2.1.2 - Biological Molecules

water is a polar molecule. what does this mean?

It has an uneven distribution of charge within the molecule H atoms more positive than O atoms causing one end of the molecules to be positive than the other

water is a metabolite. what does this mean?

It is necessary for metabolism, condensation and hydrolysis used in forming/breaking chemical bonds

what is water's purpose in reactions?

acts as a solvent

what is a covalent bond?

the sharing of electron pairs between atoms.

how does a hydrolysis reaction occur?

when a molecule is split into two smaller molecules with the addition of water.

how does a condensation reaction occur?

when two molecules are joined together with the removal of water.

what is a monomer?

a small molecule which binds to many other identical molecules to form a polymer.

what is a polymer?

a large molecule made from many smaller molecules called monomers.

state the 3 main biological molecules studied in this chapter, along with the elements found in those molecules, and its respective monomer and polymer.

carbohydrates - C, H, O - monosaccharides - polysaccharides
proteins - C, H, O, N, S - amino acids - polypeptides and proteins
nucleic acids - C, H, O, N, P - nucleotides - DNA and RNA

what are hydrogen bonds and how do they occur?

a weak interaction that can occur wherever molecules contain a slightly negatively charged atom bonded to a slightly positively charged hydrogen atom.

what are the 10 properties of water

Liquid between 0 -100°C
High Specific Heat Capacity (4200Jkg-1°C)
High Latent Heat of Vaporisation (2260Jg-1)
Density: ice is less dense than liquid water, and aquatic organisms are the same density as the water they move around in.
High surface tension.
Strong cohesion between water molecules.
Strong adhesion to surfaces.
Low viscosity: ability to flow.
Water is 'The universal solvent'
High transmission of visible light.

explain why water is a liquid at room temperature.

the hydrogen bonds between water molecules make it more difficult for them to escape to become a gas.

state 4 benefits of water being a liquid.

1. provides habitats for aquatic organisms.
2. forms a major component of the tissue in living organisms.
3. provides a reaction medium for chemical reaction.
4. provides an effective transport medium, e.g. in blood and vascular tissue.

explain why ice is less dense than water.

water becomes more dense as it gets colder until about 4 C. From 4 C to freezing point, due to its polar structure, the water molecules align themselves in a structure which is less dense than liquid water (open lattice).

state 2 benefits of ice being less dense than a water.

1. aquatic organisms have a stable environment in which to live through the winter.
2. ponds and other bodies of water are insulated against extreme cold. the layer of ice reduces the rate of heat loss from the rest of the pond.

explain how water is a good solvent for many substances found in living things.

as water is polar, the positive and negative parts of the water molecules are attracted to the negative and positive parts of the solute. the water molecules cluster around these charged parts of the solute molecules/ions, and will help to separate them and keep them apart. They are then dissolved so a solution is formed.

state 2 benefits of water being a good solvent.

1. molecules and ions can move around and react together in water.
2. molecules and ions can be transported around living things whilst dissolved in water.

explain how cohesion and surface tension in terms of water works.

cohesion - where the hydrogen bonding between the water molecules pull them together (e.g. a drop of water on a flat surface is spherical)

surface tension - where the water molecules at the surface are all hydrogen-bonded to the molecules beneath them, and hence more attracted to the water molecules beneath than to the air molecules above. thus, the surface of the water contracts and it gives the surface of the water an ability to resist force applied to it.

state 2 benefits of cohesion and surface tension.

1. columns of water in plant vascular tissue are pulled up the xylem tissue together from the roots.
2. insects like pond-skaters can walk on water.

explain why water has a high specific heat capacity.

water molecules are held together tightly by hydrogen bonds. a lot of heat is energy is required to increase their kinetic energy and temperature. this means that water does not heat up or cool down easily. the specific heat capacity of energy to raise the temperature of 1 kg of water by 1 C is 4.2 kJ.

state 2 benefits of water having a high specific heat capacity.

1. living things, e.g. prokaryotes/eukaryotes, need a stable temperature for enzyme-controlled reactions to happen properly.
2. aquatic organisms need a stable environment in which to live.

explain why water has a high latent heat of vaporisation.

the molecules are held together quite tightly by hydrogen bonds so a relatively large amount of energy is needed for water molecules to evaporate.

state 1 benefit of water having a high latent heat of vaporisation.

helps cool living things and keep their temperature stable (e.g. mammals cooled when sweat evaporates and plants cooled when water evaporates from mesophyll cells).

what is the general formula for carbohydrates?

C n H 2n O n

what are the three main functions of carbohydrates?

1. a source of energy (e.g. glucose)
2. a store of energy (e.g. starch/glycogen)
3. structural units (e.g. cellulose in plants and chitin in insects)

what are monosaccharides?

the simplest carbohydrates, monomers
simple sugars

what are monosaccharides particularly important in?

they are particularly important in living things as a SOURCE of energy.

why are monosaccharides well suited to this role?

they are well suited to this role because of the large number of C-H bonds.

describe how monosaccharides taste like and their solubility.

they are sugars so they taste sweet.
they are soluble in water but insoluble in non-polar solvents.

what are three forms that monosaccharides can exist as?

straight chained
ring
cyclic

what bond do monosaccharides form?

glycosidic bonds

what do monosaccharides join to make?

disaccharides or polysaccharides.

glucose can exist as isomers. what are isomers?

molecules with the same formula but whose atoms are arranged differently in space.

how are disaccharides made?

when two monosaccharides are linked together

State what is named when the following monosaccharides are joined together:
a-glucose + a-glucose = .......
a-glucose + fructose =.......
b-glucose + a-glucose = ......
b-glucose + b-glucose = ......

a-glucose + a-glucose = MALTOSE
a-glucose + fructose = SUCROSE
b-glucose + a-glucose = LACTOSE
b-glucose + b-glucose = CELLULOSE

when monosaccharides join together, what is formed?

a condensation reaction occurs to form a glycosidic bond

explain how a glycosidic bond is formed when monosaccharides join together

two hydroxyl groups line up next to each other, from which a water molecule is removed. this leaves an oxygen atom acting as a link between the two monosaccharide units.

how are disaccharides broken into monosaccharides?

by a hydrolysis reaction, which requires the addition of water. The water provides a hydroxyl group (-OH) and a hydrogen (H) which help the glycosidic bond to break.

what is the molecular formula of glucose (both alpha and beta)?

C6H12O6

what is the role of a-glucose in the body?

energy source
component of starch and glycogen, which act as energy stores

what is the role of b-glucose in the body?

energy source
component of cellulose, which provides structural support in plant cell walls.

what is the molecular formula of ribose?

C5 H10 O5

what is the role of ribose in the body?

component of ribonucleic acid (RNA), ATP and NAD

what is the molecular formula of deoxyribose?

C5 H10 O4 (one less oxygen atom than ribose, hence DEoxyribose)

what is the role of deoxyribose in the body?

component of deoxyribonucleic acid (DNA)

what type of sugar is both alpha and beta glucose?

hexose

what type of sugar is both ribose and deoxyribose?

pentose

what are polysaccharides?

large macromolecules formed from monosaccharides

what are homopolysaccharides? Give one example.

polysaccharides made solely of one kind of monosaccharide.
example: starch

what are heteropolysaccharides?

polysaccharides made of more than one monosaccharide.
example: hyaluronic acid

if you join lots of glucose molecules together into polysaccharides, what can you create?

a store of energy

how do plants store energy?

plants store energy as starch (amylose and amylopectin) in chloroplasts

how do humans store energy?

humans store energy as glycogen in cells of the muscle and liver

give 4 reasons why polysaccharides form good stores of monosaccharides.

1. glycogen and starch are compact so they do not occupy a large amount of space.

2. polysaccharides hold glucose molecules in chains so they can be easily 'snipped off' from the end of the chain by hydrolysis when required for respiration.

3. branched chains, such as amylopectin, tend to be more compact. they also offer the chance for lots of glucose molecules to be snipped off by hydrolysis at the same time, when lots of energy is required quickly.

4. polysaccharides are less soluble in water than monosaccharides. if many glucose molecules did dissolve in the cytoplasm, the water potential would reduce and excess water would diffuse in. they are less soluble because not only of their size but because regions which could hydrogen-bond with water are hidden away inside the molecule

what is amylose?

it's a type of starch in plants. long chain of a-glucose molecules. has glycosidic bonds between carbons 1-4.

describe the structure of amylose. explain its properties due to its structure.

amylose coils into a spiral shape with hydrogen bonds holding the spiral in place. hydroxyl groups on carbon-2 are situated on the inside of the coil, making the molecule less soluble and allowing hydrogen bonds to form to maintain the coil's structure.

what is amylopectin?

type of starch in plants. similar to amylose in that it has glycosidic bonds between carbon 1-4 but it also has branches formed by glycosidic bonds between carbon 1-6.

describe the structure of amylopectin.

coils into a spiral shape, held together with hydrogen-bonds but with branches emerging from the spiral.

what is glycogen?

like amylopectin with glycosidic bonds between carbon 1-4 with branches formed by glycosidic bonds between carbon 1-6.

describe the structure of glycogen.

he 1-4 bonded chains tend to be smaller than in amylopectin, so glycogen has less tendency to coil. however, it has more branches which makes it more compact. It is also easier to remove monomer units as there are more ends.

what is cellulose? how is cellulose made?

forms the cell walls of plants. it is a tough, insoluble and fibrous substance.It is a homopolysaccharide made from long chains of up to 15K B-glucose molecules bonded together through condensation reactions to form glycosidic bonds.

what is the difference in the general structure between cellulose chains and a-glucose.

cellulose chains are straight and lie side by side.

give 2 reasons why cellulose chains are straight in comparison to a-glucose molecules.

1. the hydrogen and hydroxyl groups on carbon 1 are inverted in B-glucose. so every other B-glucose molecule in the chain is rotated by 180 degrees. so the B 1-4 glycosidic bond helps to prevent the chain spiralling.

2. hydrogen bonding between the rotated B-glucose molecules in each chain gives the chain additional strength, preventing the spiralling.

when 60 to 70 cellulose chains are bound together, what do they form?

microfibrils

how long are microfibrils in terms of diameter?

10-30 nm

what is formed when lots of microfibrils (i.e. 400) bundle together?

macrofabrils which are embedded in pectins to form plant cell walls.

why is cellulose an excellent material for plant cell walls?

1. microfibrils and macrofabrils have very high tensile strength, both because of the strength of the glycosidic bonds but also because of the hydrogen bonds between chains.

2. macrofibrils run in all directions, like a mesh, criss-crossing the wall for extra strength.

3. it is difficult to digest cellulose because the glycosidic bonds between the glucose molecules are less easy to break.

give 4 reasons as to why the properties of cellulose help the plant cell wall to do its job.

1. plants do not have a rigid skeleton so each cell needs to have strength to support the plant as a whole.

2. there is space between macrofibrils for water and mineral ions to pass on their way into/out of the cell, making the cell wall fully permeable.

3. the cell wall has high tensile strength which prevents plant cells from bursting when they are turgid, helping to support the plant as a whole.

4. the macrofibril structure can be reinforced with other substances for extra support or to make cell walls waterproof (e.g. cutin and suberin).

describe what lipids are.

lipids contain large amounts of carbon and hydrogen, and smaller amounts of oxygen.
they are insoluble in water because they're non-polar. they do not attract water molecules but can dissolve in alcohol.

what are the three most important lipids in living things?What are they examples of?

1. Triglycerides
2. Phospholipids
3. Steroids

they are examples of macromolecules

describe the structure of a triglyceride.

made up of glycerol and fatty acids.

what are essential fatty acids?

linoleic acid and linolenic acid (omega 3 and omega 6)

describe the structure of glycerol.

has three carbon atoms.
an alcohol: it has 3 -OH groups.
partially why the final structure is called triglycerides.

describe the structure of fatty acids.

a long hydrocarbon chain with a carboxyl group attached to the end (often 15-20 carbon atoms long)

why are fatty acids 'acids'?

the carboxyl group ionises into H(+) and a -COO(-) group. this structure is therefore an acid because it can produce free H+ ions.

if a fatty acid is saturated, what does that mean?

there are no C=C bonds in the molecules.

if a fatty acid is unsaturated, what does that mean?

there is a double bond between two of the carbon atoms instead. this means fewer hydrogen atoms can be bonded to the molecule.

what is the difference between a monounsaturated fatty acid and a polyunsaturated acid?

monounsaturated fatty acid: a single C=C bond is present (e.g. oleic acid)
polyunsaturated fatty acid: more than one C=C bond is present (e.g. linoleic acid)

why do unsaturated fatty acids have lower melting points than that of saturated fatty acids?

the C=C bonds in unsaturated fatty acids change the shape of the hydrocarbon chain, giving it a kink where the double bond is. because these kinks push the molecules apart slightly, it makes them more fluid.

how many fatty acids are bonded to the one glycerol molecule in a triglyceride?

three

describe how an ester bond is formed in triglycerides.

a condensation reaction happens between the -COOH group of the fatty acid and the -OH group of the glycerol. because there are three -OH groups, three fatty acids will bond (hence 'triglyceride').

a water molecule is also produced. the covalent bond formed is known as an ester bond.

what are 5 functions of triglycerides?

1. Energy source: triglycerides can be broken down in respiration to release energy and generate ATP. the ester bonds are hydrolysed and then both glycerol and the fatty acids can be broken down completely to carbon dioxide and water.

2. Energy store: triglycerides are insoluble in water so they can be stored without affecting the water potential of the cell. 1g of fat releases twice as much energy as 1g of glucose. this is because lipids have a higher proportion of hydrogen atoms than carbohydrates and almost no oxygen atoms.

3. insulation: adipose tissue is a storage location for lipid in whales (blubber). lipid in nerve cells acts as an electrical insulator. Animals preparing for hibernation store extra fat.

4. buoyancy: fat is less dense than water so it is used by aquatic mammals to help them stay afloat.

5. protection: humans have fat around delicate organs to act as a shock absorber. the peptidoglycan cell wall of some bacteria is covered in a lipid-rich outer coat.

describe the structure of phospholipids.

they have the same structure as triglycerides, except that one of the fatty acids is replaced by a phosphate group.

where does the condensation occur in a phospholipid to form an ester bond?

a condensation reaction between an -OH group on a phosphoric acid molecule (H3 PO4) and one of the three -OH groups on the glycerol forms an ester bond.

describe the behaviour of phosopholipids in water.

when surrounded by water, the phosphate group has a negative charge, making it polar (attracted to water). however, the fatty acid tails are non-polar so are repelled by water.

which part of the phospholipids is hydrophilic and hydrophobic?

the phosphate heads are hydrophilic (water-loving).
the fatty acid tails are hydrophobic (water-hating).

why are phospholipids amphipathic?

they have a hydrophilic head and a hydrophobic tail

what kind of structure do phospholipids organise themselves as when in water?

micelles - tiny balls with the tails tucked away inside, and the head pointing outwards into the water.

how do amphipathic phospholipids arrange themselves as when forming membranes?

as a PHOSPHOLIPID BILAYER (a row of ampthipathic phospholipids on one side and a row beneath it, with fatty acid tails hidden inwards)

explain, due to the structure of phospholipids, why the cell membrane is stable.

the individual phospholipids are free to move around in their layer, but will not move into any position where their hydrophobic tails are exposed to water.

what are the benefits of having a membrane that is selectively permeable?

tt is only possible for small and non-polar molecules to move through the tails in the bilayer, e.g. oxygen/CO2. This lets the membrane control what goes IN and OUT of the cell, and keeps it functioning properly.

Describe cholesterol (4)

- it is a steroid alcohol (sterol), a type of lipid which is not made from glycerol or fatty acids

- consists of four carbon-based rings or isoprene units.

- small and hydrophobic molecule, so it can sit in the middle of the hydrophobic part of the bilayer

- regulates the fluidity of the membrane, preventing it from becoming too fluid or stiff.

- production of vitamin d, bile and steriod hormones

where is cholesterol made in animals?

cholesterol is mainly made in the liver in animals.

where is cholesterol made in plants?

plants also have a cholesterol derivative in their membranes, called stigmasterol (it has a double bond between C-22 and C-23).

name 3 steroid hormones that cholesterol makes.

1. Testosterone
2. Oestrogen
3. Vitamin D

what are proteins?

large polymers comprised of long chains of AMINO ACIDS.

name 3 functions that the properties of proteins enable.

1. They form STRUCTURAL COMPONENTS of animals in particular, e.g. muscles made from protein.

2. Their tendency to adopt specific shapes make proteins important as ENZYMES, ANTIBODIES and some HORMONES.

3. Membranes have protein constituents that act as carriers and pores for active transport across the membrane and facilitated diffusion.

animals can make some amino acids, but must ingest others. what are these amino acids called?

essential amino acids

plants can make ALL the amino acids they need, but only if....

...they can access fixed nitrogen (e.g. nitrate)

how many of the 500 amino acids are PROTEINOGENIC (found in proteins)?

20