PjProblemStrings Sequences Of ATP Supply Chains

PjProblemStrings Sequences Of Adenosine Triphosphate Supply Chains.
TECTechnics Classroom TECTechnics Overview

PjProblemsStrings Sequences Of Adenosine Triphosphate Supply Chains

PjProblemStrings Sequences Of ATP Supply Chains

Energy is the basic existential currency especially for living organisms. In other words, existence demand energy. So, there exist existential supply chains.

(a) What is Adenosine Triphosphate (ATP)?
(bi) Where in the human cell is ATP produced?
(ii) Identify the supply chains needed to produce ATP in the human body.
(iii) Indicate the PjProblemStrings Sequences of the supply chains.
(iv) Which of the 7 types of PjProblemStrings sequences are present in ATP supply chains?
(ci) How has the human body secured its ATP supply chains?
(ii) Is the security perfect?
(iii) What lessons can humans learn from how ATP supply chains are secured in the human body?
(d) ATP is a single nucleotide. Name two important macromolecules in the human body that also contain nucleotides.
(e) How is the energy ATP stores made available in cells?
(f) Briefly state the fundamental biologic cycle of energy.

The strings: S₇P₃A_3k (force -k =1, 2), S₇P₄A_4k (motion- k =1, 2, 3,4).

The math:
All Pj Problems are at play. However, Pj Problems of Interest are of types force and motion.

ATP

(a)Adenosine Triphosphate (ATP) is a nucleotide (a substance composed of a phosphate, a ribose sugar, and a nitrogen-containing base).
ATP contains three phosphates, hence the prefix, Tri. The nitrogen-containing base in ATP is Adenine (one of the four nitrogen-containing bases in nucleotides. The other three are cytosine, thymine, guanine). When the molecule contains two phosphates it is called Adenosine Diphosphate (ADP). When the molecule contains one phosphate, it is called Adenosine Monophosphate (AMP). ATP is important because it is the form in which energy is stored in the cells of living organisms. A cell will die if it has no energy to carry out its metabolism (the sum of all chemical reactions or energy exchanges in cells). Energy demand in cells is synonymous with ATP demand in cells. In other words, ATP must be presented to obtain the energy needed for cellular activities. It is for this reason that ATP is often called the energy currency of the cells.
ATP is produced in cells during cellular respiration (anaerobic and aerobic). In anaerobic respiration (respiration without oxygen), ATP is produced during glycolysis and fermentation. However, most of the ATP in human cells are produced during aerobic respiration (respiration with oxygen) in the three part processes: glycolysis, TCA cycle and electron transfer chain.

(bi) ATP is produced in the cell's cytoplasm during glycolysis and the mitochondria (matrix and innermembrane) during the TCA cycle and the end of the electron transfer reactions.

(bii) ATP supply chains can be categorized into external ATP supply chains (materials supplied originate from outside the organism) and internal supply chains (materials supplied originate from within the cell).
External Supply Chains
Supply Chain: the respiratory system
Material supplied by the respiratory system: oxygen.

Supply Chain: the digestive system.
Material supplied by the digestive system: digested food (carbohydrate, protein, lipids) and water. The food often contain vitamins and minerals.
Transporter
The circulatory system transports oxygen and nutrients.

Internal Supply Chains
Supply Chain: glycolysis

Material supplied to glycolysis: glucose.
Material supplied by glycolysis: pyruvate.

Supply Chain: transition reaction
Material supplied to the transition reaction: pyruvate
Material supplied by the transition reaction: acetyl CoA (acetyl coenzyme A)

Supply Chain: Tricarboxylic Acid Cycle (TCA cycle, also called the Kreb's cycle and the citric acid cycle).
The Tricarboxylic Acid Cycle
The Steps Of Tricarboxylic Acid Cycle
Material supplied to the TCA cycle: acetyl CoA (acetyl coenzyme A),
Material supplied by the TCA cycle: NADH (reduced coenzyme of coenzyme Nicotinamide Adenine Dinucleotide(NAD)), FADH₂ (reduced coenzyme of coenzyme Flavin Adenine Dinucleotide (FAD)).

Supply Chain: electron transport chain

Material supplied to the electron transport chain: NADH, FADH₂
Material supplied by the electron transport chain: protons.

Supply Chain:ATP Synthase
Material supplied to ATP Synthase: protons
Material supplied by ATP Synthase: ATP.
In this supply chain, Enzyme ATP Synthase moves a proton down the proton gradient created by the pumping of protons into the intermembrane space of the mitochondria during the Electron Transport Chain. The resulting energy is used to phosphorylate ADP to ATP in a process called oxidative phosphorylation: ADP + P_i -> ATP. Most of cellular ATP is produced during oxidative phosphorylation.

PjProblemString Sequences of Supply Chains
A PjProblemString Sequence is a sequence of PjProblemStrings (S_iP_jA_k: a space of interest stringed to a particular problem of interest). Supply chains are configurations of PjProblemStrings Sequences. The PjProblemString Sequence that is of primary importance is motion sandwiched between two forces (S_iP₃A_kS_iP₄A_kS_iP₃A_k). The first force is the active force and the second is resistive force. The difference between the active force and the resistive force is the resultant force (driving force) causing the motion. In some scenarios, the active force is deliberately reduced in order to reduce or stop the motion (e.g. a runner reduces speed after crossing the finishing line).
Muscles (skeletal, smooth and cardiac), hydrostatic pressure, vascular elasticity, enzyme actions, attractive and repulsive forces of atoms, electrochemical gradients are the primary sources of forces in the human body.
(biii) Supply chain: respiratory system
Motion sandwiched: movement of oxygen into lungs.
Forces sandwiching motion: atmospheric pressure and thoracic pressure.
Diaphram contraction and relaxation and intercostal muscle contraction and relaxation influence pressure in the thoracic cavity.
Diaphram contraction (movement downward) and intercostal muscle contraction (elevates the chest) increase volume of thorax. Increase in thorax volume results in decrease in thorax pressure. So, inhalation (movement of air into lungs) occurs when atmospheric pressure is greater than the decreased pressure in the thorax. In a reverse manner, diaphram relaxation and intercostal muscle relaxation decrease volume of thorax. So pressure in thorax is increased. Carbon dioxide is exhaled when thoracic pressure is greater than atmospheric pressure.
Oxygen travels in the lungs through the trachea, bronchi, bronchiole to the aveoli (tiny air sacs where oxygen and carbon dioxide exhange occurs) where it diffuses into the capillaries in the alveoli (carbon dioxide diffuses into the alveoli). Oxygen in capillaries enters the pulmonary venules and then the pulmonary vein to the left atrium of the heart.

Motion sandwiched: movement of oxygen from the capillaries of the lungs to the left atrium of the heart.
Forces sandwiching motion: pulmonary vein hydrostatic pressure and left atrium hydrostatic pressure. Pressure in the left atrium is much lower than hydrostatic pressure in the pulmonary vein . Sequential hydrostatic pressure gradient in the pulmonary vein allows the oxygenated blood to move into the left atrium of the heart and then into the left ventricle from where it is pumped into the aorta for systemic distribution.

Supply chain: digestive system
The digestive process can be grouped into six subprocesses: ingestion, propulsion, physical digestion, chemical digestion and excretion (defecation).
Motion sandwiched: movement of food through the alimentary canal which can be subdivided as follows: food movement into the mouth, stomach, small intestine and large intestine.

Motion sandwiched: food movement into mouth
Forces sandwiching motion: muscle action (usually of the hand) and muscle action of the mouth (lips,jaw). If the food or drink enters the mouth, it is either welcomed or unwelcomed. It is ejected from the mouth with the help of the tongue if it is unwelcomed. If it is welcomed, the tongue with the help of the hard palate position it for the first stage of mechanical and chemical digestion of caborhydrate and lipid. The teeth tears, grind and chew the food so as to increase its surface area (mechanical digestion). Saliva gland secretes saliva and enzyme amylase begins the digestion of caborhydrate while enzyme lingual lipase begins the digestion of lipid (chemical digestion). A bolus (round ball) is formed and prepared for entry into the stomach. Liquids (e.g. water) move to the stomach.

Motion sandwiched: food movement into esophagus
Forces sandwiching motion: tongue and pharynx muscles (effect swallowing) and peristalis (involuntary wave-like contractions and relaxations of smooth muscles in the alimentary canal). The beginning of peristalis marks the end of voluntary muscle actions in the motions in the alimentary canal prior to defecation. Peritalsis takes the food into the stomach then to the small intestine where almost all the post-digestion nutrients in the food are absorbed.

In the stomach, the circular wave-like motion of peristalsis continues the mechanical digestion of food by mixng it with digestive juices into chyme in a stomach environment of gastrin juice and hydrocholric acid (HCL). Enzymes amylase and ligual lipase continue the chemical digestion of caborhydrates and lipids. Enzyme pepsin initiates the chemical digestion of proteins. Surely but slowly and guided by neural and hormonal triggers, the stomach moves chyme through the pyloric sphincter into the duodenum (first part of the small intestine). Nutrients are not absorbed in the stomach. However, certain drugs (aspirin) and alcohol are absorbed in the stomach.

In the small intestine, the chemical digestion of caborhydrates and lipids are continued by enzymes pancreatic amylase and pancreatic lipase respectively. Brush border enzymes: α-Dextrinase, Lactase, maltase and Sucrase act on substrates, &alpha-Dextrin, lactose, maltose and sucrose respectively to produce glucose, galactose and fructose.

The majority of the chemical digestion of lipids occur in the small intestine. Enzyme pancreatic lipase breaks down each triglyceride into two free fatty acids (short chain fatty acid less than 10 or 12 carbons, and long chain fatty acid) and a monoglyceride.

Pancreatic enzymes chymotrypsin and trypsin continued the chemical digestion of protein by breaking down the bonds of specific amino acid sequences. Furthermore, brush border enzymes aminopeptidase and dipeptidase break down peptide chains to prepare them for entry into the blood stream.

Pancreatic enzymes, deribonuclease (digest DNA) and ribonuclease (digest RNA) are responsible for the chemical digestion of the nucleic acids in food. The nucleotides produced are further broken down by brush border enzymes, nucleosidase and phosphatase into pentoses, phosphates and nitrogeneous bases.

Almost 100% of ingested food, 90% of water and 80% of electrolytes are absorbed in the small intestine. The chyme passed on to the large intestine is basically, indigestable food residue (mostly plant fibers such as cellulose), some water (the large intestine absorbs some water), and millions of bacteria. The contents of the large intestine move through the rectum and are excreted through the anus.

Absorption Of Nutrients
Once digested molecules have been broken down to small absorbable sizes, the epithelial cells of the villi and microvilli of the small intestine carry out the absorption. Most of the glucose, fructose and galactose (products of carbohydrates digestion) are absorbed in the jejunum (second part of the small intestine), bile salts and vitamin B₁₂ are absorbed in the ileum (the third and terminal part of the small intestine), and the entire small intestine participate in the absorption of fatty acids, monoglycerides and water.

The absorptive motions of interest are: motions of nutrients from the lumen of the small intestine into the villi; and from the villi into the capillaries and lacteals of the villi; from the capillaries into the hepatic vein; and from the lacteals into the lymphatic vessels.

Motion sandwiched: movement (absorption) of glucose and galactose from the lumen of the small intestine into the villi.
Forces sandwiching motion: protein transporter and electrochemical gradient (implicit in the electrochemical gradient is membrane resistance). The protein transporter is sodium-dependent hexose transporter (SGLT1). The electrochemical gradient is the sodium-postassium gradient across the cell membrane. Cells do not want too much sodium (NA+) within them. They prefer to have more of potassium (K+). So, there is a regular effusion of Na+ into the extracellular space and infusion of K+ into the cell with the help of enzyme ATPase using ATP energy. This effusion of Na+ out of cells and infusion of K+ into cell is called the sodium-potassium pump (NA-K pump). The Na-K pump pumps 3Na+ out of the cell and brings 2K+ into the cell via the basolateral membrane (also called serosal, peritubular), for each ATP moleculed hydrolyzed. The electrochemical gradient allows sodium ions to cotransport with glucose into the villi via the apical membrane (also called, brush border, mucosal, luminal) with the help of SGLT1 (first binds to Na+, then to glucose, then manouvers both into the cell). The use of protein transporters in the absorption of glucose ensures the desired unidirectional movement of glucose and galactose from the lumen of the small intestine into the villi.

Motion sandwiched: movement of glucose from the villi into capillaries.
Forces sandwiching motion: protein transporter and electrochemical gradient. In this case no ATP energy is used. However, the glucose that has accumulated in the epithelial cell against its gradient exits the cell via the basolateral membrane with the help of protein transporter (GLUT) in a motion called facilitated diffusion, into the interstitial space from where it enters the capillaries via interstitial clefts. The glucose is taken to the liver via the hepatic portal vein (carrying partially deoxygenated blood) where it is processed (excess glucose is stored as glycogen, toxin removed, etc). The hepatic vein carries the processed glucose from the liver to the inferior vena cava which carries it to the heart.

The absorption of glucose is the focus. However, the absorption of the following important nutrients also occur: fructose (caborhydrate) is absorbed via facilitated diffusion (GLUT 5); amino acids (protein) via cotransport with sodium ions; short-chain fatty acids (lipid) and gycerol (lipid) via simple diffusion; long-chain fatty acids (lipid) and momoacylglycerides (lipid) diffuse into intestinal cells where they combine with protein to form chylomicrons which are then absorbed by the lacteals of the villi from where it enters the lymphatic vessels and then the blood stream through the lymphactic system; pentoses, phosphates and nitrogeneous bases (products of nucleic acid digestion) are absorbed via active transport (use protein pumps using energy from ATP to move substances across a membrane from low concentration environment to high concentration environment); water by osmotic pressure through semi-permeable membrane.

Transporter: the circulatory system (cardiovascular system).
The circulatory system is responsible for systemic distribution of the oxygen and glucose that has been brought to the heart from the respiratory system and digestive system. The medium of transport is blood contained in closed networks of vascular systems (blood vessels: arteries take oxygenated blood away from the heart and veins return deoxygenated blood to the heart). blood consists of a fluid called plasma and suspended cells (red blood cells, white blood cells and platelets).
Motion sandwiched: movement of blood containing oxygen and glucose from the heart to capillaries.
Forces sandwiching motion: pump action of the heart and hydrostatic pressure in blood vessels. Hydrostatic pressure in blood vessels is also called blood pressure (elasticity of blood vessels and volume within the vessels are implicit in the hydrostatic pressure).
The heart is a muscle and derives its power from muscular contraction and relaxation called the cardiac cycle (one heart beat). The cardiac cycle consists of atrial contraction and relaxation; ventricular contraction and relaxation; and a short pause.
The Circulatory System
The heart pumps blood from its left ventricle into the large arteries for systemic distribution during ventricular contraction (systole), then blood flows from regions of higher pressure to regions of lower pressure (from main arteries to smaller arteries, arterioles, capillaries, venules and veins). The measurement of arterial blood pressure is clinically expressed in millimeter of mercury (mm Hg) as the ratio of the systolic pressure/diastolic pressure and obtained using the brachial artery of the arm. The systolic pressure is arterial pressure during ventricular contraction when the heart pumps blood into the circulatory system; diastolic pressure is arterial pressure during ventricular relaxation. Other expressions relating to arterial pressure are: pulse and mean arterial pressure (MAP).
Where pulse = systolic pressure - diastolic pressure
Mean arterial pressure = diastolic pressure + (systolic pressure - diastolic pressure)/3 = diastolic pressure + pulse/3.
Blood flow and blood pressure is influenced by: cardiac output (volume of blood per minute being pumped by the ventricles); compliance (arterial elasticity); volume and viscosity of blood; length and diameter of blood vessel.

Physician and physiologist, Jean Louis M. Poiseuille related blood flow to pressure difference as follows:
Blood flow = (πΔPr⁴)/(8ηλ) --------(1)
Where ΔP = difference in pressure
η = viscosity of blood
λ = length of blood vessel
r = radius of blood vessel
π = the constant 3.14 approximately.

Resistance in the vascular system can be calculated given equation (1)
Blood flow = ΔP/Resistance.
So, Resistance = ΔP/blood flow -------------(2)
So, substitution of (1) into (2):
Resistance = (8ηλ)/(πr⁴ ------(3).

Motion sandwiched: movement of oxygen and glucose into interstitial space.
Forces sandwiching motion: capillary hydrostatic pressure (CHP) and hydrostatic pressure of interstial fluid (IFHP). CHP higher than IFHP, so motion is into interstitial fluid.

Motion sandwiched: movement of oxygen into cell
Forces sandwiching motion: passive diffusion and concentration gradient.
The concentration gradient that cause the driving force for diffusion also provides the restrictive force.

Motion sandwiched: movement of glucose into cell
Forces sandwiching motion: facilitated diffusion and electrochemical gradient.
The electrochemical gradient that cause the driving force also provides the restrictive force.

Supply chains: Glycolysis, TCA Cycle, Electron Transfer Chain
The motions in these internal supply chains are subtle. Enzyme actions, the attractive and repulsive forces of atoms provide the driving forces for the motions. The bond forces of substrates (the reactant molecules enzymes bind to) provide the restrictive forces.
Metabolic reactions do not normally occur spontaneously under the normal temperature and pressure inside living organisms. Enzymes (biochemical catalysts) make the reactions possible by reducing the activation energy necessary for the reactions so that the reactions can occur without thermal damage to the cells. Enzyme actions are specific, that is, an enzyme binds to a specific substrate in the specific reaction it catalyzes. Often, the objective of the enzyme when it binds to substrates is to alter their shapes or orientations in manners that will facilitate the occurrence of the reactions. When this objective is realized, the attractive or repulsive force of atoms actualize the reactions. Metabolic reactions are either catabolic (breakdown or removal of atoms or molecules), or anabolic (synthesis or addition of atoms and molecules). In essence, enzymes in their role as biochemical catalysts, facilitate the breaking of existing chemical bonds or the formation of new chemical bonds depending on whether they are catalyzing a catabolic reaction or an anabolic reaction. Metabolic reactions are usually reversible so, an enzyme can be a catalyst in acatabolic reaction and its anabolic equivalent. For example, the enzyme glucose-6-phosphatase catalyzes the addition of a phosphate group to the glucose molecule (anabolic reaction). Enzyme glucose-6-phosphatase also catalyzes the removal of a phosphate group from glucose-6-phosphate. The required by Le Chatelier's Principle is mantained in the system of subtrate, enzyme and product>.

(biv)The 7 PjProblemStrings Sequences are:
(1) Stand-alone PjProblemStrings Sequences
(2) Queueing PjProblemStrings Sequences
(3) Colliding PjProblemStrings Sequences
(4) Displacement PjProblemStrings Sequences
(5) Overlapping PjProblemStrings Sequences
(6) Hovering PjProblemStrings Sequences
(7) Linked PjProblemStrings Sequences
Stand-alone PjProblemStrings Sequences (e.g electron and proton transfers in the electron transfer chain), Linked PjProblemStrings Sequences (e.g several enzyme actions, oxygen linked to hemaglobin, Na+ linked to glucose) and Displacement PjProblemStrings Sequences (e.g displacement of carbon in glycolysis) are prevalent in ATP supply chains.

(ci)The human body established Internal control and vetting of most of the processes of the supply chains.

(ii) Security of the supply chains not perfect. They remain vulnerable to externally initiated disruptions and component failures.

(iii)Supply chains are never perfectly secured. Vulnerabilities always lurk within and outside the demand-space. Often raw materials are sourced outside the demand-space as is the case of the sourcing of oxygen and food.

(d)Nucleotides are also part of De-oxyribonucleic acid (DNA), a macromolecule involved in information storage in the human body; and Ribonucleic acid (RNA), a macromolecule involved in protein synthesis in the human body.

(e)ATP store its energy in the high energy phosphate bonds. When energy is needed in the cell, the phosphate bonds are broken. Enzyme ATPase breaks the bonds between the 2^nd and 3^rd phosphate groups: ATP --> ADP + P + energy. If more energy is needed, the bond of the 1^st and 2^nd phosphate groups is broken: ADP --> AMP + P + energy.
When energy is to be stored, enzyme ATPsynthase catalyzes the synthesis of ATP in the oxidative phosphorylation of ADP: ADP + P + energy --> ATP.

(f)Fundamental biologic cycle: photosynthesis (plants store energy in glucose molecules) -> respiration (plants and animals release the energy)->ATP (energy is stored)<-->ADP (energy s released when needed).