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Biochemistry 2 > Module 6: Unit 2-3 > Flashcards

Module 6: Unit 2-3 Flashcards

1
Q

With the lock and key analogy what is the key and what lock.

A

Enzymes have an active site that is complementary tot he substrate

Substrate - key

Active site - lock

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2
Q

How do enzymes function?

A

Enzymes = biocatalysts

  • increase reaction rate (V0) by lowering the activation energy of a chemical reaction
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3
Q

What is the activation energy?

A

Is the energy that has to be overcome for a substrate to be converted to a product.

EX: breaking apart of surprise into fructose and glucose requires a huge amount of energy. Enzymes have the ability of lowering that activation energy and, thus INCREASE the probability of that action to occur

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4
Q

What happens when there is more enzyme present?

A

The faster the reaction occurs or the faster product is formed.

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5
Q

What factors impact enzyme velocity?

What is the driving factor for enzymes?

What is the common thread in changing reaction rates?

A
  • pH
  • Temperature

Driving factor is to get the body back to homeostasis

—> Common thread is conformation change

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6
Q

The relationship between substrate concentration and reaction rate is ________

A

Hyperbolic,

A hyperbolic equation is used to analyze enzyme kinetics, acid-base behavior, and absorption processes

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7
Q

Describe a hyperbola graph

A

Starts steep and plantos with higher concentrations

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8
Q

Name the four different types of schematic depiction of inhibitor action. *Picture on slide 16 from Module 6 unit 2-3

A
  • Normal binding
  • Competitive inhibition
  • Noncompetitive inhibition (mixed)
  • Uncompetitive inhibition
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9
Q

Name the inhibitor that binds at the active site instead of substrate, has unchanged Vmax, and Increased Km.

A

Competitive inhibitor

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10
Q

Name the inhibitor that bonds at a site other than the binding site, affects the conformation of the enzyme, including the shape of the active site; decreased Vmax, increased Km

A

Mixed (noncompetitive) inhibitor

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11
Q

Name the inhibitor that binds at a site other than the binding site, but only is substrate is bound; once the inhibitor binds the reaction does not proceed; decreased Vmax, and decreased Km

A

Uncompetitive inhibitor

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12
Q

T or F

The product of one enzyme reaction can be the substrate of one or more other enzyme reactions.

A

T

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13
Q

T or F

All enzymes are regulated

A

F

Only certain enzymes are regulated (commonly first step in a pathway, or enzymes at or near ‘intersections’)
Reversible enzymes are rarely regulated

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14
Q

T or F

Enzymes in extracellular spaces are commonly catalyzed reactions independently of other enzymes.

A

T

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15
Q

T or F

Some enzymes are present in inactive form to be quickly activated when their activity is required

A

T

EX: enzymes in the digestive tract (break down nutrients to building blocks which then can be absorbed)

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16
Q

Explain the enzyme regulation overview of covalent reactions.

A

Reversible and nonreversible!!

Reversible - phosphorylation/dephophorylation… methylation/demethylation

Nonreversible - Removal of C-/N- terminal amino acids

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17
Q

Explain the enzyme regulation of non-covalent reactions.

A

Allosteric
- uncompetitive
- mixed
Competitive
- always reversible (equilibrium)

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18
Q

FITB

____-_______ and ________ are found in the intracellular realm

A

non-covalent, and reversible

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19
Q

T or F

The non-reversible modification is only found in the extrecellular realm.

A

T

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20
Q

T or F

Non-covalent is always reversible because it’s based on equilibrium situations, ligand binding interactions between the regulatory compound and the protein.

A

T

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21
Q

What is allosteric?

A

Inhibitor binds in ligand-binding fashion at a specific site that is not the active site

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22
Q

During Intracellular exhume regulation (non-covalent)

FITB

A positive modulator is _____________ (negative modulator is inhibiting)

A

Activating

The binding of the modulator affects the conformation (shape of both subunits and changes the affinity of the active site for S)

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23
Q

When a proteins conformation changes so does its _____ ______ ______

A

Change in function

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24
Q

What is an example of covalent, reversible regulation?

A

Phosphorylase phosphorylation/dephosphorylation

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25
Q

Give an example of intracellular enzyme regulation in a physiological situation.

A

Glycogen is broken down when the blood glucose levels drops due to use of glucose for energy production (NS, skeletal and heart muscle)

  • dropping blood glucose levels —> hormone glucagon activated
  • exercise —> hormone epinephrine released
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26
Q

What is the function of kinases?

A

Transfer phosphate from one molecule to another

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27
Q

What is the function of phosphatases?

A

Remove phosphate from molecules (releasing inorganic phosphate)

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28
Q

Explain Proteolytic Cleavage.

A

Involves enzymes that break peptide bonds. Hydrolysis of specific peptide bonds

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29
Q

Inactive precursors of enzymes normally have the prefix _______ and suffix _____

A

Prefix ‘pro’

Suffix ‘gen’

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30
Q

What do C- and/or N- terminal sequences of amino acids do?

A

Keep enzyme/protien inactive until they are removed by proteolytic cleavage (hydrolysis of specific peptide bonds); enzymes are proteases or peptidases

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31
Q

What are two examples within the Non-Reversible Enzyme Regulation (Proteolytic Cleavage) that we will be using in this unit?

A
  1. proteases in the digestive tract: ex; trypsin (enzyme), chymotrypsin (enzyme) (the trigger is the arrival of food)
  2. Blood clotting cascade (the natural tigger is injury in the BV; there are pathological triggers, ex; plaques in BV
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32
Q

In the example on slide 32 of proteases of the digestive tract chymotrypsinogen and trypsinogen are?

A. Active precursors
B. Median precursors
C. Regulatory precursors
D. Inactive precursors

A

D,

Because they end in the suffix ‘-gen’

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33
Q

Look at and explain the diagram on slide 32: proteases of the digestive tract. Understand the situation!!!!

A

We need a fast activation of an extracellular enzyme in the case of digestive proteases, which, it they were active all the time would actually target our own proteins in cell membranes and would start digesting our intensively tract. THATS WHY we can only have them active in the case of the presence of food.

*digestive proteases are inactive, when there is no food to digest (they would start breaking down our own proteins) —-> the arrival of food in the digestive tract triggers this series of events leading to the activation of digestive proteases.

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34
Q

What are digestive proteases?

A

Enzymes that break down proteins into smaller peptides and amino acids, facilitating digestion. Essential for various bodily functions, such as building and repairing tissues, producing enzymes and hormones, and supporting immune function.

Examples: pepsin, trypsin, chymotrypsin, carboxypeptidase, aminopeptidase

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35
Q

What is proteases?

A

Also known as proteinases or peptidases, are enzymes that catalyze the breakdown of proteins into smaller peptides or individual amino acids by cleaving the peptide bonds between the amino acids.

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36
Q

Trypsin and chymotrypsin are digestive proteases and are examples of ____-________ _________ ________ ________ through the removal of C an N-terminal sequences

A

Non-reversible covalent enzyme regulation

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37
Q

Blood clotting is an example of what enzyme regulation?
And is it intracellular or extracellular?

A

Non-reversible enzyme regulation

Extracellular

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38
Q

The blood clotting cascade is an example of what?

A

Non-reversible covalent enzyme regulation through the removal of C- and N- terminal sequences

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39
Q

In the Proteolytic cleavage in the blood clotting process, carboxylase is dependent on what?

A

Vitamin K-dependent

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40
Q

T or F

The gut microbiome is a major source of vitamin k

A

T

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41
Q

People who are on blood thinners have to be careful of what?

A

Not consuming to many green leafy vegetables, because it might mess with the concentration of their blood thinners,

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42
Q

Some blood thinners are vitamin K

A. Agonistic
B. Antagonists
C. Agonists
D. Precursors

A

B

They competitively bind to the vitamin K binding site on the glutamate carboxylase. Leads to inhibition —> less carboxylation —> less protease activity —> less fibrin formation —> less blood clotting

*antidote for this is more Vitamin K

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43
Q

Most enzymes are _____

A

Proteins

44
Q

Tempurture, pH, certain ions, and regulatory measures affect the function of enzymes by

A. Blocking their active site
B. Altering the structure of the substrate
C. Affecting their conformation
D. Increasing or lowering the activation energy

A

C

45
Q

*LOOK AT #3 on quiz 2 regarding Mechaelis-Menten kinetics equation and the parts of it

A
46
Q

Which of the following types of regulations is non-reversible?

A. Feedback inhibition
B. Competitive inhibition
C.Phosphorylation.dephosphorylation
D. Proteolytic cleavage

A

D

47
Q

In _________ inhibition, the structure of the inhibitor resembles the structure of the substrate of the affected enzyme

A

Competitive

48
Q

Which of the following types of regulations is typical for extracellular space?
A. Phosphorylation
B. Competitive inhibition
C. Proteolytic cleavage
D. Feedback inhibition

A

C

49
Q

Activation of the digestive proteases trypsin and chymotrypsin is an example of ______ regulation

A. Noncovalent, nonreversible
B. Covalent reversible
C. Covalent, nonreversible
D. Noncovalent, reversible

A

C

50
Q

T or F

The higher the pH, the higher the enzyme catalyzed reaction rate

A

F

51
Q

Warfarin, the active ingredient in the blood-thinning drug ‘coumadin’

A. Inactivates glutamate carboxylase by competitively binding instead of Vitamin K
B. Inhibits the activation of Ca2+ dependent proteases in blood-clotting cascade by chelating Ca2_ and thus making it unavailable as a cofactor
C. Inhibits fibrin molecules from cross-linking to form a blood clot

A

A

52
Q

T or F

Enzyme activity is temperature dependent

A

T

53
Q

Which portions of the Michaelis-Menten equation are constant?

A

Km and Vmax

54
Q

In an inhibition experiment the effect of the inhibitor was to decrease Km and Vmax. This indicates that the mechanism of inhibition is ___________

A. Competitive
B. Mixed
C. Uncompetitive

A

C

55
Q

Michaelis-Mentons enzyme kinetics graphs show what curves?

A

Hyperbolic

56
Q

Phosphatases catalyze

A. Redox reactions
B. The removal of phosphate groups from organic molecules
C. The transfer of phosphate groups from one molecule to another

A

B

57
Q

What is the first law of thermodynamics?

A

Energy cannot be created or destroyed

Conversion of one form of energy into another always leads to a loss of energy, typically, in the form of heat

58
Q

What is the 2nd law of thermodynamics?

A

A highly organised system contains a lot of potential energy while a system that is disorganised (high chaos = entropy) contains a low amount of potential energy

59
Q

Define metabolism, catabolism, and anabolism within bioenergetics

METABOLISM = CATABOLISM + ANABOLISM

A

Metabolism - the sum of all biochemical reactions in a cell or organism
BROKEN INTO:
—> Catabolism - the sum of all degradative reactions in a cell or organism
—> the sum of all biosynthetic reactions in a cell or organism

60
Q

What do energy catabolic pathways do?

A

Generates energy (ATP, heat) and oxidize carbon (electrons to NAD+, NADP+, and FAD);

LARGE —> SMALL

61
Q

What do energy anabolic pathways do?

A

Require energy (ATP) and reduce carbon (electrons from NADH, NADPH, and FADH2)

Small —> Large

62
Q

Within the oxidation/reduction of carbon the OXIDATION of C would be:

A

Catabolism

63
Q

Within the oxidation/reduction of carbon the REDUCTION of C would be:

A

Anabolism

64
Q

An anabolic process required more or less energy?

A

More energy than catabolic

65
Q

What are the three stages of cellular respiration?

From macronutrient to ATP

A

Stage 1 - Acetyl-CoA production (protein *amino acids, fats *fatty acids, carbs *glucose)
—> Oxidation of carbon, electrons come from stages 1 and 2

Stage 2 - Acetyl-CoA oxidation (citric acid cycle) *taking out e- to NADH and FADH2
—> Oxidation of carbon, electrons come from stages 1 and 2

Stage 3 - Electron transfer and oxidative phosphorylation into respiratory chain (ETC)
—> Reduction of oxygen

PURPOSE = FORMING ATP PRODUCTION

66
Q

Give me an overview of glycolysis.

A
  • Means the splitting of sugar
  • involves partial oxidation of C
  • Small amount of ATP
  • Primary source of metabolic energy in some mammalian tissues and cell types (brain, RBC, anaerobic muscle, sperm, …)
    -Two phase process
  • Many enzymes of glycolysis are Mg2+ dependent (magnesium)
67
Q

During the preparatory phase of glycolysis what are key elements of this phase?

A

*Phosophorylation of glucose and its conversion to glyceraldehye 3-phosphate

  • Staring point is glucose
  • Ending point is Glyceraldehyde 3-P
  • Glucose (very stable) has to be energetically activated
    —> investment of 2 ATP
  • TWO REGULATED ENZYMES
    1. Hexokinase
    2. Phophofructokinase

OVERALL - Glucose + 2 ATP —> 2 Glyceraldehyde 3-P +2 ADP

68
Q

During the pay-off phase of glycolysis what are the key elements of this phase?

A
  • Starting point: Glyceraldehyde 3-P
    The potential energy of this metabolite can now be reaped:
    —> 2 NADH/Glucose
    —> 4 ATP/Glucose
  • End point: Pyruvate
  • One regulated enzyme:
    1. Pyruvate kinase

OVERALL -
2 Glyceraldehyde 3-P —> 2 Pyruvate + 2 ATP + 2 NADH

69
Q

What is the overall final chemical formula of glycolysis?

A

Glucose +2 NAD+ + 2 ADP + 2 Pi ——————-> 2 Pyruvate + 2 NADH + 2 ATP

*Glucose gets converted to 2 Pyruvate and under the formation of 2 ATP and 2 NADH. The process requires 2 NAD+ (important to remember to understand fermentation)

70
Q

T or F

Pyruvate comes from glycolysis (breaking down of glucose)

A

T

71
Q

T or F

Acetyl-CoA gets transferred into the Cytric Acid Cycle

A

T

72
Q

FITB

Coenzyme A bond in a metabolite makes it more _______

A

Reactive

73
Q

FITB

Pantothenic acid is a ___ vitamin

A

B
Also called B5

74
Q

What are the four enzymes within glycolysis?
And what are their functions

A

Kinase - Catalyze TRANSFER of a PHOSPHATE GROUP from one organic molecule to another, usually involving ADP or ATP (most of these are non-reversible)

Phosphatase - Remove a phosphate group, yielding inorganic phosphate

Isomerase - Catalyze the formation of an isomer of the substrate (requires the breaking of a bond, reversible reactions)

Dehydrogenase - Catalyze redox reactions (coenzyme NAD+/NADH, FAD?FADH2 or NADP+/NADPH)

75
Q

In which stage of glyolysis is the citric acid cycle?

A

Stage 2, Acetyl-CoA oxidation

76
Q

*MEMORIZE figure on slide 64. The Krebs Cycle process

Where is this cycle located? What makes up this cycle?

A

Located - matrix of mitochondria

Made up of:
- 8 intermediates (metabolites)
- 8 enzymes (4 dehydrogenases (2 catalyze an oxidative decarboxylation)

77
Q

3 NAHD and 1 FADH2 are involved in which stage of glycolysis? And produce what?

A

Stage 3 and produce ATP

78
Q

In which stages it carbon completely oxidised to CO2?

A

Stages 1 and 2

79
Q

T or F

In stage 3 of oxidative phosphorylation we are going from low potential energy to high potential energy

A

F

We are going from high potential energy to low potential energy

80
Q

Oxidative phosphorylation consists of what two processes?

A

ETC and ATP synthesis

81
Q

T or F

Oxidative phosphorylation is an intercellular process

A

F

It takes place on the inner membrane of the mitochondria

82
Q

What is ubiquinone (lipid)?

A

An intermembrane electron carrier. Can receive NADH or FADH

83
Q

What are the four complexes of the ETC?

A

Membrane proteins that are redox enzymes. Use energy from redox reactions to move protons against the concentration gradient.

84
Q

What micronutrients are in conjunction with the ETC?

A

Fe2+ (Iron)
Riboflavin = Vitamin B2

85
Q

Experiments have determined that it takes ____ number of protons moving through the F0F1 complex for ____ ATP

A

4 protons
1 ATP

86
Q

Fatty acids to ATP happen in how many stages? What happens in these stages?

A

3 stages

1 - B-oxidation: four recurring enzymatic reactions; can process saturated fatty acids

2- CAC (citric acid cycle)

3 - Oxidative phosphorylation

87
Q

When we break down fat Triacylglycerol uses _______ to form 3 fatty acids + glycerol

A

Lipases

88
Q

What breaks down proteins into amino acids?

A

Proteases

89
Q

What is the overall yield of ATP per glucose?

ATP per fatty acid?

ATP per amino acid?

A

30-32 per glucose

Per FA - depends on size. larger FA the more ATP

Per AA- depends on which AA

90
Q

What is involved in the fermentation reaction?

When does it occur?

A
  • Pyruvate —> Lactate dehydrogenase —> Lactate
  • When a cell becomes anaerobic condition (in skeletal muscle) *No mitochondria (RBC)
91
Q

T or F

Fermentation occurs without oxygen, unlike aerobic respiration which requires oxygen

A

T

92
Q

How many net ATP do we get from glycolysis?

A

2 ATP

93
Q

What are the micronutrient requirements (vitamins)?

A

B1 = thiamin —> coenzyme TPP
B2 = riboflavin —> coenzyme FAD
B3 = niacin —> coenzymes NAD+ and NADP+
B5 = pantothenic acid —> coenzyme A

94
Q

What are the micronutrient requirements (minerals)?

A

Mg2+ (magnesium)
Fe2+ (Iron) (ETC)
Cu2+ (copper)

95
Q

What are the names for the Citric acid cycle?

A

CAC
TCA = tricarboxylic acid cycle
Krebs cycle

96
Q

Which of the following metabolites is the point of convergence of carbohydrate fat, and protein catabolism for the purpose of ATP production?

A. Pyruvate
B. Acetyl-CoA
C. Citrate
D. Glyceraldehyde 2-phosphate

A

B

97
Q

Which of the following coenzymes relies on riboflavin?

A. FAD
B. NADH
C. TPP
D. NAD+

A

A

98
Q

Fermentation converts NADH to NAD+ so it can be used in ___________

A

Glycolysis

99
Q

The sum of degradative reactions is called

A. Metabolism
B. Anabolism
C. Catabolism
D. Bioenergetics

A

C

100
Q

Which of the following is carbon the most oxidized?

A. Alcohol
B. CO2
C. Carboxylic acid

A

B

101
Q

Anabolic pathways

A. Require ATP and yield reduced electron carriers
B. Require ATP and reduced electron carriers
C. Yield ATP and reduced electron carriers

A

B

102
Q

Citrate is a C_____ compound

A

6

103
Q

FITB

_________ catalyze the transfer of phosphate groups from one organic molecule to another

A

Kinases

104
Q

In the CAC cycle acetyl-CoA gets combined with __________ to form citrate

A. Succinct
B. A late
C. Oxaloavetate

A

C

105
Q

Name processes in which oxidation of carbon occurs.

A
  • Krebs cycle
  • Glycolysis
  • Beta-oxidation
  • PDH (Pyruvate dehydrogenase) complex

Biochemistry 2 (21 decks)

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