[B] General Biology
[B] General Biology Biol 102
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LECTURE OUTLINES AND STUDY GUIDE FOR BIOL 102 Here you ll find outlines of all the lectures that I ll be giving Please note that they are outlines which means that they do not include all of the details that the lectures themselves contain Please don t think that reading these outlines will be a sufficient substitute for attending the lectures to do so would be a huge mistake These outlines are intended to cover the main conceptual areas that we ll discuss as well as some but not all of the details including examples They will be of most use if you read them both before and after the relevant lectures In addition I have written them in such a way that they will be useful as study guides before our three exams Note that each of the sections ends with a question or two I ve called these bullets ASK YOURSELF Do just that Being able to answer these questions will show whether your understanding of the material is around that required for an A grade Do you remember the criteria for an A from earlier Thorough comprehension39 ability to correlate the material with other ideas to communicate and to deal effectively with course concepts and new material WHAT IS SCIENCE Science is a process a way of knowing about the world and our place in it Facts and figures are not science they are products of the scientific process Science depends on public observations of natural processes and natural causes not personal feelings or revelations based on supematural powers The process of science is as follows An observation of some phenomenon in nature leads to a question such as how or why A hypothesis is a tentative answer to that question Predictions that come from the hypothesis if then are tested with data that are obtained from additional observations or from experiments We ask is the hypothesis supported or rejected by our data Note that we don t look to see if our hypothesis is proven There s always a chance that future work will lead our hypothesis to be rejected This means that scientists must be comfortable with uncertainty Louis Pasteur s famous experiment on the spontaneous generation of living things is a nice example of the scientific process in action It is also an elegant experiment meaning that it is simple yet informative 0 And of course we think in the same kind of way as a scientist on a daily basis even if we aren t really aware of it How would you go about fixing a broken ashlight What s a theory It is just the opposite of a best guess as we use the word in everyday language such as asking who will win this year s Apple Cup A theory is a multiplytested and wellsupported hypothesis or set of related hypotheses Hence we talk about such things as the theory of gravity the theory of germs and the theory of natural selection A theory is about as close to a fact as we can get in science 0 0 ASK YOURSELF Do you think that all the questions we might ask about ourselves and our world can be answered by science 39339 ASK YOURSELF Girls seem to be less likely to study science than boys Why What might we do to interest more girls in science EVOLUTION PATTERN Biological evolution refers to the observation that living things change across generations and so over time The venue of such change has both time and space components Evolution has occurred over huge amounts of time and in an ever changing environment Fossils provide evidence of two things that life on Earth is very old and that living things have changed over time That said some organisms seem to have changed very little over millions of years In addition fossils suggest connectedness among different kinds of life eg the fins of fish the fmgers of frogs and the ippers of dolphins The hypothesis of connectedness eXplains observations that simply don t make sense otherwise For example why do modern whales which lack back legs have a pelvis Could it be because their ancestors had back legs Why do early human embryos have tails and gill slits in their necks Could it be because tails and gill slits were present in our ancestors Similar structures in different species may fulfill different functions wings are for ying legs for walking Descent with modification from a common ancestor could be a natural process producing such a pattern 0 0 ASK YOURSELF Modern snakes don t have limbs but some such as boas and pythons have little spurs that contain something looking like a femur bone the top of your leg Suggest some reasons for the presence of a leg bone in animals that don t have legs 39339 ASK YOURSELF If people evolved from monkeys did they how come monkeys are still around EVOLUTION PROCESS A tiny bit of history to set the scene religious thought science and biology in the 17001800s Paley and his 6argument from design the complexity and functionality of living things could only be produced by a Creator This idea lives on today as the nonscientific notion of 6Intelligent Design Lamarck was an early evolutionist who proposed the idea of the inheritance of acquired characters But offspring don t inherit physical characters acquired during the lifetimes of their parents Lamarck observed patterns of change over time but explained them with an impossible process not the same as epigenetics see later Charles Darwin world traveler around the world by ship reader e g of Malthus book on population growth and food supply observer e g of Galapagos finches and great integrative and synthetic thinker Natural selection is a process that explains descent with modification In essence those parents that best fit the current environment will be most likely to survive and so reproduce Because offspring tend to resemble their parents the next generation should on average be better tted to the environment Alfred Wallace Darwin s contemporary and natural selection s unsung hero Artificial selection is a useful analogy for natural selection and was used by Darwin e g selection by humans for different breeds of dogs all derived from a wolfy ancestor Actually Darwin used pigeons as his main example of artificial selection And of course environments tend to vary over time and across geography The peppered moth shows us evolution in action Selection coming from predation and pollution combine to explain variation in color among populations over space and changes in color within populations over time The initial reception to Darwin s idea was mixed one big problem was Darwin s inability to explain the cause of parentoffspring resemblance there was no science of genetics in Darwin s time Many people thought incorrectly that the Earth was too young for evolution to have occurred 0 Although Darwin said nothing about human evolution in his book of 1859 many people were disturbed by the thought that humans may have descended from lower animals 0 Today Darwin s idea forms the core theory of all of biology o Pesticide and antibiotic resistance are two contemporary cevolutionary problems of huge human importance 39339 ASK YOURSELF Do you think that human beings are still evolving 39339 ASK YOURSELF Evolutionary theory provides us with a much fuller understanding of infectious diseases Might it be useful in understanding other diseases such as cancer which we ll talk about later INHERITANCE o The story begins Gregor Mendel growing peas in a monastery garden Mendel s observations In an individual inheritance units come in pairs what we refer to today as alleles of the same gene Also these units seldom blend Mendel was lucky in that no blending occurred in his peas but it does happen for certain traits in other species Most often one allele is dominant over the other only dominant alleles not recessive ones are eXpressed in the phenotype that s the eshandblood form of an individual When alleles are the same for a particular gene e g AA both dominant or aa both recessive an individual is said to be homozygous for that gene39 when alleles differ Aa an individual is said to be heterozygous for that gene Punnett squares are invaluable tools for predicting ratios of different genotypes and different phenotypes based on Mendel s observations Genes on different chromosomes are inherited independently of one another That isn t necessarily true for genes on the same chromosomes especially if they are close together Sex linkage explains why some phenotypes occur only or more frequently in one seX such as the recessive condition of color blindness Remember in humans the male is heterozygous for seX chromosomes XY A recessive allele on the X obtained from Mom can t be masked by a dominant allele on the Y obtained from Dad Some traits are discrete whereas others are continuous eg a widow s peak hairline or blue eyes versus height or IQ Discrete traits are often controlled by one or a few genes whereas continuous traits are controlled by many interacting genes A simple equation P G X E An individual s phenotype P results from interactions between its genes G and the environment E in which those genes are eXpressed For some traits genes are little affected by the environment e g eye color for others environmental factors play a larger role e g IQ ASK YOURSELF How might you study pairs of twins identical and not to determine whether a particular phenotypic character is determined more by genes than by the environment WHAT IS DNA AND HOW IS IT REPLICATED 0 Genes are found on chromosomes in almost all kinds of cells mature human red blood cells are an exception DNA deoxyribose nucleic acid not protein is what genes are made of The basic DNA unit is the nucleotide a sugar known as deoxyribose connected to a phosphate molecule and a second molecule known as a base There are four bases in DNA their names abbreviated to A T C and G their full names don t matter What does a DNA molecule look like in 3D A little intrigue involving Xrays Watson Crick Wilkins and Franklin shows the human side of doing science DNA is a double heliX of two long chains of nucleotides Weak bonds between adjacent bases called hydrogen bonds hold the two chains together A bonds with T C bonds with G These two chains unzip for DNA replication before a cell divides New nucleotides are added to each of the original chains to fOI H l two new double helices which should be identical to the original and to one another If an incorrect base is added during replication or a new base is added or an existing base is deleted then the new helices will not be faithful copies a mutation occurs Another kind of mutation occurs when a chromosome breaks perhaps then joining onto another chromosome in a very abnormal fashion Sometimes but not always mutated genes produce altered phenotypes Many mutations are detrimental but some are beneficial and so are favored by natural selection Indeed mutation is the basic source of the genetic variation upon which selection acts ASK YOURSELF In what kinds of cells must DNA mutations occur if they are to be inherited by a child from her parent FROM DNA TO PROTEINS The basic chemistry of life involves nucleic acids DNA and RNA carbohydrates lipids and proteins Proteins are made up of units called amino acids Each amino acid there are 20 in nature has a unique side group Amino acids combine with one another Via a dehydration reaction to form a polypeptide chain The 3D conformation of the chain represents a functional protein truly one of the building blocks of a phenotype Some proteins have lipid or carbohydrate molecules attached to them Now back to DNA Triplets of bases code for or correspond to particular amino acids remember there are 20 of the latter in nature In the process of transcription the DNA message in triplets of bases is converted into a codon message in mRNA or messenger RNA mRNA is a single strand of nucleotides in which the sugar ribose replaces deoxyribose and the base U replaces the base T In the process of translation which occurs on cytoplasmic structures called ribosomes mRNA combines with tRNA or transfer RNA the latter carrying specific amino acids Where mRNA codons and tRNA amino acids match adjacent amino acids connect to one another Via dehydration reactions to form a protein or more correctly a polypeptide chain The genetic code is said to be redundant meaning that more than one codon is associated with each of the 20 amino acids And that means that a mutation in DNA let s say an A base replacing a C base doesn t necessarily change the protein for which a gene codes However a change in just one base is enough to change the protein structure of hemoglobin in red blood cells from healthy to diseased The central dogma of biology states that the information needed to create a phenotype ows from DNA to RNA to protein Information cannot ow in the reverse direction and so contrary to Lamarck s idea acquired changes to the physical phenotype cannot be inherited Retroviruses are different information flows from RNA to DNA e g in HIV that causes AIDS Blocking such reverse transcription is one treatment for AIDS e g AZT therapy Mutations in the RNA of HIV can result in resistance to drug therapies 0 0 o 0 0 Remember Lamarck Acquired characters cannot be inherited It is true that say genetic changes that occur in a skin tumor can t be inherited But changes to proteins on chromosomes not the DNA bases themselves that alter gene activity may be passed to offspring For example chemical pollutants given to a pregnant female mouse may lead to changes in these proteins in the cells of her offspring with changes in the activity of associated genes After birth her offspring may pass these altered proteins on to their own young This exciting new branch of biology is called epigenetics Remember we re not talking about mutational changes to DNA bases eg replacing an A with a C ASK YOURSELF Some stretches of DNA mutate at a slow but more or less constant rate and so can act like a clock What kinds of DNA would be most clocklike stretches that code for proteins or those that don t Explain your answer ASK YOURSELF If different cells in your body have the same genetic composition except for sperm and eggs how can they look and function so differently say muscle versus nerve cells CELLS Cell theory all living things are made of one or more cells Thus many biologists do not consider Viruses to be living things Viruses aren t cells Cells are bags of life separated from the outside world An outer membrane made of fats and proteins acts as a barrier with gates Not all materials can enter or leave through the gates in the membrane Within cells different structures called organelles perform different tasks Ribosomes are the sites of protein synthesis where mRNA codons and tRNA carrying amino acids come together in the process of translation Mitochondria produce energy by respiration glucose oxygen gt carbon dioxide ATP Useable energy is released when ATP gt ADP ie when ATP loses one of its phosphate groups lriphosphate becomes diphosphate Chloroplasts in plants only produce sugars by photosynthesis carbon dioxide water sunlight gt sugars oxygen Note how the equation for photosynthesis is almost the mirror image of that for respiration What might that mean at an ecological level Cells with a distinct nucleus and organelles surrounded by membranes are called eukaryotes Cells without such as bacteria are called prokaryotes Eukaryotes and prokaryotes the analogy of slow fancy cadillacs and speedy strippeddown race cars Plant animal and bacterial cells are linked in a complex web of ecological interactions involving respiration and photosynthesis How can the diverse phenotypes of cells in a living body be produced when cells are genetically identical It all depends on which genes are turned on when and where 0 0 ASK YOURSELF The first organisms to evolve were singlecelled But today there are many whose bodies consist of multiple cells Can you think of any advantages to having a phenotype made of multiple cells CELL DIVISION AND CANCER With the exception of cells that produce sperm and eggs or gametes all cells divide by mitosis In mitosis one parent cell duplicates all of its genetic material and then divides to form two genetically identical daughter cells barring mutation of course Mitosis is part of the cell cycle the stages of which are labeled as Gl S G2 and mitosis A cell grows and does its jobs Gl copies its DNA S and then gets ready to divide G2 The cell cycle is controlled by genes Genes called oncogenes promote mitosis whereas tumorsuppressor genes inhibit mitosis Cancer arises when regulation of the cell cycle fails and mitosis becomes uncontrolled For example genes that either promote or inhibit mitosis may suffer mutations and so not function properly Cancer is a variable disease with variable causes including exposure to environmental carcinogens such as tobacco smoke and the rays coming from tanning beds Not too many cancers are caused by genetic changes that can be inherited but more may be caused by infectious agents such as viruses than we once thought The disease begins with the growth of a primary tumor that may spread to other parts of the body a process called metastasis to form secondary tumors This spread sometimes is helped by tumors stimulating the formation of new blood vessels close to them a process called angiogenesis Diagnosis often begins with a patient noticing troubling symptoms such as a persistent cough Biopsies and various forms of imaging are then used to determine the kind of cancer involved and its exact locations in the body Secondary tumors are often much harder to treat than primary tumors but new treatments for cancer are under constant development Standard therapies involve surgery andor the use of radiation andor drugs chemotherapies to slow or halt cell division For example the drug Taxol disrupts the little spindles that move chromosomes during mitosis Newer therapies are more targeted For example the drug Avastin blocks angiogenesis starving tumor cells and making metastasis less likely Another approach is to block the responses of cancer cells to o 0 o o 0 molecules that occur naturally in the body and which stimulate cell division Despite progress with particular kinds of cancer the disease overall remains the second leading cause of death in the US heart disease is number one About one out of every three Americans will develop cancer if they live long enough getting cancer isn t the same as dying from cancer You can reduce your odds of developing cancer by knowing your family history lowering your exposure to recognized risk factors such as tanning beds and getting yourself screened on an appropriate schedule A colonoscopy isn t much fun but nor is colon cancer ASK YOURSELF What measures are you taking to lower your risk of developing cancer ASK YOURSELF Mom has cancer Dad has cancer and your siblings have cancer So you must have the gene for cancer too yes Why is this conclusion not necessarily correct APPLIED GENETICS TOOLS OF THE TRADE AND DNA FORENSICS The basic strategy underlying applied genetics is what we ll call ISICU Identify Sequence Isolate Copy Use Identify and sequence the bases in genes of interest the Human Genome Project has now sequenced all of our proteincoding genes There are around 20 to 25 thousand of them Most people expected that there d be more given the complexity of the human phenotype Isolate the gene of interest restriction enzymes think of them as DNA scissors recognize particular sequences of bases A C T and G and cut the DNA where those sequences occur Thus a gene can be removed from its chromosome We can put DNA scissors to several forensic uses such as identifying criminals Repetitive sequences of bases called tandem repeat units can be cut out of the chromosomes separated and stained to make them visible They can then be used as DNA fingerprints because they are so incredibly variable among individuals in how many repeating units they possess By comparing DNA fingerprints among defendants in a criminal case we can exclude those for whom we obtain no genetic match Wrongly imprisoned people have been released from jail thanks to such exclusion When we find a match statistical methods can be used to estimate how likely that match may be due to chance The smaller that estimate the more certain we can be that the match is real Genetic samples are routinely taken from arrested people not necessarily only if or when they are found guilty and sentenced Does that sound fair And what about a nationwide DNA registry for everyone in the US people like you Does that sound like a good idea 0 39 ASK YOURSELF Let s say your employer or lifeinsurance company is able to a look at your genetic profile How comfortable do you feel with that Might there not be the threat or at least the possibility of genetic discrimination ls such discrimination illegal Do you think that it should be APPLIED GENETICS GENE TRANSFER With a gene isolated from its chromosome by cutting it free with restriction enzymes we can use the polymerase chain reaction or PCR to produce millions of identical copies accurately quickly and cheaply PCR mimics in a machine the natural process by which DNA is copied in cells we learned about that earlier Copies can then be put into recipient cells even of different species An individual carrying a gene from a different species is said to be transgenic DNA that carries a gene from a different species is said to be recombinant How does the process work Here s an example Using restriction enzymes a copy of a gene of interest is spliced into a plasmid which is a bacterial minichromosome The plasmid is then put into a bacterial cell That recipient cell and all of its descendants created by mitosis will copy the foreign gene and then can be made to manufacture the protein for which it codes In this way we can generate bacteria that produce say human insulin which can be used to treat Type I diabetes also called juvenile or earlyonset diabetes Agriculture also is using transgenic technology to produce greater quantities of higher quality food Geneticallymodified GM crops produce GM foods with tricky mixes of benefits and potential risks Are the crops safe to grow and the foods safe to eat GM crops are being grown across hundreds of thousands of acres in the US and GM foods seem acceptable to most US consumers But there s a great deal of mistrust of GM crops and foods in Europe Are we in the US being naive or are the Europeans just being paranoid Would you eat GM foods 0 0 ASK YOURSELF How can a bacterial cell make human proteins when bacteria and people shared a common ancestor hundreds and hundreds of millions of years ago 0 ASK YOURSELF Granma says We ve been genetically altering plants for years by breeding them in particular combinations that s how wheat was made So why all the fuss about GM crops What would you say to Granma 0 APPLIED GENETICS PRENATAL MEDICINE The goal is to detect and hopefully cure well at least treat certain kinds of genetic diseases Human development from fertilized egg to newborn baby and beyond can go wrong for many reasons including environmental insults eg alcohol abuse during pregnancy giving rise to fetal alcohol syndrome or genes perhaps inherited from one or both parents that do not function properly Ultrasonography can detect largescale anatomical problems But what about more subtle problems such as disorders of biochemistry Amniocentesis and chorionic villus sampling let s just call the latter CVS can be used to detect certain genetic abnormalities by looking at chromosomes and genes or by looking at gene products proteins An extra copy of chromosome 21 might be detected Such trisomy results in a disorder known as Down syndrome In addition genetic counselors advise people with known genetic diseases on the odds of having children that may be affected sickle cell anemia is a good example With that advice affected couples can then make informed decisions about whether they wish to become biological parents Amniocentesis and CVS can detect subtle problems fairly early in pregnancy but the technique of preimplantation genetic diagnosis or PGD allows detection of problems even before a very young embryo implants into its mother s womb How can that be possible In PGD cells from very young embryos produced by in vitro fertilization are screened for chromosomal abnormalities and defective genes Only those embryos whose cells reveal normal chromosomes and genes are then put into their mothers wombs Could the technique of PGD be modified to include treatment or even a cure not just diagnosis Could we transfer functional genes into cells that have defective ones And what about other uses of PGD For example do you think it would be ethical to use the technique to screen embryos for such traits as sex eye color or if we could do it future intelligence Hot off the press We now have another tool for prenatal diagnosis Believe it or not DNA from a fetus can be found in a pregnant woman s blood We can isolate that fetal DNA make copies by PCR and sequence it to see if it is normal This is a very lowrisk procedure because all it involves is taking some of Mom s blood 39339 ASK YOURSELF What kinds of consequences could arise in a society in which because families prefer boys baby girls are aborted as fetuses or left to die after birth 39339 ASK YOURSELF Should every pregnant woman have amniocentesis or CVS Explain your answer APPLIED GENETICS TOPICS LISTED BELOW WILL BE INTEGRATED GENE THERAPY o The goal is to replace a defective gene with a functional copy and so cure well at least treat a genetic disease But would the offspring of such a cured individual be guaranteed a diseasefree life Not necessarily but do you know why Remember our ISICU strategy First Isolate a functional gene then Copy it and finally Use it by putting it into an affected person Fatty blobs liposomes and gene guns can be used to put DNA into cells Viruses are also used as socalled vectors to infect human cells carrying defective genes with functional copies That s what parasitic Viruses normally do inject genetic material their own of course to infect host cells But the process isn t foolproof For example people may mount an immune response against the virus destroying both it and the good genes Or the virus may place its payload of genes into a patient s DNA but in the wrong place This might cause cancer Overall current successes for gene therapy are quite limited but there is promise for the future But could all human diseases ultimately be fixed by gene therapy And if not why ASK YOURSELF As clever genetic technologies mature and they surely will should society support those that result in genetic changes to DNA that can cross generations STEM CELLS Stem cells have the potential to develop into any kind or almost any kind of mature cell type Not surprisingly embryonic cells seem to be the most useful stem cells called totipotent stem cells Of course embryonic cells have to develop into every kind of cell present in the adult body Pluripotent stem cells are less versatile and committed stem cells are the least versatile If stem cells can be coaxed to develop into specific cell types then we may be able to devise better treatments for such conditions as Parkinson s disease a brain disorder spinal cord injury and Type I diabetes and many more There s lots of experimental work going on One troubling observation is that stem cells sometimes develop into tumors rather than the desired cell type Perhaps the bestknown success story so far it made it into all of the media was the repair of a woman s damaged windpipe using stem cells taken from her bone marrow Is it ethical to destroy a very young embryo in order to get the most valuable totipotent stem cells even if doing so benefits others Do the ends justify the means What if such embryos would be destroyed anyway The previous Bush administration put restrictions on federallyfunded research on stem cells in the US such research was very restricted but not banned Many scientists and some politicians feared that the US might lose its edge if stem cell research shifted abroad to countries with fewer regulations Some states revolted eg California with its stem cell initiative With the advent of the Obama administration restrictions on the use of embryonic stem cells were relaxed somewhat which isn t to say that regulations on and legal challenges to the use of these cells in research aren t continuing New work suggests that umbilical cord and adult stem cells may be more common and more useful than was previously thought And we now have a method of turning mature cells into pluripotent stem cells by adding just four genes that are responsible for pluripotency These altered cells are known as induced pluripotent stem cells or iPS cells 0 0 ASK YOURSELF If putting embryonic stem cells into your kidneys from an unrelated donor could potentially cure you of a particular disease would you allow the surgeon to inject you with them Explain your answer CLONING o Identical twins are natural clones they are identical genetically barring mutations of course fomied when a single embryo breaks in 0 two But are clones identical in all aspects of their phenotypes Not necessarily remember that P G X E As an aside embryos that are genetically different sometimes combine into one in the womb The result is a chimera an individual whose cells are genetically different How might I clone an individual I d take the nucleus out of a donor cell and put it into an egg whose own nucleus has been removed That egg now containing the nuclear DNA only of the donor would be put into the womb of a surrogate mother We ve been able to clone DNA for quite a while Dolly the sheep showed that we can also clone the adult DNA of a pretty advanced creature say compared to a frog a lot of scientists thought that this could not be done But Dolly suffered from premature aging perhaps because the ends of her chromosomes socalled telomeres were worn after all Dolly s chromosomes were older than Dolly herself Would it be safe to clone a person And why would you want to clone a person There are two motivations behind human cloning reproductive cloning and therapeutic cloning Pretty much everyone in the U S finds reproductive cloning to be unethical In reproductive cloning one makes a replica of the complete donor individual For example I might clone a dead child or spouse In therapeutic cloning I d clone a very early embryo from whichl would then harvest stem cells remember they are totipotent Research on therapeutic cloning is going ahead in the U S but with strict regulations Certain other countries also are moving ahead in research on therapeutic cloning Has a human been cloned yet We have cloned humans to early embryonic stages with the goal of obtaining stem cells that s therapeutic cloning Claims have been made that humans have been cloned to birth or beyond that s reproductive cloning but these claims haven t been supported by any evidence ASK YOURSELF What do you think about reproductive cloning acceptable or not If the technology was available would you clone your dead spouse And if you did would the clone really be identical to your dead wife or husband BIOETHICS 0 Our understanding of how genes and cells work now enables us to manipulate them in ways that 20 years ago would have been in the realm of science fiction Research is racing ahead we ll probably have the technology to do some amazing things pretty soon But just because we can do something doesn t necessarily mean that we should do it Under what circumstances are risks worth taking When do ends justify means Is it ethically right to destroy a young embryo even if doing so might save the life of an adult History teaches us that scientists can lose sight of ethics even here in the US in the last century eg the forced sterilization of people with low IQs and unmarried mothers and the denial of medical treatment to AfricanAmerican men with syphilis The latter was done so that scientists could study how the disease kills people Can we reach a fair and just middle ground and so avoid the polarized positions that keep emerging I believe that achieving this will only be possible with no guarantees of course if everyone has access to the information needed to make informed decisions 0 0 ASK YOURSELF Some people will die prematurely such as people with fatal diseases and prisoners on Death Row awaiting execution Why not use them in experiments after all there s nothing to lose if the experiments kill them Would you be OK with that REPRODUCTION MALE REPRODUCTION The basic players are the hypothalamus in the oor of the brain the anterior front pituitary gland attached to the hypothalamus and the two testes These structures communicate with one another and with other parts of the body Via hormones A hormone is a chemical that is produced in one part of the body and has an affect somewhere else The testis Sertoli cells nurse sperm produced by meiosis in the seminiferous tubules Situated between these tubules are Leydig cells that produce male seX hormones or androgens such as the steroid testosterone The hypothalamus controls hormone production by the anterior pituitary gland The pituitary hormone FSH stimulates Sertoli cells and is needed for sperm formation lnhibin produced by Sertoli cells regulates sperm production by negative feedback a process analogous to the control of room temperature by a thermostat The pituitary hormone LH stimulates Leydig cells to produce testosterone and other androgens Testosterone then regulates LH secretion by negative feedback the thermostat effect again Testosterone has both direct and indirect effects on male reproduction eg sperm production sexual behavior muscle growth deep voices and hairy chests Decreasing levels of testosterone with age are responsible for changes in male behavior that are sometimes called the andropause although some evidence suggests that the causal arrow is in reverse with changes in behavior causing changes in testosterone Sperm are very specialized single cells that are mobile with a tail or agellum They carry shuf ed patemal DNA in the form of 23 chromosomes that s what meiosis produces They carry mitochondria to generate energy And enzymes needed to penetrate into an egg are present in a structure called an acrosome at the front of the cell Into the outside world glands in the male reproductive tract add to sperm to form semen For example secretions of a gland called the seminal vesicle contain a sugar that fuels the swimming activity of sperm 2 ASK YOURSELF The penis is peculiar as are the people who have penises it is neither a bone nor a muscle but a blood pump The drugs Viagra and Cialis can help men with erectile dysfunction by increasing blood flow to the penis As the ads say Will you be ready when the time is right And If it lasts for longer than four hours that s not good Why Around 300 million sperm are released during seX why so many From a biological point of view but not emotional or economic or moral a male s investment in reproduction ends when one of his sperm fertilizes an egg In what ways might you interrupt the processes underlying male reproduction to develop new forms of birth control FEMALE REPRODUCTION The basic players are the hypothalamus anterior pituitary gland posterior back pituitary gland ovaries uterus or womb and mammary glands or breasts FSH from the anterior pituitary gland is needed for the maturation of an egg in an ovarian follicle by meiosis LH from the anterior pituitary gland is needed for release of that egg or ovulation and the formation of a corpus luteum which means yellow body in Latin from the empty follicle Ovarian steroid hormones estrogen is produced by the follicle before and by the corpus luteum after ovulation Progesterone is another hormone produced by the corpus luteum These hormones have effects on the uterus the mammary glands and the brain Activities of and interactions among these basic players are coordinated as the menstrual cycle in which compleX but predictable changes occur in the pituitary ovary and uterus over the course of about 28 days one lunar month In an average menstrual cycle day l the first day of menstruation or period and day 14 the day of ovulation From ovary to uterus an ovulated egg is picked up from the surface of the ovary by fingerlike fimbriae found at the ends of the Fallopian tubes As the egg moves down one of the tubes swept along by the beating of hairlike cilia it may encounter sperm and become fertilized Just one sperm fertilizes a single egg Meiosis by the egg is completed only after penetration by a sperm When the 23 paternal chromosomes join with the 23 maternal chromosomes the complete genetic blueprint for the development of a new individual is in place But remember P G X E The complexity of female reproduction in humans provides lots of opportunities for intervention of various kinds This might explain why so many methods of contraceptionbirth control are designed to disrupt processes in women rather than in men More on this a little later Getting the timing of intercourse just right is important because sperm don t live for too long in the rather hostile environment of the female reproductive tract it is rather acidic and there are lots of immune cells roaming around looking for unwanted invaders like bacteria There is some evidence suggesings that chemical signals called pheromones play a role in sexual desire and in coordinating sexual interesUattraction between men and women Early pregnancy the hormone HCG from an embryo implanted in the wall of the uterus enters the mother s blood and stimulates the corpus luteum in her ovary to keep producing estrogen and progesterone HCG carries the message Mom s pregnant and is the target of detection of pregnancytest kits If the corpus luteum fails then the wall of the uterus is lost ie a woman experiences her period A quick aside HCG is being sold as an aid to dieting Don t use it HCG hasn t been approved for this purpose and diets using it often include dangerously low numbers of calories Avoid HCG in the same way you avoid tanning salons and secondhand cigarette smoke The placenta is a complex organ in which the baby and mother s blood come very close together but do not directly mix Actual mixing would be a medical emergency Why There s a lot of exchange between the two blood supplies oxygen and nutrients moving to the baby carbon dioxide and other wastes moving to the mother Of course some unwanted things can also pass into the baby across the placenta such as alcohol and cocaine Within the uterus a ball of just a handful of cells develops into a baby consisting of billions A period of intense cell differentiation in the first 8 weeks is followed by growth in size until birth occurs about nine months after fertilization The baby initiates birth by producing stress hormones that cause contractions of the uterus muscles Then the mother contributes to the process with the homione oxytocin produced by her posterior pituitary gland causing more intense uterine contractions and dilation of her cervix a short passage connecting the uterus to the vagina and through which the baby passes during birth In addition the ligaments that hold Mom s pelvic bones together become a bit looser Successful vaginal birth requires that the baby move through the cervix head first If this doesn t occur as with a breech presentation such as butt rst then an obstetrician will perform a caesarian section to remove the baby For a woman who is unable to produce muscle contractions strong enough to eXpel the baby or whose cerviX isn t becoming sufficiently dilated an obstetrician may inject an artificial form of oxytocin called Pitocin into one of her veins When the process of birth is too painful for a woman to endure an obstetrician may inject an anesthetic into the space around her spinal cord Known as an epidural this causes the woman to feel no pain below the site of the injection The health of the newborn baby is measured according to a set of standardized Apgar scores In addition a small sample of the baby s blood is taken and tested for certain disorders such as sicklecell anemia Parents have the option of banking umbilical stem cells after birth If the child needed those cells at some time in the future they could be used with no fear of rejection by the child s immune system Lactation provides the newborn infant with nutrition The breast or mammary gland first produces colostrum which is rich in disease fighting antibodies Sometime later true milk is produced a miX of fats sugars and proteins for health and growth until weaning when the child switches to solid food well mashedup food like peas and apples A hormone called prolactin produced by the anterior pituitary gland stimulates milk production by cells in the ducts of the breast A second hormone called oxytocin and produced by the posterior pituitary gland stimulates the ejection of milk from the nipple Yes this is the same oxytocin that was involved earlier in the process of birth This hormone also may strengthen the emotional bond of the mother to her new baby And people in romantic love often have relatively high levels of oxytocin men too Levels are also increased during and after sexual activity Some have dubbed oxytocin the love hormone Growing evidence suggests that breastfeeding might provide some protection to Moms against certain diseases such as breast cancer Breastfeeding is good for both baby and Mom 0 Women go through the menopause when their ovaries produce less estrogen and progesterone in their 40s or 50s This drop in hormone levels has a number of physical and psychological effects such as loss of bone mass and irritability 39339 ASK YOURSELF Given what you know about processes underlying reproduction in the two sexes would it be easier to develop new forms of birth control in one sex rather than the other Which sex and why 39339 ASK YOURSELF Before rushing off to buy a vial of oxytocin the love hormone and you can buy it online how would you test the hypothesis that exposing someone s partner to it will make her or him love that person more Design an experiment CONTRACEPTION My goal isn t to review what you may have leamed in high school in a class such as Healthy Living Rather we want to use our understanding of how reproduction works normally to disrupt the process and so avoid unwanted pregnancies I appreciate that some of you may have religious or ethical objections to aspects of this topic Please approach the subject from the perspective of understanding the biology whether or not you agree with how that understanding may be used For males we really haven t moved much further than preventing sperm from reaching eggs Most obvious is a physical barrier such as a condom 0 Cutting the vas deferens prevents sperm from leaving the testes While easy quick and safe vasectomy should not be thought of as reversible Surgery to reverse a vasectomy is not very reliable and it is very expensive Several technologies are in development that provide removable barriers to sperm flow through the vas deferens 0 Why no chemicalbased pills for men Some are being tested experimentally but the big problem is that the chemicals used may interfere with male libidoperformance not just fertility That s not acceptable to most men 0 That s not to say that chemical forms of birth control don t sometimes in uence female libido some like the Pill can do that I wonder why we seem to care less about female libido than male libido Barrier methods of various kinds exist for use by women such as the female condom cervical cap and sponge In addition tubal ligation provides a parallel to vasectomy again think of it as permanent sterilization rather than temporary contraception But the complexity of female reproduction allows for more kinds of interventions that does the simple system of males Here are some examples Spermicides These kill sperm in the vagina Intrauterine devices IUDs These prevent a fertilized egg from implanting in the uterus probably by causing mild in ammation some IUDs contain copper Oral contaceptives or the Pill There are many different kinds with most containing a combination of artificial forms of the steroid hormones estrogen and progesterone These chemicals inhibit the release of FSH and LH from the pituitary gland Follicles fail to develop and if one gets through the net ovulation is unlikely In addition mucus in the cervix may become thick and viscous blocking the path of sperm The socalled Mini Pill contains only progesterone39 while a little less effective than combination pills it has fewer unwanted sideeffects Norplant Multiple sticklike capsules containing progesterone are placed under the skin Implanon works in a similar way but only a single capsule is needed OrthoEvra or the Patch Looking a bit like a Bandaid the patch releases hormones that pass across the skin and into the blood Vaginal ring A thin exible ring containing hormones is placed up against the cervix The hormones pass into the blood DepoProvera A shot of progesterone is injected deep into a muscle Plan B Designed as emergency contraception after unprotected sex the hormones in Plan B pills block ovulation disrupt sperm transport and make implantation less likely They do not cause the abortion of an alreadyimplanted embryo Nevertheless some pharmacists want the right to refuse to provide Plan B because the egg that fails to implant could be fertilized Is it fair for a pharmacist to refuse to provide a woman with a product that is medicallyapproved and legal RU 486 This molecule blocks the action of progesterone If taken before pregnancy it can prevent implantation More controversial is its use after implantation the time when it is used the most when it causes abortion 0 These various methods vary in terms of their acceptability effectiveness cost ease of use and risk of sideeffects 39339 ASK YOURSELF Who should be responsible for birth control if a couple doesn t want to get pregnant the man or the woman 39339 ASK YOURSELF Do you think it is ethical for governments to regulate the family sizes of their citizens in order to avoid over population HUMAN POPULATIONS For most of human history there have been fewer than one billion people on the planet It was in the 1800s that our numbers started to climb Any idea why Our global population is predicted to increase from around 6 billion in 2000 to around 10 billion ish in 2050 this year 2012 we re over 7 billion Reproductive decisions regarding fertility that are made by individuals when multiplied across all of the individuals present obviously affect population size and growth Do you think it is right and fair for governments to dictate how many children their citizens can have Female determinants of fertility include the timing of puberty use of birth control lowered fertility while breastfeeding due to the hormone prolactin but fertility doesn t drop to zero and impacts from education Of course we mustn t forget about males Availability of information and appropriate technology is crucial for both sexes to make good reproductive choices That said my focus on females isn t because I m a sexist It is because quite literally women have the babies that contribute to population size Population pyramids are diagrams that provide summaries of current population sizes The shape of a population pyramid serves as a predictor of the potential for future population growth A broad base predicts a population with a high potential for future growth A population with a fertility rate of 21 will have a rectangular population pyramid I know that sounds silly How might the size of that population change in the future The demographic transition model goes some way to explaining variation among nations The core idea is that as a nation moves toward a more developed economy a decline in death rate occurs before a decline in birth rate Thus there is the potential for a surge in population growth The greatest potential for global population growth is in developing nations many but not all of which are hotspots of biodiversity How many people can the planet support What is Earth s carrying capacity for humans An environment s carrying capacity is the maximum number of individuals that it can support in terms of space and resources An ecological footprint measures the average per capita amount of land needed to provide people with the goods and services they need or want and enable wastes to be disposed of But does a nation s ecological footprint match its ecological capacity Does the world s 39339 ASK YOURSELF Developed countries often encourage countries in the developing world to move toward becoming just like say Europe or the United States Do you think this is a good idea Justify your answer 39339 ASK YOURSELF A population with a low birth rate may put less pressure on the environment by having a smaller ecological footprint But might there also be social economic and political consequences of low birth rate Would these be good BIODIVERSITY IF TIME ALLOWS Biodiversity has a long and rather clumsy definition For us it is most easily defined in terms of a hierarchy of components diversity of genes of species of communitiesecosystems desert versus Arctic for example and of ecological processes such as predators and their prey and parasites and their hosts Species numbers often are used as an indeX of an area s biodiversity However biologists use several methods to determine whether two populations belong to the same species and results aren t always consistent Around 17 million species have been described so far with perhaps 10 million lurking out there in total On land species numbers are greatest in the Tropics many of these tropical species are endemics with geographic distributions that are naturally restricted If an endemic vanishes from its naturallyrestricted home then it s gone from everywhere unless some specimens are in a zoo or a botanical garden Why should we care about biodiversity Maybe you feel an ethical responsibility to the organisms with which we share the planet Or perhaps you care because you find biodiversity beautiful Or maybe you are more utilitarian Perhaps you value the goods and services that biodiversity provides such as pollination of crops by bees little penises with wings o 0 ASK YOURSELF Verrell loves frogs and salamanders Can you think of any goods or services that these animals might provide to we humans POLLUTION amp CHEMICAL SAFETY What is a pollutant One class of pollutant is something that is present in area where it should be absent Other pollutants may occur naturally but human activity then boosts them to abnormally high levels Pollution is a global problem across all kinds of habitats pollutants travel even to places we might think of as pristine wildernesses They flow in the water and blow in the wind Pollutants may come from either point or nonpoint sources The latter are diffuse in space and so are the hardest to monitor and regulate Pests have been a problem ever since agriculture was developed around 10000 or so years ago For years we have waged war against pests with chemicals designed to kill them But not all of these chemicals are specific to their intended targets Contamination of nontarget species Rachel Carson and the story of DDT By eating contaminated prey with DDT stored in fatty tissues DDT became bioaccumulated or bioconcentrated or biomagnified in predators at higher levels in food webs At the top of their food webs populations of many predatory birds started to decline bald eagles were hit hard Why did populations suffer Because DDT caused egg shells to thin and few live baby birds to hatch What would the population pyramid look like in such a situation Today in the US the use of DDT is very restricted because of effects in nontarget species Should we ban the use of DDT worldwide How do we test whether a chemical is safe This is a difficult job for the Environmental Protection Agency and other federal organizations Let s design a test What decisions will we have to make Who should we test Mice Frogs Bees People How should we expose our subjects Should we put the chemical in their food In their water Should we inject them with it Should we expose our subjects to large amounts of the chemical in short periods of time acute exposure or to smaller amounts over longer periods chronic exposure Which kind of exposure is the one that you and I are most likely to experience Should we expose our subjects to the chemical by itself or to a cocktail of chemical that occur together Which is more natural What should we measure as an endpoint Something obvious like death the basis of an LD50 test or cancer Or perhaps something more subtle like problems with fertility A growing number of chemicals disturb the hormonal control of reproduction either by mimicking the effects of natural hormones or blocking their effects Such hormone disrupters have been shown to affect cells growing in dishes laboratory animals and wildlife But what about us The average woman in the U S has around a oneineight chance of developing breast cancer If a man lives long enough he will probably die with prostate cancer even if not om prostate cancer Is there a link with our use of chemicals Can we be certain How should we deal with uncertainty Should we just wait and see or should we use the Precautionary Principle The latter states in its fanciest version that if the consequences of doing nothing might be sufficiently bad then maybe it is best to act now even if we aren t 100 certain whether those bad consequences will actually come about Better to be safe than sorry And shouldn t we apply this same principle to some of the incredible genetic and cellular advances that we discussed so many weeks ago ASK YOURSELF Who should determine what s safe and what s not or when we should be or need not be precautionary We the people Scientists Corporations The President Some worldwide organization or agency such as the United Nations ASK YOURSELF Should the government regulate how much fat is in the burgers and fries we eat how much sugar is in the sodas we drink or whether we can smoke cigarettes 855pm PGxEPhenotype Interaction between the genotype and the environmentHow much variation among individual is due to genesntelligence quotient 45 for children 75 for adolescentsBody mass index 48 at age 4 years 78 at age 11 yearsHeight60 80Depression45Bipolar disorder 60Schizophrenia 80 The basics of DNAWhat are chromosomes made ofAbut 33 DNA 66 proteinWhat makes this bacterium deadly to mice Protein or DNATB of mice tuberculosis ASE EnzymeLACTASE breaks down sugars in milkLlPASEbreaks down fatsPROTEASE breaks down proteinsDNASE breaks down DNADNASE 9 chromosomes DNA X destroyed Protein is okayPASE 9 chromosomes DNA is okay protein is destroyedDNA destroyed DNASEProtein is okay mickey livesProtein is destroyed mickey diesDNA a string of pearlsDNA is made up of nucleotides Sugar BaselvPhosphate vsugar9 base vrepeatsBase A T C or G Biology 102 8222012 What is science Science is a way of knowing about the world None of these ways of knowing are superior The world today past and in the futter history literature painting music religious belief What makes science different Provides us with a better way of knowing and gives us a deeper understanding It relies on observations that anyone can make No supernatural causes explain things in a natural explanation Science relies on evidence not belief What s wrong with my flashlight The scientific method observation define a problem propose hypothesis gather evidence test hypothesis Reject and develop a new hypothesis or retain hypothesis Develop theory Francis bacon and the inductive method The scientific method goes way back llThe whole of science is simply using common sensequot Einstein Louis Pasteur tried to find out why wine went sour discovered that there were microorganisms decided to heat the wine to kill the organisms and developed the idea of pasteurization He also developed a vaccine to prevent rabies He tested the hypothesis of spontaneous generation from dead material into living things When the flask was closed there was no contamination when the flask was open organisms grew Elegance in science don t make the process more complicated than is has to be A theory sa hypothesis or set of hypotheses that has been supported after multiple tests 8242012 Evolution llnothing in biology makes sense except in the light of evolution Evolution is change over time The origin of life is a mystery The oldest evidence of living things is a 34 billion year old fossil Lots of timelots of space Fossils they teach us that life on earth has a very long history the diversity of living things has changed over time They bridge gaps between present living things and past living things Ambulocetus whale ancestor has back legs In early human embryos have gill slits