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Biochem 2 > Exam 3 > Flashcards

Exam 3 Flashcards

0
Q

The energy needs of essentially all organisms are provided _________ or _______ by solar energy.

A

directly or Indirectly

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1
Q

The flow of electrons in _______-_______ _______ underlies the energy transduction a in living cells

A

Oxidation-reduction reactions

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2
Q

Living organisms are __________, exchanging energy and matter via the environment.

A

Interdependent

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3
Q

_______ must maintain life, grow, and reproduce

A

Cells

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4
Q

Cells must harness _______ and transform it into a form to do biological work

A

Energy

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5
Q

Energy transformations in cells obey the ______ of _______

A

Law of thermodynamics

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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

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7
Q

The principle of the conservation of energy

A

First law of thermodynamics

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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

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9
Q

The principle of increasing disorder

A

Second law of thermodynamics

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10
Q

According to the second law of thermodynamics in all natural process, the _______ of the universe increases

A

Entropy

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11
Q

Entropy in _______ systems tend to increase to a maximum

A

Isolated

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12
Q

The _______ of the components of a chemical system is expressed as entropy, S

A

Randomness

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13
Q

Any change in randomness is expressed as “_______________”

A

Change in entropy

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14
Q

DELTA S has a _______ value when randomness increases

A

Positive

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15
Q

DELTA S has a _______ value when randomness decreases

A

Negative

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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

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17
Q

The actual amount of energy available to do work is called the (_______) _______________

A

Gibbs free energy

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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

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19
Q

Chemical reactions can be _______ so that an energy-releasing reaction drives an energy requiring one

A

Coupled

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20
Q

Chemical reactions in a _______ system proceed spontaneously until equilibrium is reached

A

Closed

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21
Q

At _______, the rate of product formation exactly equals the rate of which product is converted to reactants

A

Equilibrium

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22
Q

At equilibrium, a _______ _______ is achieved

A

Steady state

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23
Q

In the steady state there is no _______ change in the concentration of reactants and products

A

Net

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24
Q

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

A

Temperature

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25
Q

_______ 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

A

Exergonic

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26
Q

_______ reactions require an input of energy! and their DELTA G is ______

A

Endergonic

Positive

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27
Q

DELTA G can be defined in terms of three quantities

A

Enthalpy
Entropy
Absolute temperature

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28
Q

Reflecting the number and kinds of bonds (heat evolution or absorption)

A

Enthalpy

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29
Q

Randomness of the system

A

Entropy

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30
Q

Absolute temperature is expressed in _______

A

Kelvin

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31
Q

A negative DELTA H and a positive DELTA S are _______ of favorable processes

A

Typical

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32
Q

Either a negative DELTA H or a positive DELTA S will tend to make DELTA G _______

A

Negative

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33
Q

A positive DELTA G indicates that a process is not favorable, but that the _______ process is

A

Reverse

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34
Q

_______ free energy change is directly related to the equilibrium constant.

A

Standard

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35
Q

The concentrations of reactants and products at _______ define the equilibrium constant

A

Equilibrium

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36
Q

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

A

Driving force

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37
Q

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

A

Standard

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38
Q

Biochemists define the standard state to include a pH of _______ and a water concentration 55.5M

A

Seven

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39
Q

For reactions that involve magnesium its _______ is taken to be a constant 1mM

A

Concentration

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40
Q

Physical constants based on the _____________________ are called standard _______ constants and are writer with a prime

A

Biochemical standard state

Transformed

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41
Q

The standard transformed constants distinguishes them from the _______ constants used by chemists and physicists

A

Untransformed

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42
Q

The standard free energy change of a chemical reaction is simply an alternative mathematical way of expressing the ______________

A

Equilibrium constant

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43
Q

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

A

Phosphoglucomutase

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44
Q

For the reverse reaction, ΔG’* has the same ______, but the opposite sign

A

Magnitude

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45
Q

The actual free energy change is dependent on reactant and product ______

A

Concentrations

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46
Q

_______ do not change equilibrium constants, only the _______at which the reaction proceeds in the direction dictated by _______

A

Enzymes
Rate
Thermodynamics

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47
Q

_______ is not too useful in biochem because the system is not _______

A

Entropy

Isolated

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48
Q

Cells contain several compounds that have ______ _______ free energy changes

A

Large

Negative

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49
Q

These compounds supply energy to many _______ reactions in cells. These processes include biosynthesis and transport.

A

Endergonic

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50
Q

The common energy currency of cells is in the form of _______

A

ATP

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51
Q

Formal name of ATP

A

Adenosine triphosphate

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52
Q

High energy compounds include:

A

Phosphoenolpyruvate
1,3-bisphosphoglycerate
Phosphocreatine
Acetyl-CoA

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53
Q

The donation of energy from ATP to an endergonic reaction GENERALLY involves the _______ participation of ATP in the reaction to be driven

A

Covalent

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54
Q

The donation of energy by ATP, in most cases involves _______ group transfer, and not simple ATP hydrolysis

A

Phosphoryl

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55
Q

The standard free energy change for ATP hydrolysis is _______kJ/mol

A

-30.5 kJ/mol

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56
Q

The _______ free energy of ATP hydrolysis in living cells is much larger

A

Actual

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57
Q

The actual free energy of ATP hydrolysis in cells is larger because the conditions in a cell are very different from _______ conditions

A

Standard

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58
Q

The cellular concentrations of ATP, PEP, and Pi are not identical and much _______ than 1M concentration

A

Lower

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59
Q

In addition, most enzymatic reactions that use ATP as the phosphoryl group donor, the true substrate is _______

A

MgATP

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60
Q

The magnesium in the _______ binds to ATP and ADP

A

Cytosol

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61
Q

In biochemical pathways where ATP is involved to supply energy to a reaction, the _______ step is typically shown as a single arrow

A

ATP

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62
Q

When ATP is involved to supply energy to a reaction, the reactions _______ to represent a simple hydrolysis where water displaces Pi or PPi

A

Appear

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63
Q

This ________-_______ process actually occurs

A

Two step

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64
Q

The first step is the transfer of a phosphoryl, _______, or AMP group to the substrate

A

Pyrophosphoryl

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65
Q

Phosphoryl, pyrophosphoryl, or adenylate becomes _______ attached to the substrate, thus _______ it’s free energy

A

Covalently

Raising

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66
Q

In the second step, the phosphate-containing group is _______, generating Pi, PPi, or AMP

A

Displaced

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67
Q

The ATP therefore _______ in the reaction

A

Participates

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68
Q

Sometimes direct _______ of ATP does drive a process without the covalent binding of ATP to the _______

A

Hydrolysis

Substrate

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69
Q

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

A

Noncovalent

Conformations

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70
Q

_______ _____ is either indirectly or directly responsible for all biological and biochemical work

A

Electron flow

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71
Q

Electron flow is largely mediated through _______-_______ reactions

A

Oxidation-reduction

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72
Q

What are the three ways oxidation can occur?

A

Addition of oxygen,
The removal of hydrogen,
The removal of electrons

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73
Q

What are the three ways reduction can occur?

A

Removal of oxygen
The addition of hydrogen,
The addition of electrons

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74
Q

The source of electrons in nonphotosynthetic organisms are _______ compounds

A

Reduced

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75
Q

The source of electrons in phosphosynthetic organisms is a chemical species excited by the _______ of light

A

Absorption

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76
Q

Electrons flow from the source, to various metabolic intermediates, to electron carriers, and ultimately to electron acceptors having _______ electron affinities, with energy _______

A

High

Release

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77
Q

Cells contain numerous energy _______ molecules that function to convert the energy of electron flow into work

A

Transducing

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78
Q

Different chemical species differ in their _______ for electrons

A

Affinity

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79
Q

In the electromotive force electrons flow _______ from a molecule with lower electron affinity to a molecule with high electron affinity

A

Spontaneously

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80
Q

The electron motive force is driven by a force _______ to the difference in electron affinities

A

Proportional

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81
Q

The flow of electrons is _______ due to the high affinity of oxygen for electrons

A

Exergonic

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82
Q

The electromotive force generated provides _______ to do biological work

A

Energy

83
Q

In the _______, membrane-bound enzymes use the energy from the electromotive force to produce transmembrane _______ difference

A

Mitochondrion

pH

84
Q

The proton gradient had potential energy and is called the _______-_______ force

A

Proton-motive force

85
Q

ATP in the mitochondrion uses the energy generated by the proton motive force to synthesize ATP from _______ and _______

A

ATP

Pi

86
Q

Highly _______ compounds contain a relatively large amount of hydrogen when compared with oxygen

A

Reduced

87
Q

In biological systems, oxidation is often synonymous with ______

A

Dehydrogenation

88
Q

_______ catalyze oxidation reactions

A

Dehydrogenases

89
Q

There are only a _______ universal biological electron carriers

A

Few

90
Q

The reduction of the biological electron carriers during catabolic processes _______ the free energy released by substrate oxidation

A

Conserves

91
Q

The universal biological electron carriers undergo _______ reduction

A

Reversible

92
Q

What are the four major universal electron carriers?

A

NAD+
NADP+
FMN+
FAD+

93
Q

Formal name of NAD+

A

Nicotinamide adenine dinucleotide

94
Q

Formal name of NADP+

A

Nicotinamide adenine dinucleotide phosphate

95
Q

Formal name of FMN+

A

Flavin mononucleotide

96
Q

Formal name of FAD+

A

Flavin adenine dinucleotide

97
Q

What are the other electron carriers?

A

Ubiquinone,
plasoquinone,
Iron-sulfur proteins,
Cytochromes

98
Q

NAD+, NADP+, FMN, FAD are all _______-soluble coenzymes

A

Water-soluble

99
Q

NAD+ and NADP+ easily move between a number of various _______

A

Enzymes

100
Q

The nicotinamide ring resembles pyrimidine and are called _______ ______

A

Pyrimidine nucleotides

101
Q

_______ is the source of the nicotinamide moiety

A

Niacin

102
Q

FMN and FAD are typically tightly bound to _______ and are prosthetic groups to those enzymes

A

Flavoenzymes

103
Q

Ubiquinone and plasoquinone are _______-_______ and act as electron carriers and proton donors in membranes

A

Lipid-soluble

104
Q

Iron-sulfur proteins and _______ have tightly bound prophetic groups which serve as the electron carriers

A

Cytochromes

105
Q

Formal name of PI-PLC

A

Phosphotidylinositol- phospholipase C

106
Q

__________ is the enzyme that acts on phosphotidylinositol

A

Phosphotidylinositol- Phospholipase C

107
Q

There is diversity in types of receptor tyrosine kinase, what are the diferences

A 
Class 1 and Class 3 are single subunits
And class 2 is a dimer with two subunits
108
Q

_______ _______ kinase is associated with viral transforming proteins produced by oncogenic viruses

A

Nonreceptor Tyrosine

109
Q

What is pp60^v-src?

A

Phospho-protein, 60kD, viral-origin, sarcoma-causing

110
Q

pp60^v-src has a __________ anchor to membrane of host

A

Fatty acid

111
Q

Molecule of IP3 is released to diffuse into the cytoplasm. This molecule is very _______

A

Hydrophilic

112
Q

When IP3 is released, diacylglycerol remains as a product in the membrane. DAG is very _______

A

Hydrophobic

113
Q

_______ tyrosine kinase act as an activator which will recognize phospholipase C as the substrate

A

Receptor

114
Q

What does PLC do?

A

Cleaves phosphorylation headgroup from PIP2

115
Q

In order of PLC to be active it must have phosphorylation and _______ present

A

Calcium

116
Q

_______ 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

A

Transmembrane

Physical

117
Q

What are pheromones?

A

Chemicals produced by certain species to signal others of the same species

118
Q

Pheromones can act in a _______ way by producing chemicals to attract others

A

Defensive

119
Q

_______ are important pathways that dictate cellular response in an environment

A

Pheromones

120
Q

_______ _______ is the conversion of information into a chemical change

A

Signal transduction

121
Q

Signal transductions are highly _______ and extremely _______

A

Specific

Sensitive

122
Q

The _______ of signal transduction is accomplished by precise molecular complementarity between signal and _______ molecules

A

Specificity

Receptor

123
Q

_______ means that not many signals are needed to cause a response, only one or two are needed to get a large response

A

Sensitivity

124
Q

When the _______-_______ interacts the unit illicit a a certain response together that would otherwise not occur

A

Ligand-receptor

125
Q

The sensitivity of signal transduction can be accounted to :

A

HIGH AFFINITY of receptors for signal molecules

COOPERATIVITY in the ligand-receptor interaction

AMPLIFICATION of the signal by enzyme reactions

126
Q

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

A

Amplification

127
Q

During amplification the signal strength _______ throughout the cascade

A

Increases

128
Q

The specificity of signal-transducing systems is not very specfic for _______ receptor and does not work with _______ molecules

A

one

alternate

129
Q

The amplification of the signal-transducing systems occuring with one enzyme that acts on another enzyme that produces _______ products

A

Multiple

130
Q

_______ is a feature of signal transducing systems

A

modularity

131
Q

“Mix-match” signals yield complexes with _______ functions

A

different

132
Q

In modularity, the _______ points are reversible

A

phosphorylation

133
Q

What are the five features of signal-transducing systems?

A 
specificity
amplification
modularity
desensitization & adaptation
integration
134
Q

Not all, just some systems have the ability to be turned off. This is the feature _______ of signal-transducing systems.

A

Desensitization/ adaptation

135
Q

In desensitization, when receptors become active, a feedback mechanism also gets _______ to cancel receptor activity or cause loss of receptor from the cell membrane

A

Activated

136
Q

_______ and _______ are critical in signal-transducing systems because signal cascades do not need “runaway” responses, they need a way to stop the response

A

Desensitization and adaptation

137
Q

In _______ two signals have opposite effects, the way the response is regulated, is by combined input from both receptors

A

Integration

138
Q

In the integration of signal-transducing systems multiple signals yields a _______ response

A

Unified

139
Q

What are the six general types of signal transducers?

A 
G Protein-coupled receptor,
Receptor Tyrosine Kinase,
Receptor Guanylyl Cyclase,
Gated Ion Channel,
Adhesion Receptor,
Nuclear Receptor
140
Q

What is the signal of the G Protein Coupled Receptor?

A

The ligand

141
Q

What is usual product of G-protein coupled receptors?

A

A second messenger

142
Q

In G Protein- coupled receptors, when the ligand binds to the receptor it causes a _______ change

A

Conformation

143
Q

What is the intermediate of G protein coupled receptor signal transduction?

A

A G-protein

144
Q

What is the signal transducer?

A

The receptor

145
Q

In receptor tyrosine kinase when the ligand binds it can trigger _______ which activates receptor

A

Autophosphorylation

146
Q

Some _______ _______ _______ act in order to trigger a response in the nucleus, either producing or activating transcription factors

A

Receptor tyrosine kinase

147
Q

The receptor of receptor tyrosine kinase acts as both a receptor and a _______

A

Kinase

148
Q

In the receptor Guanylyl Cyclase signal binds to the receptor it activates the receptor which functions as _______ _______

A

Guanylyl Cyclase

149
Q

What acts as a second messenger in receptor Guanylyl Cyclase?

A

The conversion Guanylyl Cyclase to cyclic GMP

150
Q

When gated ion channels are _______ ions go through

A

Open

151
Q

When when gated ion channels are _______ ions do not go through

A

Closed

152
Q

What causes gated ion channels to open?

A

Conformational changes

153
Q

The calcium channel is an example of a _______ _______ _______ which causes a calcium ion influx to the cell

A

Gated ion channel

154
Q

Another name for adhesion receptor is an _______

A

Integrin

155
Q

_______ receptors bind to molecules in the extracellular matrix which alters confirmation which alters _______ interaction with matrix molecules

A

Adhesion

Cytoskeleton

156
Q

_______ _______ will either hold on the the matrix or shed the matrix

A

Adhesion receptors

157
Q

what type of signal transducer acts like transcription factors,

A

Nuclear receptors

158
Q

The _______ and _______ of extracellular signals to the interior of cells gives rise to a number of observable biochemical events

A

Transduction and amplification

159
Q

Activation of signal transduction pathways mobilize various _______ messengers

A

Second

160
Q

What are some common intracellular second messengers?

A 
cAMP
cGMP
Ca^2+
IP3
DAG
Phosphatic acid
Ceramide
Nitric oxide
Cyclic ADP-ribose
161
Q

What are the effects of cAMP and where does is come from?

A

Effect: activates protein kinases
Source: adenylyl Cyclase

162
Q

What is the function of IP3 and what is its source?

A

Effect: activates Ca^2+ channels
Source: PLC action on PIP2

163
Q

The G-protein is _______

A

Heterotrimeric

164
Q

In G-Protein coupled signaling the G-protein mediates the activation to produce _______

A

cAMP

165
Q

In the G-protein’s inactivated state, _______ has GDP on it and a fatty acid coming off

A

Alpha

166
Q

The alpha subunit is a _______-_______ subunits

A

Lipid-modified

167
Q

The alpha subunit is an _______ fatty acid

A

Acylated

168
Q

The gamma subunit has a _______ subunit

A

Prynylated

169
Q

The prynylated subunit has a _______ lipid to keep the inner leaflet and gamma subunit associated

A

Polyprenyl

170
Q

When GDP gains affinity for _______ _______ it becomes GTP

A

Adenylate cyclase

171
Q

The formation of GTP will cause the alpha subunit to _______ affinity for the beta subunit

A

Loose

172
Q

_______ is cyclized to cAMP

A

cATP

173
Q

There is a _______ G-protein alpha subunit and an _______ G-protein alpha subunit

A

Stimulatory

Inhibitory

174
Q

Cyclic AMP binds and activates _______ to phosphorylate certain proteins

A

PKA (protein kinase A)

175
Q

cAMP can be destroyed directly to inhibit function when in its _______ form

A

5’-AMP

176
Q

G-protein BETA and GAMMA subunits _______ stimulatory pathway

A

Inhibits

177
Q

**When a biological circuit is formed, what four processes are associated?

A

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
Q

In a biological circuit oxygen is a _______ electron acceptor

A

Terminal

179
Q

IP3 is water-soluble and will _______ out of the membrane to the cytoplasm

A

Diffuses

180
Q

What is required for PKC to be activated?

A

DAG

elevated Ca^2+ concentration

Presence of PS that form anulus around PKC2

181
Q

The IP3 receptor is present in ________ endoplasmic reticulum

A

Smooth

182
Q

The pathway to activate PLC

A

Tyrosine kinase

183
Q

PLC has _______ requirement to be active through _________ pathways.

A

Calcium

Signaling

184
Q

PKC requires 3 things:

A
  1. DAG
  2. An elongated calcium concentration
  3. Presence of PS that forms an annulus (lipid-that surrounds something) around PKC
185
Q

SER have _______ ______ with binding sites for IP3, and function as _______ channels.

A

Integral proteins

Calcium

186
Q

IP3 binds ___________ with receptors

A

Simultaneously

187
Q

__________ binds to multiple calcium ions simultaneously

A

Calmoduline CaM

188
Q

When substrates become ___________ they become active

A

Phosphorylated

189
Q

GPCR

A

Gene protein couple receptor

190
Q

When IP3 is produced= _______ of calcium

A

Release

191
Q

Calcium ion concentration can be measured in ______, by the degree of __________ dependent on the amount of calcium.

A

Cells

Fluorescence

192
Q

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.

A

Oscillation

193
Q

If calcium was constantly stimulated, what would happen to the ER?

A

It would eventually run out of calcium

194
Q

Formed when PIP is phosphorylated

A

PIP2

195
Q

_______ comes from phospholipid biosynthesis pathway

A

Phosphotidylinositol PI

196
Q

What removes phosphates?

A

Inositol phosphatases

197
Q

What adds phosphates?

A

Inositol kinase

198
Q

Inositol can have ___ phosphates

A

6

199
Q

_______ modulates activity of Ca+ dependent proteins

A

Calmodulin

200
Q

Four main domains:

A
  1. Phorbol- binding domain
  2. Calcium- binding domain
  3. ATP- binding domain
  4. Substrate- binding domain
201
Q

_______ ______ are equivalent to DAG, but stay bound

A

Phorbol esters

202
Q

When PKC is inactive, it is _______, but not in the membrane.

A

Soluble

203
Q

Calcium ions are placed between ____ & ______ to allow binding by interfering with negative repulsion.

A

C2 & membrane

204
Q

High affinity of _______ for _______ molecules

A

Receptor

Signal

205
Q

Cooperativity in the _______-_______ interaction

A

Ligand-receptor

206
Q

Amplification of the _______ by _______ reactions

A

Signal

Enzyme

Biochem 2 (7 decks)

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