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Transcript
Biology Chapter 1 Basics/introduction There are certain properties (characteristics) of life such as : -growth and developement, -homeostase (regulation), -reproduction, -consumption of energy, -response to environment, -Order -Evolutionary adaption Touchstones (Grundprinzipien) of life: -Organization, Information, Energy and Matter, Interactions, Evolution Life is structured on different levels, that biologists have defined -Biosphere: consists all of life -Eco system: consists of all the living things in a particular area including non living components such as water, soil, gases, stones.. -Communities: all organisms inhabiting a particular ecosystem (plants animals bacteries) -Populations: all individuals of a species -Organisms: one individual living thing (each tree, dog..) -Organ(Systems): part of body with particular function -Tissues: group of cells that have the same job, performing a specialized function -Cell: smallest organism capeable of all functions of life -Organelles: functional components/structures in a cell -Molecules: chemical structure consisting of atoms, with specific function (zooming in is an approach called reductionism by zooming out you’ll find emergent properties. To understand these better biologist complete reductionism with systems biology, analysing the interactions among parts) Function and structure go hand in hand (correlate) because of natural selection Gene expression = (Proteinbiosynthese) entire process by which information in a gen directs the manufacture of a cellular product DNA → transcription → mRNA → translation → chain of amino acids → protein folding Energy flows through and chemicals cycle Organisms interact with each other and their environment on all levels of life. They often use the ability to self regulate by a mechanism called feedback we distinguish between Negative feedback: the response reduces the initial stimulus (blood sugar regulation) Postive feedback: The end product speeds up its own production (clotting of blood) Three domains of life Prokaryotic : no nucleus nor membrane enclosed organelles 1-Bacteria 2-Archaea (differ in molecular organization thought to be a intermediate between Bacteria and Eucaryotes) 3-Eukaryotic : nucleus & membrane enclosed organelles (organized in 4 kingdoms) -Kingdom Plantae: carry out photosynthesis -Kingdom Fungi: absorb nutrients from outside their bodies -Kingdom Animalia: ingest other organisms -Kingdom Protists: mostly unicellular & simple multicellular relatives Charles Darwin On the Origin of Species by Means of Natural Selection -Individuals in Populations vary in their traits -A Population can produce fare more offspring, than can survive -> competition -Species suit their environments Evolution accounts for the Unity in the Diversity of Life (universal genetic language of DNA ,similar skeletons) and evolutionary adaption (match of organisms to their environments) natural selection: mechanism of evolutionary adaption (individuals with traits that suit their environment have higher chances to survive and reproduce) hypothesys = explanation on trial, has to be falsifyable, can't be verified but becomes more and more plauseable after a lot of testing and experiments inductive reasoning = generalization from a large number of specific observations the sun always rises in the west or all men are mortal for example deductive reasoning = top-down-logic, reasoning from one or more statements (premesis) to reach a logically certain solution. All men are mortal, your are a man → you are mortal controlled experiment = experiment with controll group, that only differs in the one factor the experiment is testing called the independent variable (eg color of a mouse) the predation is the measured factor called dependent variable qualitative data = descriptions, not mesureable (colors, smells, appearance, texture..) quantitative date = measureable, deals with numebrs (length, time, cost, volume, area..) Ribosome = consits of proteins and large pieces of RNA Chapter 3 Water and Life Because of the way a water molecule is built it is a polar molecule with the ability to form hydrogen bonds. Because of this water has four emergent properties, witch are very important for life on earth. Hydrogen bonding keeps the molecules close to each other (cohesion)this is the reason for surface tension and how trees are able to transport water. Because the molecules are held together by these strong forces a lot of heat is neccessary to increas the temperature (high heat capacity). This helps to keep temperatures in areas close to large amounts of water relatively steady. To evaporate a water molecule has to break all bonds to other molecules with needs a lot of enrgy. This results in a high (heat of evaporization), helping animals to keep their temperature steady. When cooled below 4° there is not enough energy in the system to break hydrogen bonds, which causes the molecules to arrange in the lowest energy configuration in which each molecule is hydrogen bonded to four partners. This cristalized configuration is abour 10% less dense than at 4°. Therefore Ice floats on top of water(highest density at 4°) creating new environments and protecting fishes from freezing. Because water is polar it alows other polar molecules to be solved in it. (solvent) Chapter 4 Carbon (C) Structural isomers = have the same molecular formule (C5H12 for e.g.) but differ in the arrangement of their carbon skeletons cis-trans isomers = due to the inflexebility of double bonds the atoms cannot rotate around the bond axis if the substituents are on the same side its a cis or z isomer and if they are on opposite sides its a trans or e isomer chirality = molecules of identical composition but are non-superposeable mirror images of each other (Hands) are called chiral. Enantiomers = isomers that are mirror images of each other due to an asymmetric carbon (one that is attached to four different atoms ) Chapter 5 Struct and funct of large biological molecules Dehydration =monomers connect by a reaction in which it sets free water Hydrolysis = Polimer is disassembled by addition of water Carbonhydrates = sugars and polymers of sugars monosaccharides = multiple of H2CO e.g. glucose C6H12O6. Distinction between Ketose CO DB (Carbonylgroup) within skeleton and Aldose Carbonylgroup at the end Sugars also vary in skeleton length and spatial arangement (Glucose /Galactose) Disaccharides = Two monosaccharides joined by a glycosidic linkage Polysaccharides = up to a few thousand monosaccharides Starch = Glucose storage as granules in plastids. Two forms Amylose (not branched) and Amylopectin (somewhat (a little) branched) Glycogen = Glucose storage for animals mainly in liver and muscle cells like amylopectin but more extensively branched Cellulose = never branched; hydrogenbonds with parallel polysaccharides about 80 of these form a microfibrill; most organisms are unable to digest Chitin = Also a structural polysaccharides with HNCOCH3 Group on second carbon Lipids = Group of hydrophobic molecules including fats, waxes,steroids, some vitamins,.. Fatty acid = long carbon skeleton (usually 16-18) with a carboxyl group at one end Fats = Consiting of Fatty acid and Glycerol (propan-1,2,3-triol) Fat provides more than twice as much energy per gramm than sugar this means you have less weight to cary around plus fat protects organs and works as an insulation Phospholipids = Important for cell membrane Steroids = obtained from diet and sinthesized in liver fats impact cholesterol level Protein = proteios (=primary) make up 50% of the cell dry mass are all made up from 20 amino acids connected by peptide bonds there are tens of thousands of proteins each with its unique function and structure. Proteinstructure can be divided into four substructures -Primary structure = sequence of amino acids like letters in a word even slightest changes can cause the protein to loose its function (sickle-cell) -Secondary structure = Folding of the amino sequence because of oxygens negative and hydrogens positive charge -α-Helix delicate coil held by hydrogen bonding between every fourthamino acid -β pleated sheet hydrogen bonds between parts of the two parallel segments of the polypeptide backbone -Tertiary structure = Overall shape of a polypeptide -Quaternary structure = overall protein structure (sometimes consisting of more than one polypeptide together eg. Collagen three α-Helixes interwined or Hemoglobin including a non peptide componed called hemme with an iron atom that binds oxygen. Denaturation = Changes in physical or chemical conditions can cause the protein to un/ refold eg. High temperature (egg white) or nopolar solvent where hydrophobic regions now face outward. Chaperonins = also chaperone proteins are molecules that assist in the folding process of proteins eg. In E. Coli a big cylinder protects the aminosequence from harmful chemical conditions in the plasma so the polypept. Can fold properly there are also controll mechanisms that check if folding was proper. Misfolding is associated with diseases like alzheimer parkinsons and mad cow disease Bioinformatics = tries to predict 3d structure of polypeptides based on their aminosequence. 3D struct can be determined by X-Ray crystallography and NMR (nuclear magnetic resonance spectroscopy) Gene expression = The process by which information from a gene is used in the synthesis of a functional gene product. (mainly Proteins) DNA->RNA-> Protein Polynucleotide = phosphodiester linkage (two sugars linked by phosphate group) builtin directionality from 5' to 3' (5'-AGTT-3') RNA = Ribonucleic acid mRNA = messenger RNA conveys genetic information from the nucleus to the ribosomes tRNA = transfer RNA brings amino acids to the ribosome during polypeptidesynthesis about 80 nucleotides long. baise pairing within RNA leads to functional shape DNA = deoxyribonucleic acid Genome = entire sequence of the organisms full complement of DNA Light microscope = 1674 first living cell visualized; Magnification ~1000x; Resolution min distance to distinguish two seperate points ~0,2um; Contrast difference between light and dark areas of an image can be enhanced by dyes etc. Electron Microscope = 1950s; Resolution in practice ~2nm Scanning Electron Microscopy = 3D Image of surface Transmission Electron Microscopy = Through thin section of specimen, internal structure. Cell Fractionation = isolate components by centrifugating cells. smooth ER = Enzymes in ER synthesise lipids including oil steroids (sex-/hormones) and new plasma phospholipids. Detoxifies drugs usually by adding hydroxyl goups. Store calcium ions, whose release can trigger secretion of vesicles or contraction of muscle cells rough ER = Membrane factory (also phospholipids) production of membrane and secretory proteins, vesicels bud like bubbles from specialized region called transitional ER Identification tags such as phosphate groups added to the golgi products aid in sorting by acting like zip codes. Vesicles budded from the golci have external molecules on their membranes that recognize docking sites. Human liver cell recycles half of its macromolecules each week. Lysosomal storage diseases lack a functioning hydrolytic enzyme and become engorged with indigestible material. Central Vacuole = repository of inorganic ions (K,Cl..) growth by maintaining a suitable surface to cytosol ratio. Some vacuoles store pigments or even poisonous compounds to attract or drive away animals Endosymbiont Theory = Ancestor of Eucariotic cell engulfed an oxygen-using-nonphotosynthetic prokaryotic cell becomming an endosymbiont (cell living within another cell) merging into a single organism (cell with mitrochondiron) that then engulfed a photosynthetic prokaryote becomming a chloroplast. Evidence: both posses double membrane, own ribosomes and DNA and are autonomous (grow and reproduce) Not static as in pictures but dynamic move, grow, pinch in two Detoxify by transferring hydrogen from molecules onto O2 forming O2H2 which itself is poisonous but broken down into water by other enzymes. Can also break down fatty acids eg. In plants glyoxysomes suply energy until plant can perform photosynthesis. Cytoskeleton = network of fibers extending throughout the cytoplasm. Also provides anchorage to organelles & enzymes and help form food vacuoles out of membrane Flagella and cilia consist both of microtubuli a flagellum has a 9+2 pattern and a cilium a 9+0 pattern both are anchored by a basal body (similar to a centriole in sperms becomes a centriole) movement of the dyneins proteins is coordinaten and happens on one side of the circle at a time causing it to bend. In vertebrates many cells contain a single primary cilium acting as a signal antenna Microfilaments = build the outher cytoplasm layer called cortex and reinforce the cells shape. They are responisble for amoeboid movement as well, by extending so called pseudopodia (greek false foot) Furtehermore they are involved in cytoplasmic streaming in plant cells as well as muscle contraction in collaboration with myosin filaments. Intermediate filaments = More permantent fixtures to reinforce shape and anchor organelles stay even after death and maku up the nuclear lamina Collagen makes up to 40% of proteins in the human body. Integrins can even influence activity of genes Glycoprotein = Proteins covalently bonded to carbohydrates usually short sugars Plant Cell Walls = 0,1um to several micrometers. Young cell thin flexible primary cell wall when old hardens them by secreting cellulose and proteins bilding a matrix into the primary wall or by ading a harder secondary wall cells are connected by plasmodesmata (desma = bond) that allow communication and exchange of substances between cells. Amphipathic molecules = have both a hydrophilic and a hydrophobic region Phospholipids can travel about 2um/s proteins are slower but moving as well though some are held in place ore clustered together with other proteins of complementary function. Intregral proteins are usually transmembrane or at least embedded in the lipid bilayer whereas peripheral proteins are not embedded at all but loosely connected to the surface of the membrane. Its not only a structural but a functional mosaic as well. Cell recognition = usually established through binding to glycoproteins or sometimes glycolipids with carbohydrates of fewer than 15 sugars serving as identification tags it's crucial to organization of cells into tissues and the immunesystem. Bigger molecules such as proteins cannot pass through the membrane or transport proteins. The cell uses Exocytosis, where a vesicle fuses with the membrane and secretes it's substances (eg. Insulin, neurotransmitter or proteins and cyrbohydrates for cell walls) There are three types of Endocytosis Phagocytosis (Cell engulfs a particle by extending pseudopodia) pinocytosis (cell gulps droplets of extracellular fluid into tiny vesicles) and receptor-mediated endocytosis(ligands-molecules that bind specifically to a certain receptor- gather together and a pit forms into a coatet vesicle as in pinocytosis). Metabolism = totality of an organism's chemical reaction (greek metabole = change). A methabolic pathway begins with one or more specific molecules which are then in a series of reactions catalyzed by enzymes converted into one or more products. Are complex molecules broken down into simpler ones releasing energy it's called catabolic pathway the other way round anabolic pathway. First law of thermodynamics = energy cannot be created or destroyed only transformed Second law of thermodynamics = every energy transfer or transformation increases the entropy of the universe. An organism might decrease it's entropy by building complex molecules out of simpler ones this uses energy though and because some energy is always lost as heat it will increase the entropy of it's surroundings. Entropy = a measure of disorder/randomness A Cell does mainly three kinds of work chemical work (pushing endergonic reactions) transport work (move substances against concentration gradient) and mechanical work to do so it uses energy coupling – using an exergonic process to drive an endergonic one. ATP can be hydrolised forming ADP and HOPO3^2- ΔG =-7.3 kcal/mol (-30,5kj) under standard conditions. Unter cellular conditions ΔG is about -13kcal/mol. If an endergonic reaction is coupled with ATP hydrolysis it usually forms a phosphorylated intermediate that enables the overall process to be exergonic Enzymes work as catalysts reducing the activation energy. They are not static but subtly change their shape and even change it futher when interacting with the substrate because of intermoleculare interactions. When there are enough substrates to bind to all the enzymes it's said to be saturated at this point only adding more enzymes can increase the rate of converting substrate into products. Activiti is depending on temperature and pH because after a certain temp the enzyme substrate complex is getting torn apart because of the kinetic energy. Most Enzymes work best at pH of 6-8 but digestive enzymes need a pH of 2 Many enzymes require nonprotein helpers for catalytic activity. These adjuncts are called cofactors (eg metal atoms) if they are organic they're called coenzymes (many vitamines are coenzymes or bulding material for coenzymes). Toxins and Poisons are often irreversible enzyme inhibitors. Example -ATP inhibits several catabolic enzymes while (feedback inhibition – inhibiting it's own production) ADP activates them, speeding up catabolism, producing more ATP -Hemoglobin binding one oxygen molecule increses the affinity of the remaining binding sites fermentation = partial degradation of sugar or other organic fuels without oxygen aerobic respiration = with oxygen whereas anaerobic means without oxygen Burning glucose is basically a redox reaction in witch electons lose potential energy when bound to a more electronegative atom resulting in a G = -686kcal/mol (2,87kJ) oxidative phosphorylation accounts for about 90% of generated ATP a smaller amount is formed by substrate-level phosphorylation. For each molecule of glucose the cell forms about 32 molecules of ATP Glycolysis means sugar splitting: a glucose gets split into two three carbon sugars that are transformed into pyruvate. The process can be devided into two phases the energy investment and the energy payoff phase resulting in a net gain of 2 ATPs and 2 NADHs Each NADH transports 10H+ across the membrane. 4 are needed to generate ATP therefore each NADH synthesises 2.5 ATP. FADH2 which is lower in energy synthesises 1.5 ATP. Because the inner membrane is impermeable to NADH the electones need to be shuttled across. Depending on the shuttle this results in either NADH or FADH2. Furthermore H+ can be used to do other kinds of work reducing the ATP yield. About 34% of the potential chemical energy in glucose is transferred to ATP. Yeast (a fungus) carries out alcohol fermentation and is used in brewing baking and winemaking. Lactic acid fermentation is used to make yogurt and cheese. Muscle cells can also use it if they lack oxygen. Excess lacetate is then carried to the liver and converted back to pyruvate. Obligate anerobes carry out only fermentation whereas facultative anaerobes can do both. Brain cells can only carry out aerobic oxydation. Fats and Proteins can be used as fuel for respiration as well. In fact a gram of fat produces in more than twice as much ATP than a gram of carbohydrate. Amino acids undergo a process called deamination, where the amino group is removed and later excreted as ammonia (NH3) Naturally cellular respiration is regulated by different feedback loops in which certain enzymes are stimulated or inhibited by substrate or products (AMP derives from ADP) Autotrophs produce their organic molecules form CO2 an other inorganic materials they are refered to as producers as well. Plants are photoautotrophs Heterotrophs use organic molecules produced by other organisms also known as consumers Mesophyll = tissue inside of the leaf mesophylle cells contein multiple chloroplasts Photosynthesis uses 12 H2O molecules but forms 6 new ones. The O2 released derives from H20 and not CO2. The oxygen in water is getting oxydized and the electrons transferred to the glucose this process is endergonic. Photosynthesis can be broken down into two stages the light reaction and the calvin cycle. Carbon fixation = conversion process from inorganic carbon ( CO2) to organic compounds Pigments = Substances that absorb light Chlorophyll a is the key pigment b an accessory pigment and the carotenoids broaden the absorption spectrum but are also used as photoprotection by absorbing excessive light energy that could damage chlorophyll or interact with oxygen. Carotenoids are also used for protection in the human eye (eat carrots) The light harvasting complexes consist of pigments bound to proteins. The special chlorophyll is special becuase it is able to transfer an electron to another molecule. There are two types of photosystems. Photosystem I and Photosystem II differing in the proteins associated with the chlorophyll a molecules the one in PS I absorbing best at 700nm called P700 and the one in PS II called P680 absorbing best at 680nm. Linear electron flow is shown in the picture some photosynthetic bacteria use cyclic electron flow where only the PS I is used and the Fd shuttles the electrones to the cytochrome complex. In this case no NADPH is produced. The pH in the thylakoid space is about 5 and the stroma about 8. after 3 CO2 entering the cycle one by one (3cycles), a net output of one GP3 is generated consuming 9 ATP and 6 NADPH On a hot day most plants close their stomata limiting access to CO2 and releas of O2 that is produced, favouring a wastefull process called photorespiration. In C3 plants (first product of carbon fixation is a three carbon compound) the enzyme Rubisco is capable of binding a O2 in place of a CO2. The product splits and a two carbon compound leaves the chloroplast where it is transformed into CO2 by peroxisomes and mitochondria. Can protect the plant from excess light. C4 Plants use PEP carboxylase in a first cycle to fix CO2 onto PEP. Because PEP carboxylase has a high affinitiy for CO2 and no affinity for O2 it will also work under conditions created by partially closed stomata. The CO2 is then „pumped“ into the Calvin cycle stabilizing the CO2 concentration to make sure rubisco only adds CO2. CAM plants close their stomata during the day to minimize water loss and only open them at night, to store CO2 in organic acids. This process is called crassulacean acid metabolism (CAM). CO2 is released during the day where it is used to build sugars. The mechanism is similar to C4 where CO2 is also stored in organic acids first. Cell communication between yeast and mammal cells is strikingly similar (evidence for evolution) Endocrine signaling is like a radio station only cells with an antenna receptor can receive the signal. There are three steps reception, transduction and cellular response. The receptor usually changes it's shape triggering transduction. G protein coupled receptors (GPCR) use a G protein, capeable of binding GTP. Many hormones as well as neurotrasmitters use GPCRs that vary in their binding sites and different G Proteins inside the cell. In humans vision, smell and taste depend on GPCRs and pharmacologists found, that up to 60% of all medicines exert their effect on G protein pathways. G Proteins are also GTPprotease enzymes hydrolyzing GTP to GDP after a certain time becoming inactiv and therefore reuseable. Receptor tyrosine kinease (RTK) exists as monomers after binding they form dimers that are activated by adding Phospahte from ATP and can then trigger multiple transduction pathways, which sets them apart from GPCR. Abnormal RTK function is associated with many forms of cancer binding to phospholised tyrosine results in a change of shape of the relay molecules. Ligand-gated ion channels are important for the nervous system. In synapses they trigger the electric signal. Intracellular Receptors bind to signaling molecules small or hydrophobic enough to cross the plasma membrane. It can activate or act as a transcription factor – a protein that controls which genes are transcribed into mRNA Benefits of multiple step pathways are amplification of the signal (one relay molecule can activate numerous others before being turned inactive again), better control and coordination Activation of proteins by phosphoriylation is a widespread cellular mechanism. Each activated relay molecule (kinase) is able to activate the next molecule in the phosphorylation cascade. Protein phosphatases then remove phospate and deactivate the kinases (enzyme capable of transferring a phosphate group from ATP to a protein) again. Not all signal transducting molecules are proteins. Small water soluble molecules or ions called second messengers are important as well, as many proteins are sensitive to the concentration of aforementioned, Ca2+ and cAMP being the most important ones. CAMP concentration can boost 20-fold in a matter of seconds usually activating protein kinase A. Cholera bacteria inhibit GTP hydrolisys of the G Protein, keeping cAMP levels high. Thus cells secrete salt into the intestinals in combination with osmosis resulting in epic diarrhea. Ca2+ concentration in extracellular fluid is often more than 10'000 times higher than in the cytosol The same hormone can have different effects on different cells, because they contain different proteins. Therefore enpinephrine might cause liver cells to break down glycogen while it causes muscle cells to contract. The hormone cannot have the same effect, because they can only activate protein that are present in the cell. To increase efficiency of signal transduction scaffolding proteins are used, because relay proteins are usually large and would take for ever to find its substrate. Signal pathways can also interact with eachother Apoptosis = programmed cell death. DNA and Organelles are destroyed, packed up in vesicles and digested by specialized scavenger (Aasfresser) cells. Cell cycle mitotic phase when cell divides and interphase when cell grows. G1 cell grows. S DNA is duplicated. G2 Cell grows further. Mitosis divided into the following subphases where DNA is divided. Cytokinesis Cytoplasma is divided and two cells formed. In Plant cells Cytokinesis is different. Vesicles transport material into the middle of the cell forming a cell plate while in animal cells a ring of actin microfilaments associated with the protein myosin contracts. During anaphase the chromosome is thought to be walked along the microtubule by motor protein. There are other ways of mitosis in dinoflagellates and some yeasts where the nuclear envelope remains intact during cell division While nerve and muscle cells never divide and liver cells only do if they have to for eg because of injury, skin cells divide regularly. The cell cycle is regulated by two types of proteins protein kinases and cyclicns (named because concentration fluctuates with cyclically) Kineases depend on cyclins to become activated and are therefore called cyclin dependent kinases (Cdks) Another important checkpoint is G1. If the cell does not recieve a go ahead signal it might go into a nondividing state called G0 phase. Liver cells can be called back. At the M phase checkpoint the cell can only continue once all chromosomes are attached to microtubules, which activates the enzym separase cleaving the cohesins that hold the chromatids together. If the cell lacks an essential nutrient or growth factor it cannot divide. Most animal cells depend on anchorage . They can't divide without being attached to a substratum. Division can also be inhibited by density dependent inhibition for eg in Skin cells that only bild a single cell layer. Benign tumor = have too few genetic and cellular changes to survive at another place. Malignant tumor = are able to spread to new tissues and impair functions of morgans cells are also considered transformed cells. Spreading is called metastasis. Cancer cells are „immortal“ because they do not stop dividing whereas normal cells stop dividing afer 20-50 times and die. Most drugs inerfere with specific steps in the cell cycle interferring with normal dividing cells though. Karyotype = ordered display of all chromosomes homologous chromosomes = have the same length, centromere position and staining pattern. Autosomes = all the other chromosomes exept the X and Y the sex chromosomes. Diploid cell = containing two sets of chromosomes a maternal (mother) and a paternal (father) each consisting of 23 chromosomes (human 2n = 46) During metaphase I the arrangement of the homologous chromosome pairs is random. Generating genetic variation. For a human n=23 2^23 combinations are possible. Character = A heritable feature that varies among individuals (eg flower color) trait = each variant of a character such as white or red true breeding = varieties that over many genera tions of self-pollination produced only the same variety as the parent plant hybridization = mating/crossing of two true-breeding carieties F1 generation = first filial gnerartion (lat for son) An organism with a pair of identicall alleles for a character is said to be homozygous one with two different alleles heterozygous Allele = Alternativ versions of a gene, accounting for vatiations in inherited characters. An organism's observable traits (appearance) are called its phenotype its genetic makeup its genotype Law of dominance (uniformitätsregel) if an organism contains two allels, the dominant allele determines the organism's phenotype uninfluenced by the recessive allele Law of segregation (spaltungsregel) Two alleles for a heritable character segregate (seperate from each other) during gamet formation and end up in different gametes. Law of independent assortment (unabhängigkeitsregel) two or more genes assort independently -that is, each pair of alleles segregates independently of each other pair of alleles -during gamete formation (two alleles → 9:3:3:1 phenotypic ratio) Because of these laws mendel observed in ~1860 a 3:1 ratio when experimenting with pea plants that differet in character Testcross = if we cannot tell if an organism is homo(XX)/heterozgous(Xx) we can cross it with a homozygous(xx) organism. If theres only one phenotype (Xx) the orgenism was homozygous if it was heterozgous there would be two phenotypes (Xx/xx) 1:1: ratio monohybrid = heterozygous for the one particular character being followed in the cross dihybrid = heterozygous for the two character being followed in the cross incomplete dominance = neither allele is completly dominant F1 generation has a phenotype somewhere between those of the parents because neither is dominante the letter C is used with the allele in superscript e.g. (red(C R CR)&wite(CW CW) → pink(CR CW)) F2 generation splits up in red:pink:white in a 1:2:1 ratio codominance = two alleles affect the pheontype in separate distingushable ways meaning if two alleles are present they do not result in an intermediate but both are fully expressed eg. MN molecules on human blood cells Level dependance = if a allel is dominant or recessive depends on the level at which we examine the phenotype. the Tay-sachs disease seems recessive (die when (xx)) the intermediate pheotype (Xx) at biochemical level is of incompletet dominance because half of the proteins are working. Thus observed at the molecular level its codominant. Multiple alleles = multiple alleles for a single gene are possible. blood groups are determined by three alleles of a single gene coding for different carbohydrates. Pleitropy = Most genes have multiple phenotypic effects. Epistasis = The phenotypic expression of a gene at one locus alters that of a gene at a second locus. One gene determines color - Black(B) is dominant to brown (b) - while a second gene determines wheter or not pigments are deposited in the furr – Deposition (E) is dominant to no deposition (e). Therefore a cross might represent an F1 dihybrid cross we'd expect to end in a 9:3:3:1 ratio but because (E/e) is epistatic to (B/b) F2 offspring results in a 9:3:4 ratio. Quantitative characters = such as Height or skin color vary in gradations along a continuum they usually indicate polygenic inheritance = an additive effect of two or more genes on a single phenotypic character. E.g. if there are 3 genes with two alleles of which the dominant form adds 1 unit of darkness there would be 7 possible phenotypes. (diploid → 1-6 darkgenes +1 phenotyp for 0 dark-genes) carriers = Many diseases are inherited as simple recessive traits. Although heterozygotes usually are phenotipically normal they may transmit the allele to their offspring Enviromental Impact = leaves of a tree differ in phenotype Thomas hHunt Morgan = first to associate a specific gene with a specific chromosome. In 1907 spent two years breeding fruit flies drosophila melanogaster to find one with white eyes. Throu breeding he was then able to find, that the white eye gene was only present on the X sex chromosom. Wild Type = phenotype for a character most commonly observed in natural populations mutant phenotypes = traits alternativ to the wild type assumed to originate from mutations Gender = Mammals have two types of sex chromosomes X&Y short segments are equal to allow them to pair and behave like homologs during meiosis in the testes. In bees and ants females are diploid and unfertilized eggs (haploid) develop males. Grasshoppers have only one type of sex chromosome two → female only one → male. There are a number of x-linked recessive disorders such as red-green color blindness or Hemophilia. Barr body = Femal mammals inherit two x chromosomes of which one randomly gets inactivated by condensing into a barr body thus females are heterozygous for a sex linked trait eg. Cats with patched furr. Inactication involve dna and histone modification linked genes = genes located neach each other on the same chromosome tend to be inherited together because only crossing over could seperate them which is not likely. If genes are not linked the testcross offspring would be expected to occurr in a 1:1:1:1 ratio and if they are linked in a 1:1:0:0 ratio the experiment resulted in a ~5:5:1:1 ratio because crossing over can still cause linked genes to be seperated recombinant offspring = have new combinations of traits of their parents recombination frequency = 10 recombinants/ 100 total offspring = 10% frequency of recombination genetic map = ordered list of the genetic loci along a particular chromosome linkage map = a genetic map based on recombination frequencies. The further away two genes are the higher the probability that a crossover will seperate them. Thus the higher the recombination frequency. The recombination frequency can be at maximum 50%. It does not directly correspont to actual physical distances though. Another problem is some genes are so far apart recombination is almost certain. these genes are physically connected but still unlinked because they behave like unlinked genes. Nondisjunction = when homologous chromosomes do not separate during meiosis I or sister chromatids in meiosis II. Forming gametes with abnormal chromosome numbers aneuploidy = A zygote formed from such a gamete has an abnormal number of a particular chromosome this condition is known as aneuploidy. If it is missing a chromosome its said to be monosomic if it is present in triplicate its trisomic Down syndrome also called trisomy 21 is such an example Polyploid = if an organism contains more tan two complete chromosome sets (3n) triploid (4n£) tetrapoloid. They usually appear more normal than aneuploids Klinefelter syndrome = XXY males, abnormaly small testes thus sterile, big boobs pos Turner syndrome = X0 females, sterile, usually normal intelligence cri du chat syndrome = specific deletion in chromosome 5, severely disabled, cry that sounds like mewing of a distressed cat. Errors in meiosis or damaging agents such as radiation can cause breakage of chromosome leading to four types of alternations in chromosome structure. Chromosomal translocations have been implicated in certain cancers including chronic myelogenous leukemia (CML) Genomic imprinting = vatiations in the phenotype depending on whether an allele is inherited from the male or female parent. In mice a growth factor gene is only expressed from the paternal chromosome. Thus offspring only became dwarf when the mutant gene came from the father. Methylated (-CH3) genes ar usually inactive inthis case methylation of cytosine nucleotides activates the expression of the allel. Extranuclear genes = genes located in mitochondria, chloroplasts and other plastids contain small DNA molecules. Inherited from the mother DNA as genetic material = until 1940 proteins where beliefed to be the information holding material. Griffith found that remains of dead pathogenic (disease causing) mixed with living nonpathogenic bacterias resulted in a transformation of some of those to pathogenic ones. Research also showed that bacteriphages injected their DNA into bacterias while their protein shell remained outside. In1950 Chargaff's rules 1. base composition of DNA varies between species 2. percentages of A&T (Purines – 2 rings) and G&C (pyrimidines - single ring)Bases are roughly equal. Through X-ray christallography they found DNA to be two antiparallel strands forming a double helix In initial pairing errors occur at a rate of In initial pairing errors occur at a rate of 10^5 but polymerases proofread each nucleotide against its templat reducing error rat to 10^10. Chemical and physical agents such as X-ray can destroy the DNA and has to be continously repaird like in the nucleotide excision repair above telomers = short nucleotide sequence (Human:TTAGGG) that is repeated 100 to 1000 times at each end of the molecule. In combination with specific proteins prevent the staggered (uneven) ends from activating repair mechanisms and Protects genes from getting lost. They are thaught to be connected to aging. In germ cells telomerase enzymes catalyze the lenghtening of telomers to normal lenght. Each eukaryotic chromosome in humans everages about 1,5x10^8 nucleotide pairs and is ~4cm long. Therefore it has to be tightly packed. Even during interphase most areas are in a highly condensed state. This type of chromatin is called heterochromatin distinguished from the less dense euchromatin. Also the chromosomes seem to be organised and attached to the nuclear lamina. Genes code mostly for polypeptides that are or built together with others proteins. Some genes code for RNA that is never translated into RNA. In bacterial cells there is no RNA processing. Codons = There are only 4 nucleotide bases to specify 20 aminoacids → 4^3 = 64 information is based on a triplet code. These triplets are called codons Template strand = For each gene only one of the two DNA strands is transcribed. It is always the same strand. For other genes however the opposite strand may be the one that is always the template. Polymerase untwists the double helix exposing about 10-20 nucleotides. Transcription progesses at a rate of ~40 nucleotides per second. Amound of RNA can be increased by multiple polymerase following each other. RNA splicing = removal of large portions of RNA that is initially sequenced Exons = Regions that are expresses usually by being translated into amino acid seqs. Introns = lay between coding regions called intervening sequences get cut out Spliceosome = large complex of proteins and small RNAs that remove introns Ribozymes = RNA molecules that function as enzymes some catalyze its own intron excision. Because its a single strand it can base-pair with complementary regions in the same molecule giving it a three-dimensional structur. Some bases contrain functional goups that can participate in catalysis and hydrogen bonding with other nucleic acids adds specificity to its activity. Alternative RNA splicing = a gene can encode more than one polypeptide depending on which segments are treated as exons Domains = proteins often ahve a modular architecture consisting of discrete structural and functional regions called domains. Different exons often code for domains thus they are kind of like codes for basic units that are combined to build a protein. tRNA = translator. Single strand of RNA that forms 3 dimensional shape through hydrogen bonding. Because there are only 45 instead of 61 some tRNAs must be able to bind to more than one codon. aminoacyl-tRNA synthetase = match tRNA and aminoacids. 20 different synthetases each for a specific amino acid and its tRNA the resulting aminoacyl tRNA is also called a charged tRNA. Ribosome = consist to 2/3 out of ribosomal RNA (rRNA) giving it function and shape thus it can be regarded as a ribozyme. The subunits are assembled in the nucleolus. Eucariotic ribosomes are slightly different than bacterial ribosomes alowing certain drugs to affect only those of bacterias. Ribosomes are identical if bound or free and synthesis always begins in the cytosol on a free ribosom. Sometimes polypeptides need post translational modifications befor bilding a functional protein. (attaching sugars,lipids etc, removing amino acids …) SRP = signal-recognition particle functions as an escort to bring the ribosome to a receptor protein. Point mutations = changes in a single nucleotide pair of a gene responisble for the huge diversity of genes found among organisms. Silent mutation = no observable effect on the phenotype. Missense mutations = little effect on protein nonsense mutation = change of codon into stop codon effect depends on location of new stop codon Insertion and deletions cause a frame shift leading almost certain to nonfunctional protein. Mutagens = physical and chemical agents that cause mutations Gene = A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule. Repressible operon = usually on but can be inhibited Corepressor = small molecule that cooperates with a repressor to switch an operon off inducible operon = usually of but can be induced (stimulated) inducer = small molecule that inacitvates the repressor allolactose is an isomer of lactose formed in small amounts from lactose that enters the cell. Only if allolactose inactivates the repressor the enzymes to break down lactose are synthesised. Positive gene regulation = E.coli only use lactose if glucose is scarce. In this case cAMP accumulates and binds to an activator CAP (catabolite activator protein) that then stimulates transcription. Even if no repressor is bound without CAP not enough RNA will be synthesised. Differential gene expression = human cells typically express at maximum ~20% of their protein coding genes some even less this is why there are different cell types. Gene expression is usually regualted at transcription eucariotic cells may have additional stages where they regulate expression. Histone acetylation causes nucleosomes to become less dense thus becomming more accessible for transcription while methylation has the opposite effect. After DNA replication the daughter strands get methylated too thus inheriting the methylation pattern. epigenetic inheritance = Inheritance of traits transmitted by mechanisms not involving the nucleotide sequence itself is called. Transcription factors = RNA polymerase needes their assistance to initiate transcription. Some are used for alle protein coding genes called general transcription factors. Few of them bind do DNA most bind to other proteins or the polymerase itself. Some activators recruit proteins that acetylate histones thus promoting transcription while some repressors remoce acetyl groups reducing it also called silencing. Specific transcription factors either activators or repressors influence gene expression. Enhancer = consists on average of 10 control elements that can bind a specific transcription factor by combinating the control elements differently there is a great number of possible enhancers by using less activators. Thus gene expression is determined by the transcription factors made in a cell.