Week 3 - Enzymes Flashcards
What are the 4 types of protein structure?
1 - primary
2 - secondary
3 - tertiary
4 - quaternary
What is the structure of a polypeptide?
Specified by its amino acid sequence
The 3D structure is critical to its function
What are globular proteins?
- the polypeptide chain fold up into a compact shape like a ball with an irregular surface
- compact structure
- tertiary and quaternary structures can be quite complex
What are fibrous proteins?
- an individual protein molecule spans a large distance
- generally have a relatively simple elongated structure
What are enzymes?
They are biological catalysts as they speed up the metabolic reactions that occur within the body, without itself being changed in the process.
Most enzymes are globular proteins
Highly specific for their substrate
What are the 5 main biological function of enzymes?
1 - Metabolism
2 - Movement
3 - Digestion
4 - Cell Signalling
5 - Gene expression
What is enzymes involvement in disease?
- Any malfunction is enzyme activity disrupts homeostasis
- DNA mutations resulting in under or overproduction/deletion in a single critical enzymes results in disease - which can be fatal
- a single amino acid substation could: destabilise protein structure, disrupt bind - affect catalysis
- mutation in enzymes that regulate cell cycle control or DNA repair mechanisms can result in cancers
What is the structure of enzymes?
- mainly globular proteins
- amino acid sequence specifies 3D conformation = catalytic activity
- work optimally with range of pH’s and Temperature, denature if above or below
- contains an active site
What is the active site of an enzyme?
The region that binds the substrates
- highly specific
- form a cleft/crevice on surface of enzyme
- non-polar environment that enhances binding by multiple weak forces
What are allosteric sites?
- distinct from the active site
- binding to the allosteric site can induce a conformational change - change in the active site/rate of reaction
- mechanism of regulation
- activate or inhibit reactions
- act as a feedback mechanism within a pathway
Definition of a cofactor
any factor essentially required for enzyme activity or protein function (inorganic)
most common are metal cofactors
Definition of a coenzyme
cofactor which is directly involved in enzyme catalysed reaction (organic)
some enzymes require them for optimal activity
transiently bound
may be altered during a reaction
Definition of a prosthetic group
covalently associated non-protein constituent required for a particular function
How do coenzyme work? What do they bind with?
Apoenzymes (inactive) + coenzyme = Holoenzymes (active) which can then bind with substrates
Examples of coenzyme deficiency?
1 - scurvy - connective tissue disease, lack of vitamin C
What do oxidoreductases do?
Transfer of oxygen or hydrogen atoms or electrons from one substrate to another
What do transferases do?
Transfer functional groups from one substrate to another
What do hydrolases do?
Hydrolysis of a substrate
What do lyases do?
Addition or removal of a group to form a double bond
What do isomerases do?
Transfer of groups within a molecule
What do Ligases do?
Bond formation coupled with ATP hydrolysis
What happens during enzyme reactions?
All reactions need to overcome the energy barrier = activation energy, enzymes reduce the activation energy required for the reaction to proceed
enzymes only alter the rate of reaction not the amount of product formed
How do enzymes reduce activation energy?
1 - microenvironment
2 - orientation
3 - hydrophobic
4 - ionic bonds
5 - hydrogen bonds
6 - transient covalent bonds
7 - van der Waals
What are the 4 main catalytic mechanisms?
1 - Metal ion catalysis
2 - catalysis by approximation
3 - covalent catalysis
4 - acid-base catalysis
What happens during covalent catalysis?
The enzyme formed a covalent bond with the substrate, when the products are then formed the bond is broken
How does the cell regulate the catalytic activity of its enzymes?
- controls how many molecules of each enzyme it makes by regulating the expression of the gene that encodes that enzyme
- confining sets of enzymes to particular subcellular compartment
- covalently modified to control their actvity
- the rate of protein destruction by targeted proteolysis
- binding of small molecules (allosteric activation and inhibition)
What is feedback regulation?
Enzyme inhibition - end products inhibit earlier pathway steps
prevents build up of unnecessary metabolites and energy use
What are the types of reversible inhibition?
reversible inhibitors bind to the enzyme via weak non-covalent interactions (hydrogen/ionic bonding and hydophobic interactions)
1 - competitive
2 - non-competitive
3 - uncompetitive
How do competitive inhibitors work?
- have some affinity for the active site
- similar shape/binding properties as substrate
- substrate is competing for access to active sites
- therefore reduced rate of activity
- can be overcome by increasing S
Graphs - Vmax remain unchanged
- Km increases as binding is affected
How do non-competitive inhibitors work?
- inhibitor binds an allosteric site
- conformation of active site changes
- substrate cannot bind
- dependant on inhibitor
Graphs - Vmax is reduced
- Km does not change as it is catalytic activity that is affected
How do uncompetitive inhibitors work?
- inhibitor binds only the enzyme/substrate complex
- inhibits catalysis
Graph - Vmax reduced
- Km reduced
