Phase 2 Flashcards
(195 cards)
1
Q
What is a codon?
A
A triplet of nucleotides that codes one amino acid
2
Q
In what direction is the genetic code written?
A
5’ to 3’
3
Q
How many termination codes are there?
A
3
4
Q
How many initiation codons are there and what amino acid do they code for?
A
1, Met (Methionine)
5
Q
What is the place for protein synthesis?
A
The ribosome
6
Q
What are proteins?
A
Polymers made in the cell from the 20 alpha aminoacids
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
8
Q
What is the primary structure of a protein?
A
Its alpha amino acid sequence
9
Q
What is the most important structure of a protein?
A
Its primary structure
10
Q
What is the secondary structure of a protein?
A
An alpha helix or beta sheet
11
Q
What does a secondary structure of a protein result from?
A
Essentially from hydrogen bonding between nearby alpha aminoacids
12
Q
What constitutes the tertiary structure?
A
Folding and arrangements of secondary structures into a 3D shape
13
Q
What is a quaternary structure and how often does it occur?
A
It occurs sometimes when multiple polypeptides arrange in groups
14
Q
What are motifs?
A
Particular combinations of secondary structures that repeat even in dissimilar patterns
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
16
Q
What is the native structure of a protein?
A
Its active form
17
Q
What is the native structure of the protein determined by?
A
Different interactions between closed and distant aminoacids
18
Q
What creates kinks?
A
Weak covalent disulfide and ionic bonds
19
Q
What created hydrophobic regions a protein?
A
Non-polar R groups will create hydrophobic regions
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
21
Q
What happens when the environment of the protein is altered?
A
The protein may change its shape or even unfold
22
Q
How can the environment of the protein be altered?
A
Heat, ions, pH, etc.
23
Q
What is renaturation?
A
When an environment is reestablished, a small protein may spontaneously refold ( renaturation)
24
Q
What determines tertiary structure?
A
Primary structure
25
What led to the conclusion of what determines tertiary structure?
The fact that if an environment is reestablished, a small protein may spontaneously refold
26
What do chaperones assist with?
The folding of a protein to produce its final native state is a complex event that requires assistance from other proteins called chaperones
27
What are chaperonins?
A class of chaperones
28
What do chaperonins resemble?
A cylindrical container
29
What occurs with chaperonins?
It is basically a cylindrical container where unfolded or misfolded protein moves in and gets refolded aided by energy from ATP
30
What does chaperonin deficiency cause?
Improper folding resulting in diseases such as cystic fibrosis
31
What are enzymes?
Selective catalysts composed mostly of proteins in which their native state is essential for activity
32
What state is essential for the activity of an enzyme?
The native state of the proteins it is composed of
33
Where does the reaction of an enzyme occur?
At specific active site where the substrate binds
34
How are enzymes named?
Based on the general type of reaction they catalyze
35
What is the type of reaction catalyzed for oxidoreductases?
Transfer of electrons (Hydride ions or H atoms)
36
What is the type of reaction catalyzed for transferases?
Group transfer reactions
37
What is the type of reaction catalyzed for hydrolases?
Hydrolysis reactions (transfer of functional groups to water)
38
What is the type of reaction catalyzed for lyases?
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
39
What is the type of reaction catalyzed for isomerases?
Transfer of groups within molecules to yield isomeric forms
40
What is the type of reaction catalyzed for ligases?
Formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor
41
What is an example of oxidoreductase reaction?
Alcohol dehydrogenase
42
What is an example of transferase reaction?
Hexokinase (phosphorylation)
43
What is an example of a hydrolase reaction?
Carboxypeptidase A (peptide bond cleavage)
44
What is an example of a lyase reaction?
Pyruvate decarboxylase (decarboxylation)
45
What is an example of isomerase reaction?
Maleate isomerase (cis-trans isomerization)
46
What is an example of a ligase reaction?
Pyruvate carboxylase (carboxylation)
47
What do some enzymes need to act?
An inorganic cofactor
48
What are some examples of inorganic cofactors?
Metal ion (Mg2+, Fe2+)
49
What is an example of an enzyme with Fe and what is its role?
Cytochrome oxidase
| Oxidation-Reduction
50
What is an example of an enzyme with Cu and what is its role?
Ascorbic acid oxidase
| Oxidation-Reduction
51
What is an example of an enzyme with Zn and what is its role?
Alcohol dehydrogenase
| Helps bind NAD+
52
What is an example of an enzyme with Mn and what is its role?
Histidine Ammonia Lyase
| Aids in catalysis by electron withdrawal
53
What is an example of an enzyme with Mg and what is its role?
Many kinases
| Helps bind ATP
54
What is a coenzyme?
An organic or organometallic cofactor
55
What is a coenzyme called if it is tightly bound to the enzyme?
A prosthetic group
56
Prosthetic group + Enzyme =
Holoenzyme
57
What is an apoenzyme?
It lack the prosthetic group
58
Vitamin for Thiamine
Coenzyme for Thiamine
Reactions involving conenzyme
Vitamin B1
Thiamine pyrophosphate
Activation and transfer of aldehydes
59
Vitamin for Riboflavin
Coenzyme for Riboflavin
Reactions involving conenzyme
Vitamin B2
Flavin mononucleotide; flavin adenine dinucleotide
Oxidation-Reduction
60
Vitamin for Niacin
Coenzyme for Niacin
Reactions involving conenzyme
Vitamin B3
NAD, NADP
Oxidation-Reduction
61
Vitamin for Pantothenic acid
Coenzyme for pantothenic acid
Reactions involving conenzyme
Vitamin B5
Coenzyme A
Acyl group activation and transfer
62
Vitamin for pyridoxine
Coenzyme for pyridoxine
Reactions involving conenzyme
Vitamin B6
Pyridoxal phosphate
Various reactions involving amino acid activation
63
Vitamin for biotin
Coenzyme for biotin
Reactions involving conenzyme
Vitamin B7
Biotin
CO2 activation and transfer
64
Lipoic acid
Coenzyme for lipoic acid
Reactions involving conenzyme
Lipoamide
| Acyl group activation; oxidation-reduction
65
Vitamin for folic acid
Coenzyme for folic acid
Reactions involving conenzyme
Vitamin B9
Tetrahydrofolate
Activation and transfer of single carbon functional groups
66
Vitamin B12
Coenzyme for vitamin B12
Reactions involving conenzyme
Adenosyl cobalamin; methyl cobalamin
| Isomerization and methyl group transfer
67
Why do we have both NAD and FAD?
NAD has to carry 2 electrons while FAD can carry one or two
68
How does NADH help in a respiratory chain?
It enters and FMNH2 turns Fe2+ to Fe3+
69
Why is a thiol ester easier to hydrolyze than a regular ester?
Since O has a lot more resonance structures
70
What cycle do red blood cells not participate in and why?
They do not participate in the Krebs Cycle because they do not have mitochondrion
71
What is vitamin B3's most important function?
To introduce NAD+ so that glycolysis can proceed
72
What effect do enzymes have on reactions?
They increase the reaction rate without altering the basic 3 equilibrium steps
73
What is equilibrium?
The materials in the reaction recycle themselves. Nothing new introduced
74
What is steady state?
New materials enter and new materials exit
75
What type of control is essential for enzymatic action?
Entropy Control
76
What is the rate limiting step in a reaction?
The catalytic step
77
What is the enzymatic reaction?
E+S is in equilibrium with ES which is in equilibrium with EP which is in equilibrium with E+P
78
What must enzymes do to achieve rate enhancement?
Enzymes must preferentially stabilize the transition state to achieve rate enhancement
79
What do enzymes do to activation energy?
They lower the activation energy?
80
How do enzymes lower the activation energy?
By weak interactions between enzyme and substrate that restrict the motion of the substrate which pretty much reduces the entropy
81
How do the entropy and enthalpy of the catalyst compare to things that aren't the catalyst?
Scat > Snon
| Chat < Hnon
82
What are the 6 ways that enzymatic catalysis proceeds by?
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
What happens in covalent catalysis?
A covalent bond is formed
84
What happens in proximity effects?
Transition state may have charges so this stabilizes those
| *HIV stabilization depends on altering the transition state
85
What happens protein conformational changes?
Increasing activity of reaction center
86
What is acid base catalysis performed by?
By properly positioned functional groups within the enzyme
87
How do reaction rates of catalyzed versus un-catalyzed reactions compare?
Increases in reaction rates 5 to 17 orders of magnitude higher in catalyzed reactions
88
How does substrate concentration affect reaction rates?
Rate declines as substrate becomes product; gives a curved shape
89
On a time versus product concentration graph, how do you find the initial velocity?
A tangent at t=0 gives the initial velocity of each reaction.
90
What does kcat stand for?
Equilibrium constant
91
What does Km stand for?
Rate constant
92
What are the two equations for v?
```
v = (kcat)[Et][S] / (Km + [S])
v = Vmax[S] / (Km + [S])
```
93
What does the Michaelis constant, Km, indicate?
The substrate concentration at which the reaction rate is 1/2 Vmax
94
When is enzyme activity high?
When concentration is above Km
95
What does the turnover number, kcat, measure?
The rate of the catalytic process
96
What do you want the ratio of kcat/Km to be and why?
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
What are Km and Vmax important for?
For the study and comparison of different enzymes
98
What do Km and Vmax not provide information about?
They do not provide information about the rate, steps, and chemical nature of a reaction
99
What is kcat?
The number of substate molecules concerted to product in a given time by a single enzyme molecule
100
What is the function of acetylcholinesterase and what happens if it doesn't function?
It breaks down acetylcholine, which makes the muscles clench. So when it is unregulated the muscles cannot unclench
101
What is the average rate of diffusion of a cell?
10^8 to 10^9. It cannot be greater
102
What is the limit for the rate of a reaction dictated by?
The rate at which E and S diffuse together in aqueous solution. Some enzymes approach that rate
103
What are enzymes subject to?
They are subject to reversible inhibition by several molecules
104
What occurs in competitive inhibition?
The inhibitor competes with the normal substrate for the enzyme. Km different, Vmax the same as [I] increases
105
What is uncompetitive inhibition?
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
True or false: inhibition cannot be a combination of competitive and uncompetitive inhibition?
False. Inhibition CAN be a combination of competitive and uncompetitive inhibition
107
How are irreversible inhibitors useful?
They are useful to determine the active site of an enzyme - known as covalent modification
108
What is an example of an enzymatic reaction and what does it show?
Decarboxylation ; shows the use of nucleophiles
109
What are the two steps of a reaction for an aldehyde with an amide?
1st: Schiff base is made (has a positively charges NH+)
2nd: Schiff base carboxylated or changed back
110
What happens if we cannot produce alanine?
We cannot transport ammonia and too much ammonia in the blood leads to alkylosis
111
What is the function of histidine in serine proteases?
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
How do cysteine and serine compare in acidity?
When pure, cysteine is stronger than serine. In a polypeptide, serine is stronger than cysteine
113
What metal is mostly used in metaloproteases and what does the metal do?
Zn and it polarizes the water to make it act as a nucleophile
114
What is a Rossman fold (motif)?
A pocket of a polypeptide in which NAD+ rests
115
What are common examples of nucleophiles?
Negatively charged O, Neg charged D, carbanion, uncharged amine group, imidazole, and hydroxide ion
116
What are common examples of electrophiles?
Carbon atom of a carbonyl group, protonated imine group, phosphorous of phosphate group, proton
117
What does phosphorylation show?
Shows how substrate binding induces conformational changed in the enzyme
118
What do metals serve as in a reaction?
A polarizing agent
119
What does the HIV aspartyl protease do?
Cleaves peptide bonds using general base catalysis
120
What does the tetrahedral intermediate of a reaction do?
Has been used as the base for the design of irreversible inhibitors
121
How does enolase perform transformations?
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
What are regulatory enzymes?
Enzymes that have a greater effect on the rate of the overall sequence and have more than one function
123
What are allosteric enzymes?
Regulatory enzymes that use allosteric modulators
124
How do allosteric enzymes compare to nonallosteric enzymes?
Allosteric enzymes are normally larger and more complex
125
What do allosteric enzymes include?
They include catalytic and regulatory subunits
126
What are some enzymes regulated by?
Some are regulated by covalent modification
127
What introduces phosporyl groups to amino acids?
Protein kinases
128
What are the target residues of phosphorylation?
Tyr, Ser, Thr, His
129
What are the target residues of adenylylation?
Tyr
130
What are the target residues of acetylation?
Lys and alpha amino (amino terminus)
131
What are the target residues of myristoylation?
alpha amino (amino terminus)
132
What are the target residues of ubiquitination?
Lys
133
What are the target residues of ADP-ribosylation?
Arg, Gln, Cys
134
What are the target residues of methylation?
Glu (occurs only in glutamic acid residues)
135
What is the function of a phosphatase?
To remove phosphoryl groups
136
Is covalent modification reversible or irreversible?
Can be reversible in certain cases (ex) kinase reversible thru phosphatase)
137
What is unique about muscles
Muscles do not have phosphate so a phosphorylated glucose remains in the muscle. It is a very strong covalent bond
138
How do plasma membranes compare in different cells?
Plasma membranes differ in composition between cells
139
How are peripheral proteins bound to a membrane?
Either by being covalently linked to a lipid or by being bound by electrostatic attraction
140
What is an integral protein composed of?
Single transmembrane helix
141
What are the types of ways that particles can enter / communicate with the cell?
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
What is a chelating agent and what is an example?
Chelating agent removes integral proteins. EX) EDTA. Used in order to "soften" water because it helps remove metals
143
What is the function of urea?
Only removes peripheral proteins
144
What is type one of an integral protein?
Single span with C terminus inside cell, N terminus outside cell. Portion inside the lipid bilayer is non polar, portion outside is polar
145
What is type two of an integral protein?
Single span with N terminus inside cell, C terminus outside cell
146
What is type 3 of an integral protein?
Multiple spans
147
What is type 4 of an integral protein?
Multiple difference polypeptides assembled to form a channel
148
What is type 5 of an integral protein?
Anchored by lipid to inside the cell
149
What is type 6 of an integral protein?
Single span and lipid anchor on outside
150
What is the process of insertion of proteins into membranes?
It is a cotranslational process and requires ribosome and translocon
151
What is a translocon?
A multisubunit complex that acts as a protein conducting channel
152
What does the translocon facilitate?
It facilitates the insertion of hydrophobic regions of protein sequence into the bilayer
153
How do you identify hydrophobic and hydrophilic regions on an hydropathy index?
Hydrophobic regions are positive, hydrophilic are negative
154
What is flippase?
An enzyme that moves phosphatidylethanolamine and phosphatidylserine from outer to cytosolic leaflet
155
What is floppase?
An enzyme that moves phosphatidylethanolamine and phosphatidylserine from cytosolic to outer leaflet
156
What is scramblase?
Moves lipids in either direction, towards equilibrium
157
What is a caveole?
Type of lipid raft that are invaginations of the plasma membrane and have caveolin dimers
158
What are caveolin dimers?
Six fatty acyl, 8 cholesterol moieties
159
What is phagocytosis?
Intake of large molecules like bacterial cells to the cell
160
What is pinocytosis?
Intake of small molecules like solutes into the cell
161
What is receptor mediated endocytosis?
Receptor proteins are available to receive a target molecule
162
What is non mediated transport?
Slow mode of transport that demonstrates diffusion across a membrane is more rapid for those solutes that are hydrophobic
163
What is facilitated transport?
Diffusion of certain solutes is accelerated by specific pores, carriers, or permeases
164
What is active transport?
Couples a thermodynamically favorable process to achieve transport against a concentration gradient
165
How does delta G compare from diffusion with and without transporter?
Delta G of diffusion without a transporter is greater than that with a transporter
166
What is simple diffusion?
Nonpolar compounds only; down concentration gradient
167
What is facilitated diffusion?
Goes down the electrochemical gradient
168
What is primary active transport?
Against electrochemical gradient driven by ATP
169
What is ionophore mediated ion transport?
Down electrochemical gradient
170
What is an ion channel?
Goes down electrochemical gradient may be gated by a ligand or ion
171
What is secondary active transport?
Against electrochemical gradient, driven by ion doing down its gradient
172
What is valinomycin?
An antibiotic ionophore produced by streptomyces. Acts as a potassium ionophore
173
What is the general process for ionophores?
Encapsulate the ion, move into the cell, release the ion
174
How are ionophores produced?
By bacteria to kill competing bacteria by destroying the electrochemical gradients that store free energy
175
What are ionophores useful
| for?
Some are useful antibiotics
176
What is the structure of an ionophore?
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
What are permeases?
Also known as transporters and are membrane spanning proteins that recognize specific molecules
178
What is the normal Kt level of glucose transporters?
5
179
What are the tissues where GLUT1 is expressed, what is the Kt, and what are the roles?
Ubiquitous
3
Basal glucose uptake
180
What are the tissues where GLUT2 is expressed, what is the Kt, and what are the roles?
Liver, pancreatic islets, intestine
17
In liver and kidney, removal of excess glucose from blood; in pancreas: regulation of insulin release
181
What are the tissues where GLUT3 is expressed, what is the Kt, and what are the roles?
Brain (neuronal); Testis (sperm)
1.4
Basal glucose uptake
182
What are the tissues where GLUT4 is expressed, what is the Kt, and what are the roles?
Muscle; fat; heart
5
Activity increased by insulin
183
What are the tissues where GLUT5 is expressed, what is the Kt, and what are the roles?
Intestine (primarily); testis; kidney
6
Primarily fructose transport
184
What is symport?
Transports two solutes across the membrane in the same direction (EX) Glucose-Na+)
185
What is anti port?
Tranports two solutes across the membrane in opposite directions (2 K+ in, 3 Na+ out)
186
What reaction occurs in respiring tissues (Erythroccyte)?
CO2 + H2O reacts to form HCO3- + H+ + Cl-
187
Where does bicarbonate dissolve?
In blood plasma
188
What are the essential elements of primary active transport?
Actuator domain, phosphorylation domain, and nucleotide binding domain
189
What are the mechanics of primary active transport?
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
How do ions move in sodium/potassium ATPase?
Ions move according to polarity
191
What does intestinal transport of glucose require?
Sodium, Na/K ATPase and a glucose transporter
192
What are aquaporins?
Water channels that increase water kidney transport in some tissues: erythrocytes, salivary glands, and kidnet
193
When does plasma osmolarity vary?
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
What do aquaporins facilitate?
They facilitate rapid transport of water and thereby maintain osmotic balance within a cell while preserving critical ion gradients
195
How does water pass free of protons?
This occurs in aquaporins by electrostatic repulsion from Asn
