Topic 3: Organic and Biological Chemistry

Question 1

What are hydrocarbons? What are the main families and their suffixes?

Answer 1

The simplest class of organic compounds, composed of only carbon and hydrogen
Alkanes - contain only single bonds between carbon atoms (-ane)
Alkenes - contain double bonds between carbon atoms (-ene)
Alkynes - contain triple bonds between carbon atoms (-yne)

Question 2

In order, state the prefixes of hydrocarbons from 1-10 carbons in the main carbon chain

Answer 2

Meth-, eth-, prop-, but-, pent-, hex-, hept-, oct-, non-, dec-

Question 3

How do secondary forces affect the boiling (and melting) points of organic compounds?

Answer 3

Non-polar organic compounds only experience dispersion forces, the weakest form of secondary interactions which don’t require a lot of energy to overcome, so they have low boiling points (compared to molecules of similar mass)
Some polar organic compounds are able to form hydrogen bonds, the strongest form of secondary interactions, requiring more energy to separate the molecules and hence having a higher boiling point

Question 4

How does molar mass affect the boiling point (and melting) of an organic compound?

Answer 4

Larger molecules experience greater dispersion forces, requiring more energy to overcome them and separate the molecules, having a higher boiling point than molecules of similar polarity
Greater molar mass weakens the polarity of polar functional groups, though, due to increased size making any dipole-dipole interactions weaker, making them less soluble

Question 5

What affects the solubility of organic compounds?

Answer 5

Organic compounds are more soluble in water if they experience stronger secondary forces with them, so its size and number of polar functional groups affect how soluble it is
As the number of polar groups increases, so does solubility
As size decreases, its solubility increases as it is easier for water molecules to fully surround it and dissolve it

Question 6

How does the branching of an organic compound affect its melting point and solubility?

Answer 6

Having branches weakens the strength of dispersion forces, making it more difficult for the molecules to line up and stack neatly, resulting in relatively lower melting and boiling points.
Due to their larger mass and awkward branching, it is harder for water molecules to fully surround them, decreasing solubility

Question 7

What are alcohols and what are the three main types?

Answer 7

Alcohols are compounds that have a hydroxyl functional group/s (-OH) attached to a carbon
The three main types depend on the hydroxyl’s position.
Primary - the carbon connected to the hydroxyl group is connected to one other carbon
Secondary - the carbon is connected to two other carbons
Tertiary - the carbon is connected to three other carbons

Question 8

How do you name alcohols?

Answer 8

They use the parent alkane’s name and have the suffix -ol
If there is one hydroxyl, the -e is removed from the parent alkane and is replaced with -ol.
If there is more than one hydroxyl, the -e is kept, the hydroxyl’s positions are stated, and the suffix -diol or -triol is added

Question 9

What can acidified dichromate do to alcohols? Explain.

Answer 9

Acidified dichromate (Cr2O7(2-)) can be used to oxidise alcohols to form other compounds.
The position of the hydroxyl group determines what type of compound the alcohol is converted to.
A primary alcohol is oxidised into an aldehyde, which can then be converted to a carboxylic acid
A secondary alcohol is oxidised into a ketone, which cannot oxidise futher
Tertiary alcohols cannot be oxidised
When dichromate ions are reduced to chromate(III) ions, the solution changes colour from orange to green, allowing primary and secondary alcohols to be distinguished from tertiary alcohols

Question 10

What are aldehydes and ketones? What are the differences between them?

Answer 10

They are organic compounds that contain carbonyl functional groups (C=O)
The carbonyl groups of aldehydes are terminal, whilst those of ketones are non-terminal

Question 11

Please explain the aldehyde functional group and how you name aldehydes.

Answer 11

The aldehyde functional group includes the oxygen, carbon, and its hydrogen to indicate it being terminal.
When naming hydrocarbons, the -e is removed from the parent alkane and replaced with -al, unless it contains two aldehyde functional groups, in that case the -e is included and -dial is written at the end.
(You do not need to number the functional group/s as they will always be terminal)
The condensed structural formula for aldehyde functional groups is CHO

Question 12

How do you prepare aldehydes?

Answer 12

Aldehydes are prepared by the controlled oxidation of primary alcohols, with an oxidising agent being added drop by drop to a heated alcohol mixture
This will oxidise to form an aldehyde, which will have a lower boiling point as it will exhibit dipole-dipole interactions instead of the stronger hydrogen bonds, evaporating, preventing further oxidation into a carboxylic acid
This is then caught in a condenser and transferred to a beaker in an ice bath that prevents loss from evaporation

Question 13

Please explain the ketone functional group and how you name ketones.

Answer 13

The ketone functional group includes the carbon and oxygen and two Rs to indicate it being non-terminal
When naming ketones, the -e is removed from the parent alkane and replaced with -one, unless it contains multiple, in that case the -e is included and -dione or -trione is written at the end
These must be numbered, with the functional group/s having the lowest number/s possible
The condensed structural formula for ketone functional groups is written with CO

Question 14

Aldehydes can undergo oxidation in acidic conditions with acidified dichromate, but can also oxidise in alkaline conditions. How and with what chemical? Why is this useful?

Answer 14

Aldehydes can undergo oxidation under alkaline conditions with Tollens’ reagent (Ag(NH3)2), which results in carboxylate anions being formed instead of carboxylic acid, and also a silver mirror forms on the surface of the reaction vessel
This can be used to distinguish between aldehydes and ketones

Question 15

State the table of if this alcohol/aldehyde/ketonecan be oxidised by either of the two oxidising agents

Answer 15

(Acidified dichromate and then Tollens’ reagent)
Primary alcohols: Y N
Secondary alcohols: Y N
Tertiary alcohols: N N
Aldehydes: Y Y
Ketones: N N

Question 16

What are carboxylic acids?

Answer 16

Weak organic acids found in nature, containing a carboxyl functional group, an extremely polar group made up of a carbonyl and hydroxyl group

Question 17

How do you name carboxylic acids?

Answer 17

Remove the -e from the parent alkane and replace it with -oic acid
(you do not need to number the carboxyl group’s position as it is always terminal)
If there are two carboxyl functional groups, the -e is included, and di is added to the suffix

Question 18

Compare the physical properties of carboxylic acids to other organic compounds

Answer 18

Due to the high potential of the carboxyl group to form hydrogen bonds (as well as dipole-dipole interactions), carboxylic acids have significantly higher melting and boiling points than other organic compounds with similar molecular masses
As they are more polar, they are also more soluble in water than other polar organic compounds with similar molecular masses
However, solubility decreases as the carbon chain length increases as it becomes harder for polar water molecules to get around the non-polar carbon chain to surround the whole molecule

Question 19

In what ways do carboxylic acids react?

Answer 19

They are a weak acid due to the hydroxyl group, which can lose the H+, which bonds with water to form hydronium, leaving behind a carboxylate anion. However, as a weak acid, fewer than approx. 5% of molecules are dissociated at any one time.
The following still apply to carboxylic acids, even ones that aren’t soluble:
Acid + metal hydroxide -> salt + water
Acid + bi/carbonate -> salt + water + carbon dioxide
Acid + metal -> salt + hydrogen gas

Question 20

Discuss the solubility of carboxylate salts in comparison to carboxylic acids

Answer 20

Sodium and potassium carboxylate salts are always soluble in water
Carboxylic acids have partial charges due to the polar functional group, allowing for hydrogen bonding, but gain a full negative charge when dissociated into a carboxylate salt, allowing for stronger ion-dipole interactions, increasing solubility

Question 21

What are esters and how are they formed?

Answer 21

Esters are organic compounds that contain the ester functional group
They are prepared by reacting a carboxylic acid with an alcohol in the presence of an acid catalyst (condensation reaction)
The acid’s hydroxyl and the hydrogen of the alcohol’s hydroxyl form a water molecule, resulting in the two molecules bonding to form an ester functional group written as -COO-
Esterification is a reversible equilibrium reaction that favours the backward reaction, but by increasing the concentration of alcohol, the forward reaction is favoured, producing a higher yield of ester

Question 22

How do you name esters?

Answer 22

Esters are composed of two parts: the carboxylate anion (which includes the alcohol’s oxygen), and the alkyl group
When naming, the -anol of the alcohol is replaced with -yl, indicating the alkyl group is a hydrocarbon fragment
The second part of the name is just the carboxylate anion (carbon chain and suffix -oate)

Question 23

What is a polyester?

Answer 23

It is a polymer (poly=many) formed when a diol and dicarboxylic acid react
One diol monomer and one dicarboxylic acid monomer form a repeating unit
This is a condensation reaction, producing one water for each ester functional group

Question 24

What does it mean to ‘heat under reflux’ and what is its purpose?

Answer 24

Reflux means ‘re-flow’
Even with an acid catalyst, ester formation is slow, so heat is used to speed up the reaction
However, the reactants and prodcutSS are usually volatile, so the heating has to be controlled with a reflux apparatus
When the mixture boils, the vapours rise into the condenser and condense, falling back into the flask (re-flowing) and return to the reaction mixture to elicit a greater yield
It also allows for the mixture to be heated for an extended period without losing any compounds and maintaining optimal temperatures
Boiling should be kept to a simmer, with the flask being filled halfway and the vapours reaching only halfway up the condenser to prevent vapours from escaping

Question 25

What is hydrolysis?

Answer 25

Hydrolysis is a reaction in which a compound is broken down by water

Question 26

Compare the products of acid hydrolysis and alkaline hydrolysis of esters, and explain why and acid/alkali is required.

Answer 26

Esters can be hydrolysed, which occurs more quickly when it is refluxed with a strong acid or alkali
If an ester is refluxed with water using a strong acid catalyst, the original alcohol and carboxylic acid are formed, which is reversible
If an ester is refluxed with water and a strong alkali, the original alcohol and a carboxylate anion are formed, which is irreversible as the hydrogen of the carboxylic acid’s hydroxyl has been taken by the alkali

Question 27

Discuss the physical properties of esters

Answer 27

Unlike alcohols and carboxylic acids, ester molecules do not have hydroxyl groups and so cannot form hydrogen bonds with each other, instead experiencing dipole-dipole interactions, meaning they have significantly lower boiling points than alcohols and carboxylic acids with similar molar masses
As esters are polar, they can form hydrogen bonds with water molecules, making them soluble. However, solubility decreases with increasing carbon chain length, as the overall molecule becomes more non-polar

Question 28

What are amines, how are they classified, and how do you name them?

Answer 28

Amines are organic compounds that contain the amino functional group (which is a carbon bonded to a nitrogen with two hydrogens and a lone electron pair)
Amino groups are derivatives of ammonia, NH3
Primary amines have the nitrogen bonded to one carbon, R-NH2
Secondary amines have the nitrogen bonded to two carbons, R2-NH
Tertiary amines have the nitrogen bonded to three carbons, R3-N
(you only have to name primary amines)
The -e from the parent alkane is removed, the amino group is numbered, and then the suffix -amine is used
If there are two or three amino groups, the -e is kept, the amino acid groups are numbered, and the suffix -diamine or -triamine is used

Question 29

Discuss the physical properties of amines

Answer 29

N-C and N-H bonds are both polar, but due to the lower electronegativity, N-C bonds are weaker than C=O bonds
They can still experience dipole-dipole interactions and hydrogen bonds, having higher boiling points than other alkanes of similar molar mass, but as carbon-chain length increases, solubility decreases

Question 30

Discuss the BASE properties of amines

Answer 30

Amines are weak bases, meaning they incompletely ionise in aqueous solution
The lone electron pair can accept protons (H+ ions) to form a protonated amine
When amines react with acids, they form ionic salts

Question 31

How are amides formed? What is their functional group? How are they classified

Answer 31

Amides are formed by the condensation reaction between a carboxylic acid and an amine
When they react, the acid’s hydroxyl and the nitrogen’s hydrogen form water, and the nitrogen essentially takes the hydroxyl’s place
YOU DO NOT HAVE TO NAME AMIDES.
The amide functional group comprises of the carbonyl group (C=O) and the nitrogen and its hydrogen, as well as R and R’ on either end
Primary amides have nitrogen bonded to one carbon
Secondary amides have nitrogen bonded to two carbons
Tertiary amides have nitrogen bonded to three carbons

Question 32

Discuss the physical properties of amides

Answer 32

The amide functional group is polar (C=O and N-H bond/s) and can form hydrogen bonds with water and each other (thanks to the N-H bond/s), meaning they have a relatively high boiling point and are relatively soluble compared to alkanes of similar molar mass
Whilst small amides are soluble, solubility decreases as the length of carbon chain/s increase

Question 33

What are polyamides?

Answer 33

Polyamides are polymers formed in the condensation reaction between a dicarboxylic acid and a diamine

Question 34

Compare the products of acid hydrolysis and alkaline hydrolysis of amides

Answer 34

Amides can undergo hydrolysis like esters but require more vigorous conditions
If an amide is refluxed with a water and an acid, the original carboxylic acid and a protonated amine are formed, which is reversible
If an amide is refluxed with water and a strong base, the products are a carboxylate anion and an amine. This is not reversible as the carboxylic acid’s hydroxyl loses its hydrogen to the base

Question 35

What are proteins? What are they made up of?

Answer 35

Proteins are natural polymers that carry out many functions in the body
Monomers of proteins are called amino acids

Question 36

Of the 20 amino acids, the human body can only synthesise 10. What are the other 10 called?

Answer 36

The other 10 must be ingested and are called essential amino acids

Question 37

Explain the structure of amino acids

Answer 37

Amino acids contain a carboxyl group (-COOH), an amino group (-NH2), and ‘R’ group called a side chain, and a hydrogen atom (bonded to another carbon)
The only thing that differs between the 20 amino acids is their side chain
These side chains determine the overall polarity of the amino acids
Polar side chains contain nitrogen and oxygen atoms (etc.) and are hydrophilic
Non-polar side chains contain mostly carbon and hydrogen atoms and are hydrophobic

Question 38

What can amino acids do in acidic and basic solutions?

Answer 38

The carboxyl group is acidic and can donate an acidic hydrogen, and the amino group is basic and can accept a proton, making amino acids amphiprotic
In an acidic solution, the amino group accepts an H+ and forms a protonated amine
In an alkaline solution, the carboxyl group donates its acidic hydrogen and forms a deprotonated amine

Question 39

What do amino acids do in neutral solutions?

Answer 39

In a neutral solution, the carboxyl and amino groups of an amino acid react with each other; the carboxyl group donates a proton to the amino group
This forms a zwitterion: a molecule with positively and negatively charged functional groups, but no overall charge
Due to their ionic dipole, they have similar properties to salts, including high melting points and being generally soluble in water

Question 40

How can amino acids react with each other?

Answer 40

Amino acids undergo condensation reactions to form a protein polymer chain
The remaining amino acids in the chain are called amino acid residues
The amino group and the carboxyl group of two amino acids react to form an amide group (which includes the C=O) known as a peptide bond
Two amino acids = dipeptide, three amino acids = tripeptide, >20 amino acids = polypeptide

Question 41

Explain the four levels of structure in a protein

Answer 41

The primary structure of a protein refers to is amino acid sequence, which is responsible for the protein’s unique shape, affecting the various bonds that will form
The secondary structure of a protein is the initial folding of the chain into alpha-helices and beta-pleated sheets determined by hydrogen bonding between amino groups and carbonyl groups
The tertiary structure of a protein is a more complex folding of the protein upon itself, its overall 3D shape, created by the side chains interacting to form primary bonds (ionic or covalent) and secondary bonds (ion-dipole, dipole-dipole, hydrogen bonding, dispersion forces)
A quaternary structure is the combination of two or more polypeptide chains

Question 42

What is so important about a protein’s structure?

Answer 42

The 3D structure of a protein is critical to its function, but if it is changed such that it can no longer function, it is denatured

Question 43

How does temperature affect protein structure?

Answer 43

When proteins are heated to high temperatures, the thermal energy is able to break the secondary and primary bonds between amino acids and their side chains, disrupting the structure of the protein, resulting in its inability to function, denaturing it

Question 44

How does pH affect protein structure?

Answer 44

Many amino acids side chains are acidic or basic, so they are able to donate or accept protons
In highly acidic solutions, they may become protonated, and in highly basic solutions, they may become deprotonated, affecting the charge of the side chains and therefore their interactions, disrupting the protein’s structure which affects its function, denaturing it

Question 45

How do you define a carbohydrate? How are they classified?

Answer 45

They are formally defined as polyhydroxyaledhydes (aldoses), polyhydroxyketones (ketoses), or compounds that yield either of those when hydrolysed
‘Saccharides’, or sugars, can be classified as monosaccharides, disaccharides, or polysaccharides, depending on how many simple sugar units make up the molecule
All carbohydrates have the general formula Cx(H2O)y

Question 46

Describe monosaccharides

Answer 46

Molecular formula: C6H12O6
In an aqueous solution, they exist in an equilibrium between a chain form and a cyclic (ring) form - the cyclic form is heavily favoured
The ring forms do not contain aldehyde or ketone groups but are still carbohydrates as they yield aldoses or ketoses
Monosaccharides are crystalline solids
They have high melting and boiling points due to the hydrogen bonding between hydroxyl groups, which also allow them to form hydrogen bonds with water, making them very soluble

Question 47

What are functional group isomers?

Answer 47

Functional group isomers are molecules that have the same molecular formula but different functional groups in their structures

Question 48

Describe disaccharides

Answer 48

Molecular formula: C12H22O11
Disaccharides contain two monosaccharide monomers joined by a glycosidic bond, which is an individual oxygen atom that bridges them together, which is produced through a condensation reaction
Like monosaccharides, disaccharides have high melting and boiling points due to the hydrogen bonding between hydroxyl groups
Many, but not all, are soluble in water, although they are generally less soluble than monosaccharides due to their higher molar masses

Question 49

Describe polysaccharides

Answer 49

General formula: (C6H10O5)n
Polysaccharides are polymers consisting of many monosaccharide units joined together by glycosidic bonds
Due to their large size, polysaccharides are densely tangled together and form strong hydrogen bonds with each other, meaning water molecules cannot completely separate them, making them insoluble
However, since hydrogen bonding does occur between them, polysaccharides can absorb a significant amount of water
Heat can disrupt the polymer chains, so some polysaccharides can dissolve in boiling water

Question 50

Describe the structure of triglycerides

Answer 50

Triglycerides are made from one molecule of propane-1,2,3-triol , called glycerol, and three long-chain carboxylic acids, called fatty acids
The three hydroxyl groups of glycerol allow it to bond to three fatty acid molecules
The fatty acids have unbranched chains and can be saturated (only single bonds between carbon atoms) or unsaturated (mono or poly - one or more than one double or triple bond between carbon atoms)
When a glycerol reacts with three carboxylic acids, it forms three esters, hence the name triester or triglyceride
This is a condensation reaction that forms three water molecules per triglyceride (one for each ester group)

Question 51

Describe the products of hydrolysing triglycerides in acidic and alkaline conditions

Answer 51

Like other esters, triglycerides can be hydrolysed with an acid or alkali catalyst
In an acidic solution, triglycerides are hydrolysed to produce glycerol and free fatty acids. This process is reversible
In an alkaline solution, triglycerides are hydrolysed to produce glycerol and carboxylate anions. This process is not reversible

Question 52

Describe the physical properties of triglycerides

Answer 52

In a saturated triglyceride, the fatty acid’s chains have a tetrahedral arrangement, allowing the chains to lie parallel to each other, stacking neatly, which increases the strength of dispersion forces, resulting in them often being solids at room temperature (fats)
On the other hand, in an unsaturated triglyceride, the fatty acid chain’s carbons have a combination of tetrahedral and trigonal planar arrangements, with the double bonds also forcing the carbon chains to twist at points, resulting in the hydrocarbon chains not stacking as neatly or compactly together (kinks), resulting in weaker dispersion forces and hence lower melting points, so they are usually liquids at room temperature (oils)

Question 53

How can you determine the degree of saturation of a fatty acid?

Answer 53

The general formula for a saturated fatty acid is CnH2nCOOH
This can be used to distinguish if a fatty acid is saturated or unsaturated
If it is unsaturated, the number of missing hydrogens divided by two is how many carbon-carbon double bonds there are (one double bond displaces two hydrogens)

Question 54

What kinds of fatty acids can small diatomic halogen molecules such as bromine and iodine react with?

Answer 54

Unsaturated fatty acids (reacting with the C=C groups)

Question 55

Describe hydrogeneation

Answer 55

Liquid oil triglycerides (unsaturated) can be converted to solid fats (saturated) via hydrogenation, where hydrogen is added across C=C double bonds
This requires hydrogen gas, high temperature, high pressure, and a metal catalyst

Question 56

What is produced after a triglyceride is hydrolysed in alkaline solution? Describe its structure and what it does in water

Answer 56

When triglycerides undergo hydrolysis in alkaline solution, carboxylate anions, or ‘fatty acid anions’ are formed
These are composed of a non-polar hydrocarbon ‘tail’ which is hydrophobic as it cannot form secondary interactions with water, and a polar carboxylate ‘head’ which is hydrophilic as it can form strong ion-dipole interactions with water
When these carboxylate anions are in water, the non-polar hydrocarbon tails cluster together, and the polar anionic heads face outwards, forming a micelle

Question 57

What is the main application of fatty acid anions?

Answer 57

Carboxylates can be used to wash away non-polar substances such as grease, oil, and fat stains, as the non-polar hydrocarbon tails are able to absorb the non-polar molecules, surrounding them in a micelle with the polar carboxylate heads facing outwards, interacting with water and allowing the micelle to dissolve
With agitation, the grease lifts off the surface, and the micelles repel each other, allowing them to remain suspended in the water