enzymes (b1- foundation)

Question 1

definition of an enzyme

Answer 1

protein (biological) catalysts that increase the rate of reaction without undergoing any change themselves

OR

a protein with catalytic properties due to its power of specific activation

Question 2

definitions: substrate, active site, product, ribozymes

Answer 2

substrate: monomers that bind to the active site of an enzyme

active site: area on an enzyme where substrate binds

product: what the enzyme produces

ribozymes: RNA molecules that act as enzymes

Question 3

define the following terms:
- holoenzyme
- apoenzyme
- prosthetic group/cofactor/coenzyme
- prosthetic group
- cofactors
- coenzymes

common MCQ - parts of an enzyme

Answer 3

Holoenzyme: protein + nonprotein (helper parts it needs to function) parts of an enzyme, fully functional active enzyme

Apoenzyme: just the protein part of the enzyme. is inactive by itself and needs a helper (cofactor or coenzyme) to function.

Prosthetic group / Cofactor / Coenzyme: NON PROTEIN helper molecules that attach to the inactive enzyme to make it work properly

Prosthetic group: tightly bound cofactor or coenzyme that stays attached to the enzyme permanently, even after the reaction is complete

Cofactors: if nonprotein part is a metal ion (like Zn2+ or Fe2+), are INORGANIC (non-carbon-based) helpers
- ex. Copper in cytochrome oxidase and Fe²⁺ (Iron in catalase)

Coenzymes: if nonprotein component is a small ORGANIC (carbon based) molecule, often derived from vitamin B, like NAD⁺ and FAD

all coenzymes are derived from vitamins

So, a holoenzyme = apoenzyme (protein) + cofactor/coenzyme (helper)

Question 4

what were the 3 ways that enzymes could be named on before

Answer 4

• either have suffix -ase (glucosidase, urease)
• describe the action (lactase dehydrogenase, adenylyl cyclase)
• special cases = no hints (trypsin, pepsin)

Question 5

what is EC number of enzymes

Answer 5

each enzyme given a 4-number EC code

• first number represents the major class of the enzyme (1-6)

-2nd number: type of reaction catalyzed by enzyme but ends w/ -ase

-3rd and 4th numbers are further classifications

• does not reflect anything ab the amino acid sequence, protein structure, or chemical mechanism

idek if u need to know the details of this

Question 6

IUBMB 6 major classes for enzymes important!!

Answer 6

on the highway, Linda is lonely

EC1. Oxidoreductases

EC2. Transferases

EC3. Hydrolases

EC4. Lyases

EC5. Isomerases

EC6. Ligases

Question 7

EC1. Oxidoreductases + 4 subgroups

Answer 7

catalyze transfer of hydrogen, oxygen, or electrons from 1 substrate to another
- invovled in redox reactions = electron donor/acceptor is also required to complete the reaction (why coenzymes are required in this reaction)

example to know: Pyruvate + NADH ↔
L- Lactate + NAD+
catalyzed by lactate dehydrogenase

subgroups:
1. Oxidases: only 1 function, O2 is added to H atoms from substrate forming H2O or H2O2
- ex. xanthine oxidase, L-amino acid oxidase

2. Dehydrogenases: removal of either hydrogen or electrons from the substrate
- the hydrogen is taken up by special hydrogen acceptors such as NAD+, NADP+, FAD

3. Hydroperoxidases: 2 enzymes in this class = peroxidase and catalase
- both catalyze the decomposition of H2O2 (examples for both on another card- need to know)

4. oxygenases: incorporate O2 into the substrate (monooxygenase- responsible for detoxification, making substrate water soluble to be excreted through urine, deoxygenase)
- exs. phenylalanine hydroxylate, tryptophan dioxygenase

Question 8

EC1: oxidoreductases: hydroperoxidases- 2 enzymes reactions to know

Answer 8

catalase:
2H2O2→2H2O + O2
- rapidly breaks down hydrogen peroxide into water and oxygen, found in liver & blood cells

peroxidase:
H2O2 + AH2 → 2H2O + A
- instead of releasing oxygen, breaks down hydrogen peroxide by transferring oxygen to another molecules (AH2- a reducing agent)

Question 9

cytochrome p450 is the most important example for what class of enzymes

Answer 9

EC1. oxidoreductases

subgroup: oxygenases (specifically monooxygenases, which are responsible for detoxification)

Question 10

difference b/w oxygenase and oxidase

Answer 10

oxygenase: don’t need to remove H to add O

oxidase: need to remove an H to add an O

Question 11

EC2. Transferases + 5 subgroups

Answer 11

transfer functional group (like phosphate or methyl) from one molecule to another, excluding H or O

1. Transminases: exchange -NH2 (amine) groups b/w amino acids and keto acids
- exs. ALT, AST

2. Phosphotransferases (kinases): catalyze transfer of phosphate groups
- exs. hexokinase, creatine kinase

3. Methyl transferases: catalyze transfer of methyl groups (CH3) groups

4. Transpeptidases: catalyze transfer of amino acids or peptides

5. Transacylases: catalyze transfer of acyl groups
- ex. cholesterol acyl transferase

Question 12

example to know of a transferase enzyme

Answer 12

alanine aminotransferase (ALT)

• tested in liver function tests

tranfers amine group from alanine to alpha-ketoglutarate resulting in formation of pyruvate & glutamate

Question 13

EC3. Hydrolases + 3 subgroups

Answer 13

hydrolases: cleavage of different bonds (C-O, C-C, or C-N) by the addition of water (hydrolysis)

1. Protein hydrolyzing enzymes (proteolytic enzymes:
A. Exopeptidases: hydrolysis of terminal peptide bonds (remove amino acids from the ends of the protein)
0 tripeptidases, dipeptidases
B. endopeptidases: cut peptide bonds within the protein
- ex. pepsin, trypsin, chymotrypsin, and elastase

2. carbohydrates: hydrolyze glycosidic bonds (ex. amylase, maltase, sucrase, lactase)

3. lipid hydrolyzing enzymes: lipases, cholesteryl esterases, phospholipases

Question 14

EC4. Lyases + example to know

Answer 14

enzymes that break chemical bonds without using water (H₂O) or oxidation-reduction reactions
- usually form a double bond or a new ring structure in the process

ATP-Citrate Lyase: converts citrate into acetyl-CoA and oxaloacetate using ATP

reaction: Citrate + CoA + ATP→Acetyl-CoA + Oxaloacetate + ADP + Pi

Question 15

EC5. Isomerases + example to know

Answer 15

isomerases: rearrange atoms within a molecule to form an isomer - do not add or remove atoms, only rearrange them!

phosphoglucose isomerase: converts glucose-6-phosphate (G6P) to fructose-6-phosphate (F6P) in glycolysis

Question 16

EC6. Ligase + example to know

Answer 16

ligases: join (ligate) 2 molecules together using ATP or another energy source, forming new chemical bonds (usually C-O, C-N, C-S, or C-C bonds)

DNA ligase: seals breaks in DNA strands by forming phosphodiester bond b/w nucleotides

Question 17

structure of an enzyme

Answer 17

enzymes are proteins with a globular shape and complex 3-D structure

Question 18

coenzymes are commonly derived from what

Answer 18

vitamins

• ex. NAD+ contains niacin, and Fad contains riboflavin

Question 19

active site

Answer 19

part of an enzyme where substrate molecules bind and a chemical reaction takes place

made up of:
- binding site (area on enzyme that specifically recognizes and binds to substrate, positioning it correctly for reaction to take place at catalytic site)
- catalytic site (where chemical reaction actually occurs, facilitating catalysis of a substrate)

shape and chemical environment inside active site is what allows a chemical reaction to proceed more easily

Question 20

substrate

Answer 20

reactants that are activated by the enzyme

• enzymes are specific to their substrates; specificity is determined by active site

Question 21

activation energy (Ea)

Answer 21

difference in energy b/w the reactants and the transition state (high-energy intermediate that is formed during the conversion of reactant to product)

therefore, molecules are in transition state during this time (top of the curve is called the transition state)

Question 22

how do enzymes affect the energy of activation and the overall equilibrium of the reaction?

Answer 22

enzymes lower the activation energy, but keep the overall equilibrium the same because they do not change the free energies of the reactions or products (only make it faster to get there)

• this is because greater the energy of activation = slower the reaction and vice versa

Question 23

hyperbolic curve vs sigmoidal curbe

Answer 23

hyperbolic is when it goes up and then starts to level off
- ex. enzymes that follow michaelis-menten

sigmoidal is when it sort of looks like an S
- ex. allosteric enzymes

Question 24

Fischer’s template theory

Answer 24

also called lock and key model

• enzyme is like a LOCK while substrate is like a KEY
• active site of enzyme is a rigid structure and the exact fit substrate needs to bind to unlock it

later found that the induced fit model is a better representation as the enzyme is a bit more flexible and can also change slightly to accommodate the substrate

Question 25

Induced fit model (koshland)

Answer 25

- more updated explanation on how enzymes work when substrate comes close, active site **changes shape** slightly yo fit in better (like glove adjusting to hand) = substrate induces change in enzyme's conformation helps enzyme **hold substrate tighter** and catalyze reaction more efficiently

Question 26

the 3 steps of enzyme catalyzed reactions

Answer 26

**1. Formation of enzyme substrate complex (ES - enzyme-substrate complex)** - fischer's theory & induced fit model **2. Conversion of substrate to product (EP - enzyme-product complex)** - reactants are activated before the reaction to reach a transition state - transition state is followed by conversion of reactants to produced through the chemical reaction **3. Release of product from the enzyme** - product is release from enzyme-product complex - enzyme is reused for catalyzing other reactions

Question 27

the 4 mechanisms for catalysis

Answer 27

**1. Catalysis By Proximity**: higher the conc. of substrate molecules = greater the rate of reaction - if substrate present near enzyme = higher chance of reaction **2. Acid Base Catalysis**: Ionizable (charge can change) functional groups of the aminoacyl side chains can act as acids/bases - enzyme = proteins so active site = amino acids - diff amino acids have different charges - so need substrate & enzyme both to be the right charge (opposites attract) in order for reaction to occur **3. Catalysis by Strain**: binding of substrate in an unfavorable conformation causes bonds of substrate to strain and then break - change in shape of enzyme is acc straining the enzyme's bonds too but they dont break, only the substrate's bonds break **Covalent catalysis**: NEW temporary covalent bond between enzyme and substrate until reaction is done - holding everything in place until the reaction is over - once reaction is done = temporary bonds broken and enzyme returns to original state *to remember- think mechanism PASC the test*

Question 28

what is reaction velocity

Answer 28

rate or velocity of a reaction (v) is the number of substrate molecules converted to product per unit time - usually expressed as **μmol of product formed per second**

Question 29

what is the optimum temperature for most human enzymes

Answer 29

between **35ºC-40ºC** - normal body temp is **37ºC**

Question 30

factors affecting enzyme activity: 1. substrate concentration + graph

Answer 30

rate of reaction of enzyme-catalyzed **increases with substrate concentration** until a maximal velocity is reached (Vmax) - *graph looks like a straight line* levels off b/c high substrate conc. becomes **saturated** with substrate of all available binding sites (more substrate, not enough binding sites) - unless you add more enzymes, then it will change

Question 31

factors affecting enzyme activity: **2. effect of temp** + graph

Answer 31

temp increased = increase in **kinetic energy** - more molecules have energy to cross the energy barrier = **reaction rate goes up** - more **collisions** also occur = more chance of reaction & product formation but only good til a certain temp, then enzymes get **denatured** **most enzymes fully denature at 70ºC** *graph looks like upside down parabola*

Question 32

factors affecting enzyme activity: 3. effect of pH + graph

Answer 32

- effect of pH differs with different enzymes - **extremes** of pH can **denature** enzymes - reactions usually require that enzymes and substrates have specific chemical groups in either **ionized or unionized** (neutral) state - ex. might require NH2 (amino) group to be in protonated form (NH3+) but alkaline pH deprotonates it - rate of that reaction would decline *graph is also a bunch of upside down parabolas depending on the enzyme*

Question 33

human optimal pH; optimum pH values of pepsin & trypsin

Answer 33

**human pH**: 7.35-7.45 **pepsin**: 2 **trypsin**: around 8

Question 34

2 types of enzyme inhibitors + example

Answer 34

**irreversible**: bind to enzymes through covalent bonds - *lead = forms covalent bonds 2/ sulfhydryl side chain of cysteine in proteins* - *ferrochelatase = enzyme involved in heme synthesis, is irreversibly inhibited by lead* **reversible**: bind to enzymes through non-covalent bonds, forming enzyme-inhibitor complex - *dilution of enzyme-inhibitor complex dissociates the inhibitor and recovers enzyme activity* - 2 types: competitive & noncompetitive *inhibitors should be specific and work at low conc. (to not kill other enzymes and become dangerous)*

Question 35

3 methods of enzyme activity regulation (when asked how enzyme activity is regulated, have to write these 3 down) *different from inhibitors*

Answer 35

1. Allosteric regulation 2. Regulation by covalent modification 3. Regulation by induction/repression of enzyme synthesis

Question 36

enzyme activity regulation: **allosteric regulation**

Answer 36

allosteric enzymes are regulated by **effectors** that act [by non-covalently bonding] on a site other than the binding site (active site) - **negative effectors**: inhibit enzyme activity - **positive effectors**: increase enzyme activity - do not follow michaelis-menten kinetics (hyperbolic curve) **Act by**: - Modifying the affinity of enzyme for substrate - Modifying the catalytic activity of enzyme - Homotropic ---the substrate itself (sigmoidal curve) - Heterotropic--- feed back inhibition - (change the shape so substrate cant bind)

Question 37

homotropic vs heterotropic effectors in allosteric regulation + examples for both

Answer 37

**homotropic**: substrate itself serves as effector (allosteric regulator) - usually positive effector so said to follow **cooperative binding** - presence of substrate at one site on the enzyme enhances catalytic properties of the other substrate binding sites - show **sigmoidal curve** **example: O2 in hemoglobin**: 1 hemoglobin can bind with 4 O2 molecules, when 1 molecule of O2 binds, it makes the others' binding easier by changing shape change in entire protein **heterotropic**: effector is a different molecule from the substrate - enzyme has an allosteric site for the end product where product binds and inhibits the reactions - simply because of product accumulation = **feedback inhibition** **example: inhibition of phosphofructokinase-1 (PFK-1) by citrate**: PFK-1 is a key enzyme in glycolysis and citrate is a product of glycolysis, when citrate levels are high, citrate binds to allosteric site on PFK-1 enzyme changing its shape and reducing its activity

Question 38

regulation of enzyme activity: **2. covalent modification**

Answer 38

covalent modification mostly done by addition/deletion of **phosphate groups** to serine, threonine, or tyrosine residues of the enzyme **kinases**: enzymes that add phosphate groups using ATP as the phosphate donor **phosphatases**: enzymes that remove phosphate groups - different enzymes also respond differently to phosphorylation: - **glycogen phosphorylase** (degrades glycogen) increases its activity when phosphorylated - **glycogen synthase** (synthesizes glycogen) decreases its activity when phosphorylated

Question 39

regulation of enzyme activity: **3. induction and repression of enzyme synthesis**

Answer 39

regulate amount of enzyme present by increasing (**induction**) or decreasing (**repression**) enzyme synthesis (the amount of enzymes being made) - mostly for enzymes that are needed at one stage (*not used for enzymes that are in constant use*) - process is **slow** and can take hours to days *ex. you diet and stop eating carbs, so body starts to produce less carb metabolism enzymes* **example in book**: constantly high blood glucose levels→ elevated levels of insulin→ increase in synthesis of enzymes involved in glucose metabolism

Question 40

michaelis-menten equation

Answer 40

proposed model that describes how rate of an enzyme-catalyzed reaction depends on the substrate concentration - in this model, enzyme reversibly combines with substrate to form an ES complex that subsequently yields product, regenerating the free enzyme **V0 = (Vmax[S])/(Km+[S])** - velocity is proportional to conc. of reacting molecules

Question 41

**michaelis-menten equation**: what does Km represent and how to find it?

Answer 41

Km = equal to value of substrate when Vmax is 1/2 Km represents the **affinity of enzyme for substrate** (measures how much substrate is needed for the enzyme to work efficiently) **low Km = high affinity** (because enzyme binds tightly to substrate so it works well even at low substrate concentrations) **high Km = low affinity** (enzyme needs more substrate to work effectively) - so the Km closer to 0 is the one with more affinity (makes sense too b/c that graph is steeper too showing faster velocity)

Question 42

**Michaelis-Menten**: initial velocity, first order reaction, zero order reaction

Answer 42

**initial velocity**: as soon as enzyme and substrate are mixed **first order**: when [S] is less than Km → graph shows direct relationship (at low substrate conc.) **zero order**: when [S] is more than Km → graph is kind of trailing off (at high substrate conc.) *reference point on graph is Km point*

Question 43

line weaver-burke + equation

Answer 43

harder to find Vmax when hyperbolic curve so plot **1/Vo vs 1/[S]** instead = straight line - aka double reciprocal plot **1/V0 = (Km/Vmax[S])/(1/Vmax)** **-1/Km = x intercept 1/Vmax = y intercept**

Question 44

what do Vo and Vmax represent in Michaelis menten?

Answer 44

**Vo (initial velocity**: speed of the reaction when the substrate is first added **Vmax (max velocity)**: fastest speed the enzyme can work when all active sites are occupied

Question 45

noncompetitive inhibition vs allosteric regulation

Answer 45

both bind to sites other than active site but noncompetitive inhibition specifically **prevents enzyme function** whereas allosteric regulation **controls enzyme activity** as needed - allosteric can be inhibitory or activating but noncompetitive is always inhibitory

Question 46

competitive & noncompetitive inhibitors: effect on Vmax, Km **important**

Answer 46

**competitive**: Vmax remains the same while *Km increases* *because decreases affinity for enzyme if competing for the same spot* **noncompetitive**: *Vmax decreases* (b/c enzyme activity is reduced) and Km remains the same (affinity of enzyme for substrate remains the same)

Question 47

example of **noncompetitive inhibitor** drug

Answer 47

**oxypurinol (alluprinol)** is non competitive inhibitor of xanthine oxidase involved in purine degradation

Question 48

example of **competitive inhibitor** drug

Answer 48

**statin drugs** which compete with enzyme HMG-CoA reductase for cholesterol synthesis

Question 49

Suicide inhibition + example

Answer 49

*aka mechanism based inhibition* inhibitor is a structural analogue, converted to **more effective inhibitor by enzyme itself**, permanent complex formed *ex. allupurinol converted to alloxantlhine by xanthine oxidase*

Question 50

example of irreversible inhibitor

Answer 50

toxins and poison inhibition of **ferrochelatase** by lead - enzymes with thiol groups are irreversibly inhibited by heavy metals

Question 51

2 examples of enzyme inhibitors as drugs (hypertension & antibiotics)

Answer 51

**beta-lactam antibiotics (e.g. penicillin & amoxillin)**: inhibit enzymes involved in cell wall synthesis of bacteria - *irreversible inhibition* **angiotension converting enzyme inhibitors**: *captorpil & enalapril* for treatment of hypertension - are ACE inhibitors

Question 52

proenzymes (zymogens) + examples

Answer 52

inactive forms of enzymes that only turn on when they are required *ex. blood clot lytic enzymes only active when blood clot is formed* also: pepsinogen (inactive) becomes pepsin (active) in the stomach when there is food

Question 53

what vitamins are the following enzymes derived from: - NAD, NADP - FMN, FAD - TPP

Answer 53

**NAD, NADP**: nicotinamine **FMN, FAD**: riboflavin **TPP**: thiamine

Question 54

name the metals that the following enzymes are derived from: - Carbonic anhydrase - Hexokinase - Phosphoglucomutase - Cytochrome oxidase - Lipase - Xanthine oxidase

Answer 54

**Zinc**: Carbonic anhydrase **Magnesium**: Hexokinase **Manganese**: Phosphoglucomutase **Copper**: cytochrome oxidase **Calcium**: Lipase **Molybdenum**: Xanthine oxidase

Question 55

list 4 coenzymes and their functions

Answer 55

**Coenzyme A**: activation of fatty acids **Thiamine pyrophosphate**: Pyruvate dehydrogenase complex **Biotin**: Carboxylation reactions **Ascorbic acid**: Hydroxylation reactions

Question 56

what are isoenzymes?

Answer 56

physically distinct forms of the same enzyme that differ in their amino acid sequences & number but catalyze the same reaction *creatine kinase exists in 3 isoforms while lactate dehydrogenase on electrophoresis gives 5 bands*

Question 57

the 3 isoenzymes of creatine kinase and which one is used for diagnosing myocardial infarction

Answer 57

**CK1**: BB (present in brain, smooth muscles of GIT and urinary tract) **CK2**: MB: myocardium (35%), HIGH LEVELS IN BLOOD DURING ACUTE MYOCARDIAL INFARCTION **CK3**: MM (in skeletal muscles)

Question 58

5 Isoenzymes of LDH

Answer 58

**LDH 1**: HHHH **LDH 2**: HHHM **LDH 3**: HHMM **LDH 4**: HMMM **LDH 5**: MMMM *think no M, 1 M, 2 M, 3 M, 4 M*

Question 59

2 types of plasma enzymes

Answer 59

1. small group of enzymes **secreted into the blood by certain cells** (like the liver secreting zymogens [inactive form of enzymes] of blood coagulation 2. large group of enzymes released during **normal cell turnover** (these enzymes function intracellularly and have constant blood levels in healthy individuals) - *rate of release from damaged cells = rate of removal of enzymes from blood* - like cleanup crew, these enzymes are being disposed into blood stream but too much of them shows tissue damage or an irregularity

Question 60

increased levels of enzyme alanine aminotransferase (ALT) indicates what?

Answer 60

damage to the liver (acute hepatitis)

Question 61

plasma vs serum

Answer 61

**plasma**: physiological fluid, contains blood coagulants **serum**: prepared in lab, obtained by centrifugation of whole blood after it has been allowed to coagulate, does not contain blood coagulants

Question 62

what enzyme levels are increased in the blood during acute pancreatitis?

Answer 62

**amylase**: increased about 1000x - mild increase in mumps as well **lipase**: highly elevated, but not as much as amylase - not increased in mumps

Question 63

2 enzymes as therapeutic agents

Answer 63

**streptokinase**: treatment of myocardial infarction **asparaginase**: anti cancer

Question 64

what enzyme levels are increased in **mumps**?

Answer 64

alpha-amylase (AMS)

Question 65

what is normal cell turnover?

Answer 65

**cell turnover**: old/damaged cells are constantly being removed and replaced by new cells - when cells die, they release enzymes into the blood *small amount of enzymes is normal in blood but excessive amounts indicates diseases* **rate of release from damaged cells = rate of removal of enzymes from blood**

Question 66

what are other enzymes can be used for myocardial infraction?

Answer 66

**creatine kinase** (MB- CK2) & **troponin** (protein) - these are **specific to heart attack** *lactate dehydrogenase & AST (aspartate aminotransferase)* - not as specific to heart attack but can also be elevated

Question 67

other enzymes used for diagnosis of liver disease

Answer 67

**alanine amino transferase (ALT)**: more specific **aspartate amino transferase (AST)**: more sensitive - will rise faster when tissue is damaged while others hasn't raised yet - alkaline phosphate - gamma glutamyl transferase (GGT)

Question 68

what type of enzymes are GIT enzymes?

Answer 68

**hydrolases** - they're hydrolytic enzymes that use water to cleave chemical molecules *ex. proteases, glycosidases, lipases*

Question 69

role of hydrochloric acid in the stomach

Answer 69

to **activate pepsinogen to pepsin**