week 10, 11, 12-> test 4

What did Galileo publish in 1632? What were the 2 systems and the 3 characters of the book? What mistake did Galileo make specifically regarding the new pope and family friend? the new pope told Robert Bellormine to get the Duke of Tuscany to send Galileo once again.

- "The dialogue of the 2 great world Systems" 1. The Copernican System 2. The Ptolemaic System character 1- Simplicito(the simple one character 2- salvato(the savior) character 3- sagrado(the wise one)-listens to the other twos argument for each system and declares Salvato as the winner -he put words from the new popes into simplicitos mouth

What is differential gene expression?

- A process in which cells with the same genle express different sets of genes. Ths is because cells that are located in different part of the organism are exposed to different cell-cell signals. This process forms specialized cells, arranges them into tissues, and more.

What is DNA mehtylation? Methylated CpG sequences are recognized by... SO actively transcribed genes have ___ levels of methylated CpG near their promoters wheras non transcribed genes have ____ levels of methylated Cpg. methylation= increase packing/decrease transcription!

- A process where a group of enzymes called DNA methyltransferases add methyl groups (CH3) to cytosine C) residues in DNA. IN mammals, the sequence recognized buy these enxzymes is a C next to a G. The sequenc eis abbreviated CpG -proteins that trigger chromatin condensation !!! -low;high!!!

How do transcription factors recognize specific DNA sequences of enhancers, silencers, promotoer Proximal elements, etc? Recall: DNA bases are partially exposed in the major and minor grooves of the DNA double helix pg 386 says a methyk is on Thymine but 382 says methyklations is to C? The strenght of a proteins binding to a target is often called its ____.

- A-T and C-G base pairs present different shapes and chemical groups in grooves. SO The edges of different bsae pairs projecting into the major and minor grooves of DNA present different structures and sets of atoms. There are Atoms that participate in Hydrogen bonding with amino acids of trasncription factors project slighlty from the bse pairs in the grooves. A particular transcription factor binds to a specific enahncer sequence (or other ) because of complementary interations between its amino acids and a particular sequence of base pairs of DNA. -affinity

Who was the first person to propose chemical evolution? Oparin and Haldane published which hypothesis specifically? What was the other hypothesis that supported a prebiotoc soup? A few year later ____ published the same idea. Today the Oparin Haldane proposal is or isnt considered a scientific theory?

- Alex Oparin in 1924 - the abiogenetic hypothesis of prebiotic soup. : said early Earth was a reducing atmosphere with H2, CH4, NH3, and H2O. Said lightening and UV radiation were the enrgy sources and UV radiation would work because there was no ozone layer so the oceans were warm. All the chemicals could react togetehr to give monomers - the impactor hypothesis: early earth wsa dense in CO2 and impactors like meteros and comets would contaCt Earth and rather tha oxidizing adn vaporizig they would have broke. The dense atmosphere would slow the comets from 17000->4000 km/hr. So the comets would hut Earth. 2% of impactors carry organic matter= carbonites - JB Haldane -it is a scientific theory

Traditional definitions would say that members of one species can or cant exchange genes with members of anotehr species? Laterl gene transfer counters this because rather than genes moving "vertically" from gen to gen it moves "laterally" between differnt species

- CANNOT

What contributs to the tight assocation between histones and DNA?

- DNA is negatively charged because of its phosphate groups andhistones are positivelhy charged because they have many arganines and luysines(both + aa's)

THe idea of evolution originated by the ____ because mount olympus has fossils of marine organisms and they inferred.. THe Enlightenment occured because... THe theory of evolution was formulated by what 2 people? Who published a book that created controversy at the time because it differed from the view on the origin of life at the time? Explain what was believed at the time.

- Greeks; these fossils must be ancestors - people questined church because Galileos trial. 1. Charles Darwin 2. Alfred Wallace -Charles Darwin published his theory in 1859 in a book called "On the Origin of Species by Means of Natural Selection) - "Special Creation" which said that all species are independent so not related, life on Earth is 6000 years old, and that species are unchanging and all created by a supernatural being

Briefly explain Millers experimental setup. State the contents of eahc flask. What was his hypothesis? When at bp of water no chemical reaction occured. What did Miller due that resulted in reactions? What molecules resulted? THus the formation of a prebiotic soup is possible!!

- He connected a large and small flask with glass tubing and had a condensor conected as well. The large flask contained the reducing atmosphere - methane, ammonia and hydrogn(early atmosphere). The small flask contained 200 mL of water(the ocean). Miller boiled the water constantly in the small flask to connect the flasks. Boiling added water vapor to the mix of gases in the large flask, AS the vapor cooled and condensed it flowed back into the small flask where it boiled again. This way, water circulated the whole time. IF the molecules in th simulated atmosphere reacted with one another, the rain would carry them into the mini ocean. - if kinetic energy is added to the mix of simple molecules, reactions wil occur that produce more complex molecules, maybe even C-C bonds - Milller sent electrical discharges across the electrodes hed inserted in the atmosphere. These "lightining bolts" added pulses onf intense electrical energy. AFter a day the solution in the small boiling flask turned pink adn a week turned red. - the mini ocean or the small flask contained lots of hydrogen cyanide and formaldehyde which are poisonous but reactive and could make larger molecules. There was also some aa's including glycine

What is the orignin of the nucleur envelope thought to be?

- Invagination hypothesis : Infoldings of the PM of the eukaryotic ancestor (a prokarytoes) were thought to surround the chromsomes and eventually detached to form a eukaryotic cells with a nuclear envelope and ER that is continuous with the nuclear envelope

Make a statement about the mutant rpoB allele including fitness and adaptation and frequency

- M tuberculosis individuals with the mutant rpoB allele had higher fitness in an environment where rifampin is present. The mutant allele produces a protein that is an adaptation when the cells environment has rifampin. THe M tuberculosis population evolved because the mutant rpoB allele increased in frequency

WHat observation did not match the geocentric model? What was used to "fix" this?

- Mars moved in retrograde motion not a sphere so it had a large curve/circle that doesnt match that it should continuously move ina circle. -astronomers said that MArs goes on a epicycle(a circle on the circle) which explined retrograde motion.

Why is chromatin packaged so tightly makig it necessary for remodling so that a molecular signal can trigger the transcription of a certain gene?

- Most cells in our body have 6 million base pairs of DNA. Lined up end to end this forms a double helix 2 meters long or 6.5 feet. The nucleius of cells are only 5 um. Hence why tight packaging is needed

What did Harolds group call the protein produced by the gene the made ising reverse trasncriptase from myoblst mRNA? How does MyoD work? MyoD is a ___ ____ of msucle differentiation.

- MyoD! - the MyoD gene encodes a regulator transcription factor(protein) and that this protein , the MyoD protein, binds to enhancors location upstream of muscle specific genes - master regulator

The Roman adn Spanish inquisition was the __ ____ ___ ___ ___ now the COngregation of propegation of the fate. What was their job? How did people use the bible to support a geocentric model?

- ROman Catholic church Holy office; to identiofy and arrest heretics and get them to publiscly take back their hersy otherwise to be burned or tortured. This is why Coperncus waited to publish until he was gonna die soon anway and he did die -the took verse literally lke Psalm 104:1-5 which says Earth would not be moved

What second kind of ribozyme did the team search for? What was teh experiment done?

- Ribozymes that could catalyze the production of nucleotides because if such a thing existed these would be copied more due to local accumulation of monomers - the researchers selected for RNAs that could catalyze the addition of URacil to a ribose sugar. By round 11, the group discovered that there were ribozymes that were 50,000 times better at catalyzing the reaction than those in round 4. This showed molecular evolution.

What bacterium has begun to cause patients to geg infections from being in the ICU of hospitals? Why has this occured? The incidence of antibiotic resistance hsa risen so quickly that the World Health Organization has recently announced that world count soon enter .,... note- hundreds of fungi, bacteria, viruses and plants have become resistant to insecticides, antiviral drugs and more

- Staphylococcus aureas. They are resistant to the antibiotic vancomycin. This resistance increased greatly the more vancomycin was used. S. aureus cells are actually resistant to multiple antibiotics- multidug resistance. -a post antibiotic era

sperm penetration gives rise to 2 other axes. at the grey cresent, the cytoplasm shifts up. What causes this shift? What does this shift dertermine? THe belly is called _____ and the top or the back is called _____. THe grey cresent becomes the ____ side. What other axes is determined?what else is determined by the site of sperm penetration and that helps establish the previous axes?

- THe nucleus and centrioles of the sperm enter the egg and the centrosome begins to reorganize the cytoskelton using microtubules. THis causes the eggs cytoplasm to shift upward; the top and and the belly! -ventral;dorsal;dorsal -left and right! The sight of penetration is where the first plane of cell divsion is going to occur creating left and right. The clevage furrow will form here two make 2 cells

Who read Charles Darwins "On the origin of species" and proposed that for natural selection to occur there must be ___ _____? THere must also be ____ ____ otherwise there is nothing to select from.

- THomas Huxley;selective pressure- if theres a perfect environment natural selection cant occur

Explain how snakes lost their limbs.

- The fossil record shows that all ancesors of snakes had 4 legs. By looking at the patterns of gene expression in chick embryos they saw that that in areas where only the Hoxc6 gene was expressed, then a forelimb(arm ) forms, but when Hoxc 6 gene and Hoxcv 8 gene are expressed together, then ribs form. in a snake, Hoxc6 and hoxc8 gene are expressed together always so all they have are ribs and no forelimbs. This data suggest that a change in the regulation of where Hoxc8 gene is expressed led to the evolutipnary loss of forelimbs in snakes. also in some snakes, Hindlimb loss in snake can be due to faiulire to produce a signaling molecule encoded by the gene sonic hedgehog. defects of this gene or loss of the signal lead to disappearnce of limbs in other aninals as well

To explore the possibiilty of early formaldehyde synthesis, which then can prodiuce sugars and otehr molecules, a research group constructed... What was included in the model that was a source of energy? Why did they think this energy wouldve been present? Enrgy in photons weer able to create ____. How? The computer model included several reactions that produced free radicals. This showed that

- a computer model that included all possible reactions of Earths early atmosphere consisting of CO2, H20, N2, CO and H2. - sunlight! sunlight strikes Earth in form of packets of light energy called photons. This wouldve been present because although today Earth is protected by the ozone layer (upper atmosphere that absorbs most of the high energy photons in sunlight) , it is thought that ozone was NOT among the volcanic gases released as the molten planet cooled and so the ozone wouldnt have been in Earth early atmosphere. Based on this logic, researches infer that when chemical evolution was occuring, large quantities of high energy photons bombard the plant - free radicals: fragments that have unpaired electrons in their outermost shell and are very reactive ! recall that atoms in H2 and CO2 molecules have full valence shells and are very unreactive. However, energy in photons can breakl up molecules by knocking apart shared electrons resulting in free radicals! - large amounts of formaldehyde would have been produced! Thus the energy in sunlight could be converted to chemical enrgy by generating free radicals that spontaneoulsy formn new bond to form formaldehyde.

What is a master regulator?

- a gene or protein that can unleash a series of events that produce a specialized cell tytpe, tissue or body structure.

In evolutionary biology, an adaptation is... ADaptations increase or decrease fitness?

- a heritable trait that increases the fitness of an individual in a particular environment relative to individuals lacking the trait. -increase

What is a mediator? Explain the steps of intiation of trancription from chrmatin remodling to whn the RNA pol begins trancription.

- a large complex of proteins that helps connect actions of regulatory transciption factors and assembles in an organized fashion general transcription factors and RNA pol 11. 1. Chromatin remodeling- Transcriptional activators bind to DNA (enhancers or PPEs)and recruit chromatin remodeling complexes(knock off histones and slide nucleosomes) which decondenses the chromatin. 2. exposure of promoter and regulatory sequences- a region of DNA is exposed including the core promoter, promoter-proximal element, and enhancers 3. Assembly of proteins- other transcriptional activators then bind to the newly exposed enhancer sand promoter proximal element. the DNA is looped by DNA bending protein to allow activators bound to DNA to come together at the mediator(the mediator is between the loop in order to bond to all the activators which are on different enhancers and promoter-proximal elements) 4. Proteins contact the core promoter- general transcription factors and RNA pol II assemble on the mediator complex. THR RNA pol II binds tot he core promoter and trancrition begins

The thoery of evolution by natural selection is a scientific revolution. What does this mean? Give some other examples.

- a scientific revolution overturns an exiasitn idea aboiut how nature works and replaces it with something new. Ex: Copernicus theory of the SUn being at the center, Newtons law of motion and theory of graviation, the germ theory of diseases, etc

What the TATA box? What is TATA-binding protein( TBP)? Does the binding of TBP to a TATA box guarantee a gene will be transcribed?

- a short stretch of DNA that is a common sequence on core promoter sequences - once a core promoter with a TATA box has been exposed by chromatin remodeling, TBP binds as the first step to initiating transcription. -NO, many of other DNA sequences and proteins must work with RNA pol

What is genetic equivalence?

- all cells contain the same genes, just different genes are expressed

Why is a nucleur envelope advantageous?

- allows for control of gene expression because transcription and translation are separate! IN bacteria and archae transcription and translation occur together while in eukaryotes NRA transcripts are processed in the nucues and translated outside allowing alternative RNA splicing and other RNA processing OR maybe a slective pressure was that a double menbrane protects DNA more so than 1

Differentiation is a step by step process that is complete wehne cells...

- begin producing proteins that are specific to a particular cell type

How do biologists learn if cells are determined?

- biologist transplant them form one location to another within a developing embryo. If a cell has irreversibly commited ton becoming a certain type of cell, then moving it to a differnt location wher eit will receive new sifnals will nit change the cells path of differentiation.

Explain Darwin and Wallaces "Evolution by Natural Selection" What is "population thinking" What are some reasons the theory of evolution by natural selection was revolutionary?

- change through time -or evolution- occurs because traits vary among the individuals in a population and because individuals with certain traits leave more offspring. - the idea by Darwin that says that variation among individuals is important and connects all species? 1. It overturned the idea that species are static. Rather, species change over time and related by common ancestry 2. It replaced typological thinking with population thinking 3. It was scientific meaning it propose a mechanism that account for change over time and amde predictions that could be tested by observation and experimentation.

In the case of the finches , why was it difficult to pinpoint which genes are involved or which alleles are changing in frequency? What technique was used by Clifford Tabin to find which gene is responsible for the variation? How does Bmp4 expression effect beak shape and sieze? How did they test this idea? Lastlt, the frequincy of different alleles for what gene correlates with beak shape as well as human faciual structures?

- characteristics like body size and beak shape are polygenic meaning many genes affect the one trait. - they looked for variation in the patternof expression of cell-cell signals. Using situ hybridization showed that a cell cell singal gene called Bmp4 is expressed - lower Bmp4= small shallow beak and high Bmp4 expression=large deep beak; they increasrd Bmp4 expression in yound chikcnes and those chickens had large deep beaks -ALX1

WHat does the copy and paste transposons do? Why do these increse genome size ina spec ies over evolutionary time?

- copy and paste transposons are copied as another dsDNA and the copy is palced somewhere els ein the genome. THis gives 2 copies! This can change the DNA sequence as before and it adds nuceltpdes so it increases genome size. These transposons can also either be delterious(more often) or benefical - because it makes the genome larger. IF this happens all a species individuals then the genome increses

What other important role does gastrulation play? What does the blastopore become ? What does the oppopsite end of the gut become? WHat does the region where cells first move into the blsatopore define? MAjor body axes are also partially affectd by _____. Explain the above process.

- creating the body axes! -The anus- posterior -mouth- anterior -the dorsal or back side of the embryp -determination; Determination occurs through the action of regulatory molecules called cytoplsmic determinants or through iteractions between cells in a prodcess called induction. Determination results in differential gene expression between cells.

Retrotransposonas and copy and paste both increase ___ ___ since they increse genome size. What are teh 2 kinds of crossing over? WHich is setup by retrotransposons and copy and paste transposons? How does unequal crossing over occur?

- crossing over -equal and unequal corrsing pver; unequal crossing over - two homologous chromosomes misalign because there are two of teh same repeated sequences(may or may not be TE's) on each side of a gene. THey cross over and the reuslt is 1 chromosome with extra DNA and often genes and 1 that is lethal because it has less DNA and often genes

In summary, in organogenesis cells do what to form an organ? This whole process is controlled by ...

- divide, specialize, change shape, migrate, and some die. -signaling molecules and genetic regulatory cascades

an important source of new genes is the _____ of existing genes,a process that adds extra copies of the gene to the genomes. This process is called ___ ____. Gene duplication has most likely occured if..

- duplication; gene duplication -there are groups of genes that are similar in sequence and arrangement of exons and introns.

Explain Platos "typological thinking"

- every organism was an example of perfect essence or type created by God, and thta each type is unchanging. There may be differneces but jsut trivial deviations. books example- Genesis of the Bible

Alternative RNA splicing- we know that introns are spliced out in the nucleus as the primary transcript is being transcribed. mRNA results from splicesomes cutting introns out and splicing exons ogether. mRNA has the 5' cap added and the poly A tail added for protection. What concept accounts for alternative splicing? Splicing the same primary RNA transirpt differnt ways results in matuer mRNAS with different sequences and thus make differnt polypeptides. This is __ ____. So 1 gene codes for multiple polypeptides. HUman genome has 23000 genes but via RNA alt splicing can code for 100,000's of polypeptides!! How is alternative slicing controlled? This means that a gene is a nucleotide sequence that allows the prodction of .... EX: the Dscam gene in fruit flys produces a primary transcript that can be spliced to make 38,000 forms of mRNA

- exons may be treated as introns and intons may be treated as exons. Exons-expressed, introns -removed and non coding. -alternative splicing! -by proteins that binds to RNA in the nucleus and interact with spliceosomes to influence which sequences are cut out or left in. -one or more related RNAs or polypeptides

In addition the first eukaryotes were thought to have _____ to swim. What are the differences between the flagellum of eukaryotes and prokaryotes?

- flagellum -eukaryotic flagellum are made of microtubules and use dynein as the motor protein. THey move by undulating motion. Bacteria and archaea flagellum however are made of a protein called flagellin and it rotates.

What is considered to be one of the most dramatic -rearrangements of animal cells early in development? Later in development some animal cells break away from their original sites to form ____ _____ What is different about plant cells movement?

- gastrulation! In gastrulation, the mass of cells rearrange themselves into three layers-which then form the skin, gut, and other parts of the body\ -germ cells, pigment-containing cells, precursors of blood cells , and nerve cells -they cant move because they are in cell walls!. The directions that they divide and expand are regulated to form stems , leaves and roots

What is the reason genetically for evolutionary changes? For example, the increase in human body size must have resulted from...

- genetic changes cause evolutionary changes because genetic changes may cause a modification in regulatory signals and cascaded which both bring about development. -mutations that altered the signals, regulatory sequences in DNA, or transcription factors that are involved in the amount and timing of cell proliferation throughout the body

Puberty begins when the hypothalamus releases a hormone called ______. THis hormone stimulates the _____ to release... DO sex hormones particpate in negative feedback?

- gonadotropin releasing hormome(GnRH). This stimulate the anterior pituitary gland to release LH (leutenizing hormome)and FSH(follice stimulating hormome) which enter the bloodsrteam and stimulate testis to secrete testosteroen and stimulate ovaris to secrete estradoil. LH and FSH also stimulate gametogenesis. -yes

What did Galileo publish and in what language and why? He thought he could modernize Christianity in Catholic denominations while the Protestants would still be i Ptolemic ways giving Catholics an edge up What people were threatened and what people liked it? What did the Aristotliean philosophers do? At the time where was Galeleio working and why was this bad for him? What happened when Galileo met with the head of the HOly OFfuce of INquisition , a jesuit and Cardinal named Robert Bellormine? What did Galileo do once the old Pope died and the new Pope was a family friend?

- he published "The Stary Message" in 1610 in Italian so that all people that knew how to read could read it and so that scholars couldnt filter it - Aristotilian philosophers were threatened and the merchant class liked it -they wrote the Bishop and tattled!He was working for the Grand Duke of Tuscany where he was court philosopher in FLorence(capital of Tuscany). He even named a Jupiter star after the prince Madeche of Tuscany. Tuscany had a treaty iwth the Holy Papel States and had to send Galileo to the inquisition when they wrote to the Grand DUke - He was very angry and made Galileo sign a paper that said hed quit talking about it and so he signed but continued to find evidence the next 10 years. -he thought it would be okay to write about it.

How would LAmark explain how mosquitos become resistant to insecticides? SO he said individuals can evolve = not true How would Darwin/ natural selection explain the same thing? SO populations change/evolve over time!! individuals DO NOT evolve! Natural selection can act on individuals. Populatins evolve. Natural selection=main mechanism of evolution.

- he would say that the insecticide would be sprayed causing the environmental change. AND then the mosquitoes would have a "felt need" and that they would decide to start making more of a specific enzyme to break the insecticide -"principle of use and disuse" So he says that individuals can evolve. These mosquitos genuoles would say "make this enzyme: which would be passed to offspring and the second gen would inherit that trait and would be even more resistant than the parents because they too would change in rsponse to the insecticide. - even before the insecticide is sprayed soms mosquitos present have an allele for resistance(genetic variation). THen insecticide is sprayed (environment change) and the non resistant ones die and the few with resistance live . SO generation 2 will be more resistant as a whole because there was differential reproductive success in the 1st feneration. Insecticide caused NON random death. IF its sprayed more the 3rd generation will then have even more resitant mosquitos . The majority of the population would be resistant and a few would have mutations mkaking them unresistant.

WHat enzyme adds acetyl groups to the positvely charged lysine residues in histones? Acetylation of histnoes usually reults in ... acetylation= decrease packing deracetylation=increase packing which decreases transcription

- histone acetyltransferases(HATs); decondensed chromatin, a state assocaited with active transcription. This is becvause the added acetyl groups neautralize the positive charge on lysine residues adn this loosens the close assoication of the histones that make uo the core of the nucloeomse woth the negative charged DNA. THE addition of acetyl groups also creaes a binding site for other proteins that help opne hte chromain

What enzyme remove acetyl groups? SOO acetylkation= more transcription removing aetly groups= less trancription

- histone dacetylases(HDACs). When HDAC s renove acetyl groups from histones, this causes chroamtin to condense, a stae associaed with no transcription

What is another way chromatin condensation is controlled and hence helps regulate transcription? What has been proposed to account of these effects??

- histone modification!! there are many enzymes that add different chemical groups to specific amino acids of histone proteins. THings that may be added include acetly groups (COCH3), methyl groups, phosphate groups or short polypeptide chains. ADdition of groups to histones promotes condensed or decondensed chromatin depending in the set of modifications made to particulat histones. - the existence of a histone code!!The histone code hypothesis postulates taht particular combos of histone modifications set the state of chromartin coindensation for a aprticular gene.

Humans are microlecithas which means... What does macrolecithal mean? We study embryos of amphibians because their eggs are ____.

- human eggs have no yoke! -lots of yoke! -mesolecithal!

Explain how unequal crossing over occurs.

- if a gene lies between two of the same type of transposable elements or any DNA repeats, a crossover between misaligned copies of sequence repeats may occur. THis results in 2 normal chromosomes which come from the non sister chromatids that did not cross over. It will also result in one of the chromatids that crossed over having a deletion of the DNA segment between the sequence repeats and the homologous chromatid having a duplication of the segment/gene. The genes in this duplicated chromosomes will arrange in tandem/one after another like STR's. Note-crossing over occurs in M1. a homologous pair is made of two homologs which are all the same chromosomes just perhaps with different genes. Recall that a homolog is made of 2 chromatids. SO the 4 daughter cells will get one of the chromatids.

What is evolutionary developmental biology or ev-devo?

- it focuses on understanding how changes in developmentally important genes have led to the evolution of new forms

Why didnt Copernicuss book become very popular? Who was Galileo Galilie? What did he invent and why was he able to quit teaching after that? What did Galileo then spend his time doing? WHat key discoveries did he find with his telescope?

- it was huge and in Latin which only scholars and priests could read - a mathematician and philospher like Copernicus. He taught at Radua Italy but hated teaching. Rather he liked the solar system.; he heard about a Holland man that discovered you culd put lenses in series and magnify things so Galileo put them ina tube to make a telescope! THis made him rich and no longer have to teach -studied the sky! 1. a lunar(moon) topography meaning he looked at edge of moon and saw that it was not a perfect sphere like Aristotle said, rather there were hills and etc 2. he saw sun spots! The moon was NOT perfect. and the sun spots moved night to night 3. He discovered Jupiters moons! He looked one noght and saw 4 "fixed stars" on the stellar phase and the next night they had moved. This showed that Jupiter as not fixed, those 4 things were centered around Jupiter and not Earth. ("Earth not special") 4. THe phases of Venus! He saw that the size and shape changes. At the time people thought only the moon had phases. The Ptolemic model was unable to explain phases of Venus even with an epicycle which would make Venus appear large when close and small when far. This doesnt explain phases . A heliocentric.copernican model could explain phases though since sun was in the middle

Whats a common transposable elemnt? note-these are found in humans and animals and like retrovruses they insert into and exise from the genome leading biologiusts to beleive that LINE;s come from retroviruses.

- long interspersed nucleur elements! (LINE's)

In plants, where are stem cells located? IN animals stem cells are...

- meristems; meristems are in embryos and adults and produce the stems, roots, leaves, and flowers - in many locations in the body. STem cells proliferate to replace skin, blood, and gut cells that die and repair wounds

What kind of research Catalogs all the genes present in a complex cummunity of prokaryotes? this kind of research is able to learn the genes present, the composition of species and their abundance in communities of prokaryotes. IN recent metagenomics studies, reseachers have studied the diverusty of microbes that...

- metagenomic or environmental sequencing -live in the enviuronemnts in and on humans. THey analyzed 14 trillion bases of sequneces obtained from bacterial communitie at different sitse across healthy adults. They found variation in abundance and types of species at a given site in different people and saw difference in compositionn of bacertial communities in differient istes on the same person

After teh production of the 8 blastomere embryo, a ____ is formed. Explain how division occurs to get a morula from an 8 blastomere embryo

- morula!! The bottom 4 cells of the embryo are full of yolk and thud cell division and S phase is very slow in these, so the next division is only in the top 4. The blastomers from now on go throihg mitosis and cytokinesis and S phase independently. BEcause of the fact that the bottom blastomeres will be slower, the embryo will have lots of small cells at the top and the cells will get largertoward the vegetal side

What caused multicellularity probably? KEY about multicellularity- all cells do not express the same genes

- mutations that caused cells to stick together. Selection pressures then would act on these larger coloniakl organisms allowing them to evolve and siversify. Eventuall cells became specialized for different functins.

PROOF of evolution by natural selection What bacterium causes tuberculosis or TB? TB infects the ___ and causes.. What 2 reasons made TB to recede in early 1900s? In the 80s, TB has declared a global health emergency because strains of M. Tuberculosis were resistant to antibiotics that once were effective. Explain the young mans from Baltimore's story that helped physicians figure out the reason for resistance

- mycobacterium tuberculosis - lungs; fever, coughing, sweats , death 1. advances in NS made people better able to fight off M tuberculosis infections 2. THe development of antibiotics allowed physicians to stop infections - A man ccamein with a TB infefction. He was given antibiotics s 6 weeks and had doses od\f the antibiotic rifampin. Ten moths after therapy started, bacterial cultures from the patients ches fluid indicatd no more M. tuberculosis cells and he was normal. BUT two months after the TB tests proved normal, he was readmitted. Despite being treate with many anioiotics including rifampin, he died of respirapty failure. SAmples of fluid from his lungs showd that M tuberculois was again grwing and complety resistant to rifampin.

What was the selection event that occured during the wet season and how did this effect the population? How do they know they disappeared finches died of starvation? This event allowed for what kind of experiment? On average, survivors tended to have ___ compared to before the drought? Why was this adaptive(increase fitness)? These results showed that ____ ______ led to an increase in average beak depth in the population. What happened when breeding resumed? NOTe- in just one generation, natural selection led to measurable change in the heritbL charcteristi s of the population. Deep and large beaks were adaptations for cracking fruits and seds!!

- on the island of Daphne Major there was only 24 mm of rain when normally there is 130 mm. During the drought few plants could make seeds and 84% of the medium groundbirds disappeared -they found 38 dead very thin birds and none of the missing finches were spotted anywhere lese and did not return - a natural experiment! Instead of comparing groups created by direct manipulation under controlled conditions, natural experiment sallow researchers to compare treatment groups created by unplanned change in conditions. -deeper beaks!; at peak of drough most seeds were gone and touhg fruits of a plant was all that was available for food. These fruits are very difficult to track and normally not eaten unless seds are unavailable. INdividuals with large and deep beaks were better able to crack the fruits to survive. -natural selection ; the offspring had beaks 1/2 mm deeper on average than those in the population that existed before the drought.

miRNA is able to play a big role in siolemncing / effecting gene expression becasue...

- one type of miRNA can regulate many different mRNAs and one mRNA can be targeted by many different miRNAS.

The following are meant to debunk common myths about natural selection and adaptation. Explain what it means to say that Natural Selection does NOT change individuals. Explain why Natural Selection is NOT "Lamarckian INheritance" What is Acclimization and explain why it isnt considered adaptation! What is acclimization called when this poricess occurs in organisms in a lab?

- only populations change! Natural selection acts on individuals but evolutionary change occurs in the populations! Ex- during drought the pop of finches beaks became deeper. - Lamark said that individuals change in response to challenges of the environment and that the changed traits are then passed to the offspring. BUT, this is wrong. Darwin found that individuals dont change when they are selected. Instead they simply produce more or fewer offspring in response to environmental changes and when this happens alleles found inc certain selected individuals become more or less frequent in the population. There is no mechanism that lets natural selection edit the nucleotide sequence of an allele in an individual. An individuals heritable characteristscs dont change when natual selection occurs - Acclimatization is a change in an individuals phenotype that occurs in response to a change in natural environment conditions. For example- when a foreign hiker travels Mount everest in Asia, he or she would experience oxygen deprivation due to the low partial pressure of oxygen at high elevation. In response, their body would produce more of the oxygen-carrying pigment hemoglobin. The body doesnt normally do this because thick blood can cause chronic moutnain sickness. TH increase in RBCs and Hb is an example of acclimatization. If in a lab it would be aclled acclimation. Phenotypic changes due to acclimatization are not passed on to offspring because no alleles have changed. This means acclimatization does not cause evolution. In contrast, populations that have lived in the region for along time are adapted to this environment through genetic change. Among natives of the regions, an allele tha increases the ability of Hb to hold Oxygen has increased in frequency. That same allele is rare or nonexistent in populations not at high elevation

Explain Aristotles "Scale of Nature" Explain Jean Lamarcks "Idea of Evolution as Change through Time" *Lamarck eventually abandoned the :progressive life" view

- organisms could be ordered into a linear scheme/ladder calld the greater chain of being or scale of nature based on complexity and size. Humans were at the top with other vertebrates right below and lower plants were at the bottom. The idea of "higher" and "lower " species is still around today. - he made the first formal theory of evolution- that species are changing not static. His pattern component was based on Aristotles scale of Nature however. He said tha simple organisms origante at hte bottom of the scale by spontaneous generation and evolve by moving up teh scale over time. so evolution is always progressive and produces "better" species. Lamarck also tha species change through time via the inheritance of acquired charactes. This idea is that as an individual develops, its phenotype changes in response to challanges by the environment and these phenotypic ahnges are passed down. Ex- giraffees devlop long necks when they stretch and this is passed down

What were the first living things? WHy isnt the world an RNA world today? ___ +_____ = monolayer membrane ___ +____ + ____ + ____= phosphplipid bilayer What are liposomes? What are proteinoids? Are liposomes or proteinoids more similar to actual biological membranes?

- protobionts: had RNA based genetic systems - RNA is ss and so unstable adn easily degraded. DNA is ds and very stable. Fossil DN A of neanderthals from 30,000 years has even survived. DNA is better for faithful genetic replication. note- RNA is still needed for protein and DNA synthesis (primers) - lipids + H2O -lipids+ H2O+ protein(stabilize)+ agitation - membrane with more lipids relative to protein - membrane with more protein relative to lipid - proteinoids have permeability characteristics similar. they store charge and let solutes pass

Explain the experiment done to prove that chromatin modifications can be inherited. These findings imply that a mothers nutritional status during pregnancy and nursing is responsible for the types of chromatin modifications in her offsring!!!

- researches knew tha rats born to protein malnourished motehrs during pregnancy wer emor likely to develop diabetes. One gene associated with diabetes is the Hnf4a gene which codes for a regulaor gene involved in glucose uptake, Rats born to potein deprived mothers often develops diabtes despite havbing healthy diets trhroughout their life after being born. Researches had a control group of pregnant mothers who had a healthy diet and a treatment group that had a low protein diet. The researchers then measured the types of histone modification found at a regulatrory region of the Hnf4a gene. A regulatory region is a section o f DNA, like operatiors oin bacteria, that controls the activt of a gene. The results showed that hsitone modificstions that lead to condensed chromatin were much higher in rats born to maln ourished mothers. And that histone modifications associated with decondensed chromatin were much less in the same rat.s IN addition, the transcription of Hnf4a , an important gene that regulated glucose uptake, was much lower in the treatment group than the control group.

Some transposable elements behave like what kind of virus?

- retroviruses! however , rather than leabing th ehost cekk like retrovuruses, the copy themselves and insert the copies into new loctrions. Because they are part of the genome, transposable elemtns are passed from mother to daughter cell and parents to offspring.

What class of hormones is especially importatn to development?

- sex hormomones

which eukaryote originally is thought to have a photosynthetic orgnallele?(confused bc it said protists firs engulfed a cyanobacterium so how) However, chloroplasts also are in 4 linegaes of protists. But in these, the chloroplasts is surrounded by ... What is secondary endosymbiosis?

- since all species in the Plantae have chloroplasts with two membranes, biologists infer that the orginal endosymbiosis occurred in these species ancestors and the ancestors gave rise to various algae and land plants. -more than 2 membranes- usually 4 - protisits engulfed other protists(euk) that already had chloroplasts, resulting in 4 membranes. Sometimes 3 membranes will result by loss of a membrane.

What is the yolk graident and what doesit do? This causes egg polarities! yolk polarity vs _____ which are parralel to each other and create the ___ and ___ poles IN addition, there are two hemispheres. ____ and ____

- since gravity pulls the yolk down it makes a yolk gradient and the yolk dispalces all the cytoplas,( protein, RNA , nucleus, organelles) up to the top. -all else! animal and vegatal -animal and vegetal

What was an alternativce hypothessis? If this hypothesis were true then mitochnodmnraul genes would have derive from nucleur e=fenes in ancestal euaryotes, however....

- that mirochondrau evolved within eukaryotic cells - researchers studied the mitochndorail gens and found that gene sequences of mitochonrai are similar to alpha-proteobacteria.

Gene families are very common in the human genome. Give an example of a gene family. ______ in duplicated regions can create new genes with new functions! More often, mutations lead to... What is a pseudogene? If mutations in the duplicated sequence alter the protein product so that it performs a benefical new function, then a new gene has been added to the genome. Together these processes that create new genes are called ___ ____ _____

- the B-globin gene family! they code for proteins that form part of hemoglobin. Each coding gene in the family serves a different function -mutations!; nonfunctional genes. For example,a mutations could produce a stop codon in the middle of an exon. -a member of a gene family that resembles a working gene but does not code for functinal product because of amutation like a stop codon - duplication and divergence. So there are repeating TE's , then unequal crossing over which causes duplication and then a new gene could be made via mutations

WHat is the top pole? THe bottom?

- the animal pole;vegetal

WHich cells turn into mesoderm?

- the cells that invaginate via the dorsal lip and enter the interior of the embryo

the cells of the morula get smaller and smaller and mre and more but the size of the embryo doesnt change since it has no mouth! What important developmental process ocurrs next? What is the embryo now called?

- the embryo develops a chamber called the blastocoel! It is now called a blastula and is the same size still and the cells are still pleuripotent.

Erasmus Darwin(charles grandad) = said " __ ____ ___ ____" WHo was Charles Darwins father? WHat did he want Charles to do? What did Charles do since he hated medical school? Charles Professor got him a job on the.. What did he do on this voyage( the ships goal and Darwins job)? Where did the ship stop on way abck that had a huge impact on Charles? WHen did Charles return? What did he do when he returned? Why was th eidea of new species so different? What did Charles do after his Dad died?

- the fact of evolution!! -a famous physician names Robert Darwin ; he wanted Charles to become a Dr. as well. He sent Charles to medical school in Scotland at age 16 and Charles hated it(remeber no anesthetics at time) -he left to become an Anglican clergymen and he got a degree in divinity at Cambridge -HMS Degal(a ship); this voyage went to south america to map the coast. Charles was basically the naturalist-> he collecte specimen - The Galapagos ISlands(volcanic and new) which ahd new species adn each island had their own. He collectd them and sent them bac to ENgland - in 1836; he sent specimen to experts who confirmed they were new species. ; At time ANglicans beleived all species were md ein Genesis so no new ones. ; he got all his money and didnt have to work. He "landed gentry"(wealthy born" and just did science and was a rock pigeon breeded! HE practiced artifical selection meaning he could pick and choose which pigeons mated to get specific traits/phenotypes in the offspring.

COntorl of translation!! What is global regulation of translation? When is this done? What protein plays a crtiical role inn global regulation of translation adn how? SO- the cell can control the availability of what 3 things to control the level of translation? NOTE- if a cell is infectd with a virus it also wont provide these three things because they dont want to make viral products.

- the shutting down of translation of most mRNAs in the cytoplasm; This is done when a cell is in stressful conditions such a slow oxygen because protein synthesis take slots of energy and supplies so it is stopped to store those things. - a protein kinase called mTor(kinase adds a phosphate group from an ATP toa differnt molecule). Under stressful conditions, mTor is inactivated and doesn't add phosphate to the target proteins it regulates such as translation initiation factors. Without added phosphates, translation initiation factors are inactive and mRNAs cant be translated. Once conditions improve, mTor activated again and translation resumes. 1.initiation factors 2.elomngation factors 3. release factors

a few years later what other selection event occured and how did it change the population? High reprodictive rates means that the birds with small beaks had higher _____... SO the characterisitcs of the population changed again!!

- they received TONS of rain! plant growth was active and finches fed on small soft seeds that were in abundance. At this time, finches with small, shallow beaks had very high reproduction rates - higher fitness than those with large deep beaks because they were better able to harvest the seeds.

What is commitment? Are there different "levels" of commitment? Once a cell is locked down to become a particular type of cell, it is said to be _____.

- this occurs when an embryonic cell becomes dedicated to follow a particular path of cell specialization; YES! intitally, ciommitment is weak and can easily be reversed. OVer time, a cell become smkre and more commite till it can no longer be reversed -determined!

RECALL- mitochondrau are organelles that make adenosine triphosphate uisng pyrivate as an electron donor and Oxygen as an electron acceptor. What is the endosymbiosis theory?

- this proposes that mitochondria originats when a bacterial cell was engulfed inside anothe cell 2 billon years ago.

What is the 1000 Genomes Project?

- this sequenced more than 1000 genomes of people selected from diverse populations spread across the planet. The goal was to assess the genetic similarities and differences among people in order to understand our evolution.

What is essential for evolution to occur?

- variation among individuals in a population

Does the lateral gene transfer also seem to have occured for chloroplast?

- yes! teh chloroplst genome is small compard to the genomes of living cyanobacterium. Most of the orgnial genes were lsot or transfered to the nucleus

In some cases there are unique types of nuclei Diplomandas have ____ nuclei that look identical and it is unknown how they interact Ciliates have a ____ ______ that is involved only in reproduction and a ____ ______ where trasncription occurs. Foraminifera, red algae and plasmodial slime molds some cells have ____ nucleo. NOte- distinctive nuclei is a synapomorphy(a characteristic present in an ancestral species and shared exclusively (in more or less modified form) by its evolutionary descendants) that can be used to recognize lineages as distinct monophyletic((of a group of organisms) descended from a common evolutionary ancestor or ancestral group, especially one not shared with any other group.) groups

-2! -diploid micronucleus; polyploid macronucleus -many

Amphibian eggs are ____ tones to increase survival!

-2! it camfogs the egg since amphiboncan eggs are laid in water the bottom is light and the top is dark.

The analysis of the human genome has shows that less than ____ % of the human genome consists of protein coding exons. ___ % is made of transposable elements. and introns( some regulatory sequences like promoters, silencers, enhancors, temrination sequences) make up ___ %. What % is centromers/telomeres?

-2!;45;25;8

CLeavage divisions forms multicell embryos. For example, after its first S phase and first Mitosis we would get an embryo called a __ ____ ____ after the first cleavage! The cleavage furrow quickly or slowly gets through the yoke? IN the case of a 2 blastomere embryo, the furrow is parallel to the animal vegetal poles. SO each blstomere gets the same cytoplasm. SO if we separate these 2 cells each would still become a regular frog just smaller. Each blastomere is _______

-2-blastomere embryo -slowly! because it is inert and dense! -totipotent! meaning they can devlop into any cell in the organisms

SAy that each of the 2 cells of the embryo then each undergo their own cleavege again. The result would be a ___ ____ ____. Would these cells still be totipotent?

-4 blastomere embryo! YES! because egg plarity hasnt beet messed up at this point meaning that that the furrow is parallel to the animal vegetal pole

_____ % of the human genome is made of transposable elements. DO prokaryotes have fewer or more?This has led to the hypothesis that bacteria and archaea...

-45;far less; have the means to removve transoposable elements are can prevent their insertion

After a 3rd cleavage, a __ _____ ____ reults. Are the cells of this embryo still totipotent?

-8 blastomere embryo! NO, becaiuse this 3rd cleaveage is not parralel to the poles. It is horizontal/perpendicular to the poles and is in the animal hemisphere, thus it messes with polarity. THis means 2 types of cells are created with respect to cytoplasm. The top 4 would have lots of protein and RNA and the bottom 4 would have mostly yolk. These cells rather are pleuripotent!

___ % of the human genome is transcribed. SOme of these trancriptis code for regulatory RNAs like microRNAs.What RNA has been recently discovered and biologists are trying to find out what it does? IF long noncoding RNA play roles in regulating genome structure and expression then perhaps instead of coding for proteins , most genes produce regulatory RNAs that are never translated into proteins and play a role as RNA like rRNA, miRNA, snRNA, etc.

-90% - long nocoding RNA!

Enhancers occur in ___ eukaryotes. What are som ekey characterisitics of enhancers?

-ALL!! 1. enhancers can be more than 100,000 base pairs away from the promoter. THey can be located in introns or in untranscribed sequences(UTRs -give stability in translation) on wither the 5' or 3; side of teh gene or even wihtin the gene. 2. Like promoter proximal elements, tehre are many types of enhancers 3. most genes have more than one enhancer 4. enhancers have different bonding sites for more than one type of regulatry protein 5. Enhancers can work even if researchers flip their normal 5'->3' orientation or move them to a new location near the gene

What is the complete reaction that forms formaldehyde? NOTE- each side is equal in ernrgy because sun light is high energy and CH2O and H2O require high energy to be formed

-CO2 + 2H2 + sunlight-> CH2O + H2O

The age of ___ caused this to start to change in year 1600. Occured in the years 1200-1600. What was happening specifically that showed issues with the geocentric model?

-Exploration -using stars to navigate! people in greath authority often had to change the calender because it didnt work. 1- The Julian Calender by JUlius Caesar 2. Gregorian Calender by gregory the Pope

What is a major issue with the prebiotic soup model? If the prebiotic soup model gave rise to monomers how would polymers have come about?

-It only accounts for monomers. precurosor molecules would become diluted when they enter the ocean and without a means of localization, formaldehydye and HCN wouldnt meet ot make other molecules 1. wave splash onto warm coastlines! the early ocean was warm and full of organic monomers. THe land also wouldve been warm because of the UV's. THe ocean wouldve been splashed unto coastlines and the water would evaporate leaving increased concentration of organic monomers which would react together to give polymers. The polymers would then be washed back into ocean 2. Tidal basin evaporation! as the tide comes in the basins would fill with water. WHen the tide went out water would evaporate adn basically thr concentration of monomers would increse same as before to give polymers which would get pulled back in ocean. in both the ocean-repositorys.

Who did CHarles show his essay to? IN 1858 who wrote Charles and what did the letter say? When did Charle finally publish his ideas and what was the book? WHat was in the book? The book brought about the ..

-Lyell; Alred WAllace wrote proposing natural selection. Lyell showed the Royal Academy Charles and Wallaces ideas -in 1858 in the book"On the ORigin of Species by Means of Natural Selection" 1. evidence of evolution 2. explained natural selection as the process -Evolution revolution

Explain what it means to say that natural selection is NOT goal orientated.

-Mutations occur by chance! Mutations are the source of new alles but mutations occur by change and are random without rspect to fitness- they dont occur to solve problems . For example, the mutation that created the mutant allele that let the mt everst natives carry Hb better occured randomly, due to erroes in DNA synthesis, and jsut happend to be advantageous when the environment changed. There is no mechanisms that enables the environment to direct mistakes DNA pol makes when copying genes - Evolution is not progressive: organisms do not get better over time. yes it is true that groups tha appear later in the fossilr ecord are often more complicatd than closely related earlier groups BUT there is nothing absolute about this tendency. IN some cases, complex traits are lost as a result of evolution by natural selection. For example- whales losing limbs - There is no such thing as a higher ow lower organism! UNder Aristotle and Lamark, organisms should evolve to higher and higher levels of nature. BUT evolution by natural selection show sthat tehre is no such thing as higher or lower organisms.

Aristotles 2 spere universe become the _____ model of the universe. This was introduced by ___ who was from ____ in 200 AD. THe model was a geocentric one meaning that... What were the "concentric crystalline spheres"? What was the fermament position? The Ptolemic model became part of ____ theology.

-Ptolemic -Ptolemy;Alexandria (current Egypt) -Earth is in the center of many positions - the spheres around Earth that were transparent and the planets were lights attached to the spheres that moved around Earth and changed position each night. -the outermost sphere where fixed stars attached. -Christian

What changes in a cell commit it to a particular pathway development?

-Signals in the embryo induce cells in its area to produce regulatory transcription factors. In turn, these transcription factors alter patterns of chromatin condensation in ways that control which genes are expressed by enhancers or which are silenced.

Who made the Ptolemic model part of Christianity? He lived in _____ AD HE is known as the ____ _____ by Catholics and as the ___ ____ by historians because he put what two things together? Explain how he "christianized" greek knowledge. What was the empirir? He said that different ranks of ___ moved the different spheres that hold the planets around earth?

-St. Thomas Aquinas! -1200 -Angelic Dr; Great SYnthesizer. He put gree knowledge about nature and Christian doctrine together - he said that humans are at the center of Gods creation;heaven where God resides in the stellar spere -angels! the lowest rank=angels=moves the earths moon. next=archangels=move mercury. next= cheribs seriphs, princes, throne angels with highest rank=move outermost sphere(fermanant)

Chemical evolution remained an untested hypothesis for many years. IN 1953 who tested the prebioitic soup model?

-Stanley Miller

What model provides an explanation to how the molecules could actually have been localized? ie- it accounts for monomers and polymers What is the main idea of the surface metabolism model? What would be needed for polymers to form?

-The surface metabolism model! - reactants are attracted to a layer of reactive and negatviely charged minerals in the walls of seep sea vents. Dissolved gases are + and attracted and concentrated at the vents. -a catalyst! provides appropraite chemical environkent for eactants to react but doesnt provide enregy or change spontaneity

Natural Slection does not Lead to Perfection! 1. Traits are not always adaptive: give a few examples of this. 2. Fitness Trade off exist: What is a fitness trade off? 3. Fitness tradeoffs are considerd to constraint adaptations. . What are three other types of constraints that can effect adpatations?

-Vestigal traits such as the human coccyx(tailbone) do not increase the fitness of individuals with those traits. Teh structures arent adaptive they just exist because they were present in ancestral populations.Nonadptive tratis can also involve evolutionary changes in DNA sequences. Silent mutations in DNA sequences can be considered trait that isnt adpative because it doesnt cahnge the phenotype and thus cant be acted on by natural selection. - it is a compromise between two traits that cannot be optimized at the same time. For example , in finches there is a trade off between bright colors to attract mates and cryptic coloration to hide from predators. Tradeoffs often occur because of energetic constraints ie resources ar elimited. BEcause selection acts on many traits at once, evefry adpatation is a compromise 1. traits are genetically constrained! genetic correlations may constraint certain traits. Genetic correlations occur because of pleitropy in which a single gene effects many traits. For example, selection on a gene for one trait( increased beak depth) casued a correlated though not adaptive increase in another trait(beak width). This is why their are no finches with long and thin beaks which would be good for opening fruits. Lack of genetic variation is also a caise of genetic constraints. Exmple-humans lack the gene to regrow limbs like salamanders 2.Traits are historically constrained! All traits evolve from previous traits. Example- the ear bones of humans derived from bones of the jaw. Biologists interpret the bones as adaptations that imporove hearing. But they arent perfect. SOme otehr vertebrates have more efficent hearing canals but human ears are a good solution given a historical constraint 3. Traits are environmentally conmstrained! Natural selections occurs int he context of the changing environment. THsu,a beak shape that isn adaptive one season may not be adaptive the nexrt. There is no certain trati that is opitmal for ALL environments. IN addition, some environmental evetns are caraastophic adn organisms are wiped out regaedless of what adaptations they have. These events like volcanos can cause a change in the avergae traits of a population that are RANDOM with brespoect to fitness

Who is Nicholas Copernicus? What did he propose? Did this idea still have to use epicycles? What did he publish this in ? HE finished it in 1533 but published in 1543. Why?

-a Polish mathemetician/philospher and Roman Catholic. -the Heliocentric model! Said that earth is in the 3rd position rather than the sun and that rather the sun is in the middle! -yes because they thought orbitals were circular instead of elliptical -De Revolutionibus(comparing revolution of celestial orbs); the ROman and Spanish inquisition

What hypothesis explains the difference between genome size and organisms complexity?

-alternative splicing! Exons of a particular gene can be spliced in different ways to make different mature mRNAS and thus a single eukaryotic gene can code for multiple transcripts and multiple proteins. SO alternative splicing makes it possible for small number of genes to produce a much larger set of proteins.

IN amphibians the sperm must fertilize the egg in the ___ hemisphere!

-animal

The animal pole gives rise to the _____ "front of organism" THe vegetal pole gives rise to the _____ "back of " What lines the animal hemisphere/top?

-anterior -posterior -melanin to make it dark at th etop! its right under the PM

Programmed cell death is anothr important part of development in animals and plants. IN animals, what is it called? Give a few examples of why apoptosis is important? What was imntitally used to study apoptosis?

-apoptosis 1.Cells that are present between toes must die to form separate toes otherwise we owuld have webbed feet. 2. AT least half of embryonic nerve cells are destroyed by apoptosis to function correctly. - Caenorhabditis- worm

Most of the genes found in one species are or are not shard by many others? ONly what sort of genes are similar across all prokaryotes?

-are NOT! -genes involved in DNA replication, trancriptiom and translation

a few _____ are multicellular but mostly multicelljular species are members of the ___

-bacteria, Eukarya

The yolk is on the ______ and close to the ____ pole because it is...

-bottom ;vegetal; it is nutritous dense and sinks, it is also inert-unreactive

gastrulation is ____ ___. The embro is then called a ____.

-cell migrations; gastrula

Testosterone and estradiol bind to receptors within the cytoplasm or nucleus of traget cells. THe resulting hormone-receptor complexes bind to DNA and trigger...

-changes in gene expression

The notochord is unique to what group of animals? How does the notochord differ in some vertebrates vs other vertebrates? The notochord is also called the ___ ____ because...

-chordates! this is all vertebrates including humans - in some species of chordates the notocord is long lasting and functions as internal skeleton rod-it stiffen the body to help swimming. IN humans chickens and frogs the notochord is transient meaning only in the embryo. AS organogenesis proceeds , many of the cells in the notochord undergo programmed cell death or apoptosis. - primary inducer! recall that the dorsal lip gave rise to the first mesodermal cells which then the first mass of mesoderms become the notochord! the notochord is called the primary inducer not because it releases the first inducers( that was domne by the dorsal lip) rather, it is releases the most important inducers

Chloroplasts are thought to have origniated from ____- because they contail multiple memnbranes and photsysems I and II like the sam eabcteria. AN extenstion of the endosymbiotic theory says that the eukaryotic chloroplasts originated when ... Once isnide the protists the photosynthetic bacterium would... note - ALL photosynthetic protists have chlorplasts

-cyanobacterium -a protist engulfed a cyanobacteriujm - provide the host eukaryot with oxygen and glucoe and the host would offer protection adn light

The nuclei of these 2 different inds of cells become different because the cytoplasms are differnt and have different chemicals that were part of egg polarity. These chemicals of the cytoplasm are now called ___ _____. What are these? therefore, gene expression is regulated by ____ _____.

-cytoplasmic determinants!: they are chemicals that infuence nuclei by influencing which genes are turned on and which are turned off. THis means they affect which genes are transcribed and then produce proteins. The proteins that each cell makes is different! ie- blood cells make different proteins than hair cells -cytoplsmic determinants

Differentiation is caused by ___ ____ ___. The differential gene expression is caused by ....

-differential gene expression - signals that tell cells where they are in time and space, triggering the deployment of a complex cascade of transcription factors.

Some hypothesize that an amoebe like eukaryotes englufed a bacterium and failed to ... Howeve, origna protists ALL had ____ when they first evolved. A new hypthesis is that...

-digest it in it lysosome -mitochondria - the first eukaryotes formed at the same time as the first mitochondria because endosymbiosis occurred between an archaeal host and a bacterium(2 prok)

mutations in miRNAs genes are associated with many _____ RNA interference can be triggered by two other types of small RNA called... The origins of the 3 types of small RNAs involved in RNA interference are all ____ but all work similarly to silence gene expression through RISAC or RISC like complexes. Some piRNAs function in the nucleus to... RNA interference can be used by researchers to...

-diseases 1.short interfering RNA (siRNAs) 2. PIWI interacting RNAs (piRNAs) -different!! -control chromatin condensation and regulate epigenetic inheritance - lower the expression of particlar genes

INvagination produces the ___ ____ which is where the grey cresent was(opposite sperm penetration and where cytoplasm shifted up early in development ) What is the job of the dorsal lip? IN your anser explain the importance of migration and how it furthers differentiation. The chemicals involved that help further differentiation is part of ____ _____. Embryonic indiction is when ..... IUt creates a ________ _______ embryo.

-dorsal lip! -it is the primary organizer of the embryo. It has proteins that causes cells to come down to it and makes them take ona new identity. Migration helps cells be exposed to new cells adn chemicals like peroteins which furthurs differentiation. -embryonic induction! CHemicals from the dorsal lip affect arriving cells from the animal pole . It creates a 3 layered embryo!!

Prokaryotic organismsm regulate gene expression to respomnd to changes in their ______. ____ eukaryotes regulate gene expression in response to the environment as well. multicellular Eukaryotes dont only respond the external environment. THey also respond to...

-environment -unicellular like yeast - changes in the organisms internal environment- specifically to signals from other cells.

enhancers are primarily in _____ Transcription begins when... Enhancers and activators are in ___ control.

-eukaryortes - when regulatory proteins called transcriptional activatorys or simply activators bind to enhancors -positive

What are induced pluripotent stem cells, or iPS cells? These are involved in ___ ____ therapy.

-fully determined and fully differentiated human (or other ) cells can be changed by adding and bringing about the expression of four genes for transcription factors that are normally active in embyoic cells. This induces these cells to de-differentiate back to an eanyl embryonic cell state. SO if an adult cell could be made embryonic then perhaps these cells could be induced back imrto differentiating to form specialized cells. IF so, cells needed to replace those destroyed in diseases like diabetes, parkinsons, or heart diease could be made from iPS cells generated by patients own cells. -stem cell

Once embryoinic induction results in 3 layers during gastrulation, the embryo is called a _____

-gastrula

What occurs in ambryonic development when cleavage nears completion and cell division slows what stage if developlemtn occurs?

-gastrulation! In gastrulation extensive and highly organized cell movements and changes in cell shape rearrarange the embryonic cells into a structure called the gastrula.

Both cytoplasmic determinants and induction work by regulating ___ ______. Most gene expression patterns are maintaned through "epigenetic" mechansism that control ____ ____.

-gene expression -chromatin condensation

Within a species, genes that are similiar to each other in structure and function are considerd to be part of the same ___ ____ and have arisen from a common ancestral sequence through gene duplication.

-gene family!

Aristotle was a ___ man who lived in the GOlden age in 440 bc who observed ____. What was his 2 sphere universe? What was the "intersphere"? The outersphere?

-greek; nature THe moon is the boundary 1. Sublunar spehere is beneath the moon 2. The superlunar sphere is above. - below the moon-locus off all that is tangible, chaotic-where humans are and humans are the source of the chaos. Earth is at the center of the intersphere - source of perfection and if there is movement it is oerfect circular movement.

Galileo was tried for ____ in 1633. Galileo denied having ever signed the disjunction the first time adn he refused to ___ until.. for the rest of his life..

-heresy -recant; the Pope told inquisiotors to show Galileo the torture room, after that he recanted by admitting heresy and takes back his statements.; He was on house arrest rest of life in Tuscany unitl he died

What are the DNA associated proteins in chromatin?

-histones!!

Natural selection acts on _____, because individuals experience... Only ____ evovles. Allele frequences change in ____, not in _____.

-individuals; differential reproductive success -populations - populations, not individuals

Bacterial species that live inmanuy different kinds of habitats and use many differnt moleculs as food have ______ genomes. Parasitic species that use a hosts machinery rather than making their own molecules have ____ genomes.

-large;small

A significant proportion of many prokaryotic genomes has been acquird from other often distnlty related species. THis is called ____ ____ ____

-lateral gene transfer

Secondary endosymbios is the largest ___ _____ ______.

-lateral gene transfer

What are the sex hormones in males and females? Both are ___ and classified as____ hormones because...

-males: testosterone -females: estradiol, comes from a ckass of hormones called estrogen -steroids; gonadal hormones because they are made in the gonads. Tesosterone is made in the testes and estradiol and otehr estrogens are made in the ovaries by cells that surround developing eggs to form a structure called a folicle.

WHat causes some somite to form? what cell fo they come fom? WHat structure do they formnear? Like the notochord , somites are transient(short lastin) BUT what important structures do somites eventually produce? Explain how they become different from one another. What factors contribute to embyronic indcution of somites? IN this way neighbors of cells determine that cells identity How do somites do this? Ex of cell movement. ____ cells are determinedddd(when become irreversibly set) by embrypnic induction in organogenesis. WHJat cells are not? What is "applied development"? What causes different genes to be turned on or off in eukaryotes ?

-mesoderm! They form because of embryonic inducers from the notochord. ; the notochord -they give rise to muscle, the lower layer of the skin or the dermal layer, and give rise to part of the skeleton. THe somites form near the notochord but can detach and migrate, all being exposed to different chemicals, this is embryonic induction -1. th identity of the inducer 2. the concentration 3.the direction from which it arrives compared to others 4. the sequence relative to other tissues from other tissues. - throughout organogenesis, somite cells break away in groups that migrate to their final location in the developing embryo, inducers often change them along the way. Cell movements is very important. Ex- once in their new locations, skeletal precursor cells divide and start to make muscle specific proteins and eventually will differentiate into new cells. -ALL, not ectoderm or endoderm! - when you want to get a specific cell- start out with a stem cell and expose it to correct inducers, concentation, order and direction! cell starts off totipotent. AS its exposed to chemicals it gets more and mor specialised. Eventually, its very hard to de-differentiate -differential gene expression due to induction most often but can be cytoplasmic determinant

What processes are responsible for cell division? what initiates mitosis in cells? What helps regulate progression at each stage of the cell cycle? Cells also contorl their division by ...

-mitosis and cytokinesis -a regulatory protein complex called M phase-promotiong factor -checkpoints - social cntrols or signals from other cells

most LINES and transposable elements in the human genome no longer...

-move under their own power becasue they have mutated in a critical gene or regularory element. They litter the genome and are reerred to as molecular fossils.

As LINES or any transposable elements move from place to place (this is the books wording, make it sound like it moves ?) insertion into a new site creates a_____ that can have what effects?

-mutations! it can be negative, neutral or psotiive on fitness. This causes transpoable elemtns to shape teh structure, fucntion and evolution of genomes

The embryon inducers released by the notochord chsnge the gastrula into something called the _____. Organogenesis of the central nervous system or neurulation begins when... WHat are the cells involved then called? What helps determine which part of the ectroderm become the neural tube? Once the neural tube is in place, organogenesis proceeds along two axes- explain both of these Explain the divisions tha occur in the anterior portion.

-neurula -neural folds occur at the surface of the mebryo to form the nueural plate. Then the folds pinch together and fuse ectoderm over the folding to form the neural tube! The cells are called neuroectoderm - molecular signlaing from the notochord. 1. the anterior-posterior axis- The anterior portion of the neural tiube contributes to the brain and the posterior portion contributes to the spinal cord 2. The radial axis that runs from the center of the neural tube to the periphery. -In the anterior portion, the neural tube swells out in specific regions and then is folded back on itself to form different brain structures. aS this occurs, stem cells in the innermost layer of the neural tibe divide. In every cell division, one daughter cell remains a stem cell in the innermost layer and the other daughter cell migrates to the outermost layer of the neural tube where it differentiates. The type of cell it becomes depends on when during development the stem cell divides because the chemicals it could be exposed to is different. The resulting layer of different cells types are arranged along the radial axis of the neural tube like layers in an onion. These layers are crucial to the brain and spinal cord function.

What enzyme do cut and paste transposons use? What enzymes do all retrotransposons use? Both transposons and retrotransposons may work by a ___ __ ___ mechanism. This means that copy and paste transposons/retrotransposons can use what enzymes?

-only transpoases -rev. transcriptase and integrase -copy and paste -transposase, rev. transcriptase and integrase

In bacteria, genes that need to be regulated together are often clusterd together into a single _____ and trascribd into a single ____ In eukaryotes, co-regulated genes are not clustered together, instead... This kind of control is called ___ ____ Note- regulatory sequences are in ALL eukaryotic genes.

-operon/regulon;mRNA -each has the same regulatory DNA sequences that binds the same type of regulatory protein. So they have the same enhancers in the exact same places up or downstream of the gene. This way when activators become available from 2nd messengers by the presence of embryonic inducers all will be transcribed. ;coordinated control!

AFter gastrulation, what is the next stage? What is this process? What process is involved in organogenesis?

-organogenesis!; when cells divide, move, differentiate, and assemble imto tissues and organs using instructions in the genome and signals from other cells - embryonic induction: a process where chemicals from outside of a cell like other cells perhaps influence that cell. This is often done by receptors in signal transduction pathways. The receptors receive the 1st messenger signal which is passed to a cytosolic PM protein which activates the 2nd messenger and affects the cell

What is one maor way bologists beleie gene tranfer couldve occured? What have they documen ted to support this?

-plasmids! THey ahve documented the tranfer of plasmid bprne antiobitic resitacne gene between distantly relate bacteria.

THe cells of the morula are ____.

-pleuripotent! can become many cells but not all types.

What are general transcription factors? What is a common example?

-proteins that interact with the core promoter(where RNA pol begins transcription) and that are not restricted to particular genes or cell types. bint to many different ore promoters. So help with transcription, not regulation of it -TATA binding protein!! basal trancription factors

In modern day cells, without ribozymes what very importatn molecules couldnt be made? This suggests that the RNA world was before or after proteins? The evolution of protein enzymes would mark the end of the RNA world because.. Once protein enzymes existed what 3 characterists of lufe would be completed?

-proteins! -before! - proteins can catalyze reactions for life to become cellular! 1. Information: proteins and ribozymes were processing info stored in nucleic acids for the synthesis of more proteins 2. Replication: enzymes and maybe ribozymes were replicating the nucleic acids that stored the hereditary info 3. Evolution: random changes in the nucleic acids led to synthesis of different proteins . Selective advantages relsulted in the evolution new funtions

Pfrokaryotic genomes are frequenmtly ____ during evolution. Even closely related spcies show little similarity in gene order.

-rearrange

Just like in abcteria, the promoter in eukaryotes is a site in DNA where RNA pol binds to initiate transription. HOwever eularyotic promoters are more complex. They often contain 2 or 3 ____ ______ that serve as binding site for other proteins needed to start transcription. What exactly is a regulatory sequence? What is the core promotoer? What binds to the promoter first and attracts RNA pol? The promoter is always ____ of a gene so UTR's, exons and introns are all _____.

-regulatory sequences; any sequence of DNA or RNA that allows the bindingf of a protein to control the expression of a gene. - the specific sequence where RNA pol binds as opposed to the other sequences needed for regulation of trasncription.- basal trancription factors!! -upstream;downstream

Collectively, the proteins that bind to enhancers, silencers, and promoter proximal elements that are used to regulate gene expression are called _____ _____ _____. Sum up how different types of cells express different genes:

-regulatory transcription factors or transcription factors - it is becaue they have different transcription factors. The genes encoding transcription facotrs are expressed in response to signals that arrive from other cells during embryonic development. So if a signal reaches and early embryo cell that sys "become a muscle cell" the signal triggers a signal transduction pathway that leads to the production of transcription factors specifc to muscle cells. Because different tracnription facotrs bind to specific regulatory sequences, they turn on the production of muscle specific proteins. If no "become a msucle cell" signal ever arives then no muscle specific transxcription factors are produced and no muscle specific gene expression will take place. Differential gene expression results from the production or activation of specific transcription factors. Eukaryotic genes are turned on when transcription factors bind to enhancors and promoter proximal elements; the genes are turnd off when trasncriptin factors bind to silencers or when a particular transcription factors is not present or when chromatin is condensed

The team in Bartels lab trie to generate an RNA molecule that could catalyze template directed polymerization needed for RNA replication. This RNA would be called a RNA _____. THe team started with a ribozyme capable of joining two ribonucleotides together and generated what? Next, they incubated the mutants with free ribonucleotides and looked for ___ ____. Molecules that showed this activity were ____ and _____. Ater two weeks and 18 round of selection, the team isolated a ribozyme that added ____ nucleotides to an existing RNA strand. The population of RNAs from each round had varying characteristics that could be replicated adn passed on to the next generation of ribozymes. THe researchers were able to select the most efficient RNA as thw parents of teh next generation ton make the offpring better ribozymes. SInce the max product length made was 10% the ribozymes own length, this is not considered to be finding an RNA replicase

-replicase! -billions of copies with random mutattions introduced -replicase activity; isolated and copied;14

Chromatin must be decondensed to expose the promoter so RNA pol can bind to it. This means chromatin remodeling is the first step in gene expression. What experiment was done to prove that chromatin must decondense? These results siggesrted that in their normal or derfault state, eukaryotic genes are turned off!!!

-researchers used DNases which are enzymes that cut DNA. hypotheticallty, DNase works only if DNA is in a decondensed or opne configuation. Theybuised chicken blooc cell and theuyc ompared the chromatin of B clobulin genes and ovalbumin. On blood cells, the B globin gene is trancribed at high levels and the ovalbumin isnt at all. After trating the bloopd cells with Dnase the compared and saw that the B globuline gene DNA was cut much more the DNA odf the ovalbumin gene. This proved rhat chromatin of actively transcribed B globin gene was decondensed and tha chromatin of non transcribned ovalbumin was condensed. SO chromnatibn is decondensed in genes that are being trancribed.

Retrotransposons are similar to _____. Like retrovuruses they do ____. Example of a retrotransposon? It codes for what 2 things? Explain the steps of how a LINE copies itself The results of a retrotrasnosons are the same as of a ______ ___ ____

-retroviruses; reverse transcritptiomn. -a LINE; reverse transcriptase and integrase 1. LINE DNA is transcribed to LINE mRNA. 2. It leaves nucleus where its tranlated to produce the proteins rev. transcriptase and integrase 3. THe proteins and mRNA go back into the ucleus via NPCs 4. Rev. trasncripase used the mRNA to make dsDNA 5. integrase puts the dsDNA into a host chromosome -copy and paste- the nucletpdie sequence changs and the genome size increases

The most far back ancestral prokaryote lived in early oceans , had no cell wall and was anaerobic since ther earth had no free O2. It was also heterotrophic meaning gets food from outside sources by absorbibng Carbon adn etc. What selective pressure would have occured and the ancestral prokaryotes would have eventuall evolved into what 3kind of cells? Why would autotrophic prokaryotes increase?What did this cause? Which of the three engulfed one of the others?

-selective pressure: eventually the conditionsproviding Organic materials would cease and then the prokaryotes use up the organic amterial 1. THey could evolve into predadtors. THey could capture other organismsm by phagocytosis if no cell wall. 2. Photosynthetic prokaryote: Autotrophic! SOme evolved photosynthesis! CO2 +H2O +sunlight-> O2 + C6H12O6. THey would increse because sunlight and CO2 and H2O was not limiting. ;This caused a buildup of O2 in oceans which was eventiuallgy given off in the atmosphere. oxidizing of Eraly earths atmosphere, Oxygen was a pollutant to anaerobic proks. This O2 created a pressure and causes the 3rd type to come about 3. Aerobicxally respiring prokarytoe: would evolve in response to the O2 made by photosynthetic organisms. These are still heterotrophic but it can now combine O2 with other things. C6H12O6 +O2-> CO2 +H2O+ATP - the heterotrophic one that became a predator engulfd the eroically respiring prokaryote!

Eukaryotes also possess regulatory sequences that are similar in structure and have similar characterisitis with enhancers but work to inhibit transcription. These DNA sequences are called _____. The regulatory proteins that bind to silencers to shut down transcription are called_____. THis is calld ____ feedback

-silencers;repressors. -negative

How are cell cell interactoins involved in embryonic development?

-singaling molecules may diffuse in the watery environment that surrounds cells or may b epresent on the surface of other cells or bound to the extracellular matrix. In a developing embryo, some signals are received inside rh cells intacellular receptor. Others are received by receptors by receptors on the cell surface that trigger a ginal transduction pathway. As a result, transcription factors are activated, patterns of gene expresskon change and the embryonic developmkent cells activitr is alterd. In response to signaling molecueles, embryonc cerlls divide, differeentiate, move, chang shape,m and die.

Genome ___ and ____ vary even within species

-size and content

Most cells stop or continue to divide when they mature? What is different about stem cells? What about its division is important?

-stop! - stem cells are undifferentiated cells that never lose the potential to divide. ZWhen they divide theyb produce 2 daughter cells- 1 stem cell and 1 cell that differentiates into a specialized cell. This maintains the population of stem cells.

2 processes in gastrulation that occur are epiboly and invagination. Epiboly only involves the ____. Invagination is the ...

-surface! -interiror movement of blastomeres that creates a pouch!

who led the research done on finches nativce to the Galapagos islands? What were they investigating? What did they do to keep track of ____ finches on the Island of Daphne Major of teh Galapagos ? What and how do tehse finches eat? Beak size and shape adn body size are all ___ traits.

-the Grants - changes in beak size, beak shape, and body size - they caight, weighed and measured all the medium ground finches since th eisland is so small. THey marked each finch with a unique combination of colord leg bands. - by eating seeds, they crack them open -heritable so passed from parent to offspring

Is tehr an example today when a bacterium isnt broken down buy the cell that engulfs it? THe aerobic respirng cell detoxifed its own cytoplasm and the hosts and the host gave it protectin and NS. THis is _____ SO endosymbiosis gave rise to _____ cells. The engulfed cells we have talked about became ____ and are related to _____. What if a cell with a mitochondira had then phagocytised photosynthetic organisms?THis is ____ endosymbiosis WHat did chloroplasts evolve from?

-the Tb example -symbiosis! 2 organisms living together. Specifically, this is mutualism because both benefit. THis is evolutionary stable. They eventually go from independent to dependent -the first eukaryotic cells;mitochondria; alpha proteobacteria - This is plants! have mitochondrai and chloroplasts!; cereal -cyanobacterium

What are microfossils? What gave rise to them? Are Eukarya more closely relate to bacteria or archaea? Eukarya evolved from____.

-the earliet life forms-> prokaryotes 3.5 billion years ago;prtobionts -archaea -prokaryotes

What is the site opposite where sperm penetration occurs?

-the grey cresent!

WHo inhertied this idea from the Greeks? Who discovered "wandering stars"? What were the wandering stars actually? WHat are fiuxed stars?

-the romans! - the romans; they moved each night and were the planets; actual stars whose positinos were fixed each night relativ to each other like the big dipper

What is epigenetic inheritance?

-the term for any mechanism of inheritance that is due to something other than differences in DNA sequences!! changes in phenotype not due to inheritnce genes but rather due to the inheritance of packing pf chromatins Ex: If cells divide the patterns of DNA methyklation and histone acetlyation are passed on to the daighter cells. so, Muscle cells are different form liver cells not becaue gheyc ontai different genes byt bwcasue they haev imnherited different patterns of DNA methylation and histoen modifiactions.

THe proteins that remodel chromatin cant recognize specif DNA sequences themselves, rather they are recruited by ____ _____ How can an activator bind to DAN in the first place if chromatin is condensed?

-transcription activators- recall that they bond by the different shapes in major and minor grooves due to different sequences 1. some transcription activators bind to DNA that is associated with histones 2. DNA occasionally dissociates from the histone proteins in nucleosomes, exposing regulatory sequences to activators that represent in a certain cell type

Repeated sequences were once called "junk DNA" however now it is known that these sequences are derived from _____ _____. (discoverd by Barbara Mcclintock)

-transposable elements!- thse DNA segments can insert into new locations in a genome

A common way genes are duplicated is though the process ___ ___ ____ during meiosis. This often involves what kind of DNA sequences?

-unequal crossing over; repeated DNA seuqnces such as trasnposable elements

All bacteria and archae are singel celled. Are the furst eukaryotes thought to have been unicellular or multicellular? WHat structures were thought to be apart of the first eukaryotes?

-unicellular! -they were singled cell organisms with mitochondria, a nucleus, an endomembane system(PM, golgi, ER, lysoosme, peroxisome) and a cytoskeleton. THis is thought because ALL eukaryptes have these today. NO cell wall tho

Prokaryotic genomes have _____ coding sequences, have _____ space between genes , use ______ alot, and have few _____ ______. The bigger the genome the more or less genes?

-uninterrrupted; little, operons, regulatory sequences. more

A Distal Control ELement is a strech of DNA that can be ____ or ____ of the promoter. They are always very _____. Proximal Control ELements are always ____. PCE's are regulatory sequences that are.... SPecific genes have specific PCE's! what are the two kinds of DCE's? WHat binds to enhancers? To silencers?

-upstream or downstream!-far! -upstream; that are close to the promotor. There are regulatory proteins that binds to the regulatory sequence, in this case the Proximal element, which is a short stretch of DNA that is located upstream from the core promoter -1.enhancors: sequences that enhance transcription 2. Silencers: these inhibit transcription even if RNA pol adf basal transcription factors are present! - activators bond to enhancers and repressors bond to silencers. BOth are glycoproteins that are 2nd messengers that result from inducers

RNA replicated itself still ocurs today in some ____. How would a ssRNA be replicated?

-viruses! 1. using the oringial strand a complemtary copy is made. free ribonucleptides form H bonds to do so. The 3' hydroxyls and 5' phosphates are linked via condensation reactions to form the daighter molecule 2. a dsRNA results 3. It is then broekn apart by heatng or catalysis and they both can then serve as templates.

Millers results were inaccurate because the early atmosphere ACTYUALLY had what gases? IF used these in Millers apparatus get much less organic monomers but still some.

-volcanic gases like CO, CO2 ,H2O N2 and H2

Eukaryotic genomes sizes vary ______ but the number of genes vary ____.

-widely; little

Each chromosomes lies in its own region yes or nO?

-yes! portions of these chromosomes may fold out of its area ot reach sites of the nucleus wehre genes are activelry trsancribed and then fold back when trancription is finished

Explain the steps of how line transposable elements spread ( find put -is it moved or just becomes present in multiple places ?) sounds like it is then present i multiple locations

1. A LINE element exists in the genome 2. RNA pol transcribes the LINE producint LINE mRNA 3. LINE mRNA exits the nucleus and is translated 4. LINE mRNA and proteins(reverse transcriptase and integrase) enter nucleus 5. reverse transcriptase makes LINE cDNA from mRNA adn then makes cDNA ds. 6. Integrase cuts chromosomal DNA and inserts teh LINE cDNA 7. new copy of the LINE is integrated into a ew position in genome

Explain the steps in what happens once activators bonds to PCE's and DCE's(enhancers) Note- DCE's, PCE's and the transcription machinery are all present in eukaryotes

1. AFter the actvoators/specifc trasncription facotrs bond, a protein called a DNA bending protein loops the DNA and brings the regions of DNA close to the promoter 2.NExt, s trancriptionfactor protein called a mediator comes into play to form a tracnription machine- the activator proteins ar eattached at one end to the enhancors and to the mediator at the other end. THe mediator proteins are attached to the RNA pol and basal transcription factors. THis is a large machine and is why DNA must decondense/ be in euchromatin form to transcribe

SO the found results suggest the patient died because?

1. By chance, one or a few of the bacterial cells in the patient before the onset of drug therapy happend to have the rpoB allele with the C-> T mutation changing the RNA pol shape. In normla comndotions, the mutant form of RNA pol doesnt work as well as the normal form so it stayed at low frequency. Even while the overal popuylation grewenough to put the man in the hospital the first time 2. Therapy with rifampin began. In respomnse, the cells with normal RNA POl began to die. As a resultm the overall bacterial population declined enough for the mans symptoms to go away 3. Cells with the C-> T thta have the mutant pol continue to slowly increase after therapy ended. Eventually the population grew enough for te patients symotims to come bacl 4. Drug resistant M tuberculosis cells now were abundant and so the 2nd round of Rifampin failed.

What is some evidence of an endosymbiotic orginin of chloroplasts?

1. Chloroplasts are also multiple membranes and do fission and their own ribosomes 2. Chloroplasts have a circular DNA with 1 ori an dferw introns and with genes similar to the genes in species of cyanobacterium 3. the photosynthetic organelles in one group of protists, the glaucophyte algae, has an outer layer with the same peptidoglycan in the cell walls of cyanobacterium 4. There are examples today haev endosymbioti cyanobacterium living inside cells of protists or animals 5. The inner membrane is same as PM of cyanobacterium

What are the 6 levels of gene expression control in eukaryotes? explain in the order they occur

1. Chromatin remodling- in Eukaryotes, DNA is wrappe around proetins to create a chromatin. The stretch of DNA that has the promoter must be released from tight interactions with proteins for RNA pol to reach the promoter 2. Transcription 3. RNA processing- these are the steps required to produce a mature mRNA from a primary transcript. Recall introns are spliced out and exons splicd together. Different combos of exons are included in the mRNA- alternative RNA splicing 4.mRNA stability/longevity: mRNAs that remain in the cell a long time are ltranslated more and so their lifespanm is regulated 5. Translation 6. Post translational modification- folding, glycosaltion, activation, degradation

What are the two mechanisms involved in cell differentiation: Explain each. which is used often universally?

1. Cytoplasmic determinants: cytoplasmic determinants are regulatory molecules asymmetrically localized in the cytoplasm of a cell-often an egg- that become unequally distributed among daughter cells after cell division and then effect the activity of the genes. If a cytoplasmic determinant is segregated to one region of a cell, one of the daughter cells obtain it and the other will not. SO, the one with the determinant will then differentiate differently than the one that did not recieve the determinant. 2.Induction: This works through cell cell interaction. One of the daughter cells receives a signal that the other doestn. This causes each daughter cell to undergo different developments/differentiate into different cells. -induction. Cytoplasmic determinants are rarely used in mammals or plants.

Explain the steps of gastrulation in a frog embryo? What was used to follow cel movements in embryonic development of frogs in the 20's? Does the blastoporew or the dorsal lip become the food tube!?

1. Different regions of the frog bastula(look back at what a blastula is!!!) are specified by cytoplasmic determinants and signals that determine their fate during gastrulation. The blastula at this time contains a fluid filled interior space called the blastocoel 2. A gastrulation begins, an invagination(indention) forms on the outer surface a the cells change shape. IN frogs, this invagination starts out as a slit that forms a circular opening known as the blastopore dorsal lip( the dorsal lip is part of the blastopore! it is the dorsal border!) 3. SUrface cells continue to fold inward through the blastopore dorsal lip forming a tube that extends across the embryo. THe tube becomes the gut or digestive tract-the gut is specifically the archenteron. The blastocoel is displaced and disappears in this process. 4. The three embryonic germ layers-ectoderm,mesoderm, and endoderm- are formed as a result of the cells movement into and across the embryo, ready for organogenesis. - agar was soaked into a dye. The agar was then pressed against the surface of blastula stage embryos so that some blastomeres would become marked and the embryos cells could be tracked

Explain the 6 characterisitics of Lamark's mechanism oublished in 1809 the "Inheritance of Acquired Traits" Inhertiance of Acquired traits = wrong. It ws the first mechanism ough that was provided and suggested that organisms can change He lacked....

1. Environmental change from migration or just change 2. engenders a "felt need" in organisms 3. principle of use and disue-use some tissues more at certain times 4. Individuals change due to the principle of use and disuse 5. genuoles- particles cells of the body created and had the current status of the cells. THey were secreted into the bloodstream in animals or zylum of plants and collected at sex organs. THe genuoles then were used to make sex cekks so sex cells had info about the status of an organisms and would change over an organismsm lifetime. genuoles->sex cells-> next gen 6. inheritance of acquired taits! passed from parent to offspring. If the parent changed hair color or used braces to have straight teeth then that would go to child since that was the current status. -evidence!!

Explain generalized steps for cell differentation in the form of explaining how cells become muscle cells in your bicep. SO the fate of embryonic cells lies with what signals they are exposed to because those signals induce them.

1. Fertilization of the egg in your mother triggered cell divisions that results in an early embryo 2. Certain cells in the embryo began producing signals that triggered regulatory gene cascade that provide positional information for cells to tell them where to go. 3. Later in development, signals from cells in one particular rgion of the embryo induced the production of MyoD in neighboring cells. These MyoD producing cells than are determined by devlop into muscle and moved to regions of your arms 4. Later, these MYoD expressing cells begin to produce muscle-specific proteins and exhibit unique properties of muscle cells.

What "inspired" Darwin to reach the idea of natural selection?

1. He studied the diversity of plants and animals around the world and in England 2. He viewed his data from studying variation in the context of a changing Earth made popular by his geologist friend Charles Lyell 3. artifical selection- Dawrin crossbred pigeons and observed how characterisitics were passed to offspring, He could choose certain indivudlas with desirable traits to reproduce thus manipulaitng thie composotiion of the population 4. The book by Thomas Malthus "AN essay on the Principle of Population". Malthus studies made him conlcude that since more individuala are born than can survive, a "struggle for existence" occurs as people compete for food and other things. Malthus said the rich would win the fight once the time came when there wasnt enouhg resources

1. In 1615 (a year after 1st encounter with Galileo)what did Cardinal Bellormine do that discredited the church of the time? Note- Psalsm are poetry so Galileo interpreted it correctly 2.What occurred in 1992? 3.What are the two creation stories in Genesis (poetic style as well)?

1. He wrote a letter saying he knew the heliocentric model could be true 2. THe Pope admitted that the CHurch was wrong to Galileo (360 years later)! 3. a. older one as in written sooner i 950 bc- Ch 2 is the story of GOd in the Garden of Eden, oral tradition passed through Jewish theology b. older one as in is supposed to take place before- Ch 1. 7 days and 7 nights of creation added centuries later and written by a different author. A Babylonian creation myth altered to be Jewish . Alterd during Babylonian Exodus/exile a Levitc priest wrote the myth.

What are a few other examples of endosymbiosis? NOTE-there are 3 domains but there is lots of lateral gene transfer among them all. once , many prokaryotes shared most genes but now they all have different ones

1. Legumes and Rhizobium: Rhizobium is a soil bacterium that does N2 fixation menaing it uses N2 to ultimatlety give NO3- which is important for aa's. WE get our sources of fixed N to make aa's and N bases from eating legumes or things that ate them 2. reef coral animals and marine algae called dinoflagellate that does photosynthesis. Dinoflagelate are in the digestive tract of reef coral animals.WIthout dinoflagellate the coral animals cant make their exoskelton which is the reef which is important for fishies. 3.THere is a protist called myxotrica that lives in the gut of woodeating termites. The myxotrica have 4 flagellum for steering and cilia look alikes on their surface that is actually another bacteria called spirochaetas that are aerobically respiring and provude ATP for self and the mycotrixa. Micotrixa has another bacteria that can digest ceullulose , so it digest the wood that is in myxotrixa and in the termite

NOte- endosymbiotic relationships exist among protist (eukaryotes ) and bacteria today, often involving the bacteria alpha-proteobacteria. What structural observations about mitochondria support the endosymbiotic theory?

1. Mitochondria are similar in side to alpha-proteobacteria. 2. Mitochondria replicate by fission like bacterial cells. mitochondrial division happens independently of the cell division . 3. Mitochondria have double membranes because they were engulfed most likely 4. Mitochondria have their own genome which are circular like a bacterial chromosomes. THey code for their own proteins. have 1 ori and few introns . 5. Theyhave theirniwn ribosoems similar to those of abcteria 6. inner mem same as PM of alpha proteobacterium

WHy the theory of evolution is controversial. 3 reasons Give an example of a past argument that hasnt been learned from

1. Physchological- Equates humans to all organisms making them feel less special 2. Science claims the questino of where organisms come from but religions violate NOMA 3. George Santina said "THose who dont remember the past are doomed to repeat it" science and religion havent learned from their past arguments - The Copernican Revolution! sun is center not Earth

What can be done in post-translational control? Why is this considered a tradeoff in ways?

1. Protein activity may be changed by enzymes that add carbohydrate groups or cleave off aa's like proinsulin(tertiary structure) to insulin(quaternary since 2 chains) 2. folding must occur, chaperone proteins often needed 2. Proteins may be phosphorylated by protein kinases like mTor 3. Proteins may be targeted for destruction when enzymes add many copies of a small polypeptide called ubiquitin(named this because its common). Ubiquitons are molecular tags for destruction. Polyubiquitin are stronger signals! A macromolecular machine called a Proteasome !!! recognizes ubiquitin tags and cuts the proteins into small segments to recycle the aa's. 4. proteins may have sugars added or removed in the ER or golgi - its a waste of energy to do transcription, RNA processing and translation if the protein won't be used because those processes use lots of energy.

Explain the process of RNA intererenece through a small RNA called a microRNA(miRNA) note- only eukaryotes have miRNA not prokaryotes

1. RNA interference through miRNA begins when RNA pol transcribes the miRNA gene. THe transcript doubles back on itself to form hairpins. Hairpins form because sets of bases within the RNA are complementary. THere ar eloops where there is no H bonding 2. Hairpin-containing RNA is then bound to a RNA processing complex made of proteins. THe complex trims off the single stranded 5' and 3' ends 3. THe partially processed miRNA is exported to thy cytoplasm and is then bound by a differnt RNA processing complex that has an enzyme called dicer that cuts off the loop leaving a short (22 bas epairs) double-stranded RNA 4. THe double stranded miRNA precursor is unwound by helicase intro 2 separate strands 5. One strand is degraded ad the other is transferred to a group of proteins called teh RNA-induced silencing complex or RISC(because it silences gene expression). When The RNA strand is held by RISC it is now a mature miRNA 6. Still a part of RISc, the miRNA can bind to its complementary sequences in a target RNA 7. IF the match between the miRNA and the mRNA is perfect, an enzyme in RISC destroys the mRNA by cutting it in two. IF not a perfect match, translation of the mRNA is inhibited because the ribosome cant move along it

Explain in simple steps the surface metabolism model of chemical evolution

1. Simple molecules were present in early oceqans and hydrothermal vents because the vents have pockets whose surfaces are coverd by minerals with - charges which attract organic + molecules to give monomers. 2. Vent minerals catalyzed spontaneous reactions among high energy molecules to give polymers 3. Stimulated by heat and concentration, the products formed more complex molecules

Explain in simple steps the prebiotic soup model of chemical evolution

1. Simple molecules were present in the atmosphere of ancient Earth 2. Energy in sunlight drove reactions among the simple reactions. THey rained down into oceans 3. Stimulatd by heat, the products(like formaldehyde) formed more complex molecules in ocean.

Newspapers published about his trial!! What were the consequences of his trial? (4 things)

1. The Big Chill: All scholars stopped controversial research. Ex: Rene Descartes a french man stopped writing his book of "Everything", as all scholars stopped in the Roman Catholic regin. Many moved to Northern Europe where there was no inquisition 2. Northward shift in :intellectual center of gravity": all discoveries were made in Northern Europe 3. Exodus(departure): the exodus of educated ROman Catholics. They became Protestant or atheists. The church had been discredited 4. The Wedge: friction between theologians and scientists natural philosphy= science *less people were theologians and scientists *interpretations of passages of Bible changed in the Church-less literal

The formation of what 3 structures is necessary for organogenesis? ie. explain first steps of organogenesis WHat process forms the notochord? What structure discussed above is the 1st organ in vertebraes?

1. The notochord forms from mesodermal cells after gastrulation is complete 2. Ectoderm near the notochords folds inward because the notochord releases signal inducers 3. THe folding forms the neural tube,a tube of ectoderm that runs along the dorsal midline of the embryo and gives rise to the brain and spinal cord 4. AS organogenesis continues, mesodermal cells near the notochord become organized into somites. Somites are paired blocks of mesodermal tissue that extend along either side of the dorsal midline of the embryo ie side of the neural tube. SOmite formation is in response to cell adhesion molecules -embryonic induction -the notochord

What two models explain the kinds of reactions that may have set chemical evolution in motion? Briefly explain each

1. The prebiotic soup model-proposes that certain molecules were made from gases in the atmosphere or arrived via meteroite.Afterward, theybwould have codensed with rain and accumulated in oceans. This would result in an "organic soup" that allowed for the continued making of larger molecules. 2. The surface metabolism model- suggests that dissolved gases cam ein contact with minerals lining the walls of deep sea vents and formed more complex organic molecules.

REcall that: introns are transcribed sequences that are spliced out and exons ae transcrbiebd regions that are included in mature RNA. Reseacrhers found a regulatory sequence that enhanced transcriptions within an intron . This was remarkable because...

1. The regulator sequence was 1000 base pairs away from promoter 2.it was downstream of the promoter instead of upstream

Testing Darwins Postulates indicate that evolution by natural selection DID occur because all prove ot be true.

1. Variation DID exist in the population!. Due to mutation, both resistant and nonresistant strains of TB were present before administration of the drig 2. the variation IS heritable! The researchers showed that the variation in the phenotypes of teh two strains-drug susceptibilaty and drig resistance- was due to variation in their gemnotypes. Because the mutant rpoB gene is passed on to daughter cells when a Mycobacterium replicated, the allele an phenotype it produces drug resistance is passed on 3. Ther IS variation in survival and reproductive success! Only a tiny fraction of M tuberbulosos cells in the patient survived the first round of antiobiitosc long enouhg to reproduce. 4. Survival adn reproduction is NOT random! When rifampin was present certain cells-those with drug resistance allele- had higher reproductive success than cells with the normal allele

IN 1844 he wrote his essay. Wha are Darwins 4 postulates? Natural selection occurs when... Biologist now knwo that traits are determined by alleles or differnt versions of genes. THUS, the outcome of evolution by natural selection is a change in...

1. Variation exists among individual organisms that make up a population(such as in size) 2. SOme of the trait differences are heritable meaning passed on to offspring 3. IN nature, organismsm produce to their full biological potential.ie-as many as can even if cant support them all 4. IN nature, the size of wild populations tends to remain stable over time. This is because say theres a pond that can only hold 1000 frogs. Once this is exceeded rampant nonrandom death will occur and the populatin will drop back to a 1000. 5. Death is rampant and not random because of 1! some variations are better in certain environments 6. Differential survival-> differential reproductive success. Survival and reproductive success is highly variable. THe set of individuals that survive best and produce the most offspring are individuals with certain heritable traits that make them more likely to survive and reproduce. -individuals with certain heritable traits produce more offspring than do individuals without those traits. Thus the frequency of the certain trait increases from one generation to the next. - allele frequencies in a population over time.

1.When a research team analyzed DNA from the drug resistant strain and compared it with stored DNA from M tuberculosis cells that had been isolated from the same patient nearly a year before the biologist discovered ... 2. The rpoB gene codes for a component of.. 3.The point mutation changed a 4. Why was the shape change important?

1. a point mutation in a gene called rpoB. 2. RNA POl( trancribed DNA to mRNA) 3. cytosine to a thymine forming a new allele. This missense mutation caused a change of aa sequence of the RNA pol and caused a shape change 4. Rifampin, the antibiotic used on the patient, wprks by binding to RNA pol of M tuberculosis and interferes with transcriptiom.. Bacterial cells with the C->T mutation can continue to produce offspring even in the presence of teh drug because the drug can t bind to the mutant RNA pol.

What are 5 essential developmental processes?

1. cell division: cells divide by mitosis and cytokinesis. The timing and location of these processes are regulated 2. cell-cell interactions: signals are produced by cells that influence their neighbors to divide, differentiate, move or die 3. Cell differentiation: cells specialize at specifc times and places 4. Cell movement and coorinated cell shape changes: cells may move past one another causing changes tothe shape of the embryo. Cells may migrate to new locations. 5. Programmed cell death: the timiong and location of cell death is regulated

What are 4 other sources of genetic variation?

1. chromosomal nondisjunctin- in A1 of M1 homologous chromosomnes may not separate into adn in AII the sister chromatids may not disjoing. Aneploidy: 1 extrac or 1 less chromomes polyploidy: 4 sets of chromosomes and so on(good in plants because stronger phenotypes) 2. Translocation: part of 1 chromosomes is transloactd to a different chromosome 3. exon shuffling: exonic portions of a gene may move within a gene or into a different gene giving new alleles 4. template shifting: new alleles in S phase

What are the two kinds of transposons? WHat do the cut and paste do? WHat enzyme does it c ode for? does it code for anything else at all? What occurs as a reult of the action of transposase?

1. cut and paste 2. copy and paste - cut and paste TE's code for an enzyme called transposase only. Transposases cuts out the gene that coded for it and brings the 2 pieces together that it cut from and then reinserts the cut-out piece into a different location of the genome - it changes the nucleotide sequence of the DNA molecule its inserted into-it can be inserted into the same DNA molecule or a different one. If its inserted into a coding DNA/exon then a new allele could be created. IF it's inserted into a promoter it may prevent RNA pol from attaching. If its inserted into an exon it could be beneficial by coding for a new gene or could be bad

What are the three layers that result from gastrulation?

1. ectoderm-outermost cells 2. Endoderm-inner tissues/cells 3. mesoderm- tissue between the other two

CHromatin exists at different levels of organization! firstl, what is the "regular structure" of chromatin? What is a nucleosome?What seals the DNA of nucleosones to the structure? What is linker DNA?

1. in electron microscopy, chromatin looks like beads on a string. The beads are what are called nucleosomes.Each nuclosomes consists of 200 bas epairs of DNA wrapped twice around a core of 8 histone proteins This complex just described is a nucleosome. A histone called H1 attaches to the nucleosome to seal it and attaches on th eother side to linker DNA. Linker DNA is a strech od DNA between each pair of nucleosomes.

What are 2 things that support this?

1. infoldings of the PM occur in som ebacteria today 2. The nucleur envelope and ER are continuous in eukaryotes today.

Mito lost 70% of their genes and chloroplast lost 50%. WHy is this thought to have occured? Explain lateral gene transfer.

1. loss due to redundancy with the host genome 2. lateral gene transfer - the idea that genes from the endosymbiotioc bacterium moved into the nucleur genome. Tis is thought because mitocondiral genomes code for 50 genes and its bacterial cousins (alpha-proteobacteria) code for 1500 genes. We know this is true because the host genome have sequences similar to that of alpha proteobacterium and cyanobacterium

What are ALL the sources of genetic variation we have discussed?

1. mutation 2. crossing over 3. lateral gene transfer 4. transposable elements 5. chromosmal nondisjuntion 6. translocation 7. exon shuffling 8. template shifting

What are 4 sources of genetic variation? no genetic variation=no adaptation=extinction

1. mutation, especially in prokaryotes 2. crossing over, especially in eukaryotes inP1 3. lateral gene transfer 4. transposable elements

RNA longevity!!! What are two things that effect the survivabnility of RNAs?

1. poly-A -tail: the longer the tail the longest it survives. sO the longer the tail the more gene product/protein made. IF a cell no longer needs a certain mRNA the tail will be removed or shortened 2. RNA interferene using miRNA. this occurs when a tingly single stranded RNA help by a protein complex binds to a complementary sequence in an mRNA. Depending on how well the small mRNA matches the mRNA target, the target RNA is ether destoyed or its translation is blocked.

The first living molecule existed without being enclosed in a membrane . It had to do what two things? What is thought to be this molecule?WHy couldnt it have been DNA , the current sysstem? WHy couldnt it have been proteins?

1. provide a template that could be copied ie store info 2. catalyze polymerization reactions to link monomers into a copy. ie autocatalytic -RNA: can store info and catalyze !DNA cant catalyze.; proteins cant store information.

What 3 things may result from the gene that is longer?ALl are result of gene ____. What resuls because of gene duplication?

1. same gene so more gene product per unit time ex: cells have manyb genes that make histones needed in S phase. The additinal genes cam eabout this way ex: the rRN gene family-> many genes for rRNA(at nucleolus and on several chromosomes) 2. pseudogenes: such mutated gened where they cant make product but they resemble a functinoal gene 3. mutation could prevent a new gene with a new function! -duplication -gene families - can consist of pseudogenes, mutated new genes, and the orginianal. Can all be on the same or different chromosomes

What are two challenges when it comes to sequencing eukaryotic genomes?

1. size! when you think about how the largest bacteria gnome is 15 million base pairs compared to humans who have 3 bill base pairs this is way larger. THere is even a plant with 145 bill pairs! 2. repetitive DNA- many sequences in DNA of eukaryores are repeated many times. STRS and minisatellites both occur between genes or inside introns but dont code for product. Repeated sequences =repetiveDNA

What 2 criteria can idenitify lateral gene transfer?

1. the gene of interest is much more similar to gene in distantly related species than those closely related to its species. In the bacterium Thermotoga maritima that live in the deep sea vents , 25% of their genes are closely related to genes found in archaea that live in the same habitats. The archaea like genes occur in well defined clustors w3ithin the T maritima genomre supportint he hypothesis that these seqeuncs were transferrd in large peices between the 2 species 2. Look to see if THe proportion of C-G base pairs and A-T ba spairs in a particular gene or series of genes is different than the base comp in the rest of the genome. the proportion of C-G bas epairs in a genome is characterists of particlar genus or species.

What are the three levels of gene expression control in bacteria?

1. transcription 2. translation 3. post-translation

What are the 2 kinds of transposable elements or "jumping genes"? Whats at the end of each transposable element?

1. transposons 2. retrotransposons -inverted repeated sequences

1.What are chromatin remodling complexes? 2.DNA is called ____ when its transcriptinally active.

1.- a macrmolecular machine made of enzymes. IT uses ATP to cause nucleosomes to slide along DNA or knock histones entirley off DNA to open up streched of chromatin and allow gene transcription. 2. euchromatin! THe nucleosomes /histones dont block the transcription machinary

the sex hormones play important roles in...

1.Development of the reproductive tract and brain in embryos 2. Maturation of the reproductive tract during the transition from childhood to adulthood 3. Regulation of spermatogenesis and oogenesis in adults.

1.What are a few ways protist protect themselves? Note-These structures can serve as synapomorphies that identify monophyletic groups among protist. 2.Diatoms are surrounded by a glass like cells wall off ____ _____ that is two pieces. 3.Dinoflagellates have a ____ ____ made of cellulose plates. 4.Some foraminiferans form a _____ _____ 5Other foraminiferans and some amoebas form ______ by covering themselves with _____ 6.THe parabasalids have an ____ _____made by microtubules. 7.The euglenids have a collection of ____ _____ called a ____ that run under the PM. These are supported by microtubules. 8.All alveolates have sac like structures called ____ under the PM that stiffens the cell.

1.cells walls outside the PM, hard external shells, or rigid structures under the PM 2.silicon dioide 3.cell wall 4.carbonate shell 5.shell;sand 6internal support, 7 8. alveoli

The synthesis of what molecule has shown that perhaps the minerals in the hydrothermal vents acted as catalysts? The catalysts that perform the same ractions in modern day cells contain minerals similar to those found in hydrothermal vents .This mineral represents t a form of moleculas taken form deep sea hydrotheral vents by the...

1.the formation of acetic acid! Acetic acid can be formed under conditions similar to a hydrothermal vent 2. acetic acid is a key intermiediatwe in a metabolic pathwayay that give acetyl Coglycolysisis) - last universal common ancestor!!

WHat is the next level of organization (more organized)of chromatin?. The chromatin is then often called ______ because...

2. H1 histones interact with one another and with histones in other nuclosomes to produce a tighlty packed structure called a 30-nm fiber(thats its width). The chromatin is then called heterochromatin! heterochromatin is chromatin that is transcriptionally inactive because its unlikely although still possible for the transcription machinery to get to DNA thru histones

LEcture 29 onward! Humans have ____ different kinds of cells.

200!

Whats the 3rd level?( is this the stage most often in ??)

3. 30 nm fibers are attached at intervals along their length to proteins that form a scoffold inside the nucleus which causes coiling. THis keeps the entire chromosomes inplace and organized

The 4th level? THe chromatin that is in this state are transfcirptinally silent which means......What are BAr bodies?

4. FINALLY, scaffolded chromatin supercoil to get super condensed chromatin. THis happens when chromosomes condense before mitosis or meiosis the scaffolded chromatins are folded into even tighter packed structure (and larger overall) that lead to the chromosomes visible in cell division (X). This is also what happens to barbodies or inactive X chromosomes. Super condensed chromosomes as in mitosis or meiosis or as in barbodies are transcriptionally silent so transcription doesn't happen in mitosis or meiosis but it still occurs in G1, G2 and S phase

About ____ % of an avergage eukaryotic genome consists of repeated sequences.

50%

How does determination distinguis plant and animal development? What kind of animal cell si teh exeption and idoes not play by "oce determines always determine"?

Animals neraly always play by once edetermined always determined. Whers plants cells arent ocked into a particular fate - tumor cells are at least partially dedifferentiated and change properties back to besimilar to an embryonic cell

Compare the regulation of gene expression in bacteris vs eukaryotes.

Chromatin remodeling: bacteria- less packaging of DNA and remodeling not an issue in regulation eukaryotes- extensive packaging of DNA, chromatin must be decondensed for transcription to begin Transcription: bacteria- positive and negative control by regulatory proteins that act at sites close to the promoter. Sigma protein interacts with the promoter to attract RNA pol Euk- + and - control by regulatory proteins that act at sites close to and far from the promoter. LArge set of transcription factors interact with the core promoter and many regulatory sequences. A mediator is required RNA processing bacteria- none or rare euk- extensive, RNA alt splicing mRNA stability bacteria- rare or none euk- common, RNA interference limits life span or translation rate of mRNAs translation: bacteria- regulatory proteins(like initiation and elongation factors) bind to mRNas and ribosomes and affect translation rate euk- regulatory proteins(like initiation and elongation factors) bind to mRNAs and ribosomes and affect translation rate post translation modifications: bacteria- folding by chaperone proteins and chemical modifications euk- much more often, folding by chaperone proteins, chemical modifications (phosphorylation), and ubiquitination targets proteins

What does the ectoderm, mesoderm, and endoderm form?

Ectoderm: forms the outer covering of the body and the nervous system. THe cornea and lens ofeye, epidermis of skin, and epithelial lining of mouth and rectum Mesoderm: produces muscle, most internal organs, and connective tissue such as bone and catilage- so the skeletal system, ciruclatory system, lympathetic system, muscular system, excretory/uronary system, reproductive system, dermis of skin, lining of body cavity Endoderm:epithelial lining of digetsive tract, respiratpry trsact, reproductivec tract, urinary tract, liver , peancreas, parathyrpid gland, and thymus. basically lines all ducts that come off the food tube

Biologist today condense Darwins postulates into the following two part statement:

Evolution by natural selection occurs when heritable varaition leads to differential reproductive success

Who provided lots of support for this theory?

Lynn ,Argulis

What is differentiation?

The process by which an unspecialized cell changes to become specialised

Explain the experiment done by Barold Weintrab that proved how an embyronic cell becomes a muscle cell.

They sexperimented on myoblasts which are determoined to become muscle cells but have not yet differentiated into specialized muscle cells. They said that at myoblast must express at least one transcription factor that triggers their differentiation to muscle cells. The isea was that myoblast begin to make this muscle determining protein after they receive the right signals from nearby tissues. 1. Isolate the mRNAs from myoblasts 2. They used reverse transcriptase to convert the mRNAs to cDNAs. Because myobnlsat were prediucted to transcribe genes required for irreversible commitmnet to muscle cell differentiation, they reasoned that the cDNAs must include a muscle determining gene transcript/cDNA 3. They attached a type of promoter to the cDNAs that would ensure expression of the cDNA in any type of cell. 4. They introduced the modified cDNAS into nonmuscle cells called fibnrobklasts and others and monitored the development of tehse cells. ONe o the nyoblst derived cDNAs converted fibroblast into muscle like cells.

What hormones control puberty(transition from childhood to adulthood) in humans?

What hormones control puberty(transition from childhood to adulthood) in humans?

What is a scientific theory? What are the two components?

an explanation supported by large amounts of experimental evidence. An overarching mode that explains all the known data and isnt contradicted by anything 1. The pattern component- summarizes a series of observations about the natural world based on facts 2. the process component- a mechanism that produces the certain patterns of observations

Endosymbiosis occurs when...

an organism of one species lives inside the cells of an organism of another species. THe host cell supplies the bacterium with protection and carbon comounds and the bacterium supplies the host with ATP

What does the term fitness mean? Fitness is a ___ _____.

biological fitness is the ability of an individual to produce surviving, fertile offspring relative to that ability in other individuals in the population. -measurable quantity by comparing the number fo surviving offspring eahc individual produces

When the sperm nucleus fuses with egg nucleus it becomes fertlized and is now ____. Once it fuses, ___ ___ occurs which then allows ___ ____.

diploid! ;S phase occurs which is followed by cleavage divisions( the first cytokinesis of the organism)

SO transposable elements produce DNA that allows for ______. The Beta globin gene family consists of pseudogenes and different kinds of Beta genes that code for different types of Hb. Gene duplication allowed for the different kind of Hb that allows the fetus to get more O2 from the Mom. BUT at a time there was only 1 beta gene

duplication

What ocurs after the development fo the blastoceoel?

gastrulation!!

AS the blastocoel shrinks due to gastrulation making_____, what is formed in the endoderm layer? SO gastrulation causes cell migration so that cells that are endoderm go toward the very center and cells to invaginate from the animal pole to become mesoderm and causes ectoderm cells to wrap all the around . SO its like a ball is inside another ball which is inside another! (at the bottom is the yolk plug / blastopore where the vegetal pole was- it is full od endodermal cells) THe blastopore gives rise to endodermal cells!! THe blastopore gives rise to the gut/ anus but the dorsal blastopore lip specifically gives rise to the food tube. The yolk plug is the remaining patch of endordermal cells of the blastopore that is exposed on the vegetal side of a blastula but will eventually be coveerd by epiboly in gastrulation. When those leftover blastopore cells are beginning to be covered it is called a yolk plug

mesoderm; archenteron- endoderm surronds it, this is the primitive gut

Any regulation that occurs after transcirption is called ____ ____ ____ What 4 ways can this occur?

post transcription control 1. different ways of splicing the same RNA primary transcript 2. inhibiting the translation of many mRNAs in the cell 3. destroying certain mRNAs or altering the ability to translate them 4. altering the activity of the protein after translation

We know RNA can store info in its nucleotide sequences. And we know some RNAs are catalytic like rRNA which catalyzes peptide bonds in ribosomes. We know tRNA is autocatalytic. We know function depends on structure and is why proteins can do so much. WHat is the primary, secondary adn tertiary structure of RNA? WHaT allows RNA to act as a catalyst? There wouldve needed to be RNA that was autocatalytic adn ribozymes

primary= ss RNA secondary= hairpins: ss region formns loops when no comp pairing occurd tertiary=if theres more than one loop ; its tertiary structure! it provides active sites

What was the Human Genome Project?

sequencing and mapping of the entire human genome. (all of the nucleotide base pairs). Took 15 years and 3 billion dollars. Today sequencing a human genome would only be about a 1000.

Selection means.. is or isnt purposeful?

the passive process of differential reproduction as a result of heritable variation; it is NOT purposeful

Development:

the process that allows a multicellular individual to form from a single cell

What does symbiosis mean?

when two individuals of a different species live together

A single celled fertilized egg is called a _____. After that single cell begins to divide it is called a _____.

zygote embryo- a yound developing organism