Biology essay

Energy transfer- photosynthesis

The primary energy transfer involves the absorption of sunlight by photopigments such as chlorophyll a and b in photosystems embedded in the thylakoid membrane of chloroplasts of photoautotrophs. Light energy raises the energy level of electrons causing them to leave the chlorophyll molecules resulting in photoionisation. Electrons move down the electron transport chain and are involved in redox reactions at each electron carrier. Energy released from electrons passing down the chain, alongside energy released from the photolysis of water is used to pump protons (by AT) from the stroma into the thylakoid space. Protons move down their electrochemical gradient, from the thylakoid space into the stroma via ATP synthase which spins to catalyse the production of ATP. If it weren't for the photoionisation of chlorophyll and photolysis of water, from the energy transferred from light, then not enough energy would be available to pump protons into the thylakoid space to create a large enough chemiosmotic gradient. Insufficient NADH and ATP would be synthesised for the LIDR and so less G3P could be reduced to TP, so less TP available to convert into glucose and fructose to assimilate sucrose.

Mass transport of sucrose

Any sucrose produced moves by facilitated diffusion from chloroplasts into companion cells. Sucrose molecules are then moved by cotransport alongside hydrogen ions from companion cells into sieve tube elements in the phloem. Mass transport mechanisms of translocation can then occur. Sucrose causes the sieve tubes to have a lower water potential, causing water to move by osmosis out of the xylem and into the sieve tubes. This raises the hydrostatic pressure within them at the source. At respiring cells, sucrose is hydrolysed or actively transported back into companion cells. Water moves by osmosis out of the sieve tube and into the companion cells resulting in lower hydrostatic pressure at the sink. If it weren't for the transfer of sucrose into the sieve at the source and the removal of sucrose at the sink there would be no hydrostatic pressure gradient created. Sucrose would not move by mass flow to respiring tissues of the plant. Less sucrose would be available to be hydrolysed into glucose and so less aerobic respiration would occur and insufficient ATP produced. Less energy released in plants would lead to reduced cell division and stunted growth.

Digestion+ glycolysis

Energy can be transferred from plants to primary consumers by feeding and digestion. Starch is composed of amylose and amylopectin. The glycosidic bonds within these carbohydrate polymers are hydrolysed by salivary amylase, to produce the disaccharide maltose which is subsequently hydrolysed by maltase into alpha glucose. If heterotrophs were unable to hydrolyse starch in plants then they would have insufficient sources of glucose for glycolysis. The cytoplasm of cells, glucose is phosphorylated into glucose phosphate via the hydrolysis of ATP into ADP and Pi. This provides energy to activate glucose and lower the activation energy for the enzymatic reactions which follow. Phosphorylated glucose is split into two triose phosphate molecules which are then oxidised, releasing hydrogens passed onto to NAD forming NADH. Each triose phosphate molecule is converted into pyruvate and energy release catalyses the formation of ATP. Per glucose molecule in glycolysis there is a net production of 2 pyruvate, 2 ATP and 2 NADH. As glycolysis does not require oxygen, it is of vital importance in the release of energy and so survival of organisms in anaerobic conditions. If it didn't occur, no ATP or pyruvate could be produced during aerobic respiration, so insufficient energy would be released for vital processes such as active transport.

Sodium-potassium pump resting potential

Active transport as an energy transfer process is essential in controlling the membrane potential of cells at rest. When a sodium-potassium pump binds three sodium ions, it triggers the hydrolysis of ATP into ADP and Pi. Inorganic phosphate attaches to the pump, phosphorylating it and causing it to conformationally change shape so it is open towards the extracellular space, instead of the intracellular space. The pump loses its affinity for sodium ions, causing them to be released into the tissue fluid. It now has a higher affinity for potassium ions, to which it binds two of, triggering the release of the phosphate group. The pump returns to its original shape and in doing so, pumps two K+ into the cytoplasm. This results in a negative potential difference of -70mV across neuronal membranes, as more Na+ at out than K+ in. If active transport was not to occur along the axon of a neuron, the resting potential could not be maintained. This means that depolarisation could not occur properly to the extent of thresholds being reached and action potentials being able to fire. If they were to fire, the neurons would not be able to re-establish the resting potential and so overcome the period of hyperpolarisation post-firing, hindering further transmission of impulses. This would lead to the body unable to fire or control impulses sent for muscle contraction leading to muscle paralysis.

Plasma membrane structure

A typical plasma membrane takes the form of a phospholipid bilayer. The hydrophilic phosphate heads attract water and point outwards and the hydrophobic fatty acid tails point inwards in repulsion. This means the centre of the bilayer is hydrophobic and doesn't allow hydrophilic substances to simply diffuse through it. Only small, non-polar, lipophilic substances are able to pass independently across cell membranes. The plasma membrane is therefore adapted with intrinsic proteins, like channel proteins which are filled with water and enable the facilitated diffusion of polar substances such as glucose.

GLUT4

When the hormone insulin binds to receptors on the cell-surface membrane, vesicles containing GLUT4 channel protein fuse with the membrane, embedding it as a channel. Glucose can then be transported into the cell via this channel protein down its concentration gradient. In this example, the plasma membrane is vital for the regulation of blood glucose levels. If glucose was unable to be transported across the membrane when insulin binds, then blood glucose levels would remain too high (hyperglycaemia). This would lower the water potential of the blood, causing water to diffuse by osmosis out of erythrocytes into the plasma, causing them to become crenated. If RBC are damaged in this way they can't transport oxygen as effectively, so less aerobic respiration can occur and not enough ATP can be produced for e.g. active transport.

Cisternae

Cisterna describes the complex system of flattened membranes of the endoplasmic reticulum and golgi apparatus. The stacked membranes of the rough endoplasmic reticulum (RER) provide a large surface area for the attachment of ribosomes for protein synthesis. The RER also folds and processes proteins made before transporting them to the golgi apparatus. The membranes of the golgi apparatus are polar structures, with the cis face being thinner and convex in shape to maximise the endocytosis of proteins. Proteins are sorted and packaged into vesicles which leave the apparatus at the thicker, concave trans face. Vesicles transport the proteins and fuse to the cell-surface membrane to release them by exocytosis. If it weren't for the cisternae, the immune response would be hindered as antibodies would not be able to be secreted from plasma cells. Without the excretion of antibodies, which agglutinate pathogens, then phagocytes would not be able to identify foreign antigens as quickly to be able to engulf and destroy them. This means that a pathogen could easily replicate within an organism and overcome its defense mechanisms, leading to cell death.

inner-mitochondrial membrane

Folded into extensions called cristae, the inner mitochondrial membrane acts as the site of oxidative phosphorylation in eukaryotes. Electrons released from the oxidation of NADH and FADH flow down the electron transport chain and lose energy at each carrier molecule embedded in the cristae. Energy released is used to pump protons (via AT) from the matrix into the intermembrane space, creating an electrochemical gradient. The folded, semi-permeable structure of the inner mitochondrial membrane ensures this proton motive force can be established, as the hydrophilic protons are unable to pass through the hydrophobic centre of the bilayer. Protons are therefore forced to move down their chemiosmotic gradient via ATP synthase from the intermembrane space into the matrix. ATP synthase changes shape, driving the condensation of ADP with Pi--->ATP. If it weren't for the inner-mitochondrial membrane, then no ATP would be produced during oxidative phosphorylation. The only ATP produced would be the small amount from glycolysis, meaning insufficient energy would be released for the contraction of muscles and cell division.

Horizontal transmission

The plasma membrane has a vital role in the horizontal transmission of genes for survival in bacteria. Bacteria replicate genes for antibiotic resistance found in the form of plasmid DNA. In a process called conjunction, the plasma membrane facilitates the transferal of this plasmid DNA between distinct bacteria. Small membrane projections called pilus are transcribed which make contact with neighboring bacteria. This stimulates the structure of the membrane of the recipient bacterium to change by means of the formation of a pore and the plasmid DNA can be passed on, in linear form, from one bacterium to another via a continuous protein tube. Once in the recipient bacterium, plasmids become circular again. Thanks to this membrane conjunction, the recipient bacterium now also contains genes for antibiotic resistance. So if one bacteria has a plasmid that carries the code for penicilinase, the plasmid can be replicated and passed via horizontal transmission. Now both cells are resistant to penicillin. Without horizontal transmission via plasma membranes, colonies of bacteria would not be able to develop resistance as quickly and they would be more likely to be destroyed by antibiotics.

Proteins- antibodies

Proteins, in the form of antibodies, are integral to the humoral immune response in mammals. Following the clonal selection of B-cells, which divide by mitosis into plasma cells, monoclonal antibodies can be secreted against a particular non-self antigen. Composed of two heavy and two light chains, the antibody's specificity is of vital importance as a polymeric protein. The variable region of each antibody has a unique shaped polypeptide structure which acts as binding site to the specific, complementary shaped antigen. On binding, an antigen-antibody complex is formed. As each antibody has two hypervariable regions, two antigens can be bound and neutralised at the same time- this can cause the agglutination of pathogens which makes it easier for phagocytes to locate and destroy them as they are less spread out in the body. If it weren't for antibodies, which act like markers for phagocytes, the immune response would be much slower because pathogens would be less easily detected and destroyed. Viruses would be able to invade, inject their capsids and replicate within host cells more freely, causing cells to burst and die.

ATP synthase

ATP synthase (located in the inner-mitochondrial membrane) controls the production of ATP during oxidative phosphorylation. Energy released from redox reactions of the electron transport chain is used to pump protons (via AT) from the matrix into the intermembrane space, creating an electrochemical gradient. Protons move down their chemiosmotic gradient via ATP synthase from the intermembrane space into the matrix, leading to the production of ATP. The way in which ATP synthase is able to catalyse this reaction relates to its specific quaternary structure. ATP synthase can be split into two portions. The Fo complex embedded in the inner mitochondrial membrane and the F1 complex which projects into the matrix. As protons move down their electrochemical gradient, the energy they release rotates the Fo complex in a clockwise direction which triggers a series of conformational changes in the polypeptides of the F1 complex, catalysing the condensation of ADP with Pi--->ATP. Without ATP synthase, no ATP would be produced, so no energy would be available for vital processes such as active transport and cell division. Cells would not be able to repair and synthesise new molecules and metabolism would cease leading to the death of the organism.

Adrenaline action

This ATP synthesized is able to interact with proteins during homeostasis in the regulation of blood glucose. Adrenaline is a hormone released by the adrenal glands of the kidney in response to low blood glucose levels during times of high stress or exercise. Like glucagon, in order to bring out a response, adrenaline acts by a second messenger. Adrenaline binds to complementary receptors of a transmembrane protein outside of a hepatocyte. This causes the protein to conformationally change inside the membrane and activates adenylate cyclase which converts ATP into a chemical "second messenger", cyclic AMP. cAMP binds to protein kinase A, inducing a change in shape which activates a cascade that carries out glycogenolysis.

The interactions of adrenaline demonstrate the importance of proteins working together to generate a specific response. Without adrenaline, organisms would be less able to flee from predators. This is because insufficient glucose would be released into the blood to meet increased respiration rates for the production of ATP. Less energy would be available for rapid and then sustained muscle contraction and the organism would be more likely to be killed and eaten by its predator.

--- Fast twitch fibres

Haemoglobin

The oxygen required for increased respiration has to be transported by the quaternary carrier protein, haemoglobin. Haemoglobin is composed of four separate folded polypeptide chains, two alpha and two beta with a haem group in the centre containing an iron ion. Haemoglobin saturation depends on the partial pressure of oxygen. At the lungs, high oxygen concentration causes haemoglobin to have a high affinity to oxygen to which it readily combines. In respiring tissues, oxyhaemoglobin unloads its oxygen where there is a lower pO2. As well as being essential for oxygen transport, the ability of haemoglobin to change shape is vital for maximising the uptake and release of oxygen to meet different respiratory demands. Binding of the first oxygen molecule induces a conformational change in haemoglobin which uncovers a second binding site, making it easier for more oxygen molecules to bind. This is known as positive cooperativity. Conversely, haemoglobin changes shape and becomes less affinitive to oxygen in higher CO2 concentration due to lower pH levels(Bohr shift). Haemoglobin therefore maximises the amount of oxygen unloaded at respiring tissues, where pCO2 is high and pO2 is low.

If it weren't for haemoglobin, there would be reduced transfer of oxygen so fewer electrons move down electron transport chain as O2 acts the final electron acceptor in oxidative phosphorylation. Less energy would be released to pump H+ into intermembrane space so less of a proton motive force would be generated so less ATP produced.

Organisms at different stages of development can have haemoglobin with different affinities for oxygen. Human fetuses have haemoglobin F which has a higher affinity for oxygen compared with adult haemoglobin (HbA). This ensures that oxygen can bind, even in the relatively lower pO2 in the blood reaching the placenta. If fetal haemoglobin was not of higher affinity to oxygen, then there would be no incentive for oxygen to transfer from maternal blood to fetal blood, and the fetus would be starved of oxygen and die.

protein synthesis

Transferring information by means of the synthesis of proteins demonstrates the importance of intracellular communication. After the double helix of DNA unwinds in the nucleus, free-floating RNA nucleotides are attracted to and bind to their exposed complementary base, present on the antisense strand of DNA. RNA polymerase catalyses the formation of phosphodiester bonds between these nucleotides and so the Pre-mRNA strand is transcribed. Pre-mRNA is spliced to remove introns in eukaryotes, leaving a mature mRNA which is able to transfer genetic information from the nucleus to the ribosome, by exciting through a nuclear pore. mRNA binds to the ribosome which moves across it, translating codons, allowing for two tRNA molecules with complementary anticodons to bind at a time. tRNA molecules carry amino acids which join via the formation of a peptide bond.

If it weren't for the transferal of base sequences by mRNA then genes would not be able to be translated into sequences of amino acids and so polypeptide chains would not be able to fold into proteins such as antibodies. The immune system would be hindered, unable to agglutinate and destroy pathogens in the body, resulting in cellular destruction and disease.

Glucagon

Transferal of information between and within cells is of vital importance during homeostasis. If alpha cells of islets of langerhans detect a state of hypoglycaemia, they increase glucagon secretion. Glucagon binds to complementary receptors of transmembrane proteins on hepatocytes, inducing a conformational change to the protein on the intracellular side. This activates adenylate cyclase which binds to ATP, converting it into a chemical "second messenger", cyclic AMP. cAMP binds to protein kinase A, causing it to change shape, triggering a cascade which results in glycogenolysis. This is an example of amplification. Glucagon binds to receptors outside the cell but transfers information to the inside of the cell, activating a chain of reactions leading to the hydrolysis of glycogen and release of glucose into the blood. If it weren't for this transfer of information regarding low blood glucose levels, then glucose would not be readily released into the blood in response. There would be less glucose available for glycolysis, so less glucose converted into pyruvate and less acetyl coA produced. The Krebs cycle would slow, resulting in less NADH and FADH produced. Less NADH FADH available for redox reactions of the electron transfer chain would mean less energy released to generate an electrochemical gradient during oxidative phosphorylation. A smaller proton-motive force would mean less ATP produced as a result. Less ATP means less muscle contraction, leading to weakness and fatigue.

Microtubules and movement

Microtubules, hollow tubes made of alpha and beta tubulin, have a key role in forming the mitotic spindle and so controlling the movement of chromatids during mitosis. During prophase, chromosomes condense into sister chromatids, the nuclear envelope breaks down and spindle apparatus is formed. Astral microtubules radiate out from the centrosome to the cell membrane and hold the spindle in place. Polar microtubules link centrosomes and hold chromosomes apart. Chromatids attach to kinetochores microtubules at their centromere at the equator of the cell. During anaphase, when the centromere divides, spindle fibres contract to pull individual chromatids apart, to opposite poles allowing for progression into telophase. If it weren't for microtubes, spindle apparatus would not form so there would be no attachment or separation of chromatids, and so they would not move to opposite sides of the cell. After the cytoplasm divides, one daughter cell would receive double/ more than diploid number of chromosomes. The daughter cells would not be able to carry out mitosis properly themselves, hindering growth and repair. Knowledge of microtubules is important in terms of cancer. Cancer drugs such as chemotherapy poison microtubules in order to prevent mitotic spindle production and impede cell division.

Tau protein

From outside of the specification, the Tau protein is essential for stabilizing microtubules in neurons. Microtubules are dynamic tubulin protein structures which are able to alter the shape of the cell. This drives neuron cells to grow and form new connections. The tau protein is crucial in stabilizing tubulin molecules within microtubules to allow for this to be possible. We can see the importance of tau functioning properly as when it doesn't, it can drive the progression of dementia. Following post-translational modification, tau can become detached from tubulin due to phosphorylation or proteolysis. This causes microtubules to become unstable and collapse. Detached tau aggregates together, clogging up the inside of the neuron and preventing essential transport of proteins. Action potentials are unable to fire so the neuron dies. Tau aggregates can spread between neurons, blocking areas of the hippocampus leading to memory loss.

bonding in DNA

Bonding within DNA is crucial in dictating its stability. Phopshodiester bonds between deoxyribose sugar of one nucleotide and phosphate group of the next join polynucleotides of antiparallel strands, allowing for the double helix structure to form. The high bond enthalpy of these covalent bonds, means they require a high quantity of energy to overcome. In this way, the phosphodiester bonds of the sugar-phosphate backbone protect the more chemically reactive nitrogenous nucleotide bases. Between complementary bases, hydrogen bonds form and release energy, leading to higher entropy. Although weak individually, these hydrogen bonds give high relative strength collectively and form rungs between the two strands, ensuring that they are unlikely to separate spontaneously. As hydrogen bonds are able to be broken by DNA helicase, they also enable for two antiparallel strands to be unwound during semi-conservative replication. If it weren't for hydrogen bonding, free-floating nitrogenous bases would not bond with their complementary partner. The accuracy of replication would be hindered and there would be reduced genetic continuity between cells. Mutations would be more likely- genes would not be copied properly resulting in the transcription of non-functional proteins like ATP synthase- unable to produce ATP.

Transpiration stream

Hydrogen bonds are of vital importance in the transpiration stream of the xylem. When water vapour that has accumulated in spaces between cells in the leaf, moves down its concentration gradient out of the stomata, negative tension is induced in the xylem. This negative tension pulls more water molecules up from the soil into the roots and into the xylem. As the more electronegative oxygen atoms pulls electron density away from hydrogen atoms, the high-polarity of water allows hydrogen bonds to form. This makes them highly cohesive so when some are pulled into the leaf, others follow. Water molecules also form small electrostatic forces of attraction to the cellulose microfibrils making them adhesive to the walls of the xylem tube. A continuous column of water can therefore be pulled into the stem through the roots. If it weren't for the cohesion and adhesion of water molecules thanks to H-bonds, then when water evaporates from stomata, limited water would be pulled into the xylem. The water potential of the xylem would be lowered, so water would move by osmosis from other cells into the xylem, causing these cells to be plasmolysed. Less minerals such as ammonium ions would be taken into the plant causing it to become deficient. The plant would eventually shrivel up and die.

ATP synthase bonding

The importance of bonding in proteins can be applied to ATP synthase in oxidative phosphorylation. Peptide bonds allow for a specific sequence of amino acids to form the primary structure of its polypeptide chains. Alpha helices and beta pleated sheets form depending on the location of hydrogen bonds between slightly positive hydrogen atoms of amine groups and slightly negative oxygen of carbonyl groups of amino acids. Polypeptide chains are folded into more specific 3D tertiary structures as more hydrogen bonds form, as well as ionic bonds and disulfide bridges (between sulfur atoms). ATP synthase is a quaternary protein and therefore hydrogen bonding joins multiple polypeptide chains and prosthetic groups together and so ATP can split into two portions- the Fo complex embedded in the thylakoid membrane and the F1 complex projected into the matrix. If it weren't for specific bonding placement, ATP would not be synthesised. This means that when protons flow down their electrochemical gradient, the F0 complex would not spin to induce the correct conformational changes in the F1 complex. The active site would not be complementary in shape to bind ADP and pi and so ATP synthase would not catalyse the formation of ATP. Without ATP, no muscle contraction could occur and the organism would be paralysed.

Actin-myosin crossbridges

In muscle contraction, the formation of actin-myosin cross bridges is of paramount importance. When calcium ions bind to troponin, tropomyosin uncovers the actin-myosin binding site on the actin filament. Globular myosin heads are attracted to the actin-binding site and so temporary covalent bonds, in the form of actin-myosin cross bridges are created. Energy released from the hydrolysis of ATP causes the myosin head to bend, and thanks to the crossbridge, in doing so pulls actin filament along in a rowing action.

The ability of the crossbridge to be impermenent and break ensures that mysoin can detcah and rebind further along actin in order to shorten the muscle fibres further.

If no actin-myosin bridges formed then actin filament would not be pulled across the myosin and the sarcomere would not shorten. If sarcomere units did not shorten, then muscle fibres would not shorten and the overall muscle would not contract. If the heart muscle did not contract, it would lead to heart failure. No oxygenated blood could be pumped around the body and no aerobic respiration could occur. The organism would die.

Chymotrypsin and Trypsin

In the digestion of proteins, endopeptidases are enzymes which hydrolyse the peptide bond within polypeptide chains, other than terminal ones. Synthesised at the pancreas, the serine endopeptidase chymotrypsin is essential. Chymotrypsin is first secreted as its inactive form, chymotrypsinogen, but once in the small intestine, the enzyme trypsin converts it into its active form. Chymotrypsin has a highly specific shaped active site including a hydrophobic pocket to which only hydrophobic amino acid side chains can bind, such as phenylalanine. On binding, the active site changes shape slightly for a better fit and an intermediate is formed. The intermediate then reacts, to enable the catalytic hydrolysis of the peptide bond and so a large polypeptide chain can be split into smaller chains. If chymotrypsin was not activated by trypsin then the hydrolysis of polypeptides would be much slower. Amino acids would not be released as quickly by exopeptidases as there would be fewer ends for them to hydrolyse from. Fewer amino acids would be taken up into the blood by cotransport and so less protein synthesis could occur. Conversely, if chymotrypsin was secreted already in its active form, this could lead to the self-digestion of the pancreatic duct, leading to acute pancreatitis.

Rubisco

In plants, rubisco is the primary enzyme in the calvin cycle. The active site on rubisco binds carbon dioxide and catalyses the attachment of it to ribulose bisphosphate. A long unstable 6 carbon chain is initially formed and so rubisco works to clip the chain into two identical glycerate-3-phosphate molecules. If it weren't for rubisco, glycerate-3-phosphate would not form rapidly enough. Less glycerate-3-phosphate would be converted to triose-phosphate. As the majority of triose phosphate (⅚ molecules) is converted back into RuBP, then less RuBP would form and carbon dioxide would build up in air spaces in the leaf. Less triosephosphate would be available to be converted into glucose (2TP) and sucrose. Less sucrose means less mass transport via mass flow to respiring tissues. Fewer glucose sources available means less respiration in the plant, and less ATP produced. Less energy available for cell division resulting in stunted growth of the plant.

RNA polymerase

Amino acids ingested are a source of nitrogen for the production of new RNA molecules. RNA polymerase is vital for the transcription of DNA base sequences into RNA molecules, like mRNA, tRNA and rRNA. RNA polymerase initiates transcription by wrapping around a specific promoter region of DNA. It then proceeds to unwind the double helix of DNA into two template strands. As DNA strands move through RNA polymerase, RNA polymerase catalyses the formation of phosphodiester bonds between RNA nucleotides that are attracted to their complementary exposed bases. Finally, when RNA polymerase detects a terminal sequence, the RNA strand is released. If it weren't for RNA polymerase, mRNA would not be synthesised. There would be no sequence of bases to be read by the ribosome. As no tRNA produced, base sequences would not be translated into amino acids, joined to form polypeptide chains. Genes therefore would not be transcribed into proteins such as antibodies, essential for agglutinating pathogens to destroy them during the immune response.

Chloride ions

Chloride ions are of crucial importance in thinning mucus produced by goblet cells in the trachea and so aiding the function of mucociliary clearance. If working properly, the CFTR protein, an ion channel embedded in the plasma membrane, allows for chloride ions to diffuse from inside the cell to outside the cell. Chloride ions lower the water potential of the mucus and so water molecules move down their water potential gradient out of cells into the mucus by osmosis. Increase in water content thins the consistency of the mucus and allows for cilia to waft back and forwards, sweeping mucus up and out of the airways to be swallowed. We can see the importance of chloride ions when they are not able to be transported. In cystic fibrosis, a mutation occurs to the CFTR causing it to be non-functional and there is no movement of chloride ions out of cells. The water potential of the cells is lower than the mucus and so water moves by osmosis out of mucus into cells. The mucus becomes very thick, causing it to flatten the cilia. Cilia are unable to sweep mucus away and so it becomes stuck in the airways. Bacteria become trapped in the mucus leading to infections and form a biofilm. The surface area for gas exchange is reduced and so is the tidal volume of air, so less oxygen can diffuse into the blood and less aerobic respiration can occur as oxygen acts as the final electron acceptor in oxidative phosphorylation

Sodium-glucose transport

Sodium ions are paramount in the absorption of glucose in the ileum epithelium. As the concentration of glucose in the lumen of the small intestine is usually lower concentration than in the blood, it must be taken up by active transport- specifically cotransport with sodium ions. Sodium ions are initially pumped out (via active transport) of the ileum epithelium and into the blood by a sodium-potassium pump. This creates a concentration gradient where there is a higher concentration gradient of sodium ions in the lumen of the ileum than inside the cell. Sodium diffuses down its concentration gradient via a cotransport protein which binds glucose at the same time. The concentration gradient of sodium is used to transport glucose against its concentration gradient into the cell. The concentration of glucose increases inside the cell, and so glucose can diffuse down its concentration gradient into the blood through a protein channel via facilitated diffusion. If it weren't for sodium ions, a limited amount of glucose would be absorbed. Less glucose would be available to be converted into pyruvate during glycolysis and so less ATP and NADH would be produced. There would be less energy available for important processes such as muscle contraction.

Calcium ions in muscle contraction

Calcium ions are vital for muscle contraction. When an action potential is induced across the sarcolemma of the muscle, the sarcoplasmic reticulum is stimulated to release calcium ions into the sarcoplasm. A calcium ion binds to troponin causing it to conformationally change shape. In doing so, tropomyosin is moved to uncover the actin-myosin binding site to which it had previously blocked. Thanks to calcium ions, globular myosin heads can then bind to form an actin-myosin cross bridge. If it weren't for calcium ions which also activate ATP hydrolase, ATP wouldn't be hydrolysed to release the energy needed for the myosin head to bend to pulls the actin filament across and so the sarcomere would not shorten and the muscle fibres would not contract. Without the active transport of calcium ions back out of their binding sites and into the sarcoplasmic reticulum, then muscles would remain contracted because tropomyosin would not move back to block the actin-myosin binding site. Therefore without calcium ions, we would not be able to control our muscle contraction. Wouldn't be able to control the contraction of e.g muscles in the iris so can't control amount of light which enters the pupil and hits the retina. In bright light, pupil unable to be constricted resulting in bleaching of photopigments to an extent which damages the retina leading to blindness.

AT in root hair cells

The active transport of hydrogen ions is further required during the absorption of mineral ions in the root hair cells of plants. Any cations present in clay rich soil will remain tightly bound to the negatively charged clay particles. This makes it difficult for cations to be absorbed by the root hair cells. To overcome this problem, epidermal tissues are lined with proton pumps which actively transport protons out of cells against their electrochemical gradient into the soil. If it weren't for the active transport of protons, then the protons would not bind to the negatively charged clay particles to release the cations. The cations are then able to diffuse by facilitated diffusion into root hair cells. Furthermore, if active transport of protons did not occur then the concentration of hydrogen ions in the soil would not increase relative to the root hair cells. The plants would not be able to use co-transport of hydrogen ions down their concentration gradient back into the cells as an energy source to move anions against their gradient into the root hair cells. The plant therefore would absorb less cations such as magnesium and less anions such as phosphates, leading to deficiency which limits the amount of photosynthesis which the plant can carry out. Less photosynthesis means less ATP and NADPH produced during the LDR to reduce GP into TP during the LIDR. Less TP can be converted into glucose for energy storage and respiration.

If organic ions.Hdrogen not only produces the electrochemical gradient but also...

are produced by the photolysis of water. When two electrons attach to a magnesium ion in chlorophyll, water is broken down and hydrogen ions are released. Together with the electrons, the hydrogen ions are used to reduce NADP in the light-dependent reaction in the thylakoid. In LIDR hydrogen ions are used to reduce GP into TP as well.

What actually is wrong in cystic fibrosis?

mutant recessive allele results in the loss of an amino acid in the transmembrane conductance regulator protein coded by the CFTR gene. This causes the protein to break down before it is fully processed so never reaches the cell membrane to be embedded.