| MOVEMENTS INSIDE CELLS | MOVEMENTS INSIDE CELLS |
| THE DIFFERENT WAYS IN WHICH ORGANISMS USE INORGANIC IONS | THE DIFFERENT WAYS IN WHICH ORGANISMS USE INORGANIC IONS |
| Inorganic ions | Inorganic ions are charged particles that do not contain carbon atoms bonded together. While organisms are mainly built from carbon-containing molecules, their functions rely on inorganic ions such as nitrate, hydrogen and calcium. |
| Nitrogen cycle | The availability of fixed nitrogen in the soil limits the productivity in an ecosystem
Nitrogen fixing bacteria in the roots of leguminous plants reduce atmospheric nitrogen to ammonium using ATP + NADH2
The ammonium ions released into the soil are oxidised by nitrifying bacteria into nitrite,and then to nitrate
plants can use nitrates to produces many useful molecules including amino acids, DNA and ATP
The formation of these ions forms part of the ecological nitrogen cycle which plays a key role in sustaining life on this planet |
| Photosynthesis | Plants are the producers for an ecosystem
They photosynthesise co2 + h20 and produce energy in the form of carbohydrates and other molecules.
Plant absorbs water with their roots from the soil using mineral ions such as nitrate produced by the nitrifying bacteria
Hydrolysis of ATP releases energy for processes such as active transport of the nitrate ions (and others such as potassium etc) from the soil into root hair cells, a process that lowers water potential and is used to draw water into the plant from the soil.
In leaves, photosynthesis involves the photolysis of water, which involves the attachment of 2 e- to a magnesium ion in chlorophyll and the production of h ions from the breakdown of water.
Together with the e-, the h ions are used to reduce NADP in the light-dependent reaction in the thylakoid. The h ions and e- are used to reduce gp to form tp and glucose.
H ions also play a role in the production of ATP in the ETC. They are pumped into the inter-membrane space creating a proton gradient that provides energy to combine ADP and inorganic phosphate ions to form ATP |
| Respiration | The glucose, proteins and other molecules produced by the plants can be consumed by animals
The glucose undergoes respiration in cells in three different stages, each involving inorganic ions.
Hydrolysis of ATP produces ADP + a phosphate ion which can be used to phosphorylate glucose in the cytoplasm during glycolysis.
This phosphorylation makes the glucose more reactive and prevents it from leaving the cell.
Following the transfer of h ions to coenzymes such as NAD, the pyruvate formed enters the mitochondrion + is decarboxylated + oxidised, in the process transferring its h ions + e- to NAD + FAD.
These h ions are pumped into the inter-membrane spaces of the cristae and are used to create a proton gradient to form ATP as part of oxidative phosphorylation. |
| The nerve impulse | Hydrolysis of ATP provides energy that is used to pump out 3 s ions + pump in 2 p ions into the axon of a neurone through a specific cation pump by AT
A reduction of the membrane permeability to s ions maintains a resting potential of -70mV on the inside of the axon.
Generation of an action potential also uses the charges from ions. S gated channels open in the axon membrane allowing s ions to enter.
This causes the membrane to depolarise until the threshold voltage of +40mV opens p gated channels. This causes p ions to leave repolarising, and eventually hyperpolarising the cell.
This wave of depolarisation caused by these ion movements allows the passage of nerve impulse and coordination of the animal within its environment |
| Skeletal muscle | This movement involves the contraction of muscles, another process that uses ions, calcium.
Calcium ions bind to tropnin, which causes tropomyosin to move away from the myosin head binding site on actin filaments.
Actomyosin cross-bridge is formed, actin filament slides into myosin, calcium ions activate ATPase to hydrolyse ATP to ADP and phosphate ions, a process that releases energy for the detachment and reformation of cross bridges.
Contraction of the muscle sarcomere allows the contraction of skeletal muscle, allowing the animal to move.
Muscles contractions are also used by animals in processes such as controlling light entry into the eye blood flow in arterioles in maintenance of homeostasis.
All these processes require nervous coordination and contraction, emphasising the importance of the inorganic ions for proper function |
| Ventilation | Contraction of intercostals muscles allows ventilation of the lungs to take place in mammals.
This introduces o2 to the gas exchange surface, the epithelium of the alveoli of the lungs.
In order to maintain a high conc grad, the o2 is rapidly removed, a process involving another mineral ion, iron.
Iron ions are attached to haem groups on haemoglobin inside red blood cells. The iron can form bonds to o2, allowing haemoglobin to load o2 in the lungs when the pp0 is high.
Each molecule of haemoglobin can bind 4 O2 mols allowing a rapid saturation and the production of oxyhaemoglobin.
On contraction of the ventricles, the pressure forces the red blood cells through the body to regions where pp0 is lower.
Here, the haemoglobin unloads, making o2 available for aerobic respiration and the production of ATP. |
| DNA AND THE TRANSMISSION OF INFORMATION | DNA AND THE TRANSMISSION OF INFORMATION |
| DNA | Deoxyribonucleic acid, carries the genetic code for all living organisms on this planet. It is variation in the info it carries in form of genes and alleles that produces the wide diversity of life |
| Stucture | Polymer, double helix of 2 polynucleotide strands bonded together by h bonds. Each nucleotide comprises of a phosphate group attached to a 5c deoxyribose sugar and an nitrogen-cotaining organic base. These bases can be either A, T, G, C. Adjacent nucleotides are joined by a condensation reaction to form the phosphate-sugar backbone of a polynucleotide strand. Two complementary strands then join by specific base pairing (A to T, C to G), which then wind together to form the double helix which provides strength and stability to the molecule.
The information in DNA is encoded in the sequence of bases along the template strand. A gene is a sequence of bases on DNA that codes for the sequence of amino acids in a polypeptide chain.
Proteins determine the functions and structures of cells, so DNA code controls all cell activities.
Organisms of the same species carry the same genes at loci, but individuals carry different slightly different versions, alleles.
Variation in these alleles results in intraspecific variation within a species. |
| Semi conservative replication | DNA must be replicated by semi-conservative replication to transfer genetic material into daughter cells as the organism grows or repairs.
Helicase breaks h bonds in DNA, dividing the 2 polypeptide strands, exposing the bases, act as templates. DNA-nucleotides then bind to exposed bases by specific base pairing with h bonds.
DNA polymerase then joins adjacent nucleotides with a condensation reaction forming the phosphate-sugar backbone.
DNA molecule contains one strand from the original DNA molecule and one new strand. So this helps to minimise mutations when copying the code.
In prokaryotic cells the DNA is free in the cell cytoplasm, but in eukaryotes it is bound within a nucleus and joined to histones.
Forms chromosomes , these are separated into daughter cells to carry the same genetic information as the parent cell. |
| Mitosis | - Separates the two copies of each chromosome
- Prophase the chromosomes coil up and become visible, the nuclear envelope disappears and the chromosomes attach to spindle fibres at the equator of the cell using their centromere in metaphase. In anaphase the centromere divides and the spindle contracts drawing the chromatids to opposite poles of the cell. After telophase and cytokineis, two new daughters are formed, each containing an identical copy of the DNA code; hence the encoded information has been transmitted vertically. Bacteria also possess the ability to transmit some of their genes horizontally. Conjugation tubes can form between two bacterial cells and the plasmid, small loops of DNA that carry codes for antibiotic resistance, can pass between the two cells. So if one bacteria owns has a plasmid that arries the code for penicilinase, the plasmid can be replicated and passed via conjugation to another. Now both cells are resistant to penicillin. |
| The genetic code | The information on DNA is encoded as triplets of bases, called codons. Each triplet can code for one amino acid in a polypeptide chain. So for example, if GCA codes for the amino acid alanine and TAC codes for glycine, then the code GCAGCATACGCA would code for a polypeptide with the sequence ala-ala-gly-ala. As there are over twenty different amino acids in nature, a triplet code allows coding of up to 64 amino acids. Such a code is termed redundant and in reality each amino acid is coded for by several different codes. This minimises mutation rates as, for example, if GCC also codes for alanine, then a mutation from CA to CC would have no effect on primary structure. Each of the codons is translated in sequence as the code is non-overlapping, but first the genetic information must be transcribed, and then transferred out of the nucleus. It is transferred as an RNA molecule, a single-stranded polynucleotide containing the base uracil instead of thymine, and the five-carbon sugar ribose. |
| Transcription | - Produces copy of a gene in the form of mRNA
- Helicase binds to the gene locus causing DNA to unwind and reveal a template strand
- RNA-nucleotides bind by specific base pairing and RNA polymerase joins them by condensation to form a strand of pre-mRNA.
- Introns are removed, exons are spliced together with enzymes to form the mRNA
- Now small enough to diffuse through the nuclear pore and bind to a ribosome on the rough endoplasmic reticulum |
| Translation | The process of protein synthesis, or translation can now begin. In the cytoplasm, a transfer RNA (tRNA) molecule binds to a specific amino acid and two such complexes deliver their amino acids to the ribosome. The anticodon on tRNA binds to the complementary codon on mRNA by specific base pairing (A to U, C to G). An enzyme now forms the peptide bind between the amino acids by condensation using energy from ATP and the process is repeated building up the polypeptide chain. Alterations of the base sequence of the gene, mutations alter the structure of the mRNA and so possibly altering the primary structure of the polypeptide coded for. These can be substitutions, deletions of additions. The greatest corruption of the code occurs with the latter two which cause frame shifts that are catastrophic to the base sequence and the primary structure of the coded protein |
| Sexually reproducing organisms | Sexually reproducing organisms transmit their genes in the form of haploid gametes (ova and sperm, or pollen) formed by meiosis. This reductive cell division halves the chromosome number so the diploid number of chromosomes can be regenerated on fertilisation. Meiosis introduces variation through crossing over and independent segregation of chromosomes, and random fusion ensures further variety in the offspring produced. In this way the genetic information is transmitted from generation to generation introducing a diverse range of alleles that adds not only variety, but helps ensure a population can survive and adapt to any environmental changes |
| THE PART PLAYED BY ENZYMES IN THE FUNCTIONING
OF DIFFERENT CELLS, TISSUES AND ORGANS | THE PART PLAYED BY ENZYMES IN THE FUNCTIONING
OF DIFFERENT CELLS, TISSUES AND ORGANS |
| Globular proteins | - Enzymes are globular proteins which have a specific tertiary structure that has a complementary shape to substrate
- The lock and key model is used to describe enzyme action. For example the enzyme lactase has an active site (a lock) that is complementary only to lactose (the key).
- Sucrose, a similar disaccharide has a different shape to lactose and so cannot bind to lactase’s active site. On binding to the active site, an enzyme-substrate complex is formed and reaction takes place.
- The products have a different shape and can no longer remain bound.
- In the induced fit model, the active site is not complementary to the substrate, but on binding the shape changes and the active site forms, molding itself to the substrate a tight glove would mould to a hand. |
| Digestive system | - Humans gain the molecular building blocks they need for energy and growth from digestion of food by the digestive system.
- System of organs that is adapted for the hydrolysis of food molecules and the absorption of their products.
- Amylase in the saliva hydrolyses starch to maltose, which is digested in the intestinal epithelium to α-glucose.
- In the stomach endopeptidases such break down proteins in smaller peptides, and exopeptidases further hydrolyse these into amino acids in the small intestine.
- Glucose is then absorbed by sodium-glucose transport, a type of AT that involves the enzyme ATPase which hydrolyses ATP to ADP and Pi releasing energy to pump sodium ions out, and potassium into epithelial cells creating diffusion gradient for sodium and glucose uptake. |
| Enzyme role in digestion | Enzymes also play a key role in digestion of large insoluble food molecules into smaller, more soluble products that can be transported and assimilated in fungi and bacteria. Decomposers in the ecosystem, the fungi and bacteria, release hydrolytic enzymes such as lipase, carbohydrase and protease (to digest triglycerides, carbohydrates and proteins respectively). The soluble products of this extracellular digestion (e.g. fatty acids, glucose, and amino acids) can then be absorbed and assimilated into useful compounds. |
| Replication | All organisms carry the genetic code for their functions as a DNA molecule. Before a cell divides by mitosis, the DNA must undergo semi-conservative replication to produce two identical copies for the daughter cells. Enzymes play a key role here. Helicase binds to the DNA, breaking the hydrogen bonds that hold the two polynucleotide chains together. This reveals two template strands which have exposed bases which bind to DNA-nucleotides. A second enzyme, DNA polymerase then forms a phosphate-sugar backbone by joining adjacent nucleotides with a condensation reaction |
| Insulin | Some cells, such as β-cells of the pancreas synthesise and secrete protein hormones such as insulin. In order for the genetic code on DNA to be expressed and the insulin formed, the DNA must be transcribed as a pre-mRNA molecule, spliced to form mRNA and transcribed as a protein. Enzymes are involved in each step. Helicase binds to the gene locus and cause the gene to unwind exposing the template strand. RNA polymerase joins adjacent nucleotides in a condensation reaction to form the pre-mRNA strand. Enzymes in the nucleus remove non-coding introns, and splice together the coding exons leading to the formation of an active mRNA which binds to a ribosome on the rough endoplasmic reticulum. Transfer RNA complexes line up with their anticodons on the codons on mRNA and bring two amino acids in contact with an enzyme in the ribosome that condenses them together by forming a peptide bond. The process is repeated to build up the primary structure of the insulin molecule. The action of the hormone insulin also involves phosphorylase enzymes which cause the condensation of glucose molecules into the storage polysaccharide glycogen in the liver by glycogenesis. |
| Respiration | All living cells release the energy in substrate molecules using aerobic or anaerobic respiration. The respiratory process is a sequence of interconnected enzyme controlled steps called a metabolic pathway. Other pathways include photosynthesis and the synthesis of steroid hormones such as oestrogen from cholesterol. During glycolysis, the link reaction and the Krebs cycle, some of the steps include oxidation by dehydrogenase enzymes. This oxidation involves the transfer of hydrogen ions and electrons from the substrate and passing them to a coenzyme which becomes reduced. For example, in the cytoplasm, when triose phosphate molecules are oxidised to pyruvate as part of glycolysis, the coenzyme NAD is reduced forming reduced NAD. The coenzyme forms part of the active site of the dehydrogenase enzyme allowing it to function as a catalyst and |
| The ATP formed as part of respiration | The ATP formed as part of respiration is used in a wide variety of contexts in biology. For example in order for an animal to move and hunt for food within its environment, it has to contract its muscle tissue. The tissue is composed of cells containing actin and myosin filaments which move relative to each other to contract a sarcomere. For this to happen, actomyosin cross-bridges form between the actin and myosin. Once activated by calcium ions, the enzyme ATPase then hydrolyses ATP to ADP and Pi releasing energy for the detachment and formation of more cross-bridges, giving rise to the sliding filament theory of muscle contraction. This enzyme also helps release energy from ATP in a wide variety of contexts, such as in the active transport of sodium ions out of an axon through sodium-potassium cation pump in the generation of a resting potential, or in the active transport of nitrate ions into a root hair cell to lower water potential to draw in water to generate a root pressure. |
| THE PART PLAYED BY THE MOVEMENT OF SUBSTANCES ACROSS CELL MEMBRANES IN THE FUNCTIONING OF DIFFERENT ORGANS AND ORGAN SYSTEMS | THE PART PLAYED BY THE MOVEMENT OF SUBSTANCES ACROSS CELL MEMBRANES IN THE FUNCTIONING OF DIFFERENT ORGANS AND ORGAN SYSTEMS |
| Cell surface membrane | The cell surface membrane is a plasma membrane composed of a phospholipid bilayer. It acts as a hydrophobic barrier that prevents the passive diffusion of hydrophilic species such as glucose and amino acids into the cell. Hydrophilic channel proteins are embedded in the bilayer which provides a route by which polar substances can enter, either down a concentration gradient by facilitated diffusion or against a concentration gradient by active transport. The relative movements of the lipid molecules together with the random arrangement proteins give rise to the term the fluid mosaic model of the cell surface membrane. |
| Diffusion | Non-polar molecules such as fatty acids, oxygen and carbon dioxide are able to dissolve directly through the membrane and enter the cell by diffusion. This process is used in the lungs whose function is the gas exchange of carbon dioxide and oxygen across the epithelium of the alveoli. Contraction of the intercostal muscles and the flattening of the diaphragm move the rib cage up and out, increasing the volume of the thorax. This decreases the pressure allowing air to be drawn into the lungs down a pressure gradient. This ventilates the epithelial cells of the alveoli allowing oxygen to diffuse through the membrane through the cells. The oxygen then continues to diffuse through the membrane of the red blood cells where it loads to haemoglobin forming oxyhaemoglobin. The carbon dioxide follows the reverse route and is expelled from the lungs during expiration as the intercostal muscles relax. |
| ATP | The oxygen helps cells to release energy as ATP during aerobic respiration. The oxygen helps to increase the permeability of the mitochondrial membrane allowing pyruvate formed in glycolysis to enter the matrix of the mitochondrion. The reduced NAD also formed passes its electrons down an electron transport chain in a series of redox reactions from one carrier molecule to the next. In doing so it increases the permeability of channel protein the inner membrane to hydrogen ions, which then pass into the inter-membrane space. This lowers the pH and helps to generate an electrochemical gradient which activates ATPase to combine ADP and Pi to form ATP. |
| Active transport | All organisms use ATP as an immediate energy source for processes such as active transport. In plants, the roots are an organ system whose purpose is the uptake of mineral ions and water, and its movement though to the endodermis and xylem via the apoplast and symplast pathways. The root hair cells have specific channels for ions such as nitrate and potassium. These channels have the enzyme ATPase which hydrolyses ATP and releases energy to absorb the ions against a concentration gradient into the cell. This movement into the cell from the soil lowers the water potential of the roots hair cells allowing water to enter by osmosis. Movement of this water then takes place via the symplast pathways (through cell cytoplasm) and apoplast pathways (via gaps in the cell walls. Water crosses the junctions of adjacent cells through plasmodesmata, smallgaps that allow its smooth passage to the endodermis. Active transport of the mineral ions into the xylem allows the water to enter the xylem by osmosis generating a hydrostatic pressure called the root pressure. This creates a push, which together with the cohesion-tension pulls water up the xylem in a column through the hollow lignified xylem vessels. |
| Waste products/osmosis | Animals use an excretory system to remove any waste products such as urea. The role of one key organ, the kidney, is to form a more concentrated urine and reabsorb glucose, sodium ions and water while excluding the urea. The membranes of the kidney tubules are adapted to allow this function. The narrowing of the afferent arteriole generates a hydrostatic pressure at the glomerulus which forces blood against the capillary network. Water and small molecules pass through the pores while proteins and cells are excluded by the process of ultrafiltration. These smaller molecules enter the Bowman’s capsule and the proximal convoluted tubule, which has many sodium and glucose channels. These allow the selective reabsorption of these materials into the surrounding tissues. This lowers the water potential so water moves out of the tubule by osmosis and is reabsorbed with the ions into the capillaries that surround the tubules. As the membrane does not have channels for urea, urea remains in the tubule increasing in concentration. The ascending limb of the loop of Henle is impermeable to water. Sodium and chloride ions are actively transported out onto the surrounding tissues through a specific channel using ATP. This lowers water potential creating a water potential gradient that draws water from the descending limb by osmosis. This counter current multiplier further contributes to the reabsorption of water, one of the key functions of the kidney. A protein hormone, ADH is released by the pituitary gland and binds to specific receptors on the collecting ducts of the kidney in situations when the blood water potential is too low. This increases the membranes permeability to water effectively increasing the volume reabsorbed at the same time decreasing the volume of urine produced. |
| Example | One example of the consequences of uncontrolled ions movements is when the bacterium, Vibrio cholerae releases its toxin in the large intestine. The protein binds to and opens a chloride ion channels on the epithelium surface. Chloride ions flood out into the lumen lowering water potential causing rapid loss of water, chronic diarrhoea and severe dehydration. In the absence of the toxin these ions would have remained inside the epithelial cells. Water alone cannot be used to rehydrate the sufferer as it cannot easily be absorbed through the intestinal epithelium. The reabsorption of water requires sodium and glucose, two key components of oral rehydration solutions. These species are taken up by co-transport in the small intestine region of the digestive system which lowers water potential sufficiently to allow the absorption of water and the rehydration of the sufferer. |
| MOVEMENTS INSIDE CELLS | MOVEMENTS INSIDE CELLS |
