biochemistry Flashcards
Define Metabolism
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.
Define catabolism
Catabolism – the breakdown of complex molecules into simpler molecules. Such processes release energy.
Define Anabolism
Anabolism – the synthesis of more complex molecules from simpler precursor molecules. Such processes require energy.
What is anaerobic respiration known as in yeast?
Give Equation
Anaerobic respiration in yeast is known as fermentation
C6H12O6(aq) → 2CO2(g) + 2C2H5OH(l)
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.
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
What reaction creates all biological molecules?
Biological macromolecules and polymers (biopolymers), such as proteins, lipids and DNA, are formed by enzyme-controlled CONDENSATION reactions
What do condensation reactions involve?
These involve the reaction between the functional groups of two smaller molecules to form one large molecule with the release of a water molecule.
What two types of reactions does a condensation reaction involve?
Condensation reactions are an addition reaction followed by an elimination reaction.
What is the condition necessary for condensation polymerisation to occur?
For condensation polymerization (Figure 23.6) to occur each of the reacting molecules must possess at least two reactive functional groups
Give 3 examples of condensation reactions
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.
What conditions do hydrolysis reactions need to occur?
The hydrolysis reactions can also occur in the presence of acid without the presence of enzymes.
In what two ways can amino acids be classified?
Amino acids can be classified based on their polarity and their acid–base properties
What stereoisomer property do all amino acids exhibit, what is the exception?
With the exception of glycine (2-aminoethanoic acid), all of the 2-amino acids contain a chiral carbon atom and therefore exhibit optical isomerism.
What for do amino acids take under standard conditions?
Amino acids are white crystalline solids under standard conditions.
When do amino acids exist as zwitterions?
They exist in the solid state and in neutral aqueous solution as zwitterions
How do amino acids form zwitterions?
This is due to an internal acid–base reaction. A hydrogen ion is released from the carboxyl group and protonates the amine group.
What bonding does the zwitterion form cause?
The presence of zwitterions leads to ionic bonding in crystalline amino acids involving electrostatic forces of attraction between oppositely charged ends of the zwitterions.
What does the ionic bonding and electrostatic attraction of zwitterions result in?
This results in high melting (or decomposition) points and good solubility in water.
Do peptide bonds experience restricted rotation?
YES
Peptide bonds experience restricted rotation (Figure 23.12) due to resonance (π delocalization), giving rise to two possible conformations
Which conformation of an amino acid is generally more stable?
the trans conformation is generally more stable.
What must be done to sequence an entire protein?
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
What is done with the smaller protein fragments?
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.
What can amino acids be classified as in terms of acid-base theory?
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)
Why do amino acids have two pKa values?
Amino acids have two pKa values, one for the carboxyl functional group and one for the amine functional group
When will amino acids have 3 pKa values?
Amino acids with basic or acidic side-chains will have a third pKa value.
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
What are amino acids separated on the basis of in electrophoresis?
During electrophoresis, amino acids are separated based on their pI values.
What charge does a zwitterion carry?
It is neutral
What happens to a zwitterion when the pH of a solution decreases?
forms a cation
What happens to a zwitterion when the pH of a solution increases?
forms an anion
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
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.
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.
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
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
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)
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
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
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.
What are globular proteins composed of?
Globular proteins, for example, hemoglobin (Figure 23.21) are polypeptide chains that are coiled into compact shapes.
What are structural proteins?
Structural proteins, such as keratin, are fibrous proteins that provide structural rigidity in nails and hair.
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.
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.
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.
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.
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
WHat two techniques can be used to identify the structure of a protein?
Chromatography and electrophoresis both separate and identify substances in complex mixtures.
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.
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.
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.
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.
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.
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.
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.
How can lipids be extracted?
Lipids can be extracted from cells, using non-polar solvents, such as ethers and hydrocarbons.
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).
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
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.
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.
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.
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).
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.
What part of the phospholipid condenses with the glycerol?
phosphate group has condensed with the third –OH group of glycerol
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.
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 .
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.
What can be hydrogenated?
Unsaturated oils can be hydrogenated, for example, in the production of margarine.
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
How may hydrogenation make oils “unhealthy”?
However, during the hydrogenation process partial hydrogenation may occur, leading to the production of trans-unsaturated fats
Why are trans-unsaturated fats “unhealthy”?
These increase the formation of LDL cholesterol which raises the risk of heart disease.
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.
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
How can transesterification be achieved?
Transesterification of triglycerides can be achieved via either acid or base catalysis to produce biodiesel
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.
What two ways can lipids become rancid?
Lipids become rancid as a consequence of hydrolytic or oxidative processes.
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.
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.
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.
what does oxidative rancidity produce?
Unpleasant smelling and tasting ketones, alcohols and aldehydes are produced
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.
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
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.
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
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.
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
What is the general formula of carbohydrates?
Carbohydrates are important in nutrition and have the general formula Cx(H2O)y.
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
What is the role of monosaccharides?
Monosaccharides are used to release energy during respiration or act as precursors for other biomolecules.
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)
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.
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
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.
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.
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.
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.)
How many stereoisomers does glucose have?
Glucose is one of 16 stereoisomers, 8 pairs of enantiomers, which include fructose and galactose.
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
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
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.
What does Benedicts show, if reducing sugars in high amounts are present?
A red-brown precipitate of copper(I) oxide is formed.
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.
Vitamins definition
Vitamins – organic micronutrients that cannot (except for vitamin
D) be synthesized in the body and must be obtained from appropriate food sources.
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.
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).
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
What are examples of fat-soluble vitamins?
Fat-soluble vitamins include vitamins A, D, E and K
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.
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.
What are examples of water-soluble vitamins?
. Vitamin B group members (of which there are eight) and vitamin C are water-soluble molecules
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.
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
What is a function of vit A?
Involved in the visual cycle of the eye; particularly important for night vision (low light intensity)
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
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.
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.
