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by: AK315

LS15 - FINAL STUDY GUIDE Life Science 15

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The best study guide out there for LS15!
Life: Concepts and Issues
Professor Phelan
Study Guide
Life Science, LS15, finals, complete
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This 38 page Study Guide was uploaded by AK315 on Thursday March 10, 2016. The Study Guide belongs to Life Science 15 at University of California - Los Angeles taught by Professor Phelan in Winter 2016. Since its upload, it has received 103 views. For similar materials see Life: Concepts and Issues in Biology at University of California - Los Angeles.


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Date Created: 03/10/16
Life Science 15 - Study Guide Week 1 
 About Science • Scientific thinking is essentially an organized, empirical (by observation), methodical way to understand anything. • To understand something that puzzles us, we often use a framework called the scientific method. It’s a flexible process that shows us how science is carried out. 
 Carry out Make Formulate Predict Draw Observation a outcomes an conclusions Hypothesis experiment A hypothesis in simple terms is an ‘educated guess’ for how things work. It’s the starting point of scientific investigation.
 Usually phrased as “If _____ is ______ then _______ will _______ “ (though not always). The key thing is, a good hypothesis is one that is clearly defined and testable which means it should allow you to measure what you do and what happens. So a good hypothesis might be “If students sleep more than 8 hours a day then they will perform better during exams”. In the case above, you can easily measure how many hours of sleep a student gets (surveying them) + you can also measure their performance in exams (by looking at their exam scores).
 • A notable example is the question “Does it rain more on Saturdays?” which started off by someone observing that each Saturday, their plans to go out were ruined by rain.
 This ‘dumb hypothesis’ was later found to be TRUE ! A study published in Nature revealed that based on 43 years of data (the experiment data gathering part) - it was indeed found that it rained more on Saturday. Based on this data, scientists inferred that this was a result of particulate matter building up from the exhaust fumes from cars (in cities). Throughout the week, this particulate matter would build up in the atmosphere causing heavy rainfall to occur nearing the weekend (that explains all those ruined weekends!). The critical experiment • The critical experiment is the very core of the scientific method. It’s designing an experiment that puts your hypothesis to the test, whose results can decisively decide whether a hypothesis is correct.
 • An example was when scientists wanted to test the hypothesis as to whether the maze running ability of mice was genetic.
 They built a maze and timed a large number of rats. They made them compete against each other and then took the top 20% and bottom 20% of mice. They made these mice breed and eventually these mice gave birth to a set of offspring. After repeating this process for many generations, they found that the ‘bright’ mice (whose parents were in the top 20%) made HALF the number of errors of the ‘dumb’ mice (whose parents were in the bottom 20%). • Treatment - The experimental condition applied to test subjects. This is like giving them doses of Vitamin C or shaving their eyebrows etc. • Experimental group - this is the group of subjects that are exposed to the particular treatment. For example - the individuals who are asked to take cold medicine after being exposed to a cold virus. • Control group - this is the group of subjects who are treated identically to the experimental group EXCEPT they are NOT EXPOSED to the treatment. These are individuals who are given placebos (Ex. fake pills or sham surgeries). • Variables - the factors in an experiment that can change. For example when measuring vitamin C doses given to individuals, variables that can change are; the amount of vitamin C, the method in which it’s given (tablet, injection etc.), the time at which it is given etc. Making the experiments better 1. Randomize - This means subjects of experiments are randomly assigned into control and experimental groups. This ensures that researchers have no influence into the composition of groups they are studying.
 2. Control variables - In any experiment, you will have the dependent and independent variables that you can change and observe the results for. All other variables are called controlled variables because they must NOT CHANGE. We must ensure that all other factors that could change the outcome of the experiment are kept constant. If we want to attribute the difference between 2 groups in an experimental treatment, there must be no underlying difference between the 2 groups. 3. Double-blind design - This is a common feature of experiments involving pharmaceutical drug treatments. Essentially it’s an experiment where any information that may influence the behavior of the experimenter or the subject is withheld until after the test. Basically, neither the experimenter nor the subjects know which treatment a subject is receiving (it could be the actual treatment or it could be a placebo but they’ll only know once the test is completed). It eliminates bias and preferential checking. Are lab experiments always better? • If scientists discover the potential for a certain chemical to fight the AIDS virus (the virus responsible for HIV in humans) - is it better to conduct experiments in a lab or in the real world?
 The question is tricky - in a lab it is much easier for scientists to control all other variables which means that they can better determine whether the chemical is indeed effective at fighting the aids virus. In real life, however, individuals receiving treatment are exposed to all kinds of external factors in their environment (from diet to exercise to pollution and so on) that makes it hard to tell whether the treatment developed in a lab will definitely help fight the AIDS virus in the real world.
 The better we control an experiment, the more confidence we should have in its results. But as experiments are better controlled, they are often poorer models of the situations of interests. Beware of Pseudoscience • Scientific thinking is powerful but can be costly, time consuming and difficult which is why there exists cheating which we call pseudoscience. This is essentially a collection of beliefs or practices that people mistakenly think are based on actual scientific methods. • For example, years ago, the chewing gum brand Trident ran a slogan saying “4 out of 5 dentists recommend our sugarless gum to chew!”. 
 It seems like a fairly ordinary statement but you know what’s wrong with the statement? It leaves out all the important details like: - How many dentists were asked? - How were these dentists selected?
 - What alternatives were they given? (If the dentist had to pick between Trident gum vs acid - it’s pretty easy to see that they would pick the gum. While this example is obviously exaggerated, the point is - they don’t disclose the alternatives). Without knowing the kind of information above, it’s super easy to get tricked into thinking a brand is legit just because they claim that some doctors/dentists recommend their product. That is pseudoscience and they are unfairly taking advantage in our trust of medical professionals. • Another cool (but freaky) example is that of ‘Radithor’ - a medicinal product sold from 1918-1928 by college dropout William Bailey. The product was essentially water mixed with radium (a highly radioactive and dangerous element). Bailey sold the product to many people claiming it was therapeutic and perfectly safe. Eben Byers was a wealthy athlete and socialite from Yale who consumed over 1000 bottles of radithor over a span of 3 years. It was all working fine … until his teeth started to fall off. That wasn’t the worst though, because Byers died a painful and agonizing death as his bone tissue started to disintegrate and holes started to form in his skull as a result of acute radium poisoning.
 Beware of Anecdotes • We often hear anecdotes in our day to day lives - striking stories that we hear about based on what other people saw, heard or did. These anecdotes are emotionally powerful and they can greatly shape our beliefs by suggesting links between events and occurrences. For example you may notice that if you wear a ‘lucky shirt’ you tend to do better on exams or you’ve heard ‘drinking 7 glasses of water’ makes your skin glow.
 More often than not, that is BS. The only thing we should rely on for scientific explanations is data (objective) and not anecdotes (that are subject and vary from person to person). • A common example of this is the recent fears that have developed about vaccines causing autism in infants. 
 Although scientific data shows NO correlation between vaccines and autism (backed up by numerous scientific studies), the observations of a few individuals that the symptoms of autism developed at a young age coincidentally around the time they were administered vaccines, led these individuals to believe that vaccines were the cause of autism. Without even knowing the facts, they jumped to faulty and erroneous conclusions - which translated into a widespread fear amongst misinformed parents across the US. Pseudoscience and Anecdotal observations often lead people to believe that there are links between 2 phenomena even when there are no such links. Week 2 & 3 Darwin’s Ideas He wrote the 1859: Origin of species (which was his work that was published - check out the last paragraph !) A trait can change over time within a species if there is: 1. Variation for a trait (Darwin observed this) 2. Heritability (Darwin couldn’t quite explain this which is where Mendel came in) 3. Differential reproductive success Gregor Mendel He was a monk and he experimented with peas to study heritability. Often credited as the father of ‘genetics’. Mendel gave a talk in 1965 on the “Inheritance in Pea plants”. However, the ordinary people could not wrap their head around his way of thinking and eventually he came to believe that he didn’t figure it out. Only 35 years later scientists understood that Mendel figured it out. Generic Cell • A chromosome is a linear strand. Humans have 23 unique chromosomes. We have 2 copies of each chromosomes (a pair). They number the chromosomes by size. • Under the microscope, the chromosomes look like X’s (but we can try to visualize them as spaghetti strands). • The chromosome looks like an X because essentially it’s a chromosome + a copy of itself coiled up and connected. • Humans have 23 homologous pairs. • Karyotype - a picture of all chromosomes in a cell. • You might want to look at a karyotype to determine based on the chromosomes if babies develop problems. • For instance having an extra copy of a chromosome which is trisome 21 (3 copies of chromosome 21) leads to down’s syndrome. • Both the maternal and paternal copy of the chromosomes contain many genes each (many instruction sets to produce a particular trait). Mendel’s Laws Law of Segregation • A gamete receives only 1 allele for each gene (Even though the organism general has 2). • Fertilization re-establishes the diploid number. A diploid (contains 2 of each allele) and a haploid (contains only 1 of each allele) • Albino organisms have 2 copies of the pigment gene that doesn’t produce any pigment. Use a punnet square for assessing the cross. For mM x Mm case: Genotype ratio is 1:2:1 Phenotype ratio is 3:1 (pigmented:albino) assuming that M was the dominant gene and ‘m’ (albino pigment gene) was the recessive one. The law of segregation points out that a gamete receives only one copy of each gene from both parents. Law of Independent Assortment The allele you pass on for one trait has no effect on which allele you pass on for some other trait If an individual shows the dominant phenotype, how can you determine their genotype? We see a dominant trait phenotype > B__ = BB or Bb What cross would help? X homozygous recessive gene The test cross allows you to determine whether individuals showing the dominant trait are homozygous or heterozygous. Sex determination How is the sex of a baby determined by the father? Girl vs Boy XX (maternal) vs X (maternal) & Y (paternal) So sperm can carry either X or Y chromosome whereas females always contribute an X chromosome. Methods of sex determination: • Male heterogamety • Female heterogamety (honey bees can control the sex of their offspring - if they fertilize their eggs with sperm then female but if the choose not to fertilize their eggs then the unfertilized eggs go on to become males) • Ploidy • Incubation temperature If men only have one X chromosome, are they more or less likely to exhibit a sex-linked recessive trait? What about dominant?   White eyed female (Xr Xr) vs Red-eyed male (XR vs Y) females = Xr x XR = Red eyes (dominant) males = Xr x Y = White eyes (Recessive) Sex linked traits have different patterns of expression in males and females Trade off between survival and reproduction Australian mother spider gives birth to many spiders that proceed to suck her dry. It is necessary to ensure offspring live but the spider does not survive. Theory of Kindness Kindness leads to: 1. Shared Genes 2. Reciprocity Why are people nice to other people? 1. Because allele X in you causes you to act in such a way that you increase the reproductive success of other individuals that carry Allele X (Shared genes/Kin selection). 2. Because allele Y in you causes you to help other people who will return the favor, thereby benefitting allele y (Allele Y buffers itself from an uncertain future by storing goodwill in others. 2 ways in which an Allele can increase the market share: 1. Direct fitness (increase the number of offspring I produce) 2. Indirect fitness (increase the number of offspring my kin have; they also carry many of my alleles). If I paid my sister and she was able to take care of herself and have more kids, then because she shares the same alleles from my parents - it would increase the number of offspring my kin has. Inclusive fitness = direct fitness + indirect fitness Hamilton’s Rule How much do we expect individuals to help various relatives? (Hamilton’s rule) equation: B*r > C B - benefit to relatives r - coefficient of relatedness (the probability that an allele that you carry is carried within this individual because of a common ancestor - measured from 0.0-1.0). C - Cost to me (the decrease in my own reproductive output based on my actions) For situations in which this equation is true, we expect the ‘kind’ act to occur. Belding’s ground squirrels: 1. Yell when a predator approaches (sometimes) 2. Hide when they hear a yell (always) 3. 10% of predator attacks end with a dead squirrel 4. 50% of the dead squirrels were the ones yelling Which squirrels are making alarm calls? Adult females (they have tons of relatives - parents, sisters). (male squirrels relocate to a different community at maturity. Females don’t) The more kin a squirrel is likely to have nearby, the more it will act ‘altruistically’.  Hamilton’s rule helps us to predict when we will see ‘kindness’ (When something that benefits someone else comes at a cost to you) ‘r’ is a measure of the proportion of our genes we have in common with our relatives. Rules for calculating ‘r’; 1. UP UP UP and DOWN DOWN DOWN - Never reverse the directions on the path from one individual to another 2. All paths are created equal - dont forget a path. 3. Multiply within and add between paths. example; from parent to offspring r = 0.5 example ; from sibling to sibling r = (0.5*0.5) + (0.5*0.5) = 0.5 (we add the paths from BOTH parents) example; from sibling to half sibling r = (0.5*0.5) = 0.25 example; from cousin to cousin r= 0.125 Altruism requires kin recognition - spatial association (treat those around you as main) - social association (treat those from childhood as kin) - phenotype matching (treat those who resemble you as kin) SUPPOSE you capture an old female ground squirrel and move her to a new neighborhood far away, will they make alarm calls. THE CORRECT ANSWER IS YES. It’s a mistake and what biologists call maladaptive behavior because this squirrel is risking her life and the other squirrels aren’t even her relatives ! This is built in natural selection. What can you conclude? We call it maladaptive behavior because this is an event that hasn’t occurred in her evolutionary history and she’s not yet adapted to it. Behavioral rules of thumb Predictions of Kin Selection: IN MURDER CASES: - Spouses and non-relatives had the GREATEST risk of homicide as opposed to off- spring and parents IN INFANTICIDE CASES: - Children in step-families inured or killed more frequently than those living with their biological parents IN BEQUESTS (WILL/LEAVING INHERITANCE): - individuals will leave more of their estate to close kin than distant kin Week 4 Altruism Among unrelated individuals selfishness is the rule, kindness is the exception Bicycle sharing programs V1.0 - Various bike sharing programs were abandoned due to the bikes being stolen - It was an act of kindness to provide the bike but selfish humans stole them Can we see animal friendship? Co-operation among kin is almost non-existent in the animal world. Vampire bats - they suck blood for food - 10% of adults and 33% of juveniles fail to find a meal on any given night - A bat will starve to death if it doesn’t get food on more than two consecutive nights - sometimes a ‘full’ bat will sometimes regurgitate blood into a hungry bat’s mouth (it comes at a cost to the full bat but it’s ultimately helping to save it’s other friend). This is just one extremely rare example of friendship The question is ‘which bats get a free lunch from another’? - Scientists found that a bat is significantly more likely to give food to bats that have previous helped it - Bats shun individuals that do not help them. Take home message 1; Co-operation is very rare in the Animal kingdom Does unconditional love among unrelated individuals exist? Not really. What conditions are conducive to reciprocal altruism? 1. Repeated interactions
 2. High benefit to recipient relative to the cost to the actor 3. Ability to keep tabs on people (and to punish cheaters) What is the big impediment to kindness (from a biological perspective)? FREELOADERS You are very vulnerable (from a fitness perspective) when you do something kind for another person. A cheater can take the favor and run. The market share of the the cheater’s genes increases The market share of the altruist’s genes decreases Effective altruists can remember the cheaters.  What are some design features we’d expect to see in the human brain? What skills should we be good at? 1. We ought to excel at recognizing faces Vampire bats: 100 individuals  Humans: thousands! 2. We ought to be good at keeping track of cheaters 3. We ought to be voracious consumers of social information. Gossip and social information • Why are our brains so good at keeping track of social info? • Why do we keep tabs on people we will never meet Our brains were built for a world in which we encountered only a small number of people (~100) and we may have needed any one of them. Humans recognize faces, keep track of kindness/selfishness and live for a long time this makes reciprocal altruism possible. Your avenues to enhancing cooperation: • Tinkering with the perceived costs and benefits ◦ Reduce the perceived cost to the other person (example: let’s ‘swing by’ the post office and then go to lunch) ◦ Accentuate the benefit that you’ll receive from co-operation
 Our level of kindness/selfishness is influenced by how we perceive the benefit to the individual. • Distinguish cheaters and kind people ◦ Facilitating the building of reputations (allow others to know that someone is a generous person). Someone donating blood is rated as significantly more unselfish as compared to non-donors. If you increase your reputation, you’re gonna see more acts of kindness around you. ◦ Use ‘honest’ signals that can’t be faked. ◦ Keep track of and punish cheaters (cheapskate story) • Reduce the perceived vulnerability of partners ◦ Make the first step: gifts ◦ Acknowledge debts clearly and concretely  ◦ Receiving gifts an favors properly is as important as giving gifts. ▪ Thank you notes; essential ▪ acknowledgment of debts; essential ▪ eye contact; essential ▪ Use their thank you notes
 Assurances of future reciprocity are motivating (its not about the money, it’s about the reciprocation or expectation). Unexpected co-operation (Ants, bees, wasps) Female = diploid and male = haploid Daughters all get all of father’s genes and only get half of mothers genes. Coefficient of relatedness mother vs daughter = 0.5 female vs sister = 0.75 Result - better to forego reproduction and care for sisters Examples of Naked mole rats. They have: • A queen • Non-reproductive workers Even after generations and generations, all mole rats are almost all interrelated to each other with a coefficient of relatedness close to 1 Because of hundred (maybe thousands) of generations of inbreeding, all individuals in a populations have extremely high coefficient of relatedness with each other Take home message: When ‘r’ is really high (as in the cases of inbreeding), co- operation is extreme. Example of A mother’s love for a child - is it the most unconditional thing? Coefficient of relatedness is 0.5 Fetus - Pumps out a hormone (hPL) that dilates mother’s blood vessels this gives the fetus more food. Mother - Increases insulin production. This removes food from the bloodstream. Escalation ensues. Gestational diabetes occurs if mother can’t mount sufficient response to the fetus manipulation. When r<1.0 some conflict is likely. Example of WWI Truces Individual units facing each other across trenches initiated mini-truces without formal exchanges. First, one side made a gesture. However punishment for violation is necessary. Generals could not advance a war with all the truces. So they moved the soldiers around so that they didn’t have repeated interactions (a condition for reciprocation) so they didn’t have any truces because the soldiers never figured out the altruism behind it. Only happened when same troops faced each other for a long time. Ultimatum game Proposer: 35$ me 5$ you OR 15$ me 25$ you Accepter: Decides whether to accept or reject If proposer then pick generous  If responder then accept generous and accept stingy Most people accepted the stingy offers AND over 25% proposed the generous offers! contrary to what economists thought (because they believed people will always maximize utility). The results; Some people make very generous offers. Some people turn down free money. Our emotional responses - such as justice & gratitude reflect reciprocal calculations and insure fair play. 
 We didn’t accept the stingy offer because it wasn’t about the money but our perception that the other person was ‘greedy’ and that we were willing to forsake cash in order to ‘punish’ the other individuals for being greedy. When a computer proposed the same offer, people didn’t hesitate to accept the stingy offer! Week 5 DNA fingerprinting Why are we interested in DNA fingerprinting? ◦ Real fingerprints not left behind in many crimes ◦ They are essentially unique
 What are the uses? ◦ Solve unsolvable crimes ◦ Resolve paternity issues ◦ Can prove innocence of people unjustly convicted ◦ Immigration issues About DNA • DNA is a long sequence of ‘letters’ that carry the info of how to build molecules for the body
 • It’s essentially 2 strands (the backbones) and the rungs.
 • Comparing the DNA fingerprints means seeing how much ‘spelling’ difference there is between individuals. ◦ Almost no difference - 99.9% identical ◦ 0.1% of base pairs is different (0.1% of 3 billion base pairs = 3 million base pairs and this is enough for identifying individuals)
 • On average, individuals differ in their DNA sequence at 0.1% of their bases; 3 million differences out of 3 billion base pairs.
 • We have DNA from several samples. How can we tell if the DNA came from the same person. Short Tandem Repeats (STR’s) • What are STR’s (Short tandem repeats) which is repeating units 4-5 nucleotides long (so it’s a small sequence within the DNA somewhere)     • Everyone has STR 1 (for example ATGCC) but it repeats a different time for each person (5/11 repeats OR 3/6 repeats OR 13/7 repeats etc.) STR 2 (for example may be AGAT).
 • For an STR locus - many (2 or 3 dozen or even more!) alleles exist within the population, but each individual can only have two of them.
 • Simply comparing 1 STR for an allele won’t yield any results when matched up because odds are low. ◦ But if choose 6 features for which individuals vary a lot. ◦ Compare DNA sample for those 6 features. If they are the same at all of them, then the samples came from the same individuals.
 • Creating a DNA fingerprint ◦ The DNA fragment containing each STR region is amplified using PCR. This results in huge number of those fragments. ◦ The fragments are separated by size using electrophoresis (using gel - the big STR’s move slow through the gel as a result of electric current pulling it through the gel to the positive charge and the small STR’s move fast, essentially this forms a pattern). ◦ PCR > You take a strand > Heat it up > Stands separate and you add more nucleotides (throw in alphabets - PRIMERS that attach to the strand) > cool it down > you now have doubled the DNA > do it multiple times
 • Human paternity testing ◦ Analyzing one’s locus ◦ What do the bands represent? ▪ A band tells you what allele it represents and it tells you how many time an STR repeats itself based on the distance it moves down the gelatin. ▪ The width of the band is the same, however.
 Important issues • Difficulties and controversies with DNA fingerprinting ◦ Overlap of STR’s (it takes judgment to determine if STR’s are same or slightly different since they are overlapping) ◦ How many STR’s should we compare? ◦ How likely is a match?
 p(one band)*p(another) …. can juries understand this? ◦ Are there sub-population differences (in allele frequencies)? ▪ P = (0.1)*(0.1)*(0.1)*(0.1)=1/10,000
 2 loci, 10 alleles each
 P = (0.1)*(0.1)*(1/1)*(1/1) =1/100 ▪ Need to take into account geographical factor that many people of higher genetic relatedness will be living in same area
 ◦ Do humans make mistakes? ▪ Cops planting evidence ◦ How sure do we want to be? ▪ What is a ‘reasonable’ level of certainty to warrant imprisoning someone? ◦ Should we keep DNA databases? Who should have access to them? ▪ Probable cause (attack on privacy) vs larger database ▪ Insurance companies can exploit the data to identify known disease causing sequences and then deny insurance to those individuals (because they’d have to pay them if they get the disease) Week 6 Fuel • What are some things that living systems need? ◦ Raw materials for growth ◦ Energy to do things that won’t happen spontaneously • How do we power machines? ◦ We use gasoline and many other fuels ◦ Their structures are Hydrocarbons (a mixture of hydrogen with 5-12 carbons) ◦ Automobile engines combust the hydrocarbons, forming new bonds, releasing energy that can be used ◦ biofuels: natural oils from plants, sugar, or starches modified into ethanol ◦ Essentially - you break bonds > reform them > and make use of the energy released in that process (Breaking the bonds and reforming new bonds releases energy that can be harnessed to do ‘work’ making things happen that would not happen spontaneously) • The origins of fuel ◦ Fuel comes from energy stored in chemical bonds ◦ Photosynthetic organisms create it initially Lipids • These are macromolecules  • They have many features ◦ Not water soluble ◦ Major storehouses of energy ◦ good insulators • Lipids are used for storing and generating useful energy • We use them for creating cell membranes • Major types: ◦ Fats/triglycerides ◦ Phospholipids ◦ Sterols • Saturated fats vs Unsaturated fats ◦ Depends on whether there are double bonds in hydrocarbon tail ◦ If anywhere on the hydrocarbon tail there is a double bond, then it’s an unsaturated fat! (these are better than saturated fats) ◦ Hydrogen is the saturator so if you add the max number of hydrogens you can give then its a saturated fat, if not then its unsaturated ◦ Most plant fats are unsaturated and animal fats are saturated (they are mostly solid at room temperature e.g. bacon fat) ◦ Many snack foods contain ‘partially-hydrogenated’ vegetable oils. Why might it be desirable to add hydrogen atoms to a vegetable oil? Why might there also be some less desirable consequences? ◦ Saturated fats are very easy to store away (make links) but very difficult for your body send an enzyme in there to break through so to access that energy it’s tough. ◦ They add the hydrogen to make it saturated to make it slightly solid but then the moment foods like chocolate etc. are put in your mouth, the heat melts them (they are solid but BARELY) and food chemists tweak it in such a way that they bring about this effect ◦ In saturated fats - fatty acid molecules are tightly packed hence tend to be solid at room temp ◦ In unsaturated fats - kinks in the hydrocarbon tail means that molecules are not tightly packed and hence tend to be liquid at room temperature
 • Lipids are water-insoluble molecules important in energy storage, in membranes and as hormones
 Human taste preferences • We have a high preference for fatty foods (sugar is different; not TOO sweet but not TOO unsweet either) • Ancestral humans vary in preferences • Questions we ask are; ◦ Who is less likely to starve - fatties ◦ Who leaves more offspring - fatties (if alive) will pass on the genes ◦ Who are our ancestors? - fatties - they leave behind the kids • The same amount e.g. 1 gram of protein vs 1 gram of fat give different caloric values; 1 g of fat = 9 cals and 1 gram of protein = 4 cals!
 • Evolution has shaped our food preferences, making us love energetically rich fats. Carbohydrates • Macromolecules # 2 is carbohydrates (it’s a carbon chain bonded to hydrogen H and OH groups) • Primary function is to serve as FUEL • Mono-saccharides are simple sugars (orange juice, white rice) - within minutes your blood sugar goes up and you get a lot of energy easily. • Our body has a very easy time in breaking down glucoses (carbohydrates) so we are able to QUICKLY get energy from carbs.         • Starch and polysaccharides are complex sugars and take a lot more work from your body to break them down. There is a slow, long release (more energy). ◦ For instance, when you want to study for hours in a row - getting such type of carbs means that your body releases the energy slowly rather in short busts which sustains you for a longer duration of time. • Disaccharides = 2 molecules and polysaccharide = 2 or more molecules • Carbohydrates give us easily accessible energy Proteins • Proteins = construction (fats = energy storage and carbs = fuel) • We can’t get the simple sugars from cellulose molecules because we can’t break through them easily and thus they just pass through our digestive system. • Notice that the basic amino acid structure contains an ’N’ which is Nitrogen! We need nitrogen for protein. This is why for plants to grow - all fertilizers used are made of Nitrogen! • Valine and phenylanine • Certain amino acids code for certain types of hair; curly or straight. • These can be altered semi-permanently • Cells and tissues are primarily built from proteins, sequences of amino acids Diet variation amongst animals • Herbivores (Zebras) - only eats plants • Plants can’t run away so they evolve to have defenses against Herbivores (poisonous chemicals etc.) • Carnivores (Tiger) - only eats animals • Omnivores (Crows/Humans) - eats plants and animals But processing and deriving energy from the food is exactly the same Metabolism • The kilocalories = 1000 calories (a calorie is energy required to raise 1 gram of water  by 1 degree celsius (C)) • How many are needed? ◦ Human female = 1800-2400 Kcal ◦ Human male = 2400-3200 Kcal ◦ Guys need more because they are bigger ◦ When you think harder, you also burn more calories!
 • BMR (Basal metabolic rate) = energy needed to maintain life without activity. Generally we need twice as much. ◦ For females = 1400 kcal/d ◦ For males = 1700 kcal/d ◦ 1700 kcal = a 75 watt light bulb for 24 hours ◦ In humans: 1 calorie/g/hr ◦ In shrews: 35x as high. Heart rate ~ 500 beat/min ◦ Why is it higher for shrews? One theory is they are warm blooded, if they are losing heat quickly then they need to compensate by having a high metabolism rate to retain heat (Surface area of body) ◦ 5g shrew * 35 cal/g/hr * 24 hrs * 2 = ___ kcal/g ◦ Carbo = 4 kcal/g, protein = 4kcal/g, Fat = 9 kcal/g ◦ Shrews prefer fatty foods as it can eat less (But fatty food) and gain same calories leaving more time for them to mate etc.
 • Basal Metabolic rate is the energy expenditure necessary to keep a resting animal alive. It depends on size and species. Digestion and Absorption • Digestion is breaking down the food into it’s component parts (the taking apart of food molecules) ◦ Mouth = 2 functions ▪ Mash up food (mechanical breakdown) ▪ Partially digest starch (amylase - enzyme that breaks down carbs found in saliva) ◦ Stomach = 3 functions ▪ More food mashing (HCL, pepsin) ▪ Start protein digestion ▪ Secretes acid: denature protein, kill bacteria ▪ Acid denatures proteins and causes it unfold ◦ Small intestine = 4 functions ▪ Neutralize chyme pH (with bicarbonates) ▪ Finish protein/starch digestion (Breaking starches into simple sugars AND proteins into individual amino acids) ▪ emulsify & digest lipids (bile) ▪ absorb nutrients & H2O (these are absorbed into our bloodstream and transported around our body) ▪ Animals can increase the surface area of small intestine to absorb and extract more from their foods, if they are on low-calorie diet. ◦ Large intestine = 3 functions ▪ Absorb H2O (water) & Salts ▪ Push chyme into rectum for excretion ▪ Absorb nutrients produced by bacteria ◦ Harsh conditions help break down foods. This frees the food to interact w/ enzymes. Humans aid this process by: ▪ Cooking food at high temps ▪ Marinating in harsh acids (Lime juice/vinegar) ◦ What is indigestion? How do antacids cure it? ◦ Why does diet coke lose its sweetness if it gets too hot? Diet coke is sweetened from nutrisweet (made of 2 amino acids stuck together)
 • Harsh mechanical (Chewing/churning) and chemical (HCL and amylase) processes aid in the first steps of digestion. • Most nutrients are absorbed in the small intestines. H2O is absorbed in the large intestines.
 Fiber • What is fiber? - Cellulose, lignin, pectins, gums (plant structures that CANT be digested by humans) • But it is helpful (despite being a mass of material that’s not going to be digested): ◦ Helps move food through your gut (stimulates the intestine muscles that tries to push the fiber and subsequently the food out) ◦ It also bonds with bile which eliminates bile and this reduces our ability to absorb cholesterol. ◦ May lower cholesterol (see point above) ◦ May reduce colon cancer risk ◦ Too much fiber = a lot of undigested food is moved out but too little water is extracted so the resulting fecal matter has a lot of water (Diarrhea) ◦ Too little fiber = too much water extracted as food not pushed out properly and this means fecal matter moves more slowly and is tougher to push out (constipation) Why vegetarians are at a higher risk for protein deficiency • Are all proteins created equal? NO. • There are 20 different amino acids needed by Animals. We can produce 11 of them. You need to eat the 9 others because our bodies cannot produce them. • Milks, egg, meat have ALL 9 of the ‘essential amino acids’ - as these are essential to your diet. • Corn has only 6 amino acids (it has protein but this is made of LESS of the essential amino acids) • Beans also have 6 amino acids (but this is NOT the same as the ones that corn has) • It’s not sufficient just to get certain amount (Grams) of protein; you ALSO need to get all the different amino acids. That’s why you can be protein deficient even though you eat a lot of protein but lack all 9 amino acids. Soy, quinoa etc. are all complete proteins (they have all the 9 amino acids). • Nearly all plants have incomplete proteins. Essential nutrients • vitamins are necessary organic molecules ◦ They assist in chemical reactions ◦ Fat soluble ▪ A - precursor to eye pigment ▪ D - calcium absorption ▪ E - antioxidant function ▪ K - blood clotting ◦ Water soluble ▪ B - coenzymes in metabolism ▪ C - collagen formation protection from oxidative damage ◦ You either have the sufficient amount of vitamins or you DON’t. Buying and eating additional supplements, doesn’t help you! ◦ In fact, in the US - almost no adults suffer from any vitamin and mineral deficiency diseases. ◦ Excess consumption of ▪ Vitamin A: Can lead to hair loss in men ▪ Vitamin D: can lead to growth retardation
 • Minerals are necessary inorganic elements ◦ Ca - nerve propagation ◦ P - ATP ◦ K, Na, Cl - action potentials, etc. • Our metabolism is basically involved in modification; breaking down or building up molecules ◦ For example to build eye colors in fruit flies takes 20 steps! • Who might need vitamin supplements? ◦ Pregnant or breast-feeding women ◦ People on extreme caloric restriction ◦ People with low milk consumption and extremely low sun exposure may need extra Vitamin D. ◦ Women who lose unusually large amounts of blood during menstruation may need extra iron! More about mutations • Central dogma - the flow of information from the DNA moving to messenger mRNA >>> protein. The DNA is nucleus and mRNA is leave nucleus. • DNA in 23 pairs of chromosomes. • 2 chromosome lines - but both are double stranded and they may be slightly different from one and another. • If they have 2 different bases (like G and T) on the strands then that individual is heterozygous for that trait.
 • Mutation - random alteration to DNA.
 If it happens at intergenic regions (Where no trait is really there) then mutation effects are minimal. ◦ Silent mutation example = No amino acid change (ATCCGG = ATGCGG) where ATC = Lysine and CGG = Tryptophan ◦ Point mutation example - a change in a single nucleotide ◦ Mis-sense mutation = change amino acid (so Lysine may become Arginine) ◦ Non-sense mutation - premature stop (truncated protein). The shape of a protein is generated by how it folds and how it folds is determined by the properties of amino acids. So if you change an amino acid (like one that likes to be around water) to an amino acid that doesn’t - it could affect the folds and hence the shape of the protein. ◦ Insertion and deletions can ensure that the reading frame does not change. Lest, any insertion would shift all the triplets by one place which would change.
 • What can mutations do to our phenotypes? ◦ loss of functions = recessive phenotypes ◦ Gain a function ◦ Neutral and Lethal mutations
 • Remember: Red foxes always jump over logs
 add XX to it:
 frame shift: XXR edfox esalwa ysju mpov eslogs Week 7 Hormones and how they work
 • Hormones are chemical signals, secreted into body fluids. • May reach many cells, but only target cells respond. • They only have an effect if that cell has a receptor (Which is a molecule that receives chemical signals from outside the cell) • Hormones elicit specific responses in target cells • Who secretes them? ◦ Pineal - melatonin ◦ Hypothalamus -  ◦ Pituitary ◦ Adrenal - adrenaline, cortisol ◦ Pancreas - Insulin ◦ Ovaries - estrogens, progesterone ◦ Testes - androgens, testosterone • Cortisol ◦ Make glucose available (From non-carbs) ◦ Act on skeletal muscle (break down protein) ◦ High dose • Adrenaline ◦ Senses danger - heart rate goes up ◦ Increases glycogen breakdown (in liver and muscles). Releases fatty acids from fat cells. ◦ Increase rate/volume of heart-beats ◦ Dilates bronchioles in lungs - delivers more oxygen to cells • Oxytocin ◦ A peptide hormone ◦ Produced in hypothalamus; released fro pituitary gland ◦ Influences people’s trust in others. ◦ Encourages social attachments Hormones can affect thoughts and behaviors • Mental rotations ◦ MALE score - 3.5 ◦ FEMALE - 1.3 • Object memory ◦ MALE score - 13.7 ◦ FEMALES score - 15.5 • Testosterone influences mental rotation capabilities in men + Estrogen helps females with object memory Week 8 Sex behavior predictions • More investment > More determining ◦ Demand honest signals or health ◦ Value fighting ability ◦ Elicit a commitment to invest ▪ Females make male do courtship dances ▪ Asking males to get her nuptial gifts (insects do this) ◦ Because female reproductive investment is initially higher, they are vulnerable early on. We expect the evolution of choosiness and demands for investment ◦ Example: Bush cricket lose 1/3 of their weight when they mate! Therefore they are highly constrained on their mating ability and thus making a bad decision about who to mate with can drastically affect their fitness, which is why they are gonna be extremely choosy and demanding when it comes to finding the right mate!
 • Lower reproduction investment > more competition and need for paternity certainty ◦ Competition for access ◦ Mate guarding/extended mating (in humans - wedding ring for example is a signal that the person is married. Hickey/Facebook status/holding hands/chastity belt) ◦ Sperm competition/anti-sperm ▪ Observation: Lots of cuckoldry ▪ Evolutionary response: produce more sperm ▪ They measured testes size of gorilla (it was found to be small) ▪ Physical manifestation: Gorillas (all females choose to mate mate with 1 male) ▪ Chimps? (females have sex w/dozens of partners) - chimps had large testes and produced a lot more sperm!] ▪ Why do males exhibit more mate guarding than females? Paternity uncertainty ▪ Initial low reproductive investment and paternity uncertainty lead to male-to-male competition for access to females, indiscriminate male mating, mate guarding and sperm wars. ▪ Extreme nature examples - black widow spider males break their sex organ off into females preventing the male and the female from mating with anyone else. ▪ Think about why many females aren’t partners at law firms - they realize that 7 years of work for the final payout may not be worth as much! Could be due to final outcome and weighing that outcome
 • Mating system definitions ◦ Polygyny: (high variance in Male Rs/ low variance in female Rs) so one male bonds with multiple females. Most mammals are polygynous ◦ Polyandry: (low variance in Male Rs/ high variance in female Rs) so one female bonds with multiple males. Very rare but example is mouse lemur, bush cricket example etc. ◦ Monogamy: low variance in both, low number of mates each so one female bonds with one male. Most birds are monogamous. • Sexual dimorphism is considered a very good predictor of mating systems. Why? ◦ Biological constraints make reproductive investment asymmetric ◦ The more asymmetric the investment:
 • Why would we see more monogamy in birds than mammals? ◦ They are sexually dimorphic - there is no need to be so choosy when they look similar. ◦ Birds feed their babies food, they cannot lactate like mammals. Both MALE AND FEMALE can feed their kids so reproductive investment is SHARED. It’s divided up better! which explains why monogamy works. ◦ Mating systems - monogamy, polygyny and polyandry describe the variance in mate number of males and females in a population.
 • Normal development requires: ◦ Stable environment ◦ Good genes ◦ Heterozygotes can develop normally even in a turbulent and variable environment. ◦ Homozygotes don’t develop that normally…. ◦ How can we spot abnormal development? ▪ as deviations from bilateral symmetry ▪ this is called asymmetry ▪ Measured as for example :(difference between size of right index finger - left index finger)/average size of index finger ◦ Another study was done with scorpion flies (symmetric scorpion flies produce sexier pheromones) - where pheromones from male flies were given and females chose the more symmetric males. This was done with human males too. ◦ Study 2: Women smelled shirts worn by different men and rated ‘most attractive’ - found to be for more symmetric guys ◦ Study 3: Relation between increased orgasms and increased symmetry ◦ Study 4: Who are the most symmetrical people? ▪ Bi-racial individuals tend to be much more symmetrical ▪ people who are symmetric (grow quicker, produce better orders, have more sexual partners, are better lovers, produce more babies) ▪ symmetric horses are faster runners ▪ symmetric flowers produce more nectar About the nervous system • Your body has 2 systems for responding to stimuli and co-ordinating info within the body; Hormones and Neurons
 • Central nervous system CNS and the peripheral nervous system PNS
 • Neurons are the cells that transmit nerve impulses. ◦ When we do something injurious or dangerous, we feel pain. Pain is crucial because those nerve impulses that transmit the pain, tells our body that whatever we are doing is going to be harmful to us. It’s an adaptive behavior, which is why it is important for the body to be able to feel pain. ◦ Plants do NOT have neurons and they don’t feel pain ◦ Cool stuff: Surgery to correct tremors = planting electrodes within certain parts of brain. ◦ A vertebrate neuron - dendrites (receive signals) > through the axon > conducts information out of the terminal buttons ◦ Neurons release neurotransmitters (chemicals that basically carry the signal across a synapse from one neuron to another neuron, muscle cell or gland cell) ◦ 10-15x gleal cells compared to neurons ◦ How neurons work: ▪ Signal - initiated somewhere else in body in response to external stimuli. Travels from dendrite through cell body and down the AXON ▪ Axon - electrical signal (Na+ in, K+ out) travels down until (also Axons are extremely long - the cell can stretch from spinal cord to fingertips) ▪ Synapses with: ▪ A muscle: causing contraction ▪ Another neuron: causing firing/no firing ▪ Neurons, in some cases (rare), have been found to grow and regenerate. However, for the most part, neurons do die ▪ London cab drivers - had larger hippocampus (used for spatial memory). • Action potential  - is a short-lasting event in which the electrical membrane potential of a cell rapidly rises and falls, following a consistent trajectory.
 • Myelin sheath = insulator
 • What do babies and individuals with multiple sclerosis have in common?
 • An action potential is a self propagating, all-or-none change in the membrane potential that travels down an Axon.
 • We detect the MAGNITUDE of stimulation based on the number of neurons that were activated/involved. However, the process and action potential returns the exact same.
 • What are sensory cells? ◦ They are all the same thing ▪ modified dendrites ▪ interacting with the outside word ▪ and sending info to our brain ◦ The senses: ▪ smell - chemoreceptors ▪ taste - chemoreceptors ▪ vision - photoreceptors ▪ hearing - mechanoreceptors ▪ touch - mechanoreceptors + thermo-receptors ▪ others - electricity, magnetism etc. Week 9 The synapse • Action Potential comes down Axon • Calcium channels open (calcium that is at higher potential outside rushes in to the lower potential area inside) • Neurotransmitter dumped in synapse • NT diffuses across synapse • Binds to receptors • Causing Na+ influx and depolarization • At the synapse, an action potential is converted to a chemical signal releasing NT to stimulate tissue or another neuron The pleasure centers • There are pleasure centers in animal brains • In 1954, James Olds put electrodes to the mesolimbic area of bats brains and found that rats loved the sensation and would self-stimulate till the point of death from starvation (more than 700 times per hour!) • What good does it do an animal to have a set of neurons that makes them feel real good? • Which behaviors are tied to human pleasure centers? Why? ◦ Sex = pleasure. It maximizes reproductive success, although we don’t partake in sex with the expectation of maximizing reproductive success ◦ Adrenaline-filled activities; Bungee jumping etc. • What is going on in pleasure centers? ◦ Neuron is stimulated (in response to your behavior) ◦ dopamine is released into the synapse ◦ receptors on adjacent cell binds dopamine and fire ◦ happiness occurs Drugs • Cocaine ◦ Cocaine binds to re-uptake receptors. Blocks them. ◦ Dopamine remains in synapse. ◦ Pleasure is intensified ◦ The message ‘something good is going on’ is not going to stop
 • Our brains are built with pleasure centers. Stimulating them is so pleasurable, we want to behave in ways that repeat and maximize that stimulation.
 • Serotonin ◦ This is another neurotransmitter ◦ It’s usually inhibitory ◦ Affects appetite, sleep, anxiety and mood. ◦ Makes you content and satiated ◦ What if you block serotonin re-uptake transported protein? ▪ No more depression ▪ Prozac, Zoloft, Paxil etc. help prevent the re-uptake of serotonin and are used as anti-depressants. ▪ Wellbutrin, however, blocks the re-uptake of dopamine
 • How can a drug make us feel less tired and more alert? ◦ Caffeine ◦ Adenosine is a chemical produced as a by-product of cellular metabolism. It is like ‘cellular exhaust’. ◦ Over the course of a day, adenosine builds up n brain synapses, ◦ When adenosine receptors are filled, the ion channels open and the cell becomes less likely to fire. ◦ Adenosine is like a brake to brain activity (And when you sleep, it is re- absorbed) ◦ When you sleep, adenosine gets taken away and you feel refreshed. Then throughout the day it builds up and shuts down your cells so you feel sleepy. ◦ Caffeine masquerades as adenosine but doesn’t make a neuron less likely to fire! ◦ Additional caffeine effects; ▪ Athletic endurance- 19.5% more endurance with caffeine consumption, 1 hour before bike race ▪ Learning - increased performance in maze learning by rats given caffeine. ◦ By interfering with normal neuron functioning, drugs can change the way we feel and function (for better or worse) ◦ There is no evidence of negative consequences of caffeine long term.
 • Why use Botox and how does it work? ◦ It gets into the terminal button at neuron/muscles synapses ◦ It degrades several proteins required for fusion of vesicles with the terminal button membrane ◦ this prevents the release of acetylcholine (neurotransmitter) ◦ And if this neurotransmitter doesn’t release, then the muscles that is meant to be contracted, does NOT contract! (it paralyzes the muscles) ◦ So basically, Botox prevents the muscle contraction
 ◦ LSD: Mimics serotonin ◦ Ecstasy: Increases serotonin production and blocks serotonin re-uptake ◦ Permanently damages serotonin producing cells in cerebral cortex (used in learning) and the hippocampus (used for memory) ◦ Crystal meth - stimulates dopamine and serotonin release ◦ Oxycontin - mimics an opium-like neurotransmitter in pain neurons, blocking their function.
 • By interfering with normal neuronal operation, drugs can alter how we look/feel/function Alcohol • Alcohol is a molecular everyman ◦ Alcohol reduces anxiety ▪ GABA is an inhibitory neurotransmitter. When GABA docks, cells won’t fire. So releasing it calms you down. Alcohol mimics GABA and thus enhances its efficiency ◦ Alcohol produces stimulated energized feelings ▪ Alcohol increases dopamine. Dopamine makes us happy ◦ It blocks pain ▪ Alcohol stimulates endorphins release. Endorphins block pain signals ◦ It reduces depression ▪ Alcohol stimulates serotonin receptor activity. Serotonin makes us more content. ◦ Alcohol slows you down ▪ Glutamate is a NT. Alcohol blocks Glutamate receptors: slow/ slurred speech + reaction times are slowed down
 • Alcohol has multiple physiological effects because it mimics activity at numerous different synapses
 • How do our bodies process alcohol ◦ Ethanol - our body produces alcohol dehydrogenase (ACD) that binds to this, breaking ethanol down to ….. ◦ Acetaldehyde - our body produces aldehyde dehydrogenase (ALD) that binds to this, breaking acetaldehyde to ….. ◦ Acetic acid 
 • Asians and alcohol = Asian glow (they turn red) ◦ 50% produce an inactive form of aldehyde dehydrogenase (this is coded for by our genes) ◦ Acetaldehyde levels increase (and because the aldehyde dehydrogenase isn’t working and breaking the acetaldehyde down). This build up causes consequences which are: ▪ Rapid pulse ▪ Sweating ▪ skin flushing ▪ nausea ◦ 2 versions; fast flushing (2 defective ALD genes) and slow flushing (1 defective and 1 active ALD Gene) meaning that the slow flushers can handle the drinks slowly but if they take it fast then they’re gonna have problems ◦ In fact, interestingly, it can be considered beneficial that having a defective ALD Gene makes alcohol more unpleasant for you thus lowering your risk of alcoholism
 • Many genetic diseases - or beneficial conditions - are the result of a non- functioning metabolic pathway • How might you make a drug that helps treat alcoholism? ◦ Antabuse - blocks the action of ALD. It has kind of a low success rate though because since the Antabuse pill needs to be taken everyday, alcoholics can just choose not to take the pill. ◦ Aspirin - blocks ACD which means ethanol build up occurs causing you to get drunk faster
 • Humans are polymorphic for the dopamine receptor gene ◦ Long version of gene - more responsive receptor ◦ Short version of gene - less responsive receptor ◦ Wo


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