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Cells and Their Housekeeping Functions – Metabolic Process Shu-Ping Lin, Ph.D. Institute of Biomedical Engineering E-mail: [email protected] Website: http://web.nchu.edu.tw/pweb/users/splin/ Metabolism Cell metabolism: sum of all chemical reactions in living cell used for production of useful energy and subsequent synthesis of cell constituents Intake of food by cells from bloodstream: messenger substances (hormones) released from endocrine glands into blood stream to affect metabolism of cells that have receptors for that hormone Hormone: Anabolism: cells steadily remodel and replace their structures Catabolism: structures worn out and no longer needed are broken down into small molecules and either reused or excreted Alter permeability of cell membrane to extracellular substances, Ex: glucose Alter activity of key intracellular enzymes (pacemaker enzymes) controlling major chemical pathways, Ex: insulin increases glucose uptake by muscle cells and increases storage of glycogen. Type 1 diabetes (insulin deficiency) – depress glucose uptake and increase glycogen breakdown, causing abnormally high levels of glucose in blood ↑osmotic pressure Remove tissue water, cellular dehydration, and electrolyte loss Cells break down structural lipids and proteins when glucose starves. Protein deficiency and weight loss in type 1 diabetes Animals in low blood glucose levels Secreting epinephrine (adrenaline) from adrenal gland and glucagon from pancreas Lead to an increase in conversion of glycogen to glucose in liver. Opposite directions: glucagon and insulin establish levels in circulation Excess nutrients not immediately used are stored as glycogen (in liver and skeletal muscle; sufficient for a few hours) and fat reserve-triglyceride (sufficient fat stored for several weeks of starvation) Generation of Useful Energy from Food First stage of metabolism: large molecules split into smaller units in digestive tract, no useful energy is produced; Ex: proteins 20 amino acids, carbohydrates glucose, fats glycerol and fatty acids Second stage: occurs in cytoplasm small organic units convert into simple units, Ex: sugars, fatty acids, glycerol, and amino acids are converted into acetyl unit of acetyl CoA; process does not require oxygen, yields small amount of ATP Third stage: useful food energy, citric acid cycle and oxidative phosphorylation carried out under aerobic conditions in mitochondria Oxygen for contracting muscle cells is insufficient, pyruvate convert to lactate releasing useful energy But accumulation of lactate in muscle tissues is responsible for muscle cramps. Yeast (anaerobic organisms), pyruvate transform into ethanol Oxidation-Reduction Reactions Oxidation-reduction or redox reaction: food degradation, chemical reactions in which one or more electrons are transferred from one reactant to another, each reaction requires an electron donor and an electron acceptor Oxidation Give up e- by removing H, loss of electrons Adds O Called an electron donor or a reducing agent (reduces the accepting molecule, makes it more -) Releases energy - exergonic Reduction Gain e-(more -), addition of electrons Removes O Called an electron acceptor or oxidizing agent (oxidizes donor molecule) Stores energy - endergonic Oxidation Xe- + Y X + YeReduction Xe- is being oxidized (losing e-), acts as a reducing agent because it reduces Y Y is being reduced (gaining e-), acts as an oxidizing agent because it oxidizes Xe- Electron-transfer potential of NADH convert into phosphate-transfer potential of ATP NAD+(oxidized form) +RH2 NADH (reduced form) +H++R Redox potential: Oxidized form X reduced form X- G 0' nFE 0' Chemical reactions: degradation of food are exergonic redox (△G<0) NAD+ Oxidized form NADH Reduced form Degradation of Glucose Glucose metabolism: C6H12O6 + 6O2 6CO2 + 6H2O + energy Blocks indicate 4 separate pathways in cellular energy process, each pathway is composed of multiple consecutive reactions catalyzed by enzyme. Anaerobic Respiration Glycolysis in cytoplasm, others in mitochondria (called (Respiration without O2) cellular respiration) Glycolysis: consists of 10 reactions to convert glucose into 2 molecules of 3-carbon compounds (i.e. pyruvic acid and pyruvate) First 5 reactions consume energy: 2 ATP molecules are used to phosphorylate and activate glucose to 3-carbon sugar phosphate Aerobic Respiration nd 2 set of reactions: hydrogen atoms are removed (Respiration using O2) (oxidation) by NAD+ forming NADH (reduction): 2NAD+ + 4H (oxidation) 2 NADH (that’s a total of 4 e) -- Four ATP were produced from energy released by substrate-level phosphorylation Exergonic process with ∆G = -140kcal/mol Glycolytic pathway do not involve oxygen Glucose+ 2Pi+ 2ADP+ 2NAD+ 2 pyruvate+ 2ATP+ 2NADH+ 2H++ 2H2O Glycolysis is highly regulated. blood to meet the need for ATP. Cells acquire enough glucose from Vesicular Transport mechanism The transport mechanism which proteins use to progress through the Golgi apparatus Cisternal maturation model: the cisternae of the Golgi apparatus move by being built at the cis face and destroyed at the trans face. Vesicular transport model: Vesicular transport views the Golgi as a very stable organelle, divided into compartments in the cis to trans direction. Vesicular Transport Type Description Exocytotic vesicles Example Vesicle contains proteins destined for extracellular release. After packaging the vesicles bud off and immediately move (continuous) towards the plasma membrane, where they fuse and release the contents into the extracellular space in a process known as constitutive secretion. Antibody release by activated plasma B cells Secretory vesicles Vesicle contains proteins destined for extracellular release. After packaging the vesicles bud off and are stored in the cell until a signal is given for their release. When the appropriate signal is received they move towards the membrane and fuse to release their contents. This process is known as regulated secretion. Neurotrans mitter release from neurons Lysosomal vesicles Vesicle contains proteins destined for the lysosome, an organelle of degradation containing many acid hydrolases, or to lysosome-like storage organelles. These proteins include both digestive enzymes and membrane proteins. The vesicle first fuses with the late endosome, and the contents are then transferred to the lysosome via unknown mechanisms Digestive proteases destined for the lysosome (regulated) Metabolic Process and Mitochondria Degradation of Glucose Glucose metabolism: C6H12O6 + 6O2 6CO2 + 6H2O + energy Blocks indicate 4 separate pathways in cellular energy process, each pathway is composed of multiple consecutive reactions catalyzed by enzyme. Anaerobic Respiration Glycolysis in cytoplasm, others in mitochondria (called (Respiration without O2) cellular respiration) Glycolysis: consists of 10 reactions to convert glucose into 2 molecules of 3-carbon compounds (i.e. pyruvic acid and pyruvate) First 5 reactions consume energy: 2 ATP molecules are used to phosphorylate and activate glucose to 3-carbon sugar phosphate 2nd set of reactions: hydrogen atoms are removed (oxidation) by NAD+ forming NADH (reduction): 2NAD+ + 4H+ (oxidation) 2 NADH + 2H+ (that’s a total of 4 e-) -- Four ATP were produced from energy released by substrate-level phosphorylation Exergonic process with ∆G = -140kcal/mol Aerobic Respiration (Respiration using O2) Glycolytic pathway do not involve oxygen Glucose+ 2Pi+ 2ADP+ 2NAD+ 2 pyruvate+ 2ATP+ 2NADH+ 2H++ 2H2O Glycolysis is highly regulated. blood to meet the need for ATP. Cells acquire enough glucose from Mitochondria Mitochondrion (singular): organelles that release energy ATP by burned (oxidized) food molecules – aerobic respiration Have their own DNA and synthesize some of their own proteins, its ribosomes similar in composition to prokaryotic ribosomes, change shape easily and move efficiently to provide ATP to sites of high ATP consumption, roughly of the size of a bacterial (0.5~10 μm in diameter), divide asexually, live and maintain by nucleus and cytoplasm Highly metabolic cells such as liver cells contain up to 2,000 mitochondria 2 membranes: Smooth outer membrane (Transport protein porin allow small proteins and molecules to enter intermembrane space) Inner membrane (impermeable to ions, innermembrane proteins selectively transport molecules into matrix) with many folds separating into 2 compartments – internal matrix space and narrower intermembrane space. Less lipid and much more protein than cell membrane (membrane-bound proteins= enzymes). Membrane-bound proteins produce ATP and facilitate the entry of pyruvate and fatty acids into matrix. Pyruvate Oxidzation Enzymes on inner mitochondrial membrane oxidized pyruvate (CH3COCO2) to acetate (CH3COO-) and yield free energy and CO2 Part energy from oxidization is saved by the reduction of NAD+ to NADH+ H+, some is stored by linking acetate to an enzyme – coenzyme A (CoA) to produce energy-rich compound acetyl CoA (C23H38N7O17P3S) Coenzyme A (CoA) also plays a central role in metabolism. Terminal sulfhydryl group in CoA is reactive site. Acetyl CoA donate acetate to acceptors, much as ATP can donate phosphate to various acceptors. Hydrolysis of Acetyl CoA ΔG0’ for the hydrolysis of acetyl CoA has a large value comparable to that of ATP. Carriers such as ATP, NAD and CoA mediate the interchange of activated groups in many biochemical reactions. Conversion of pyruvate to acetyl CoA are catalyzed by a complex of enzymes consisting of 72 subunits and 24 different proteins. Enzyme complex cooperates with coenzymes, such as thiamin Higher animals lost capacity to synthesize vitamins, organic molecules, and obtain them in their diet. Most water-soluble vitamins are components of coenzymes such as CoA. Degradation of Glucose Glucose metabolism: C6H12O6 + 6O2 6CO2 + 6H2O + energy Blocks indicate 4 separate pathways in cellular energy process, each pathway is composed of multiple consecutive reactions catalyzed by enzyme. Anaerobic Respiration Glycolysis in cytoplasm, others in mitochondria (called (Respiration without O2) cellular respiration) Glycolysis: consists of 10 reactions to convert glucose into 2 molecules of 3-carbon compounds (i.e. pyruvic acid and pyruvate) First 5 reactions consume energy: 2 ATP molecules are used to phosphorylate and activate glucose to 3-carbon sugar phosphate Aerobic Respiration nd 2 set of reactions: hydrogen atoms are removed (Respiration using O2) (oxidation) by NAD+ forming NADH (reduction): 2NAD+2 + 4H (oxidation) 2 NADH (that’s a total of 4 e-) -- Four ATP were produced from energy released by substrate-level phosphorylation Exergonic process with ∆G = -140kcal/mol Glycolytic pathway do not involve oxygen Glucose+ 2Pi+ 2ADP+ 2NAD+ 2 pyruvate+ 2ATP+ 2NADH+ 2H++ 2H2O Glycolysis is highly regulated. blood to meet the need for ATP. Cells acquire enough glucose from Citric-Acid Cycle (Aka Krebs Cycle) Begins when acetyl CoA combines with oxaloacetate (a 4-C molecule) to produce citric acid and releases Coenzyme A Each turn of the citric acid cycle consumes one acetyl CoA molecule (originally a pyruvate, since glycolysis produces 2 pyruvates, 1 glucose molecule produces 2 turns of the citric acid cycle ) One turn of the Krebs cycle oxidizes the remaining citric acid, or citrate, producing 1 ATP, 3 NADH, 1 FADH2, and the byproduct 2 CO2 which is exhaled Glucose Metabolism The citric-acid cycle of glucose produces: 4 CO2, 2 ATP, 6 NADH, 2H+, and 2 FADH2 Glucose+ 2Pi+ 2ADP+ 2NAD+ 2 pyruvate+ 2ATP+ 2NADH+ 2H++ 2H2O 2X 2X 2X Respiratory Chain FADH2 & NADH are energy carriers and used to produce ATP. Couple oxidization of NADH or FADH2 to produce ATP 1 NADH H O2 NAD H 2O 2 Intermembrane space G 52.4 Matrix ADP Pi nH P ATP nH N kcal mol Oxidization of NADH by oxygen is exergonic. (Hydrolysis of ATP=-12kcal/mol) Occur on inner membrane of mitochondria (capable of rapid electronexchange, i.e. oxidation & reduction) and involve sequential transfer of electrons through membrane-associated molecules http://www.life.illinois.edu/crofts/bioph354/lect10.html Electron-transport system (ETS): high energy electron-carrying enzyme deliver electrons to more electronegative enzyme Each successive carrier is more electronegative than the last so electrons are pulled downhill One carrier reduces another, energy released is used to pump hydrogen ions across the membrane into the intermembrane space Remaining energy is used to reduce the next carrier ElectonsETSSynthesize ATP Proton (H+) accumulate in the intermembrane space Cause concentration gradient and charge gradient across membrane Concentration gradient forces protons to pass channel protein ATP synthase Relaxation of the proton flux couples formation of ATP. Free-energy change (△G) in transporting uncharged molecule from concentration 1 to 2 is: (R:gas constant=1.987 cal/mol, T:absolute temperature in Kelvin= 273.15 °+ ℃) G RT ln( C 2 ) C1 Membrane electric potential and ion concentration gradient provide driving force for moving ions (charged particles) across membrane. △G of transporting ion might be large enough to drive other processes. (Z:electrical charge of transported species, △V:potential in volts(V) across membrane 12, F:Faraday constant=23.062 kcal/Vmol ) G RT ln( C 2 ) ZFV C1 ATP Synthase ATP synthase catalyzes the formation of ATP Proton-conducting unit F0 spans the lipid bilayer. ATP synthesizing unit F1 faces matrix. Hydrogen flow form intermembrane space to matrix through F0. 3 catalytical β subunits of F1 are structurally identical but in different configurations at any particular point Catalytic site in open (O) form (configuration): little affinity for substrates Loose (L) form: bind to either ATP or ADP+Pi loosely and is catalytically inactive Tight (T) form: bind to either ATP or ADP+Pi tightly and is active Energy input from proton flux converts T site to O site O site to L site L site to T site: New L site binds new ADP and phosphate and begins a new reaction sequence Proton flux: not needed in ATP from ADP+Pi, but can release tightly bound ATP and cycle continues △G<0 in intermembrane space Flow protons through ATPase and ADP+Pi bind to ATPase Enzyme catalyzes formation of ATP ATP detaches from ATP synthase when proton flux http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/metabolic-pathways/atp-synthase.html http://www.sigmaaldrich.com/sigma-aldrich/areas-of-interest/life-science/metabolomics/learning-center/metabolic-pathways/atp-synthase/atp-animation.html Summary of Glycolysis and Cellular Respiration Respiratory Chain: Anaerobic Respiration (Respiration without O2) 4ATP+10NADH + 2FADH2= (4+ 3X10+ 2X2) = 38 ATP Total Yields Aerobic Respiration (Respiration using O2) Mitochondria are highly efficiently as energyprocessing plants. Glucose 2 pyruvates + 2 ATP (in cytoplasm) Pyruvates imported into mitochondrion and oxidized by O2 to produce 30 ATP (3ATPX10=30; since NADH 3ATP molecules, FADH2 2ATP molecules) Photosynthesis Photosynthesis: anabolic reaction, convert light energy to chemical energy of organic compounds – raw materials: water, carbon dioxide (CO2, inorganic) and energy (sunlight) Products: glucose (energy rich carbon compounds) and oxygen (side product) http://en.wikipedia.org/wiki/Photosynthesis 6CO2 + 12H2 O + energy C6H12O6 + 6H2 O + 6O2 H2O: used as reactant and released as a product 2 pathways: driven by light energy in 1st pathway; entrapment of energy received from photons into ATP molecules in subsequent pathway Light: radiant energy (packets of photons) E=h c/ λ (E:energy, c:3x1010cm/s, h:Planck’s constant 1.584x10-34cal s) λ:400~700nm; violet (high “E”), blue, green, yellow, orange, red Energy of molecule absorbing photon rises from ground state to excited state and drives electrons to away from nucleus Loosely held electron then get transferred to other molecules in subsequent reactions, resulting in the production of ATP from ADP Common to the degradation of glucose http://www.overidon.com/wpcontent/uploads/2010/06/wavelength-light1.jpg Common Themes in Metabolic Pathways Central themes of metabolism: 1) 2) 3) 4) ATP is the universal currency of energy. Hydrolysis of ATP increase equilibrium ratio of products to reactants in energy-requiring reaction by a factor of about 108. ATP is generated by the oxidation of fuel molecules such as glucose. Chemical energy in carbon bonds using electron carriers to create proton gradient across inner membrane of mitochondria to synthesize ATP. Metabolic pathways generate ATP and transfer high-potential electrons to electron carriers such as NADH also provide building blocks for macromolecules. Biosynthetic and degradative pathways are almost always separate and utilize different enzymes. Biosynthetic pathway is made exergonic by hydrolysis of ATP. Recurring motifs in these reactions 1) 2) 3) Flow of molecules down metabolic pathway is determined by amounts and activities of certain enzymes. First irreversible reaction in metabolic pathway is committed step Enzymes catalyzing committed steps are typically regulated by the end product. Regulatory enzymes in metabolic pathway are controlled by phosphorylation. Proteosomes control protein concentration by degradation. Metabolic pathways involve compartmentalization of chemical reactions. Whether they are in cytoplasm or in mitochondria, compartmentalization is a useful tool in separating degradative pathways from biosynthetic pathways. Molecular Motors & Membrane Potential Molecular Motors ATP hydrolysis drive many metabolic or anabolic reactions that require energy, such as ATP hydrolysis to mechanical work Motor protein: an enzyme and use the resulting energy to drive a chemical or mechanical change Mechanical energy (form of kinetic energy of motion or elastic energy stored in the system) – energy-transformation mechanism: protein motors become strained during transitions, free energy is partly stored as internal elastic energy and released for driving force for forward or upward movement. Motor proteins: convert chemical energy into mechanical energy by ATPase: ATP ADP; use chemical energy in ATP, a fuel to cause movement, to cause positional change relative to substrate or track Myosin and kinesin: have similar structure Myosin: cause movement in relation to actin-rich thin filaments Kinesin: cause movement along microtubules Myosin Kinesin Myosin Motors & Actins Myosin: molecular motor of muscle; together with actin and regulatory proteins for muscle contraction, cell motility, and extension of cell projections; myosin molecules in muscle cells aggregate and their tails form thick filaments Actin: most abundant in cell(10% of cell content); highly conserved ancient protein of eukaryotes; actin from different species polymerizes readily to form thin filaments; asymmetrical arrangement in microfilament: the end to which actin monomers added differs from the others(directional + - end); actin decorated with head region of myosin, all heads in the same direction and give decorated filament flight of an arrow Myosin and actin have contractile roles in all eukaryotic cells; nonmuscle cells contain 10- to 100-fold less myosin than actin; motor domains of “unconventional” myosin hydrolyze ATP, and have variations in tail can interact with different proteins: actin-based vesicular transport and hearing http://www.sigmaaldrich.com/life-science/metabolomics/enzymeexplorer/learning-center/structural-proteins/myosin.html Skeletal Muscle Structure Myosin II: building block of thick filaments, made of 6 polypeptide chains: 2 identical heavy chains (230 kDa each), 4 light chains (20 kDa each); 2 oval-shaped heads of about 60 nm and a long tail of about 130 nm Tails: bind together and form backbone of thick filaments Heads: contain binding sites for actin and ATP (hydrolysis products: ADP and Pi) α-helical neck region between head and tail: regulate activity of head region Thick filaments: 16 nm in diameter and 1.5 um long; myosin heads (cross-bridges) protrude from filament at intervals of 14.3 nm along filament axis Regulates activity of head region Myosin Filament (Thick Filament) LMM: myosin molecule embedded in body of thick filaments of muscle fibers HMM: portion of myosin protruded from body of thick filament Mechanism of force generation and movement in cells: heads protrude and interact with active sites on thin actin filaments pulling them against external load thereby causing muscle contraction Sarcomere: repeating contraction unit in muscle cells, composed of thick myosin and thin actin filaments arranged in parallel Central region of thick filament (H band) spans 150 nm and is devoid of projecting crossbridges Myosin heads on each side of bare zone point toward center of thick filament (thick filament is inherently bipolar) Sarcomere 150 nm 1.5 um Actin Filaments (Thin Filament) Major component is actin, which has high affinity for myosin. 1/3 of mass of thin filaments is tropomyosin and troponin complex. Each thick filament is surrounded by 6 thin filaments that overlap thick filament. Relaxed muscle (low Ca2+): tropomyosin prevents actin from interacting with myosin heads Signal for muscle contraction from nervous input through neuromuscular junctions Results in release of intracellular Ca2+ from specialized ER found in muscle cells Myosins bind to actin filament Muscle contracts (myosin heads pull thin filaments toward the center of sarcomeres, resulting in shortening of muscle) Sarcomere http://www.sigmaaldrich.com/life-science/metabolomics/enzymeexplorer/learning-center/structural-proteins/myosin.html Work Stroke of a Crossbridge Muscle shortening during contraction: relative movement of actin filaments with respect to myosin filaments Relative movement: reversible interaction of myosin heads protruding from thick filaments with actin binding sites on thin filament Myosin head has strongest affinity to ATP than actin: (a), (b), and (c): indicate myosin interacts with actin and produces force and movement, called attached states (e) and (d): myosin is free of actin, called detachment Chains of circles: ATP and ADP; smaller circles: phosphate groups ATP hydrolysis occurs while myosin head is free of actin Change in configuration of myosin head Allow to interact with actin Hydrolysis product Pi Strongly attached state in which myosin head pulls thin filament toward center of sarcomere Detachment of ADP Binding of ATP to same site and subsequent detachment of myosin from actin and continuation of cycle Myosin Kinetics Using In-Vitro Motility Systems Myosin-coated beads move unidirectionally on oriented actin cables in the presence of ATP, having the same sense of direction Beads coated with skeletal muscle myosin move with speed of 5 um/s and is estimated that 25 myosin molecules on each bead are sufficient to actuate motion Actin filaments can move on glass decorated with myosin in the presence of ATP. Forces generated by a single motor: myosin head can generate 5 pN and myosin molecule can catalyze hydrolysis about 20 ATP molecules per second during muscle contraction Kinesin Motors Kinesin: motor protein that powers transport of intracellular organelles along microtubules (100 eukaryotic motor proteins interacting with microtubules), facilitate chromosome movement during cell division Motile organelles such as mitochondria and vesicles use kinesins to propel them along microtubules. Consist of 2 heavy (globular) and 2 light chains, resulting in 400 kDa: 2 globular regions contain ATPase active site and microtubule-binding site: ATPase activity strongly promoted by microtubules Presence of microtubules, kinesin hydrolyze up to 100 ATP per second Globular tail domain: contain binding site for cargo (organelle, chromosome, etc.) Various kinesin genes all contain microtubule-binding sites and have ATPase activity, but differ in their cargo-binding sites Direct movement toward “+” end of microtubules, but some are minus-end-directed motors http://www.imb-jena.de/~kboehm/Kinesin.html Kinesin Cycle Their associated cargo move along microtubules for several micrometers = Kinesin-induced microtubules motion Organelle uses kinesin for transport can fall off microtubule and reattach if confronted with obstacle (same microtubule can simultaneously support “+” and “-” end-directed motion; kinesin-dependent vesicle transport from “-” to “+”) Kinesin motion is reminiscent of human walking: both heads translocate in turn by 16-nm steps, each translocation moves center of mass 8 nm forward; during the translocation motion of one head, the other remains bound to microtubules Glass coated with kinesin support gliding of individual microtubules in-vitro: kinesin binds to cargo-binding region (tubulin) immobilized to slide and microtubule moves 1 um/s, maximum force produced by kinesin ~5 pN http://homepage.ntlworld.com/malcolmbowden/kinesin.htm Dynein Another family of microtubule-based motor protein http://people.virginia.edu/~rjl6n/dynein.htm 2 identical heavy chains of about 530 kDa each (dark blue): contain 4 ATPbinding sites, movement along microtubules and microtubule binding site; 2X 74 kDa intermediate chains (magenta and yellow); 4X 53-59 kDa intermediate chains (green) 74 kDa intermediate chains are thought to bind the dynein to its cargo, cargo is membrane-bounded vesicle in neuron, golgi vesicle, kinetochore or mitotic spindle astral microtubule – force to move cargo along microtubule toward its minus end Ciliary dynein: power flagella motion in some motile single-cell eukaryotes and is responsible for beating cilia in some tissues of multicellular organisms Cilia on surface of cells in oviduct are used to move egg, cilia in cells of respiratory system are used to move mucus. http://bernstein.harvard.edu/research/motor_protein.htm http://people.virginia.edu/~rjl6n/dynein.htm Muscle Contraction http://www.maprepaphysique.fr/dossiers/physiologie/l a-contraction-musculaire.htm http://en.wikipedia.org/wiki/File:Sarcomere.svg Signal for muscle contraction from nervous input through neuromuscular junctions Results in release of intracellular Ca2+ from specialized ER found in muscle cells Myosins bind to actin filament Muscle contracts (myosin heads pull thin filaments toward the center of sarcomeres, resulting in shortening of muscle)