A Genetic Genealogy Community
Y-DNA, Mt-DNA, Autosomal DNA
Y-DNA, Mt-DNA, Autosomal DNA
You can discuss some non-genetic or non-genealogical things here. Pull up a chair and have a beer! But if you bring up politics or religion, the barman will cut you off. The forum rules do apply here especially regarding civility.
Mysterious Chorus Voice: You do not look your best today?
Writer: I cannot write. I need a can opener.
Mysterious Chorus Voice: I do not know how to help? Can you give me more details?
Writer: Over the last, 30 years there has been considerable investigation in cooking and health. Frying foods have received considerable bad remarks. In a simple Internet search, one can discover one of these cooking products of concern is acrylamide. Acrylamide forms from sugars and an amino acid that are naturally in food; it does not come from food packaging or the environment. Acrylamide has probably always been in some foods, but this wasn’t known until Swedish scientists first found it in certain foods in 2002. Acrylamide was discovered in foods in April 2002 by Eritrean scientist Eden Tareke in Sweden when she found the chemical in starchy foods, such as potato chips (potato crisps), French fries (chips), and bread that had been heated higher than 120 °C (248 °F). It was not found in food that had been boiled or in foods that were not heated. It is classified as a Group 2A carcinogen by the IARC.
In animal models, exposure to acrylamide causes tumors in the adrenal glands, thyroid, lungs, and testes. Toasting bread to a light brown color, rather than a dark brown color, lowers the amount of acrylamide. Very brown areas contain the most acrylamide. Acrylamide forms in coffee when coffee beans are roasted, not when coffee is brewed at home or in a restaurant. So far, scientists have not found good ways to reduce acrylamide formation in coffee. This search continues the pondering of the human condition, and what we should eat.
Mysterious Chorus Voice: Why do you need a can opener?
Writer: I want to eat more uncooked seafood.
Mysterious Chorus Voice: What about water pollution?
Writer: This is serious. I cannot write without a can opener?
Mysterious Chorus Voice: What do you mean?
Writer: During the ninetieth century, scientist considered "medieval science" to be as civilization taking a nap after the developmental years of Greek philosophy and Roman engineering. The expansion of the Indo-European culture into Europe led to barbaric wars augmented to the wars of revenge in what was called the Holy lands of ancient religions. While property and heritage created social stratification in the past, the guild system has offered improved social rank through technology.
By 1750, the industrial revolution allowed nations to shift from a slave economy to a worker economy freeing the wealthy owners from the daily care of the lower class while creating a new source of income from everyday workers needing such survival things as food and lodging. This exchange for individual free time away from the owners became extremely popular as it allowed for social advancement already expressed in a "people's movement" of enlightenment seen in the early guild system. This guild system of an apprentice taking over his master's work continued in many fields of science as seen with Michael Faraday.
At first he did not read the Latin writings concerning the 1820 discovery of electro-magnetism of Hans Christian Oersted as stated in his later writings, “I have very little to say on M. Oersted’s theory, for I must confess I do not quite understand it.” Oersted belonged to the German school of naturphilosophie which did not influence people like Faraday who were interested in the chemistry as taught by their teacher. For example, we read from Faraday's journal,". . . On a sudden Sir H Davy observed the diamond to burn visibly . . . This phenomenon of actual and vivid combustion, which has never been observed before, was attributed by Sir H Davy to be the free access of air; it became more dull as carbonic acid gas formed and did not last so long." (From the journal kept by Faraday of his continental tour with Sir Humphry Davy. In Brian Bowers and Lenore Symons (eds.), Curiosity Perfectly Satisfied: Faraday's Travels in Europe 1813-1815 (1991), 75-6.).
The atomic theory too did not include ancient Greek ideas of the electric. However, Faraday discovered the chemical he called bicarbuet of hydrogen (c1825), and later called by Eihard Mitscherlich benzin or benzene. This chemical had strange properties which needed to be checked out. Not only did benzene have strange properties, so did ionic compounds like table salt. On 29 August 1831, he discovered electro-magnetic induction. This idea appeared to be important in chemistry as well as in physics. As in any new field, someone had to determine how things were going to be named.
Michael Faraday corresponded with William Whewell concerning names as revealed in the following prose, ". . . All your names I and my friend approve of or nearly all as to sense & expression, but I am frightened by their length & sound when compounded. As you will see I have taken deoxide and skaiode because they agree best with my natural standard East and West. I like Anode & Cathode better as to sound, but all to whom I have shewn them have supposed at first that by Anode I meant No way. (Letter to William Whewell, 3 May 1834. In Frank A. J. L. James (ed.), The Correspondence of Michael Faraday (1993), Vol. 2, 181.). And so for ionic compounds and batteries, the words were finalized, ". . . the names used are anode cathode anions cations and ions . . ." (Letter to William Whewell, 15 May 1834. In Frank A. J. L. James (ed.), The Correspondence of Michael Faraday (1993), Vol. 2, 186.). Eventually, after the washings, the solid state must exhibit these properties too, " . . . The former I now call Paramagnetic & the latter are the diamagnetic. The former need not of necessity assume a polarity of particles such as iron has with magnetic, and the latter do not assume any such polarity either direct or reverse . . ." (Letter to William Whewell, 22 Aug 1850. In L. Pearce Williams (ed.), The Selected Correspondence of Michael Faraday (1971), Vol. 2, 589.). ". . . all this being a consequence of the solitary & isolated system of investigation . . ." (Letter to C. Ransteed, 16 Dec 1857. In L. Pearce Williams (ed.), The Selected Correspondence of Michael Faraday (1971), Vol. 2, 888.).
During this time, the term "dielectric" was finalized with Michael Faraday by William Whewell. In the solid state, a dielectric is an electrical insulator that may be polarized by the action of an applied electric field. If a dielectric is composed of weakly bonded molecules such that the dipole is characterized by its dipole moment, those molecules not only become polarized, but also reorient so that their symmetry axis aligns along the field. This is a type of dipolar polarization that is a polarization particular to polar molecules. Another type is ionic polarization which is a polarization caused by relative displacements between positive and negative ions in ionic crystals. Every material has a dielectric constant labeled by k and characterized by the ratio of the field without the dielectric (Eo) to the net field (E) with the dielectric: k = Eo/E. E is always less than or equal to Eo, so the dielectric constant is greater than or equal to 1. The larger the dielectric constant, the more charge can be stored. Experimentally, completely filling the space between capacitor plates with a dielectric increases the capacitance by a factor of the dielectric constant: C = k Co, where Co is the capacitance with no dielectric between the plates. This type of thought differs from the medieval science of the middle ages, and the so called liberal "party" culture of the early twenty-first century when people used this technology.
Mysterious Chorus Voice: I think we better find a can opener.
Writer: You see what I mean?
Mysterious Chorus Voice: Are you alright?
Writer: Yes, my headache is going away.
sVD Dew Singers: "When you say sVD Dew, just put your mind on hold.
Do what you're told, and open a cold,
refreshing sVD Dew. Just watch your life go by.
No need to try. When you've got sVD Dew." Ohhhhh sVD Dew!"
Mysterious Chorus Voice: You have to do something.
Writer: I can copy some things from the Internet.
Mysterious Chorus Voice: What about?
Writer: Insects and muscles . . .
Mysterious Chorus Voice: Why?
Writer: . . . . because they act alike.
How insects use oxygen by an insect expert who posted on the Internet:
Insects require oxygen (diatomic molecule) to live, and produce carbon dioxide (a molecular compound of carbon and oxygen) as a waste product, just as we do. To say insects breathe, though, might be a stretch. They don't have lungs, nor do they transport oxygen through their circulatory systems. Instead, insects use a series of tubes called a tracheal system to perform gas exchange throughout the body. Gas (no definite shape nor volume) exchange, or what we think of as breathing, is accomplished mostly by simple diffusion through the cell walls. Air (a mixture) enters the spiracles, and moves through the tracheal system. Each tracheal tube ends in a moist tracheole, a specialized cell for exchanging gases with another cell in the body. When air reaches the tracheole, oxygen (molecules of an element) dissolves into the tracheole liquid. Through simple diffusion, oxygen then moves to the living cell and carbon dioxide enters the tracheal tube. Carbon dioxide (molecules of a compound), a metabolic waste, exits the body through the spiracles. This explains the movement of gases, but can insects control their respiration? Yes, to some degree. The insect opens and closes the spiracles using muscle contractions. An insect living in a dry, desert environment will keep the spiracle valves closed to prevent moisture loss. Insects can also pump muscles throughout their bodies to force air down the tracheal tubes, thus speeding up the delivery of oxygen. In heat or under stress, insects can even vent air by alternately opening different spiracles and using muscles to expand or contract their bodies. Still, diffusion places some limits on the insect body. The rate of gas diffusion cannot be controlled, and only proves efficient for small organisms. This limiting factor probably benefits us, as otherwise we might find ourselves living with giant-sized insects! As long as insects breathe using simple diffusion, they aren't likely to get much larger than they are now.
How muscles work by Internet expert:
There are three types of muscle:
* Skeletal muscle or "voluntary muscle" is anchored by tendons to bone and is used to affect skeletal movement such as locomotion and in maintaining posture. Though this postural control is generally maintained as a subconscious reflex, the muscles responsible react to conscious control like non-postural muscles. An average adult male is made up of 40-50% of skeletal muscle and an average adult female is made up of 30-40%.
* Smooth muscle or "involuntary muscle" is found within the walls of organs and structures such as the esophagus, stomach, intestines, bronchi, uterus, urethra, bladder, and blood vessels, and unlike skeletal muscle, smooth muscle is not under conscious control.
* Cardiac muscle is also an "involuntary muscle" but is a specialized kind of muscle found only within the heart.
Cardiac and skeletal muscles are "striated" in that they contain sarcomeres and are packed into highly-regular arrangements of bundles; smooth muscle has neither. While skeletal muscles are arranged in regular, parallel bundles, cardiac muscle connects at branching, irregular angles. Striated muscle contracts and relaxes in short, intense bursts, whereas smooth muscle sustains longer or even near-permanent contractions.
Skeletal muscle is further divided into several subtypes:
* Type I, slow oxidative, slow twitch, or "red" muscle is dense with capillaries and is rich in mitochondria and myoglobin, giving the muscle tissue its characteristic red color. It can carry more oxygen and sustain aerobic activity.
* Type II, fast twitch, muscle has three major kinds that are, in order of increasing contractile speed:
o Type IIa, which, like slow muscle, is aerobic, rich in mitochondria and capillaries and appears red.
o Type IIx (also known as type IId), which is less dense in mitochondria and myoglobin. This is the fastest muscle type in humans. It can contract more quickly and with a greater amount of force than oxidative muscle, but can sustain only short, anaerobic bursts of activity before muscle contraction becomes painful (often incorrectly attributed to a build-up of lactic acid). N.B. in some books and articles this muscle in humans was, confusingly, called type IIB.
o Type IIb, which is anaerobic, glycolytic, "white" muscle that is even less dense in mitochondria and myoglobin. In small animals like rodents this is the major fast muscle type, explaining the pale color of their flesh.
(From Guest Lecturers: Dr. A. Scott Connelly, William H. Carpenter, M.S.)
I. Fuel Utilization During Exercise
Under most circumstances, fat and carbohydrate are the fuels utilized during exercise. The degree to which each fuel acts as the primary or secondary source of energy and the efficiency with which energy is utilized depends on the prior nutrition of the athlete and the intensity and duration of the exercise. At low levels of prolonged exercise most energy needs come from fat and lesser energy needs come from carbohydrate. At higher intensity carbohydrate plays a greater role but is limited in its duration of action. Protein plays only a minor role at very high levels of energy utilization, but adequate protein intake is critical for maintenance of lean body mass to enable exercise performance.
Energy is extracted from foods in the body by converting the chemical energy stored in chemical bonds to high energy phosphate bonds in ATP (Adenosine Triphosphate). This high energy bond can be used in a number of biochemical reactions as a fuel with the conversion of ATP to ADP (adenosine diphosphate). If ADP begins to accumulate in muscle then an enzyme is activated in muscle to break down phosphocreatine (PCr) in order to restore ATP levels (PCr + ADP ® ATP + Cr). The creatine released from this reaction is converted to creatinine and excreted in the urine. The stores of PCr are extremely limited and could only support muscle ATP levels for about 10 seconds if there were no other sources of ATP. Since ATP is provided from other sources, PCr ends up being a major energy source in the first minute of strenuous exercise. PCr has the major advantage of being localized in the muscle so that it can rapidly restore and maintain ATP levels for intense exercises such as sprinting, jumping, lifting, and throwing.
II. Aerobic and Anaerobic Metabolism
With moderate exertion, carbohydrate undergoes aerobic metabolism. Under these conditions, oxygen is used and the carbohydrate goes through both the Embden-Meyerhoff pathway of anaerobic metabolism in which glucose is converted to lactate, but, prior to the conversion of pyruvate to lactate, pyruvate enters the Krebs Cycle in mitochondria where oxidative phosphorylation results in a maximum extraction of energy from each molecule of glucose. If there is plenty of oxygen available and the exercise is of low to moderate intensity, then the pyruvate from glucose is converted to carbon dioxide and water in the mitochondria. Approximately 42 ATP equivalents can be produced from a single glucose molecule compared to only 4 ATP with anaerobic metabolism. Aerobic metabolism supplies energy more slowly than anaerobic metabolism, but can be sustained for long periods of time up to 5 hours. The major advantage of the less efficient anaerobic pathway is that it more rapidly provides ATP in muscle by utilizing local muscle glycogen. Other than PCr, it is the fastest way to resupply muscle ATP levels. Anaerobic glycolysis supplies most energy for short term intense exercise ranging from 30 seconds to 2 minutes. The disadvantages of anaerobic metabolism are that it cannot be sustained for long periods, since the accumulation of lactic acid in muscle decreases the pH and inactivates key enzymes in the glycolysis pathway leading to fatigue. The lactic acid released from muscle can be taken up by the liver and converted to glucose again (Cori Cycle), or it can be used as a fuel by the cardiac muscle directly or by less active skeletal muscles away from the actively contracting muscle.
Mysterious Chorus Voice: We have to start Act 3.
Merlin’s parallel database query thing: My big headache from calculating these trajectories is better after that delicious drink.
Writer: Okay, I think I can do it.
Mysterious Chorus Voice: What are you doing with the book?
Writer: I getting ready to write the words for act 3.
Missy Mom Laurie: You have spent too much time with your silly friends. You need to do your chores around the house and do your report.
Writer: Why do I have to do the report now? I want to do the story.
Missy Mom Laurie: No report, no story . . .
Writer: I have been working on it. It is almost ready.
Missy Mom Laurie: Almost is not good enough . . . I have been waiting on your history report long enough. Let’s hear it now.
Writer: Written language starts with sounds people here, and things people see. The object becomes a reference which becomes sounds and then multiple sounds which are now drawn into figures in what is known as a letter sound in some type of ancient reference which become letter shapes with letter names. Our best records go back to people keeping records of the cattle trade and such . . .
~ 10 kya: Mid-eastern monuments and clay tokens for record keeping
~ 6.0 kya: Mesopotamian cuneiform (writing system beginning with clay food tokens)
~ 4.7 kya: Egyptian hieroglyphs (22 hieroglyphs to represent the individual consonants + one for word-initial or word-final vowels)
~ 4.0 kya: Central Egyptian Semitic alphabetic script
~ 3.6 kya: Pictorial Canaanite letters with specific meanings such as “ox” and “house” based upon what they thought was important.
~ 2.8 ~ 1.1 kya: Phoenician alphabet and cultural separation between Greek and Hebrew alphabet from the Phoenician where the order of Greek and Phoenician letters was the same with some letters now representing vowels such as "a, e, i, o, and y (upsilon)." To accommodate all twelve Greek vowels things like diphthongs were used which include the big O, omega. The phi, chi, psi constants were added because the Phoenician language had no known aspirates, and omega was added to account for the long "o" vowel sound. The new letters were placed at the end of the Greek alphabet. Some letters disappeared over time mostly because of popularity within western and eastern geographic boundaries all along the Mediterranean shores. The letter sigma became the popular variant over san which became obsolete in time while the number sampi, 900, became obsolete as a letter. It was thought to be a combination of san and pi. Another letter was the digamma or wau or fau, and it had an "F" look because it was derived from the Phoenician letter waw or vav. It later became the Latin letter "F" while the Phoenician variant also became "V, and later U, W, and Y" in Latin or the Roman language. Another interesting letter was the Phoenician Qoph. It is thought to come from a pictogram of a monkey with a body and tail, and it developed into the Greek letter Qoppa which is round like a head with a tail like a neck. It too became obsolete in Greek but in Latin it became the letter Q. The Latinas ended up in dropping four letters from the Western Greek alphabet while adapting the Etruscan letters "G" and zigzagged "S" along with other such complication. The letters J, U, W, Y, and Z were added to make the modern English alphabet which seems to be based upon the sounds each letter makes.
We now separate the alphabet by its vowels and the water or snake signs m & n which are in the middle of the alphabet. It looks like the following:
The "a" vowel group: A B C D;
The "e" vowel group: E F G/H;
The "i" vowel group: I J K L;
The ancient origin myth group: M N;
The "o" vowel group: O P Q R/S/T;
The "u" vowel group: U V W/X Y/Z
Missy Mom Laurie: That is a very good story even though it is sketchy. You can write your story now.
Writer: Thanks Missy . . . I mean mom . . . I mean Laurie . . .
Missy Mom Laurie: Have you eaten your veggies today?
Writer: No . . .
Missy Mom Laurie: Well, you are not writing that story until you finish all of your veggies.
Writer: It tastes like rabbit food.
Missy Mom Laurie: Fiber helps control your sugar spikes.
Writer: . . . but it still tastes like rabbit food.
Missy Mom Laurie: When you eat fiber like veggies your glucose is less likely to go over 140 when you complete your meal. You can then eat other things like meats or high protein veggies before you finish up with your high carbohydrate foods. This will help to keep your belly flab around your waist to a minimum and your BMI less than 23. Also long and regular sleeping habits while eating at regular times is helpful when you stay active increasing your muscle mass with exercise. You need muscles to absorb your sugar you know, and you need to keep your blood flowing after you eat. You just cannot sit all day long writing or those glucose spikes will cause hardening of arteries. They will also change and mutate your DNA. Do not you realize all bears do not write stories?
Writer: Okay, I’ll eat some veggies if I can eat some candy.
Missy Mom Laurie: You can only have your candy after you eat your veggies.
Writer: Oookay . . .
Missy Mom Laurie: People in different DNA groups eat different diets, and people who eat different diets look differently. Just like people who live in different climates and geographical topologies look differently. After all many indigenous people are often the first people who interbreed and look differently than the original people.
Writer: I’ll eat it. Look, I am eating it now . . . (yuck).
Mysterious Chorus Voice: Do you really want me to say “ . . . that breathless charm?”
Mysterious Chorus Voice: Have you ever tried saying that?
Writer: What do you mean?
Mysterious Chorus Voice: It has too much tongue and lip motions to do to make good sense. It’s easy to get tongue tied.
Writer: Now really, think about it for a second. It is all about its sentimental meaning.
News flash <Beep Beep Beep>: Attention, attention, . . . , this is a new alert. Stupid Mouse is missing, and he is not available for this Sunday’s award show. Once again, Stupid Mouse is missing. If anyone has seen him, please report to Captain Wagg at your local police department. Stupid Mouse is unavailable for the award show this Sunday!
Mysterious Chorus Voice: How horrible! I was hoping he would win best actor again. Remember what he said about the tangent of theta?
Write: Yeah . . . Huh?
Mysterious Chorus Voice: I guess it is hard to think about the law of proportions, y1/x1 = y2/x2, when you are in the midst of an evil cloud.
Writer: It might be a publicity stunt for the show tomorrow.
Mysterious Chorus Voice: Yeah? He might be the first actor to win an award for not appearing!
Writer: Hum, I do not imagine how that is possible, but you might be correct knowing Stupid Mouse.
Missy Mom Laurie: When are you going to eat those greens I got for you?
Writer: I am still looking for a can opener.
Missy Mom Laurie: You have been using that can opening excuse for some time.
Writer: It is true. I need a can opener.
Missy Mom Laurie: Why don’t you get one?
Writer: I tried.
Mysterious Chorus Voice: Take mine . . . yuck, I can’t stand this anymore.
Missy Mom Laurie: See, your strange and mysterious friend had one. Why didn’t you ask?
Writer: I guess I was worried about the story so much. I did not ask.
Missy Mom Laurie: Well, now you know. Ask before you whine . . . let that be a lesson to you.
Writer: Well, okay.
Missy Mom Laurie: Did you finish cleaning the toilet?
Missy Mom Laurie: Did you finish vacuuming the sofa?
Missy Mom Laurie: Did you finish your genetics report?
Missy Mom Laurie: You heard me. Update me on your progress . . .
Writer: Okay, First genetic genealogy . . . social rank is determined by your parents and past history based upon generation:
Parents (first three generations, Filiations [Rank in family], Agnomen [Personal nickname]);
Family (first eight generations, Cognomen [Sept or family's nickname]);
Relatives (first sixteen generations [Nomen: Clan or name of tribe]);
Tribe (first thirty to forty generations [Praenomen: Given name from parents]);
Language haplogroup (first 90 - 150 generations)
Migration group (150 - 400 generations)
Late Pleistocene (various early haplogroups [not understood in 2009 by the dog guy online, debatable results])
Early Metal Age Hg (12 kya)
Older Dryas Hg (15 kya)
World Homo Dominance (18 -25 kya)
Divergent Homo Groups (35-45 kya)
The Homo sapiens' Journey (~60 kya)
Missy Mom Laurie: Hummm . . . where do you get those generations numbers from . . . ?
Writer: They are educated guess based upon feedback I have heard.
Missy Mom Laurie: Where these poor or well to do families or both?
Writer: I would guess mostly educated people who had to work for a living.
Missy Mom Laurie: For an unscientific study, it certainly has its aspects of provoking the thoughts. What else can you say?
Writer: All living things exchange material with their surroundings, and there are terms to study.
troph = nourishment
autotroph (inorganic) and heterotroph (organic)
organotrophic (Lewis base contains organic compounds for energy production such as to form reduced coenzymes) and lithotrophic (Lewis base contains inorganic compounds for energy production such as to form reduced coenzymes)
chemotroph (oxidizes of electron donating molecules using organic and inorganic compounds as its principle energy source) and phototrophs (solar energy)
Chemoautotrophs (synthesize all organic compounds from carbon dioxide) and Chemoheterotrophs (essential organic materials must be ingested ~ amino acids (PVT Tim Hall), lipids, sugars such as glucose)(various types of nucleo-tide-synthesis)
Writer: Carbon, hydrogen, and oxygen compounds seem to be important.
a-D-Glucose - -> glucose-6-phosphate - -> ribulose-5-phosphate can reversibly isomerize to ribose-5-phosphate
5-Phospho-a-D-ribosyl 1-pyrophosphate (PRPP) [in liver cytosol, replacement of pyrophosphate by amide(#9 on #1 beta of sugar) group of glutamine] - -> 5-Phosphoribosylamine [rate-limiting step] - -> IMP
Writer: This leads to DNA.
AMP <- - (aspartate to fumerate) IMP (glutamine to glutamate)- -> GMP
Purines [IMP](amino nitrogen of aspartate [#1], 10-formyl THF [#2,8, folate one-carbon pool (methanoyl group)], amide nitrogen of glutamine [#3,9], glycine [#4,5,7], carbon dioxide [#6, carboxyl group], glucose [ribose 5-P connected to #9], ATP energy)
Pyrimidine [Carbamoyl Phosphate - -> Orotic Acid (with PRPP)- -> UMP - -> UTP (Glutamine to Glutamate) - -> CTP](carbon dioxide's carbon [#2] and glutamine's amide nitrogen [#3] via carbamoyl phosphate, aspartate [#4,5,6,1], sugar phosphate [from PRPP] attached to ring nitrogen [#1])
Bases (Purines and Pyrimidines) - - -> Nucleosides - - -> Nucleotides - - -> Polynucleotides (Primary Structures)
Adenine = 6-amino purine
Guanine = 2-amino-6-oxy purine
Hypoxanthine = 6-oxy purine
Xanthine = 2,6-dioxy purine
Uracil = 2,4-dioxy pyrimidine
Thymine = 2,4-dioxy-5-methyl pyrimidine
Cytosine = 2-oxy-4-amino pyrimidine
Orotic acid = 2,4-dioxy-6-carboxy pyrimidine
If a sugar, either ribose or 2-deoxyribose, is added to a nitrogen base, the resulting compound is called a nucleoside. Carbon 1 of the sugar is attached to nitrogen 9 of a purine base or to nitrogen 1 of a pyrimidine base. The names of purine nucleosides end in -osine and the names of pyrimidine nucleosides end in -idine. The convention is to number the ring atoms of the base normally and to use l', etc. to distinguish the ring atoms of the sugar. Unless otherwise specificed, the sugar is assumed to be ribose. To indicate that the sugar is 2'-deoxyribose, a d- is placed before the name.
Inosine - the base in inosine is hypoxanthine
Adding one or more phosphates to the sugar portion of a nucleoside results in a nucleotide. Generally, the phosphate is in ester linkage to carbon 5' of the sugar. If more than one phosphate is present, they are generally in acid anhydride linkages to each other. If such is the case, no position designation in the name is required. If the phosphate is in any other position, however, the position must be designated. For example, 3'-5' cAMP indicates that a phosphate is in ester linkage to both the 3' and 5' hydroxyl groups of an adenosine molecule and forms a cyclic structure. 2'-GMP would indicate that a phosphate is in ester linkage to the 2' hydroxyl group of a guanosine. Some representative names are:
AMP = adenosine monophosphate = adenylic acid
CDP = cytidine diphosphate
dGTP = deoxy guanosine triphosphate
dTTP = deoxy thymidine triphosphate (more commonly designated TTP)
cAMP = 3'-5' cyclic adenosine monophosphate
Missy Mom Laurie: Okay, only the words and research is missing. I am sure you will write more later?
Writer: I am sleepy . . .
Missy Mom Laurie: What are you doing? I thought you were going to write your paper.
Writer: I am looking at television. I have writers block, and I just cannot complete my thoughts.
Missy Mom Laurie: What did you see?
Writer: The combined absorption spectra of the red/far-red light receptors (phytochromes) and the blue light receptors (cryptochromes and phototropins) overlap with those of the photosynthetic pigments, allowing coordinated control of development and energy production in plants. Some plants grow best in the shade while other grow best in the sun. Of course they look different. The assumption is that it has to do with their exposure to the sun. The observation of so called shade plants and sun plants studies have been extended to the morphological study of bushy blue light plants (guard cells proton pump, stomata opening, H+-ATPase activation) and long stem red light plants (photosystems I & II). As early as 1880, Charles Darwin had noted: "no one can look at the plants growing on a bank or on the borders of a thick wood, and doubt that the young stems and leaves place themselves so that the leaves may be well illuminated." On the basis of molecular genetic studies in Arabidopsis, it is now clear that there are two types of blue light receptors in plants: cryptochromes and phototropins (Plant Cell. 2002; 14(Suppl): s207–s225.). Cryptochromes work together with phytochromes to regulate photomorphogenic responses, including the regulation of cell elongation and photoperiodic flowering; phototropins, on the other hand, mediate movement responses including the phototropic curvature that attracted Darwin's attention more than a century ago (1881 by Darwin).
I was looking at a television special the other day, and the researcher discovered that in order to keep up with the world today, education was now becoming a continuous endeavor. While the exact mechanism of growth and light beginning with germination still is unknown. Significant progress has been made towards a solution. The website for leoLED had a good review. Blue light makes plants bushier and compact, reducing internode length. It can slow down photosynthesis slightly overall by hiding chloroplast at high intensity while producing healthier and nutrient richer plants and helps set the circadian rhythm.
Blue light is of course a main contributor to photosynthesis via chlorophyll, but it also influences a plant in other ways. Blue light is typically encountered in nature at midday, when the angle of the sun is directly vertical or close to it. This would usually be a time of peak intensity and heat, therefore in many plants high intensities of blue light cause the chlorophylls to migrate to the bottom of the cell for shielding. Moreover, cryptochrome is a phytochemical that absorbs the blue spectrum and initiates phototropism (growing towards light), plus sets a plants circadian rhythm (in combination with phytochrome and the photoperiod). Interestingly, strong blue light reduces leaf intermodal length in a plant and causes it to grow compact and bushy, not wasting energy on stem length, which would be unnecessary in blue dominant full sun conditions. Many growers use blue light to keep plants compact and under control. In addition plant stomata number increases with the intensity of the blue light fraction, possibly increasing photosynthetic rates further.
Red light is the second main contributor to photosynthesis, but similarly to blue it produces unique results in plant physiology. Red light exists most when the sun is low in the sky, which is winter, morning and evening. You can imagine that a plant will know what time of day it is by the presence of red light, and you would be right. Phytochromes are phytochemicals that carefully observe red and far red light, specifically the balance between them, and set many decisions based on this balance, such as elongating stems to beat crowing via other plants, setting seasonal or daily flowering period, budding, and contributing to plant circadian rhythm. Red light is special in that it can deliver high growth to a plant, but without the limiting effect of blue that obscures the chloroplast to protect it from high-blue midday sun. Therefore red is very efficient at producing fast growing tall and strong plants and indeed produces some of the most impressive growth rates of height and stem width in plants.
The Grobo website also has some interesting information. Multiple studies have been conducted on how different colors of lights can have varying effects on the growth of a plant. Thanks to the recent developments in LED (light emitting diode) technology, specific light wavelengths can now be isolated in order to control the different physical properties that a plant displays as it develops throughout its life cycle. These properties include, but are not limited to, height, weight, color, and texture, as well as the chemical composure of the plant itself. As a plant grows, you can use LED grow lights to manipulate these physical properties depending on the plant characteristics that you desire.
Ultraviolet (200 nm to 380 nm): No exposure produces better growth;
Violet (380 nm to 445 nm): Enhances the color, taste, and aroma of plants;
Blue (450 nm to 495 nm): Increases the growth rate of plants;
Green (495 nm to 570 nm): Enhances chlorophyll production and used as a pigment for proper plant viewing;
Yellow (570 nm to 590 nm): Plants exhibit less growth compared to blue and red light;
Red (620 nm to 720 nm): When combined with blue light it yields more leaves and crops, depending on what you are growing;
Far Red (720 nm to 1000 nm): Speeds up Phytochrome conversion which reduces the time a plant takes to go into a night time state. This allows the plant to produce a greater yield.
A regular plant has a phytochrome system (a light detection system) which regulates its growth, adjusting itself depending on the type of light that it is exposed to. In this system, there are two predominant forms of plant protein: its biologically inactive form (Pr), and its biologically active form (Pfr). When a plant perceives the red light, Pr transforms into Pfr, and if a plant receives the far-red light, its Pfr changes to Pr.
Pfr is important because it triggers plant growth, but it slowly reverts back to Pr over time when the plant is located in the dark. At the end of the day, a plant’s flowering and vegetative growth is directly influenced by the Pr to Pfr ratio.
Missy Mom Laurie: They call the TV, the idiot box you know.
Mr. Hertz: What??? One dollar per episode for each actor!!! Are you crazy?
Methyl: That is what they said . . . They want big cash if you want those ratings to go up again.
Mr. Hertz: We just cannot sell enough Mello to pay for that.
Methyl: Yes, Mello with fruit is great. And it will always always always wiggle and shake before it slides down the throat, but there is something else?
Mr. Hertz: Aw, What can be as good as Mello sliding down your throat?
Methyl: Well, you are going to need your veggies, and you are on the run, grab a bottle of this? And then just gulp it down.
Mr. Hertz: Okay, <gulp>, Come on! What are you talking about?
Methyl: Guess the first letter . . .
Mr. Hertz: “Z”
Methyl: Err, you are wrong, oh feverous one. Try again.
Mr. Hertz: “V”
Methyl: Sounds good to me, try again.
Mr. Hertz: “D”
Methyl: Sounds good to me, try again.
Mr. Hertz: “E”
Methyl: Sounds good to me, try again.
Mr. Hertz: “I”
Methyl: Sounds good to me, try again.
Mr. Hertz: “G”
Methyl: Sounds good to me, try again.
Mr. Hertz: “H”
Methyl: Sounds good to me, try again.
Mr. Hertz: “T”
Methyl: Sounds good to me, try again.
Mr. Hertz: “y”
Methyl: Sounds good to me, try again.
Mr. Hertz: “J”
Methyl: Sounds good to me, try again.
Mr. Hertz: “U”
Methyl: Sounds good to me, try again.
Mr. Hertz: “I”
Methyl: Sounds good to me, try again.
Mr. Hertz: “C”
Methyl: Sounds good to me, try again.
Mr. Hertz: “E”
Methyl: You got it.
Mr. Hertz: Wow, this VD Eighty Juice is great!
Methyl: What did I say . . .
Mysterious Chorus Voice: What are you doing?
Writer: I was really really hungry, and I had so much fun playing my new game.
Original Score Begins Playing:
Dinglying Dinglying Dinglying . . .
Poottay Flakes, the stuff of champions, are more than pretty good. They are the breakfast cereal with something more than get up and go because they have the secret ingredient we call zappo making them the Lucky Stripes of great taste. So, the next time when you are in the cereal aisle of your favorite grocery store do not resist picking up some delicious smoking good Poottay Flakes; Umm Umm tremendous.
Preamble of Show
It all began in the usual way. It was a dark and clear sky night. It had been a long hard day's work. Now, it was a little past midnight. Strange glowing lights appeared in the sky falling in the distance. The weary eyes of David Architect burned with fatigue, stopping him in his daily quest home. As he regained his sight, the glow faded as he pledged to return in the morning.
When the bright glowing sun rose early in the morning, it was not hot. It was not cold. It was not wet. It was not dry. It was nice. It was very nice. Looking out the window, the birds were playful. It was as if they were laughing, laughing as if there were overtones of something joyful. It was an oath of something so incredible; it was nested within something we all think about when we are in love. Love such as what is found within the heart of someone who was cleaning oneself into something new and happy and playful. Birds entreat each day to waiting ears: the truth. Such faithfulness is a sound of joy, and it signals growth in compassion beyond the meaning of what has been really done.
The all new Tasty Stink-a- ogie Chop presents “I am Hungry” in all new wonderful rainbow colors, a WezyMu production!
Starring: The Incredible Snowflakes; The Marvelous Goatheads; The Awesome Holy Ones; Capt. Wagg and the other officials; And introducing David Architect, Palmolive, Stealthy Platarat, JJJ, She Imp, the Dame, the usual gang of extras, and our special guest stars the Unpredictable PPs..
My applesauce, it’s my real applesauce! . . . Served with our Tasty Stink-a- ogie Chops too. And to cook those chops try picking up our new stick-free copper plated cooking pan. This is the real thing. It spreads the heat to cook those tasty slices in less than five minutes on each side. And do not worry about cleaning with our amazing Alice technology. Just toss it in the stink, and zap, bam, whammo . . . all cleaned and dried. Perfect for those hungry stomach sounds; and far cheaper than those other imitations; just call our number for a sales pitch to see how low we will go.
Act 4, Introduction: I Began to Write
Missy Mom Laurie: Have fun with your strange friends, and write a nice story.
Mysterious Chorus Voice: You have to stall. Everybody is coming back from lunch.
Writer: I found some good things to take up time.
Stink-a-ogie Singers: Stink . . . Stink, Stink . . . Stink, Stink-a- ogie, Stink, Stink . . . Stink, Stink . . . Stink, Stink-a- ogie, Stink, Stink, Stink-a-ogie . . . Ahhhhh!!!!
The difference between skotomorphogenesis and photomorphogenesis is that skotomorphogenesis is (botany) the development of a seedling in the dark while photomorphogenesis is (biology) the regulatory effect of light on the growth, development and differentiation of plant cells, tissues and organs.
In August of 1771, Joseph Priestley, an English Chemist, put a sprig of mint into a transparent closed space with a candle that burned out the air (oxygen was not discovered yet) until it soon went out. After 27 days, he relit the extinguished candle again and it burned perfectly well in the air that previously would not support it. And how did Priestley light the candle if it was placed in a closed space? He focused sun light beams with a mirror onto the candle wick (Priestley had no bright source of light, and had to rely on the sun). Today, of course, we can use more sophisticated methods to light the candle like focusing light from a flood light through converging lens, or by an electrical spark.
So priestly proved that plants somehow change the composition of the air.
In another celebrated Experiment from 1772, Priestley kept a mouse in a jar of air until it collapsed. He found that a mouse kept with a plant would survive. However, we do not recommend to repeat this experiment and hurt innocent animals.
These kinds of observations led Priestley to offer an interesting hypothesis that plants restore to the air whatever breathing animals and burning candles remove.
Light absorption does not correlated to photosynthesis rate.
chloroplasts contain a third membrane — the thylakoid membrane — that is the site of photosynthesis
photosynthetic process in plants into four stages, each occurring in a defined area of the chloroplast:
(1) absorption of light,
(2) electron transport leading to the reduction of NADP+ to NADPH,
(3) generation of ATP ( This use of the proton-motive force to synthesize ATP is identical with the analogous process occurring during oxidative phosphorylation in the mitochondrion ), and
(4) conversion of CO2 into carbohydrates (carbon fixation).
All four stages of photosynthesis are tightly coupled and controlled so as to produce the amount of carbohydrate required by the plant.
There are four main photosynthetic pigments found in the chloroplast of the plant called chlorophyll a, chlorophyll b, xanthophylls, and carotenes.
An initial experiment showed that all the pigments at peak absorbance showed violet/blue light at the highest level, orange/red light as the second highest, and yellow/green having the lowest level of absorption.
Similarities Mitochondria and chloroplast both have:
A double membrane surrounding the organelles.
Purportedly prokaryotic origins according to the endosymbiotic theory which suggests that mitochondria and chloroplast were once prokaryotic bacteria engulfed by endocytosis in early eukaryotes.
Their own circular DNA which codes for certain enzymes required for the chemical reactions that take place in this organelles.
Their own 70S ribosomes made up of 50S and 30S subunits to translate proteins
The enzyme ATP synthase which utilizes the energy released from the movement of protons across it (proton-motive force) to phosphorylate ADP to ATP. (Thus, another similarity would be that they both produce ATP)
Electron transport chains, which are embedded in the inner mitochondrial membrane and thylakoid membrane in mitochondria and chloroplasts respectively.
Both organelles have chemical cycles in which the initial acceptor is regenerated at the end of the cycle. In mitochondria, the Krebs cycle occurs after which oxaloacetate is regenerated at the end of the reaction. In chloroplasts, the Calvin cycle occurs in which ribulose bisphosphate (RuBP) is regenerated at the end of the reaction.
Obvious structural and naming differences that you should be able to figure out from the diagram above.
Mitochondria are involved in cellular respiration whereas chloroplasts are involved in photosynthesis. Thus, the overall chemical reactions for the processes occurring in them are different and reversed.
- Respiration: C6H12O6+6O2 ---> 6CO2+6H2O+ATP
- Photosynthesis: 6CO2+6H2O --->C6H12O6+6O2
Mitochondria are found in all animal and plant cells. Chloroplasts, however, are found in only specific types of plant cells, such as the palisade mesophyll and spongy mesophyll cells of leaves. These cells are the ones involved in carrying out photosynthesis. Other types of plant cells, such as root cells do not contain chloroplasts.
Chloroplasts contain pigments such as chlorophyll a, chlorophyll b and carotenoids. Mitochondria do not contain any such pigments.
The ATP synthase in mitochondria and chloroplast are orientated differently. ATP synthase in mitochondria points into the matrix, with protons flowing from the intermembrane space to the matrix. In chloroplasts however, ATP synthase points towards the stroma, and protons flow from the thylakoid space into the stroma.
The types of electron acceptors present in mitochondria and chloroplast vary. While mitochondria contain NAD and FAD, chloroplasts contain NADP.
The sources of energy used to synthesize ATP in mitochondria and chloroplasts are different. In mitochondria, this energy comes from the oxidation of glucose, and is hence termed oxidative phosphorylation. In chloroplast, this energy comes from light, so it is called photophosphorylation.
Mitochondria function under both light and dark conditions. Chloroplasts, on the other hand, do need light to function.
Electron transport chains: The final electron acceptor in mitochondria is oxygen, whereas the final electron acceptor in chloroplasts is NADP.
In mitochondria, the root source of electrons is generally glucose (it could be other substrates depending on what was utilized). In chloroplasts, however, the root source of electrons is the photolysis of water occurring at photosystem II. Water (H2O) is broken down to release 2 protons, 2 electrons and a molecule of oxygen.
Mitochondria give out carbon dioxide from the decarboxylation (removal of carbon)reactions that occur during the link reaction and Krebs cycle but chloroplasts give out oxygen due to photolysis as explained above.
Agronomy 2017, 7, 25; doi:10.3390/agronomy7010025
Because plant life relies on solar radiation as an energy source, plants have acquired a light-sensing mechanism to maximize the availability of light for photosynthesis [1,2]. Specifically, germination does not occur in deep subterranean darkness and occurs only when the plant senses a low amount of light under the ground at depths close to the surface of the soil. The post-germinative seedlings in the soil elongate the hypocotyl with a closed hook, and yellowish cotyledons move toward the surface of soil.
Upon reaching the surface and absorbing light, seedlings start photomorphogenic development, in which hypocotyl elongation ceases, the hook and cotyledons start to open, and chloroplasts begin developing to maximize light capture and autotrophic growth. This developmental transition from a dark-grown seedling to a light-grown seedling is called de-etiolation. Even aboveground plants must sense the presence and proximity of neighboring plants and compete with them for solar energy through a response called Shade Avoidance Syndrome (SAS). Plants detect shade from neighboring plants as alterations in the light quantity and quality, and, in response, they elongate the hypocotyl, petiole, and internode to bring the photosynthetic organs to more favorable conditions for photosynthesis. Plants also perceive the day length to control the transition from the vegetative phase to reproductive phase. As exemplified above, light as an environmental signal regulates plant development throughout the plant life cycle. The blue (B) and red (R) light regions of the light spectrum are most efficiently utilized for the photosynthesis; thus, B light-sensing cryptochrome (cry) and R light-absorbing phytochrome (phy) play major roles in regulating plant light responses, such as light dependent seed germination, de-etiolation, SAS and photoperiodic flowering [3–5].
1. Chen, M.; Chory, J.; Fankhauser, C. Light signal transduction in higher plants. Annu. Rev. Genet. 2004, 38, 87–117. [CrossRef] [PubMed]
2. Kami, C.; Lorrain, S.; Hornitschek, P.; Fankhauser, C. Light-regulated plant growth and development. Curr. Top. Dev. Biol. 2010, 91, 29–66. [PubMed]
3. Franklin, K.A.; Quail, P.H. Phytochrome functions in Arabidopsis development. J. Exp. Bot. 2010, 61, 11–24. [CrossRef] [PubMed]
4. Wang, X.; Wang, Q.; Nguyen, P.; Lin, C. Cryptochrome-mediated light responses in plants. Enzymes 2014, 35, 167–189. [PubMed]
5. Yang, Z.; Liu, B.; Su, J.; Liao, J.; Lin, C.; Oka, Y. Cryptochromes orchestrate transcription regulation of diverse blue light responses in plants. Photochem. Photobiol. 2017, 93, 112–127. [CrossRef] [PubMed]
6. Gururani, M.A.; Ganesan, M.; Song, P.S. Photo-biotechnology as a tool to improve agronomic traits
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