C1.1: Enzymes and Metabolism

Enzyme

Biological catalysts made of proteins or rRNA, increase the rate of biochemical reactions without being changed

Without them, necessary processes for life would occur very slowly

*convert substrates to products*

Metabolism

Complex network of interdependent and interacting chemical reactions in living organisms

Arranged as a series of reactions that are catalyzed by unique enzymes at each step, can exist as wither chains or cycles

Enzyme Specificity

Enzymes are specific and catalyze only one specific reaction.

Organisms require many different enzymes to survive, and cells control rxn rate by making more/less of different enzymes

Metabolic Pathways

Most enzymes produce small changes in pathways, significant transformations happen in a sequence of small steps

Can be a linear pathway (chain) or a cyclical pathway (cycle)

Chain Pathway

A linear metabolic pathway, ex. glycolysis converts glucose to pyruvates

Cyclical Pathway

More common, a cycle in which every intermediate is a product of previous rxns and substrate of next rxn

ex. calvin and krebs cycle

What makes enzymes?

ribosomes

Enzyme Locations

Extracellular or Intracellular

Extracellular Enzymes

exoenzymes, made by attached ribosomes on ER and released from cell.

They break down larger macromolecules, ex in digestive system or fungi that secrete enzymes to absorb nutrients bc can't do endocytosis

Intracellular Enzymes

Made by free ribosomes in cytoplasm and used within cell, ex glycolysis

Some are used inside organelles like in krebs cycle in mitochondrial matrix

Types of Reactions

Catabolism and Anabolism

Catabolism

Breakdown, polymers to monomers via hydrolysis

Exergonic, releases energy (deltaG < 0), reactants have more energy than products.

Spontaneous

ex. digestion/cellular respiration

Anabolism

Synthesis, monomers to polymers via condensation reaction

endergonic, requires energy (deltaG > 0), reactants have less energy than products

Enzyme Structure

Globular protein with specific 3D shapes

Active sites display substrate specificity, the two are complimentary in shape and chemical property and once bound, substrate becomes product

Enzyme Active Sites

Active sites consist of only a few AAs, made by unique folding of polypeptide, and AAs that make up active site are not found next to each other in AA chain

Importance of Enzyme Structure

If any part of structure altered, overall shape and active site may change, and the enzyme will lose its function

Induced-Fit Binding

When substrate and enzyme are close enough, their chemical properties attract each other

This interaction causes BOTH to change in bond angles and bond length, leading to INDUCED FIT

*if there is a second substrate, it binds to another part of the active site, causing it to change shape again*

Brownian Motion

Molecules move randomly in aqueous solutions, substrate and active site must collide for rxn to occur and the two must be aligned for bonding

Attractive forces only work over short distances

**substrates typically move more than enzyme due to smaller size, membrane embedded enzymes don't move at all**

Byproduct of Metabolism

Heat

-transfer of energy never 100% efficient, therefore excess energy lost as heat

-mammals and birds use heat to maintain body temp.

If too much heat...

Body sweats (evaporative cooling)

If not enough heat...

Body shivers, involuntary muscle contractions, or body activates brown fat tissue which has many mitochondria to carry out cellular respiration

Structure Equals Function

Enzyme-substrate specificity, some enzymes are absolutely specific and bind to same substrates only, others are less specific and bind to a group of substrates

*enzyme structure determines its function*

-changes in different parts of the enzyme (even not at active site) will likely change the active site

-changes in active site prevents substrate from binding and therefore stops reaction

Denaturation

Can occur when changes in enzyme structure are too significant to be reversed

What can affect enzyme reaction rates?

Temperature, pH, Substrate Concentration

Temperature

Increase thermal energy = increase kinetic energy = increase particle motion = increase #collisions (and bond vibration rate) = increase reaction rate

-Optimal temperature about 37 C, body temp

Peak enzyme activity = greatest # of molecular collisions

-higher temp (too high) disrupts H-bonds, causing enzyme to denature, active site loses shape and enzyme loses function

*lower temp decreases rxn rate*

pH

adding or removing H+ changes pH

-pH measure {H+}, logarithmic scale, changing pH by 1 alters soln by 10x

Optimal pH

-moving away from this range decreases enzyme activity

-affects enzymes charge and disrupts ionic bonds

-denaturation changes overall shape and decreases enzyme function

-most human enzymes; pH 6-8

-pepsin, pH 2-3

Substrate Concentration

Increase substrate [] = increase enzyme activity = increase rxn rate

-higher substrate [] allows more frequent collisions w/ enzymes, although at some point rxn rate eventually plateaus when all active sites become occupied (saturated) and are unavailable until product is released

**rxn has reached its maximum rate or Vmax (velocity maximum)

Activation Energy

Amount of energy required to begin a chemical reaction, enzymes increase reaction rate by decreasing activation energy

-enzyme binding stresses and destabilizes bonds of substrate, reducing its energy level so less energy required to become a product

*net amount of energy in rxn the same*

How do enzymes affect activation energy?

By acting as templates to allow substrates to reach optimal orientation and place stress on necessary bonds

By acting as suitable microenvironments to maintain certain pH

Types of Inhibition

Non-competitive, Competitive, End-Product Inhibition, Mechanism-Based Inhibition

Non-Competitive Inhibition

Inhibitor binds to allosteric site and changes overall shape of enzyme and therefore its active site

-sometimes the changes activates the enzyme (activator), but typically inhibits

Substrate cannot bind since two are no longer complementary

-because inhibitor does not "compete' with substrate, increase in [substrate] doesn't overcome inhibition

Competitive Inhibition

Inhibitor is structurally and chemically similar to substrate and binds to active site, prevents substrate from binding and remains bound longer than substrate

-increase in [substrate] usually overcomes inhibition

*covalently bonded inhibitors irreversible tho*

Competitive vs Non-Competitive Inhibitors

Competitive: Increasing [substrate] will alter the effect of competitive inhibition bc attaches to same active site, therefore Vmax is eventually the same but Km ([substrate] when rxn rate is 50% of Vmax) is lower

Non-Competitive: Increasing [substrate] will not alter the effect of non-competitive inhibition bc different site, therefore the Vmax is lower in the end

End-Product Inhibition

In chain/cycle pathway, product of one enzyme is used by next enzyme in metabolic pathway until final product made

-if too much final product, the final product acts as a noncompetitive inhibitor by binding to 1st enzyme's active site, stops production

-Once product levels decrease, the increase in [substrate] dislodges the inhibitor and pathway resumes to make product, or substrate attaches to second allosteric site and acts as an activator to cause inhibitor to release

Feedback inhibition regulates amount of final product to conserve energy, intermediate products are not made and do not accumulate

Mechanisms-Based Inhibition

Irreversible Inhibitors, inhibitor permanently binds to active site via covalent bond, results in stable enzyme-inhibitor complex that never forms a product

-may kill organism if the inhibited enzyme is vital

ex. penicillin to kill most gram-positive bacteria (thick cell wall)