Chapter 4 - Enzymes and Energy Flashcards
Enzymes are considered what type of organic molecule? Be specific
protein; quaternary structure of protein
Label this reaction (substrate and products)
What does the enzyme react with?
C <- A + B
A + B: substrate
C: product
Enzyme reacts with the substrate
A chemical reaction can still occur without an enzyme present. How would this reacion be different in comparison to a chemical reaction with an enzyme present?
with enzyme: rate of rxn would proceed faster
without enzyme: rate of rxn would still proceed, but much slower
What are the building blocks of enzymes?
amino acids
enzymes are considered a protein; therefore, they must be composed of amino acids
What do enzymes do?
- enzymes catalyze (speed up) chemical reactions by increasing the reaction rate throusands of times faster
- enzymes are NOT changed or used up by the reaction (so can be used again)
How do enzymes speed up/catalyze chemical reactions?
enzymes lower the activation energy (Ea) of the rxn
Define activation energy (Ea)
the “initial energy” that a chemical reaction has to overcome for reaction to occur
The lower the Ea, the ____ it is to overcome it -> chemical reaction will occur ____
easier
faster
Define an active site
a region of an enzyme that binds to a substrate during a reaction
The function of an enzyme is dictated by its ______
structure
protein structure -> protein function
Describe the appearance of an enzyme
- 3-D shape
- pockets that serve as active sites (substrates bind to active site)
What happens when a substrate binds to the active site of an enzyme?
the original bonds of the substrate become weak and allows them to break easily
Compare the shape/structure of an enzyme before and after the chemical reaction
the shape/structure of the enzyme remains the same before and after the chemical reaction
only the substrates change shape
How would you identify an enzyme?
Give examples of some enzymes
usually ends in suffix “-ase”
the first part of the name applies to function of enzyme
ex: catalase, amalase, carbonic anhydrase
What are the functions of the different types of enzymes?
DIKP
- dehydrogenases: remove hydrogen atoms
- isomerases: rearrange the atoms
- kinases: add phosphate group
- phosphatases: remove phosphate group
kinases and phosphatases are antagonistic
isomerases - “-iso” means “the same”
What factor do you look at to determine enzyme activity?
enzyme activity is measured by the rate at which a substrate is converted to a product
What factors can influence enzyme activity?
TP CoCes Si
- temperature
- pH
- concentration of cofactors and coenzymes
- concentration of enzyme and substrate
- stimulatory/inhibitory effects of products on enzyme function
Describe the effects temperature has on enzyme activity
an increase of temperature will increase the rate of reactions (until the temperature reaches a few degrees above body temperature)
after reaching max activity, denaturation occurs
All enzymes operate best at an optimum/preferred temperature. What will likely happen to the enzyme past the optimum temperature? What will likely happen to the enzyme below the optimum temperature?
past optimum temperature: denaturation
below optimum temperature: slow rate of enzyme activity -> slower chemical reaction
True or false: All human enzymes have the same optimum pH. Explain why true or false.
False, the ideal pH depends on the pH of the fluid the enzyme is found in
stomach (acidic: 1-2)
saliva (neutral: 7)
small intestine (alkaline: 9-10)
Enzymes exhibit peak activity within a ________ pH range
narrow
What will happen if the pH changes away from the optimal pH?
- rxn will proceed slower bc enzyme activeity is slowed
- enzyme can also denature and lose its shape ->loss of function
What are co-factors?
- non-protein molecules
- include metal ions (Ca2+, Mg2+, Cu2+, Zn2+) or coenzymes (small organic molecules, usually vitamins)
Where do cofactors and coenzymes attach?
cofactors attach away from the active site (allosteric site)
coenzymes attach at the active site
What is the function of cofactors/coenzymes in relation to enzyme activity?
help to maintain shape of enzyme and active site so enzyme can bind to substrate
almost all enzymes require cofactors
Compare the different types of enzymes in regards to cofactors
apoenzyme - enzyme without a cofactor
holoenzyme - enzyme with a cofactor
zymogen (proenzyme) - inactive form (precursor) of an enzyme; needs to be modified to become active form of enzyme
zymogen is an inactive and immature protein and must be modified into its useful form
Where is zymogen found?
How do you identify it?
Give an example of a proenzyme that is found in the body
- zymogen is usually found in the digestive system
- end in “ogen”
- ex. pepsinogen -> pepsin
pepsinogen is the immature/inactive form; pepsin is the enzyme and is mature and active
Explain phosphorylation vs. dephosphorylation
enzymes can be activated or inhibited either by adding a phosphate group (phosphorylation) or removal of phosphate group (dephosphorylation)
kinases will add a phosphate group, while phosphatases remove a phosphate group
a phosphorylated enzyme and dephosphorylated enzyme can either be active or inactive
True/False: Phosphorylate enzymes are activated enzymes (enzymes that are turns “on”)
False; phosphorylated enzymes can either by active or inactive
Sometimes a single enzyme can drive a reaction in ___ directions depending on the ______ of substrate or product
two
concentration
This is a reversible reaction. The enzyme is carbonic anhydrase. Explain which way the reactions will proceed if the concentration of CO2 + H20 are high. Which way will it go if the concentration of carbonic acid is high?
CO2 + H2O - H2CO3
if the concentration of CO2 + H2O are high, rxn proceeds right
if the concentration of H2CO3 is high, rxn proceeds left
True/False: Most chemical reactions in the body occur by a series of chemical reactions
true; one chemical reaction leads to a series of other chemical reactions
What are metabolic pathways?
a series of enzyme-catalyzed reactions
begin with initial substrate, and end with a final product, with many enzymatic steps along the way
What are the different types of metabolic pathways?
linear metabolic pathway
branched metabolic pathway (most common); includes branches where several products can be produced
Describe end product inhibition
a final product inhibits the branch point enzymes and shifts the chemical reaction toward an alternate path (negative feedback)
In end product inhibition, how does the final product(s) inhibit an enzyme? How does this effect the pathway?
What is this process known as?
the product binds to the enzyme away from active site (allosteric site) -> 3D shape of enzyme changes -> substrate cannot bind due to active site change
one pathway will become favored
allosteric inhibition
Define “inborn errors of metabolism.” What will happen within the chemical reaction?
inborn errors of metabolism: occur when an abnormal gene (DNA) makes a defective enzyme (protein)
substrate will not be able to bind to the enzyme, and there is no chemcal reaction: leads to a loss of one end-product, and lead to the accumulation of a different end product (can be lethal or non-lethal)
Describe Tay-Sachs Disease (what is it, what causes it, effects)
GM2 ————————-> GM3
hexosaminidase A
- inherited, neurological disorder (fatal)
- caused by a mutation in gene that codes for hexosaminidase A (is a required enzyme, deficient in it)
- accumulation of GM2 (fatty material) and decrease in GM3 -> bulging lysosomes -> damaged neuron
What is Tay-Sachs Disease also known as?
Why is it known as this?
lysosomal storage disease
known as this because lysosomes become bulged due to increase in fatty substance (GM2)
How to identify Tay-Sachs disease
- symptoms around 6 months
- exaggerated startling response to noise
- progressive blindness; cherry red spots in macula
- narrow eye blood vessels
Define enzyme kinetics
study of the rates of enzyme-catalyzed chemical reactions
What is labeled on the x and y axis of a substrate concentration graph?
What are the effects of substrate concentration on reaction rates? Does this mean the graph will have a plateau? Why/why not
x-axis: substrate concentration
y-axis: reaction rate
as substrate concentration increases -> reaction rate increase initially -> stops increasing after certain substrate concentration
will have a plateau because there is a limited supply of enzyme concentration, meaning it will plateau when all active sites are occupied
What is labeled on the x and y axis of an enzyme concentration graph
What are the effects of enzyme concentration on reaction rate? Does this mean the graph will have a plateau? Why/why not?
x-axis: enzyme concentration
y-axis: rate of reaction (speed)
as enzyme concentration increases, the reaction rate increases
no plateau because there is unlimited supply of substrate and enzyme, meaning rxn rate increases indefinitely
The Michaelis-Menten Enzyme Kinetics is a mechanism that explains the _______ of enzyme-catalyzed reactions
velocity
What is Km
is the substrate concentration (on x-axis) at 1/2 vmax
it measures the enzyme “affinity” for a substance (bond strength with substrate)
Km indicated how “_________” the enzyme is
potent
Describe the relationship between km and affinity.
inverse relationship
lower km -> higher affinity (strong bond, enzyme is effective in catalyzing rxn)
higher km -> lower affinity (weak bond, enzyme NOT effective in catalyzing rxn)
How does the lineweaver-burk plot different from a michaelis-menten enzyme kinetics graph?
- it is straightens curves of m-m graph
- double reciprocal plot (1/[S] x-axis, 1/V for y-axis)
What is the main purpose of the lineweaver-burk plot?
helps to visualize the effects of different types of enzyme inhibitors on an enzyme-catalyzed reaction
- competitive enzyme inhibitor
- noncompetitive enzyme inhibitor
Compare the different types of enzyme inhibition
competitive inhibition
- binds at active site -> blocks substrate
- mimics substrate (imposter)
- enzyme shape not changed
non-competitive inhibition
- binds at allosteric site -> changes enzyme shape -> enzyme is non-functional
- substrate will never be able to bind to enzyme
- AKA allosteric inhibitor
What does a competitive inhibitor do?
Can this reach Vmax? Why/why not?
competes with substrate for the active site -> reduces rate of rxn
competitive inhibitors can be overcome at a higher substrate concentration (vmax can be reached)
What does a noncompetitive inhibitor do?
Can this reach Vmax? Why/why not?
- does NOT use active site of enzyme
- changed conformational shape of enzym e
- substrate will NEVER be able to bind to enzyme
noncompetitive inhibitors cannot be overcome.
increasing the [substrate] will still increase the reaction rate, but because the enzyme is permanently altered, further increasing the [substrate] will never allow for the same Vmax to be reached
Why can we overcome the effects of a competitive inhibitory, but not the effects of a non-competitive inhibitor? What must be done to overcome the effects of a competitive inhibitor?
NCI cannot be overcome because they permanently alter the shape of the active site of an enzyme, meaning the substrate will never be able to bind to it. Competitive inhibitors do not change the shape of the enzyme, but instead, they compete with the normal substrates for the active site.
To overcome the effects of the competitive inhibitor, increasing [S] will increase the likelihood of substrate binding to active site as normal.
