topic 2

Question 1

2.9 Formation of proteins

Answer 1

• Proteins are made from long chains of amino acids (monomers).
• A dipeptide and water is formed when two amino acids join together.
• A polypeptide and water is formed when more than two amino acids join together.
• Proteins are made up of one or more polypeptides.

Question 2

2.9 Describe the basic structure of an amino acid

Answer 2

• carboxyl group (-COOH), an amine or amino group (-NH2) and a carbon-containing R group
• 20 amino acids (only difference is the R group)

Question 3

2.9 Formation of polypeptides

Answer 3

• amino acids are linked together by condensation reactions and a water molecule is released
• peptide bonds between amino acids
• reverse reaction is hydrolysis (addition of water molecule to break down the polypeptide bond)

Question 4

2.9 Describe the primary structure of a protein

Answer 4

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

Question 5

2.9 Describe the secondary structure of a protein

Answer 5

H bonds form between the amino acids in the chain. Coiled and folded (alpha helix or beta pleated sheets).

Question 6

2.9 Describe the tertiary structure of a protein

Answer 6

• the coiled or folded chain of amino acids is often coiled and folded further
• more bonds form between different parts of the polypeptide chain (H bonds, ionic bonds and disulfide bridges)
• for proteins made from a single polypeptide chain, the tertiary structure forms their final 3D structure
• globular

Question 7

2.9 Different bonds in the tertiary structure of proteins

Answer 7

• Ionic bonds: attractions between negative and positive charges on different parts of the molecule
• Disulfide bonds: two molecules of the amino acid cysteine come close together, the sulfur atom in one cysteine bonds to the sulfur in the other cysteine, forming a disulfide bond
• Hydrophobic and hydrophilic interactions: hydrophobic groups are close together in the protein, they tend to clump together which means that hydrophilic groups are more likely to be pushed to the outside, which affects how the protein folds up into its final structure
• Hydrogen bonds

Question 8

2.9 Describe the quaternary structure of a protein

Answer 8

made of several different polypeptide chains held together by bonds. The quaternary structure is the way these polypeptide chains are assembled together, protein’s final 3D structure

Question 9

2.9 What are globular proteins and what is their structure?

Answer 9

• round, compact proteins made up of multiple polypeptide chains
• coiled so hydrophilic R groups are on the outside of the molecule and hydrophobic R group face inwards
• soluble, easy to transport in fluids
• involved in catalysing activities (enzymes)

Question 10

2.9 Give an example of a globular protein

Answer 10

• haemoglobin
• made up of four polypeptide chains
• iron-containing haem groups that bind to oxygen and carries the oxygen around the body in the blood
• soluble, easily transported around the blood

Question 11

2.9 What are fibrous proteins and what is their structure?

Answer 11

• large and long polypeptide chains that are tightly coiled round each other to form a rope shape
• insoluble as the hydrophobic R groups are on the outside of the molecule
• chains are held together by lots of bonds (e.g. disulfide and hydrogen bonds)
• strong
• mainly found in supportive tissue
• mainly secondary structure and involved in structural functions

Question 12

2.9 Give an example of a fibrous protein

Answer 12

• collagen is a strong
• forms connective tissue in animals
• made up of 3 polypeptide chains

Question 13

2.9 What is the importance of the primary structure of a protein?

Answer 13

• the different types of amino acids determine the types of bonds such as disulphide bridges/bonds, hydrogen bonds, ionic bonds and hydrophilic and hydrophobic interactions.
• the position of amino acids determines position of these bonds
• the shape of the active site is determined by position of amino acids (active site: complementary to the binding substrate which forms enzyme-substrate complexes)
• hydrophilic R groups are on the outside so they are soluble
• globular proteins have a high number of polar/small R groups

Question 14

2.10 What are enzymes?

Answer 14

biological catalysts which speed up chemical reactions without being used up itself by providing an alternate pathway with a lower activation energy

• can be intracellular/extracellular
• globular proteins with an active site that has a specific shape
• forms enzyme-substrate complexes

Question 15

2.10 What is the Lock and Key Theory?

Answer 15

where the substrate fits into the active site of the enzyme in the same way that a key fits into a lock
- the substrate and active site are complementary to each other

Question 16

2.10 What is the Induced Fit Model?

Answer 16

• When the substrate enters the active site, the enzyme/active site changes shape slightly, fitting more closely around the substrate. The shape of the active site becomes complementary after the substrate binds to the enzyme.

Question 17

2.10 Define activation energy

Answer 17

minimum energy required to break bonds and start chemical reactions

Question 18

2.10 Describe and explain the effect of temperature and enzyme activity

Answer 18

• Low temp: low kinetic energy, few enzyme substrate collisions, rate of reaction is low
• Increased temp: high kinetic energy, more enzyme substrate collisions, rate of reaction is high
• At optimum temp: rate of reaction is at its highest
• Exceeding optimum temp: bonds in enzymes break, active site changes shape, substrate no longer fits and no longer are complementary, no enzyme-substrate complexes formed, DENATURED

Question 19

2.10 Describe and explain the effect of pH and enzyme activity

Answer 19

• At optimum pH: rate of reaction is the highest
• If pH changes too much, the bonds in enzymes break, rate of reaction is low
• Active site changes shape, DENATURED, no enzyme-substrate complexes form

Question 20

2.10 Describe and explain the effect of substrate concentration and enzyme activity

Answer 20

• At low substrate concentrations: substrate is the limiting factor, rate of reaction is low
• Increase in substrate concentrations: increases rate of reaction, higher kinetic energy, frequent enzyme substrate collisions, more enzyme-substrate complexes form
• Graph has a PLATEU because enzyme concentration becomes the limiting factor (active sites are full)

Question 21

2.10 Describe and explain the effect of enzyme concentration and enzyme activity

Answer 21

• At low enzyme concentrations: substrate is the limiting factor, rate of reaction is low
• Increase in enzyme concentrations: increases rate of reaction, higher kinetic energy, frequent enzyme substrate collisions, more enzyme-substrate complexes form
• Graph has a PLATEU because substrate level becomes the limiting factor (not all active sites are full)

Question 22

2.10 Describe the structure of an enzyme

Answer 22

• polypeptides formed by a sequence of amino acids joined together by peptide bonds (primary structure)
• the sequence of amino acids determines she shape of the specific active site which is complementary to its substrate so enzyme-substrate complexes can form
• the tertiary structure of an enzyme has hydrogen bonds, ionic bonds, disulfide bridges and hydrophilic and hydrophobic interactions between the R groups
• hydrophilic R groups are on the outside and hydrophobic R groups on the inside as enzymes are globular proteins, making them soluble