biochemistry Flashcards
(288 cards)
1
Q
Define Metabolism
A
Metabolism – the total of all the enzyme-catalysed reactions in a cell or organism. It involves the breakdown of molecules with the release of energy and the synthesis of molecules that are required by the cell.
2
Q
Define catabolism
A
Catabolism – the breakdown of complex molecules into simpler molecules. Such processes release energy.
3
Q
Define Anabolism
A
Anabolism – the synthesis of more complex molecules from simpler precursor molecules. Such processes require energy.
4
Q
What is anaerobic respiration known as in yeast?
Give Equation
A
Anaerobic respiration in yeast is known as fermentation
C6H12O6(aq) → 2CO2(g) + 2C2H5OH(l)
5
Q
The blood plasma of a typical human adult contains 20.00g of glucose. Calculate the mass of oxygen needed to completely oxidize it to water and carbon dioxide.
A
amount of glucose = 20.00g / 180.16 g mol–1
= 0.111mol During aerobic respiration:
1 mole of glucose requires 6 moles of oxygen to react with it, so the amount of oxygen required is
6 × 0.111mol = 0.666mol
hence the mass of oxygen required is
0.666mol × 32.00gmol–1 = 21.3g
6
Q
What reaction creates all biological molecules?
A
Biological macromolecules and polymers (biopolymers), such as proteins, lipids and DNA, are formed by enzyme-controlled CONDENSATION reactions
7
Q
What do condensation reactions involve?
A
These involve the reaction between the functional groups of two smaller molecules to form one large molecule with the release of a water molecule.
8
Q
What two types of reactions does a condensation reaction involve?
A
Condensation reactions are an addition reaction followed by an elimination reaction.
9
Q
What is the condition necessary for condensation polymerisation to occur?
A
For condensation polymerization (Figure 23.6) to occur each of the reacting molecules must possess at least two reactive functional groups
10
Q
Give 3 examples of condensation reactions
A
Examples include the condensation of amino acids to form proteins, the condensation of nucleotides to form DNA, the condensation of propane-1,2,3-triol (glycerol) and fatty acids to form lipids and the condensation of glucose to form starch and cellulose.
11
Q
What conditions do hydrolysis reactions need to occur?
A
The hydrolysis reactions can also occur in the presence of acid without the presence of enzymes.
12
Q
In what two ways can amino acids be classified?
A
Amino acids can be classified based on their polarity and their acid–base properties
13
Q
What stereoisomer property do all amino acids exhibit, what is the exception?
A
With the exception of glycine (2-aminoethanoic acid), all of the 2-amino acids contain a chiral carbon atom and therefore exhibit optical isomerism.
14
Q
What for do amino acids take under standard conditions?
A
Amino acids are white crystalline solids under standard conditions.
15
Q
When do amino acids exist as zwitterions?
A
They exist in the solid state and in neutral aqueous solution as zwitterions
16
Q
How do amino acids form zwitterions?
A
This is due to an internal acid–base reaction. A hydrogen ion is released from the carboxyl group and protonates the amine group.
17
Q
What bonding does the zwitterion form cause?
A
The presence of zwitterions leads to ionic bonding in crystalline amino acids involving electrostatic forces of attraction between oppositely charged ends of the zwitterions.
18
Q
What does the ionic bonding and electrostatic attraction of zwitterions result in?
A
This results in high melting (or decomposition) points and good solubility in water.
19
Q
Do peptide bonds experience restricted rotation?
A
YES
Peptide bonds experience restricted rotation (Figure 23.12) due to resonance (π delocalization), giving rise to two possible conformations
20
Q
Which conformation of an amino acid is generally more stable?
A
the trans conformation is generally more stable.
21
Q
What must be done to sequence an entire protein?
A
In order to sequence an entire protein, the polypeptide chain is broken down into smaller fragments using either chemicals (concentrated acid or alkali), or proteases
22
Q
What is done with the smaller protein fragments?
A
The resulting smaller fragments are then sequenced. The complete sequence is assembled by analysing overlapping fragments generated by cleaving the polypeptide chain with different reagents.
23
Q
What can amino acids be classified as in terms of acid-base theory?
A
Amino acids are amphoteric or, more specifically, amphiprotic, because, depending on pH, they can act as either an acid (via proton loss at the carboxyl group), or as a base (via protonation at the amino group)
24
Q
Why do amino acids have two pKa values?
A
Amino acids have two pKa values, one for the carboxyl functional group and one for the amine functional group
25
When will amino acids have 3 pKa values?
Amino acids with basic or acidic side-chains will have a third pKa value.
26
What is the isoelectric point of an amino acid?
The isoelectric point (pI) of an amino acid is the pH at which the concentrations of the zwitterionic form reaches its maximum value
27
What are amino acids separated on the basis of in electrophoresis?
During electrophoresis, amino acids are separated based on their pI values.
28
What charge does a zwitterion carry?
It is neutral
29
What happens to a zwitterion when the pH of a solution decreases?
forms a cation
30
What happens to a zwitterion when the pH of a solution increases?
forms an anion
31
What is the secondary structure of a protein?
The secondary structure of a protein refers to three-dimensional conformations of localized regions of the protein, in particular, an α-helix or a β-pleated sheet
32
What is the tertiary structure of a protein?
The tertiary structure of a protein is the arrangement of the α-helix or β-pleated sheet into a configuration characteristic of the protein.
33
What is the difference in bonding between parallel and anti-parallel B-pleated sheets?
In a parallel β-pleated sheet the hydrogen bonds run in the same direction; in an antiparallel β-pleated sheet the hydrogen bonds run in the same direction.
34
What is a hydrogen bond, in terms of tertiary structure?
hydrogen bond weak intermolecular force common in polypeptide chains that helps to stabilize the protein molecule
35
What is a disulfide bond, in terms of tertiary structure?
disulfide bond strong covalent bond formed by the oxidation of
–SH groups of two cysteine side chains
36
What are dispersion forces , in terms of tertiary structure?
dispersion forces - these come into play when two or more molecules are very close (0.3–0.4 nm apart)
37
What is an ionic bond, in terms of tertiary structure?
weak electrostatic interaction between oppositely charged ions: may often be broken by changing the pH
38
What is the difference in bonding between a beta pleated sheet and alpha helix?
hydrogen bonds occur closer together in alpha helix, than in bet pleated sheets
39
What are fibrous proteins composed of?
Fibrous proteins, for example, collagen (Figure 23.20), consist of linear polypeptide chains that are bundled and associated together.
40
What are globular proteins composed of?
Globular proteins, for example, hemoglobin (Figure 23.21) are polypeptide chains that are coiled into compact shapes.
41
What are structural proteins?
Structural proteins, such as keratin, are fibrous proteins that provide structural rigidity in nails and hair.
42
How do enzymes achieve their catalysis?
Enzymes achieve their catalysis via the stabilization of the transition state (activated complex) formed by the reactants (substrate) during the reaction.
43
How does pH affect enzyme activity?
structure of protein changes when a change of pH alters the ionic charge on –COO– (acidic) and –NH3+ (basic) groups in the polypeptide chain, so the shape of the active site is lost
Large deviations in pH lead to denaturation of the enzyme due to changes in the ionization of amino acid residues and the disruption of non-covalent interactions, especially hydrogen bonds.
44
How does temperature affect enzyme catalysed reactions?
Temperature affects the rate of enzyme-catalysed reaction by increasing the average kinetic energy of the substrate molecules. This increases the proportion of molecules with sufficient kinetic energy to overcome the activation barrier and hence increases the rate of the reaction.
In addition, the kinetic energy of the component molecules of the enzyme is increased, which leads to an increased rate of denaturation of the enzyme protein due to the disruption of the non-covalent interactions holding the structure together.
45
What type of bond do inhibitors form?
Inhibitors which bind irreversibly to an enzyme often form a covalent bond to an amino acid residue at or near the active site, and permanently inactivate the enzyme.
46
What amino acids are susceptible to inhibitors? What reacts with them?
Susceptible amino acid residues include serine and cysteine residues which have reactive –OH and –SH groups, respectively.
Heavy metals and their ions react with the side-chain of cysteine residues
47
WHat two techniques can be used to identify the structure of a protein?
Chromatography and electrophoresis both separate and identify substances in complex mixtures.
48
What must first be done before chromatography/electrophoresis?
. The protein is hydrolysed to amino acids by boiling with concentrated hydrochloric acid in a sealed tube for six hours.
49
What technique can be used to identify the 3D structure of a protein?
The three-dimensional tertiary structure of the protein can be confirmed by X-ray analysis of the crystalline protein.
50
Basic process of chromatography for amino acids
In paper chromatography, the mobile phase (a solvent mixture) moves the amino acids over the stationary phase (hydrated cellulose). Separation occurs by the transfer of amino acids to the stationary phase by portioning between the two liquids.
51
How are amino acids identified via chromatography?
The amino acids are identified by their retention values (Rf) after they have been made visible by reaction with the locating agent ninhydrin.
52
What does two-dimensional chromatography consist of?
Two-dimensional chromatography consists of two successive acts of chromatographic separation, done with different solvents, in directions at 90° to each other. It operates on the principle that amino acids left unseparated by one solvent will be resolved by the second.
53
Basic process of gel electrophoresis for amino acids?
In gel electrophoresis (Figure 23.28) the mixture of amino acids is supported on a semi-solid gel. The amino acids molecules are charged and move in an applied electric field, where they separate according to their charge and the shape and size of their molecules.
54
Why are lipids grouped together?
Lipids are a structurally diverse group of biological compounds that are grouped together due to their poor solubility in water and excellent solubility in organic solvents.
55
How can lipids be extracted?
Lipids can be extracted from cells, using non-polar solvents, such as ethers and hydrocarbons.
56
Roles of lipids
Lipids act as structural components of cell membranes (as phospholipids), in energy storage (as adipose tissue), thermal and electrical insulation (around nerves) and as transporters of lipid-soluble vitamins and as hormones (vitamin D).
57
What does the melting point of lipids depend on?
The melting points and other properties of lipids depend on the identity of the fatty acid groups. Fats containing unsaturated fatty acids melt at lower temperatures than those with saturated fatty acids
58
Why does melting point decrease with carbon double bond introduction?
This trend is a steric effect and occurs because the introduction of a carbon– carbon double bond prevents the triglyceride molecules from approaching each other closely and hence interacting via London dispersion forces.
59
What type of fatty acid chain will have the greatest melting point and why?
Long-chain saturated fatty acids have a regular tetrahedral arrangement of carbon atoms and so can pack closely together. The dispersion forces between chains are strong because of their extended surface area.
60
What melting point will unsaturated fatty acids have and why?
In unsaturated fatty acids the bond angle in the chains changes around the double bond and the structure becomes rigid at that point. This introduces a kink in the chain (Figure 23.31) and they are unable to pack so closely together.
61
How are phospholipids formed?
Phospholipids are formed by the condensation of two fatty acid molecules and a phosphate group (or a derivative of a phosphate group).
62
WHat is the simplest type of phophoglyceride?
The simplest type of phosphoglyceride is a phosphoric acid monoester, called a phosphatidic acid. Phosphoglycerides that contain choline are called lecithins.
63
What part of the phospholipid condenses with the glycerol?
phosphate group has condensed with the third –OH group of glycerol
64
What is hydrolytic rancidity?
Hydrolysis of lipids occurs slowly to produce fatty acids and other products with a rancid smell. This is termed hydrolytic rancidity.
65
What is saponification?
The alkaline hydrolysis of fats and oils by sodium hydroxide produces soaps: the sodium salt of fatty acids. The process is called saponification .
66
How is the saponification value of a liquid measured? What can this method also be used to find?
The saponification value of a lipid is a measure of the amount of fatty acids that is formed when one gram of lipid is completely hydrolysed by a strong base. This technique can be used to find the fatty acid composition of food.
67
What can be hydrogenated?
Unsaturated oils can be hydrogenated, for example, in the production of margarine.
68
What do oils contain and are they considered "healthy" / "unhealthy"?
Oils contain cis-unsaturated fatty acids which are ‘healthier’ than saturated fats as they increase levels of HDL cholesterol
69
How may hydrogenation make oils "unhealthy"?
However, during the hydrogenation process partial hydrogenation may occur, leading to the production of trans-unsaturated fats
70
Why are trans-unsaturated fats "unhealthy"?
These increase the formation of LDL cholesterol which raises the risk of heart disease.
71
What is the iodine value and how is it determined?
Fats and oils can undergo addition reactions with iodine (in the presence of a non- polar solvent). The iodine value is a measure of the degree of unsaturation.
72
What is the iodine number?
The iodine number is the mass of iodine in grams that reacts with 100 g of an unsaturated lipid. A moles calculation can be used to deduce the number of carbon–carbon double bonds since each mole reacts with 1 mole of iodine molecules
73
How can transesterification be achieved?
Transesterification of triglycerides can be achieved via either acid or base catalysis to produce biodiesel
74
Oleic acid, [CH3(CH2)7CH=CH(CH2)7COOH, is present in many animal and vegetable fats and oils. Calculate the iodine number.
It is monounsaturated and hence each carbon–carbon double bond reacts with one molecule of iodine.
molar mass of oleic acid = (18 × 12.01) + (34 × 1.01) + (16.00 × 2)
= 282.52 g mol–1
molar mass of iodine = (126.90 × 2)
= 253.80 g mol–1
282.52g of lipid reacts with 253.80g of iodine; by ratios, 100g of fat reacts with
(253.80 × 100) / 282.52 = 90g of iodine, and
hence the iodine number is 90.
75
What two ways can lipids become rancid?
Lipids become rancid as a consequence of hydrolytic or oxidative processes.
76
Hydrolytic rancidity:
- when does it occur?
- what does it produce?
Hydrolytic rancidity occurs where ester links are broken by water, producing glycerol and unpleasant smelling/tasting fatty acids.
77
What conditions favour hydrolytic rancidity?
This condition is favoured by high water content, acidic or alkaline conditions, high temperature and the presence of lipase enzymes.
78
Oxidative rancidity
- When does it occur?
occurs where fatty acid chains are broken down when oxygen reacts with the C=C bonds of unsaturated lipids.
79
what does oxidative rancidity produce?
Unpleasant smelling and tasting ketones, alcohols and aldehydes are produced
80
What conditions favour oxidative rancidity?
This condition is favoured by a high proportion of unsaturated fatty acids, high temperature, a high oxygen availability, high light intensity and the presence of metals such as copper and nickel.
81
What is cholesterol? Where is it found?
Cholesterol is present in animal cell membranes (where it controls fluidity) and has the characteristic fused four-ring structure possessed by all steroids
82
What is the structure of cholesterol?
This is a tetracyclic system, involving three six-membered rings and one five-membered ring that form a rigid system.
83
How is cholesterol oriented within the plasma membrane?
Cholesterol molecules have a hydroxyl (–OH) group and a hydrocarbon chain on either side of the carbon ring structures. Each cholesterol’s hydroxyl group aligns with the phosphate heads of the phospholipids, and the hydrocarbon chain with the fatty acid chain on the nearest adjacent phospholipid
84
What does cholesterol's orientation within the plasma membrane cause?
This helps maintain a stable structure on the outer surface of the membrane, making it less permeable to very small water-soluble molecules that could otherwise easily pass through.
85
How is cholesterol transported around the body?
Cholesterol is transported around the body in the blood plasma by lipoproteins. HDL and LDL like in biology
86
What is the general formula of carbohydrates?
Carbohydrates are important in nutrition and have the general formula Cx(H2O)y.
87
What are the 3 types of monosaccharides?
The simplest carbohydrates are monosaccharide sugars: trioses (C3 sugars), for example, ribose, C5H10O5, pentoses (C5 sugars), and hexoses (C6 sugars), for example, glucose and fructose, C6H12O6
88
What is the role of monosaccharides?
Monosaccharides are used to release energy during respiration or act as precursors for other biomolecules.
89
How can monosaccharides be classified?
Monosaccharides are classified as aldoses (containing a terminal aldehyde group), for example, glucose, or as ketoses (containing a ketone group)
90
Are monosaccharides and disaccharides v. soluble? How do they compare with polymers?
Monosaccharides and disaccharides are very soluble because their hydroxyl groups form hydrogen bonds with water molecules. Polysaccharides, such as starch and glycogen, have limited solubility and therefore make better food storage materials.
91
Structure of starch and its use (same as biology)
Starch is the food storage material of plants. It is a polysaccharide, which occurs in two forms: amylose and amylopectin. Both are condensation polymers of glucose and poorly soluble in water.
Amylose is an unbranched polymer of glucose molecules linked by α-1,4-glycosidic bonds. Amylopectin is a branched polymer of glucose, but has many branches arising from α-1,4-glycosidic bonds. Starch contains variable amounts of amylose and amylopectin
92
Structure of glycogen (same as biology)
Glycogen, the food storage material in an animal, is a polysaccharide which is similar in structure to amylopectin (a component of starch), but more branches occur. Glycogen is stored in the liver and muscles.
93
Structure of cellulose (same as biology)
Cellulose (Figure 23.45) is the structural component of plant cell walls. It is a polysaccharide consisting of glucose units joined by 1, β-4-glycosidic linkages. Few animals have the cellulose enzyme that can hydrolyse these linkages, so allowing them to digest cellulose.
94
Why are cellulose molecules linear?
Cellulose molecules are linear because of the orientation of the glucose residues. The molecules are held together by hydrogen bonds between hydroxyl groups and are assembled into cellulose fibres which give tensile strength to plant cell walls.
95
How can polysaccharides be hydrolysed i.e. conditions?
Polysaccharides can be hydrolysed by heating with dilute hydrochloric
acid. Polysaccharides can also be hydrolysed by specific enzymes, which convert polysaccharides to monosaccharides when required by the cell.
(Hence the chemical energy stored in these molecules is available to the organism.)
96
How many stereoisomers does glucose have?
Glucose is one of 16 stereoisomers, 8 pairs of enantiomers, which include fructose and galactose.
97
How do glucose molecules exist in solution, i.e. what forms? Which form is favoured?
The glucose molecule exists in solution as an equilibrium between a straight chain form (with a free aldehyde group) and the more favourable six-membered pyranose ring, which exists in α and β forms and can be represented by Haworth projections
98
Why are aldoses categorised as reducing sugars?
Aldoses, such as glucose, are reducing sugars in solution because they contain a terminal carbonyl (aldehyde) group and are easily oxidized under relatively mild conditions
99
What can be used to test for reducing sugars?
Benedict’s solution and Fehling’s solution (both of which contain copper(II) ions) are used to test for reducing sugars with an aldehyde, –CHO, group.
100
What does Benedicts show, if reducing sugars in high amounts are present?
A red-brown precipitate of copper(I) oxide is formed.
101
How can starch be tested for?
The presence of starch (even at low concentrations) can be detected using iodine: an intense blue- black complex is formed.
102
Vitamins definition
Vitamins – organic micronutrients that cannot (except for vitamin
D) be synthesized in the body and must be obtained from appropriate food sources.
103
What are micronutrients? What are macronutrients?
Micronutrients are substances required in tiny amounts by the body unlike protein, carbohydrates and lipids, which are termed macronutrients.
104
What is the role of micronutrients and give examples of them
They mainly function as co-factors for enzyme activity and include not only vitamins but trace minerals such as iron (Fe), iodine (I2) and zinc (Zn).
105
What features decrease solubility in water, but increase fat solubility?
Non-polar groups such as hydrocarbon rings (cycloalkenyl groups, for instance) and long alkyl chains decrease water solubility but increase fat solubility
106
What are examples of fat-soluble vitamins?
Fat-soluble vitamins include vitamins A, D, E and K
107
Where can fat-soluble vitamins accumulate?
They can accumulate in the fatty tissues of the body; sometimes an excess of a fat-soluble vitamin can be as detrimental to good health as a deficiency.
108
What features increase water solubility?
The presence of functional groups capable of taking part in hydrogen-bonding promotes water solubility; these include hydroxyl, carboxyl, amine and amide groups.
+ and/or several very electronegative atoms (such as nitrogen or oxygen) are generally water-soluble.
109
What are examples of water-soluble vitamins?
. Vitamin B group members (of which there are eight) and vitamin C are water-soluble molecules
110
Can water-soluble vitamins be stored? Why/Why not?
As a result of their solubility, these vitamins are excreted readily in the urine, they do not accumulate in the body and so require regular daily intake from the diet.
111
What is a function of vit c?
Acts as a co-factor in some enzyme reactions; important in tissue regeneration and wound healing; can act as an antioxidant
112
What is a function of vit A?
Involved in the visual cycle of the eye; particularly important for night vision (low light intensity)
113
What is a function of vit D?
Stimulates the absorption of calcium from the gut; important in whole body calcium homeostasis and the health of bones and teeth
114
How do some vitamins respond to heat? Are these vitamins water/fat soluble?
Some vitamins, particularly those that are water soluble, vitamin C and thiamin (vitamin B1), are highly sensitive to heat; they decompose or are chemically altered at temperatures involved in food processing and cooking, causing them to lose their biological effect. Note also that water-soluble vitamins may leach into cooking water and be lost.
115
Why do fat-soluble vitamins stay not decompose or are not chemically altered at higher temperatures?
The hydrocarbon backbones of the fat-soluble vitamins A and D are relatively stable to heat and do not decompose significantly when food is steamed or boiled. Over-cooked or fried food can lose more than 50 per cent of its fat-soluble vitamin content and virtually all its vitamin C.
116
Which vitamins, A/D/C are more sensitive to light? Why?
Vitamins A and C, containing carbon–carbon double bonds and –OH groups, are more sensitive to light and air than vitamin D as they are susceptible to free radical and redox reactions.
117
Which vitamin has the WHO determined as the greatest deficiency?
The World Health Organization (WHO) has identified vitamin A as the most important vitamin deficiency in global health terms.
118
What are typical reasons for vitamin deficiency?
harsh agricultural conditions
n famine
n poverty
n lack of prolonged periods sunlight for part of year (vitamin D only) n poor access to or supply of vitamin supplements.
119
Scurvy today
Scurvy, which involves a deficiency of vitamin C, is one of the accompanying diseases of malnutrition and thus is still widespread in areas of the world depending on external food aid. Though rare, there are also documented cases of scurvy due to poor dietary choices by people living in industrialized nations.
120
Why is it difficult to solve the vitamin A deficiency? Why can increasing vit A via biofortification not simply solve the problem?
Programmes involving the biofortification of diet using crops rich in pro-vitamin A have shown the complexity of the dietary situation where people are under- nourished. Vitamin A is fat soluble, so if the level of body fat is low then the vitamin is not absorbed. An adequate fat intake is essential for the β-carotene from golden rice – a variety of rice rich in provitamin A – to be absorbed.
121
How are foods fortified with vit A, and how has it been promoted?
Fortification of foods with vitamin A has proved a successful strategy for combating this deficiency. Programmes also exist to encourage farmers to grow varieties of foods richer in β-carotene (provitamin A; which can be converted into vitamin A in the body) – this is called biofortification. For instance, the introduction of orange-fleshed sweet potato into Uganda to replace the indigenous white-fleshed variety has met with some success in reducing vitamin A deficiency. The provision of golden rice should also help with reducing vitamin A deficiency.
122
How are foods fortified with vit D and how has it been promoted?
Mandatory vitamin D fortification is increasing; fortification is usually applied to milk and margarine, as the vitamin is fat soluble. Fortification of dairy products with vitamin D means that deficiency is now rare in some industrialized countries; though not all European countries do this and vitamin D tablets may need to be prescribed to some individuals.
123
What are breakfast cereals usually fortified with?
Many foods, such as breakfast cereals, are fortified with niacin and thiamin (vitamin B), and deficiency is rare in developed countries.
124
What is another version of biofortification apart from the addition of vitamins to food-stuffs? What has it been used to produce?
A more controversial form of biofortification involves genetic modification (GM) of foodstuffs to make them richer in a particular vitamin. Genetic modification has been used to produce golden rice, fortified with vitamin A. It is hoped that the use of golden rice will make a significant difference to vitamin A deficiency in countries such as India, Bangladesh and Vietnam.
125
How can education help to reduce vitamin deficiencies?
Debate is widespread on the extent to which a balanced diet
can provide sufficient quantities of vitamins, or whether supplementation is necessary for optimum health. The existence of conflicting information and advice, and the pressure of advertising, can make it difficult for individuals
to make an informed choice. Apart from vitamin D, there is little need for supplements for people with a good mixed diet – but there are problems of low vitamin A intake in many developing countries, as well as iron and iodine. Results from intervention trials with antioxidant supplements (especially β-carotene and vitamin E) in developed countries are mixed, with many studies showing increased all-cause mortality among those taking antioxidant supplements.
126
How may medical programmes decrease vitamin deficiencies?
Scientists have a duty to share their findings with the public in ways that help people to understand the issues and make valid judgements.
127
What is a simple method of combatting vit D deficiency?
Vitamin D deficiency it is still a problem in some developing countries where intake of dairy products may be low or where religious or social customs or climatic conditions prevent an adequate exposure to sunlight. More widespread use of sunscreen lotions during the summer months seems to have resulted in greater concern over an increase in vitamin D deficiency even in affluent populations. Current recommendations for vitamin D intake are greater than can be achieved readily from diet, especially in winter above about 40°N or S.
128
What does host-guest chemistry involve?
Host–guest chemistry involves the design, synthesis and investigation of simpler organic compounds that imitate the working features of naturally occurring compounds: molecular recognition, transport, regulation and catalysis.
129
What can a molecules recognition process be described as?
A molecular recognition process can be described as a specific interaction between two molecules through multiple non-covalent contacts (via intermolecular forces).
130
What are examples of molecular recognition in biology?
Molecular recognition forms basis for many processes in biology: receptor–substrate binding; enzyme catalysis (e.g. lock and key principle); assembly of multi-protein complexes, e.g. ribosomes; and transport across cell membranes.
131
What is a host?
The host is an organic molecule containing convergent binding sites.
132
What are convergent binding sites?
These are synthetic counterparts to receptor sites in enzymes, genes and antibodies.
133
What is the guest?
he guest is a molecule or ion containing divergent binding sites.
134
What are the divergent binding sites?
The binding sites are the counterparts to substrates, inhibitors, cofactors and antigens.
135
What holds the host and guest components together in solution?
The host and guest components of a complex are held together in solution (Figure 23.47) by an enthalpy contribution and an entropic contribution to their combination.
136
What is the enthalpy of contribution?
The enthalpy contribution: consists of electrostatic forces of interaction such as ion-pairing, hydrogen bonding, metal ion-to-ligand attraction, ring-stacking, dipole–dipole interaction, and London (dispersion) forces.
137
What is entropic contribution?
The entropic contribution: results from the process of desolvation – an increase in entropy due to the freeing up of solvent molecules as the host and guest associate.
138
What is the host-guest complex also known as?
The host–guest complex is also known as a supramolecule.
139
What have host-guest complexes been used for?
Host–guest complexes have been used to deliver poorly soluble drug molecules more effectively in patients by increasing the solubility and bioavailability of the drug
140
What are cyclodextrins and how do they act as a host?
Cyclodextrins are chemically stable, water-soluble oligosaccharide hosts derived enzymatically from starch. Because their interiors are relatively lipophilic and their exteriors hydrophilic, cyclodextrins can complex hydrophobic guests to form inclusion complexes in aqueous solution.
141
How is host-guest chemistry used in the environment?
Host–guest systems have been utilized to remove hazardous substances from the environment. They can be made in different sizes and different shapes to trap a variety of chemical guests. One application is the ability of BOBCalix6 to trap a caesium ion
142
What is caesium 137?
Caesium-137 is radioactive and there is a need to remove it from nuclear waste in an efficient manner.
143
Apart from caesium 137, what has host-guest chemistry been used to remove?
Host–guest chemistry has also been used to remove carcinogenic aromatic amines, and their N-nitroso derivatives from water.
These waste materials are used in many industrial processes and found in a variety of products such as pesticides, drugs and cosmetics.
144
What is an example of host-guest chemistry that can be used in the exam?
You will need to be able to give a named example of host–guest chemistry
the calixarenes are such an example: used to remove radioactive caesium-137 from waste water by forming ion–dipole interactions.
145
What are xenobiotics?
Xenobiotics are chemicals found in organisms which are not normally present or are present in higher than usual concentrations.
146
What are examples of xenobiotics, general compounds?
They are chemical compounds, often drugs (including antibiotics which enter the water supply and those given to livestock), pesticides or carcinogens that are foreign to the living organism.
147
Are xenobiotics natural or pollutants?
BOTH
Some xenobiotics may be natural compounds, but most are pollutants.
148
What are 3 cases of xenobiotics?
Three well-studied classes of xenobiotics are dioxins, dioxin-like substances, such as polychlorinated dibenzodioxins (PCCDs, Figure 23.50), and polychlorinated biphenyls (PCBs, Figure 23.51).
149
When are dioxins produced?
Dioxins are produced as by-products in the manufacture of some chlorinated organic compounds and the incineration of plastics.
150
Why are dioxins harmful?
They are highly carcinogenic, especially the chlorinated dioxins, and they can disrupt the endocrine system (hormone action) and lead to cellular and genetic damage.
151
What is the structure of PCB's and what were they used for?
PCBs contain one to ten chlorine atoms attached to a biphenyl molecule (Figure 23.51). They are highly stable, with high electrical resistance and were used as coolants, plasticizers, lubricants and insulating liquids.
152
What is the major issue with xenobiotics?
A major issue with xenobiotics is biomagnification, which involves an increase
in concentration as a substance passes up the food chain via digestion and assimilation
153
Define biomagnification
the increase in the concentration of the pollutant as it moves up through the food chain.
154
What is a named example of a chemical involved in biomagnification?
. DDT (Figure 23.52) (dichlorodiphenyltrichloroethane) is an insecticide (now banned in many countries) against the malaria mosquito which accumulates in birds of prey and makes their eggs non-viable
155
Apart from DDT, what substances may be involved in biomagnification?
Heavy metals, such as mercury compounds, can also be involved in biomagnification in marine environments.
156
Bioaccumulation definition
Bioaccumulation – the increase in the concentration of a pollutant
in an organism as it absorbs or it ingests it from its environment
157
A 500.0 cm3 water sample is analysed for DDT using chromatography and mass spectrometry. The water sample undergoes chromatography and is then rinsed with 20.0 cm3 of water. The DDT-containing fraction is removed with 20.0 cm3 of methanol, evaporated and then transferred to a 2.00cm3 volumetric flask using methanol. A 20μdm3 aliquot is injected for analysis and the concentration of DDT in this extract is found to be 27.1ngcm–3.
Determine the concentration of DDT in ngdm–3 in the water sample, assuming 100% transfer efficiency.
mass isolated in DDT extract = (27.1ngcm–3)(2.00cm3) = 54.2ng
(note that 2.00cm3 = final extract volume)
initial water volume = 500.0cm3 = 0.500dm3
initial water concentration = mass of DDT isolated / water volume
= 54.2 ng / 0.500 dm3
= 108 ng dm–3
158
What does green chemistry promote?
Green chemistry promotes the design and application of chemical products and chemical processes that are compatible with human health and preserve the environment.
159
When can green chemistry be used?
The areas in which green chemistry can operate to improve environmental quality include choices of solvents and reagents for chemical reactions, development of alternative processes and improvements in existing chemical processes or practices.
160
What are the 6 principles of green chemistry?
(You are not expected to learn this list, or the 12 principles of green chemistry, but you will be expected to be able to discuss the broad issues and apply them in a discussion of the ‘greenness’ of a particular product.)
- It is better to avoid producing waste than to clean or treat it after it has been created.
- When synthesizing new substances, the method used should generate as little waste as possible. The substances generated should have little or no toxicity to human health or towards the environment.
- Catalysts that allow the use of common and safe chemical reagents should be used whenever possible.
- The raw materials for chemical processes should be renewable feedstock when it is technologically and economically feasible.
- Auxiliary substances, such solvents, should be eliminated or made as harmless as possible.
- Chemical processes should be designed to be as energy efficient as possible, avoiding high temperatures and pressures.
161
An ultrasound imaging agent can be made by the reaction of butane and fluorine as shown in the following equation.
C4H10 + 10F2 → C4F10 + 10HF
Calculate the atom economy for the formation of decafluorobutane, C4F10, to
three significant figures.
atom economy (%) = (molecular mass of atoms in useful products / molecular mass of atoms in reactants) × 100
= (238 × 100) /438 = 54.3%
162
What are synthetic plastics usually based on?
Synthetic plastics are organic and usually based on hydrocarbons
163
Therefore are synthetic plastics biodegradable?
Thus they are generally not biodegradable and cause pollution in the sea and in landfills.
164
What is classified as a biodegradable plastic?
Biodegradable plastics are plastics capable of being decomposed by bacteria
and fungi, ultimately to carbon dioxide and water.
165
What are biodegradable plastics composed of?
They are based on naturally occurring polymers usually with ester functional groups, such as PLA (polylactic acid) or glycosidic (ether) linkages, such as starch.
166
What is bioremediation?
Bacterial and fungal enzymes can be used to degrade biological pollutants, such as the hydrocarbons released in crude oil spills, a process known as bioremediation.
167
What is used in washing powders and why are they useful?
Proteases, lipases and other enzymes are used in biological washing powders. Biological detergents allow for use at lower temperatures than non-biological ones and so save energy. Immobilized enzymes (enzymes attached to a solid support) have been used in the clean-up of industrial waste water.
168
How is the active site "built"?
At the active site of the enzyme, the amino acid side-chains of the folded protein are precisely positioned so they favour the formation of the high-energy transition states that the substrate(s) must pass through to be converted to product.
169
What are saturation kinetics?
When reaction rate is plotted against substrate concentration, a hyperbolic curve with an asymptotic plateau is reached. This is known as saturation kinetics (Figure 23.56) and occurs when the rate at which substrate enters active sites is equal to the rate at which products leave active sites.
170
What are the two parameters developed by MIchaelis-Menten?
The kinetics of enzyme-controlled reactions (known as Michaelis–Menten kinetics) identifies two important parameters: Vmax and Km
171
What is Km?
(the Michaelis constant), the concentration of substrate that results in half the maximum rate.
172
What does a low Km show?
A low value of the Michaelis constant, Km, indicates that the enzyme works efficiently even if the concentration of the substrate is low,
173
What does a high Km show?
while a high value of the Michaelis constant indicates that the enzyme requires a high concentration of the substrate before being relatively active.
174
What does an enzyme assay measure?
An enzyme assay measures the conversion of substrate to product, under conditions when the enzyme is optimally active.
175
Why does an enzyme assay use high substrate concentrations?
High substrate concentrations are used so that the initial rate is proportional to the enzyme concentration.
176
What is measured in the enzyme assay?
Either the rate of appearance of product or the rate of disappearance of substrate is measured, often by following changes in absorbance using a spectrophotometer.
177
Define competitive inhibiton and its effect on Vmax and Km
Competitive inhibition – involves a molecule binding to the active site of an enzyme and thus preventing substrate from binding. The inhibitor has a similar structure to the substrate. Competitive inhibition does not affect the value of Vmax but increases Km.
178
Define non-competitive inhibiton and its effect on Vmax and Km
Non-competitive inhibition – involves a molecule binding to the enzyme at a site distinct from the active site. This alters the shape of the enzyme, affecting the active site so that it no longer binds the substrate. Non- competitive inhibition decreases the value of Vmax but has no effect on the value of Km.
179
What is feedback inhibition?
One of the most common forms of inhibition is feedback inhibition (Figure 23.58), in which an enzyme early in a metabolic pathway is inhibited by its binding to one of the metabolic pathway’s end products.
180
What are the main ways of immobilising enzymes?
Most of the enzymes used in industry are extracellular and secreted by bacteria into the growth medium. The main methods of immobilizing enzymes are cross-linking, entrapment and adsorption
181
Why are immobilised enzymes used?
Isolated enzymes are used commercially and their effectiveness is increased if the enzyme is immobilized. Immobilized enzymes can be readily removed from a reaction mixture to avoid feedback inhibition by products. Immobilization of an enzyme can also improve its thermal stability.
182
When can immobilised enzymes be used?
Immobilized enzymes are important in biosensor and diagnostic tests.
183
What components of biological fluids act as buffers?
The major components in most biological fluids are the dihydrogen phosphate ion (H2PO4–, pKa 6.82) and the hydrogencarbonate ion (HCO3–, pKa 6.35).
184
What biological molecules also act as buffers?
However, many biological molecules, including amino acids, proteins, nucleic acids and lipids have multiple acid–base groups that are effective at buffering in the physiological pH range (pH 6–8).
185
How do amino acids act as buffers?
The carboxyl and amino groups bonded to the central carbon-2 atom of an amino acid act as acid–base groups, donating or accepting a proton as the pH is changed (Figure 23.60).
At LOW pH, both groups are fully protonated, (NH3+) but as the pH is increased first the carboxylic acid group and then the amino group lose
a hydrogen ion (H+). Those amino acids with an ionizable side-chain with an additional side-chain have an additional acid–base group with a distinctive pKa. (COO-)
186
When does an amino acid not act as a buffer?
It is important to realize that an amino acid does not act as a buffer around its isoelectric point because there is only one species present.
187
What does an a) acidic b) alkaline solution of amino acids contain?
Solutions with an acidic pH (pH < pI) contain a mixture of the zwitterion and the cation, while alkaline solutions (pH > pI) contain zwitterions and anions
188
How to calculate the pH of an amino acid buffer?
pH = pKa + log [conjugate base] / [conjugate acid]
For amino acid buffers, this can be adapted as follows: acidic pH (pH < pI)
pH = pKa1 + log [zwitterion] / [cationic form]
alkaline solutions (pH > pI)
pH = pKa2 + log [anionic form] / [zwitterion]
189
How can the concentration of proteins in a solution be determined?
The concentration of a protein in solution can be determined by UV–Vis spectroscopy (Figure 23.62).
190
What is done to the amino acid solution before spectroscopy and why?
Proteins are colourless and only weakly absorb UV radiation so the protein is complexed with a dye or redox reagent to form a highly coloured complex.
191
What is the Beer-Lambert?
The principle of quantitative spectroscopy depends on the Beer–Lambert law (Figure 23.63). This states that for dilute solutions at a fixed wavelength absorbance is directly proportional to concentration:
log10 (I/I0) = ε lc
192
What do the symbols stand for in the Beer-Lambert equation?
where I0 is the intensity of the incident radiation, I is the intensity of the transmitted radiation, ε the molar absorption coefficient (cm–1 mol–1 dm3), l is the path length (in the cuvette) of the absorbing solution (usually 1 cm) and c is the concentration (mol dm–3) of the solution.
193
How can spectroscopy be used to determine the concentration of the protein solution?
To determine the concentration of the solution of the protein with an unknown concentration, it is necessary to obtain a calibration curve (line) by using a range of known concentrations of a specific purified soluble protein (such as serine albumin from a cow) and measuring the associated absorbance values.
A line of best fit (Figure 23.64) is constructed and once the absorbance of the unknown sample has been measured its concentration can be determined by interpolation of the graph.
194
What charge do nucleotides have under physiological conditions?
The nucleotides themselves are made from a pentose sugar, a nitrogen-containing base and a phosphate group (which is ionized and negatively charged under physiological conditions).
195
What is the difference in structure between purines and pyrimidines?
The nitrogenous bases present in RNA and DNA nucleotides are heterocyclic ring structures classified as purines or pyrimidines. The pyrimidines (thymine, uracil and cytosine) contain just a single ring (Figure 23.65), whereas the purines (guanine and adenine) contain two fused rings (Figure 23.65).
196
What stabilises the double helix structure of DNA? (2)
The pairing is mediated through hydrogen bonding which stabilizes the double helix structure(; note that the AT pairing involves two hydrogen bonds, whereas the GC pairing involves three such bonds.)
London (dispersion) forces due to the presence of the flat-ringed bases stacked above and below each other also contribute to maintaining the secondary structure of DNA.
197
If a given sample of double-stranded DNA is analysed for its base composition and shown to contain 40% cytosine, what is the expected percentage of adenine?
By Chargaff’s ratios, 40% cytosine means the sequence must have 40% guanine as C always pairs with C. That leaves 20% of the bases as being A and T. Again, by Chargaff’s pairing ratios, the %A must equal %T (A always pairs with T). Therefore, A and T split the remaining 20%, and there must be 10% adenine and 10% thymine in the DNA.
198
How does RNA differ from DNA?
RNA (Figure 23.68) has an almost identical structure to DNA, except that the sugar is ribose, thymine is replaced by uracil, and it is single stranded and less chemically stable than DNA.
199
Replication, Transcription and Translation
In bio flashcards
Details of transcription and translation are not required for the examination. For the examination limit your revision of the expression of DNA to the concept of a 4-unit base code determining a 20-unit amino acid sequence.
200
DNA storage
nucleosomes, histones etc, stored as chromosome - in bio flashcards:
The genetic material of cells with nuclei is contained in a set of paired chromosomes, each formed from a long DNA molecule with many genes. Chromosomes consist of DNA bound to specializeDd, highly basic proteins which help fold the DNA into a compact form. These basic proteins are known as histones and they have a high content of amino acid residues with basic positively charged R-groups. The first level of association between the DNA strand and histones is the formation of nucleosomes. A nucleosome consists of a length of DNA of about 150 base pairs, wrapped around a core of eight histones. These nucleosomes are spaced along the DNA, and thus form a ‘string of beads’ referred to as chromatin. Nucleosomes help to supercoil the DNA while still ensuring appropriate access to it. Figure 23.75 shows the relationship between the DNA strand, the nucleosomes, and a chromosome.
201
Define GMO
Genetically modified organisms (GMOs) – organisms that have genetic material that has been changed in some way by genetic engineering. This can often be the result of the insertion of DNA from a different species.
202
Define recombinant DNA
Recombinant DNA (rDNA)
– these molecules are DNA molecules formed by laboratory methods of genetic recombination which bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome.
203
What does the universal nature of the genetic code allow for?
The universal nature of the genetic code makes it possible for DNA from one organism to be expressed by directing protein synthesis when it is transferred into the DNA of a different species. This is the basis of genetic engineering which gives rise to genetically modified organisms (GMOs).
204
What does recombinant DNA allow for?
Recombinant DNA technology allows biochemists to pick out a specific gene from a cell’s genome and determine the molecular structure of the gene. An important technique is the ability to cut a long DNA molecule into a specific and reproducible set of fragments using restriction enzymes (Figure 23.76), each of which cuts the DNA double helix only at a particular nucleotide sequence.
205
What does nucleic acid hybridisation allow for?
DNA fragments can be separated from one another on the basis of size by gel electrophoresis. Nucleic acid hybridization (Figure 23.77) can detect any specific RNA or DNA sequence in a mixture of nucleic acid fragments. This technique relies on the fact that a single strand of DNA or RNA will form a double helix only with another nucleic acid strand of the complementary nucleotide sequence.
206
How is the foreign gene introduced into the vector (plasmid)?
Genetic engineers isolate, cut out and transfer genes between organisms. In order to transfer DNA in a living cell the DNA is introduced by a vector, usually a plasmid (circular DNA from bacteria). Once the foreign DNA is inside the host cell it may be incorporated by the host cell. Genes in the foreign DNA are expressed using the host cell’s ribosomes. The foreign DNA is replicated (copied) each time the cell divides.
207
What two methods can be used for rapid replication of modified DNA?
Molecular cloning and PCR are two techniques for the rapid replication of modified DNA. The fundamental difference between the two methods is that molecular cloning involves replication of the DNA within a living cell (often a bacterial cell), while PCR replicates DNA in the test tube, free of living cells.
208
What is the most common application of recombinant DNA?
The most common application of recombinant DNA is in basic research, but many additional practical applications of recombinant DNA are found in industry, food production, human and veterinary medicine, agriculture and bioengineering. Some specific examples are listed below.
209
Discuss recombinant human insulin
This form of insulin has almost completely replaced insulin obtained from animal sources for the treatment of insulin- dependent diabetes. Recombinant insulin is synthesized by inserting the human insulin gene into E. coli, or yeast (Saccharomyces cerevisiae), which then produces insulin for human use. This example is of importance because of its impact on patients and the fact that it was essentially the first successful application of this ground-breaking technique. A similar approach has been taken in the following cases.
210
Discuss recombinant human growth hormone (HGH, somatotropin)
Recombinant HGH is now administered to patients whose pituitary glands generate insufficient quantities to support normal growth and development. The use of the recombinant protein eliminated problems associated with HGH from cadavers (dead corpses), which had been the previous source.
211
Discuss Recombinant hepatitis B vaccine
Recombinant hepatitis B vaccine contains a form of the hepatitis B virus surface antigen that is produced in yeast cells. The development of this recombinant vaccine was an important and necessary development because hepatitis B virus, unlike other common viruses such as the polio virus, cannot be grown in vitro.
212
How can GMO's be used commercially?
However, a number of GMOs have been developed for commercial use involving animals and plants that produce pharmaceuticals or other compounds. Within the field known as pharming, intensive research has been conducted to develop transgenic animals that produce biotherapeutics.
213
What is an example of the first human biological drug produced from an animal?
The first human biological drug produced from such an animal, a goat, is the drug anti-thrombin (ATryn), which is an anticoagulant that reduces the probability of blood clots during surgery or childbirth. The anticoagulant is extracted from the goat’s milk.
214
What is biotechnology?
Biotechnology is the manipulation of organisms and cells for the benefit of people in agriculture, medicine and food production. Biotechnology is used to modify plants used in food production
215
What are techniques of inter-species DNA transfer?
- add a gene to yield a new product
- inactivate a gene to remove undesired an undesired property
- modify a gene for higher yields of its protein.
216
What are examples of GM foods?
Examples include corn which contains a bacterial gene that produces a natural pesticide, herbicide-resistant crops, rice which produces higher concentrations of vitamin A (‘golden rice’), and tomatoes that remain fresh for longer.
217
What are 6 benefits of GMO's?
- longer shelf-life
- improved flavour, texture and nutritional value
- increased resistance to diseases and pests, reducing the use of pesticides
- produce a supply of substances such as vitamins and vaccines
- increased crop yields
- tolerance of a wider range of growing conditions, such as drought resistance.
218
What are 6 concerns over GMO's?
- lack of information about long-term effects
- changes to the natural ecosystem through cross-pollination
- possible links to increased allergies
- risk of altering natural composition of food
- concerns of breeding species that are resistant to control
- in some cases lack of information through food labelling.
219
What are biological pigments?
Biological pigments are coloured compounds which are produced by metabolism
220
What is melanin?
Melanin is a biological pigment responsible for the colour of skin, hair and eyes.
221
What colour do pigments absorb?
The colour of pigments results from the absorption of certain wavelengths of visible light. All pigment molecules have intense absorption bands in the visible region of the spectrum. The colour seen is the light that is not absorbed but instead is reflected (Figure 23.79).
222
What are chromophores?
Groupings within organic molecules that cause colour are chromophores.
223
What are chromophores composed of?
They are typically delocalized electron systems, often benzene rings or with functional groups with lone pairs, such as >C=O, –N=N– and –NO2
224
What is a common chromophore?
A common chromophore is an arrangement of alternating single and double carbon–carbon bonds
225
How does the energy and wavelength absorbed change with more extensive conjugation?
The more extensive the conjugation, the lower the energy (longer the wavelength) of the light (photons) absorbed.
226
What happens to electrons when light is absorbed
The absorption of light (of specific energy) causes electrons in π-bonds or lone pairs (n) being excited and undergoing a transition to a molecular orbital of higher energy, usually an anti-bonding orbital
227
When does conjugation occur in terms of orbitals?
Conjugation occurs when three or more p orbitals overlap. This can be achieved via π–σ–π bonds or can be achieved by an atom (such as nitrogen or oxygen) with a lone pair that is sp2 or sp3 hybridized.
228
What are anthocyanins?
Anthocyanins are aromatic, water-soluble polyphenol pigments found in fruits, vegetables and flowers.
229
What are the structure of anthocyanins based on?
Their structures are based on the hydrocarbon flavan structure (Figure 23.83) which has a C6–C3–C6 skeleton with two benzene rings (conjugated systems) isolated by an oxygen-containing pyran ring.
230
What affects the colour of anthocyanins? Therefore what can they acts as?
The colour of anthocyanin molecules is affected by the presence of cations, pH and temperature. They can act as acid–base indicators.
231
What can anthocyanins act as in terms of Lewis acid-base theory?
Anthocyanin molecules can act as ligands (Lewis bases) via their oxygens and can coordinate to cations, such as aluminium, iron(II) and iron(III) to form intensely coloured complexes.
232
In what forms do anthocyanins exist in equilibrium in aqueous solution?
A complex equilibrium exists in aqueous solution (Figure 23.84) with four different structural forms with different extents of conjugation:
A ⇋AH+ ⇋B⇋C
quinoidal base ⇋ flavylium cation ⇋ carbinol ⇋ chalcone
purple/red ⇋ red ⇋ colourless ⇋ yellow
233
What form do low and high values of pH favour in anthocyanins?
Low values of pH favour the red flavylium form; high values of pH favour the yellow chalcone form
234
What forms does an intermediate pH favour in anthocyanins?
At intermediate pH values the purple quinoidal base and colourless carbinol form are at high concentrations in the equilibrium mixture.
235
What form of anthocyanins is favoured at low and high temperatures?
At low temperatures the red flavylium form predominates; at high temperatures the yellow chalcone form predominates.
236
What are carotenoids?
Carotenoids are lipid-soluble plant pigments involved in the absorption of blue light during photosynthesis.
237
Where is the conjugation system in carotenoids?
The conjugated system in carotenoids is due to the presence of a long hydrocarbon chain consisting of an alternating series of single and double carbon–carbon bonds.
238
What are carotenoids derived from?
Many carotenoids, such as beta-carotene (Figure 23.85), are derived from a polyene chain containing 40 carbon atoms, which may have terminal cyclic groups and oxygen-containing functional groups.
239
What is B-carotene, where is found and what is its structure?
β-Carotene (a precursor to vitamin A) is found in carrots and has a characteristic orange colour. It has a conjugated π-system involving 11 conjugated carbon– carbon double bonds. It appears orange when viewed in white light since its molecules absorb strongly in the violet-blue (400–510nm region) of the electromagnetic spectrum.
240
Why are carotenoids vulnerable to oxidation? WHat is the reaction catalysed by?
Owing to their polyunsaturated nature, carotenoids are susceptible to oxidation. This is a complex free radical reaction catalysed by light, transition metal cations and hydroperoxides (ROOH).
241
What happens to carotenoids at high temperatures?
At high temperatures carotenoids isomerize from the all-trans form into a mixture of cis isomers.
242
What are porphyrins?
The porphyrins are a series of related nitrogen-containing macrocyclic (large single ring with multiple donor sites) conjugated ligands that are able to strongly coordinate a specific metal cation.
243
What are examples of porphyrins?
Examples of porphyrins and their cations are chlorophyll (Mg2+), hemoglobin (Fe2+), myoglobin (Fe2+) and the cytochromes (Fe2+ and Fe3+, depending on their oxidation state).
244
What is hemoglobin?
Hemoglobin is a protein found in mammals that transports molecular oxygen in the red blood cells
245
In what way does oxygen bind to hemoglobin?
xygen binds cooperatively to hemoglobin, resulting in a sigmoidal (S-shaped) oxygen dissociation curve
246
What is the structure of hemoglobin?
It is a tetrameric protein – four protein molecules associated together. Each of the four globin proteins contains a heme group with an iron(II) ion at the centre
247
What 4 factors affect oxygen saturation of hemoglobin?
pH, CO, CO2, Temperature
248
How does pH affect oxygen saturation of hemoglobin, give equation
Hemoglobin can be protonated (at an amino acid side-chain) at a low value of pH (high concentration of protons), resulting in the dissociation (release) of oxygen as the protein undergoes a conformational change:
HbO2 +H+ ⇋HbH+ +O2 (low pH curve to right?)
249
How does CO affect oxygen saturation?
Carbon monoxide is a competitive inhibitor of oxygen at the iron(II) ion in the heme group. Hemoglobin has a higher affinity for carbon monoxide than oxygen. A strong coordinate bond is formed between the iron(II) ion and the lone pair of electrons on the carbon atom of carbon monoxide.
250
What does carbon dioxide react with water to form?
Carbon dioxide reacts reversibly with water to form carbonic acid (H2CO3), which dissociates to form hydrogen carbonate, HCO3–(aq) and hydrogen ions, H+(aq).
251
What is the result of the products of carbon dioxide with water?
This lowers the pH so that more H+ binds to hemoglobin and causes a release of oxygen.
252
Does Hb bind CO2?
YESHemoglobin also binds carbon dioxide, but not at a different site from oxygen. This carbon dioxide reacts with the –NH2 group on the terminal amino acid of each polypeptide chain that makes up hemoglobin (Figure 23.88) which releases H+ and also changes the shape of the protein; both of these reduce the affinity of hemoglobin for oxygen.
253
How does temperature affect oxygen saturation?
The dissociation of oxyhemoglobin (HbO2 → Hb + O2) is an endothermic process. Hence, the position of equilibrium will shift to the right as the temperature is increased and less oxygen binds to hemoglobin.
254
How does foetal hemoglobin differ from adult hemoglobin?
Fetal hemoglobin is a different form of hemoglobin only present in the blood of the developing fetus. It has a higher affinity for oxygen than maternal hemoglobin (which replaces it after birth) (Figure 23.89). This adaptation allows the efficient transfer of oxygen from the mother’s blood to the fetal blood in the placenta.
255
How does myoglobin differ from adult hemoglobin?
Myoglobin also has an oxygen dissociation curve to the left of that of hemoglobin, which means it has a greater affinity for oxygen and can accept oxygen from hemoglobin for storage (in the striated muscles).
256
What are cytochromes?
Cytochromes are a varied group of electron transport proteins that contain a heme group which has an iron ion that alternates between iron(II) and iron(III).
257
What is the role of cytochromes?
It is able to accept electrons from one substance and donate them to another (with
a less negative electrode potential), functioning as part of the electron transport chain which is involved in the last step of the aerobic respiration of glucose.
258
Give an equation for the role of cytochrome c
Cytochrome c passes its electrons to the terminal acceptor oxygen with the formation of water:
4Fe2+(cytochrome c) + 4H+ + O2 → 4Fe3+(cytochrome c) + 2H2O
259
Is the dissociation curve for myoglobin sigmoidal?
NO
The dissociation curve for myoglobin is not sigmoidal in shape as there can be no cooperative binding within its one heme structure.
260
What is chlorophyll?
Chlorophylls are the main photosynthetic pigments in leaves and are involved in absorbing the light needed in the process of photosynthesis.
261
How does chlorophyll participate in the ETC?
Chlorophyll molecules ionize and donate an electron to the electron transport chain.
262
In what forms does chlorophyll occur in plants?
Chlorophyll (Figure 23.90) occurs in plants in two closely related forms: chlorophyll a (blue green) and chlorophyll b (yellow green).
23.9 Biological pigments 109 myoglobin
fetal hemoglobin normal hemoglobin
263
Where does chlorophyll absorb light strongly?
Chlorophyll absorbs light strongly in the blue part of the spectrum and to a lesser extent in the red (see Figure 23.91) and hence leaves appear green (when viewed in white light).
264
What is the chromophore in chlorophyll?
The chromophore is the conjugated porphyrin ring system.
265
What is the stability of chlorophyll affected by?
The stability of chlorophyll is affected by pH and temperature
266
What happens to chlorophyll in highly acidic conditions?
in highly acidic conditions (pH < 3) the central magnesium ion, Mg2+, is replaced by a proton (H+).
267
What happens to chlorophyll at high temperatures?
Chlorophyll will undergo decomposition at high temperatures and in the presence of high intensity ultraviolet radiation.
268
What is chromatography based on and what is it used for?
Chromatography is based upon the differential retention of compounds in a mobile phase as they pass through or across a stationary phase. It can be used to separate, identify, identify and quantify the component pigments (or dyes) in a mixture.
269
What is the main principle of chromatography?
In paper chromatography, the stationary phase is a liquid adsorbed onto the surface of the paper. The paper has many pores that can adsorb and strongly hold hydrogen bond water molecules to form the stationary phase. The water can be displaced by other liquids to give different stationary phases.
Pigments that are more soluble in the solvent than they are in the water molecules of the stationary phase move rapidly up the paper, while those that are more soluble in the water are not carried as far up the paper (Figure 23.92).
270
What is the principle of thin layer chromatography?
Thin layer chromatography (TLC) uses a stationary phase of silica or alumina particles bonded to a thin layer of glass or plastic. TLC (Figure 23.93) separates a mixture of pigments based on how strongly they are adsorbed on the stationary phase and dissolved in the mobile phase (a liquid or mixture of liquids). This equilibrium is known as partitioning. The greater the affinity of the pigment
for the stationary phase, the more slowly it moves along the surface of the TLC plate.
271
What are enantiomers?
Enantiomers are a pair of molecules related as non-superimposable images (‘mirror images’).
272
What molecules show chirality?
Molecules with sp3 hybridized carbon atoms bonded to four different atoms/ groups show chirality due to their tetrahedral shape.
273
Can amino acids exist as enantiomers?
YES
All amino acids can exist as a pair of enantiomers except glycine (2-amino ethanoic acid).
274
What are Fischer projections?
Fischer projections (Figure 23.95) attempt to show three-dimensional structure using a two-dimensional framework of vertical and horizontal bonds.
275
How are Fischer projections meant to be viewed?
The main carbon chain is drawn as a vertical line, and bonds to all substituents (atoms or groups of atoms) are drawn as horizontal lines. All vertical lines represent bonds behind the plane of the page, and horizontal lines bonds coming out of the plane towards the viewer.
276
How can amino acids be termed L and D isomers?
When shown in Fischer projection, if the –OH group on the highest numbered chiral carbon is on the right, the molecule is assigned the label d; if the –OH group is on the left, it is given the label l. These notations are known as absolute configurations and often used to describe amino acids and monosaccharides.
277
How are Fischer projections used for monosaccharides?
Fischer projections are a method of representing the structure of any straight- chain forms of a sugar by projection on to a plane. In a Fischer projection, the sugar molecule is shown with the carbon numbered 1 at the top – according to the normal naming rules the aldehyde/ketone group will be given the lowest possible number (Figure 23.96).
278
What are anomers, for monosaccharides?
The conversion of sugars in the straight-chain form to the ring form creates α- and β-isomers (Figure 23.96) known as anomers.
279
How do monosaccharide anomers differ?
These differ by the relative position of the hydroxyl substituent attached to the carbon atom derived from the aldehyde or ketone carbon in the open chain form of the sugar.
280
What extra component is formed when a sugar cyclises from straight-chain form?
When a sugar cyclizes from the straight-chain (linear) form, an extra chiral carbon is formed (Figure 23.98).
281
What happens to the lone pair of electrons?
The lone pair of electrons on the oxygen atom on carbon 5 can attack the carbonyl group (>C=O) from either above the plane of the group or below.
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What does the ability of the lone pair from oxygen to attack above or below the plane lead to?
Two cyclic molecules can therefore be formed: α- and β-forms.
If the –OH on the new chiral carbon (anomeric carbon) is above the ring when the structure is drawn with the ring oxygen at the rear then it has β configuration (the –OH is on the same side of the ring as carbon-6), and if it is beneath then it is α.
283
What is the visual cycle?
The visual cycle (Figure 23.99) is a process by which light (photons) are converted into an electrochemical signal in the cells of the retina lining the eye
284
What does rhodopsin consist of?
Rhodopsin consists of the protein opsin and a covalent bonded co-factor retinal, which is synthesized from vitamin A
285
What does retinal act as in the visual cycle?
Retinal acts as the chromophore.
286
What does the absorption of light do to retinal in the visual cycle?
The absorption of light converts the cis form of retinal (11-cis-retinal) to the trans form (all trans-retinal)
287
What does the trans isomer do in the visual cycle?
This causes the all-trans-isomer to dissociate from the opsin, which ultimately causes a nerve impulse to the brain.
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How is rhodopsin generated?
Rhodopsin is regenerated from opsin and 11-cis-retinal after the all-trans form has isomerized back to the 11-cis form in a series of steps catalysed by enzymes.
