Biochem Block 2

Front 1

How is activity obtained?

Back 1

Activity obtained by determining the rate of enzyme-catalyzed reaction under defined conditions

Front 2

What is velocity rate?

Back 2

Velocity (rate) v is generally expressed as rate of conversion of substrate to product per minute

Front 3

What is a holoenzyme? Apoenzyme?

Back 3

Holoenzyme enzyme with cofactor
Apoenzyme protein portion of holoenzyme

If cofactors absent apoenzyme typically does not show biological activity

Front 4

What is an example of prosthetic group?

Back 4

Biotin in carboxylases

Front 5

When is a high energy intermediate formed?

Back 5

Free energy of activation
This peak represents transition state

High-energy intermediate is formed

Front 6

What is transition state stabilization?

Back 6

1. transition state stabilization
active site frequently acts as flexible molecular template for the substrate
geometry representing activated transition state
greatly increases the concentration of reactive intermediate

Front 7

Oxidoreductase

Back 7

Oxidoreductase – catalyzes redox reactions e.g. lactate dehydrogenase

Front 8

Transferase

Back 8

Transferase – transfers C,N or P containing groups e.g. serine hydroxymethyl transferase

Front 9

Hydrolase

Back 9

Hydrolase – cleavage of bonds by addition of water e.g. urease

Front 10

Lyase

Back 10

Lyase – cleavage of C-C C-S or N-C bonds e.g.pyruvate decarboxylase

Front 11

Isomerase

Back 11

Isomerase – racemisation of optical or geometric isomers e.g. methylmalonyl CoA mutase

Front 12

Ligase

Back 12

Ligase – formation of new bonds between C and O,S or N

Front 13

What are coenzymes?

Back 13

May be metal ions, or organic molecules (coenzymes)

Front 14

What is a prosthetic group?

Back 14

Type of cofactor that A tightly bound coenzyme that doesn’t dissociate

Front 15

What is an example of Cofactor?

Back 15

Cofactor- NADH

Front 16

What happens if the energy barrier is high?

Back 16

If the barrier is high, few molecules will have enough energy to react, and the reaction will proceed slowly.

Front 17

What is velocity?

Back 17

Velocity is the number of S molecules converted per unit time. Usually in μmol/min

Front 18

What is the vmax?

Back 18

Velocity increases as [S] is increased up to a maximum, Vmax when the enzyme is saturated.

Front 19

What is a type of allosteric enzyme?

Back 19

Hemeglobin

Front 20

How does temperature affect V?

Back 20

Increase of V with T
Simple effect due to increased numbers of sufficiently energetic substrate molecules.

Front 21

What happens to V if temp. increases?

Back 21

Decrease with further increase in T
Enzymes are denatured at high temperatures

Front 22

How is Km associated to S?

Back 22

KM is numerically equal to [S] at ½ the maximal velocity

Front 23

How is Km associated with enzyme []?

Back 23

KM does not vary with enzyme concentration
If KM is small the affinity of E for S is high
A low [S] is able to half-saturate the enzyme
If KM is large, the affinity is small.

Front 24

What is the effect of E on velocity?

Back 24

Effect on Velocity by [E]
Rate is directly proportional to [E] at all S concentrations
If [E] is halved, Vo and Vmax will be halved too.

Front 25

What is the effect of Vmax from Competitive inhibition?

Back 25

Effect on Vmax
At a sufficiently high [S] the Substrate will “win out” and the enzyme exhibits its full Vmax i.e. Vmax is unchanged.

Front 26

What is the effect of Km from Competitive inhibition?

Back 26

Effect on Km
Increases the apparent Km.
In the presence of inhibitor, we need more substrate to achieve ½ Vmax
That is, the behaviour is as if the enzyme has a lower affinity for substrate.

Front 27

What are examples of competitive inhibition?

Back 27

Competitive Inhibition
HMG-CoA reductase inhibitors
e.g. Lipitor, Crestor, lovastatins inhibits by competing

Front 28

What is the effect on Vmax of non-competitive inhibitor?

Back 28

Non competitive
Effect on Vmax
Cannot be overcome by high [S]
Therefore Vmax decreases

Front 29

What is the effect on Km of non-competitive inhibitor?

Back 29

Effect on Km
The inhibitor does not interfere with the binding of substrate to enzyme, so the Km is not changed.

Front 30

What is the effect on Vmax of uncompetitive inhibitor?

Back 30

Effect on Vmax
However the ESI complex is non-productive so Vmax lowered.

Front 31

What is the effect on Km of uncompetitive inhibitor?

Back 31

Effect on Km
The Inhibitor only binds to ES so it stimulates formation of ES and increases binding of substrate to enzyme so Km is reduced.

Front 32

What is an example of homotropic effector?

Back 32

Example glycogen phosphorylase is activated by Pi which is also its subsrtate.

Front 33

What is an example of heterotropic effector?

Back 33

Example: Phosphofructokinase inhibited by citrate

Front 34

What are examples of covalent modification?

Back 34

E.g. glycogen phosphorylase (degrades glycogen) Phosphorylation activates,
Glycogen synthase is deactivated by phosphorylation

Front 35

How is creatine kinase involved in heart disease?

Back 35

CK is released when muscle is damaged.
CK is found as three isoenzymes, CK1, CK2, CK3
CK2 is only produced by the myocardium, plasma levels peaking around 24 h after infarction.
In addition, lactate dehydrogenase peaks 36 to 48h after infarction.
Both are used to determine the existence of damage and to asses its extent.

Front 36

What is AST?

Back 36

Liver enzymes
AST – Aspartate aminotransferase
Greater amounts so more sensitive
Also in muscle so less specific

Front 37

What is ALT?

Back 37

Liver enzyme
ALT – Alanine aminotransferase
Smaller amounts – less sensitive
Mainly liver so more specific

Front 38

What do AST & ALT determine??

Back 38

Some evidence that AST / ALT > 1 indicative of alcoholic liver damage (this is not universally agreed upon)

Front 39

What is GGT & ALP?

Back 39

GGT and ALP are other liver function enzymes measured (elevated in cholestasis)

Front 40

What is the equation for delta G?

Back 40

ΔG = ΔH - TΔS

Front 41

What is enthalpy, entropy?

Back 41

Enthalpy (H): Heat content
Entropy (S): Amount of disorder

Front 42

What is the enthalpy change?

Back 42

Enthalpy Change (ΔH): heat flow. If heat leaves the system ΔH is negative. (The heat and hence the vibrational entropy of the surroundings increases).

Front 43

What is the entropy change?

Back 43

Entropy change (ΔS): Change in disorder. If the system becomes more disordered ΔS is positive.
Both of these (ΔH negative and ΔS positive) favour a reaction as written.

Front 44

What is the rule if delta G is negative or positive?

Back 44

Rule: if ΔG is negative, the reaction will proceed spontaneously as written.


Rule: if ΔG is positive, the reaction will proceed spontaneously in the reverse direction.

Front 45

When is a reaction endergonic?

Back 45

ΔG is positive – reaction is endergonic, not spontaneous.

Front 46

When is a rxn exergonic?

Back 46

ΔG is negative – reaction is exergonic, spontaneous.

Front 47

What happens to Keq If ΔGo is large and negative?

Back 47

If ΔGo is large and negative
Keq will be large (>>1)
much more product than reactant at equilibrium

Front 48

What happens If ΔGo is large and positive?

Back 48

If ΔGo is large and positive
Keq will be small (<< 1)
much more reactant than product at equilibrium

Front 49

What is the difference b/w aldose and ketose?

Back 49

Aldose has CO on either end
Ketose has CO in the middle

Front 50

What is the suffix of ketose? Function?

Back 50

Ketose suffix is ulose

Function:immediate energy source, cell membrane structure, cell signaling

Front 51

What is monosacchride?

Back 51

Monosaccharides (simple sugars) have a carbon skeleton of 3 or more carbons depending on the monosaccharide. The most familiar monosaccharide is Glucose (C6 H12 O6).

Front 52

What is disacchride?

Back 52

Disaccharides. Disaccharides consist of two monosaccharides linked together by a dehydration synthesis.

Ex. Sucrose, Galactose, Lactose

Front 53

What is an oligosaccharide?

Back 53

Few simple sugars linked together.

usually found on cell membranes

Front 54

What is a polysaccharide?

Back 54

Starch, many sugars linked togeher

Front 55

Disaccharides, Oligosaccharides and Poly are linked by....

Back 55

Glycosidic bonds

Front 56

Why is the chair form more stable of the carbohydrates?

Back 56

The chair form is more stable because of less steric hindrance as the
axial positions are occupied by hydrogen atoms.

-due to the OH groups arrangement

Front 57

What are epimers? What is d-mannose?

Back 57

Epimers
- Stereoisomers differ in the position of the hydroxyl group
at ONLY ONE of their asymmetric carbons

D-mannose is c2 epimer

Front 58

What is b-D-glucose?

Back 58

B-D-Glucose is equatorial;

Front 59

What is the only L sugar present in polysaccharide?

Back 59

L fructose is th only L sugar present in polysaccharide

Front 60

What are the most common amino sugars?

Back 60

1 or more OH replaced by amino group
- Eg: D-glucosamine, D-galactosamine are most
common
- N-Acetylneuraminic acid (C9) in glycoproteins
&glycolipids

Front 61

What is the difference b/w maltose and lactose?

Back 61

Maltose-mjr degradation product of starch---a-1,4) glycosidic bond

Lactose-galactose and glucose in a β–(1,4) glycosidic bond.

Front 62

What is homopolysaccharides?

Back 62

homopolysaccharides –have single type of residue
- Eg : starch, glycogen –glucose residues, Inulin –fructose residues

Front 63

The deficiency of PDH complex in infants leads to delayed development and
Reduced muscle tone often associated with ataxia and seizures. Some infants have
Congenital malformations of the brain

Back 63

Brain needs ATP to properly develop b/c pyruvate is shuttled to the lactic acid. Thus
Improper conversion causes lactodema or lactoacidosis. Prolong life by reducing
Carbohydrates in the diet.

Front 64

Deficiency of Thiamine pyrophosphate (TPP) is

Back 64

Thiamine pyrophosphate (TPP
coenzyme B1

common in alcoholics.

Front 65

What is allosteric modification? What is feedback inhibition?

Back 65

Allosteric – when something binds to an allosteric site allowing the enzyme to make a conformational change
Feedback inhibition  need 3 enzymes for the rx to happen and 2 to regulate it. All present in the PDH complex.
Inhibition: 1)Direct inhibition of PDH enzyme and 2)promoting inactive form, by stimulating the kinase. Negative feedback inhibition by is VERY STRONG b/c 2 ways that product is inhibiting rx.
PDH(active) –NADH-Energy----PDH-Inactive-noenergy

Front 66

What is the 1st intermediate of TCA?

Back 66

Citrate by citrate synthase

Front 67

How does Flouride affect glycolysis?

Back 67

This is used in the measurement of blood glucose. Tubes which hold a blood draw have Fluoride in them which inhibits glycolysis. In addition we have anticoagulant which prohibits the blood from clotting.

Front 68

Hexokinase/Glucokinase

Back 68

Irreversible reaction
Requires ATP
Phosphorylate other sugars
Hydrophilic- needs transporter b/c cant enter membrane bilayer
“branch point” – b/c it can enter other pathways

Front 69

EIF2-kinase

Back 69

inhibitor of tyrosine kinase

Front 70

Liver has what two enzymes?

Back 70

HK--low Km, high affinity
GK-High Km, low affinity

Front 71

Islet celss of pancreas have what enzyme?

Back 71

GK (glucose sensor)

After meal GK senses if high amt of glc to statr secreting insulin to remove

Front 72

What enzyme does the brain have?

Back 72

Hexokinase

Front 73

Phosphoglucose isomerase

Back 73

isomerase
reversible
essential

Front 74

Fructose 6 phosphate

Back 74

Irreversible
Major role in regulating the rate of Glycolysis
First committed step of the pathway unlike G6P (which can enter other pathways) it is committed to glycolysis
Requires ATP

Front 75

Glyceraldehyde 3 P Dehydrogenase (GAPDH)

Back 75

-Reversible

-2 reactions
-oxidation (aldehyde to acid)
- Addition of iP (Pi)

-Generation of Ist high energy molecule(biphosphoglycerate)

- NADH generation

Front 76

Phosphoglycerate kinase

Back 76

The dehydration then Enolase makes PEP which is a ~hi e compd. 2nd mol of ATP is generated in PEP pyruvate

Front 77

Pyruvate kinase

Back 77

- Irreversible

- Generation of 2nd ATP molecule (Substrate level phosphorylation)

Front 78

What inhibits GK?

Back 78

Fructose 6 Phosphate

Front 79

Glycogen sysnthesis requires?

Back 79

Glycogen synthesis
Requires an activated form of glucose, uridine diphosphate glucose (UDP-glucose),
Added to the nonreducing end of glycogen molecules.

Front 80

Glycogen degradation steps?

Back 80

Glycogen degradation consists of three steps:
The release of glucose 1-phosphate from glycogen,
The remodeling of the glycogen substrate to permit further degradation, and
The conversion of glucose 1-phosphate into glucose 6-phosphate for further metabolism.

Front 81

What are the hormone regulators of blood glucose?

Back 81

Insulin, glucagon, and epinephrine – regulators to maintain blood glucose

Front 82

What is the active glucose donor in Glycogenesis?

Back 82

Utilizes uridine diphosphate glucose (UDP-glucose) as the activated glucose donor.

Front 83

What is UDP-glucose synthesized from and catalyzed by?

Back 83

Synthesized from glucose 1-phosphate and uridine triphosphate (UTP)
Catalyzed by UDP-glucose pyrophosphorylase

Front 84

What is the metabolic junction in carb metabolism? What is the primer? What aa is added on the free OH? purpose? How are they attached?

Back 84

Glc-6-p is the metabolic junction in carbohydrate metabolism
Glycogenin is a protein that acts as a primer. Tyroxine residue is on the end with a free OH group and is responsible for the attachment of UDP-glc. UDP leaves and glc is attached by alpha 1,4 linkage.

Front 85

What is the key regulatory enzyme of glycogen synthesis? What is req in order to add residues?

Back 85

Glcogen synthase
Can add glucosyl residues only if the polysaccharide chain has more than four residues  requires a primer.
Priming function carried out by glycogenin

Front 86

What does the enzyme 6 Phosphogluconate result in?

Back 86

Pentose phosphate pathway

Front 87

What does the enzyme glucose 1 phosphate result in?

Back 87

UDP glucose

Front 88

What is the fate of G6P when glucose is brought in by Muscle & Liver? What transporters do they use?

Back 88

Muscle-Glut 4
Liver Glut 2

G6P can catalyze
F6P-->Glycolysis

6Phophsogluconate -->
Pentose phosphate

G1P<--> UDP glucose

Front 89

. After a meal, blood glucose enters cells and is stored as glycogen, particularly in the liver. Which of the following is the donor of new glucose molecules in glycogen?

Back 89

UDP-glucose

Front 90

What is required for Glycogenolysis?

Back 90

The efficient breakdown of glycogen to provide glucose 6-phosphate requires four enzyme activities:
One to degrade glycogen,
Two to remodel glycogen so that it remains a substrate for degradation, and
One to convert the product of glycogen breakdown into a form suitable for further metabolism

Front 91

When is glycogenolysis conducted?

Back 91

Used during the starving state or an overnight fast…max of storage in liver is 10 hrs of fasting..

Front 92

What is glycogen phosphorylase? PLP?

Back 92

Glycogen phosphorylase,
Key enzyme in glycogen breakdown,

PLP=pyridoxal phophate=Vitamin B6 is the integral part of the enzyme

Front 93

What enzymes remodel glycogen for cont. degradation?

Back 93

Two additional enzymes remodel glycogen for continued degradation by the phosphorylase
Transferase and
α-1,6-glucosidase

Front 94

What does phosphoglucomutase do?

Back 94

A phosphoryl group is transferred from the enzyme to the substrate, and a different phosphoryl group is transferred back to restore the enzyme to its initial state

Front 95

Where is glucose-6-phosphatase found? Function?

Back 95

A major function of the liver is to maintain a near constant level of glucose in the blood
In liver  glucose 6-phosphatase cleaves the phosphoryl group to form free glucose
Located in smooth endoplasmic reticulum membrane
Glucose 6-phosphatase is absent from most other tissues.

Front 96

What are the principal enzymes of glycogen metabolism?

Back 96

Principal enzymes are –
Glycogen phosphorylase &
Glycogen synthase

Front 97

Where is glucagon secreted?

Back 97

Glucagon is secreted by islet of Langerhans is a hypoglycemic hormone only in liver, absent in linver. Epinephrine is in both. B2 adrenergic receptor – EPI.

Front 98

What inhibits glycogenin synthesis?

Back 98

Gycogenin synthesis is inhibited by glucagon and epinephrine.

Front 99

Function of insulin?

Back 99

Insulin stimulates PP1 and removes the phosphate group for glycogen synthase b to make glycogen synthase a ACTIVE. Insulin stimulates glucogenesis and glucagon and epinephrine inhibit it.

Insulin inhibits glucogen degradation/glycogenolysis by stimulating PP1 makes glycogen phosphorylase b inactive

Front 100

What enyzyme becomes active without phosphorylation? When?

Back 100

Phosphrylase kinase B

High [] of AMP in muscle during severe muscular exercise, glycogen phosphorylase b becomes active.

Front 101

What inhibits phosphodiesterase? PPD do?

Back 101

Caffeine inhibits phosphodiesterase(which degrades cAMP) which increases the level of cAMP of stops the cAMP to remain. If cAMP is increased then degrades glycogen which increases bld glc level.

Front 102

Protein phosphatase 1 function? Process?

Back 102

Key role in regulating glycogen metabolism.

Accelerates glycogen synthesis

Insulin Activates Protein Phosphatase 1
Binding of insulin to its receptor  activation of PP1  association of PP1 with glycogen molecule  dephosphorylation of glycogen synthase, phosphorylase kinase, and phosphorylase inc glycogen synthesis and dec degradation

Front 103

A man goes on a hunger strike and confines
himself to a liquid diet with minimal calories. Which
of the following would occur after 4 to 5 h?

Back 103

Increased cyclic AMP and increased liver glycogenolysis

Front 104

Von Gierkes disease -Type 1
Defective enzyme?
Organs affected?
Cause
CF

Back 104

Defective enzyme- Glucose 6-phosphatase
Organ affected- Liver and kidney
Increased amount, normal structure of glycogen
Clinical features- Massive enlargement of the
liver
Failure to thrive
Severe hypoglycemia
Ketosis-ketone body formation due to glc 6-P going to another pathway

Hyperuricemia-Glc-6-P to glc is blocked so it goes to purine catabolismuric acid
Hyperlipemia--glc6P goes to glycerol synthesis

Growth retardation and delayed puberty
AR

Front 105

Pompe's disease-Type 2
Enzyme?
Organs
Cause
CF

Back 105

α 1,4-Glucosidase (lysosomal)
All organs
Massive increase in amount, normal structure
of glycogen.
Cardio respiratory failure causes death, usually
before age 2.
Characterized by accumulation of
glycogen in heart muscle

--Muscle weakness

Front 106

What is the distinguishing CF b/w type 3 & 4 glycogen storage disorders?

Back 106

Hpatosplenomegaly in Cori's

Andersons-death before 2, liver failure

Front 107

Tauri's disease-Type 7
Enzyme?
CF
Organs?

Back 107

Muscle Phosphofructokinase deficiency
Affected organ- Muscle
Increased amount of glycogen
Clinical features are Like type V, but milder
Course

Front 108

18 year old graduate student experiences easy fatigue and muscular weakness when he does short duration of exercise. He also develops muscle cramps if he continues his exercise. The boy is suffering from which of the following glycogen storage disorder?

Back 108

McArdles due to painful cramps not present Tauri's