Title: InkBiology / Biological molecules, water and inorganic ions
On every note of this deck, unless a note says otherwise:
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Front: DEFINE
Define: Monomer.
Back: A small molecule from which a larger one is built by joining many of them together.

Front: CHECK YOURSELF
A student writes that water is important in biology because it is a liquid that living things can dissolve substances in and cool themselves with. Rewrite that answer so that every claim in it is explained from the structure of the water molecule.
Back: Water molecules are polar: the oxygen pulls the shared electrons closer than the hydrogens do, so the oxygen end is slightly negative and the hydrogen ends slightly positive, and the molecule is bent so the two positive ends lie on the same side.
Those charges attract the ions of an ionic compound and the charged parts of polar molecules, pulling them apart and holding them in solution. That is why glucose, amino acids and ions are transported in blood, and why non-polar lipids are not.
The same polarity lets each molecule hydrogen bond to four others. Evaporating water means breaking those bonds, which takes a great deal of energy, so a small mass of sweat evaporating removes a large amount of heat.
The same bonding gives water a high specific heat capacity, so the temperature of a cell or a lake changes slowly, which is a separate point from cooling and earns its own mark.

Front: DEFINE
Define: Denaturation.
Back: The loss of a protein's specific three-dimensional shape through disruption of the hydrogen bonds, ionic bonds and hydrophobic interactions holding it, so the function is lost, while the primary structure is unchanged.

Front: DEFINE
Define: Lipid.
Back: A biological molecule that is largely non-polar, insoluble in water and soluble in organic solvents such as ethanol.

Front: CHECK YOURSELF
Starch and cellulose are both polymers of glucose, and a plant makes both. Explain why one of them can be used as an energy store and the other cannot, and why cellulose is strong enough to hold a cell in shape.
Back: Starch is built from α-glucose and cellulose from β-glucose, which differ only in the position of the hydroxyl group on carbon 1.
In cellulose that position forces every second glucose to be rotated through 180 degrees, so the chains are straight rather than coiled. Straight chains lie alongside one another and form many hydrogen bonds between them, building microfibrils with a high tensile strength.
Starch coils and branches instead, so it is compact and insoluble: useful as a store because it exerts no effect on water potential and is hydrolysed back to α-glucose when the cell needs it.
The plant's enzymes hydrolyse α-1,4 bonds and do not fit the β-1,4 bonds of cellulose, so the wall is not digested by the cell it surrounds.

Front: DEFINE
Define: Latent heat of vaporisation.
Back: The energy needed to change one kilogram of a liquid into a gas without a change in temperature.

Front: DEFINE
Define: Secondary structure.
Back: The regular coiling or pleating of the backbone into an α-helix or β-pleated sheet, held by hydrogen bonds between the C=O of one peptide group and the N–H of another.

Front: DEFINE
Define: Hydrogen bond.
Back: A weak attraction between a slightly positive hydrogen atom of one molecule and a slightly negative atom of another.

Front: DEFINE
Define: Hydrophobic.
Back: Not attracted to water: non-polar, so it is excluded from water rather than dissolving in it.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Proteins are made of amino acids, so a protein's job comes from which amino acids it contains.
Back: The order fixes the fold and the fold does the job. Two proteins can contain the same amino acids in different orders and do unrelated things, so the function follows from the shape rather than from the list of residues.

Front: DEFINE
Define: Polar molecule.
Back: A molecule with an uneven distribution of charge, so that one part is slightly negative and another slightly positive.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Unsaturated means the fatty acid is shorter, with fewer carbon atoms in it.
Back: Unsaturated is about bonding, not length. Saturated means no carbon to carbon double bond, so the tail lies straight and packs closely; unsaturated means at least one, which bends it permanently. Stearic and oleic acid both have eighteen carbons, and only one of them is an oil.

Front: DEFINE
Define: Monosaccharide.
Back: A single sugar unit, the monomer from which disaccharides and polysaccharides are built.

Front: DEFINE
Define: Ester bond.
Back: The covalent bond formed by condensation between a hydroxyl group of glycerol and the carboxyl group of a fatty acid.

Front: CHECK YOURSELF
A triglyceride and a phospholipid are made from the same three kinds of component, and only one of them forms a bilayer in water. Explain why, and explain why a triglyceride is the better energy store of the two.
Back: A phospholipid has two fatty acids and one phosphate group where a triglyceride has three fatty acids, so the two molecules differ at one position only.
The phosphate group is charged and therefore hydrophilic, while the fatty acid tails are non-polar and hydrophobic. A phospholipid therefore has one end attracted to water and one end not, and in water the arrangement that keeps the fewest tails in contact with it is a bilayer, heads out and tails in.
A triglyceride is hydrophobic at every point, so it forms droplets rather than a sheet.
As a store, the triglyceride carries a third hydrocarbon tail rather than a charged group, so it holds more energy per gram, and being wholly insoluble it has no effect on the water potential of the cell storing it.

Front: DEFINE
Define: Quaternary structure.
Back: The arrangement of two or more polypeptides, and any non-protein groups, in a functioning protein.

Front: DEFINE
Define: Polymer.
Back: A large molecule made of many similar monomers joined together.

Front: DEFINE
Define: Condensation.
Back: A reaction that joins two molecules with a covalent bond and releases a molecule of water.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Water is a good solvent because it is a liquid, so things can move about in it.
Back: Being liquid is not enough: shake sugar with cooking oil and nothing dissolves. Water dissolves ionic and polar solutes because its own molecules are polar, so their charged ends surround an ion and hold it away from its neighbours. A lipid carries no charge, so nothing separates it.

Front: DEFINE
Define: Hydrophilic.
Back: Attracted to water: charged or polar, so it interacts with water molecules.

Front: DEFINE
Define: Amino acid.
Back: A molecule containing an amine group, a carboxyl group and a variable side chain attached to the same carbon.

Front: DEFINE
Define: Polysaccharide.
Back: Many monosaccharides joined by glycosidic bonds into one large molecule.

Front: DEFINE
Define: Disaccharide.
Back: Two monosaccharides joined by a glycosidic bond.

Front: DEFINE
Define: Protein.
Back: One or more polypeptides folded into a specific three-dimensional shape.

Front: DEFINE
Define: Hydrolysis.
Back: A reaction that breaks a covalent bond between two molecules using a molecule of water.

Front: DEFINE
Define: Polypeptide.
Back: A chain of amino acids joined by peptide bonds.

Front: DEFINE
Define: Glycosidic bond.
Back: The covalent bond formed by condensation between two monosaccharides, joining them through an oxygen atom.

Front: DEFINE
Define: Tertiary structure.
Back: The overall three-dimensional fold of a single polypeptide, held by hydrogen bonds, ionic bonds, disulfide bridges and hydrophobic interactions between side chains.

Front: DEFINE
Define: Triglyceride.
Back: One glycerol molecule joined to three fatty acids by three ester bonds.

Front: DEFINE
Define: Primary structure.
Back: The sequence of amino acids in a polypeptide, held by peptide bonds.

Front: SPOT THE ERROR
Say what is wrong with this claim:
Starch and cellulose are made of different sugars, which is why one is food and the other is not.
Back: Same sugar, different bond. Both are chains of glucose: starch of α-glucose, cellulose of β-glucose, which differ only in where one hydroxyl group sits on carbon 1. That flips every second glucose in cellulose, straightens the chain, and leaves the enzymes that hydrolyse starch unable to fit it.

Front: CHECK YOURSELF
Two proteins are made from exactly the same set of amino acids, in different orders. Explain why one might be an enzyme that works in blood plasma while the other is a structural fibre.
Back: The order of amino acids is the primary structure, and it fixes which side chains end up next to each other once the chain folds.
In the enzyme, the folding brings hydrophilic side chains to the outside and hydrophobic ones to the core, giving a compact globular shape that dissolves in plasma, with an active site of a specific shape.
In the fibre, a repetitive sequence lets the chain form long regular strands that pack together rather than folding into a ball, so it is insoluble and strong.
Same components, different order, different fold, different job. That is why the sequence and not the inventory is what matters.

Front: DEFINE
Define: Specific heat capacity.
Back: The energy needed to raise the temperature of one kilogram of a substance by one kelvin.