Chapter 4 - Enzymes and Energy

Question 1

Enzymes are considered what type of organic molecule? Be specific

Answer 1

protein; quaternary structure of protein

Question 2

Label this reaction (substrate and products)
What does the enzyme react with?

C <- A + B

Answer 2

A + B: substrate
C: product

Enzyme reacts with the substrate

Question 3

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?

Answer 3

with enzyme: rate of rxn would proceed faster
without enzyme: rate of rxn would still proceed, but much slower

Question 4

What are the building blocks of enzymes?

Answer 4

amino acids

enzymes are considered a protein; therefore, they must be composed of amino acids

Question 5

What do enzymes do?

Answer 5

• 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)

Question 6

How do enzymes speed up/catalyze chemical reactions?

Answer 6

enzymes lower the activation energy (Ea) of the rxn

Question 7

Define activation energy (Ea)

Answer 7

the “initial energy” that a chemical reaction has to overcome for reaction to occur

Question 8

The lower the Ea, the ____ it is to overcome it -> chemical reaction will occur ____

Answer 8

easier
faster

Question 9

Define an active site

Answer 9

a region of an enzyme that binds to a substrate during a reaction

Question 10

The function of an enzyme is dictated by its ______

Answer 10

structure

protein structure -> protein function

Question 11

Describe the appearance of an enzyme

Answer 11

• 3-D shape
• pockets that serve as active sites (substrates bind to active site)

Question 12

What happens when a substrate binds to the active site of an enzyme?

Answer 12

the original bonds of the substrate become weak and allows them to break easily

Question 13

Compare the shape/structure of an enzyme before and after the chemical reaction

Answer 13

the shape/structure of the enzyme remains the same before and after the chemical reaction

only the substrates change shape

Question 14

How would you identify an enzyme?
Give examples of some enzymes

Answer 14

usually ends in suffix “-ase”

the first part of the name applies to function of enzyme

ex: catalase, amalase, carbonic anhydrase

Question 15

What are the functions of the different types of enzymes?

Answer 15

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”

Question 16

What factor do you look at to determine enzyme activity?

Answer 16

enzyme activity is measured by the rate at which a substrate is converted to a product

Question 17

What factors can influence enzyme activity?

Answer 17

TP CoCes Si

• temperature
• pH
• concentration of cofactors and coenzymes
• concentration of enzyme and substrate
• stimulatory/inhibitory effects of products on enzyme function

Question 18

Describe the effects temperature has on enzyme activity

Answer 18

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

Question 19

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?

Answer 19

past optimum temperature: denaturation

below optimum temperature: slow rate of enzyme activity -> slower chemical reaction

Question 20

True or false: All human enzymes have the same optimum pH. Explain why true or false.

Answer 20

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)

Question 21

Enzymes exhibit peak activity within a ________ pH range

Answer 21

narrow

Question 22

What will happen if the pH changes away from the optimal pH?

Answer 22

• rxn will proceed slower bc enzyme activeity is slowed
• enzyme can also denature and lose its shape ->loss of function

Question 23

What are co-factors?

Answer 23

• non-protein molecules
• include metal ions (Ca2+, Mg2+, Cu2+, Zn2+) or coenzymes (small organic molecules, usually vitamins)

Question 24

Where do cofactors and coenzymes attach?

Answer 24

cofactors attach away from the active site (allosteric site)

coenzymes attach at the active site

Question 25

What is the function of cofactors/coenzymes in relation to enzyme activity?

Answer 25

help to maintain shape of enzyme and active site so enzyme can bind to substrate almost all enzymes require cofactors

Question 26

Compare the different types of enzymes in regards to cofactors

Answer 26

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 ## Footnote zymogen is an inactive and immature protein and must be modified into its useful form

Question 27

Where is zymogen found? How do you identify it? Give an example of a proenzyme that is found in the body

Answer 27

- zymogen is usually found in the digestive system - end in "ogen" - ex. pepsinogen -> pepsin ## Footnote pepsinogen is the immature/inactive form; pepsin is the enzyme and is mature and active

Question 28

Explain phosphorylation vs. dephosphorylation

Answer 28

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

Question 29

True/False: Phosphorylate enzymes are activated enzymes (enzymes that are turns "on")

Answer 29

False; phosphorylated enzymes can either by active or inactive

Question 30

Sometimes a single enzyme can drive a reaction in ___ directions depending on the ______ of substrate or product

Answer 30

two concentration

Question 31

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

Answer 31

if the concentration of CO2 + H2O are high, rxn proceeds right if the concentration of H2CO3 is high, rxn proceeds left

Question 32

True/False: Most chemical reactions in the body occur by a series of chemical reactions

Answer 32

true; one chemical reaction leads to a series of other chemical reactions

Question 33

What are metabolic pathways?

Answer 33

a series of enzyme-catalyzed reactions begin with initial substrate, and end with a final product, with many enzymatic steps along the way

Question 34

What are the different types of metabolic pathways?

Answer 34

linear metabolic pathway branched metabolic pathway (most common); includes branches where several products can be produced

Question 35

Describe end product inhibition

Answer 35

a final product inhibits the branch point enzymes and shifts the chemical reaction toward an alternate path (negative feedback)

Question 36

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?

Answer 36

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

Question 37

Define "inborn errors of metabolism." What will happen within the chemical reaction?

Answer 37

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)

Question 38

Describe Tay-Sachs Disease (what is it, what causes it, effects) GM2 -------------------------> GM3 hexosaminidase A

Answer 38

- 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

Question 39

What is Tay-Sachs Disease also known as? Why is it known as this?

Answer 39

lysosomal storage disease known as this because lysosomes become bulged due to increase in fatty substance (GM2)

Question 40

How to identify Tay-Sachs disease

Answer 40

- symptoms around 6 months - exaggerated startling response to noise - progressive blindness; cherry red spots in macula - narrow eye blood vessels

Question 41

Define enzyme kinetics

Answer 41

study of the rates of enzyme-catalyzed chemical reactions

Question 42

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

Answer 42

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

Question 43

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?

Answer 43

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

Question 44

The Michaelis-Menten Enzyme Kinetics is a mechanism that explains the _______ of enzyme-catalyzed reactions

Answer 44

velocity

Question 45

What is Km

Answer 45

is the substrate concentration (on x-axis) at 1/2 vmax it measures the enzyme "affinity" for a substance (bond strength with substrate)

Question 46

Km indicated how "_________" the enzyme is

Answer 46

potent

Question 47

Describe the relationship between km and affinity.

Answer 47

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)

Question 48

How does the lineweaver-burk plot different from a michaelis-menten enzyme kinetics graph?

Answer 48

- it is straightens curves of m-m graph - double reciprocal plot (1/[S] x-axis, 1/V for y-axis)

Question 49

What is the main purpose of the lineweaver-burk plot?

Answer 49

helps to visualize the effects of different types of enzyme inhibitors on an enzyme-catalyzed reaction 1. competitive enzyme inhibitor 2. noncompetitive enzyme inhibitor

Question 50

Compare the different types of enzyme inhibition

Answer 50

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

Question 51

What does a competitive inhibitor do? Can this reach Vmax? Why/why not?

Answer 51

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)

Question 52

What does a noncompetitive inhibitor do? Can this reach Vmax? Why/why not?

Answer 52

- 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

Question 53

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?

Answer 53

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.