ENZYMES:

- Cell have mechanisms that regulate biochemical reactions to ensure the final product is not overproduced or
underproduced
- Enzymes are protein molecules that catalyse biochemical reactions and regulate biochemical pathways
- The specific nature of enzymes ensures that particular enzymes only bind to particular substrates, catalysing
specific chemical reactions
- Enzyme activity is altered by the environment around the enzyme and sometimes by the availability of
cofactors

FEATURES OF ENZYMES:
- Most enzymes are globular-type protein molecules → they are formed from long chains of amino
acids that coil and fold into a compact structure
- Most globular proteins are soluble, they also have a large number of atoms

- The main features of enzymes are there specificity for a substrate their catalytic power and their
capacity to a catalyse repeated reaction
➔ Specificity- different enzymes act as catalysts for different biochemical reactions by binding to a
specific type of molecule, called substrate. Although some enzymes have evolved to be highly specific,
binding to only one substrates and catalysts one specific reaction, other enzymes can act on multiple
substrates that are similar and catalyse multiple reactions

- A substance is a molecule upon which an enzyme acts. The enzyme can break down the substance into
smaller molecules, or join the substrate with other molecules to make a larger molecule
- Catalysts are substances that accelerate the rate of any chemical reaction without themselves being charged
→ enzymes are a subgroup of catalysts that catalyse reactions in living things

- Enzymes are not consumed when they catalyse reactions; they are recycled and used again many times

ENZYME SPECIFICITY:
- An important structure of enzymes is their active site
- This is a pocket or groove-like depression in the enzyme’s structure formed from the tertiary (3D) folding of
the protein
- Each enzyme’s active site is a complex 3D shape that interacts with a specific substance to catalyse a
specific reaction
- When the active site binds to the substance, it forms an enzyme-substance complex

Enzyme-substrate interaction model:

Two models describe enzyme-substrate interaction

- Lock and Key model: describes the active site and the specific substrate as fitting together like a lock
and key. If the key (substrate) does not fit into the lock (enzyme’s active site), then no reaction occurs.
Older version , now thought to be inaccurate.
- Induced fit model( more accurate) l: states when a substrate binds to the active site of an enzyme, the
active site changes shape. We know that the active site is flexible, capable of changing its shape to
conform to the shape of the substrate and achieve a tighter fit

Enzymes and energy in reactions:

- Metabolism is the collection of all the biochemical (metabolic) reactions that occur in living cells
- Metabolic reactions can be:

Catabolic reactions:
- break down substrates
- catholic reactions are exergonic because they release energy

Anabolic reactions:
- produce larger molecules from smaller substrates
- are endergonic because they require energy to form bonds between molecules

- To address this need for energy input, biochemical pathways sometimes couple a reaction that releases
energy with a reaction that requires energy

Plant Enzymes
- Plant carry out many biochemical reactions such as photosynthesis and cellular respiration.
- These biochemical reactions need to be regulated in plant cells just as in animal cells
- Different enzymes catalyse biochemical pathways in plants but many of these enzymes have similar
features to those in animal cells

Photosynthesis:
- Enzymes play a role in photosynthesis, particularly during the light-independent stage of photosynthesis
- Because the light-independent reactions of photosynthesis are catalysed by enzymes, the rate of reaction
changes as enzyme activity changes

Other plant enzymes:

- some herbicides (chemicals that kill plants) work by blocking plant enzyme activity.
- A tiny herbicide molecule can attach to the site of an enzyme and stop it from working
- such molecules are called irreversible inhibitor
- some plants have adapted to herbicides by changing 1 or 2 amino acids in their enzymes, which allows the
enzymes to adjust their structure and continue working, and as a result these plants have become herbicide
resistant.
- Insectivorous plants such as Venus fly traps produce a sticky liquid that attracts and traps insects. This liquid
contains digestive enzymes which break down the insect body by supplying extra nutrients to the plant.

Fruit Enzymes:
- Many fruits, such as pineapple, papaya, fig, kiwi, contain enzymes called proteases
→ Proteases speed up the breakdown of proteins

FUNGI ENZYMES:
- Many fungi are saprotrophic, which cause decay by releasing enzymes onto the dead animal or plant,
which breaks down complex compounds into simple soluble compounds that can absorbed by the
decomposer. Example: fungus growing on bread releases amylase enzymes to digest the bread starch
into maltose and then absorbs the maltose
- Disease causing fungi infect plants and animals with their action usually coming from the enzymes
secreted by the fungi to obtain the nutrients they need. The fungus group includes organisms known as
mould, rot and yeast.
- Fungi and their enzymes are a vital part of decomposition cycle in environment
- The combined actions of the diverse microbe community ( fungi and their secreted exo enzymes)
convert complex organic compounds into easily assimilated nutrients for other species.
- These microbial communities are ubiquitous in nature, inhabiting both terrestrial and aquatic
ecosystems.
- Cycling of elements from dead organic matter by heterotrophic soil microbes is essential for nutrient
turnover and energy transfer in terrestrial ecosystems.

FACTORS THAT AFFECT ENZYME ACTIVITY:

- When cells produce too much or too little of particular substances, or are unable to properly break down
substances, the whole organism can suffer
- To account for energy and resource wastage, to account for this cells have mechanisms that regulate
biochemical reactions (metabolism) to ensure final product is not overproduced or underproduced
- If the regulatory mechanisms fail, a variety of problems energy for a human body-from milk to fatal
- Enzymes control metabolism through the catalysis of reactions at every step of a biochemical or metabolic
pathway
→ a whole pathway can be regulated through control of one enzyme; this is why it is important to
understand that enzyme activity is affected by its environment
- When these conditions are optimal, enzyme activity is at its highest, the rate of reaction is at its fasted, and
the biochemical pathway is operating at maximum efficiency
- The amount of final products and the speed at which they are produced in a biochemical pathway can
therefore be controlled through the regulation of the pathway’s enzymes and individual reactions

TEMPERATURE:
- Rate of enzyme catalysed reactions will generally increase as the temperature increases.Warmer the
particles during a reaction, more rapidly they move, which makes successful collisions and reactions
between them more likely to happen
- But, proteins, including enzymes, can become denatured at high temperatures. When this occurs
hydrogen bonds and hydrophobic interactions that create the coiled globular, tertiary (3D) shape of the
enzyme are broken. Shape of the enzyme molecule is changed so the substrate cannot bind to it and
the reaction cannot occur. Even induced-fit process does not provide an active site on the enzyme for
the substrate molecule.
- Optimum activity of human enzymes happens at 36-38 degrees because it matches their normal body
temperature .
- Animal enzymes usually begin to denature at temperatures above 40 degrees celsius
- Some enzymes have optimum temperatures much higher than this. E.g Taq polymerase (enzyme
found in bacteria living in volcanic hot springs and has optimum temperature at 70 degrees celsius)
- Enzymes of each species have evolved over time to enable the species to live successfully in their
natural environment.
- If enzymes are cooled below their optimum temperature the rate of reaction will slow down because
particles will move more slowly at cooler temperatures making successful collisions less likely
- Chemical bonds are not as flexible at cooler temperatures and conformational changes do not occur,
however enzymes are not denatured at low temperatures.
- If an enzyme’s environment increases in temperature, its activity and reaction rate will also increase.
(this is why decomposition of food slows in the fridge)
- DENATURATION: loss of the characteristic of 3-D shape of protein such as an enzyme. This prevents
the functioning of the enzyme and is irreversible. This can happen if enzyme is heated above optimum
temperature.

INCLUDE FIGURE 3.4.18

Enzymes at extreme temperatures

- Sooty grunter: fish that inhabit large freshwater streams, preferring rapidly flowing water with a rocky
bottom and sparse, aquatic plant cover. This species is also found in hot springs. They tolerate acidic
conditions to a pH of 4.1 and water temperatures range from 12-34 degrees celsius. The wide
tolerance range of these fish is due to their metabolic enzymes being able to function in these extreme
environments.
- Psychrophilic: bacteria and fungi adapted to extreme cold of Antarctica and Arctic. Function at low
optimum temperatures which allows their cells to grow and carry out metabolic processes at the
constant low temperatures of their cold environments.
- Thermophiles: prokaryotes from Archaea domain, which tolerate hot environments and contain
enzymes with high optimal temperatures than those of mammals

Enzyme and substrate concentration:

- The concentration of enzyme compared to substrate affects the rate of reaction
- If the enzyme concentration is high compared to that of the substrate, the reaction will occur over a short
period of time
→ this is because the more enzyme molecules that are available, the more active sites there will
be for the substrate to bind to, and so the rate of reaction will be faster until saturation point is
reached
- If enzyme concentration is lower that the substrate concentration, then the reaction rate will be slow
and will continue for longer
→ this is because there are few active sites compared to the number of substrate molecules
- Controlling the enzyme or substrate concentration in an organism’s body is a way to regulate the speed of a
biochemical pathway

Cellular Compartmentalisation
- Helps create an environment in which conditions are optimal for enzymes to catalyse reactions
- Each organelle has different function and within it the molecules involved in biochemical pathways are
related to the organelle’s function are brought close together for reactions to take place.
- Also makes different environments possible within each organelle such as different pH and cofactor
chemicals that support activity of particular enzymes.
- There will be high concentrations of the enzymes and substrates for that organelles function, such as in
the chloroplasts for photosynthesis and mitochondria for cellular respiration.
- In animal cells lysosomes (specialties sac with digestive enzymes called acid hydrolases), these
enzymes are delivered to lysosomes via vesicles that bud off the Golgi apparatus.
- Lysosomes contain about 40 types of enzyme that break down and recycle proteins, lipids and nucleic
acids and more. These enzymes function optimally in the acidic lysosomal environment. Lysosome
digest cell components that are past their use by date.

Inhibition of enzyme activity:

- Enzyme activity can also be changed by inhibitor molecules that bind to the enzyme’s active site, preventing
the substance from binding
- The inhibition of enzyme activity by an inhibitor molecule can be reversible or irreversible, depending on the
strength of the bonds between the enzymes and inhibitor
- Enzyme inhibition is also classified as being competitive inhibition or non-competitive inhibition, depending on
where the inhibiting molecule binds to the enzyme
- Feedback inhibition occurs when a product that is produced late in a biochemical pathway is also an inhibitor
of an enzyme earlier in the pathways
- As the level of the inhibiting product reduces, less of it will bind to the enzymes, allowing them to function
again
→ Feedback inhibition is an important mechanism in controlling enzyme activity

Phosphorylation
- Phosphorylation: binding of a phosphate group to a protein
- Dephosphorylation: removal of phosphate group from protein
- Most common regulatory mechanism of protein function, with as many as one third of all proteins in the
human body being substrates for phosphorylation at some point
- Phosphorylation and Dephosphorylation both change the structure of proteins and therefore both can
regulate enzymes
- E.g. phosphorylation of glycogen synthase inhibits its ability to interact with glucose.

Cofactors and Coenzymes:

- Some enzymes needc
- These components, called cofactors, bind to the enzyme
- Cofactors can be inorganic ions such as iron, magnesium or organic molecules like proteins and vitamins
- Small, non-protein organic cofactors are known as coenzymes
- For certain enzymes a specific coenzyme is required to catalyse reactions
- Often the coenzyme is structurally altered during the reaction, but afterwards reverts to its original form,
which allows it to be reused
- There are many types of coenzymes, including vitamins, ATP, nicotinamide adenine dinucleotide (NADH),
flavin adenine dinucleotide (FADH) etc.
- Except for vitamin C, all other vitamins must be modified in the body before they can function as coenzymes