Exam 3 Flashcards
(207 cards)
0
Q
The energy needs of essentially all organisms are provided _________ or _______ by solar energy.
A
directly or Indirectly
1
Q
The flow of electrons in _______-_______ _______ underlies the energy transduction a in living cells
A
Oxidation-reduction reactions
2
Q
Living organisms are __________, exchanging energy and matter via the environment.
A
Interdependent
3
Q
_______ must maintain life, grow, and reproduce
A
Cells
4
Q
Cells must harness _______ and transform it into a form to do biological work
A
Energy
5
Q
Energy transformations in cells obey the ______ of _______
A
Law of thermodynamics
6
Q
_______is the quantitative study of the energy transductions that occur in living cells and the nature and function of the chemical processes that underlie these transductions
A
Bioenergetics
7
Q
The principle of the conservation of energy
A
First law of thermodynamics
8
Q
The first law of thermodynamics states that for any physical or chemical change, the total amount of energy in the universe remains constant; energy may change form or it may be transported from one region to another, but it cannot be _______ or _______
A
Created or destroyed
9
Q
The principle of increasing disorder
A
Second law of thermodynamics
10
Q
According to the second law of thermodynamics in all natural process, the _______ of the universe increases
A
Entropy
11
Q
Entropy in _______ systems tend to increase to a maximum
A
Isolated
12
Q
The _______ of the components of a chemical system is expressed as entropy, S
A
Randomness
13
Q
Any change in randomness is expressed as “_______________”
A
Change in entropy
14
Q
DELTA S has a _______ value when randomness increases
A
Positive
15
Q
DELTA S has a _______ value when randomness decreases
A
Negative
16
Q
The central issue in bioenergetics is the means by which energy from metabolism or light capture is coupled to _______-_______ reactions
A
Energy-requiring
17
Q
The actual amount of energy available to do work is called the (_______) _______________
A
Gibbs free energy
18
Q
The amount of free energy required will differ from the theoretical amount of energy because some energy is dissipated as the _____ of ______
A
Heat of friction
19
Q
Chemical reactions can be _______ so that an energy-releasing reaction drives an energy requiring one
A
Coupled
20
Q
Chemical reactions in a _______ system proceed spontaneously until equilibrium is reached
A
Closed
21
Q
At _______, the rate of product formation exactly equals the rate of which product is converted to reactants
A
Equilibrium
22
Q
At equilibrium, a _______ _______ is achieved
A
Steady state
23
Q
In the steady state there is no _______ change in the concentration of reactants and products
A
Net
24
The energy change in the system as it moves from its initial state to equilibrium, with no changes in ________ or pressure is given as change in free energy
Temperature
25
_______ reactions are reactions that occur spontaneously and the products have less free energy than the reactants, thus the reaction releases free energy, which is available to do work
Exergonic
26
_______ reactions require an input of energy! and their DELTA G is ______
Endergonic
| Positive
27
DELTA G can be defined in terms of three quantities
Enthalpy
Entropy
Absolute temperature
28
Reflecting the number and kinds of bonds (heat evolution or absorption)
Enthalpy
29
Randomness of the system
Entropy
30
Absolute temperature is expressed in _______
Kelvin
31
A negative DELTA H and a positive DELTA S are _______ of favorable processes
Typical
32
Either a negative DELTA H or a positive DELTA S will tend to make DELTA G _______
Negative
33
A positive DELTA G indicates that a process is not favorable, but that the _______ process is
Reverse
34
_______ free energy change is directly related to the equilibrium constant.
Standard
35
The concentrations of reactants and products at _______ define the equilibrium constant
Equilibrium
36
When a reacting system is not at equilibrium, the tendency to move toward equilibrium represents a _______ _______, the magnitude of which can be expressed as the rate free energy change
Driving force
37
Under _______ conditions when reactants and products are initially present at 1M concentrations the force driving the system toward equilibrium is defined as the standard free energy change
Standard
38
Biochemists define the standard state to include a pH of _______ and a water concentration 55.5M
Seven
39
For reactions that involve magnesium its _______ is taken to be a constant 1mM
Concentration
40
Physical constants based on the _____________________ are called standard _______ constants and are writer with a prime
Biochemical standard state
| Transformed
41
The standard transformed constants distinguishes them from the _______ constants used by chemists and physicists
Untransformed
42
The standard free energy change of a chemical reaction is simply an alternative mathematical way of expressing the ______________
Equilibrium constant
43
Chemical analysis shows that for the reaction of glucose-1-phosphate to glucose-6-phosphate it is catalyzed by the enzyme _______, the final equilibrium mix contains 1mM glucose-1-phosphate and 19mM glucose-6-phosphate
Phosphoglucomutase
44
For the reverse reaction, ΔG'* has the same ______, but the opposite sign
Magnitude
45
The actual free energy change is dependent on reactant and product ______
Concentrations
46
_______ do not change equilibrium constants, only the _______at which the reaction proceeds in the direction dictated by _______
Enzymes
Rate
Thermodynamics
47
_______ is not too useful in biochem because the system is not _______
Entropy
| Isolated
48
Cells contain several compounds that have ______ _______ free energy changes
Large
| Negative
49
These compounds supply energy to many _______ reactions in cells. These processes include biosynthesis and transport.
Endergonic
50
The common energy currency of cells is in the form of _______
ATP
51
Formal name of ATP
Adenosine triphosphate
52
High energy compounds include:
Phosphoenolpyruvate
1,3-bisphosphoglycerate
Phosphocreatine
Acetyl-CoA
53
The donation of energy from ATP to an endergonic reaction GENERALLY involves the _______ participation of ATP in the reaction to be driven
Covalent
54
The donation of energy by ATP, in most cases involves _______ group transfer, and not simple ATP hydrolysis
Phosphoryl
55
The standard free energy change for ATP hydrolysis is _______kJ/mol
-30.5 kJ/mol
56
The _______ free energy of ATP hydrolysis in living cells is much larger
Actual
57
The actual free energy of ATP hydrolysis in cells is larger because the conditions in a cell are very different from _______ conditions
Standard
58
The cellular concentrations of ATP, PEP, and Pi are not identical and much _______ than 1M concentration
Lower
59
In addition, most enzymatic reactions that use ATP as the phosphoryl group donor, the true substrate is _______
MgATP
60
The magnesium in the _______ binds to ATP and ADP
Cytosol
61
In biochemical pathways where ATP is involved to supply energy to a reaction, the _______ step is typically shown as a single arrow
ATP
62
When ATP is involved to supply energy to a reaction, the reactions _______ to represent a simple hydrolysis where water displaces Pi or PPi
Appear
63
This ________-_______ process actually occurs
Two step
64
The first step is the transfer of a phosphoryl, _______, or AMP group to the substrate
Pyrophosphoryl
65
Phosphoryl, pyrophosphoryl, or adenylate becomes _______ attached to the substrate, thus _______ it's free energy
Covalently
| Raising
66
In the second step, the phosphate-containing group is _______, generating Pi, PPi, or AMP
Displaced
67
The ATP therefore _______ in the reaction
Participates
68
Sometimes direct _______ of ATP does drive a process without the covalent binding of ATP to the _______
Hydrolysis
| Substrate
69
An example of direct hydrolysis of ATP without covalent binding of ATP of the substrate is the _______ binding of ATP or GTP to drive some proteins between two different _______. This results in mechanical motion
Noncovalent
| Conformations
70
_______ _____ is either indirectly or directly responsible for all biological and biochemical work
Electron flow
71
Electron flow is largely mediated through _______-_______ reactions
Oxidation-reduction
72
What are the three ways oxidation can occur?
Addition of oxygen,
The removal of hydrogen,
The removal of electrons
73
What are the three ways reduction can occur?
Removal of oxygen
The addition of hydrogen,
The addition of electrons
74
The source of electrons in nonphotosynthetic organisms are _______ compounds
Reduced
75
The source of electrons in phosphosynthetic organisms is a chemical species excited by the _______ of light
Absorption
76
Electrons flow from the source, to various metabolic intermediates, to electron carriers, and ultimately to electron acceptors having _______ electron affinities, with energy _______
High
| Release
77
Cells contain numerous energy _______ molecules that function to convert the energy of electron flow into work
Transducing
78
Different chemical species differ in their _______ for electrons
Affinity
79
In the electromotive force electrons flow _______ from a molecule with lower electron affinity to a molecule with high electron affinity
Spontaneously
80
The electron motive force is driven by a force _______ to the difference in electron affinities
Proportional
81
The flow of electrons is _______ due to the high affinity of oxygen for electrons
Exergonic
82
The electromotive force generated provides _______ to do biological work
Energy
83
In the _______, membrane-bound enzymes use the energy from the electromotive force to produce transmembrane _______ difference
Mitochondrion
| pH
84
The proton gradient had potential energy and is called the _______-_______ force
Proton-motive force
85
ATP in the mitochondrion uses the energy generated by the proton motive force to synthesize ATP from _______ and _______
ATP
| Pi
86
Highly _______ compounds contain a relatively large amount of hydrogen when compared with oxygen
Reduced
87
In biological systems, oxidation is often synonymous with ______
Dehydrogenation
88
_______ catalyze oxidation reactions
Dehydrogenases
89
There are only a _______ universal biological electron carriers
Few
90
The reduction of the biological electron carriers during catabolic processes _______ the free energy released by substrate oxidation
Conserves
91
The universal biological electron carriers undergo _______ reduction
Reversible
92
What are the four major universal electron carriers?
NAD+
NADP+
FMN+
FAD+
93
Formal name of NAD+
Nicotinamide adenine dinucleotide
94
Formal name of NADP+
Nicotinamide adenine dinucleotide phosphate
95
Formal name of FMN+
Flavin mononucleotide
96
Formal name of FAD+
Flavin adenine dinucleotide
97
What are the other electron carriers?
Ubiquinone,
plasoquinone,
Iron-sulfur proteins,
Cytochromes
98
NAD+, NADP+, FMN, FAD are all _______-soluble coenzymes
Water-soluble
99
NAD+ and NADP+ easily move between a number of various _______
Enzymes
100
The nicotinamide ring resembles pyrimidine and are called _______ ______
Pyrimidine nucleotides
101
_______ is the source of the nicotinamide moiety
Niacin
102
FMN and FAD are typically tightly bound to _______ and are prosthetic groups to those enzymes
Flavoenzymes
103
Ubiquinone and plasoquinone are _______-_______ and act as electron carriers and proton donors in membranes
Lipid-soluble
104
Iron-sulfur proteins and _______ have tightly bound prophetic groups which serve as the electron carriers
Cytochromes
105
Formal name of PI-PLC
Phosphotidylinositol- phospholipase C
106
__________ is the enzyme that acts on phosphotidylinositol
Phosphotidylinositol- Phospholipase C
107
There is diversity in types of receptor tyrosine kinase, what are the diferences
```
Class 1 and Class 3 are single subunits
And class 2 is a dimer with two subunits
```
108
_______ _______ kinase is associated with viral transforming proteins produced by oncogenic viruses
Nonreceptor Tyrosine
109
What is pp60^v-src?
Phospho-protein, 60kD, viral-origin, sarcoma-causing
110
pp60^v-src has a __________ anchor to membrane of host
Fatty acid
111
Molecule of IP3 is released to diffuse into the cytoplasm. This molecule is very _______
Hydrophilic
112
When IP3 is released, diacylglycerol remains as a product in the membrane. DAG is very _______
Hydrophobic
113
_______ tyrosine kinase act as an activator which will recognize phospholipase C as the substrate
Receptor
114
What does PLC do?
Cleaves phosphorylation headgroup from PIP2
115
In order of PLC to be active it must have phosphorylation and _______ present
Calcium
116
_______ signaling is the ability of cells to receive and act on signals from beyond the cell membrane without having the _______ signal itself cross the membrane
Transmembrane
| Physical
117
What are pheromones?
Chemicals produced by certain species to signal others of the same species
118
Pheromones can act in a _______ way by producing chemicals to attract others
Defensive
119
_______ are important pathways that dictate cellular response in an environment
Pheromones
120
_______ _______ is the conversion of information into a chemical change
Signal transduction
121
Signal transductions are highly _______ and extremely _______
Specific
| Sensitive
122
The _______ of signal transduction is accomplished by precise molecular complementarity between signal and _______ molecules
Specificity
| Receptor
123
_______ means that not many signals are needed to cause a response, only one or two are needed to get a large response
Sensitivity
124
When the _______-_______ interacts the unit illicit a a certain response together that would otherwise not occur
Ligand-receptor
125
The sensitivity of signal transduction can be accounted to :
HIGH AFFINITY of receptors for signal molecules
COOPERATIVITY in the ligand-receptor interaction
AMPLIFICATION of the signal by enzyme reactions
126
The _______ of the signal by enzyme cascades occurs by a signal molecule binding to the receptor triggering enzymes that produce signals then secondary signals, each with multiple products
Amplification
127
During amplification the signal strength _______ throughout the cascade
Increases
128
The specificity of signal-transducing systems is not very specfic for _______ receptor and does not work with _______ molecules
one
| alternate
129
The amplification of the signal-transducing systems occuring with one enzyme that acts on another enzyme that produces _______ products
Multiple
130
_______ is a feature of signal transducing systems
modularity
131
"Mix-match" signals yield complexes with _______ functions
different
132
In modularity, the _______ points are reversible
phosphorylation
133
What are the five features of signal-transducing systems?
```
specificity
amplification
modularity
desensitization & adaptation
integration
```
134
Not all, just some systems have the ability to be turned off. This is the feature _______ of signal-transducing systems.
Desensitization/ adaptation
135
In desensitization, when receptors become active, a feedback mechanism also gets _______ to cancel receptor activity or cause loss of receptor from the cell membrane
Activated
136
_______ and _______ are critical in signal-transducing systems because signal cascades do not need "runaway" responses, they need a way to stop the response
Desensitization and adaptation
137
In _______ two signals have opposite effects, the way the response is regulated, is by combined input from both receptors
Integration
138
In the integration of signal-transducing systems multiple signals yields a _______ response
Unified
139
What are the six general types of signal transducers?
```
G Protein-coupled receptor,
Receptor Tyrosine Kinase,
Receptor Guanylyl Cyclase,
Gated Ion Channel,
Adhesion Receptor,
Nuclear Receptor
```
140
What is the signal of the G Protein Coupled Receptor?
The ligand
141
What is usual product of G-protein coupled receptors?
A second messenger
142
In G Protein- coupled receptors, when the ligand binds to the receptor it causes a _______ change
Conformation
143
What is the intermediate of G protein coupled receptor signal transduction?
A G-protein
144
What is the signal transducer?
The receptor
145
In receptor tyrosine kinase when the ligand binds it can trigger _______ which activates receptor
Autophosphorylation
146
Some _______ _______ _______ act in order to trigger a response in the nucleus, either producing or activating transcription factors
Receptor tyrosine kinase
147
The receptor of receptor tyrosine kinase acts as both a receptor and a _______
Kinase
148
In the receptor Guanylyl Cyclase signal binds to the receptor it activates the receptor which functions as _______ _______
Guanylyl Cyclase
149
What acts as a second messenger in receptor Guanylyl Cyclase?
The conversion Guanylyl Cyclase to cyclic GMP
150
When gated ion channels are _______ ions go through
Open
151
When when gated ion channels are _______ ions do not go through
Closed
152
What causes gated ion channels to open?
Conformational changes
153
The calcium channel is an example of a _______ _______ _______ which causes a calcium ion influx to the cell
Gated ion channel
154
Another name for adhesion receptor is an _______
Integrin
155
_______ receptors bind to molecules in the extracellular matrix which alters confirmation which alters _______ interaction with matrix molecules
Adhesion
| Cytoskeleton
156
_______ _______ will either hold on the the matrix or shed the matrix
Adhesion receptors
157
what type of signal transducer acts like transcription factors,
Nuclear receptors
158
The _______ and _______ of extracellular signals to the interior of cells gives rise to a number of observable biochemical events
Transduction and amplification
159
Activation of signal transduction pathways mobilize various _______ messengers
Second
160
What are some common intracellular second messengers?
```
cAMP
cGMP
Ca^2+
IP3
DAG
Phosphatic acid
Ceramide
Nitric oxide
Cyclic ADP-ribose
```
161
What are the effects of cAMP and where does is come from?
Effect: activates protein kinases
Source: adenylyl Cyclase
162
What is the function of IP3 and what is its source?
Effect: activates Ca^2+ channels
Source: PLC action on PIP2
163
The G-protein is _______
Heterotrimeric
164
In G-Protein coupled signaling the G-protein mediates the activation to produce _______
cAMP
165
In the G-protein's inactivated state, _______ has GDP on it and a fatty acid coming off
Alpha
166
The alpha subunit is a _______-_______ subunits
Lipid-modified
167
The alpha subunit is an _______ fatty acid
Acylated
168
The gamma subunit has a _______ subunit
Prynylated
169
The prynylated subunit has a _______ lipid to keep the inner leaflet and gamma subunit associated
Polyprenyl
170
When GDP gains affinity for _______ _______ it becomes GTP
Adenylate cyclase
171
The formation of GTP will cause the alpha subunit to _______ affinity for the beta subunit
Loose
172
_______ is cyclized to cAMP
cATP
173
There is a _______ G-protein alpha subunit and an _______ G-protein alpha subunit
Stimulatory
| Inhibitory
174
Cyclic AMP binds and activates _______ to phosphorylate certain proteins
PKA (protein kinase A)
175
cAMP can be destroyed directly to inhibit function when in its _______ form
5'-AMP
176
G-protein BETA and GAMMA subunits _______ stimulatory pathway
Inhibits
177
**When a biological circuit is formed, what four processes are associated?
Glucose as the electron source
Glucose is enzymatically oxidized
Electrons are released and flow through a series of electron-carrier intermediates
Electrons ultimately are "captured" by an electron acceptor, such as oxygen
178
In a biological circuit oxygen is a _______ electron acceptor
Terminal
179
IP3 is water-soluble and will _______ out of the membrane to the cytoplasm
Diffuses
180
What is required for PKC to be activated?
DAG
elevated Ca^2+ concentration
Presence of PS that form anulus around PKC2
181
The IP3 receptor is present in ________ endoplasmic reticulum
Smooth
182
The pathway to activate PLC
Tyrosine kinase
183
PLC has _______ requirement to be active through _________ pathways.
Calcium
| Signaling
184
PKC requires 3 things:
1. DAG
2. An elongated calcium concentration
3. Presence of PS that forms an annulus (lipid-that surrounds something) around PKC
185
SER have _______ ______ with binding sites for IP3, and function as _______ channels.
Integral proteins
| Calcium
186
IP3 binds ___________ with receptors
Simultaneously
187
__________ binds to multiple calcium ions simultaneously
Calmoduline CaM
188
When substrates become ___________ they become active
Phosphorylated
189
GPCR
Gene protein couple receptor
190
When IP3 is produced= _______ of calcium
Release
191
Calcium ion concentration can be measured in ______, by the degree of __________ dependent on the amount of calcium.
Cells
| Fluorescence
192
Another calcium flux "__________" can occur if there is a stimulation of a pathway, which is then inhibited, and once inhibited the inhibitor turns off allowing presence of calcium.
Oscillation
193
If calcium was constantly stimulated, what would happen to the ER?
It would eventually run out of calcium
194
Formed when PIP is phosphorylated
PIP2
195
_______ comes from phospholipid biosynthesis pathway
Phosphotidylinositol PI
196
What removes phosphates?
Inositol phosphatases
197
What adds phosphates?
Inositol kinase
198
Inositol can have ___ phosphates
6
199
_______ modulates activity of Ca+ dependent proteins
Calmodulin
200
Four main domains:
1. Phorbol- binding domain
2. Calcium- binding domain
3. ATP- binding domain
4. Substrate- binding domain
201
_______ ______ are equivalent to DAG, but stay bound
Phorbol esters
202
When PKC is inactive, it is _______, but not in the membrane.
Soluble
203
Calcium ions are placed between ____ & ______ to allow binding by interfering with negative repulsion.
C2 & membrane
204
High affinity of _______ for _______ molecules
Receptor
| Signal
205
Cooperativity in the _______-_______ interaction
Ligand-receptor
206
Amplification of the _______ by _______ reactions
Signal
| Enzyme
