lecture 7: enzymes and metabolism Flashcards
What is metabolism?
Thousands of different chemical reactions linked through a NETWORK of metabolic pathways
not isolated pathways, they are all linked
ex: carbohydrate metabolism, amino acid metabolism, lipid metabolism, energy metabolism, etc
What’s a metabolic pathway?
Pathway composed of steps where each step is CATALYZED by a specific ENZYME
- Each step has its own enzyme
- Starting molecule A —> Reaction 1 + Enzyme 1 —> B —> Reaction 2 + Enzyme 2 —> C —> Reaction 3 + Enzyme 3 —> Product D
2 types of metabolic pathways
- Anabolic pathways: builds larger molecules from smaller components
- Synthesis, building
- Require inputs of energy —> so, involve ENDERGONIC REACTIONS —> uphill - Catabolic pathways: breakdown of molecules & RELEASE of energy
- Involve EXERGONIC reactions —> downhill
Primary vs Secondary metabolism
- Primary = ESSENTIAL for cell SURVIVAL + REPRODUCTION in organisms
ex: producing ATP - Secondary = synthesis of secondary metabolites that are NOT essential for cell survival and reproduction but can HELP an organism survive & reproduction
- for competition, to increase fitness for evolution, adaptations (ex: colours, flavours in plants and fruits)
6 types of reactions
- Oxidation-Reduction
X + Y —> X- + Y+ - Group transfer
X + YZ —> XZ + Y - Hydrolysis: add H2O to split bond
HY + H2O —> H-OH + H-Y - Cleavage: split bond without H2O
XY —> X + Y - Isomerization: transfer into an isomer
XYZ —> XZY - Condensation/dehydration: remove water to form bond
X-OH + H-Y —> XY + H2O
2 requirements for reactions to happen
- Right orientation: Need reactants to COLLIDE in a PRECISE ORIENTATION to allow them to interact and create new bonds
- Enough energy: Need reactants to have enough KINETIC ENERGY to reach the TRANSITION STARE —> more energy than activation energy
What is the transition state?
- Intermediate condition: between braking old bonds and forming new ones
- Stare where repulsive forces need to be overcame and where there are molecules with a combination of old and new bonds
- Activation energy (Ea) = amount of energy required for reactants to reach transition state
- the more unstable the transition state = the bigger Ea = the slower it is to reach Ea = the slower the exergonic reaction proceeds
2 characteristics of chemical reactions
- Direction of reaction (forward or inverse):
a) Change in potential energy
b) Change in disorder (entropy)
—> both determine change in free energy (∆G)
- Influenced by temperature (not too relevant in bio bc stable temp.) and concentration of reactions and products - Rate
Governed by:
a) Temperature
b) Concentrations of reactants
c) CATALYSIS —> enzymes
Effect of temperature on rate of chemical reaction?
Higher temperature = Higher kinetic energy = More molecules have the change to have enough energy bigger than Ea
Effect of concentration on rate of chemical reaction?
Higher concentration of reactants = More collisions = More chance to collide int he right orientation
What are catalysts and what do they do to the rate of chemical reactions?
- Substance that provide an alternate reaction route (mechanism) with a LOWER activation energy —> thus INCREASES RATE of reaction as MORE reactants will have the kinetic energy to reach the transition state
- Some reactants will still take the original route with a higher Ea
- Transition state = stabilized —> so required less activation energy bc of the catalyst
- Speeds up an already spontaneous reaction as even some reactions are spont. they happen too slowly —> need catalyst to speed it up
3 characteristics of catalysts important
- Only required in small amounts
- Are NOT consumed in the reaction and can be RECYCLED and used again and again
- Do NOT influence the change in free energy & DIRECTION of chemical reaction —> only influence the rate/speed of the chemical reaction
What are biological catalysts?
- Catalysis = vital function of proteins and some RNAs
- Protein catalysts = enzymes —> typically increase rate of a reaction 10^8 to 10^13 fold
- RNA catalysts = ribozymes
Why is catalysis important biologically?
Most biological chemical reactions occur at meaningful rates only in the presence of enzymes
- By providing an alternate reaction mechanism with lower activation energy —> more reactants have enough energy—> increase rate of reaction
6 enzyme groups
- Based on the types of reactions that they catalyze
1. Oxidoreductases: catalyze oxidation-reduction reactions
2. Transferases: catalyze transfer of C, N, or P containing groups
3. Hydrolases: catalyze cleavage of bonds by addition of water
4. Lyases: catalyze cleavage of C-C, C-O, C-S and certain C-N bonds
5. Isomerases: catalyze isomerization reactions
6. Ligases: catalyze formation of bonds in dehydration/condensation reactions
