Chapter 6 - Energy & Life Flashcards
1
Q
What is metabolism?
A
The whole range of biochemical processes that occur within a living organism. Metabolism consists of anabolism (the buildup of substances) and catabolism (the breakdown of substances)
2
Q
What is a metabolic pathway?
A
A metabolic pathway is a linked series of chemical reactions occurring within a cell.
3
Q
What are catabolic pathways?
A
Metabolic pathways that release energy by breaking down complex molecules to simpler compounds.
4
Q
What are anabolic pathways?
A
Metabolic pathways that consume energy to build complicated molecules from simpler ones; they are some- times called biosynthetic pathways.
5
Q
What is a major catabolic pathway?
A
Cellular respiration, in which the sugar glucose and other organic fuels are broken down in the presence of oxygen to carbon dioxide and water. (Pathways can have more than one starting molecule and/or product.)
6
Q
What is are 2 examples of an anabolic pathways in the human body?
A
The synthesis of an amino acid from simpler molecules and the synthesis of a protein from amino acids
7
Q
Define energy?
A
The capacity to cause change
8
Q
What is kinetic energy?
A
Energy that is associated with the relative motion of objects.
9
Q
What is thermal energy?
A
Thermal energy is kinetic energy associated with the random movement of atoms or molecules; thermal energy in transfer from one object to another is called heat. Light is also a type of energy that can be harnessed to perform work, such as powering photosynthesis in green plants.
10
Q
What is chemical energy?
A
Chemical energy is a term used by biologists to refer to the potential energy available for release in a chemical reaction. For example glucose in food.
11
Q
True or False? Organisms are energy transformers.
A
True
12
Q
What is thermodynamics?
A
The study of the energy transformations that occur in a collection of matter.
13
Q
What is an isolated system?
A
unable to exchange either energy or matter with its surroundings outside the thermos.
14
Q
What is an open system?
A
Energy and matter can be transferred between the system and its surroundings.
15
Q
True or False? Organisms are isolated systems.
A
False, organisms are open systems
16
Q
What is the first law of thermodynamics?
A
The energy of the universe is constant: Energy can be transferred and transformed, but it cannot be created or destroyed. also known as the principle of conservation of energy.
17
Q
What is the Second law of thermodynamics?
A
Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, as a bear runs, disorder is increased around its body by the release of heat and small molecules that are the by-products of metabolism.
18
Q
Why can’t organisms simply recycle their energy over and over again?
A
during every energy transfer or transformation, some energy becomes unavailable to do work. In most energy transformations, the more usable forms of energy are at least partly converted to thermal energy and released as heat.
19
Q
What is entropy?
A
Entropy is a measure of uncertainty or randomness. The more randomly arranged a collection of matter is, the greater its entropy
20
Q
If entropy is increased is your reaction more or less favoured?
A
More favoured.
21
Q
What is a spontaneous process?
A
A process that can proceed without requiring an input of energy. Signifying that it is energetically favorable. -DELTA G
22
Q
Do spontaneous reactions all occur at the same speed?
A
No for example an explosion is much faster than a car deteriorating over time.
23
Q
What are non-spontaneous reactions?
A
A process that, on its own, leads to a decrease in entropy as it will happen only if energy is supplied. +DELTA G
24
Q
how does the second law of thermodynamics help explain diffusion, the random thermal motion of particles, across a membrane?
A
The second law is the trend toward randomisation, or increasing entropy. When the concentration of a substance on both sides of a membrane are equal, the distribution is more favoured than when they are unequal.
25
What is the function of the Gibbs free energy of a system (without considering its surroundings)? G
The Gibbs free energy (G) of a system is a measure of the amount of usable energy (energy that can do work) in that system. The change in Gibbs free energy during a reaction provides useful information about the reaction's energetics and spontaneity (whether it can happen without added energy)
26
What is free energy?
Free energy is the portion of a system’s energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell. We can think of free energy as a measure of a system’s instability- its tendency to change to a more stable state.
27
The change in free energy, ∆G, can be calculated for a chemical reaction by applying the following equation?
∆G = ∆H - T∆S
∆H symbolises the change in the system’s enthalpy (in biological systems, equivalent to total energy); ∆S is the change in the system’s entropy; and T is the absolute temperature in Kelvin (K) units
28
What can we use delta G to determine?
Whether a reaction will be spontaneous or not. processes with a negative ∆G are spontaneous.
29
What is the equation for delta G?
∆G = Gfinal state - Ginitial state
30
When a reaction goes away from equilibrium what happens to the value of the free energy?
It increases. Therefore G increases
31
A change from the equilibrium position will have a positive or negative G?
Positive as this is a non-spontaneous reaction and requires energy.
32
What are exergonic reactions?
“energy outward” An exergonic reaction proceeds with a net release of free energy. Because the chemical mixture loses free energy (G decreases), ∆G is negative for an exergonic reaction. This reaction is spontaneous
33
What are endergonic reactions?
“energy inward” An endergonic reaction is one that absorbs free energy from its surroundings. Because this kind of reaction essentially stores free energy in molecules (G increases), ∆G is positive. Such reactions are non-spontaneous,
34
True or False? The greater the decrease in free energy, the greater the amount of work that can be done.
True
35
If ∆G = -686 kcal/mol for respiration, which converts glucose and oxygen to carbon dioxide and water what would the reverse reaction be?
The conversion of carbon dioxide and water to glucose and oxygen must be strongly endergonic, with ∆G = +686 kcal/mol. Such a reaction would never happen by itself.
36
How do plants make the sugar that organisms use for energy?
Plants get the required energy—686 kcal to make a mole of glucose—from the environment by capturing light and converting its energy to chemical energy. Next, in a long series of exergonic steps, they gradually spend that chemical energy to assemble glucose molecules.
37
What is metabolic equilibirum?
When metabolic reactions in an isolated system eventually reach equilibrium and can then do no work
38
What happens when a cell reacher metabolic equilibrium?
It is dead
39
Is a living cell in equilibrium?
No or else it would be dead. The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life.
40
Why do metabolic cells barely ever reach equilibrium?
The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium, and the cell continues to do work throughout its life.
41
Why do some of the processes in cellular respiration never reach equilibrium?
Because the product of a reaction does not accumulate but instead becomes a reactant in the next step of cellular respiration. As long as our cells have a steady supply of glucose or other fuels and oxygen and are able to expel waste products to the surroundings, their metabolic pathways never reach equilibrium and can continue to do the work of life.
42
Is cellular respiration endothermic or exothermic?
It is an exothermic reaction because it creates chemical energy in the form of ATP. Although there is an endothermic step in glycolysis. Glycolysis is the breakdown of glucose into 2 pyruvate molecules.
43
What 3 types of work do cells do?
Chemical work, transport work, and mechanical work
44
What is chemical work?
The pushing of endergonic reactions that would not occur spontaneously, such as the synthesis of polymers from monomers
45
What is transport work?
The pumping of substances across membranes against the direction of spontaneous movement
46
What is mechanical work?
Such as the beating of cilia, the contraction of muscle cells, and the movement of chromosomes during cellular reproduction
47
What is energy coupling?
The use of an exergonic process to drive an endergonic one. ATP is responsible for mediating most energy coupling in cells, and in most cases it acts as the immediate source of energy that powers cellular work.
48
What does ATP contain?
The sugar ribose with the nitrogenous base adenine and a chain of 3 phosphate groups bonded to it.
49
True or False? ATP is one of the nucleoside triphosphate's used to make RNA.
True!
50
How are the bonds between the phosphate groups of ATP broken and what is the result of this?
Hydrolysis, the addition of a water molecule results in a molecule of the inorganic phosphate leaving the ATP resulting in ADP. This reaction is exergonic as it released 7.3 cal of energy per mole of ATP hydrolized.
51
What is the reaction for the production of ADP?
ATP + H2O > ADP + P (Inorganic phosphate group)
52
What are the phosphate bonds of ATP sometimes referred to and why?
High-Energy phosphate bonds because their hydrolysis releases energy but this is misleading because these bonds of ATP are not usually that strong. Rather it is ATP and H2O (reactants) that are high-energy relative to the products, ADP & P (Inorganic phosphate group) .
53
Why is ATP useful to the cell?
Because the energy it releases on losing a phosphate group is somewhat greater than the energy most other molecules could deliver.
54
Why does the hydrolysis of ATP release so much energy?
The 3 phosphate groups of ATP are negatively charged and these like charges are held closely together, this contributes to the instability of this region of the ATP molecule which is why it releases so much energy during hydrolysis.
55
What is the triphosphate tail of ATP the chemical equivalent to?
A compressed spring.
56
What is a cool way ATP hydrolysis works when organisms are shivering?
The hydrolysis of ATP releases energy therefore releases heat to the surroundings. The process of shivering uses ATP hydrolysis during muscle contraction to warm the body. This can be a potentially bad way for the body to warm itself and instead the cells proteins are more likely to harvest ATP for other types of cellular work.
57
True or False? The cell can use the energy from ATP hydrolysis to drive chemical reactions that by themselves are endergonic .
True
58
What is phosphorylation?
The transfer of a phosphate group from ATP to some other molecule such as the reactant. The recipient molecule with this group covalently bonded to them is then the phosphorylated intermediate.
59
What is the phosphorylated intermediate?
The recipient of the phosphate group during phosphorylation which has this molecule covalently bonded to them.
60
What is the key to coupling exergonic and endergonic reactions?
The formation of the phosphorylated intermediate which is more reactive (less stable and more free energy) than the original unphosphorylated molecule.
61
True or False? Transport and mechanical work in the cell are also nearly always powered by the hydrolysis of ADP in the cell.
False! They are nearly always powered by ATP.
62
How does ATP power mechanical work in the cell?
In most instances involving motor proteins 'walking' along the cytoplasm, a cycle occurs in which ATP is first bound non-covalently to the motor protein. Next ATP in hydrolysed releasing ADP and P then another ATP molecule can bind. At each stage the motor protein changes its shape and ability to bind the cytoskeleton resulting in movement of the protein across the cytoskeletal track.
63
How does ATP power transport work in the cell?
ATP phosphorylates transport proteins causing a shape that allows the transport of solutes.
64
What is the ATP cycle?
Where energy released by breakdown reactions (catabolism) in the cell is used to phosphorylate ADP, regenerating ATP. As chemical potential energy stored in the ATP drives most cellular work
65
If ATP could not be regenerated by the phosphorylation of ATP what would happen?
Humans would nearly use up all of their body weight each day.
66
Is the regeneration of ATP endergonic or exergonic?
Endergonic (+7.3 under standard conditions) Therefore it is not a spontaneous reaction.
67
True or False? Free energy must be spent to regenerate ATP.
True!
68
What pathways provide the energy for the endergonic process of making ATP?
Catabolic exergonic pathways especially cellular respiration.
69
What do plants use to make ATP?
Light energy
70
How does ATP typically transfer energy from an exergonic to an endergonic reaction in the cell?
ATP usually transfers energy to an endergonic process by phosphorylating (adding a phosphate group to) another molecule. (Exergonic processes, in turn, phosphorylate ADP to regenerate ATP.)
71
Which of the following has more free energy: glutamic acid + ammonia + ATP or glutamine + ADP + P
glutamic acid + ammonia + ATP
72
If a reaction is spontaneous does this essentially mean it will go fast?
No
73
What are enzyme catalysts
Enzymes that speed up metabolic reactions by lowering energy barriers. It is not consumed in the reaction
74
True or False? Ribosomes can act as enzymes
True
75
Without the regulation by enzymes what would happen?
Chemical traffic through the pathways of metabolism would become terribly congested because many chemical reactions would take such a long time.
76
What is activation energy?
Also known as the free energy of activation this is the energy requires to contort the reactant molecules so that the reaction can begin.
77
When the reactant molecules have absorbed enough thermal energy due to collision what condition are they in?
They are then in an unstable condition known as the transition state. They are then activated and their bonds can be broken or formed and then the atoms can settle into their new more stable bonding arrangements.
78
Which complex cellular molecules are rich in free energy?
Proteins, DNA, and others. These have the potential to decompose spontaneously.
79
Heat can increase the rate of a reaction and allow reactants to attain the transitional state more often, so why does this not work well in biological systems?
The high temperature denatures the proteins and kills cells and this heat would speed up all reactions not just those that are needed in a system.
80
Instead of heat for reactions what do organisms use?
Catalysis
81
What is catalysis?
A process by which a catalyst (For an example an enzyme) selectively speeds up a reaction without itself being consumed. This allows reactions to reach the transitional state at moderate temperatures.
82
Does an enzyme change the delta G for a reaction?
No
83
Can enzymes make and endergonic reaction exergonic?
No
84
True or False? Enzymes can catalyse any reaction
False. Enzymes are very specific with what reactions they catalyse.
85
The reactant an enzyme acts on is called what?
A substrate
86
What forms when an enzyme binds to its substrate?
An enzyme-substrate complex.
87
What happens while the enzyme and substrate are binded?
The catalytic action of the enzyme converts the substrate to the product of the reaction. The overall reaction is: Enzyme + Substrate >< Enzyme-Substrate complex >< Enzyme + Product
88
What do the names of most enzymes end in?
-ase
89
What does the enzyme sucrase do?
Catalyses the hydrolysis of the disaccharide sucrose into its two monosaccharides, glucose and fructose.
90
True or False? An enzyme can recognise its specific substrate even among closely related compounds.
True
91
How do enzymes have molecular recognition
Most enzymes are proteins and proteins are macromolecules with unique three-dimensional configurations. Therefore the specificity of an enzyme results from its shape which is a consequence of its amino acid sequence.
92
What region of the enzyme binds to the substrate?
The active site which is typically a pocket or groove on the surface of the enzyme where catalysis occurs.
93
How is the active site of an enzyme formed?
Usually by only a few amino acids.
94
What is the specificity of an enzyme attributed to?
The complementary fit between the shape of its active site and the shape of the substrate.
95
True or False? An enzyme binded to a substrate is a stiff structure.
False, in-fact research has shown these enzymes to 'dance' between different shapes in dynamic equilibrium with slight differenced in free energy for each 'pose'.
96
What bonds form then the substrate enters the active site?
Weak interactions (Hydrogen bonds and ionic bonds) with the enzymes inducing a change in the shape of the protein.
97
What is induced fit?
The tightening of the binding after initial contact when the substrate enters the active site of the enzyme.
98
What groups of the amino acids in the active site catalyse the conversion of the substrate to product?
The R-groups
99
After the conversion of the substrate to product what happens?
The enzyme is then free to take another substrate molecule into its active site.
100
How fast can a single enzyme typically act on 1,000 substrate molecules?
1 Second
101
True or False? Most metabolic reactions are reversible.
True
102
When there are two or more reactants what do the catalytic enzymes do?
The active site provides a template on which the substrates can come together in the proper orientation for a reaction to occur between them. As the active site holds the substrates the enzyme may stress, bend and stretch the substrate molecules towards their transitional state form which reduces the amount of free energy that must be absorbed to reach that state.
103
True or False? Amino acids in the active site directly participate in the chemical reaction.
True, sometimes this process even involves brief covalent bonding between the substrate and the site chain of the amino acid of the enzyme.
104
True or False? The more substrate molecules that are available, the more frequently they access the active sites of the enzyme molecules.
True
105
What does it mean when a enzyme is said to be saturated?
When it has a substrate concentration where as soon as the product exits the active site another substrate molecules enters
106
When are enzyme population is saturated how do you increase the rate of reaction?
By adding more enzymes
107
What affects how efficiently an enzyme functions?
General environmental factors such as temperature and pH. Chemicals can also influence the enzyme.
108
True or False? The 3-Dimensional structures of proteins are sensitive to their environments.
True
109
What are optical conditions?
Conditions that favour the most active shape for the enzyme.
110
If the temperature is to hot for a reaction involving enzymes what happens?
The speed of the enzymatic reaction drops sharply and it disrupts the weak interactions that stabilise the active shape of the enzyme causing the protein molecule to eventually denature.
111
What optimal temperatures do most human enzymes have?
35-40 which is close to human body temperature
112
what optimal pHs do most enzymes have?
Between 6-8 but there are exceptions
113
What is pepsin?
A digestive enzyme in the stomach that is an exception to the optimal pH of most enzymes are it works best in environments with very low pHs
114
What are cofactors?
Non-protein helpers for catalytic activity . They may be bound tightly to the enzyme as permanent residents or they may be bound loosely are reversibly along with the substrate.
115
What is the cofactor of an enzyme more specifically referred to as?
A co-enzyme
116
What are competitive inhibitors?
Reversible inhibitors that resemble the normal substrate molecule and compete for admission into the active site. They reduce the productivity of enzymes by blocking substrates from entering the active sites. This type of inhibition can be overcome by increasing the concentration of substrate so that the active sites become available and more substrate molecules are around to gain entry.
117
What are non-competitive inhibitors?
These inhibitors do not directly compete with the substrate to bind to the enzyme at the active site instead they impede (delay) enzymatic reactions by binding to another part of the enzyme. This causes the enzyme to change its shape in such as way that the active site becomes much less efficient at catalysing the conversion of substate to product.
118
What are some irreversile enzyme inhibitors?
Toxins and poisons
119
Are enzyme inhibitors bad?
Not always, In fact, molecules naturally present in the cell often regulate enzyme activity by acting as inhibitors. Such regulation—selective inhibition—is essential to the con- trol of cellular metabolism
120
What can mutations in the genes do to enzymes?
In the case of an enzyme, if the changed amino acids are in the active site or some other crucial region, the altered enzyme might have a novel activity or might bind to a different substrate.
121
How can a cell tightly regulate its metabolic pathways by controlling when and where its various enzymes are active?
It does this either by switching on and off the genes that encode specific enzymes or by regulating the activity of enzymes once they are made
122
What is allosteric regulation of enzymes?
These behave something like reversible noncompetitive inhibitors: These regulatory molecules change an enzyme’s shape and the functioning of its active site by binding to a site elsewhere on the molecule, via non-covalent interactions. This may result in either inhibition or stimulation of an enzyme’s activity.
123
What do allosteric activators stabilise?
The active form of the enzyme
124
What does the allosteric inhibitor stabilise?
The inactive form of the enzyme
125
What happens if ATP binds to a catabolic enzyme allosterically?
This lowers the enzymes affinity for substrate and thus inhibits its activity.
126
What happens if ADP binds to a catabolic enzyme allosterically?
ADP functions as an activator of the enzymes.
127
Does catabolism or anabolism function in the regeneration of ATP?
Catabolism
128
What is cooperativity?
Where a substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all the subunits, thereby increasing catalytic activity at the other active sites
129
Is cooperativity an allosteric regulation?
Yes
130
What is feedback inhibition?
Feedback inhibition is the phenomenon where the output of a process is used as an input to control the behavior of the process itself, oftentimes limiting the production of more product. This can prevent the cell from making more product than is necessary and thus wasting chemical resources.
131
What are the function of enzymes inside the matrix of the mitochondria?
Enzymes involved in the second step of cellular respiration
132
What are the function of enzymes inside the inner membrane of the mitochondria?
Enzymes involved in the third step of cellular respiration
