are heavily linked to breast cancer IF you have this mitation --> *50-80%* of developing breast cancer
Amoxicillin
bubblegum flavored medicine kids used to take No longer effective against 50% of E. Coli due to selective pressures (coevolution)
How are electrons excited during photosynthesis?
by *photons* photons hit pigments which elevate electrons to a higher energy level (an unstable state), then they come back down and pass it on to an electron acceptor molecule which will convert it through a series of enzyme-catalyzed steps to chemical energy
Most of the energy used in photosynthesis is used up in the
calvin cycle
behavior bottom line
cascade of genes + environment control behavior Natural selection affects genes, genes can produce behavior directly (instinct) or can affect ability to learn (unpredictable events) Inheritance defines the limit with which learning can occur flexibility of behavior
G0 phase
cell cycle arrest (terminally differentiated) Restriction checkpoints deems the cell ill-fit for mitosis Some cells ware designed to stay in this stage ex. nerve cells, muscle cells
evolution
change in genetic make-up of a population over time
pheremones
chemical signals released by organisms when they are ready to breed
Pheromones
chemical signals that trigger certain behavior in species --- type of *sign stimulus* --- * Ex* female insects send out pheromones to attract males as *small molecules* so they will diffuse rapidly and disperse farther
types of learning that involve a punishment or reward [RECHECK]
classical conditioning trial & error
Blood groups
classified according to the presence, or absence, of certain *antigens*; four major *phenotypes* are A, AB, B, and O
cursive i blood genotype
codes for a nonfunction protein (At position 258 of 1062, it is missing a guanine [frameshift mutation])
molecular phylogeny
comparative analysis of the nucleotide sequences of genes and the *amino acid* sequences and structural features of *proteins* from which evolutionary histories and relationships can be inferred --- aka looking at biological particles to determine evolutionary relationships
interspecific competition
competition between members of different species
Trisomy 21
condition in which an individual has *three number 21 chromosomes*, resulting in *Down syndrome* 1 out of 666 babies Correlated with the age of the mother (higher the age, higher the likelihood of DS) --- likely b/c the eggs are always in the woman and will degrade over time
Polyploidy
condition in which an organism has extra sets of chromosomes --- increases the number of full sets of the genome you can have (ex. humans have two sets, polyploidy would be any more than the normal amount --- typically found in flowering plants/certain animals (flatworms, snails, earthworms) Types: 1) Autopolyploidy 2) Allopoluploidy
you made to the end!
congratulatory frogmouth
hybridization (in biology)
crossing of two differnet species ot form a hybrid species
Location of glycolysis
cytosol (out in cytoplasm)
Population cannot increase indefinitely. Either the birth rate will (increase/decrease) or the death rate will (increase/decrease).
decrease increase
Growth is human population is largely due to
decreased death rate caused by improvements in a) sanitation, b) medicine, andc) nutrition
Expressivity
degree to which the gene is expressed (labeled *mild, moderate, severe*)
How do monosaccharides combine?
dehydration reaction glycosidic linkage
Phylogenetic Tree
diagram that shows evolutionary relationships among different groups of organism --- "tree of life" → *predictive* (placing a new species onto an existing tree will allow scientist to infer information about the species through its evolutionary cousins)
4 F's
dictates most animal behavior fighting fleeing feeding ****ing (quizlet auto-sensors don't blame me)
Diversity
different combinations that solve a problem linked to a species' survival - --- different means to the same end
cyst
dormant stage in protist --- to protect against harmful conditions
Protease Inhibitor
drug that blocks HIV *late in its life cycle* --- treats AIDS by inhibiting the activity of *protease* so it doesn't cut viral parts into the right shape making them unusable
Fusion Inhibitors
drug that prevents HIV from successfully fusing with CD4 (helper T) cells
Integrase Inhibitors
drugs that block the integration of HIV DNA into the nucleus
Nucleoside RT Inhibitors (NRTI)
drugs that end HIV *early in its life cycle* --- *tricks reverse transcriptase* into thinking it is done replicating; essentially blocking RNA → DNA synthesis
sister chromatids
duplicated chromosomes held together at the centromere --while joined, 2 sister chromatids make up one chromosome --chromatids eventually separate during mitosis or meiosis II
Mendel's Law of Independent Assortment
each allele pair segregates independently during assortment --- Mendel was able to figure this out from his data even though they didn't know of meiosis yet (b/c the distribution would not occur if they were linked on the same chromosomes) the inheritance of one character has no effect on the inheritance of another
Red Queen Hypothesis
each species has to run (evolve) as fast as possible just to stay in place -- because predators, competitors, and parasites also continue to evolve --- an ever-growing *evolutionary arms race* between predator and prey --- as soon as one gains an advantage, the other finds a way to counteract it and so on
Sea Lamprey
eel-like fish that latches on to other fish and act as a parasite. Invaded Great Lakes. People put chemical TMF that disrupts ETC into the water, killing most lamprey except the ones that were resistant Eventually, the resistant species became prevalent
Is it possible to have 5 Parents
egg donor, sperm donor, surrogate mom, intended parents
Cause of Natural Selection
environment --- there is not one best phenotype because the enironment is always changing
Learned Behavior
environmentally-induced behavior modified by experience
RNA Polymerase
enzyme that links together the growing chain of mRNA nucleotides during* transcription* using a DNA strand as a template
Explaining the logistic growth graph in the context of the logistic growth equation
equation: *∆N/∆t = rN(K-N)/K* When the population is really low, N approaches 0 → ∆N/∆t = (rN)(K-0)/K = (rN)K/K = 1(rN) --- this looks like a standard exponential growth graph, which explains the behavior of the graph at low population values When N=K → ∆N/∆t = (K-K)/K = 0/K = 0; the curve is flat --- explains what happens when the graph approaches K When N>K → (K-N)/K would be negative -- leas to negative growth --- explains that if N were to ever go above K the rate of the line would start to decrease until it reaches K
G2 checkpoint
evaluates accuracy of DNA replication. Checks for mitosis promoting factor levels to proceed
"Biology does not make sense except through the concept of ______________"
evolution
Adaptive Radiation
evolution from a common ancestor of many species adapted to diverse environments numerous species emerged from common ancestor classic example: Darwin's finches --- found 14 different species --- specialized for different type of food (6 seeds, 6 insects, 2 bugs/fruit) --- pair of *ground-feeding (seed) finches were the ancestor to all of them --- founding party from South Africa, isolated for thousands of years --> construct new gene pool [allopatric speciation] --- the birds on the island don't mix gene pool b/ reproductive isolation form time they were apart
Lab retriever coat color
example of Epistasis *Gene1: B* --- BB or Bb → black --- bb → choclate *Gene2: E* --- AA or Aa → normal color development --- aa → yellow lab NO MATTER WHAT aa is epistatic over B --- has *veto powers
EDR-TB
extremely-drug resistant TB
type 2 survivorship curve
fairly constant mortality rate throughout life --- lizards, songbirds, gulls, hydra --- young individuals ae just as likely to dies as old individual
fecundity
fertility ONLY WITH FEMALES
Vertical Gene Transfer
flow of genetic information from one generation to the next --- parent to offspring
gene
forms of alleles
Pneumocystis
fungi that live in the lungs; typically held back by the immune system When the immune system is compromised, it causes PCP (Pneumocystis pneumonia) pneumonia --- opportunistic infection
Comparing r and k selected species
further explaining some of them here: # lifetime reproduction event: r - once (a big bang reproduction) k - several (has offspring at different times) General Strategy: r - productivity (get as many offspring out there) k - efficiency (puts all resources into making sure its few offspring survive)
Reduction
gain of e⁻
Point mutation
gene mutation in which a single base pair in DNA has been changed --- replace 1 nucleotide with another *3 Types:* a) silent mutation b) missense mutation c) nonsense mutation
Modifier gene (RECHECK)
genes that enhance or dilute the effects of other genes --- in reality, no expression is fully determined by one gene Standard example: eye color --- typically B → brown eyes, bb → blue eyes --- BUT other genes will also modify eye color (ex. green are have the gene for blue eyes but have a bunch of other shit going on)
Genotype
genetic makeup of an organism
Innate Behavior
genetically induced behavior that is fixed for life --- aka instinct
Population genetics
genetics on a large scale --- the study of how populations change genetically over time
phenotypes are formed through the interactions between ______________ and _____________
genotype environment
sucrose → ____________ + ____________ maltose → ____________ + ____________
glucose (+) fructose glucose (+) glucose
Age Distribution Graph
graphical representation of the population in each age group *3 Types* (labeled differently on this picture) 1) Growing 2) Stable 3) Declining
retrovirus
group of RNA viruses which inserts a DNA copy of their genome into the host cell in order to replicate, e.g. HIV a) lives inside a cell b) have a *single-stranded RNA *used to make DNA
Population
group of individuals of the same species in an area where they are *capable of interbreeding*
guild
group of species that exploit same resources in different ways
anti-codon
group of three bases on a tRNA molecule that are complementary to an mRNA codon --- contains U --- identical to template strand but with U
In every organism, energy is split between ____________, ___________, and _____________
growth maintenance reproduction (% of energy dispersed to each category changes depending on the species)
G1
growth period *right after mitosis* in interphase --- chromosomes are not replicated yet --- synthesis and growth --- *G1 Restriction Checkpoint*: Determines whether the cell will proceed with mitosis --- If not, the cell goes into *G0*
HAART
highly active antiretroviral therapy (aka cART [combination antiretroviral therapy]) use of combinations of drugs that are effective against AIDS --- turned AIDS from a death sentence to a manageable disease --- now there are one-a-day pills to combat AIDS (contains 3 drugs
Strength of Selection
how strongly a particular trait or set of traits is selected for --- compare in a common environment --- measuring *fitness*
Thermoodynamics
i misspelled thermodynamics in the last term but this is funny to me idk why ignore this term
Consequences of increased CO₂ levels in the atmosphere
ice caps melting tropics --> accelerated spread of deserts/disease impacts suitability of cold-weather species
Paternity test and blood type
important to look at genotype as well as phenotype
Autosomal Dominant
inheritance pattern of a dominant allele on an autosome --- only need 1 bad allele One mutated copy of the gene in each cell is sufficient for a person to be affected by an autosomal dominant disorder. In some cases, an affected person inherits the condition from an affected parent. In others, the condition may result from a new mutation in the gene and occur in people with no history of the disorder in their family. *(Typical) Characteristics:* a) affected individuals typically have 1/2 normal, 1/2 affected offspring b) normal children of affected individuals only have normal children c) males = female (affected in similar proportions) d) each sex equally likely to transmit diseases Ex. *Huntington's Disease*
Autosomal Recessive
inheritance pattern of a recessive allele on an *autosome* --- must have two recessive alleles (aa) In autosomal recessive inheritance, both copies of the gene in each cell have mutations. The parents of an individual with an autosomal recessive condition each carry one copy of the mutated gene, but they typically do not show signs and symptoms of the condition. Autosomal recessive disorders are typically not seen in every generation of an affected family. *(Typical) Characteristics:* a) parents clinically normal b) siblings only affected in family c) males = female (affected in similar proportions) d) parents may be consanguineous Ex.*cystic fibrosis*, Ty-Sachs, Phenylketonuric (genetic disorder in which the body lacks the enzyme necessary to metabolize phenylalanine [amino acid])
r
intrinsic rate of increase *r = avg. birth rate - avg. death rate* When the population size is *decreasing*, r is *negative* When the population size is *increasing*, r is *positive* When the population size is *constant*, r is *0*
Energy is _______________ proportional to wavelength.
inversely --- E ~ 1/ lambda --- longer wavelength, less energy
NADex = NADH
just pointing that out
What causes Huntington's disease?
lethal dominant allele *Trinucleotide Repeat* of *CAG* sequence --- 9-35 copies --> normal --- 40-180 copies ---> Huntington's (more repeats, quicker the onset of the disease) Leads to destruction of brain cells
Alteration of Generations (NOT DONE)
life cycle that has two alternating phases—a haploid (N) phase and diploid (2N) phase plants/protist/fungi
Chlorea exampe see notes
life threatening diarrhea caused by bacteria *Vibrio* --- delivered fecal-orally (gets in there somehow) --- big deal, there has been 7 pandemics due to cholera IF you are blood type O are more susceptible to cholera While AB are practically resistant If O is suspebtiple to this major disease, what hasn't NS wiped out O yet? B/c if you are type O you are more resistant to *malaria* as well as syphillis (high O blood type in Native American b/c this)
Meiosis II (overview)
like mitosis but with a different ending *Prophase II* --- ya know *Metaphase II* ---- chromatids not neccessarily identical b/ crossing over *Anaphase II* --- chromatids separate (now chromosomes b/c the have there own centromere) *Telophase II* --- 4 new haploid cells
how to count the frequency of an allele or genotype
literally just (#of target allele or genotype)/(total # of alleles or genotype)
Organ involved with degrading cholesterol?
liver
biotic factors
living parts of an ecosystem
Oxidation
loss of e⁻
If cellular respiration is 32% efficient, what happened to the remaining 68%?
lost as *body heat* for the most part --- can be partially retained a bit if warm-blooded
age-specific fecundity
m_x average # of daughters per female at age X --- only deals with *females* the average number of female offspring produced by a female in each age class
mRNA
messenger RNA A type of RNA, synthesized from DNA, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein.
Trial & Error (operant conditioning)
mistakes are punished // correct responses rewarded
Besides glycolysis which occurs in the cytosol, aerobic respiration occurs entirely in the...
mitochondria
Cytochrome C
mitochondrial respiratory enzyme Found in all organism that breather oxygen (aerobic) Model protein for molecular phylogeny because it is not "sensitive" aka it changes very slowly - implying that it is ideal for identifying organism that are evolutionarily distant; however, for the same reason it is NOT ideal at comparing specimen that of evolutionarily close --- ex. Cytochrome C has 104 amino acids in both humans and chimp showing that the two are evolutionarily close, but more data is needed to show the finer ways that the two species are distinct from one another
transposable elements
mobile pieces of DNA that can copy themselves into entirely new areas of the chromosomes
Nucleotide
monomer of nucleic acids
cigarrette smoking
most common cause for carcinogens entering the body die about a decade early 1 cigarette ~ *14 day* off your life
gene flow
movement of alleles from one population to another --- *can increase OR decreases genetic variation* *Increasing GV* --- a new individual can bring in new genes *Decreasing GV* --- constrains evolution by homogenizing gene pool --- prevent local adaption --- ex. imagine two pops with very different allele frequencies; when they come together, eventually the allele frequencies will start to match
MDR-TB
multidrug-resistant tuberculosis
degenerate code
multiple codons encode a single amino acid ex. Proline = CCC/CCU/CCA
ultimate source of genetic variation
mutation (random)
Finding out which of the 5 HW was the cause of a change in allele frequency (ignore this)
mutation is usually not significant sex/non-random mating --- sex does not change allele frequency, just changes it up Migration --- Genetic Drift --- when population size is small, drift can be more important than selection
frameshift mutation
mutation that shifts the "reading" frame of the genetic message by inserting or deleting a nucleotide --- add/delete nucleotide --- generally more disastrous b/c changes entire reading frame
Disruptive Selection
natural selection in which individuals at the upper and lower ends of the curve have higher fitness than individuals near the middle of the curve --- *both* extreme phenotypes are favored
Complementation
needing both dominant alleles to be expressed tandard example: crossing two white, sweet peas (AAbb×aaBB) → F₁ all purple → F₂ 9 purple:7 whites
After the first 3 stages of aerobic respiration, how much ATP has been produced?
net 4 ATP --- 2 from Glycolysis --- 2 from Kreb
R₀
net reproduction rate --- used in discrete exponential growth (# of females produced)/(# of females currently) - When the population size is *decreasing*, R₀ is *less than 1* [each woman is statistically producing less than one daughter] - When the population size is *increasing*, R₀ is *more than 1* - When the population size is *constant*, R₀ is *1* [each woman is statistically producing more than one daughter ]
r-selected
organisms geared towards rapid completion of life in an unpredictable environment --- reproduce early --> lots of offspring --- main cause of death is *density-independent factors* --- *high r values* (which is where it gets its name) organisms that reproduce early in life and often have a high capacity for reproductive growth. In short: discover habitat, reproduce rapidly, disperse young (even if it cost them their life ex. salmon)
k-selected
organisms that reproduce later in life, produce fewer offspring, and devote significant time and energy to the nurturing of their offspring. --- geared toward *competing for resources in a stable environment* --- pop is near K (carrying capacity) [this is where it gets its name from] --- success of kids depends on competitive abilities rather than sheer numbers (offspring need to be more competitively viable then other offspring) --- few, well-supervised offspring --- main cause of death is *density-dependent factors* In short: offspring to competitively seize and hold part of the environment
PEPFAR (President's Emergency Plan for AIDS Relief)
organization that helps cover CART cost
peppered moth
originally, the majority of these moths were light-colored, due to natural selection and then when the trees turned black due to the Industrial Revolution in England, the black colored moths came into the majority because of natural selection Two Types: light and dark (melanic) --- feed at night, rest in lichen tree trunks during day (white trees) --- industial revolution lead to soot-covered trees 1848 - 1st melanic moth found ( only though light existed) 1895 - 98% moth pop is melanic in industrial areas HBD Kettwell - Mark-RElease-Recapture experimetn --- Released 500 of each moth, sed lgith traps to recollect them *% recapture* Unpolluted --> 12.59% light and 6.3% dark Polluted-1953 --> 13.1% light and 27.5% dark Polluted-1955 --> 25% light and 53.29% dark [consistent 2:1 survival ratio towards favorable moth] Lights are coming back to to clean air laws --- Liverpool went from 90% melanic to 10% melanic
F₁
part of ATP Synthase that allows for H⁺ movement
explaining complementation
pathways need two proteins to achieve final state Standard example: crossing two white, sweet peas (AAbb×aaBB) → F₁ all purple → F₂ 9 purple:7 whites
POPs
persistent organic pollutants Toxins that alter the endocrine system and were linked to gender problems (ex. males have femenine tracks, no sperm-producing genitals) Banned worldwide in 2004
genetic counselor
person trained to collect, analyze, and explain data about human inheritance patterns
PKU
phenylketonuria autosomal recessive PKU patients have mutation in gene PAH - codes for enzyme that turns Phe into Tyr 1 out of 10,000 babies affected in US --- phetalalynine bu8ilds up in body since it can't be broken down, which inteferes with brain function --- babies with this can drink Phe-free formula
PGAL
phosphoglyceraldehyde a three-carbon molecule (3c) formed in the mid-step of glycolysis that can leave the cycle and be used to make other organic compounds
Light energy comes in the forms of ____________
photons
Inducible Defenses [RECHECK]
physical, chemical, or behavioral defensive traits that are induced in the prey in response to the presence of a predator (He gave the example of a clam shell in class which doesn't fit with this definition since a shell isn't "induced" at the signs of a predator, instead it's always there. Idk maybe I'm missing something??? Something I would say is more applicable would be skunk's spray or porcupine quills)
Spotted Knapweed
plant with roots that kill all nearby plants --- interference competition
The formation of biological molecules, with the exception of lipids, are all ________________
polymers
Proteins
polymers of amino acids *Always* consist of C, H, O, N *Sometimes* consist of P, S, Mg, Fe
allopolyploidy (RECHECK)
polyploidy resulting from the contribution of chromosomes from two or more species Species A 2N = 14; N = 7 Species B 2N = 12; N = 6 Offspring: 7 +6 = 13 ---> 2N = 26
Cost of pre/post zygotic RIMs
prezygotic have *little cost* postzygotic have *heavy cost* --- have to spend resources --- gives resources to offspring that are already doomed
concordance rate
probability that a pair of individuals (Ex. twins) will have a certain trait --- Monozygotic twin --> 100% identical rate --- Dizygotic/Siblings/Parents ---> 50% identical rate --- Aunt/uncle (2nd degree) ---> 25% identical --- First cousin (3rd degree) ---> 12.5%
Classifications on Food Chain/Web
producers (autotrophs) consumers (eat other species) detrivores (decomposers)
____________ set the energy "budget" for an ecosytem
producers (b/c energy is lost at every subsequent trophic level)
Group
set of conspecifics (belonging to the same species) that remain together for some period of time and potentially interact (social behavior)
monosaacharide
single sugar molecule Three important types (based on # of C atoms): --- 3c: Triose --- 5c: Pentose --- 6c: Hexose
Anaphase
sister chromatids seperate via shortening of spindle fibers
chaisma
site of crossing over
genetic equilibrium
situation in which allele frequencies remain constant *allele frequencies will not change* (see fly example)
Eubacteria
something or another ill get to this later
r is a feature of the ____________, while K is a feature of the _______________
species environment
Telophase
spindle apparatus disappears nuclear membrane reforms around each set of chromosomes chromosomes uncoil
If both starch and cellulose are made of exclusively glucose monomers, what is the major difference between their structures
starch is branched while cellulose is unbranched
metabolism
storage and use of chemical energy
Eugenics
study of factors that influence the hereditary qualities of the human race and ways to improve those qualities define undesirable traits and eliminate them --- certain people fear that pre-natal screening + abortion will lead to an age of eugenics
Behavioral Ecology
study of the evolution of animal behavior (aka how natural selection shapes behavior)
Ethology
study of the mechanisms behind animal behavior --- focused on instinct and learning --- subsect: behavioral ecology
antigens
substances that the immune system can respond to --- Immune system recognizes your own antigens, but not foreign antigen (which is why blood transfusions need specific donors)
Function of NADre amd FADre during cellular respiration
temporary electron carriers
Formation of Acetyl-CoA
the 2 pyruvates (3c) from glycolysis cross into the *mitochondria matrix* *Pyruvate Oxidation* occurs → ends up with *2 Acetyl-CoA (2c)* + 2*NADre* + *2CO₂* (slight correction not image: 2 of each reactant and product is present)
template strand
the DNA strand that gets copied during transcription
What happens to the ATP formed by glycolysis?
the NADre from glycolysis floating around the cytosol and need to cross the mitochondrial membrane to reach the ATP Synthase which requires 1 ATP So glycolysis ATP only accounts for 1.5 ATP
Chargaff's Rule
the amount of adenine equaled and amount of thymine and the amount of guanine equals the amount of cytosine A=T and C=G
Taxonomy
the branch of biology that deals with classifying and naming organisms
free energy change (∆G)
the change in energy between the start end and end of the reaction *NOT* affected by enzymes
Exponential Growth
unrestricted growth, no environmental restrains --- rate depends on the number of individuals (larger population = higher rate) In nature, no population can maintain exponential growth for a long time due to *resource limitations* --- only found in nature during early growth phases (ex. invasion of new environment) Exponential growth can be *discrete* or *continuous*
Twin Studies
used to investigate complex traits (ex smoking) b/c 1) genetically similar (See term above) 2) environment raise is usually similar Flaws 1) environment not always similar 2) epigenetics - express/repress genetic expression ---> EXPIERIENCES CAN CHANGE THE WAY GENES ARE EXPRESSED *WITHOUT CHNAGING THE DNA* --- cna even be transferred to offsprings Identical twins raised apart help you define the importance of genetics b/c the residual similarities b/w twins despite difference in upbringing can be attributed to *genetics*
type 3 survivorship curve
very high juvenile mortality --- sea turtles, oysters, insects *r-selected*
HPV is a type of ___________ responsible for ______% of cervical cancer
virus 85
Theory
well-supported body of knowledge that *makes testable predictions* --- theory of evolution has been tested
inbreeding depression
when individuals with similar genotypes - typically relatives - breed with each other and produce offspring that have an impaired ability to survive and reproduce
Codominance
when two alleles are found together in a heterozygote and neither gene is silent (repressed), they are both expressed independently
Modes of Selection
which phenotype is favored in the following generation 1) Directional Selection 2) Disruptive Selection 3) Stabilizing Selection
Cystic Fibrosis is most common among what group of people?
white people (1 out of every 3000)
1 ATP ~ how much E?
~7.3 *kcal*
Population Rate with Continuous Exponential Growth [Annual Rate of Population Growth]
∆N/∆t = rate change in # of individuals over time N = population size r = intrinsic rate of increase (avg birth rate - avg death rate)
6 Kingdoms
○ *Archaebacteria* ○ *Eubacteria* ○ Protista ○ Plantae ○ Fungi ○ Animalia
Taxonomic Ranks
○ *D*omain ○ *K*ingdom ○ *P*hylum ○ *C*lass ○ *O*rder ○ *F*amily ○ *G*enus ○ *S*pecies *D*ear *K*ing *P*hilip *C*ame *O*ver *F*or *G*reat *S*ex
Biological Hierarchy
○ Biosphere ○ Ecosystem ○ Community ○ Population ○ Organism ○ Organ System ○ Tissues ○ Cells ○ Organelles ○ Chromosomes ○ DNA/RNA most complex → least complex BECPOOTCOCD