12.3D Chemistry of Life

Question 1

Amino acids

Answer 1

are an important group of compounds that all contain the amino group (−NH2) and the carboxylic acid group (−COOH)

• are the monomers that make up proteins
• contain both an acidic group and a basic group, they are amphoteric

Question 2

Zwitterion

Answer 2

The resulting species with two ionized groups has net zero charge

Question 3

Physical properties of Amino acids

Answer 3

• The ionic nature of the zwitterions gives amino acids relatively** strong intermolecular forces of attraction**
• soluble in water
• insoluble in non-polar organic solvents such as hydrocarbons
• crystalline solids with high melting points
• tend to decompose before they melt ~200 - 300°C

Question 4

Peptides

Answer 4

the –COOH group of one amino acid reacts with the –NH2 group of another, a molecule of water is released and a peptide linkage is formed (condensation reaction)

Question 5

The hydrolysis of peptides

Answer 5

• by an acid or an alkali
• refluxed with HCl or NaOH solution, to hydrolyse it
• products of hydrolysis: carboxylic acid and a primary amine
• acid reflux; products of hydrolysis: its original 2-amino-carboxylic acids.
• ammonium salts
• an excess of alkali, aqueous NaOH, refluxing produces the sodium salts of the original 2-amino-carboxylic acids.

Question 6

Primary structure (1º)

Answer 6

the sequence of amino acids in the polypeptide chain
is held together by covalent bonds

Held together by peptide bonds, this forms the covalent backbone of the molecule.

Question 7

Secondary structure (2º)

Answer 7

a regular structural arrangement stabilised by hydrogen bonding between the NH group of one peptide bond and the CO group of another peptide bond

Hydrogen bonding (between NH group and CO group) of the peptide backbone causes the amino acids to fold into a repeating pattern

• the side-chains of the amino acids are not involved.
• two types of secondary structure are:
  the α-helix (alpha-helix)
  β-pleated sheet (beta-pleated sheet)

Question 8

Tertiary structure (3º)

Answer 8

the further folding of the polypeptide chain into a 3D shape.
This 3D shape is stabilised by attractive forces and bonding between the amino acid side-chains

• hydrogen bonds, ionic attraction, Van der Waals’ forces, disulphate bridges
  -interactions between the R groups (side chains).
• protein’s conformation
• the most stable arrangement of the protein

Question 9

The complex 3-D shape is stabilised by

Answer 9

• Hydrophobic interactions – between non-polar side chains
• Hydrogen bonding – between polar side chains
• Ionic bonding – between side chains carrying a charge
• Disulphide bridges – between the sulphur-containing amino acid cysteine. These are covalent bonds, and hence the strongest of these interactions
  or
  Stabilised by:
• disulphide bridges – these are covalent (S–S) bonds
• weak van der Waal’s forces
• relatively weak hydrogen bonds
• ionic bonds (salt bridges)

Question 10

Denaturation

Answer 10

When a protein loses its specific tertiary structure as a result of such disruptions as changes in temperature, pH, or the presence of metal ions.

the process by which the 3D structure of a protein or other biological macromolecule is changed, often irreversibly. Relatively high temperatures, extremes of pH and organic solvents often cause denaturation

Question 11

Quaternary structure (4º)

Answer 11

Some proteins comprise more than one polypeptide chain

• similar forces and bonds to tertiary structure – hydrophobic interactions, hydrogen bonds, ionic bonds, and disulphide bridges.

Question 12

Cofactor

Answer 12

a small molecule which is not a substrate, but which is essential for an enzyme-catalysed reaction.

Question 13

Competitive inhibition

Answer 13

enzyme inhibition by molecules that bind to the active site, preventing the normal substrate from reacting. They have a structure similar to the substrate molecule. The inhibition is reversible.

Question 14

Enzyme

Answer 14

• a protein molecule that is a biological catalyst
• most act on a specific substrate

Question 15

Lock-and-key mechanism

Answer 15

a model used to explain why enzymes are so specific in their activity
it is suggested that the active site of the enzyme has a shape into which the substrate fits exactly – rather like a particular key fits a particular lock

Question 16

Non-competitive inhibition

Answer 16

a type of enzyme inhibition in which the inhibitor molecule binds to a region of the enzyme surface, often at a region other than the active site, allosteric site.
It distorts the shape of the active site or blocks the active site permanently so that the active site no longer functions

Question 17

Prosthetic group

Answer 17

an ion/molecule that is permanently bound to part of an enzyme

Question 18

Specific features of enzymes

Answer 18

• more efficient than inorganic catalysts
• very specific
• enzymes do not produce by-products
• mild conditions, 35ºC pH 7,
• can be regulated

Question 19

The non-covalent interactions needed for the ‘chemical fit’ at the active site include:

Answer 19

• hydrophobic interactions,
• dipole–dipole attractions,
• hydrogen bonds, and
• ionic attractions.

Question 20

Induced fit model

Answer 20

the shapes of the enzyme’s active site and its substrate are not exactly complementary, but when the substrate enters the active site, a conformational changeoccurs which induces catalysis

Question 21

Factors affecting enzyme activity

Answer 21

• Heavy metal ions
  (Ag+,Hg+, Cu2+, Pb2+) react with one or more -SH (sulfhydryl) groups of enzymes and inhibit their activity because the tertiary structure of the protein is altered
• Denaturation
• Temperature
• pH
  disruption of the tertiary structure as ionic bonds break
  affecting the ionisation
  there is no possibility of forming ionic bonds

Question 22

Examples of denaturation

Answer 22

Increase of temperature:
- cooking of egg
Change of pH
- caesin in milk goes solid

Question 23

Codon

Answer 23

a set of three successive bases in mRNA which codes for a specific amino acid in protein synthesis.

Question 24

Genetic code

Answer 24

a code made up of sets of three consecutive nitrogenous bases that provides the information to make specific proteins

Question 25

Messenger RNA

Answer 25

a type of RNA which is synthesised using part of the DNA strand as a template.
The sequence of triplet bases along the mRNA codes for the sequence of amino acids in a protein.

Question 26

Nucleotide

Answer 26

a compound consisting of a nitrogenous base, a sugar (ribose or deoxyribose) and a phosphate group.
Nucleotides form the basic structural units of DNA and RNA

Question 27

Ribosomal RNA rRNA

Answer 27

this forms part of the structure of the ribosomes.
rRNA binds ribosomal proteins which take part in the various reactions at the ribosome and helps binds mRNA.

Question 28

Transcription

Answer 28

the process by which the genetic message encoded on the template strand of DNA is ‘copied’ to make a strand of messenger RNA.

Question 29

Transfer RNA

Answer 29

a type of RNA which transfers amino acids to a lengthening peptide chain during protein synthesis by interaction with mRNA and the ribosomes.

Question 30

Translation (in protein synthesis)

Answer 30

the process by which the genetic message encoded by mRNA is translated at the ribosomes into a sequence of amino acids in the polypeptide chain. mRNA, tRNA and ribosomes are all involved in the process.

Question 31

Key point about DNA structure

Answer 31

• backbone of alternating sugar and phosphate units
• the two strands run in opposite directions (antiparallel) to each other
• the two strands are twisted to form a double helix
• the nitrogen-containing bases link the two strands by hydrogen bonds
• the bases are positioned at right angles to the long axis of the helix (rather like a pile of coins)

Question 32

Complementary base pairs

Answer 32

➢ A always pairs with T
(forming 2 hydrogen bonds between them)
➢ G always pairs with C
(forming 3 hydrogen bonds between them)

Question 33

The structure of DNA is kept stable by

Answer 33

✓ hydrogen bonds between the
base pairs
✓ van der Waals’ attractive forces between one base pair and the next

Question 34

A mutation is a change in the original DNA sequence.

Answer 34

Spontaneous: (mismatch)
Radiation:
• UV-light
• X-rays
• 𝛾-rays (gamma)
• 𝛼- and 𝛽-radiation
Chemicals:
• in tobacco smoke
• synthetic materials
• pollution
• benzene
• formaldehyde
• carbontetrachloride
Infectious agent:
• Viruses
• Bacteria

Answer 35

1. POINT MUTATION (one base is substituted for another)
   ➢ If a point mutation changes the amino acid, it’s called a MISSENSE mutation.
   ➢ If a point mutation does not change the amino acid, it’s called a SILENT mutation.
   ➢ If a point mutation changes the amino acid to a “stop,” it’s called a NONSENSE mutation
2. INSERTION (an extra base, or bases, is inserted)
3. DELETION (a base, or bases, is lost)

• Deletion and insertion may cause what’s called a FRAMESHIFT, meaning the reading frame changes. These are typically one of the most serious types of mutations.