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Biology 111 > Chapter 8 > Flashcards

Chapter 8 Flashcards

1
Q

Metabolism

A

Totality of an organism’s chemical reactions

An emergent property, involves several molecules

Never reaches equilibrium, defining feature of life

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2
Q

Activation Energy

A

amount of energy needed to start a chemical reaction

EA

Usually supplied in form of heat from surroundings

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3
Q

Substrates

A

Reactant that the enzyme acts on

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4
Q

Catabolic Pathways

A

break complex molecules into simpler ones by releasing energy

ex. cellular respiration

Release free energy in a series of reactions

Catabolic reactions in cell provide energy to phosphorylate ADP

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5
Q

Anabolic Pathways

A

build complex molecules from simper ones by absorbing energy

ex. photosynthesis, synthesis of macromolecules

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6
Q

Closed System

A

isolated from surroundings

ex. liquid in thermos

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7
Q

Open System

A

energy and matter can be exhanged between system and surroundings

ex. organisms

Reactions in open systems (living cells) are constantly trying to reach equilibrium, but never do

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8
Q

First Law of Thermodynamics

A

“Energy can be transferred and transformed, but it cannot be created nor destroyed”

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9
Q

Second Law of Thermodynamics

A

“Every energy transfer or transformation increases the entropy (disorder) of the universe”

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10
Q

Free energy

A

energy that can do work when temperature and pressure are uniform (homeostasis)

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11
Q

Change in free energy and how it’s related to everything else

A

change in free energy = delta G (difference in free energy between products and reactants)

delta G = delta H - T delta S (change in entropy)

Free energy decreases, stability increases

As free energy decreases, work increases

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12
Q

Equilibrium

A

state of maximum stability

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13
Q

Spontaneous processes

A

don’t require energy input and can happen quickly or slowly

A process is spontaneous and can perform work only if it is moving towards equilibrium

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14
Q

Exergonic reaction

A

spontaneous, releases energy

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15
Q

Endergonic reaction

A

nonspontaneous, absorbs free energy from surroundings

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16
Q

3 main kinds of work by a cell

A

chemical, transport, mechanical

Powered by hydrolysis of ATP

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17
Q

Energy coupling

A

use of exergonic process to drive an endergonic one

(it’s how cell manage energy resources)

(mediated by ATP)

In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction

Overall, coupled reactions are exergonic

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18
Q

Composition of ATP

A

Adenosine triphosphate

Ribose (sugar), adenine (a nitrogenous base), and 3 phosphate groups (nucleotide)

Bonds can be broken by hydrolysis (energy is released)

Release of energy comes from chemical change (to a lower state of energy), not phosphate bonds themselves.

ATP + H2O -> ADP + Pi + energy

ATP is a renewable resource (add P to ADP)

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19
Q

How does ATP drive endergonic reactions?

A

Phosphorylation (transferring a phosphate group to some other molecule, like a reactant) (recipient molecule is now phosphorylated)

ex. Transport work - ATP phosphorylates transport proteins

Mechanical work - ATP binds noncovalently to motor proteins, then is hydrolyzed

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20
Q

Chemical potential energy

A

temporarily stored in ATP, drives most cellular work

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21
Q

Catalyst

A

chemical agent that speeds up reaction without being consumed by reaction

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22
Q

Enzymes

A

Enzymes are catalytic proteins

-ase endings are enzymes

Speed up reactions by lowering activation energy (does not affect delta G)

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23
Q

Polymerase

A

synthesis of DNA or RNA

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24
Q

Nuclease

A

destroy DNA molecule

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25
Exonuclease
outside DNA molecules, cut DNA into specific pieces
26
RNase
destroys RNA a nuclease
27
DNase
Destroys DNA a nuclease
28
Proteinase K
destroys proteins
29
Transition State
when reactants absorb energy, they become unstable
30
Enzyme-substrate complex
when an enzyme binds to the substrate
31
Active site
the region on the enzyme where the substrate can bind (lock and key relationship)
32
Induced fit of a substrate
brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
33
The active sity of an enzyme lowers activation energy by:
* orienting substrates correctly * straining substrate bonds * providing a favorable microenvironment * covalently bonding to a substrate
34
Process of substrate binding to an enzyme
1. substrates enter active site; enzyme changes shape to completely enfold substrate (induced fit) 2. substrates held in active site by weak interactions (hydrogen and ionic bonds) 3. Active site can lower EA and speek up reaction 4. Substrates converted to products 5. Products are released 6. Enzyme is now available for 2 new substrate molecules
35
What is enzyme activity affected by?
General environmental factors (temp, pH, chemicals), ions (Mg+ (DNA polymerase), K+ (Sodium-Potassium Pump))
36
ideal pH of cell
6.8 - 7.2 (aqueous solution) 3 (stomach)
37
Thermophillic
heat-tolerant
38
Trypsin
intestinal enzyme
39
Taq DNA polymerase
specific to thermophillic bacteria
40
Cofactors
nonprotein enzyme helpers, can be organic (coenzymes -\>vitamins) or inorganic (a metal in ionic form)
41
Competitive Inhibitors
bind to the active site of the enzyme, competing w/ substance
42
Noncompetitive Inhibitors
binds to a different part of the enzyme, causing it to change shape (modifying it) (not reversible) (makes active site less effective)
43
How does a cell regulate metabolic activities?
By turning on/off genes that encode specific enzymes or by regulating activity of enzymes
44
Allosteric Regulation
Inhibits OR stimulates enzyme activity Happens when a regulatory molecule binds to a protein at one site and affects the protein's function at another Made from polypeptide subunits Binding of activator stabilizes active from Binding of inhibitor stabilizes inactive form
45
Cooperativity
amplifies enzyme activity. Binding of 1 substrate to active site stabilizes favorable conformational changes at all other subunits
46
Allosteric regulators
are attracive drug candidates for enyme regulation
47
Inhibition of proteolytic enzymes (one that simply acts on proteins) called caspases
may help management of inappropriate inflammatory responses
48
Cysteine
amino acid that contains sulfur
49
Feedback Inhibition
end product of a metabolic pathway shuts down the pathway Prevents a cell from wasting chemical resourses by synthesizing more product than needed (conserves energy within system)
50
Some enzymes act as ?
structural componenets of membranes Eukaryotic: some reside in specific organelles (enzymes for cellular respiration in mitochondria)
51
Totality of an organism's chemical reactions An emergent property, involves several molecules Never reaches equilibrium, defining feature of life
Metabolism
52
amount of energy needed to start a chemical reaction EsubA Usually supplied in form of heat from surroundings
Activation Energy
53
Reactant that the enzyme acts on
Substrates
54
break complex molecules into simpler ones by releasing energy ex. cellular respiration Release free energy in a series of reactions Catabolic reactions in cell provide energy to phosphorylate ADP
Catabolic Pathways
55
build complex molecules from simper ones by absorbing energy ex. photosynthesis, synthesis of macromolecules
Anabolic Pathways
56
isolated from surroundings ex. liquid in thermos
Closed System
57
energy and matter can be exhanged between system and surroundings ex. organisms Reactions in open systems (living cells) are constantly trying to reach equilibrium, but never do
Open System
58
"Energy can be transferred and transformed, but it cannot be created nor destroyed"
First Law of Thermodynamics
59
"Every energy transfer or transformation increases the entropy (disorder) of the universe"
Second Law of Thermodynamics
60
energy that can do work when temperature and pressure are uniform (homeostasis)
Free energy
61
change in free energy = delta G (difference in free energy between products and reactants) delta G = delta H - T delta S (change in entropy) Free energy decreases, stability increases As free energy decreases, work increases
Change in free energy and how it's related to everything else
62
state of maximum stability
Equilibrium
63
don't require energy input and can happen quickly or slowly A process is spontaneous and can perform work only if it is moving towards equilibrium
Spontaneous processes
64
spontaneous, releases energy
Exergonic reaction
65
nonspontaneous, absorbs free energy from surroundings
Endergonic reaction
66
chemical, transport, mechanical Powered by hydrolysis of ATP
3 main kinds of work by a cell
67
use of exergonic process to drive an endergonic one (it's how cell manage energy resources) (mediated by ATP) In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, coupled reactions are exergonic
Energy coupling
68
Adenosine triphosphate Ribose (sugar), adenine (a nitrogenous base), and 3 phosphate groups (nucleotide) Bonds can be broken by hydrolysis (energy is released) Release of energy comes from chemical change (to a lower state of energy), not phosphate bonds themselves. ATP + H2O -\> ADP + Pi + energy ATP is a renewable resource (add P to ADP)
Composition of ATP
69
Phosphorylation (transferring a phosphate group to some other molecule, like a reactant) (recipient molecule is now phosphorylated) ex. Transport work - ATP phosphorylates transport proteins Mechanical work - ATP binds noncovalently to motor proteins, then is hydrolyzed
How does ATP drive endergonic reactions?
70
temporarily stored in ATP, drives most cellular work
Chemical potential energy
71
chemical agent that speeds up reaction without being consumed by reaction
Catalyst
72
Enzymes are catalytic proteins -ase endings are enzymes Speed up reactions by lowering activation energy (does not affect delta G)
Enzymes
73
synthesis of DNA or RNA
Polymerase
74
destroy DNA molecule
Nuclease
75
outside DNA molecules, cut DNA into specific pieces
Exonuclease
76
destroys RNA a nuclease
RNase
77
Destroys DNA a nuclease
DNase
78
destroys proteins
Proteinase K
79
when reactants absorb energy, they become unstable
Transition State
80
when an enzyme binds to the substrate
Enzyme-substrate complex
81
the region on the enzyme where the substrate can bind (lock and key relationship)
Active site
82
brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction
Induced fit of a substrate
83
* orienting substrates correctly * straining substrate bonds * providing a favorable microenvironment * covalently bonding to a substrate
The active sity of an enzyme lowers activation energy by:
84
1. substrates enter active site; enzyme changes shape to completely enfold substrate (induced fit) 2. substrates held in active site by weak interactions (hydrogen and ionic bonds) 3. Active site can lower EA and speek up reaction 4. Substrates converted to products 5. Products are released 6. Enzyme is now available for 2 new substrate molecules
Process of substrate binding to an enzyme
85
General environmental factors (temp, pH, chemicals), ions (Mg+ (DNA polymerase), K+ (Sodium-Potassium Pump))
What is enzyme activity affected by?
86
6.8 - 7.2 (aqueous solution) 3 (stomach)
ideal pH of cell
87
heat-tolerant
Thermophillic
88
intestinal enzyme
Trypsin
89
specific to thermophillic bacteria
Taq DNA polymerase
90
nonprotein enzyme helpers, can be organic (coenzymes -\>vitamins) or inorganic (a metal in ionic form)
Cofactors
91
bind to the active site of the enzyme, competing w/ substance
Competitive Inhibitors
92
binds to a different part of the enzyme, causing it to change shape (modifying it) (not reversible) (makes active site less effective)
Noncompetitive Inhibitors
93
By turning on/off genes that encode specific enzymes or by regulating activity of enzymes
How does a cell regulate metabolic activities?
94
Inhibits OR stimulates enzyme activity Happens when a regulatory molecule binds to a protein at one site and affects the protein's function at another Made from polypeptide subunits Binding of activator stabilizes active from Binding of inhibitor stabilizes inactive form
Allosteric Regulation
95
amplifies enzyme activity. Binding of 1 substrate to active site stabilizes favorable conformational changes at all other subunits
Cooperativity
96
are attracive drug candidates for enyme regulation
Allosteric regulators
97
may help management of inappropriate inflammatory responses
Inhibition of proteolytic enzymes (one that simply acts on proteins) called caspases
98
amino acid that contains sulfur
Cysteine
99
end product of a metabolic pathway shuts down the pathway Prevents a cell from wasting chemical resourses by synthesizing more product than needed (conserves energy within system)
Feedback Inhibition
100
structural componenets of membranes Eukaryotic: some reside in specific organelles (enzymes for cellular respiration in mitochondria)
Some enzymes act as ?

Biology 111 (9 decks)

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