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Biochem > Lecture 2- Enzymes To Glycolysis > Flashcards

Lecture 2- Enzymes To Glycolysis Flashcards

1
Q

RNA with catalytic activity is called

A

Ribozyme

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2
Q

The 6 major classes of enzymes

A 
Oxidoreductase
Transferase
Hydrolase
Lyase
Isomerase
Ligase
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3
Q

Difference between Lyase and Ligase?

A

Lyase lyses and ligase joins together

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4
Q

Synthetase vs Synthase

A

Synthetase requires ATP

Synthase does not require ATP

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5
Q

What does phosphatase do?

A

Removes a phosphate group

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6
Q

Difference between phosphorylase and kinase

A

Phosphorylase adds a phosphate group using Pi,

Kinase uses ATP

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7
Q

What does Oxidase do and how?

A

Catalyze redox rxns using O2 as the electron acceptor but oxygen atoms are not incorporated into the substrate

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8
Q

Oxygenase- what and how it works

A

Oxidizes a substrate by transferring oxygen atoms to do it

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9
Q

What is an enzyme?

A

A protein catalyst that increases the rate of a rxn without being consumed by the rxn

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10
Q

Holoenzyme vs apoenzyme

A

Holoenzyme- enzyme with its nonprotein component (active)

Apoenzyme- enzyme without its nonprotein component (inactive)

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11
Q

Cofactor vs coenzyme, and examples

A

Cofactor tends to be inorganic nonprotein moeity (metals)

Coenzyme is a subfactor of cofactor and are small organic, frequently derived from vitamins (NAD+ and FAD)

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12
Q

What is a prosthetic group?

A

Refers to a coenzyme that is permanently associated with the enzyme

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13
Q

What is a cosubstrate?

A

Refers to a coenzyme that only transiently associate with the enzyme

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14
Q

What is an allosteric enzyme?

A

An enzyme that changes its conformation when bound by an effector at a site other than the active site. (Enzyme can then become activated or inhibited)

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15
Q

What does an enzyme do?

A

Lowers the activation energy

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16
Q

Factors that affect the reaction velocity in enzymes

A

Substrate concentration
Temperature
pH

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17
Q

Difference in graph shape between enzymes following Michaelis-Menten kinetics vs allosteric enzymes

A

Michaelis-Menten show a hyperbolic curve

Allosteric enzymes show a sigmoidal curve

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18
Q

Explain effects that occur in enzyme activity with increased temperature

A

Increased reaction velocity as it is easier for molecules to reach activation energy.
Begins to decrease once temperature gets too high and begins to denature the enzyme

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19
Q

Explain pH and enzymes

A

Specific enzymes tend to have a specific pH at the which they have optimal function.
Too high or low could lead to denaturation, or
a specific AA may need to be protonated or deprotonated in order to function

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20
Q

Michaelis-Menten equation (simple idea and actual equation)

A

E + S ES –> E + P k1/k-1 and k2 respectively

V0 = (Vmax [S]) / (Km + [S]). Km = (k-1 + k2)/k1

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21
Q

What does the Michaelis-Menten equation describe?

A

How the reaction velocity varies with respect to substrate concentration

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22
Q

If Km is high, this means that the affinity of the substrate to the enzyme is…?

A

Low affinity

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23
Q

Simply put, Km is equal to what?

A

Half of Vmax

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24
Q

Where on the Michaelis-Menten graph do we see first and zero orders? And what do they mean?

A

First order before Km (V is proportional to [S], zero order after Km (V is constant and independent of [S].

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25
Q

What is the Lineweaver-Burk plot equation?

A

1/V0 = (Km/Vmax [S]) + (1/Vmax)

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26
Q

Lineweaver-Burk plot,
X-axis intercept =?
Y-axis intercept =?

A 
X-axis = -1/Km
Y-axis = 1/Vmax
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27
Q

Substance that can diminish the velocity of an enzyme-catalyzed reaction is called…

A

An inhibitor

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28
Q

What type of bonds are typically made to enzymes by reversible inhibitors?

A

Noncovalent bonds

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29
Q

What Bond is made to enzymes typically by irreversible inhibitors?

A

Covalent bonds

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30
Q

Competitive vs noncompetitive inhibitors

A

Competitive competes with substrate for active site

Noncompetitive binds the E or E-S at a different site other than the active site

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31
Q

What happens to Km in the presence of a competitive inhibitor?

A

Km is increased, (lower affinity)

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32
Q

What happens to Vmax during competitive inhibition?

A

Vmax stays unchanged

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33
Q

What happens to Km during noncompetitive inhibition?

A

Km remains unchanged

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34
Q

What happens to Vmax in presence of a noncompetitive inhibitor?

A

Vmax decreases (moves higher on lineweaver-burk plot)

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35
Q

Homotropic effectors….?

A

When the substrate itself serves as an effector

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36
Q

Heterotropic effectors…?

A

Effectors that are different than the substrate

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37
Q

Regulation of enzymes by covalent modification is most frequently done by addition or removal of phosphate groups from which 3 AA residues of the enzyme?

A

Serine
Threonine
Tyrosine

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38
Q

What type of enzyme is involved in phosphorylation?

A

Protein kinase

39
Q

What type of enzyme is involved with dephosphorylation?

A

Phosphoprotein phosphatases

40
Q

Bioenergetics

A

The study of energy transfer in biological systems

41
Q

Free energy equation and what each variable represents

A 
^G= ^H - T^S
G energy available to do chemical work and a measure of the spontaneity of chemical rxns
H enthalpy, total heat content
T temperature
S entropy, measure of disorder
42
Q

What is equation for ^G for rxn
A+B –> C+D
Incorporating ^G0

A

^G = ^G0 + RT ln [C][D]/[A][B]

R= 1.987 cal/mol x degK

43
Q

What is the standard free energy of hydrolysis of ATP, ^G0?

A

-7.3 kcal/mol

44
Q

Final products of the electron transport chain?

A

CO2 and water

45
Q

The two energy rich coenzymes in he electron transport chain are?

A

NADH and FADH2

46
Q

Oxidative phosphorylation results in the formation of what?

A

ATP

47
Q

Where does glycolysis take place?

A

Cytoplasm

48
Q

Where does the TCA cycle take place?

A

Matrix of mitochondria

49
Q

Where does the electron transport chain take place?

A

Inner membrane of the mitochondria

50
Q

1 NADH allows how many H+ to pass through in the ETC?

A

10

51
Q

FADH allows how many H+ to pass through during ETC?

A

6

52
Q

In the ETC, electrons from complex I and II are transferred to what?

A

Coenzyme Q

53
Q

In which complex is O2 reduced to water?

A

Complex IV

54
Q

Incomplete reduction of oxygen to water can produce?

A

Reactive oxygen species

Ex superoxide or hydroxyl radical

55
Q

Example of an enzyme to combat the production of reactive oxygen species

A

Superoxide dismutase
Catalase
Glutathione peroxidase

56
Q

What determines the direction of electron flow in the ETC?

A

Standard reduction potential, E0

Electrons flow from the pair with the more negative E0 to the more positive E0

57
Q

^G0 for the phosphorylation of ADP to ATP is how much?

A

+7.3 kcal/mol

58
Q

What happens at complex V?

A

Protons are pumped into the matrix, coupled with the phosphorylation of ADP to ATP and pumped into the intermembrane space

59
Q

Complex V has how many domains and what are the names?

A

2

F0 at the base and F1 on the matrix side

60
Q

Where are uncoupling proteins (UCPs) found in humans?

A

Inner mitochondrial membrane

61
Q

What do UCPs do and what is the process called?

A

Allow protons to re-enter the matrix without energy being captured as ATP and instead releases heat

Nonshivering Thermogenesis

62
Q

Isomer vs epimer

A

Isomers are compounds that have the same chemical formula but different structures

Epimers are isomers that differ in configuration around only one specific carbon atom

63
Q

Where is the location of the determining -OH group on a sugar that is a D and L isomer?

A

L is on the left

D is on the right

64
Q

Anomeric carbons in ring:

What position is the determining OH group when in the alpha position?

A

Pointing DOWN, or whichever is TRANS to the projecting CH2OH group

65
Q

If the hydroxyl group of the anomeric carbon of the cyclized sugar is not linked to another compound by a glycosidic bond, the ring can open and is then termed…?

A

A reducing sugar

66
Q

The bond that links sugars is called

A

Glycosidic bond

67
Q

What enzymes are used to bind sugars?

A

Glycosyltransferases

68
Q

Enzymes that rapidly digest carbohydrates are called

A

Glycosidases

69
Q

What is the glycosidic bond formed in cellulose that humans cannot digest?

A

B(1->4)

70
Q

Where in the body does the digestion of carbohydrates occur?

A

In the mouth and the small intestines

71
Q

In the small intestine, what transport system is used to transport glucose, galactose and fructose across the mucosal lining into the blood vessels? (Not into the mucosal layer from the lumen)

A

GLUT-2

72
Q

What is the result of undigested disaccharides reaching the large intestine?

A

Water is drawn into the large intestine leading to
Diarrhea
Bacterial fermentation of the remaining carbohydrate plus large volumes of CO2 and H2 gas causing abdominal cramps and flatulence

73
Q

What two monosaccharides make up lactose?

A

Glucose + galactose

74
Q

What percentage of the world adult population are lactose intolerant?

A

75%

75
Q

What enzyme breaks down lactose?

A

Lactase

76
Q

The sum of all the chemical changes occurring in a cell…

A

Metabolism

77
Q

Which specific tissues employ the glycolytic pathway?

A

ALL tissues

78
Q

What is the end product of glycolysis?

A

Pyruvate

79
Q

GLUT-1 through 4;

What type of transport system and where each is located

A

All Na+ independent facilitated diffusion transports for glucose
GLUT-1 - erythrocytes, blood brain barrier
GLUT-2 - pancriatic B-cells, liver, kidney
GLUT-3 - neurons
GLUT-4 - adipose tissue, skeletal muscle

80
Q

In the gut, what transport system is used to transport glucose, and what type of transport is it?

A

It is a Na+ dependent co-transporter system called
Sodium Dependent Glucose Transporter (SGLT)

Occurs in the epithelial cells of the intestine

81
Q

Two main phases of glycolysis

A

Energy investment phase

Energy generation phase

82
Q

First step of glycolysis

A

Glucose is phosphorylated by hexokinase (glucokinase in liver and pancreas) to produce glucose-6-phosphate (G6P)
*Irreversible step

83
Q

In glycolysis, G6P is converted to fructose-6-phosphate (F6P) via what enzyme?

A

Phosphoglucose isomerase

84
Q

What is the most important control point in glycolysis and what exactly is happening?

A

3rd step in glycolysis where F6P is converted to fructose-1,6-bisphosphate (F1,6BP) via phosphofructokinase-1 (PFK-1)

*first committed step to overall pathway

85
Q

In glycolysis, a 6 carbon molecule is cleaved into two 3 carbon molecules. What molecules are involved and enzyme used

A

4th step;
Fructose 1,6-bisphosphate is cleaved by ALDOLASE to produce
Glyceraldehyde-3-phosphate (G3P) and
Dihydroxyacetone phosphate (DHAP)

86
Q

What happens to DHAP? What enzyme used?

A

DHAP isomerized to G3P via

Triose Phosphate Isomerase

87
Q

What happens to glyceraldehyde-3-phosphate (G3P) in glycolysis?

A

G3P is oxidized by glyceraldehyde-3-phosphate dehydrogenase, using NAD+ and an organic Pi to produce 1,3-bisphosphoglycerate (1,3BPG)

88
Q

Overall concept of Arsenic poisoning

A

Competes with Pi for G3P dehydrogenase leading to 3-phosphoglycerate formation directly therefore bypassing the ATP making step

89
Q

What happens next to 1,3-bisphosphoglycerate (1,3BPG) in glycolysis?

A

1,3BPG is converted to 3-phosphoglycerate (3BPG) by
Phosphoglycerate kinase
*the removed phosphate group synthesizes an ATP in this step

90
Q

Step 8 in glycolysis, what happens to 3-phosphoglycerate?

A

3-phosphoglycerate is converted to 2-phosphoglycerate via

Phosphoglycerate mutase

91
Q

Step 9 of glycolysis, what happens to 2-phosphoglycerate?

A

2-phosphoglycerate is dehydrated to phosphoenolpyruvate (PEP) by
Enolase

92
Q

What can inhibit enolase?

A

Fluoride

93
Q

Step 10 in glycolysis,

What happens to phosphoenolpyruvate (PEP) and why is this step significant?

A

PEP is converted to pyruvate by
Pyruvate kinase
Producing an ATP
*the third irreversible step in glycolysis

94
Q

What is the NET equation of glycolysis?

A

Glucose + 2 Pi + 2ADP + 2 NAD+ =

2 pyruvate + 2 NADH + 2 ATP (net)

Biochem (8 decks)

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