Exam Preparation Notes

MIDTERM I In animals but not in plants: lysosomes centrioles flagella tonoplast encloses the vacuole Bound ribosomes make proteins that either destined for insertion into membranes, for packaging within certain organelles such as lysosomes or for export from the cell. Endoplasmic reticulm in a biosynthetic factory Smooth Endoplasmic reticulm produce lipids, carbohydrate metabolism, detoxification of poisons by adding a hydroxyl group. Golgi apparatus substitutes sugar monomers and modifies glycoproteins. Manufacterer of macromolecules. Some lysosomes come from the budding of trans face of the golgi apparatus. There is still a back and forth movement even after dynamic equilibrium. If a cell without a wall, such as an animal cell is emmersed in an evirnoment that is isotonic to a cell, there will be no net movement of water across the plasma membrane. Facilitated diffusion is always considered passive, whether it is a carier protein or channel or simple diffusion. In a salty solution, there aren't as many free water molecules since the water tends to attach to the salt molecules. Since there is more free water molecules inside the cell that is emerged, it is goes to want to balance out. If we emerge a cell that is balance salt/water in a pure water solution. Since there are more free water molecules on the outside, it will want to enter the cell. exergonic are spontaneous reactions (Catabolic) 0>G, therefore -G, oxidation is exergonic: energy released endergonic are non-spontaneous reactions (Anabolic) G>0, reduction is endergonic: reactions that require energy. Elastin is a structural protein that provides fibrous framework. Serine, Asparagine, theoronine, tyrosine, cysteine, glutamine are polar amino acids [[cst tag]] The sandwich model by david and danielli proposed that two protein coats surrounded the inside and outside of the phosphlipid bilayer. Singer and nicolson proposed that they are embedded Cell at equilibrium is dead. This means that it has a minimum of 'g' and can do no work Energy in a molecule or in a system that can preform work has 'free energy' g. the gretaer the decrease in free energy, the greater the amount of work that can be done Enzymes do not change the G, G never changes. How fast a reaction goes does not depend on G, in other words, rate of reaction is independent on G. nonprotein organic enzyme helpers are called coenzymes inorganic nonprotein enzyme helpers are called cofactors. free ribosomes make proteins that are for the cytosol. bound ribosomes make proteins for the insertion of membranes or for transport. Perixisomes are not part of the endomembrane system but they are bound by a single membrane The basal body is a 3 x 9 triplets The cilia or flagellum 2 x 9 with 2 in the middle doublets A typical pattern for endergonic reactions is that the biproduct or product of the reaction is less complec than that of the reactions A + B => C, disorder has decreased and is symbolized by -S* something like A => a + B is exergonic because the reaction required energy to break the bonds. Allosteric enzymes are senstive to envirnomental conditions because they are proteins, and proteins denature. In the cell, the hydrolysis of ATP, meaning: the break down of ATP by water is coupled (or happens) to other endergonic reactions that require heat. Therefore, heat isn't lost all at once. Allosteric inhibitors DO NOT bind to the active site, only substrates do.* Peptide formation involves dehydration synthesis (condenstation) where the H of the amino group of an adjacent amino acid combines with a hydroxyl of the C-terminus of the carboxyl group. This happens in the primary structure, covalent bond formation, this can also be seen as translation. These initial bonds will determine how this protein will look, its 3D conformation and thus its function. In translation, the formation of peptide bonds is known as peptidyl-transferase activity. Ester linkages are formed in when, for example, gylcerol and a fatty acid attach to each other, glycerol providing an -OH hydroxyl and the fatty acid providing the C=O-H* Carboxyl. MIDTERM II & BEYOND Cell-cell signaling used today evolved before the first multicellular organism. Engelmann's experiment determined which wavelegths of light are most effective at causing photosynthesis. In other other words, he measured the action spectrum. tRNA is a small RNA molecule consisting of about 80 nucleotides long Triploid: having three sets of chromosomes in the somatic cells Diploid A mother A father = AA Triploid A mother A father A from somewhere else = AAA Remember that each 'A' represents an allele so have three alleles means that sexual reproduction went very wrong. Incomplete dominance occurs when the phenotypes of two heterozygotes are mixed, their traits for instance, such as colour. Pleiotropy refers to the ability of certains genes to affect multiple characterists. For example, if an error in genetic code codes for one bad protein, this bad protein and result in complicated variations shown in other characteristics. This is shown in sickle-cell anemia where one base sequences affects many of the phenotypic characterists of an individual. Polygenes are any of a group of genes that act together cumulatively to produce a trait, as stature or skin pigmentation. In other words, if you have a gene in one area of the DNA, another gene may be related to the other one. When a protein is produced as a result, the two proteins come together cumulatively to produce a trait. Polygenic inheritance involves a continuum. Characters that vary along a continuum, following a normal distribuation, are often controlled by multiple genes each contributing to a phenotype in an additive fashion. Epistatis occurs when the gene at one loci alters the phenotypic expression of a gene at another locus. such as albinism and hair coat. epinephrine involves the g-linked protein receptor 4 types of bases, 4, and is read for every three nucleotide bases, 3, 4^3. RNA Polymerase is less accurate at 'doing business' than DNA polyermase. Therefore more errors than DNA Polymerase. Ribonucleoside triphosphate are the 'energy givers' when transcription takes place. Nucleoside triphosphates are the building blocks of the mRNA, fragments that come together during transcription. Helper proteins push the mRNA transcipt off when it reaches a termination sequence. The anticodon and the template strand of the DNA that was transcribed are the same; [[anticodon (tRNA) = template (DNA)]]. The codon and the anti-template of the DNA (the part that wasn't trascribed) are the same.The anticodon still has U instead of T. [[mRNA codon = antitemplate (DNA)]] The tRNA is a molecule that is charged after it has a amino acid binded to it, not from the amino acid but from ATP which loses two of its phosphates (pyrophosphates). Remember, the amino acid is attached to the 3' end of the tRNA (the hydroxyl end -OH). When the tRNA reaches the codon of the mRNA, it forms a hydrogen bond with the codon. It beholds a anti-codon. The tRNA finds it destination by first entering a ribosome, a ribosome is made up of protein and rRNA and are held together by hydrophobic forces and ionic bonds. The large subunit has 3 rRNA's and the smaller one has 1 rRNA. Translation involves elongation factors. When the terminator sequence is introduced, no tRNA codes for it. Instead, a release factor + water come in to from a carboxyl C-terminus. Another note on rRNA, ribozymes are also considered rRNA which play catalytic roles and structural roles in protein, like a ribosome. Just like mRNA has small nuclear ribonucleoic acid, a pre-rRNA contains small nuclearor ribonucleic acid SNR RNA deals with peptide recognition of the endoplasmic reticulm germ line mutations ONLY can be passed on. missense, amino acid substituation AUG => AGG [[point mutations]] nonsense, new stop codon formed by simple substituation, would most likely involve the first nucleotide base in a triplet codon. A frameshift mutation is also a point mutation but is further subdivided into insertion or deletion transcription favours euchromatin. Chromatin modification do not alter the DNA but are still passed on to future generations, this is called epigentic inheritance. acetalyation of the histones +ve tail makes the structure neutral, no more bonding to near by nucleosomes. This belongs to the Histone code hypothesis. Chromatin modifying enzymes make the chromatin more or less able to bind transcription machinery. Enchancers not found in prokaryotes. Repressors try to slow down transcription by moving into the enchancer region and blocking activators. Repressors are also proteins that inhibit transcription by affecting chromatin structure. Co-expressed genes (coordinetly-expressed) are on the same chromosome. Other genes will have the same enhancers, (a proximal or distal control element) and respond to the same activators when available. The life span of an mRNA, the time before it is degraded all depends on 'untranslated regions' (UTR's) that trail or lead the mRNA. If not, mRNA will be destroyed by single stranded micro RNA, siRNA. These guys find base pairs on the mRNA and either degrad it or block transcription. Genes that normally regulate cell growth and division including growth factor genes, their associated receptors and signaling molecules are often cancer causers. p53 gene encodes a tumor surpressor protein which acts a transcription factor than stimulates the production of a cell-cycle inhibiting protein. If DNA is hurt, been exposed to UV radiation for instance, he will send out an intracellular signal via a protein kinase to stimulate the p53 gene which goes on to produce a transcription factor protein that simulates the production of another protein which inhibits the cell cycle. Mutation knocks out this gene, making no more tumor surpressors. The broken DNA will remain in such a way and be transcribed even when broken thus leading to point mutations (silent, nonsence, missence, frameshift (insertion, deletion)). coletorial cancer: ras gene produced via a proto-oncogene. Possibly a point mutation on the gene itself or on the enchancer, and another mutation such as gene amplification made the production or ras possible. Polyp is formed. => adenoma big begign, => spreading malignant. YES you can inherit mutant oncogenes or tumor surpressor allele. simple sequence dna, that accounts for repetive non-coding regions are also known as satelites. Found in the centromere and telemere, may play a chromosol strucural role. 3% 15% codes for non-coding DNA in general identical or similar genes belong to multigene families that are uniformly aligned 'tandemly' one after another, such as those that code for RNA products. Each coding gene is in one copy per haploid set. This means that if you have a gene from your mothers initial haploid gamete, you will only find it once throughout the remaining 23. growth hormones use tryrosine receptors. The backbone of a peptide chain is the side that is not the amino acid. Most fibris proteins have alpha protein configurations Most globular proteins have beta pleated sheets. This is also seen in fibruous proteins too. Receprocal crosses show that male and female contribute equally QUAN. NOT QUAL. when it came to mendel Allele are different forms of a gene. They both code for the same trait, but they come from two different parents. Since us humans, for example, mate male and female, we will have two alleles no matter what for a certain characteristics. This doesn't mean that two genes cannot code for a single characteristic. Instead, if you do have two genes that code a characteristic, you will have both of those genes on both of the alleles. If you are not true-breeding on the other hand, this means that the genes will have different sequences, so what? However, there are organisms that are very simply like flower that are either white or purple. If both mating organisms are PP meaning pure breed, then they will produce an organism that is also true-breed. pp and PP and true breed homozygous Pp are not true breed The law of segregations says that a gamete, a sex cell recieves one member of each allele. [P]p, gamete [p] Monohybrid cross is Pp with Pp, testing for heterozygotes only. dihybrid cross takes into account additional characteristics that are heterzygoteous.SsYy Second law states that copies of different genes (alleles of different genes) are distributed independtly of each other. This is called the law of independent assortment of two genes Meosis I = second law Meoisis I & II = first law when one allele is not fully dominant over the other, this leads to codominance, incomplete dominance, and complete dominance All due to allele interaction. Complete dominance is when you have a domanant allele and a recessive allele, pea colour. Incomplete domanance is when the heterozygote of two true breed species come toegther, the heterzygote is basically a mixture, in some way going towards the blending hypothesis. Codominance takes into effect when both versions of the gene are domanant yet different, for example, white is dominant and so is brown. A mixture comes about. RR + WW => RW. Put another way, both phenotypes are expressed in heterozygotes mutant alleles are less common then wildtype account for 99%. if less than 99% say 70%, then the species is polymorphic most genetic disorders are multi-factored, some are single allele huntington disease is inherted in the mendalian way. when both genetics and envirnomental components are a cause of a disease or cancer, it does not follow simple mendelian inheritance. Multifatorial disorders associates with polygenes. This is where a group of genes come together to produce a phenotype. Darwin - 1809-1882, 5 year trip, beagle The phrase desent with modification involves 'ansestors with altered chacateristics, not only traits.' the three inferences and 5 observations state that 1. population sizes would expontenitally increase if all the individuals reproduced. 2. Besides that, populations are general stabize, not considering seasonal changes. 3. In an envirnoment, resourses are limited. [Inference] Over production than the envirnoment can handle will lead to only a fraction to survive. Charateristics in an individual of a population are very different, never exact. These are heritable. This leads to the observation(s) 1. that those who inherit traits that are best suited for the envirnoment have a better chance of surviving and will leave more offspring, and these are the traits that will be passed on to further generations. Unequal ability will lead to gradual change. Endemic means that they are found no where else in the world. This explains why two islands with similar envirnoments in different parts of the world are populated not by closely related species but rather by species that resemble those of the nearest mainland, where the envirnoment is often quite different. A drug does not create resistant pathogens; it seletes for resistant individuals that were already present in the population. Second, natural selection depends on time and place. It favours those characterists in a genetically variable population that increase fitness in the current, local envirnoment. Observations of molecular homologies did not change his thinking, like DNA change. Theory generally applies to an idea that attempts to explain many related phenomena. A theory is more comprehensive. The wings of a bird and those of an insect is NOT homology. Envirnomental factors vary from place to place and from time to time. Life changes the planet it inhabits. Plants releasing co2. Life is defined partly by two properties: accurate replication and metabolism. Amino acids polymerization when added to hot sand or clay. reducing atmosphere goes from inorganic to organic. Early RNA served as the first form of genetic material. It served as a template for aligning amino acids in polypeptid synthesis, liek mRNA today, and for aligning nucleotides in a primitive form of self-replication. These eraly RNA would have been more affective at using resources and would increase in number by natural selection. crestaceous mass extinction: 65 million years ago -> mesoczoic and cenozoic doomed more than half of all the marine species. The permian claimed 96% of marine animal species. Terriestrial like was also affected and this happened during the paleozoic and mesozoic eras. The early earth was thought to have lacked oxygen since prokaryotes did not require oxygen. The following are explaination of how deep-sea vents may have been important factors in the origin of life: They may have been the source of some of the carbon-containing compounds that cells use in energy metabolism. Sulfides of iron and nickel common in deep-sea vents are excellent catalysts. The high temperatures associated with deep-sea vents were a source of energy for the reactions necessary for the formation of protobionts. prokaryotes inhabited this earth for 3.5 - 2.0 billion years ago. A layer of iridium, probably from the collision of an asteroid with Earth, is found at the Mesozoic-Cenozoic boundary. cyanobacteria are the closest relatives to plastids, and the proteobacteria are the closest relative to mitochondria. Types of electron transport systems existed before the oxygen revolution. The answer to this question is a specific electron transport system. Genetic annealing is a term used to term used to describe the horizontal transfer of genetic material between bacterial and archaeal lineages 1.5 billion years ago - common multicellular eukaryote ancestor archea do not have peptidoglycan, so theyare not gram + fimbrea are more numerous and shorter than pili. Some fimbria is used to fasten itself to the mucous membranes of its host. Pili are used to link during conjunctions, a time where dna is transfered to another organism. towards nutrients or oxygen (positive chemotaxis) or to members to form colonies. photosynthesis prokaryotes are cyanobacteria. 1-3 hours, reproduction occurs by budding. a new generation passes every 20 minutes. plasmids replicate independently from chromosomes away from toxic substance (negative chemotasxis) Plants and algea including some prokaryotes like cyanobacteria are photoautotrphs who use CO2 and sunlight to make its own nutriuents. Chemoautotrphs also require CO2 but do not use light for eneergy. Instead, they oxidize inorganic substances, such as hydrogen sulfide. Unique to prokarotes. Photoheterotrophs get their CO2 not directly but through other organic organisms, use light too. Prokaryotes Chemoheterophos get their energy and CO2 from inorganic: prokaryotes plus protists, fungi, animals, and some parasite. Obligate anerobes is o2 and die from poisining. Most of their chemical energy is extracted by fermentations, other s by aneorbic respestion where so42- and no3 are the final electron acceptor. downhill. proteobacteria and gram positive parkaryotes are a part of domain bacteria. mathogens are anerobes, (obligate) that use co2 to oxidize H2 and then releasing methane as a wasteproduct. => marsh gas made off mathane. exotoxins can produce disease even if their manufactorer is not there. botulism gram-positive (canner foods) proteobacterium endotoxins- gram negative lipopolysaccride components. Released only when cells die. samonella Eukaryotic flagella are extensions of the cytoplasm, consisting of bundles of microtubules covered by the cell's plasma membrane. There are quite different from prokarytic flagella, which are filaments composed of the globular protein glagellin to the cell surface. diplomads and parabasilids: both lack plastids, mitchondria don't contains dna, electron transport chain, or enzymes. Mitochondira are very small and produce cofactors. anaerobic envirnoments. perhaps faciltavie anerobes. parabasalid -vagina infection caused by protist a diverse clade that include predatary heterotrphs, photosynthethis autotrophs, and pathogenic parasites. distinguishable by the presense of a spiral or cystalline rod inside their flagella.