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Phase 2 Flashcards

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1
Q

What is a codon?

A

A triplet of nucleotides that codes one amino acid

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2
Q

In what direction is the genetic code written?

A

5’ to 3’

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3
Q

How many termination codes are there?

A

3

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4
Q

How many initiation codons are there and what amino acid do they code for?

A

1, Met (Methionine)

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5
Q

What is the place for protein synthesis?

A

The ribosome

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6
Q

What are proteins?

A

Polymers made in the cell from the 20 alpha aminoacids

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7
Q

What are the steps of DNA to protein?

A

DNA (Hexokinase gene) -> transcription of DNA into complementary RNA -> mRNA -> translation of RNA on ribosome to polypeptide chain -> unfolded hexokinase -> folding of polypeptide chain into native structure of hexokinase -> catalytically active hexokinase

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8
Q

What is the primary structure of a protein?

A

Its alpha amino acid sequence

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9
Q

What is the most important structure of a protein?

A

Its primary structure

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10
Q

What is the secondary structure of a protein?

A

An alpha helix or beta sheet

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11
Q

What does a secondary structure of a protein result from?

A

Essentially from hydrogen bonding between nearby alpha aminoacids

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12
Q

What constitutes the tertiary structure?

A

Folding and arrangements of secondary structures into a 3D shape

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13
Q

What is a quaternary structure and how often does it occur?

A

It occurs sometimes when multiple polypeptides arrange in groups

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14
Q

What are motifs?

A

Particular combinations of secondary structures that repeat even in dissimilar patterns

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15
Q

What are Domains?

A

Regions of a protein that have different functions (binding, catalysis, etc.) Remember they can be independent in stability and movement

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16
Q

What is the native structure of a protein?

A

Its active form

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17
Q

What is the native structure of the protein determined by?

A

Different interactions between closed and distant aminoacids

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18
Q

What creates kinks?

A

Weak covalent disulfide and ionic bonds

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19
Q

What created hydrophobic regions a protein?

A

Non-polar R groups will create hydrophobic regions

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20
Q

Where do hydrophobic regions of a protein tend to concentrate?

A

In the interior of a globular protein away from the aqueous outside environment

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21
Q

What happens when the environment of the protein is altered?

A

The protein may change its shape or even unfold

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22
Q

How can the environment of the protein be altered?

A

Heat, ions, pH, etc.

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23
Q

What is renaturation?

A

When an environment is reestablished, a small protein may spontaneously refold ( renaturation)

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24
Q

What determines tertiary structure?

A

Primary structure

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25
Q

What led to the conclusion of what determines tertiary structure?

A

The fact that if an environment is reestablished, a small protein may spontaneously refold

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26
Q

What do chaperones assist with?

A

The folding of a protein to produce its final native state is a complex event that requires assistance from other proteins called chaperones

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27
Q

What are chaperonins?

A

A class of chaperones

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28
Q

What do chaperonins resemble?

A

A cylindrical container

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29
Q

What occurs with chaperonins?

A

It is basically a cylindrical container where unfolded or misfolded protein moves in and gets refolded aided by energy from ATP

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30
Q

What does chaperonin deficiency cause?

A

Improper folding resulting in diseases such as cystic fibrosis

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31
Q

What are enzymes?

A

Selective catalysts composed mostly of proteins in which their native state is essential for activity

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32
Q

What state is essential for the activity of an enzyme?

A

The native state of the proteins it is composed of

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33
Q

Where does the reaction of an enzyme occur?

A

At specific active site where the substrate binds

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34
Q

How are enzymes named?

A

Based on the general type of reaction they catalyze

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35
Q

What is the type of reaction catalyzed for oxidoreductases?

A

Transfer of electrons (Hydride ions or H atoms)

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36
Q

What is the type of reaction catalyzed for transferases?

A

Group transfer reactions

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37
Q

What is the type of reaction catalyzed for hydrolases?

A

Hydrolysis reactions (transfer of functional groups to water)

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38
Q

What is the type of reaction catalyzed for lyases?

A

Cleavage of C-C, C-O, C-N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds

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39
Q

What is the type of reaction catalyzed for isomerases?

A

Transfer of groups within molecules to yield isomeric forms

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40
Q

What is the type of reaction catalyzed for ligases?

A

Formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor

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41
Q

What is an example of oxidoreductase reaction?

A

Alcohol dehydrogenase

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42
Q

What is an example of transferase reaction?

A

Hexokinase (phosphorylation)

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43
Q

What is an example of a hydrolase reaction?

A

Carboxypeptidase A (peptide bond cleavage)

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44
Q

What is an example of a lyase reaction?

A

Pyruvate decarboxylase (decarboxylation)

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45
Q

What is an example of isomerase reaction?

A

Maleate isomerase (cis-trans isomerization)

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46
Q

What is an example of a ligase reaction?

A

Pyruvate carboxylase (carboxylation)

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47
Q

What do some enzymes need to act?

A

An inorganic cofactor

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48
Q

What are some examples of inorganic cofactors?

A

Metal ion (Mg2+, Fe2+)

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49
Q

What is an example of an enzyme with Fe and what is its role?

A

Cytochrome oxidase

Oxidation-Reduction

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50
Q

What is an example of an enzyme with Cu and what is its role?

A

Ascorbic acid oxidase

Oxidation-Reduction

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51
Q

What is an example of an enzyme with Zn and what is its role?

A

Alcohol dehydrogenase

Helps bind NAD+

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52
Q

What is an example of an enzyme with Mn and what is its role?

A

Histidine Ammonia Lyase

Aids in catalysis by electron withdrawal

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53
Q

What is an example of an enzyme with Mg and what is its role?

A

Many kinases

Helps bind ATP

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54
Q

What is a coenzyme?

A

An organic or organometallic cofactor

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55
Q

What is a coenzyme called if it is tightly bound to the enzyme?

A

A prosthetic group

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56
Q

Prosthetic group + Enzyme =

A

Holoenzyme

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57
Q

What is an apoenzyme?

A

It lack the prosthetic group

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58
Q

Vitamin for Thiamine
Coenzyme for Thiamine
Reactions involving conenzyme

A

Vitamin B1
Thiamine pyrophosphate
Activation and transfer of aldehydes

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59
Q

Vitamin for Riboflavin
Coenzyme for Riboflavin
Reactions involving conenzyme

A

Vitamin B2
Flavin mononucleotide; flavin adenine dinucleotide
Oxidation-Reduction

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60
Q

Vitamin for Niacin
Coenzyme for Niacin
Reactions involving conenzyme

A

Vitamin B3
NAD, NADP
Oxidation-Reduction

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61
Q

Vitamin for Pantothenic acid
Coenzyme for pantothenic acid
Reactions involving conenzyme

A

Vitamin B5
Coenzyme A
Acyl group activation and transfer

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62
Q

Vitamin for pyridoxine
Coenzyme for pyridoxine
Reactions involving conenzyme

A

Vitamin B6
Pyridoxal phosphate
Various reactions involving amino acid activation

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63
Q

Vitamin for biotin
Coenzyme for biotin
Reactions involving conenzyme

A

Vitamin B7
Biotin
CO2 activation and transfer

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64
Q

Lipoic acid
Coenzyme for lipoic acid
Reactions involving conenzyme

A

Lipoamide

Acyl group activation; oxidation-reduction

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65
Q

Vitamin for folic acid
Coenzyme for folic acid
Reactions involving conenzyme

A

Vitamin B9
Tetrahydrofolate
Activation and transfer of single carbon functional groups

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66
Q

Vitamin B12
Coenzyme for vitamin B12
Reactions involving conenzyme

A

Adenosyl cobalamin; methyl cobalamin

Isomerization and methyl group transfer

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67
Q

Why do we have both NAD and FAD?

A

NAD has to carry 2 electrons while FAD can carry one or two

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68
Q

How does NADH help in a respiratory chain?

A

It enters and FMNH2 turns Fe2+ to Fe3+

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69
Q

Why is a thiol ester easier to hydrolyze than a regular ester?

A

Since O has a lot more resonance structures

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70
Q

What cycle do red blood cells not participate in and why?

A

They do not participate in the Krebs Cycle because they do not have mitochondrion

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71
Q

What is vitamin B3’s most important function?

A

To introduce NAD+ so that glycolysis can proceed

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72
Q

What effect do enzymes have on reactions?

A

They increase the reaction rate without altering the basic 3 equilibrium steps

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73
Q

What is equilibrium?

A

The materials in the reaction recycle themselves. Nothing new introduced

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74
Q

What is steady state?

A

New materials enter and new materials exit

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75
Q

What type of control is essential for enzymatic action?

A

Entropy Control

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76
Q

What is the rate limiting step in a reaction?

A

The catalytic step

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77
Q

What is the enzymatic reaction?

A

E+S is in equilibrium with ES which is in equilibrium with EP which is in equilibrium with E+P

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78
Q

What must enzymes do to achieve rate enhancement?

A

Enzymes must preferentially stabilize the transition state to achieve rate enhancement

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79
Q

What do enzymes do to activation energy?

A

They lower the activation energy?

80
Q

How do enzymes lower the activation energy?

A

By weak interactions between enzyme and substrate that restrict the motion of the substrate which pretty much reduces the entropy

81
Q

How do the entropy and enthalpy of the catalyst compare to things that aren’t the catalyst?

A

Scat > Snon

Chat < Hnon

82
Q

What are the 6 ways that enzymatic catalysis proceeds by?

A

1) General acid/base catalysis (GABC)
2) Covalent catalysis
3) Electrostatic stabilization
4) Proximity effects
5) Preferential stabilization of the transition state
6) Protein conformational changes

83
Q

What happens in covalent catalysis?

A

A covalent bond is formed

84
Q

What happens in proximity effects?

A

Transition state may have charges so this stabilizes those

*HIV stabilization depends on altering the transition state

85
Q

What happens protein conformational changes?

A

Increasing activity of reaction center

86
Q

What is acid base catalysis performed by?

A

By properly positioned functional groups within the enzyme

87
Q

How do reaction rates of catalyzed versus un-catalyzed reactions compare?

A

Increases in reaction rates 5 to 17 orders of magnitude higher in catalyzed reactions

88
Q

How does substrate concentration affect reaction rates?

A

Rate declines as substrate becomes product; gives a curved shape

89
Q

On a time versus product concentration graph, how do you find the initial velocity?

A

A tangent at t=0 gives the initial velocity of each reaction.

90
Q

What does kcat stand for?

A

Equilibrium constant

91
Q

What does Km stand for?

A

Rate constant

92
Q

What are the two equations for v?

A 
v = (kcat)[Et][S] / (Km + [S])
v = Vmax[S] / (Km + [S])
93
Q

What does the Michaelis constant, Km, indicate?

A

The substrate concentration at which the reaction rate is 1/2 Vmax

94
Q

When is enzyme activity high?

A

When concentration is above Km

95
Q

What does the turnover number, kcat, measure?

A

The rate of the catalytic process

96
Q

What do you want the ratio of kcat/Km to be and why?

A

You want it to be a large ratio because you want Km (concentration of substrate) to be high and you want the rate of the catalytic process to be high.

97
Q

What are Km and Vmax important for?

A

For the study and comparison of different enzymes

98
Q

What do Km and Vmax not provide information about?

A

They do not provide information about the rate, steps, and chemical nature of a reaction

99
Q

What is kcat?

A

The number of substate molecules concerted to product in a given time by a single enzyme molecule

100
Q

What is the function of acetylcholinesterase and what happens if it doesn’t function?

A

It breaks down acetylcholine, which makes the muscles clench. So when it is unregulated the muscles cannot unclench

101
Q

What is the average rate of diffusion of a cell?

A

10^8 to 10^9. It cannot be greater

102
Q

What is the limit for the rate of a reaction dictated by?

A

The rate at which E and S diffuse together in aqueous solution. Some enzymes approach that rate

103
Q

What are enzymes subject to?

A

They are subject to reversible inhibition by several molecules

104
Q

What occurs in competitive inhibition?

A

The inhibitor competes with the normal substrate for the enzyme. Km different, Vmax the same as [I] increases

105
Q

What is uncompetitive inhibition?

A

The inhibitor competes with the intermediate ES, not the substrate, so it affects the transition state. Km and Vmax both differ as [I] increases

106
Q

True or false: inhibition cannot be a combination of competitive and uncompetitive inhibition?

A

False. Inhibition CAN be a combination of competitive and uncompetitive inhibition

107
Q

How are irreversible inhibitors useful?

A

They are useful to determine the active site of an enzyme - known as covalent modification

108
Q

What is an example of an enzymatic reaction and what does it show?

A

Decarboxylation ; shows the use of nucleophiles

109
Q

What are the two steps of a reaction for an aldehyde with an amide?

A

1st: Schiff base is made (has a positively charges NH+)
2nd: Schiff base carboxylated or changed back

110
Q

What happens if we cannot produce alanine?

A

We cannot transport ammonia and too much ammonia in the blood leads to alkylosis

111
Q

What is the function of histidine in serine proteases?

A

To extract proton from serine to make it a nucleophile that can break the peptide bond. This makes an ester that is then broken by water as a nucleophile

112
Q

How do cysteine and serine compare in acidity?

A

When pure, cysteine is stronger than serine. In a polypeptide, serine is stronger than cysteine

113
Q

What metal is mostly used in metaloproteases and what does the metal do?

A

Zn and it polarizes the water to make it act as a nucleophile

114
Q

What is a Rossman fold (motif)?

A

A pocket of a polypeptide in which NAD+ rests

115
Q

What are common examples of nucleophiles?

A

Negatively charged O, Neg charged D, carbanion, uncharged amine group, imidazole, and hydroxide ion

116
Q

What are common examples of electrophiles?

A

Carbon atom of a carbonyl group, protonated imine group, phosphorous of phosphate group, proton

117
Q

What does phosphorylation show?

A

Shows how substrate binding induces conformational changed in the enzyme

118
Q

What do metals serve as in a reaction?

A

A polarizing agent

119
Q

What does the HIV aspartyl protease do?

A

Cleaves peptide bonds using general base catalysis

120
Q

What does the tetrahedral intermediate of a reaction do?

A

Has been used as the base for the design of irreversible inhibitors

121
Q

How does enolase perform transformations?

A

Uses Mg and acid-base catalysis to perform the transformation from an -ol to something with an -ene such as 2-phosphoglycerate to phosphoenolpyruvate

122
Q

What are regulatory enzymes?

A

Enzymes that have a greater effect on the rate of the overall sequence and have more than one function

123
Q

What are allosteric enzymes?

A

Regulatory enzymes that use allosteric modulators

124
Q

How do allosteric enzymes compare to nonallosteric enzymes?

A

Allosteric enzymes are normally larger and more complex

125
Q

What do allosteric enzymes include?

A

They include catalytic and regulatory subunits

126
Q

What are some enzymes regulated by?

A

Some are regulated by covalent modification

127
Q

What introduces phosporyl groups to amino acids?

A

Protein kinases

128
Q

What are the target residues of phosphorylation?

A

Tyr, Ser, Thr, His

129
Q

What are the target residues of adenylylation?

A

Tyr

130
Q

What are the target residues of acetylation?

A

Lys and alpha amino (amino terminus)

131
Q

What are the target residues of myristoylation?

A

alpha amino (amino terminus)

132
Q

What are the target residues of ubiquitination?

A

Lys

133
Q

What are the target residues of ADP-ribosylation?

A

Arg, Gln, Cys

134
Q

What are the target residues of methylation?

A

Glu (occurs only in glutamic acid residues)

135
Q

What is the function of a phosphatase?

A

To remove phosphoryl groups

136
Q

Is covalent modification reversible or irreversible?

A

Can be reversible in certain cases (ex) kinase reversible thru phosphatase)

137
Q

What is unique about muscles

A

Muscles do not have phosphate so a phosphorylated glucose remains in the muscle. It is a very strong covalent bond

138
Q

How do plasma membranes compare in different cells?

A

Plasma membranes differ in composition between cells

139
Q

How are peripheral proteins bound to a membrane?

A

Either by being covalently linked to a lipid or by being bound by electrostatic attraction

140
Q

What is an integral protein composed of?

A

Single transmembrane helix

141
Q

What are the types of ways that particles can enter / communicate with the cell?

A

Transporter: Allows small ions and molecules through
Enzyme: has a specific binding site that transforms substrate to something else
Cell surface receptor: Cell has specific binding sites that, when bound, signal to inside the cell
Cell surface identity marker: help to differentiate cells
Cell to cell adhesion: connects two cells when the integral proteins combine
Attachment to cytoskeleton

142
Q

What is a chelating agent and what is an example?

A

Chelating agent removes integral proteins. EX) EDTA. Used in order to “soften” water because it helps remove metals

143
Q

What is the function of urea?

A

Only removes peripheral proteins

144
Q

What is type one of an integral protein?

A

Single span with C terminus inside cell, N terminus outside cell. Portion inside the lipid bilayer is non polar, portion outside is polar

145
Q

What is type two of an integral protein?

A

Single span with N terminus inside cell, C terminus outside cell

146
Q

What is type 3 of an integral protein?

A

Multiple spans

147
Q

What is type 4 of an integral protein?

A

Multiple difference polypeptides assembled to form a channel

148
Q

What is type 5 of an integral protein?

A

Anchored by lipid to inside the cell

149
Q

What is type 6 of an integral protein?

A

Single span and lipid anchor on outside

150
Q

What is the process of insertion of proteins into membranes?

A

It is a cotranslational process and requires ribosome and translocon

151
Q

What is a translocon?

A

A multisubunit complex that acts as a protein conducting channel

152
Q

What does the translocon facilitate?

A

It facilitates the insertion of hydrophobic regions of protein sequence into the bilayer

153
Q

How do you identify hydrophobic and hydrophilic regions on an hydropathy index?

A

Hydrophobic regions are positive, hydrophilic are negative

154
Q

What is flippase?

A

An enzyme that moves phosphatidylethanolamine and phosphatidylserine from outer to cytosolic leaflet

155
Q

What is floppase?

A

An enzyme that moves phosphatidylethanolamine and phosphatidylserine from cytosolic to outer leaflet

156
Q

What is scramblase?

A

Moves lipids in either direction, towards equilibrium

157
Q

What is a caveole?

A

Type of lipid raft that are invaginations of the plasma membrane and have caveolin dimers

158
Q

What are caveolin dimers?

A

Six fatty acyl, 8 cholesterol moieties

159
Q

What is phagocytosis?

A

Intake of large molecules like bacterial cells to the cell

160
Q

What is pinocytosis?

A

Intake of small molecules like solutes into the cell

161
Q

What is receptor mediated endocytosis?

A

Receptor proteins are available to receive a target molecule

162
Q

What is non mediated transport?

A

Slow mode of transport that demonstrates diffusion across a membrane is more rapid for those solutes that are hydrophobic

163
Q

What is facilitated transport?

A

Diffusion of certain solutes is accelerated by specific pores, carriers, or permeases

164
Q

What is active transport?

A

Couples a thermodynamically favorable process to achieve transport against a concentration gradient

165
Q

How does delta G compare from diffusion with and without transporter?

A

Delta G of diffusion without a transporter is greater than that with a transporter

166
Q

What is simple diffusion?

A

Nonpolar compounds only; down concentration gradient

167
Q

What is facilitated diffusion?

A

Goes down the electrochemical gradient

168
Q

What is primary active transport?

A

Against electrochemical gradient driven by ATP

169
Q

What is ionophore mediated ion transport?

A

Down electrochemical gradient

170
Q

What is an ion channel?

A

Goes down electrochemical gradient may be gated by a ligand or ion

171
Q

What is secondary active transport?

A

Against electrochemical gradient, driven by ion doing down its gradient

172
Q

What is valinomycin?

A

An antibiotic ionophore produced by streptomyces. Acts as a potassium ionophore

173
Q

What is the general process for ionophores?

A

Encapsulate the ion, move into the cell, release the ion

174
Q

How are ionophores produced?

A

By bacteria to kill competing bacteria by destroying the electrochemical gradients that store free energy

175
Q

What are ionophores useful

for?

A

Some are useful antibiotics

176
Q

What is the structure of an ionophore?

A

The exterior contains hydrophobic amino acids and the interior is a polar environment that is specific for binding ions for the size of K+

177
Q

What are permeases?

A

Also known as transporters and are membrane spanning proteins that recognize specific molecules

178
Q

What is the normal Kt level of glucose transporters?

A

5

179
Q

What are the tissues where GLUT1 is expressed, what is the Kt, and what are the roles?

A

Ubiquitous
3
Basal glucose uptake

180
Q

What are the tissues where GLUT2 is expressed, what is the Kt, and what are the roles?

A

Liver, pancreatic islets, intestine
17
In liver and kidney, removal of excess glucose from blood; in pancreas: regulation of insulin release

181
Q

What are the tissues where GLUT3 is expressed, what is the Kt, and what are the roles?

A

Brain (neuronal); Testis (sperm)
1.4
Basal glucose uptake

182
Q

What are the tissues where GLUT4 is expressed, what is the Kt, and what are the roles?

A

Muscle; fat; heart
5
Activity increased by insulin

183
Q

What are the tissues where GLUT5 is expressed, what is the Kt, and what are the roles?

A

Intestine (primarily); testis; kidney
6
Primarily fructose transport

184
Q

What is symport?

A

Transports two solutes across the membrane in the same direction (EX) Glucose-Na+)

185
Q

What is anti port?

A

Tranports two solutes across the membrane in opposite directions (2 K+ in, 3 Na+ out)

186
Q

What reaction occurs in respiring tissues (Erythroccyte)?

A

CO2 + H2O reacts to form HCO3- + H+ + Cl-

187
Q

Where does bicarbonate dissolve?

A

In blood plasma

188
Q

What are the essential elements of primary active transport?

A

Actuator domain, phosphorylation domain, and nucleotide binding domain

189
Q

What are the mechanics of primary active transport?

A

1) Ca2+ and ATP bind; N domain moves
2) Phosphoryl group transferred to Asp351 in P domain
3) Phosphorylation leads to conformational changes; releasing Ca2+ to the lumen
4) A domain moves, causing the release of ADP
5) P domain becomes dephosphorylated
6) A domain resets
7) P, T, and S domains reset to E1 conformation

190
Q

How do ions move in sodium/potassium ATPase?

A

Ions move according to polarity

191
Q

What does intestinal transport of glucose require?

A

Sodium, Na/K ATPase and a glucose transporter

192
Q

What are aquaporins?

A

Water channels that increase water kidney transport in some tissues: erythrocytes, salivary glands, and kidnet

193
Q

When does plasma osmolarity vary?

A

It varies considerably as the erythrocyte moves through lungs, capillaries, and kidneys, so rapid transport of water is critical to prevent rupture of the erythrocyte membrane

194
Q

What do aquaporins facilitate?

A

They facilitate rapid transport of water and thereby maintain osmotic balance within a cell while preserving critical ion gradients

195
Q

How does water pass free of protons?

A

This occurs in aquaporins by electrostatic repulsion from Asn

Bio 3100 (6 decks)

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