bio year 1: water, ions, sugars (biological molecules part 1)

what does electronegativity mean?

the tendency of an atom of an element to attract shared electrons in a chemical bond

why is water a polar molecule?

• oxygen is more electronegative than hydrogen, so the electrons are more strongly attracted to the oxygen than the hydrogens and spend most of their time closer to the oxygen

• this means oxygen is slightly negative (delta-negative) and the hydrogens are slightly positive (delta-positive)

how are hydrogen bonds formed between water molecules?

• since water is polar, the slightly negative end of one water molecule is attracted to the slightly positive end of another water molecule

• this results in weak hydrogen bonds

what are the properties of water?

• ice floats in water

• water has a high boiling point

• water is adhesive (sticks to the sides of a container) and cohesive (sticks to each other), creating surface tension (when the surface of water contracts to the smallest possible surface area)

• the temperature of large bodies of water (i.e. lakes, rivers, etc) stays stable

• it has a high specific heat capacity

• water is a solvent for salts

why does ice float in water?

• H₂O is denser in liquid form than solid form because, at freezing temperatures, the hydrogen bonds fix the positions of the molecules slightly farther apart by forcing them into a giant, fixed, open structure

• this means ice is less dense than water

why does water have a high boiling point and specific heat capacity?

• since there are so many hydrogen bonds, there is strong attraction between the water molecules which requires a lot of thermal energy to overcome (or loosen for the sake of increasing the particles’ kinetic energy)

why can insects like pond skaters walk on water?

• the hydrogen bonds between water molecules causes them to be very cohesive (they tend to stick together)

• this creates surface tension so the water’s surface is film-like and the insect doesn’t sink

why does water move up the xylem vessel in plants?

• transpiration pull: the evaporating water molecules at the surface of the water pull water molecules up (due to the cohesion caused by hydrogen bonds)

• capillary action: the adhesion between the water molecules and the sides of the vessel (caused by hydrogen bonds between water and hydrophilic cellulose) means the water molecules stick to the vessel + the cohesion between water molecules (caused by hydrogen bonds between water molecules) causes the water molecules to pull each other up

why can water dissolve salts?

• water is a good solvent for ionic compounds because it is polar, so its slightly negative end attracts positive ions while its slightly positive end attracts negative ions

• this breaks up the ionic lattice of salts

why do lakes, rivers, etc have a stable temperature?

• when the environment is colder, a layer of ice forms over the large body of water

• this is because ice is less dense than water, so it floats on top of the water

• this means it insulates the lake/river/etc

why is sweating used as a cooling mechanism by some animals?

• large amounts of energy are needed to overcome the hydrogen bonds between water molecules, so when sweat evaporates, a lot of thermal energy leaves the animal

why doesn’t oil mix with water?

• it’s hydrophobic

• it is non-polar while water is polar, so it doesn’t form hydrogen bonds with water

what is the biological role of Ca²⁺?

• nerve impulses

• muscle contraction

what is the biological role of K⁺?

• nerve impulses

• opening and closing of stomata

what is the biological role of H⁺?

• catalyst for reactions

• determining pH

what is the biological role of Na⁺?

• nerve impulses

• kidney function

what is the biological role of NH₄⁺?

• production of nitrate (NO₃^-) ions by bacteria

what is the biological role of NO₃^-?

• nitrogen for plants to make amino acids

what is the biological role of HCO₃^-?

• blood pH maintenance

what is the biological role of OH^-?

• catalyses reactions

• determining pH

what is the biological role of PO₄^3-?

• makes up cell membranes

what is the biological role of Cl^-?

• balances the positive charge of Na⁺ and K⁺ in cells

what elements are proteins made up of?

CHONS

what elements are nucleic acids made up of?

CHONP

what is the difference between alpha glucose and beta glucose?

• alpha: the OH at C₁ is below the ring’s plane, and the glucose is less stable because the hydroxyl groups are closer together and so repel each other more

• beta: the OH at C₁ is above the ring’s plane, and the glucose is more stable because the hydroxyl groups are farther apart and so repel each other less

what does the term ‘‘hexose monosaccharide’’ tell you about the carbohydrate?

• 6 carbons

• one sugar monomer

what is a glycosidic bond?

a covalent bond between two carbohydrate molecules

is this glucose alpha or beta?

beta

what is a condensation reaction?

the joining of two monomers by covalent bonds, removing water in the process

E.g. 2C₆H₁₂O₆ → C₁₂H₂₂O₁₁ + H₂O

(glucose → maltose + water)

what is a hydrolysis reaction?

the breaking of covalent bonds between two monomers by adding water

what is a dimer?

two monomers joined together

what are the two polysaccharides that starch is made up of?

• amylose (unbranched alpha glucose)

• amylopectin (branched alpha glucose)

which carbons in amylose are being used to link the molecules together?

• C₁ and C₄

• (alpha 1,4 glycosidic bonds)

which carbons in amylopectin are being used to link the molecules together?

• C₁ and C₄

• C₁ and C₆

• (alpha 1,4 and 1,6 glycosidic bonds)

what are the benefits of amylose’s structure?

• the angle of the 1,4 glycosidic bond gives it a helix shape that coils up so more amyloses can be packed together

• since it has many hydrogen bonds, its structure is stable

• amylose is therefore very compact and insoluble (unlike glucose)

what are the benefits of amylopectin’s structure?

• since it’s branched, there are more terminal glucose molecules

• this gives more sites that enzymes can act on to hydrolyse amylopectin into glucose more quickly

• this means glucose is released for respiration faster

what is the structure and properties of glycogen?

• alpha 1,4 glycosidic bonds

• branched

• compact due to having more branches than amylopectin

• insoluble

what is the structure of cellulose?

• beta 1,4 glycosidic bonds

• some molecules are rotated 180 degrees for the hydroxyl group on C₁ to interact with the one on C₄

what is the test for reducing sugars like glucose, galactose, fructose or maltose?

• put the same volume of each sample into a different boiling tube, then use a dropping pipette to add a set volume of Benedict’s reagent to each one

• place all the boiling tubes into a water bath for four minutes (taking notes after each two minutes)

• positive result: a brick-red precipitate forms (because the soluble blue copper(II) oxide has been reduced by the sugar, forming insoluble red copper(I) oxide)

• negative result: the solution remains clear and blue

what is the test for non-reducing sugars like sucrose?

• put the same volume of each sample into a different boiling tube and use a dropping pipette to add Benedict’s reagent

• place all the boiling tubes into a water bath for four minutes and see if there are reducing sugars present

• use a dropping pipette to add a small set volume of HCl to fresh samples and mix

• neutralise the acid by slowly adding sodium hydrogencarbonate, stirring with a glass rod after each addition

• check the pH by dipping indicator paper into the sample (not the foam on top): if it is now neutral or slightly alkaline, stop adding sodium hydrogencarbonate

• using a dropping pipette, add a set volume of Benedict’s reagent to each one and record your observations

• place all the boiling tubes into a water bath for four minutes (taking notes after each two minutes)

• positive result: (having already received a negative result for the reducing sugars test) a brick-red precipitate forms (because the HCl hydrolysed the glycosidic bonds in the carbohydrate, leaving monosaccharides that can reduce the soluble blue copper(II) oxide to form insoluble red copper(I) oxide)

• negative result: the solution remains clear and blue

what do cellulose chains form when they make hydrogen bonds with each other?

microfibrils

what do microfibrils form when they join?

macrofibrils

what do macrofibrils form when they join?

strong, insoluble cellulose fibres