Biology Exam ll (Chapter 6) Flashcards


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1

Bioenergetics

Energy in biological systems

2

Flow of Energy

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3

What is energy in the form of?

Energy is in the form of a photon.

4

Energy

The ability to do work which means to move matter against opposing forces such as gravity and friction

5

Carbon Cycle

Transforms carbon dioxide into glucose

6

First Law of Thermodynamics

Energy cannot be created or destroyed

7

Potential Energy

ATP, an electrical/ion gradient, concentration gradient, NADH, Chemical Bonds
Water being held behind a dam
Stored energy
Due to structure or location

8

Pi + ADP ==> ATP

It has a change in free energy that is greater than 0. That means it has a delta G that is positive and therefore the reaction is endergonic.

9

Kinetic Energy

Movement
Na+ and K+ molecules moving through a transport protein

10

Noncompetitive Inhibitor

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It lowers the Vmax and has no affect on the Km.
Fits into the Allosteric site to change the shape of the enzyme
Can cause a conformation change which will affect the enzyme's ability to bind to a substrate

11

Altering the three-dimensional structure of an enzyme might

Prevent the substrate from binding the enzyme's active site

12

Enzymes

Increase the rate of the reaction by reducing the activation energy.
They don't change the direction of the reactions
They do not change the amount of free energy available
It lowers the energy barrier needed for reactants to achieve the transition state or lowers the energy of activation of a reaction
Typical biological catalyst
Have a high affinity or high degree of specificity for a substrate
Can be recycled over and over

13

What are enzymes made of?

Mostly proteins but some are RNA molecules possess enzymatic functions called ribozymes

14
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This enzyme's optimal function is at about 37 degrees C, the enzymatic activity of the enzymes slows down around 40 C

15

NAD+ + H+ --> NADH
What has happened to NAD+?

It has been reduced

16

Free energy
∆G

The amount of available energy that can be used to promote change do work

17

How do you overcome the effect of a competitive inhibitor on enzyme activity

Increase the amount of substrate (Km) for the enzyme

18

Positive ∆G

Favors formation of reactants

19

Negative ∆G

Favors formation of products

20

Steps of an enzyme-catalyzed reaction

1. substrates bind to enzyme; 2. enzyme and substrate reach transtition state; 3. substrates are converted to products; 4. products are released

21

Active Site of Enzyme

Where the chemical reaction takes place
Where a competitive inhibitor competes to bind to

22

Second Law of Thermodynamics

Every chemical reaction must increase the total entropy of the universe. Every chemical reaction represents a transfer of energy, which increases entropy

Energy must be spent to retain order - this spending of energy usually releases heat, which increases the entropy elsewhere

23

Competitive Inhibitor

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Only raises the Km
Tries to bind to the active site
Slows down the Vmax when it binds to the allosteric site

24
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Exergonic

25

NADH is converted to NAD+ and H+. What has happened to NADH?

It has been oxidized.

26

Entropy

Measure of disorder

27

Exergonic Reaction

∆G is negative/less than zero
Spontaneous reaction (doesn't mean it will occur rapidly)
Favor making products (going from left to right)
Releases free energy

28

Endergonic Reaction

∆G is positive/greater than zero
Not spontaneous
Absorbs free energy
Favors making reactants
When you go from reaction to products, you have to add energy by coupling it with an exergonic reaction to make the overall ∆G negative

29

ATP (Adenosine Triphosphate)

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Universal energy molecule
Monomer of nucleic acids
Adenine, Ribose, and 3 phosphate groups connected to each other in a sequence
Energy intermediate
Is exergonic
Gets coupled with endergonic reactions (phosphorylation) -- Gives net negative free energy change
Source of energy for 20% of proteins
Undergoes 10,000 cycles of hydrolysis and re-synthesis every day
Likely underestimated because there may be other types of ATP-binding sites
A noncompetitive inhibitor for enzymes
The "energy currency" and how that we get work done

30

Change in free energy determines what?

The direction of chemical reactions

31

∆G =

∆H - T∆S

32

∆G

Free energy

33

∆H

Total energy

34

T

Absolute temperature

35

∆S

Entropy

36

Energy emitted through _______ is not usable.

Heat

37

Energy Systems

Are not efficient

38

Hydrolysis of ATP requires what to be exergonic?

Water and enzymes
The ∆G = -7.3 kcal/mole

39

Glucose + Phosphate --> glucose-phosphate + H2O

ΔG = +3.3 Kcal/mole and it is an endergonic reaction

40

Glucose + ATP → glucose-phosphate + ADP

Coupled Reaction

41

Phosphorylation

Direct transfer of a phosphate group from ATP to a substrate (an example being glucose)
It energizes the molecule

42

Spontaneous Reaction

Does not imply anything about its speed
Exergonic
Does not require inout of energy
Does require an enzyme

43

Catalyst

Speed up rate of reaction without being consumed

44

Names of enzymes usually end in ________ and typically describe what is going on.

-ASE

45

Activation Energy

Initial input of energy to start a reaction
Allows molecules to get close enough to cause bond rearrangement

46

Transition State

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Bonds are stretched/strained

47

2 ways to overcome activation energy:

1. Large amounts of heat
2. Using enzymes to lower activation energy

48

How to measure enzyme activity:

Measure your substrates and your products

49

VMax

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Velocity of reaction near maximum rate

50

Km

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Substrate concentration at which VMax is at half of max rate
Shows how good your enzyme is

51

If Km is high, the enzyme needs ______. This means the enzyme has a low affinity for the substrate.

A lot of substrate

52

Saturation

Plateau where nearly all active sites are occupied by substrates

53

Why do cells use inhibitors?

To turn off or slow down an enzyme

54

Coenzyme

Enzyme "helper"
Organic molecule
Vitamins
Carry electrons
Tightly bounded to the active site or bounded loosely

55

Cofactor

Enzyme "helper"
Inorganic molecule
Carry electrons
Tightly bounded to the active site or bounded loosely

56

Enzyme helpers (coenzymes and cofactors) will _______.

Bind to the enzyme or participate in the reaction

57

Vitamin C

Functions in muscle formation (collagen)
Deficiency causes scurvy (loss of teeth, pale skin, and sunken eyes)

58

Vitamin B3

"Nicotine acid"
Functions in the coenzymes NAD and NADP
Deficiency causes pellagra (skin lesions)

59

Which structures do enzymes most heavily depend on?

Tertiary and quaternary

60

Denature

When structure is lost due to heat
Once a certain temperature is reached, bonds maintaining the 2o, 3o, and 4o structure of the protein collapse and the protein loses function

61

The shape of the enzyme is altered by _____?

1. pH - Measure of H+ (0-7 is acidic and 8-14 is basic)
2. Temperature (typically when temperature increases, rate of reaction will increase, but not always) (as temperature increases, the enzyme's active site may become unstable and function poorly)
3. Coenzymes/Cofactors

62

Metabolism

Each step is coordinated by a specific enzyme

63

2 types of metabolism

1. Catabolic Pathways (Reactions)
2. Anabolic Pathways (Reactions)

64

Catabolic Pathways (Reactions)

Breaks down reactants
Used for recycling macromolecules
Used to obtain energy for endergonic reactions
Metabolic pathway is complex
Lots of intermediates (ATP & NADH)
Lots of energy transfer steps
Spontaneous, but does not happen without correct enzyme

65

Anabolic Pathways (Reactions)

Promote synthesis (builds up, not breaks down)
Endergonic reactions
Must be coupled to an exergonic reaction

66

Protease

Turns proteins into amino acids (catabolic pathway)

67

Nuclease

Breaks down RNA into nucleotides (catabolic pathway)

68

Hydrolysis of ATP ______ energy.

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Releases
Is exergonic
The bonds are broken
When the terminal phosphate bond is broken, a molecule of inorganic phosphate (Pi) is formed which forms adenosine diphosphate, ADP + (Pi) which generates free energy

69

Synthesis of ATP _______ energy.

Requires
Is endergonic
Can be through substrate level phosphorylation or chemiosmosis

70

Phosphorylation (substrate level)

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Finds a free floating Pi and takes it, which converts ADP to ATP

71
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ATP Synthesis

72

Chemiosmosis

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Deals with an electrochemical gradient

73

Intermediates

Compounds formed between initial reactants & products

74

Thermodynamics

Study of energy transformation

75

Enzyme-Substrate Complex

When an enzyme and a substrate come together
Held by hydrogen and/or ionic bonds

76

Enzyme action time is proportional to the concentration of the substrate:

The more substrate you have, the faster the reaction rate will be (until you reach saturation)

77

Enzyme Inhibitors

Chemicals that interfere with enzyme function
Are used to slow down/or stop an enzyme
Usually reversible in cells (when hydrogen or ionically bonded)

78

Allosteric site

Site on the enzyme that isn't the active site
Where noncompetitive inhibitors bind to

79

Energy Intermediates: Redox
Redox Reaction

Electron is removed from one molecule and added to another molecule

80

Oxidation (oil)

Removal of electrons

81

Reduction (Rig)

Addition of electrons

82

Ae- + B → A + Be-
A has been?

Oxidized (electron removed)

83

Ae- + B → A + Be-
B has been?

Reduced (electron added)

84

Energy Intermediates: NAD

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NAD is a type of nucleic acid
When NAD is reduced, NADH is formed
It's really easy to move electrons back and forth between NAD and NADH
Often coupled with reactions to give or remove energy

85

Electrons are synonymous with ______ in chemical reactions.

Energy

86

Where is energy found in molecules?

Bonds

87

Regulation of metabolic pathways

3 types:
1. Gene regulation
2. Cellular regulation
3. Biochemical regulation

88

Gene Regulation

Turn genes on or off

89

Cellular Regulation

Cell-signaling pathways like hormones

90

Biochemical Regulation

Feedback Inhibition- Product of pathway inhibits early steps to prevent over accumulation of product

91

Concentration Gradient

Refers to a differences of solutes (dissolved substances) in an adjacent area

92
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Enzyme-Catalyzed Reaction

A. Substrate binding
B. Transition State (induced-fit and Ea is lowered)
C. Substrate converted to product
D. Product is released