Essays on molecules and cells

Model answer

The function of a protein depends on its tertiary structure, the three-dimensional shape held by hydrogen bonds, ionic bonds and disulfide bridges between R-groups. Many proteins work because this shape changes when another molecule binds, and these changes are important throughout organisms.

Enzymes work by the induced-fit model. The active site is not exactly complementary to the substrate, but when the substrate binds the active site changes shape slightly to mould around it, forming an enzyme-substrate complex. This puts strain on bonds in the substrate, or brings reacting groups close together, so the activation energy is lowered. Changes in enzyme shape also control metabolism. A non-competitive inhibitor binds to a site other than the active site and changes the shape of the active site, so substrates can no longer bind; this allows the end product of a pathway to switch off an earlier enzyme. Harmful changes in shape also matter: high temperature breaks hydrogen bonds and extremes of pH disrupt ionic bonds, so the enzyme is denatured. This is why mammals keep a stable core temperature and blood pH.

Haemoglobin is a protein with a quaternary structure of four polypeptides, each with a haem group that binds one oxygen molecule. When the first oxygen binds, the shape of haemoglobin changes so that it becomes easier for further oxygen molecules to bind (cooperative binding). This produces the S-shaped oxyhaemoglobin dissociation curve, so saturation changes a lot over a small range of partial pressures of oxygen; haemoglobin loads oxygen readily in the lungs and unloads it readily in respiring tissues. Carbon dioxide also changes the shape of haemoglobin: it lowers the pH, which reduces haemoglobin's affinity for oxygen (the Bohr effect), so more oxygen is unloaded where cells are respiring fastest. Different haemoglobins differ in how readily they bind oxygen: animals that live where oxygen is scarce have haemoglobin with a higher affinity, so their dissociation curve lies to the left and their haemoglobin still becomes saturated.

Carrier proteins in cell membranes change shape to move substances. In active transport, a molecule or ion binds to a specific carrier, ATP is hydrolysed and a phosphate attaches to the carrier, which changes shape and releases the substance on the other side of the membrane. The sodium-potassium pump moves three sodium ions out of a cell for every two potassium ions moved in. This is important because it maintains the sodium ion gradient used in co-transport, for example when glucose is absorbed by epithelial cells in the ileum against its concentration gradient, and it helps to maintain the resting potential of neurones.

Channel proteins that open by changing shape allow cells to respond to stimuli. In a Pacinian corpuscle, pressure deforms the lamellae and stretches the membrane of the sensory neurone, so stretch-mediated sodium ion channels open; sodium ions diffuse in and produce a generator potential. At a cholinergic synapse, acetylcholine binds to receptor proteins on the postsynaptic membrane, which change shape and open sodium ion channels, depolarising the membrane. Acetylcholinesterase then hydrolyses the acetylcholine, so the channels close again. This is important because it means a response occurs only when a stimulus or neurotransmitter is present, and it stops continuous stimulation of the postsynaptic neurone. Some drugs act on these receptors: a drug that binds to the acetylcholine receptor but does not cause the change in shape that opens the channel blocks transmission, which is how some muscle relaxants used in surgery work.

Muscle contraction depends on changes in protein shape. When an action potential reaches a muscle fibre, calcium ions are released from the sarcoplasmic reticulum and cause tropomyosin to move, exposing the binding sites on actin. Myosin heads bind to actin, forming actinomyosin cross-bridges. Each myosin head then changes angle, pulling the actin filament towards the centre of the sarcomere as ADP and phosphate are released. ATP binds and the head detaches, and hydrolysis of ATP returns the head to its original position, ready to bind again. These repeated changes in shape shorten sarcomeres, so muscles can contract and move parts of the skeleton.

Changes in the shape of proteins also control gene expression. The steroid hormone oestrogen is lipid-soluble, so it diffuses through the cell-surface membrane and binds to a site on a transcription factor in the cytoplasm. This changes the shape of the transcription factor, releasing it from an inhibitor molecule. It can then enter the nucleus and bind to the promoter of a target gene, stimulating RNA polymerase to transcribe it. This is important because only cells with the right receptor respond, so one hormone can control specific genes in specific tissues.

Changes in protein shape can also be harmful. Prions are abnormally folded forms of a normal brain protein. When a prion contacts the normal protein, it causes it to fold into the abnormal shape, so the abnormal form accumulates, forms insoluble clumps and kills neurones, causing diseases such as variant CJD. This shows how completely a protein's function depends on its shape.

Model answer

In complex multicellular organisms, cells become specialised for particular functions and are organised into tissues, organs and systems. Specialisation is important because a cell that does one job, with a structure suited to it, does that job far more efficiently than a cell that does everything.

Cells become specialised during development. All the cells of an organism contain the same genes, but totipotent cells in the early embryo translate only part of their DNA as they divide, so different cells produce different proteins and develop different structures. Transcription factors switch particular genes on in particular cells, and epigenetic changes such as increased methylation of DNA keep other genes switched off. This is important because it produces the many different cell types needed by the organism, and it means that once a cell is specialised it usually stays that way.

Epithelial cells lining the ileum are specialised for absorbing the products of digestion. Their cell-surface membrane is folded into microvilli, which greatly increase its surface area, and contains many carrier proteins, as well as membrane-bound disaccharidases and dipeptidases that complete digestion at the surface. The cells contain many mitochondria, which provide ATP for the active transport of sodium ions out of the cell into the blood. This keeps the sodium ion concentration in the cell low, so sodium ions diffuse in from the lumen through co-transporter proteins, carrying glucose or amino acids with them, even against their concentration gradients. These features are important because they allow almost all of the glucose and amino acids in the gut to be absorbed into the blood.

Mammalian red blood cells are specialised for carrying oxygen. They lose their nucleus and most organelles as they mature, leaving more space for haemoglobin, and their small size and biconcave shape give a large surface area to volume ratio and a short diffusion distance. Haemoglobin binds oxygen cooperatively, so it loads readily at the high partial pressure in the lungs and unloads readily at the low partial pressure in respiring tissues. Because red blood cells have no mitochondria, they respire anaerobically and do not use the oxygen they carry. The cost of this specialisation is that red blood cells cannot divide or repair themselves, so they are replaced continuously by stem cells in the bone marrow. People who live at high altitude produce more red blood cells, which increases the oxygen-carrying capacity of their blood.

In plants, sieve tube elements and companion cells work together to translocate sucrose. Sieve tube elements have lost their nucleus and most organelles, leaving a column of cytoplasm through which solution flows easily, and their end walls form sieve plates. Each depends on a companion cell, which has a nucleus and many mitochondria; the companion cell provides the ATP used to load sucrose into the sieve tube. This lowers the water potential of the sieve tube, water enters by osmosis and the resulting hydrostatic pressure moves the solution by mass flow to sinks such as roots. This division of labour is important because the sieve tube element offers little resistance to the flow of sap, while the companion cell carries out the metabolism that both cells need, so sucrose made in the leaves can be supplied to roots, growing tips and storage organs that cannot photosynthesise.

Rods and cones in the retina are specialised in different ways. Rods contain the pigment rhodopsin, which is broken down by low light intensities, and several rods are connected to one bipolar neurone. Their generator potentials can combine (summation) to reach threshold, so rods give high sensitivity in dim light, but low visual acuity because the brain cannot tell which rod was stimulated. Cones contain iodopsin, which needs higher light intensities, and each cone usually connects to its own bipolar neurone, giving high visual acuity. There are three types of cone with different iodopsins, sensitive to red, green or blue light, so cones also give colour vision.

Skeletal muscle fibres are specialised for contraction. Each fibre is a multinucleate cell containing many myofibrils made of sarcomeres, with actin and myosin filaments that slide past each other. The sarcoplasmic reticulum stores calcium ions and releases them throughout the fibre when it is stimulated. Muscle fibres are further specialised into two types. Slow fibres have many mitochondria, much myoglobin and a good blood supply, so they contract for long periods using aerobic respiration, as in muscles that maintain posture. Fast fibres have more glycogen and phosphocreatine, so they contract powerfully for short periods, for example when sprinting. Having both types of fibre is important because the body can maintain its posture for hours without fatigue and can also produce sudden, powerful contractions, using ATP regenerated from phosphocreatine without waiting for oxygen to be delivered.

Plasma cells are specialised B lymphocytes that secrete antibodies. They have a very large rough endoplasmic reticulum and Golgi apparatus, many mitochondria, and they transcribe the genes for one antibody at a very high rate. This is important because thousands of antibody molecules can be released each second during the primary immune response. When the infection is over most plasma cells die, but memory cells remain.

Model answer

Plant cells have a cellulose cell wall, chloroplasts and a large permanent vacuole, and they store starch rather than glycogen. These features are important because plants cannot move, must make their own organic molecules and need support without a skeleton.

The cell wall is made of cellulose. Beta-glucose molecules are joined by 1-4 glycosidic bonds, with alternate molecules inverted, to form long, straight chains. Many parallel chains are held together by hydrogen bonds to form microfibrils with great tensile strength. When a plant cell is in a solution with a higher water potential than its cytoplasm, water enters by osmosis and the protoplast pushes against the wall, but the wall resists expansion, so the cell becomes turgid instead of bursting. Animal cells have no wall and would burst, so mammals must control the water potential of their blood using ADH and the kidneys. Turgor is important because turgid cells press against each other and support non-woody stems and leaves, holding leaves up to the light. If water is lost, cells become flaccid and the plant wilts; in a solution of lower water potential the protoplast shrinks away from the wall (plasmolysis). Cellulose also matters to animals: most cannot digest it, and herbivores such as cows rely on microorganisms in their gut that produce enzymes to hydrolyse it, which is one reason why the efficiency of energy transfer from plants to herbivores is low.

The large vacuole, surrounded by its own membrane, contains cell sap, a solution of sugars, ions and other solutes. Its water potential is important in water uptake and in maintaining turgor. Guard cells use this to control gas exchange. When guard cells take up potassium ions, using ATP, their water potential falls, water enters by osmosis and they become turgid. Because the inner walls of guard cells are thicker than the outer walls, the cells bend apart and the stoma opens, so carbon dioxide can diffuse in for photosynthesis. When water is short, the guard cells lose turgor and the stomata close, limiting water loss by transpiration. This shows the compromise between efficient gas exchange and limiting water loss.

Chloroplasts are the most important feature of plant cells, because they make plants autotrophs. Their thylakoid membranes contain chlorophyll, which absorbs light and loses electrons (photoionisation); the energy is used to make ATP and reduced NADP, and photolysis of water releases oxygen. In the stroma, rubisco catalyses the reaction of carbon dioxide with ribulose bisphosphate, and ATP and reduced NADP are used to reduce glycerate 3-phosphate to triose phosphate, from which glucose and other organic molecules are made. This is important for the whole ecosystem, because the chemical energy fixed by plants as gross primary production is the source of energy for almost all other organisms, through food chains and decomposers.

Plant cells store carbohydrate as starch, in starch grains in the cytoplasm or in chloroplasts. Starch is made of alpha-glucose: amylose is unbranched and coils into a compact helix, and amylopectin is branched. Because starch is insoluble, it does not lower the water potential of the cell or diffuse out of it. Starch is less branched than glycogen, so glucose is released from it more slowly, which suits plants, whose metabolic rate is lower than that of animals; large amounts can be stored compactly in storage organs and seeds and hydrolysed to glucose when needed, for example when a seed germinates.

The cell wall also allows plant cells to grow by elongation. Growth in shoots and roots depends on cells near the tip taking in water into the vacuole and elongating. Indoleacetic acid (IAA) controls this. In a shoot lit from one side, IAA moves to the shaded side, where it stimulates cell elongation; IAA is thought to cause hydrogen ions to be pumped into the cell wall, which loosens the bonds between cellulose microfibrils so that the wall stretches as water enters. The shoot bends towards the light (phototropism), so leaves receive more light for photosynthesis. In roots, a high concentration of IAA inhibits elongation, so roots bend downwards (gravitropism) and grow into the soil to obtain water and mineral ions.

Plant cells are also connected to neighbouring cells by plasmodesmata, strands of cytoplasm that pass through pores in the cell walls, so substances can move from cell to cell without crossing membranes. This matters in the phloem. Sieve tube elements have lost their nucleus and most organelles, and their end walls form sieve plates, so sucrose solution flows through them easily by mass flow. Each sieve tube element depends on a companion cell, connected to it by many plasmodesmata, which has a nucleus and many mitochondria and supplies the ATP used to load sucrose at the source.

Finally, many mature plant cells remain totipotent. Unlike most specialised animal cells, a small piece of plant tissue placed on a medium containing nutrients and growth factors can divide and develop into a whole new plant. This is important because plants can regenerate parts that are eaten or damaged, and growers use tissue culture to produce large numbers of genetically identical plants with desirable features.

Model answer

Some molecules and cells in an organism last for years, while others are broken down or replaced within seconds, minutes or days. Differences in life span are important: long-lived molecules and cells store information and energy, while short-lived ones allow an organism to respond quickly and to switch processes off again.

DNA is a very stable molecule. Its two polynucleotide strands are held together by many hydrogen bonds between complementary bases, the bases are protected inside the double helix by the sugar-phosphate backbones, and in eukaryotes the DNA is wound around histones inside the nucleus. This stability is important because DNA must carry the genetic information of a cell throughout its life and be copied accurately by semi-conservative replication each time the cell divides. mRNA, in contrast, is a short, single-stranded molecule that contains ribose, which makes it less stable, and each mRNA molecule is translated for only a limited time before it is broken down. This is important because when a gene stops being transcribed, the protein it codes for soon stops being made, so a cell can change the proteins it produces as conditions change. RNA interference shortens the life of particular mRNA molecules: a small RNA molecule, held in a protein complex, binds to an mRNA with a complementary base sequence, which is then hydrolysed before it can be translated, so the gene is silenced.

ATP is also short-lived. It is not used as a long-term energy store; instead, each ATP molecule is hydrolysed by ATP hydrolase soon after it is made, and a cell contains only a small amount, which is continuously resynthesised from ADP and phosphate by ATP synthase during respiration. A human recycles a mass of ATP close to their own body mass each day. This is important because ATP releases energy in small amounts, in a single reaction, immediately where it is needed. It also means that cells must respire all the time: if respiration stops, for example when cyanide inhibits the electron transfer chain, ATP runs out quickly and cells die. Long-term energy stores are different molecules. Triglycerides are insoluble and can be stored in large amounts for months, so a hibernating mammal can survive the winter on its fat reserves, whereas the glycogen in the liver is a short-term store that lasts only about a day without food.

Neurotransmitters must have a very short life. At a cholinergic synapse, acetylcholine released from the presynaptic neurone diffuses across the cleft, binds to receptors on the postsynaptic membrane and opens sodium ion channels. Acetylcholinesterase then hydrolyses it into choline and ethanoic acid, which diffuse back into the presynaptic neurone and are recombined into acetylcholine using ATP. The short life of acetylcholine is important because the postsynaptic membrane is not stimulated continuously, so each impulse that arrives produces a separate response. Some insecticides inhibit acetylcholinesterase; acetylcholine then accumulates, and the continuous stimulation of muscle fibres can cause paralysis.

Hormones are also removed from the blood, so their effects stop when they are no longer needed. After a meal, insulin is secreted and causes target cells to take up glucose and convert it to glycogen. As the blood glucose concentration falls, the beta cells secrete less insulin, and the insulin already in the blood is broken down within minutes, mainly in the liver. If insulin lasted much longer, its effect would continue after the concentration had returned to normal, and blood glucose would fall too low. ADH is removed in the same way, so when the water potential of the blood rises again, less water is reabsorbed in the kidneys. The short life of hormones therefore allows negative feedback to keep conditions close to their normal values.

The life span of lymphocytes is also important. During an immune response, B cells with complementary receptors divide to form a clone, and many of the cells become plasma cells, which secrete antibodies. Most plasma cells live for only a few days, so antibody production stops once the pathogen has been destroyed and resources are not wasted. Memory cells, however, survive for many years. If the same antigen enters the body again, they divide rapidly, so the secondary response is faster and produces more antibody, which is the basis of vaccination. Passive immunity, in which a person receives antibodies made by another organism, is short-lived because the antibodies are broken down and no memory cells are formed.

Finally, many specialised cells are short-lived and must be replaced. Mature red blood cells have no nucleus, so they cannot divide or repair themselves, and they last only about four months. They are replaced by the division and differentiation of multipotent stem cells in the bone marrow, and the epithelial cells lining the small intestine are replaced every few days in a similar way. The life span of a line of dividing cells is limited too. Each time a body cell divides, the repeated sequences at the tips of its chromosomes (telomeres) become a little shorter, and after a certain number of divisions the cell stops dividing. Many cancer cells switch on the gene for telomerase, an enzyme that adds the repeats back, so their descendants never reach this limit; together with mutations in proto-oncogenes and tumour suppressor genes, this lets a tumour keep growing.