Proteins and enzymes

Explain how DNA structure determines the specific shape of enzymes.[8] #

• DNA codes for , protein / polypeptide ;
• transcription and translation (or described) ;
• enzyme is globular (protein) ;
• 3 bases 1 amino acid ;
• sequence of , bases / triplets , determines , sequence of amino acids / primary
• structure ;
• coiling / helix / pleated sheet / particular secondary structure ;
• determines projecting side groups ;
• folding / bonding , for tertiary structure ;
• 3-D structure is tertiary structure ;
• e.g. ref. active site related to shape
• 2 or more genes produce quaternary structure

Difference between globular proteins and Fibrous proteins[8] #

GLOBULAR PROTEIN	FIBROUS PROTEINS
It has polypeptide chains with irregular sequence of amino acids	It has polypeptide chains with regular repetitive sequences of amino acids
Its shape is a compact globule of polypeptides	It has long chins running parallel
It is chemically less stable and its activity if affected by factors such as its concentration,pH and temperature	It is chemically stable and relatively unaffected by temperature, concentration and pH
Each molecule of the same type of globular proteins has a specific sequence	Each molecule of the same type of fibrous proteins may vary in length with slightly different sequences of amino acids
It is water soluble	It is insoluble in water
It is involved in various body systems such as the digestive system, the endocrine system and the immune system	Its roles is mainly in helping to maintain structure and providing support

Explain the mode of action of an enzyme. [8] #

ZIMSEC November /2003/2/10(a)]

• Enzyme are very specific
• Globular shape
• Substrate fits into active site
• Active site are specific
• Enzyme-substrate complex formed
• Enzyme-substrate complex held by hydrogen bonds / ionic bonds /hydrophilic interactions
• The product no longer fits on the active site
• lowering of activation energy
• ref to lock and key hypothesis and induced fit mechanism

With reference to a named example, describe one model of enzyme action. [6] #

ZIMSEC -/12(a)

• Enzyme are very specific
• They are specific e.g. the enzyme amylase will only act on starch converting it to maltose
• Although the enzyme molecule is large, overall, only a small region of it is functional.
• This is known as the active site.
• Active site-small hollow depression
• Substrate –molecule on which enzyme acts e.g starch for the enzyme salivary amylase
• Substrate fits into depression to form an enzyme- substrate complex
• Substrate molecule is held within the active site by bonds that form between certain amino acids and the active site
• One model, the lock and key model proposes that enzymes work in the same way as a key operates a lock
• Substrate only fit the active site of one particular enzyme e.g. starch on amylase only Shape of substrate exactly fits the active site

Describe how competitive and non-competitive inhibitors affect enzyme activity. [8] #

[ZIMSEC November /2003/2/10(b)]

Explain the effect of inhibitors on the enzyme reaction[6][ ZIMSEC /12(b)]

• Competitive inhibitor
  • Competes with substrate for the site.
  • Inhibitor and substrate have similar structure/ shape
  • Enzyme-complex usually has no end product.
  • Substrate cannot occupy enzymes active site i.e reaction rate decreases with increase in inhibitor concentration
  • Increase in the substrate concentration affect the rate of reaction
• Non-competitive inhibitor
  • They have no structural similarity with substrate.
  • Non- competitive inhibitors bind to other parts of enzyme
  • Inhibitor binding on the enzyme distorts enzyme structure
  • Substrate-enzyme complex is not formed
  • The reaction rate decreases with increase in inhibitor concentration
  • Increase in the substrate concentration does not affect the rate of reaction

Describe how you would measure the rate of a reaction catalyzed by the enzyme catalase. [8] #

ZIMSEC June 2004/2/12(a)

• Ref to a named substrate
• Amount/ concentration of enzyme
• Amount/ concentration of substrate
• Maintenance of optimum conditions eg temperature
• Count the numbers of bubbles of oxygen produced in a given time more than once
• Determination of the mean number of bubbles
• Divide number of bubbles produced by the time

Describe the secondary and tertiary structure of an enzymatic protein, such as lysozymes #

• secondary
  • regular order/pattern, based on H-bonds ;
  • between CO– group of one amino acid and NH– group of another ;
  • alpha-helix and β-pleated sheet ;
• tertiary
  • folding coiling ;
  • interactions between, R groups side chains ;
  • two correctly named bonds ; e.g. hydrogen bonds, disulfide, bonds/bridges, ionic bonds, hydrophobic interactions
  • further description of bonds ; e.g.
    disulfide between cysteine (S–H) groups
    hydrogen between polar groups (NH– and CO–)
    ionic between ionised amine and carboxylic acid groups
    hydrophobic interactions between non-polar side chains
  • ref. active site, specific/precise, shape ;
  • ref. globular/AW, shape ; A spherical/ball
  • ref. amino acids with, hydrophilic/polar, R groups facing to outside ;

With reference to molecular structure, explain the specificity of enzymes. #

• active site;
• with specific shape;
• formed by only a few amino acids;
• ref to 3D structure;
• tertiary structure;
• complementary structure of substrate and active site ;
• ref to ‘lock and key’;
• induced fit;
• only accepts one substrate / type of substrate;
• enzyme-substrate complex;