What is “oxidative phosphorylation”?

1. #1 What is “oxidative phosphorylation”? First, some basic definitions. When you take hydrogen ions or electrons away from a molecule, you “oxidize” that molecule. When you give hydrogen ions or electrons to a molecule, you “reduce” that molecule. When you give phosphate molecules to a molecule, you “phosphorylate” that molecule. So, oxidative phosphorylation (very simply) means the process that couples the removal of hydrogen ions from one molecule and giving phosphate molecules to another molecule. How does this apply to mitochondria?

2. As the Kreb’s cycle runs, hydrogen ions (or electrons) are donated to the two carrier molecules in 4 of the steps. They are picked up by either NAD or FAD and these carrier molecules become NADH and FADH (because they now are carrying a hydrogen ion).  They carry the hydrogen ions to the inner mitochondrial membrane (cristae). This is where the electron transport complexes are embedded in the membrane.  The following cartoon shows what happens next.   The NADH and FADH essentially serve as a ferry in the lateral plane of the membrane diffusing from one complex to the next. At each complex site is a hydrogen (or proton) pump which  transfers hydrogen from one side of the membrane to the other.  This creates a gradient across the inner membrane with a higher concentration of Hydrogen ions in the intercristae space (this is the space between the inner and outer membranes).

4. In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.[1]

7. Hypertonicity A hypertonic solution contains a greater concentration of impermeable solutes than the solution on the other side of the membrane.[1] When a cell’s cytoplasm is bathed in a hypertonic solution the water will be drawn into the solution and out of the cell by osmosis. If water molecules continue to diffuse out of the cell, it will cause the cell to shrink. Hypotonicity A hypotonic solution contains a lesser concentration of impermeable solutes than the solution on the other side of the membrane.[1] When a cell’s cytoplasm is bathed in a hypotonic solution the water will be drawn out of the solution and into the cell by osmosis. If water molecules continue to diffuse into the cell, it will cause the cell to swell. Isotonicity Isotonic solutions contain equal concentrations of impermeable solutes on both sides of the membrane.

8. The taxonomic classification of the Red Panda has been controversial since it was discovered. French zoologist Frédéric Cuvier initially described the Red Panda in 1825, and classified it as a close relative of the Raccoon (Procyonidae), even though he gave it the genus name Ailurus "cat" based on superficial similarities with domestic cats. The specific epithet is the Latin adjective fulgens "shining".[20] At various times it has been placed in Procyonidae, Ursidae, with Ailuropoda in Ailuridae, and in its own family, Ailuridae. This uncertainty comes from difficulty determining whether certain characteristics of Ailurus are phylogenetically conservative or are derived and convergent with species of similar ecological habits.[21] Evidence based on the fossil record, serology, karyology, behavior, anatomy, and reproduction reflect closer affinities with Procyonidae than Ursidae. However, ecological and foraging specializations and distinct geographical distribution in relation to modern Procyonids support classification in a separate family (Ailuridae).[21][22][23] Recent molecular-systematicDNA research also places the Red Panda into its own family Ailuridae, which is in turn part of the broad superfamily Musteloidea that also includes the Mephitidae (skunks), Procyonidae (raccoons), and Mustelidae (weasels) families.[3][23][24] It is not a bear, nor closely related to the giant panda, nor a raccoon, nor a lineage of uncertain affinities. Rather it is a basal lineage of musteloid, with a long history of independence from its closest relatives (skunks, raccoons, and otters/weasels/badgers). —Flynn et al. , Whence the Red Panda,[3] p197

9. A pulmonary vein is a large blood vessel of the human circulatory system that carries blood from the lungs to the left atrium of the heart. There are two pulmonary veins, two from each lung. They carry oxygenated blood, which is unusual since almost all other veins carry deoxygenated blood.

10. Triglycerides are formed from a single molecule of glycerol, combined with three fatty acids on each of the OH groups, and make up most of fats digested by humans. Triglycerides, as major components ofvery low density lipoprotein (VLDL) and chylomicrons, play an important role in metabolism as energy sources and transporters of dietary fat. They contain more than twice as much energy (9 kcal/g) as carbohydrates and proteins. In the intestine, triglycerides are split into monoacylglycerol and free fatty acids in a process called lipolysis, with the secretion of lipases and bile, which are subsequently moved to absorptive enterocytes, cells lining the intestines.

11. The salivary glands in mammals are exocrine glands, glands with ducts, that produce saliva. They also secrete amylase, an enzyme that breaks down starch into maltose. In other organisms such as insects, salivary glands are often used to produce biologically important proteins like silk or glues, and fly salivary glands contain polytene chromosomes that have been useful in genetic research.

13. Decomposition of Organic Matter in Soil - Fungi alongwith other microbes, chiefly bacteria (including actinomycetes) play vital role in the decomposition of organic matter in soil, thus releasing the nutrients locked up in the dead organic matter of plant, animal and microbial matter and bringing about the recycling of nutrients in nature.In soil, microbes oxidise organic carbon to CO2 and liberate bound materials.

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16. Linnaeus: classification system from kingdom to species • Buffon: species shared ancestors rather than arising separately • E. Darwin: more-complex forms developed from less-complex forms • Lamarck: environmental change leads to use or disuse of a structure • #13 There were many important naturalists in the 18th century.

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18. Angiosperms, the flowering plants, represent the most advanced condition among terrestrial plants. While their sexual organs -flowers- are unquestionably their crowning achievement, their origin remains a topic of considerable debate. There is general agreement that the precursor to the ancestoral flower was a modified whorl of leaves, and that extant flowers with multiple parts of indefinate number probably represent the ancestoral condition. For an interesting discussion on the origin of flowering plants, the reader is referred to Peter Crane, et.al. (1995) (See references). The angiosperm life cycle possesses the following advances over conifers: • Reproductive structures are flowers rather than cones. • Ovules embedded in female sporophylls rather than lying bare on the surface • Gametophyte still further reduced • Double fertilization to produce a diploidtriploid endosperm nutritive material • Seeds enclosed in fruits that develop from the ovary or related structures

20. The sporophyte is the dominant phase for seed plants.

21. The spore-producing plant is the mature sporophyte. • sporophyte phase is diploid • begins with fertilized egg • spores produced through meiosis • The gamete-producing plant is the mature gametophyte. • gametophyte phase is haploid • begins with spore • gametes produced through mitosis

22. 15 Learning is adaptive. • Animals that can learn can better adapt to new situations. • In associative learning, a specific action is associated with its consequences. • Trial and error • Conditioning is one type of associative learning • Classical conditioning: previously neutral stimulus associated with behavior triggered by different stimulus • Operant conditioning: behavior increased or decreased by positive or negative reinforcement

23. Innate behaviors are triggered by specific internal and external stimuli. (instinct) • An instinct is a complex inborn behavior. • Instinctive behaviors shareseveral characteristics. • innate, or performedcorrectly the first time • relatively inflexible

24. Many behaviors have both innate and learned components. • Learning takes many forms. • Habituation occurswhen an animallearns to ignore arepeated stimulus. • Imprinting is a rapidand irreversiblelearning process. • critical period • Konrad Lorenzand graylag geese

25. In imitation, animals learn by observing the behaviors of others. • young male songbirds learn songs by listening to adult males • snow monkeys and potato-washing behavior

26. Unlike learning by trial-and-error, insight learning is solving problems not based on actual experience (like trial and error steps) but on trials occurring mentally. Often the solution is learned suddenly, such as when a person is in a problem for a period of time and suddenly learns the way to solve it. • This was observed in the experiments of Wolfgang Kohler in 1900s involving chimpanzees. Kohler found that chimpanzees could use insight learning instead of trial-and error to solve problems. In one example, a banana was placed high out of reach that the chimpanzees found a way to reach it. They stack boxes on top of each other to reach it and used sticks to knock the banana down.

27. 16 • In biochemistry, • allosteric regulation is the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site (that is, a site other than the protein's active site). Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.

28. 17 • Lysosomes are spherical organelles that contain enzymes (acid hydrolases). They break up food so it is easier to digest. They are found in animal cells, while in yeast and plants the same roles are performed by lytic vacuoles. • The size of lysosomes varies from 0.1–1.2 μm.[2] At pH 4.8, the interior of the lysosomes is acidic compared to the slightly alkaline cytosol (pH 7.2). The lysosome maintains this pH differential by pumping protons (H+ ions) from the cytosol across the membrane via proton pumps and chloride ion channels. The lysosomal membrane protects the cytosol, and therefore the rest of the cell, from the degradative enzymes within the lysosome. The cell is additionally protected from any lysosomal acid hydrolases that leak into the cytosol as these enzymes are pH-sensitive and function less well in the alkaline environment of the cytosol. • Hydrolysis is a chemical reaction during which molecules of water (H2O) are split into hydrogencations (H+) (conventionally referred to as protons) and hydroxideanions (OH−) in the process of a chemical mechanism.[

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30. 19 • An adaptive radiation is a rapid evolutionary radiation characterized by an increase in the morphological and ecological diversity of a single, rapidly diversifying lineage. Phenotypes adapt in response to the environment, with new and useful traits arising.[1] This is an evolutionary process driven by natural selection. • Four of the 14 finch species found on the Galápagos Archipelago, are thought to have evolved by an adaptive radiation that diversified their beak shapes to adapt them to different food sources.

31. 20 • Cephalization is an evolutionary trend, whereby nervous tissue, over many generations, becomes concentrated toward one end of an organism. This process eventually produces a head region with sensory organs.[1] • Cephalization is intrinsically connected with a change in symmetry.

32. 21 • The solubility of oxygen in water is temperature-dependent, and about twice as much (14.6 mg·L−1) dissolves at 0 °C than at 20 °C. To illustrate, recall bubbles forming in a pot of water right before it begins to boil; these bubbles are oxygen that was dissolved at room temperature, but is being ejected as the temperature rises. Oxygen can slip into the crevasses or “holes” that exist in the loose hydrogen-bonded network of water molecules without forcing them apart. A very physical perspective on solubility of oxygen in water is that when the water is colder, the water molecules move less, and the oxygen remains trapped in the aqueous solution.

33. 22 • Proteins are made on the ribosomes which are located on the rough ER. • Then they move to the Golgi apparatus/ complex that packages them and ships them out • They go to a vesicle and then plasma membrane

34. 23 • A laboratory centrifuge is a piece of laboratory equipment, driven by a motor, which spins liquid samples at high speed. There are various types of centrifuges, depending on the size and the sample capacity. • Like all other centrifuges, laboratory centrifuges work by the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density.

35. 24 • Dicotyledonous plants (dicots) are the second major group of plants within the Angiospermae division (flowering plants with seeds protected in vessels). The other major group is the monocots. • In contrast to monocots, dicots have an embryo with two cotyledons, which give rise to two seed leaves. The mature leaves have veins in a net-like pattern, and the flowers have four or five parts.

36. 25 • In biology, anaerobic respiration is a way for an organism to produce usable energy without the involvement of oxygen; it is respiration without oxygen.[1] Respiration is a redox reaction that processes energy in a form usable by an organism, chiefly the process of producing ATP,[2] the "universal energy currency of life".[3] It employs an electron transport chain, with inorganic molecules other than oxygen used as a final electron acceptor. Anaerobic respiration should therefore not be confused with fermentation, as in ethanol fermentation and lactic acid fermentation.

37. 26 AIDS/HIV • The virus, entering through which ever route, acts primarily on the following cells:[70] • Lymphoreticular system: • CD4+ T-Helper cells • Macrophages • Monocytes • B-lymphocytes • Certain endothelial cells • Central nervous system: • Microglia of the nervous system • Astrocytes • Oligodendrocytes • Neurones – indirectly by the action of cytokines and the gp-120

38. 27 • Chemo: chemical • Auto: self • Tropic: feeding • Deep sea vents have no light. Chemoautotrophs generally only use inorganic energy sources. Most are bacteria or archaea that live in hostile environments such as deep sea vents and are the primary producers in such ecosystems. Evolutionary scientists believe that the first organisms to inhabit Earth were chemoautotrophs that produced oxygen as a by-product and later evolved into both aerobic, animal-like organisms and photosynthetic, plant-like organisms.

39. 28 • Plants have a mitochondria and a chloroplast

40. 29 • Egg • Frogs and Toads tend to lay many many eggs because there are many hazards between fertalization and full grown frogness! Those eggs that die tend to turn white or opaque. The lucky ones that actually manage to hatch still start out on a journey of many perils.Life starts right as the central yolk splits in two. It then divides into four, then eight, etc.- until it looks a bit like a rasberry inside a jello cup. Soon, the embryo starts to look more and more like a tadpole, getting longer and moving about in it's egg.Usually, about 6-21 days (average!) after being fertilized, the egg will hatch. Most eggs are found in calm or static waters, to prevent getting too rumbled about in infancy!Some frogs, like the Coast foam-nest treefrog, actually mate in treebranches overlooking static bonds and streams. Their egg masses form large cocoon-like foamy masses. The foam sometimes cakes dry in the sun, protecting the inside moisture. When the rain comes along, after developement of 7 to 9 days, the foam drips down, dropping tiny tadpoles into the river or pond below.

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42. hydrogen ions flow through a channel in the thylakoid membrane • ATP synthase attached to the channel makes ATP • The light-dependent reactions produce ATP.

43. A molecule of glucose is formed as it stores some of the energy captured from sunlight. • carbon dioxide molecules enter the Calvin cycle • energy is added and carbon molecules are rearranged • a high-energy three-carbon molecule leaves the cycle

44. The second stage of photosynthesis uses energy from the first stage to make sugars. • Light-independent reactions occur in the stroma and use CO2 molecules.

45. Glycolysis is needed for cellular respiration. • The products of glycolysis enter cellular respiration when oxygen is available. • two ATP molecules are used to split glucose • four ATP molecules are produced • two molecules of NADH produced • two molecules of pyruvate produced

46. The Krebs cycle produces energy-carrying molecules.

47. 31 • Atoms: smallest piece of matter • Molecules: two or more atoms • Cells: smallest living unit • Organism: living thing made of one or more cells • ecosystem: An environment made of both biotic and abiotic factors.

48. 32 Analogous structures • Two structures in biology are said to be analogous if they perform the same or similar function by a similar mechanism but evolved separately. • Similar structures may have evolved through different pathways, a process known as convergent evolution, or may be homologous. The wings of pterosaurs (1), bats (2) and birds (3) are analogous: they serve the same function and are similar in structure, but each evolved independently.

49. Homologous structures • homology refers to any similarity between characteristics of organisms that is due to their shared ancestry.

50. Divergent evolution • Divergent evolution is the accumulation of differences between groups which can lead to the formation of new species, usually a result of diffusion of the same species adapting to different environments, leading to natural selection defining the success of specific mutations.