Proteins, Enzymes and Denaturation

Question 1

What are proteins in the stomach broken down by?

Answer 1

Pepsin, where a hydrolysis reaction is used to break the long chain.

Question 2

How are proteins metabolised in the body?

Answer 2

Protein - (Hydrolysis) > Amino acids - (Condensation) > Protein

Question 3

Heat denaturation

Answer 3

Increased kinetic energy of polypeptide chains (increase vibration)
Hydrogen bonds broken between secondary, tertiary and quaternary structures
Primary structures are not disrupted (covalent)

Question 3

Protein

Answer 3

Found in every cell
The body needs to synthesise or ingest it

Question 4

Essential amino acids

Answer 4

Cannot be made in the body
Has to be ingested

Question 5

Amino acids

Answer 5

Made from amino group and carboxyl group
Central carbon bonded to an R group
Known as 2-amino acids or a-amino acids

Question 6

R group properties

Answer 6

Non-polar and Polar
Proton donors and acceptors

Question 7

Essential and non-essential amino acids

Answer 7

Can synthesis 11/20
Other nine must be provided from food
Hence, a balanced diet is required

Question 8

Zwitterions

Answer 8

Contains polar amino and carboxyl functional groups
NH2 acts as a base, accepting a proton to become NH3
COOH acts as an acid, donating a proton to become COO-

Question 9

How does a zwitterion form?

Answer 9

NH2 is a weak base, COOH is a weak acid
In solution (water), a zwitterion forms, which is a dipolar ion

Question 10

What is the neutral pH level?

Answer 10

7

Question 11

Zwitterion buffering action

Answer 11

In an acidic solution, it acts as a base
In a basic solution, it acts as an acid

Question 12

Forming polypeptides

Answer 12

Condensation reaction between carboxyl and amino groups
CONH/peptide link forms
50 or more is a protein

Question 13

N-terminal

Answer 13

Free amino group at the start of a polypeptide chain

Question 14

C-terminal

Answer 14

Free carboxyl group at the end of a polypeptide chain

Question 15

How are proteins broken down?

Answer 15

Hydrolysis
Breaks the peptide bonds into its constituent amino acids

Question 16

Name and describe structures of proteins

Answer 16

Primary structure: covalent bonds, creating a chain
Secondary structure: helices, folds, pleats due to H-bond betwewen C=O and N-H
Tertiary structure: 3D packing structure of proteins due to bonding between Z groups (H-bonding, ionic, disulfide bridges)

Question 17

Primary structure

Answer 17

Starts with an N-terminal and ends with a C-terminal
Straight chain in a protein
MENTION THAT THEY HAVE COVALENT BONDS

Question 18

Secondary structure

Answer 18

Colliding and pleating of sections
Hydrogen bonds between polar NH groups in the peptide link and the C=O in another forms at regular intervals

Question 19

a-Helices

Answer 19

The hydrogen bonds between the NH and the C=O to every 4th peptide link
Shapes like a spring

Question 20

b-Pleated sheets

Answer 20

Happens when two or more parts of the polypeptide chains line up parallel to each other
They can form hydrogen bonds again with the NH and C=O

Question 21

Five types of attraction in tertiary structures

Answer 21

H-bonds between polar R groups with OH or NH bonds
Ionic attraction between R groups with NH3 and COO- groups
Disulfide links between R groups with -SH groups (covalent bonds)
Dispersion forces between non-polar R groups
Dipole-dipole interactions between polar R groups (-S-H, -O-H or -N-H)

Question 22

Quaternary Structure

Answer 22

Formed when proteins contain two or more polypeptide chains and may potentially interact with non-protein molecules to produce quaternary structures
E.g. haemoglobin

Question 23

Mentioning tertiary structures…

Answer 23

‘they contribute to the unique 3D shape by interaction of R groups via (a type of bonding attraction - dispersion forces/H-bonding)

Question 24

pH denaturation

Answer 24

If pH level is altered, ionic interactions of tertiary and quaternary structures are altered
Primary structures are unaffected

Question 25

Alcohol’s effect on denaturation

Answer 25

Alcohol disrupts the secondary and tertiary structure of a protein
Due to H-bonding in the secondary and tertiary structures being disrupted
Rather than forming bonds within the protein it forms H-bonds with the alcohol instead
This destroys the structure of the protein

Question 26

Hydrolysis’ effect on denaturation

Answer 26

Denaturation doesn’t affect the primary structure, the peptide links aren’t broken
During hydrolysis however, the primary structure is affected

The reaction goes as follows:
Polypeptides -> Dipeptides -> Amino acids

Question 27

Enzymes

Answer 27

Biological catalysis that speeds up the rate of reaction - related to proteins
Needed in a relatively small amount
Aren’t used up or changed at the end of a reaction (unless it is exposed to high temperatures or varying pHs)
Doesn’t alter the equilibrium position
Provides an alternate pathway that lowers the activation energy of a reaction
More substrate will have required activation energy to undergo a reaction

Question 28

The difference between organic and inorganic catalysts

Answer 28

Inorganic catalysts used in multiple reactions with different reactants
Organic catalysts are used only for particular reactions, or a reaction that involves a particular type of bond (this is much more specific)

Question 29

Lock and Key model

Answer 29

Active sites where only reactant molecules fit into
Substrate (reactant molecules) rearranges into new products
Enzymes are specific to only one substrate

Reaction goes as such:
Enzyme + substrate <-> enzyme-substrate complex <-> enzyme + products

Question 30

Induced fit model

Answer 30

Enzymes are are to slightly alter their shapes

Question 31

Substrate and enzyme bonds are held in place by:

Answer 31

Dispersion forces between non-polar groups
Hydrogen bonding between enzyme and substrate (NH and C=O groups)
Ionic interactions between COO- and NH3+
Dipole-dipole interactions

Question 32

The effect of optical isomers on enzymes

Answer 32

Substrates have more than one chiral centre
Hence, the way they interact with an enzyme is specific

The enzyme can distinguish between the enantiomers of a chiral substance
Hence, only one enantiomer will fit into a particular enzyme and participate in the reaction

Question 32

The effect of optical isomers on enzymes

Answer 32

Substrates have more than one chiral centre
Hence, the way they interact with an enzyme is specific

The enzyme can distinguish between the enantiomers of a chiral substance
Hence, only one enantiomer will fit into a particular enzyme and participate in the reaction

Question 33

Co-enzymes

Answer 33

Some enzymes can’t function without a cofactor
A factor could be a metal ion or another non-protein organic compound called a coenzyme

Question 34

Physical interactions of coenzymes

Answer 34

The enzyme is inactive until the coenzyme binds to it and changes the shape of the active site.
Once the coenzyme is bound to the enzyme then it becomes active and can break down the substrate.

The substrate now attaches to the active site and the reaction can be catalysed.

Question 35

Chemical interactions of coenzymes

Answer 35

The coenzyme can donate electrons (undergo oxidation) and get reformed via reduction. The coenzyme donates electrons to the enzyme-substrate complex to facilitate the reaction.

Question 36

Types of coenzymes (Don’t think you need to know)

Answer 36

NAD+ (from niacin, vitamin B3): Acts as a carrier of electrons
FAD (from riboflavin, vitamin B2): Acts as a carrier of electrons
Coenzyme A (from pantothenic acid, vitamin B5): Acts as a carrier of acetyl group, -COCH3
Thiamine pyrophosphate (from thiamine, vitamin B1): Acts as a carrier of the aldehyde group, -CHO
Biotin: Acts as a carrier of CO2
Cobalamin (from vitamin B12): Acts as a carrier of the methyl group, -CH3

Question 37

Enzyme activity

Answer 37

Amount of substrate that’s converted to product per unit time
Depends on the quantity of the active enzyme and it’s given conditions

Conditions that affect enzyme activity are:
pH, temperature, concentrations of the enzyme and concentrations of the substrate

Question 38

pH for enzymes

Answer 38

pH range at which an enzyme works best is very narrow
Optimum pH at which the enzyme is most efficient
Different enzymes have different optimum pHs

Question 39

pH’s effect on secondary structures

Answer 39

Strong acids can have an impact between the N-H and C=O in the secondary structure of proteins

Question 40

Optimal temperature for enzyme activity

Answer 40

Roughly 37C is known as the optimum termpereature
Above and below that the enzyme’s function is affected

Question 41

How does temperature affect enzymes?

Answer 41

At high temperatures, enzymes gain a lot of kinetic energy
If the molecules gain too much energy it can break the intermolecular bonds holding the enzymes structure in place

Question 42

Denaturing enzymes

Answer 42

If the tertiary structure of an enzyme permanently changes, we say that the enzyme has been denatured.