IB Chemistry/Option Definitions
Option B – Medicine and Drugs - SL
Addiction: Problem with opiates, in which a dependency on a drug is created.
Adrenaline: A naturally occurring hormone and stimulant. Released during stress. Responses: 1) Increased pulse; 2) dilation of pupils; 3) sweating; 4) diversion of blood to muscles; 5) decreased blood clotting time. Fat insoluble. Both amphetamine and adrenaline are based on the framework of a benzene ring with a two carbon chain and an amine (NH2 or NH) group at the end.
AIDS: Acquired Immune Deficiency Syndrome. Develops from HIV.
Alginates: Often combined with antacids. Prevent acid in stomach from rising into esophagus and causing ‘heartburn.’
Amine: Primary amines have one R group attached to N atom. Secondary have two on at least one N atom. Tertiary have three on at least one N atom.
Amphetamine: Fat soluble molecule which mimics noradrenaline. Similarity is so strong that it can replace noradrenaline in its storage sites, resulting in a flood of displaced noradrenaline molecules that bind to other neural proteins and set of a number of signals euphoria.
Analgesic, mild: Have triad of properties: 1) analgesic (pain relief); 2)antipyretic (fever reduction); 3) anti-inflammatory (reduces swelling). Believed that they work by blocking synthesis of prostaglandins.
Analgesic, strong: Analgesics that bind with specific chemical receptors in brain that receive pain messages stopping the transmission of pain. They are almost all related to morphine. Family is called the opium alkaloids.
Analgesic: A drug which relieves pain without the aid of sleep. Two types: 1) mild; 2)strong.
Antacids: Bases that neutralize excess acid. They are just barely soluble neutralize gradually.
Antibiotics, broad spectrum: Antibiotics that are effective against a wide range of bacteria. This is initially prescribed until the specific diagnosis is found.
Antibiotics, narrow spectrum: Antibiotics only effective against certain types of bacteria. Prescribed once the specific diagnosis is found.
Anti-coagulant: Has blood-thinning properties.
Antivirals: Three possible approaches: 1) Trojan Horse (joins the replication process, inhibiting replication of the virus. Selectively toxic as it is activated by viral enzyme); 2) Retrovirus inhibitor (inhibits RNA from acting as a template for DNA replication); 3) blunting (preventing escape of new viruses by inhibiting neuraminidase enzyme which cuts open cell membrane).
Aspirin: Derived from salicylic acid, which was unpleasant to use due to its acidity. The phenol group is substituted with an acetyl group in aspirin, but it is still acidic due to its alkanoic acid group. Has anti-coagulant properties, but there can be allergic reactions to it and it can induce Reye’s Syndrome in children, a potentially fatal liver and brain disorder.
Bacteria: Have slightly different structure to mammalian cells: have a cell wall. Penicillin prevents this wall from being made, and the internal pressures within the cell builds up and causes it to burst.
Benzodiazepenes: Class of depressants, including valium, prozac and mogadon. Benzodiazepenes work on chemical receptors in brain by binding to a special protein at the synapse of nerve junctions, causing gap between nerves to widen prevents nerve cell from producing signal. The ethanol works on a different part of the same protein. The synergistic effect of these two working together can result in neural shutdown.
Blood-brain barrier: Can only by passed by fat soluble molecules.
Caffeine: A tertiary amine. Can 1) promote mild dependence; 2) act as a mild diuretic; 3) increase anxiety (when taken in excess); 4) cause insomnia. Known as respiratory stimulant, as it increases rate of respiration, by blocking inhibition of ATP. It does so by mimicking the shape of the ATP and causes the inhibiting enzyme to bind to it instead.
Cephalosporins: Variants of penicillin created to overcome the action of penicillinases. Broad spectrum antibiotics.
CNS: Central Nervous System.
Codeine: Derived from morphine by replacing H in one of alcohol groups with methyl group.
Depressant: Drugs which depress CNS by interfering with transmission of nerve impulses in the neurons. Effects depend on dosage: no effect tranquilizing effect sedative sleep-inducing lethal.
Designer drugs: Modifications to structure of natural drugs.
Dimethicone: An anti-foaming agent often used with antacids. Allow gas bubbles to coalesce and be expelled.
Drug administration: Five methods: 1) Oral (subjected to digestive process; easiest); 2)Rectal (efficient, cultural biases); 3) inhalation (drug can only be absorbed through lungs); 4) Parenteral (see PARENTERAL); 5) Patches (absorbed directly through skin barrier, allow absorption to take place gradually).
Drug development: A disease is selected, and targets along the disease process are identified, which may be vulnerable to interference by a drug. Lead molecules are considered, and selected according to the drugs which seem most effective, easiest to manufacture, have an advantage over existing drugs and are profitable. Phase I trials assess toxicology of drug. Phase II trials are clinical; the efficacy and dosage are determined. Phase III trials give the drug to thousands of closely monitored patients. If approved at this stage, drug is launched, after which comes the Phase IV trials, which is the post-launch monitoring of drug, which may lead to product extension.
Drug: A chemical which does one or more of the following: 1) alter mood or emotions; 2) alter incoming sensory sensations; 3) alter physiological state.
Endorphins: Pain killers produced in the brain. Explain how people under great trauma feel little pain despite terrible injuries. Withdrawal symptoms of a heroin addict might be behavior of body without any endorphins at all.
Ethanol: Mild depressant in which side effect mask the main effect in moderate doses. Physiological effects: 1) decreasing inhibitions; 2) short term reduction in reaction speed; 3) short term hangover; 4) long term liver damage. Social and economic effects: 1) violent behavior; 2) increase in car accidents; 3) absenteeism; 4) cost of intensive medical care. The amount of alcohol that can be safely drunk depends on 1) body mass; 2) tolerance.
Gas chromatography: Test for ethanol. Under pressure, sample can be passed through thin tube containing inert material. Components of sample separate and can be identified.
Heroin: Derived from morphine by replacing H’s from both alcohol groups with acetyl (-COCH3) groups. More soluble in fatty tissue due to removal of both -OH groups.
HIV: Human Immunodeficiency Virus. Specific proteins on HIV bind to receptor protein on certain WBC’s called T cells. Quick mutation.
In vitro: Testing potency of molecule and selectivity; done in a laboratory environment.
In vivo: Meaning “in life.” Tests conducted in living species, to test for side effects and the effect of the body on the drug.
Intoximeter: Test for ethanol. Work by infrared spectroscopy, where the vibration of OH bond in ethanol can be detected.
LD50 value: The Lethal Dose of a substance that kills of 50% of a population. The lower the number the more toxic the substance.
Maximum daily tolerance: How much of a chemical can be taken into the body before undesirable symptoms occur. Related to rate at which body’s biochemistry is able to get rid of the same agent. Minimum doses should be used due to body’s increasing tolerance to drug.
Medicine: A drug used to cure a disease.
Nicotine: Sympathomimetic. Quickly reaches CNS. Short term effects: 1) Increased pulse and BP; 2) reduction in urine output; 3) decrease in reflex times, 4) increases concentration; 5) relieves tension. Long term effects: 1) Risk of heart disease; 2) coronary thrombosis; 3) peptic ulcers; 4) number of diseases, incl. lung cancer. Nicotine is a tertiary amine.
Noradrenaline: Variation of adrenaline which is produced in the brain. A neurotransmitter which sends signals to brain by binding with neural proteins.
Opiate: Cause addiction and lead to tolerance. Short-term effects: 1) euphoria; 2) depression of CNS; 3) high doses coma/death. Long-term effects: 1) constipation; 2) loss of sex drive; 3) social problems (e.g. theft, prostitution, etc).
Paracetamol: Has none of the side effects of aspirin given that the correct does is used. If doses are exceeded, it can induce massive liver damage. Acetaminophen.
Parenteral: Administering drugs by injection. Can be administered locally reducing dose necessary and also possibility that body will alter molecular structure. Often required medically trained staff to administer. Three types: 1)intravenous (bypasses digestive system, quick arrival; still spreads out dose); 2) subcutaneous (directly into body fat – only for fat soluble molecules); 3)intramuscular (into muscle tissue).
Pathogen: Organism or virus that causes disease.
Penicillin: Discovered by Alexander Fleming, who noticed that some of the bacteria in his petri dish had died off after some foreign appearance. Prevent cell walls from being made in bacteria; does not affect mammalian cells or viruses as they do not have a cell wall selectively toxic. [Relatively] narrow spectrum antibiotic.
Penicillinases: New enzymes produced by bacteria to counter the action of penicillin. Degrade penicillin molecule.
Physiological state: Includes consciousness, activity level and co-ordination.
Placebo effect: A drug with no chemical effects. Used to test brain’s ability to influence physiology and to test the efficacy of new drugs.
Prostaglandins: Local action hormones which have a range of functions in body. One of these may be pyrogenic (raise body temperature). Also responsible for altering of signals across synapse junctions of nerves. Mild analgesics are believed to work by blocking the synthesis of these prostaglandins.
Retrovirus: Virus that contains RNA instead of DNA. Selective toxicity: The process of inhibiting processes vital to the pathogen, but absent in the host (see PENICILLIN).
Side effects: Unwanted effects of a drug. Risk-to-benefit ratio has to be considered. Thalidomide had an unacceptable ratio, while chemotherapy – causing hair loss and nausea – still has life-saving potential.
Stimulant: Drugs that increase a person’s state of mental alertness.
Sympathomimetic amine: Amines which mimic chemical behavior of hormones of the CNS.
Synergistic effect: Creating a cumulative effect greater than the sum of each individual effect. Benzodiazepenes have synergistic effect with ethanol. Ethanol also has synergistic effect with aspirin (may cause stomach bleeding).
Thalidomide: Morning sickness drug sold in many countries (1958-1962) until severe side-effects were discovered. Early clinical trials had shown no problems. Later withdrawn, but many children had been born with absent or malformed limbs (phocomelia). Currently used for treatment of some cancers, leprosy and other conditions where its inhibition of blood vessel formation is beneficial.
Tolerance: The body’s adaptation to the action of a drug, resulting in a requirement for larger doses to achieve original effect.
Toxicology: Poisonous effect of drug.
Trial, blind: A trial of drugs where half of the patients are given the real drug and the other half a placebo. The administering doctors know which patient receives which drug.
Trial, double blind: Similar to blind trial except that neither the administering doctor nor the patient knows which patient receives which drug.
Virus: Contains DNA but cannot replicate by itself. Works by sticking to the outside of a cell, and inject its own DNA, effectively causing cell to replicate the virus for it. New viruses break through cell and infect other cells. All viruses have a central core of DNA or RNA surrounded by a capsid of regularly packed protein units (capsomeres). Have no nucleus or cytoplasm.
Option B – Medicine and Drugs - HL
Anesthetic, general: An anesthetic that renders the patient unconscious so that they can feel no pain. First anesthetic to be used was ether. This was highly inflammable, so later chloroform and nitrous oxide (laughing gas) was used. Chloroform was found to possibly lead to liver damage, while nitrous oxide was not very efficient. Objectives for anesthetic: 1) able to put patient to sleep; 2) non-toxic; 3) non-inflammable; 4) volatile; 5) stable. Halothane was found to satisfy these requirements, but it is a CFC, which can cause damage to ozone layer.
Anesthetic, local: An anesthetic that blocks pain in a specific area without affecting overall level of consciousness.
Cannabis, arguments for/against: 1) Cannabis addictive: contested. 2) May lead to harder drugs. 3) Toxic. 4) If cannabis legalized demands to legalize other drugs. 5) Should be legalized to remove profits from criminals. 6) Ensure correct dosage.
Chiral auxiliary: The main component of a technique used to obtain only a desired enantiomer. Attaching an auxiliary which is itself optically active creates the stereochemical conditions for the reaction to form only one enantiomer.
Cisplatin: Cis form of a chemical which is highly effective in the treatment of testicular and ovarian cancers. Transplatin is not as effective an anti-cancer drug. Causes alteration in the cancer cell’s DNA cannot replicate properly.
Cocaine: First anesthetic to be used. Work by suppressing nerve transmissions. Side effects: 1) anxiety; 2) nausea; 3) headaches; 4) possible coma/death.
Combinatorial library: A technique to form a library of combinations of aa or other types of active molecules, by use of mix and split process.
Form, cis-: Geometric isomer where the similar groups are on the same side.
Form, trans-: Geometric isomer where the similar groups are on different sides.
Hallucination: Distortions in sound and visual perceptions.
Hallucinogen: Causing hallucinations.
Indole ring structure: A common structure in many hallucinogenic drugs such as LSD and psylocybin.
Isomers, geometric: Stereoisomerism where the isomers differ in positions of a group relative to the double bond.
LSD: Does not occur naturally. Believed to work by blocking serotonin, one of the compounds responsible for transmitting impulses across synapses in brain. Short term effects: 1) restlessness; 2) dizziness; 3) hallucinations. Long term effects: 1) severe depression; 2) recurrences of LSD effects (flashbacks).
Marijuana: Cannabis when dried. Not based on indole ring. Causes feeling of relaxation and enhanced auditory and visual perception. Synergistic effect with depressants. Long term effects: 1) apathy; 2) lethargy (state of sluggishness); 3) reduced fertility.
Mescaline: One of oldest known hallucinogens. Causes hallucinations, and decrease in appetite. Synergistic effect with alcohol.
Mix and split: Coupling resulting in a combination of active molecules. Gives all permutations possible.
Partial pressure: The pressure a gas would exert if it occupied the total volume on its own. Found by mole fraction of gas multiplied by total pressure.
Procaine and lidocaine: Derivatives of cocaine.
Psilocybin: Mildly hallucinogenic. Tolerance may develop but it is not addictive. Biggest danger lies in inability to recognize “magic mushrooms” correctly; similar looking fungi are poisonous.
Racemic mixture: A mixture containing equal amounts of both enantiomers.
Thalidomide: One enantiomer helped against morning sickness, while the other was responsible for causing fetal deformities.
Virtual library: Modeling permutations virtually.
Option C – Human Biochemistry - SL
Amino acid: A compound in which an amino group and a carboxylic acid group are present. There are 20 aa that occur naturally. Can be polymerized to form proteins. Exists as a zwitterion at their isoelectric point. All except glycine can show optical activity. aa
Amino acids, essential: Aa’s that our body is not able to produce and we need to have them as nutrients. There are 10 of these.
Amino-acids, non-essential: Aa’s that we are able to produce in our body.
Anabolic steroids: All steroids contain characteristic four-ring structure. Have similar structure to testosterone. Build up muscle.
Anabolic: Processes in which complex molecules are made from simpler ones, such as in photosynthesis.
Calorie: The energy required to raise the temperature of 1g of water by 1 oC.
Calorific value: The energy content of food.
Carbohydrates: Produced by photosynthesis in plants. Used to 1) provide energy; 2) store energy (starch is stored in liver in form of glycogen); 3) precursors for important biological molecules (e.g. they are components of nucleic acids).
Catabolic: Processes in which molecules are broken down into simpler ones, such as aerobic respiration.
Denaturation: When the three-dimensional conformation of the structure is destroyed, and the protein becomes biologically inactive. Denaturing agents are:
1) heat; 2) UV-radiation; 3) strong acids and bases; 4) concentrated salt solutions; 5) heavy metals (no, not that kind… examples are Pb, Hg, etc).
Diet: Well-balanced diet consists of about 60% carbohydrate, 20-30% protein and 10-20% fat. Should include essential vitamins and fifteen essential minerals. Amount of food required depends on age, weight, gender, and daily activity.
Eluent: The solvent in which the chromatographic paper is placed in paper chromatography.
Fats: Solid triglycerides at room temperature. Contain only saturated carboxylic acid groups. Uses of fats: 1) efficient way to store energy (in adipose tissue); 2) thermal insulation; 3) protection; 4) form part of cell membranes, 5) source of energy (can be oxidized more than carbohydrates).
Fatty acid: Long chain carboxylic acids.
Feedback mechanism: When a product of a process or a hormone reaches a certain level, it inhibits (negative feedback) or promotes (+ feedback) a further response.
Food calorimetry: Measuring the energy content of food.
Furanose: Five membered ring containing an oxygen atom, such as in fructose.
Glucose: A hexose monosaccharide. Form of glucose found in nature is D-glucose, which can exist in two separate crystalline forms: 1) -D-glucose (OH groups are down, down, up, down; following carbon chain); 2) -D-glucose (up, down, up down). C6H12O6
Glycosidic link: Link between two sugar in a polysaccharide, formed by condensation reaction.
GM food: Genetically modified food. Benefits: Improve flavor, nutritional value, and shelf life. Could incorporate anti-cancer substances. Could make plant more resistant to disease. Concerns: unpredictable outcome. May cause antibiotic-resistance. May alter balance of ecosystems.
Hard water: Contains Mg2+ or Ca2+. Prevents soap from working efficiently as it reacts with the anion of the soap, producing a precipitated salt.
Hormone, adrenalin: Responsible for ‘fight or flight’ response (goose bumps, increased pulse/BP). Produced in adrenal medulla.
Hormone, insulin: Made up of 51 aa residues. Decreases glucose levels in blood by making liver absorb glucose in the form of glycogen. Insulin produced in -cells of Islets of Langerhans.
Hormone, thyroxine: Regulates metabolism. Produced in thyroid gland. Hypothalamus releases local hormone which tells anterior pituitary to release thyroid SH (+ feedback). TSH tells thyroid glands to release thyroxine (+ feedback). When the concentration of thyroxin reaches a certain level, a – feedback is sent to hypothalamus, ceasing production of the local hormone.
Hormones, sex: Responsible for development of secondary sexual characteristics. Both estrogen and testosterone produced in testes (males) and ovaries (females). They are all steroids contain characteristic four-ring structure.
Hormones: Chemicals produced in glands and transported to specific target cell by blood stream, and binds to a receptor site on or within the target cell produces a specific physiological response. Glands are controlled by pituitary gland, which in turn is controlled by the hypothalamus. Hormones act as chemical messengers.
Hydrophilic: Describing part of molecule that is attracted to water.
Hydrophobic: Describing part of molecule that repels water.
Iodine number: Number of grams that reacts completely with 100g of a triglyceride. The higher the iodine number, the more unsaturated the triglyceride.
Isoelectric point: The pH value at which the average charge on the molecules of a compound is zero.
Lactose: Disaccharide in which -D-galactose and -D-glucose are joined by glycosidic link.
Lipids: Biological substances that are soluble in non-polar solvents (generally). Lipases in digestive system degrade lipids.
Menstrual cycle: Pituitary gland releases follicle SH, which travels to ovaries causing release of estradiol. Two weeks later, – feedback stops release of FSH and triggers release of luteinizing hormone, which travels to ovaries and releases progesterone. Progesterone causes egg to be transported to uterus. If egg is fertilized, it embeds itself on uterine wall and hormone levels rise dramatically, otherwise hormone levels fall and menstruation occurs.
Metabolism: The network of biochemical reactions that supports life.
Micelle: The particle formed when the hydrophilic tail dissolves in oil or grease.
Ninhydrin: An organic dye. Causes coloration of aa’s. Used to see how far aa’s have moved in both paper chromatography and electrophoresis.
Nutrient: Substances that are required by an organism as food.
Oils: Liquid triglycerides at room temperature. Contain at least one double bond, i.e. they are unsaturated. The more unsaturated, the lower the m.p. due to its inability to pack so closely together the surface area decreases decrease in the van der Waals’ forces between the molecules. Number of C=C bonds can be determined by addition reactions with I2. See IODINE NUMBER.
Oral contraceptives: Most common ‘pill’ contains a mixture of estradiol and progesterone mimics the high hormonal levels of pregnancy, in turn preventing the release of more eggs.
PAGE: Polyacrylamide gel electrophoresis.
Phospholipid: Form major part of plasma membranes. Phosphate group is hydrophilic while lipid part is hydrophobic.
Polyunsaturated oils: An oil containing several double bonds.
Protein structure, electrophoresis: Electrophoresis is carried out on a medium called PAGE. Sample is placed in center of gel, and a potential difference is applied across it. The movement of the aa depends on the pH of the buffer: at low pH, the amine group will be protonated, while at high pH, the carboxylic acid is deprotonated. At the isoelectric point – characteristic for each aa – the aa exists as a zwitterion, and will not move (charges balanced). When satisfactory separation is complete, the aa can be sprayed with ninhydrin, and their isoelectric points can be compared.
Protein structure, paper chromatography: When a piece of chromatographic paper containing a small sport of the unknown aa is placed in an eluent, the eluent rises up the paper (capillary action). The different aa’s spread out to different extents, and move up the paper at different rate.
Proteins: Large macromolecules of chains of 2-amino acids. Formed by aa’s bonding to each other by peptide bonds. 1) The primary structure of the proteins is their strict sequence of aa residues. 2) The secondary structure describes how the chain folds itself due to intramolecular hydrogen bonding (can be -helix -– hydrogen bonds within single chain, causing spiraling – or -pleated – hydrogen bonds between chains). 3) The tertiary structure describes overall folding of the chain, giving the protein its three-dimensional shape (may be due to hydrogen bonds, van der Waals’, and ionic attraction. Two Cys residues can form disulphide bridges). 4) The quaternary structure results from the interactions between separate polypeptide chains. Uses of proteins: 1) Many are enzymes; 2) can give structure; 3) source of energy; 4) regulation hormones.
Pyranose: Six-membered monosaccharides such as glucose.
Retention factor: The ratio of the distance traveled by the sample to the distance traveled by the solvent in paper chromatography. Each aa has a specific Rf value.
Saccharide, mono-: Simple sugars. Empirical formula CH2O. Water soluble. Two families: 1) hydroxyaldehydes (contain aldehyde group and at least 2 OH groups. Reducing sugars); 2) hydroxyketones (contain ketone group and at least 2 OH groups. Non-reducing sugars). Monosaccharides containing more than 5 C-atoms can make cyclic molecules.
Saccharide, oligo-: Containing 2-9 monosaccharides.
Saccharide, poly-: Polymers of monosaccharides. Formed by condensation reactions, forming glycosidic links.
Saponification: The process in which a triglyceride is hydrolyzed, forming soap. Reverse of esterification.
SH: Stimulating Hormone.
Soap: The sodium or potassium salt of the fatty acids produced from the saponification process. Functions because of hydrophilic head and hydrophobic tail. The tail dissolves in oil or grease to form a micelle. Surrounded by hydrophilic heads, which makes it soluble in water.
Starch: Polymer of -D-glucose. Exists in two forms: 1) amylose (water soluble); 2) amylopectin (water insoluble). Most plants use starch as a store of carbohydrates.
Structure-function relationship: The structure of a chemical compound is adapted to its function by evolution.
Sucrose: Disaccharide in which -D-glucose and -D-fructose are joined by glycosidic link between the C1 from the glucose and the C2 from the fructose.
Synthetic detergents: Soap molecules of which the calcium or magnesium salts are soluble that they can work well in hard water as well. Cause more pollution than soaps.
Triglyceride: Formed from condensation reaction between glycerol and fatty acids.
Vitamin A: Retinol. Found in cod liver oil, green vegetables and fruit. Fat soluble despite OH group, due to long hydrocarbon chain. Not broken down readily by cooking. Aids night vision. Retinol is oxidized to retinal in body. Retinal combines with protein opsin to form rhodopsin, the active agent for converting light signals into electrical signals that travel along optical nerve to brain. Deficiency xerophtalmia or night-blindness.
Vitamin C: Ascorbic acid. Found in fresh fruit and vegetables. Water soluble. Involved in biosynthesis of the protein collagen (found in connective tissue). Deficiency scurvy.
Vitamin D: Calciferol. Found in fish liver oils and egg yolk. Can be formed on surface of skin by UV light reacting with 7-dehydrocholesterol. Involved in uptake of Ca2+ and PO43+ ions from food, and in formation of bone structure. Deficiency rickets.
Vitamins, fat soluble: A, D, E, F and K. Characterized by long non-polar hydrocarbon chains or rings.
Vitamins, water soluble: C and the 8 B’s. Contain NH or OH groups has ability to hydrogen bond to water. Do not accumulate in body.
Vitamins: Vitamin D is the only vitamin that the body is capable of synthesizing. Can be defined as: 1) fat soluble or 2) water soluble. Vitamins containing C=C bonds and OH groups are readily oxidized. Refrigeration slows this process.
Water equivalent: The equivalent addition of energy to water as released when burning 1.00g of a food, causing a temperature increase.
Zwitterion: Ion with + and – charge. Aa’s exist as zwitterion at their isoelectric point.
Option C – Human Biochemistry - HL
Active site: The part of the protein that is involved in the catalysis.
ADP: Adenosine diphosphate. Made of base A, ribose, and two phosphate groups. Addition of another phosphate group makes ATP.
ATP: Adenosine triphosphate. Made up of base A, ribose, and three phosphate groups bonded together by high-energy phosphate bonds. Breaking the last of these bonds releases energy for use in cells, leaving ADP.
Chromosome: A structure composed of DNA and associated proteins.
Codon: Each of 64 permutations of the triplet code.
Coenzyme: Organic cofactors. Example: B-vitamins. Two types: 1) permanent coenzymes (always bonded to enzymes); 2) non-permanent coenzymes (only bonded to enzymes during catalysis).
Cofactor: A substance that is a part of the active site, and that is involved in the catalysis. Can be: 1) inorganic (metal ions); 2) organic (coenzymes).
Concentration, effect of: 1) Increasing concentration of the substrate: proportional increase in rate, but eventually evens out as all active sites of enzyme become saturated. 2) Increasing concentration of enzyme: proportional increase in rate.
Cyanide: A poison which works by blocking cytochrome oxidase, which is vital for aerobic respiration.
Cytochrome: Oxidizing enzymes in mitochondria. Contain Cu2+/Cu+.
Deoxyribose: The pentose sugar found in DNA.
DNA profiling: Using a small amount of cellular material, DNA is extracted and broken down into minisatellites using restriction enzymes. Splits where there are no coded messages in the base sequence are unique to the person giving the sample, and so this can be used to identify them.
DNA replication: DNA in cell begin to partly unzip as hydrogen bonds between the bases break. New sugar base units are taken up from the aqueous solution. Due to set pairs (AT and CG), the new strands will be identical to the original one.
DNA: Deoxyribonucleic acid. Double-stranded. Made up of nucleotides. Have – charge due to phosphate group. Cannot penetrate nucleus.
Electron transport: Occurs in inner membrane of mitochondria, which contains different proteins and enzymes, incl. cytochromes. The H+ ions from the NADH2 (product from the citric acid cycle) move along cytochromes by repeated redox reactions, due to presence of stronger oxidizing agents. Enzyme cytochrome oxidase causes H+ ions, e- and O2 to react to form water, releasing energy in the process.
Enzyme saturation: When all the active sites of the enzymes are occupied by a substrate. At this saturation, increasing substrate concentration has no effect.
Enzyme, factors affecting: 1) Enzyme concentration; 2) substrate concentration; 3) temperature; 4) pH; 5) inhibitors (reversible/irreversible).
Enzyme: Proteins that act as biological catalysts, for specific substrates.
Gene: A specific sequence of DNA which codes for the synthesis of a protein.
Glycolysis: First phase of breakdown of glucose in respiration. Occurs in cytoplasm.
Haemoglobin: Found in RBC’s. Contains four large polypeptide groups and four Fe2+ ions surrounded by hem groups. At high oxygen concentrations, oxygen bonds onto the iron in hem group as an extra ligand. At low concentrations, the reverse occurs. Hb
Heavy metal ions, effect of: Can poison enzymes by reacting with –SH groups replacing the hydrogen atom with a heavy metal atom or ion. Enzyme is denatured.
Induced fit theory: The active site can alter its shape to allow for a better fit with the substrate. An enzyme-substrate complex is created, and the catalyzed reaction takes place, leaving an enzyme-product complex. The products are released, and the enzyme reverts to its original shape.
Inhibition, competitive: Reversible inhibition. Resemble the substrate in shape, but cannot react. Slow down reaction by occupying active site. Does not affect Vmax but does affect Km.
Inhibition, irreversible: The inhibitor reacts with a part of the enzyme, and a covalent bond is formed between the inhibitor and enzyme. Enzyme activity is permanently destroyed. Example: nerve gases work by alkylation of an OH-group in the active site of an enzyme.
Inhibition, non-competitive: Reversible inhibition. Prevents enzyme reactions by binding to another part of the enzyme than the active site. This causes the enzyme to alter its shape and be unable to receive its substrate. Does not affect Km but does affect Vmax.
Inhibition, reversible: The inhibitor makes weak (intermolecular) bonds with the enzyme. The enzyme can become biologically active again. Two types: 1)competitive; 2) non-competitive.
Metal ions: Examples of important ions: Na+ and K+ (nerve impulses and water balance); Ca2+ (bones and teeth); Cu2+ (enzymes); Co2+ (vitamin B12); Fe2+ (Hb). All depend on one of the following: 1) difference in charge density between two ions; 2) variable oxidation states; 3) forming complexes with ligands.
Michaelis-Menten constant: The substrate concentration when the rate of the reaction is at ½ Vmax. The constant will always be the same for a particular enzyme and particular substrate. Km
mRNA: Messenger of genetic information (transcription).
Nucleotide: Repeating base-sugar-phosphate units that make up the nucleic acids. The base can be one of four nitrogen-containing bases, adenine (A), guanine (G), cytosine (C) or thymine (T). In RNA, uracil (U) replaces T. The phosphate bonds to the C4, while the base bonds to the C1.
pH, effect of: The pH value affects the tertiary structure. Enzymes have an optimum pH; outside of this, they can be denatured. More subtly, pH affects the electrostatic charge of the enzyme, which may affect the binding of substrate to enzyme, or the chemistry of the active site.
Phosphodiester bond: Bonding between nucleotides in a polynucleotide. Each nucleotide is joined between the C3 of the sugar and the neighboring phosphate group.
Phosphorylation: Addition of phosphate group. Phosphorylation in the sodium-potassium pump causes shape of pump to change.
Protein synthesis: Happens in ribosomes. 1) Transcription in nucleus; followed by 2) processing by mRNA; 3) translation by ribosome.
Ribose: The pentose sugar found in RNA. Same as deoxyribose, except with an extra O bonded to the C2.
Ribosome: Particle that causes protein synthesis. Sequence of aa’s determined by nucleotide sequence in mRNA.
RNA: Ribonucleic acid. Single stranded. Contains base U instead of DNA’s base T. Two functions: 1) transcription (messenger of genetic information); 2) translation (translating gene information into protein synthesis).
Sodium-potassium pump: Protein structure in cell membrane act as valves pumping Na+ ions out of cell and K+ ions into the cell. Works due to difference in charge density between Na+ and K+. The Na+ binds to three sites on the protein molecule. Energy is extracted from ATP by hydrolyzing to ADP, and the phosphorylation causes the pump to change its shape. Na + ions are expelled, and K+ ions bind to two sites on the protein molecule. The loss of the phosphate causes the pump to change its shape again, expelling the K+ ions into the cell.
Substrate: The substance on which an enzyme acts.
Temperature, effect of: Increasing temperature will initially increase rate of enzyme-catalyzed reactions (greater proportion of reactants will have the minimum activation energy). Optimum temperature for most enzymes is ca. 40C. Above this temperature enzymes rapidly denature.
Transcription: Copying of DNA onto a strand of RNA by unwinding temporarily due to the action of RNA polymerase. Takes place in nucleus.
Translation: The reading of the base sequence of the mRNA by ribosomes to make a sequence of aa’s to form a polypeptide.
Triplet code: A sequence of three bases that represents one aa.
tRNA: RNA that brings the right aa’s to the ribosomes.
Vmax: The maximum rate at which enzyme activity can occur, given a constant enzyme concentration. This is when the active sites of the enzyme are saturated.