a.cyclohexane.molecule

Most text taken from lecture slides.

The alimentary canal consists of, in order of food processing, (1), (2), (3), (4), (5), and (6). (7) glands—the (8), (9), (10), and (11)—secrete digestive juices. (12) are digested throughout the alimentary canal; (13) are digested starting in the stomach by (14); (15) and (16) are digested in the (17) by (18) and (19). Nutrients are absorbed in the small intestine, where the surface area is maximized by protrusions of villi and microvilli. The (20) side of (21) absorbs these nutrients and transmits them through their (22) to capillaries and hence into the circulatory system.

The production of pepsin in the stomach is an example of postivie feedback. (23) secrete protons and chloride ions into the (24), forming hydrochloric acid, while (25) secrete pepsinogen, the inactive precursor to pepsin. HCl helps convert pepsinogen to pepsin; once formed, pepsin cleaves pepsinogen to form more pepsin.

A diverse gut microbiome is important for health, and low microbial complexity in the gut is correlated with high metabolic disease risk and chance of obesity. The bacterium (26) causes stomach ulcers and (27) the diversity of the stomach microbiome.

  Gas exchange is mediated by (1). (2) are inflated air sacs in the lungs that enable the large surface area required for efficient (3); a layer of (4) coats the (2), keeping them inflated. Too high a (5) leads to collapse of the (2) and hence respiratory distress syndrome.

Blood is pumped throughout the body in the (6) and (7) circuits, the former through the body and the latter through the lungs. Deoxygenated blood passes through the (8), and oxygenated blood through the (9). (10) carry blood to the heart, while (11) carry blood away from the heart. Blood cells are differentiated through life: stem cells in bone marrow form (12) and (13) cells: from (12) cells are derived (14) (red blood cells), (15), and (16) (white blood cells), whereas from (13) cells are derived (17) and (18) cells.

The heart is a pump, contracting and relaxing. Contraction is known as (19), relaxation as (20). (21) (0.1 s) followed by (22) (0.3 s) allows the storage of blood in the ventricular chambers; subsequent (24) (0.4 s) allows for the pumping of blood through the systemic and pulmonary circuits; this cycle is known as the cardiac cycle. The progress through the cardiac cycle can also be tracked electrically via (25). [Look at an electrocardiogram and identify each of the pulses.]

The circulatory system is regulated by epinephrine. (26)—G-protein coupled receptors—on (27) cells in the heart bind to epinephrine, making the (27) cells oscillate faster and hence increasing the heart rate. (26) on muscle cells around arteries also bind to epinephrine, allowing for (28) and hence a larger blood supply to muscles in conjunction with the increased heart rate.

  The basic functional unit of the kidney is (1). (2) have shorter loops, whereas (3) have longer loops. After forced osmosis through (4), the filtrate enters (5), during which nutrients are absorbed into (6). The filtrate then descends the (7), during which water leaves the filtrate via (8) in the membrane. Reascending the loop, dissolved ions are (9) out of the filtrate to maintain the (10) in the intercellular fluid. In the descending (11), the membrane is highly permeable to (12) but not very permeable to (13); in the ascending (14), the membrane is no longer permeable to (15) but is permeable to (16). In (17), more nutrients and ions are absorbed from the filtrate and waste products are introduced into the filtrate. Finally, the filtrate descends down through (18)), variably permeable to water and permeable to salt and urea, both of which are important for maintaining the (19) in the intercellular fluid.

Antidiuretic hormone (ADH) is produced by the (20) as the result of a (21) feedback loop. (22) in the (23) are sensitive to changes in the blood osmolarity (with a normal value of ~300 mOsm/L) and trigger the release of ADH upon a (24) in blood osmolarity, activating (25), increasing the permeability of the collecting duct to water via (26) receptors and thus increasing water reabsorption. (27) also generates a sensation of thirst, signaling for water intake; both mechanisms serve to regulate blood osmolarity.

The kidney also serves to regulate blood pressure. The contraction of (28) in the heart causes a (29) in pressure, which drives the flow of blood away from the heart and through the arteries. The resistance to flow in (30) reduces the blood pressure of blood in veins to nearly nothing. Blood pressure can be regulated by changing the diameter of the arteries—via (31) or (32), increasing and decreasing blood pressure respectively—and by changing blood volume—increasing the volume of extracellular fluid by drinking water, for example, (33) blood pressure, whereas becoming dehydrated (34) blood pressure.

Sensors in (35) detect changes in blood pressure. If a decrease in blood pressure is detected, (35) releases (36), which leads to the generation of (37), which binds to the muscle around arteries, leading to constriction and hence an increase in blood pressure. (37) also binds to (38), leading to the release of (39), which binds to (40) and increases the reabsorption of water and ions, increasing blood volume and blood pressure. This is the (41) pathway.

Blood pressure control medication targets the (41) pathway. For example, ACE (angiotensin-converting enzyme) inhibitors inhibit the conversion of (42) to (43), (44) blood pressure. Other inhibitors block the (37) receptor and (39).

    Hormones are secreted (1) that travel through the blood. In contrast to neurons and (2) signaling, hormones are (3)-acting but can produce (4)-lasting responses. Hormones come in three main classes: those derived from eicosanoids (fatty acids), from peptides, and from lipids. Water-soluble and lipid-soluble hormones enter cells via different pathways: water-soluble hormones are stored in (5), expelled into blood, and bind to (6) receptors on a cell; lipid-soluble hormones are released without (7), bind to (8) in blood, diffuse into cells, and bind to receptors in the (9).

Hello! Forgot entirely about posting yesterday, sorry. Here are some cloze passages in physiology; some wording is taken entirely from lecture slides and is not mine.

Signal transduction occurs between signaling molecules and receptor proteins. Four types of cell signaling occur in animals: (1), where hormones flow through the bloodstream and are picked up by receptors in the target cell; (2), where cell signaling is short-ranged and local; (3), where signaling occurs via neurons; and (4), where signal molecules are membrane-bound.

GTP-binding proteins, also called G-proteins, play a major role in signal transduction. Signal transduction pathways involving G-proteins require the action of G-protein-coupled receptors (GPCRs), which contain seven transmembrane domains. When activated by a signaling molecule, the receptor (5) to a (6), resulting in the exchange of (7) for (8), after which (6) activates a (9) and hence initiates cellular response. (6) then undergoes (7), restoring it to its original state. Examples of GPCRs include (10), which bind to epinephrine and norepinephrine, and (11), which are found mainly in the tongue, but also in the pancreas and intestines.

Alternative means of signal transduction include (12), which involves protein kinases and (13). ATP is converted into ADP, and (14) is added onto one of three amino acids: (15), (16), or (17). Such is the case with receptor tyrosine kinases (RTKs). When one receptor tyrosine kinase binds to a signaling molecule, it (19), activating the receptor and initiating (12). Once fully activated, these RTK proteins bind to relay proteins and lead to cellular responses.

A common signaling pathway involves endocrine signaling and insulin and glucagon production in the (20). Between meals, blood (21) levels decrease, and production of (22) by (23) is increased. (24) is hence hydrolyzed into (21) and secreted into blood. After a meal, blood (21) levels increase, and production of (25) by (26) via a (27) pathway is increased. (21) is hence absorbed into cells by (25).

All cells in the body derive from a single cell and thus share the same genetic material. Development covers four processes: cell division, during which cells multiply; (1), the limiting of potential cellular fates; (2), the generation of ordered form and structure; and (3), the establishment of the coordinate system of the body.

Cell fate determination occurs when cells become specialized in structure and function, the molecular basis being asymmetric cell division and (4). For example, the absorption of differing amounts of epidermal growth factor (EGF) lead to different cell fates. Another growth factor is nerve growth factor (NGF), which gives rise to (5). Both NGF and EGF receptors are examples of (6) receptors. Stem cells bypass (1) and are capable of continued division; (7) cells can give rise to any tissue in an organism, embryonic or extra-embryonic, (8) cells can give rise to all adult cells, (9) cells can give rise to a few cells, and (10) cells can only give rise to a single cell type. Embryonic stem cells are (11), whereas adult stem cells are (12). Stem cells grown in culture require nutrients provided by “feeder cells”, usually (13).

During fertilization, sperm penetrate the protective layer around the egg, receptors on the egg surface bind to molecules on the sperm surface, and changes at the egg surface prevent polyspermy, the entry of multiple sperm nuclei into the egg. The (14) is triggered when the sperm meets the egg, during which the (15) releases hydrolytic enzymes that digest material surrounding the egg. Signaling molecules on the sperm bind to receptors on the egg, stimulating (16) and ultimately resulting in (17), which removes (18) from the egg (to prevent polyspermy) and re-activates the egg, allowing for fusion of the nuclei and resumption of the cell cycle. (Unfertilized eggs are frozen after (19) in the cell cycle.)

Fertilization is followed by (20), a period of rapid cell division without growth. (20) partitions the cytoplasm of one large cell into many smaller cells known as (21), which then form into (22), a ball of cells with a fluid-filled cavity, a (23). (24) occurs when (22) forms inward and results in three germ layers, the (25), (26), and (27), each further on the outside than the previous, exemplifying (2). (25) forms the (28) lining of the digestive, respiratory, excretory, and reproductive tracts, and the (29), (30), and (31) glands. (26) forms most organ systems, the (32) of skin, and the (33). (27) forms the (34) of skin and its derivatives, the (35) and (36) systems, the (37) gland and (38), jaws and teeth, and germ cells.

Another biology post, as I must review for upcoming midterms.

Entropy is a powerful concept, made all the more subtle for its far-reaching implications. Although the idea of entropy spans multiple fields, the connections between these entropies are not often made clear, and entropy is made out to be an abstruse, mystical force. A brief historical development of entropy, intending to clarify key misconceptions, follows.

Error propagation formulae stem from differential calculus, in which we can treat our measurements as variables and our calculations as functions. Instead of memorizing a long list of formulae (for use in an exam, say), we can simply derive them from first principles. We know from single-variable calculus that the differential...

The infinite sum of reciprocal squares has a difficult-to-find limit. We focus here on Euler’s non-rigorous proof, being the easiest to understand and requiring the least sophistication in higher mathematics. We start by considering...

The Franck-Condon principle is a quantum-mechanical rule that deals with electronic transitions. An electronic transition occurs when an electron is excited from one energy level to another via absorption of a photon; a vibronic (vibr[ational] + [electr]onic) transition is an electronic transition that also involves changes in vibrational energy levels.

The Franck-Condon principle states that, because molecular excitation and vibration takes place on a much shorter timescale (around 10-15 s) than that of molecular motion, vibronic transitions that involve changes in electronic position are less likely than transitions that do not.

Source: Franck-Condon Principle, Wikipedia

E0 and E1 represent the main energy levels corresponding to molecular orbitals, and v′ and v′′ the vibrational sub-levels. E0 and E1 are not generally aligned, E1 being higher up in energy and further from molecular nuclei. The blue arrow represents a vibronic excitation: note that a transition to E1 with v′ = 2 is more probable than one with v′ = 0, because v′′ = 0 has more vertical overlap with v′ = 2 than with v′ = 0. Vertical overlap allows for position-invariant vibronic transitions, in line with the Franck-Condon principle.

After the excitation, the electron falls from v′ = 2 to v′ = 0 via intermolecular collisions; at v′ = 0, the electron can then relax and fall back down to E0. Just as with excitation, however, the electron is more likely to fall into a non-zero vibrational sublevel, here v′′ = 2.

Source: Franck-Condon Principle, Wikipedia

Molecular bonding is commonly described by two complementary theories, molecular orbital (MO) theory and valence bond (VB) theory. Valence bond theory, using Lewis dot diagrams, provides a simple qualitative understanding of molecular geometry and structure; molecular orbital theory, using molecular orbital diagrams, provides a simple qualitative understanding of molecular stability and reactivity.

Valence bond theory is by far the simpler, and provides a reasonable first approximation as to molecular geometry, which is harder to obtain from molecular orbital theory. Molecular orbital theory spans a wide range of difficulty, depending on whether a qualitative (simple MO diagram) or quantitative (quantum chemical computation using density functional theory, etc.) approach is taken. The simplest of these approaches is still more difficult than the general application of valence bond theory; however, molecular orbital theory provides further insight in bonding and in reactivity.

Introduction Heisenberg’s Uncertainty Principle is a statistical relationship between uncertainties in position and momentum (or, equivalently, energy and time), and reflects a natural inability to determine a particle’s exact position and momentum. …

A complex number z = a + bi has real part Re(z) = a and imaginary part Im(z) = b. Since a complex number has two independent parts, we may represent it on the xy-plane by plotting Re(z) on the x-axis and Im(z) on the y-axis; this xy-plane is called the complex plane,…

This was intended to be a comprehensive guide on systems of acid-base equilibria, but as of now it’s incomplete.

A = sd

When a 2-D curve is rotated about an axis, the surface area A of the resulting surface is equal to the arc length s of the curve multiplied by the distance d travelled by the centroid of the curve. 

V = Ad

When a 2-D surface is rotated about an axis,...

I have attempted to cover here double integrals, triple integrals, line integrals, surface integrals, integral applications, and Green’s, Stokes’, and the Divergence Theorems. Much is left to the reader; only a brief overview is provided. 

Introduction

Carnot’s theorem states that, “if we conduct a heat engine that is to operate between two temperature reservoirs, then that engine will have the maximum possible efficiency if it operates via a Carnot cycle. (1)”

Carnot’s corollary states that, “if there are several cyclic heat engines, some of which are reversible, operating around cycles between the same temperatures TH and TL, all the reversible ones have the same efficiency, while the nonreversible ones have efficiencies which can never exceed the efficiency of the reversible engines. (2)”

The statement of Carnot’s theorem is not confusing. The statement of Carnot’s corollary, however, is.

The inexperienced reader concludes that all reversible thermodynamic cycles whose highest temperature reached is TH and whose lowest temperature reached is TL have the same efficiency, although this is true only for Carnot cycles. Why is Carnot’s corollary not valid in such situations?

Logical Analysis

We must consider the corollary’s wording carefully. Particularly, “temperatures TH and TL” really refer to two–and only two–reservoirs at temperatures of TH and TL. Knowing this, we can show that the only reversible cycle that is governed by Carnot’s corollary is the Carnot cycle, and thus that Carnot’s corollary applies only to Carnot cycles.

The corollary requires that the reversible cycle be in contact with two thermal reservoirs, which translates to an isothermal expansion and an isothermal compression. Any non-isothermal contact with the reservoirs would indicate irreversibility.

The corollary further requires that the reversible cycle not be in contact with any other thermal reservoirs, which is only satisfied by an adiabatic expansion and an adiabatic compression. Any non-adiabatic process would require heat transfer, which requires contact with a thermal reservoir.

We thus have a cycle of two isotherms and two adiabats, which defines a Carnot cycle. This means that Carnot’s corollary is only valid for Carnot cycles. Thus we conclude that (a) all Carnot cycles with the same two operating temperatures are equally, and (b) all other cycles, reversible or irreversible, are less efficient.

Graphical Analysis

An alternative justification of Carnot’s corollary can be done graphically. While we often consider cycles using a P-V diagram, it is more instructive to use a T-S diagram in this case because a Carnot cycle is a rectangle when graphed in terms of T and S. (This can be proven mathematically via Jacobean transformations, or physically via the definition of a Carnot cycle as having two isotherms and two adiabats, or isentropes. Because adiabatic processes do not transfer heat, they also do not transfer entropy, and thus they are also isentropic processes.)

The efficiency of a cycle is work done on the surroundings divided by heat input, both of which have a graphical representation.

A thermodynamic cycle on a T-S diagram.

From the first law, the work done on the surroundings is equivalent to the heat input minus the heat output. The heat input is the integral of (the upper curve of) TdS between Smin and Smax, and is equal to the area of A + B. The heat output is the integral of (the lower curve of) TdS between Smin and Smax, and is equal to the area of B. The efficiency is then A/(A + B).

A thermodynamic cycle on a T-S diagram with boundary lines drawn.

We are only comparing cycles that work between temperatures of TH and TL, so we are restricted to cycles that lie between TH and TL. In order to maximize the efficiency, we must maximize A and minimize B, which is accomplished when A is a rectangle. While we have no entropic restrictions, B will increase at least by the same factor as A if we try to modify our bounds on entropy. Thus, we can create artificial bounds on entropy knowing that the most efficient cycle with bounds on entropy will be the same as that without bounds on entropy. We can see from the graph that the maximum efficiency results when A is the rectangle bounded by Tmin and Tmax, and by Smin and Smax. Then A is a Carnot cycle, and we have thus shown that the Carnot cycle is the most efficient cycle within two temperatures TH and TL.

(1) The efficiency of reversible heat engines. J. Chem. Educ., 1991, 68 (3), p 208 (2) Thermodynamics, E. Fermi (3) Engineering Thermodynamics, V. Kirillin, V. Sychev, A. Sheindlin