Exam 1 Flashcards
1
Q
(COVALENT/NONCOVALENT) bonds are strong, short, and share electrons.
A
Covalent
2
Q
(COVALENT/NONCOVALENT) bonds are weak, long, and are by attraction only.
A
Noncovalent (interactions)
3
Q
Covalent bonds that hold monosaccharides (carbohydrates) together to create polysaccharides are…
A
Glycosidic bonds
4
Q
Covalent bonds that hold fatty acids plus glycerol or sphingosine derivatives together to from phospholipids or triacylglycerol are called…
A
Ester bonds
5
Q
Covalent bonds that hold amino acids together to form polypeptides are called…
A
Peptide bonds
6
Q
Covalent bonds that hold nucleotides together to form oligonucleotides or polynucleotides are called…
A
Phosphodiester bonds
7
Q
The strength of a covalent or non covalent bond is measured by the _______ needed to break the bond.
A
Energy
8
Q
Put the following bonds in order from weak to strong–
A. Salt bridges; Hydrogen bonds
B. Covalent bonds
C. Van der Waals interactions
A
- C
- A
- B
9
Q
The strength of a bond can depend on the ________ between atoms.
A
Distance
10
Q
How do we measure how attractive 2 ions are to each other in a vacuum?
A
Use Coulomb’s Law – F = k q1q2
——-
r(squared)
11
Q
In Coulomb’s Law, F = Force between ions in Newtons. If F > 0 that means the ions are (ATTRACTIVE/REPULSIVE), and if F < 0 that means the ions are (ATTRACTIVE/REPULSIVE).
A
Repulsive
Attractive
12
Q
If we want to measure how attractive the 2 ions are to each other in a biological environment, what do we need to add to Coulomb’s Law?
A
Relative permittivity
***Add D (dielectric constant) to the denominator (in air = 1)
13
Q
What is the energy required to separate two ions?
A
Energy of interaction
**If E < 0 then there is an attraction
14
Q
A dipole means having a ______ charge.
A
Partial
15
Q
Dipoles can be _______ (polar) or _______ (polarizable).
A
Permanent
Induced
16
Q
With this type of bond, an electron pair is shared.
A
Covalent bonds
17
Q
What is the average distance of a covalent bond?
A
1 angstrom
18
Q
What types of bonds interact through charge attraction?
A
Charge and/or dipole interactions
van der Waals interactions
19
Q
What is the average distance of the charge and/or dipole interactions?
A
3 angstroms
20
Q
What is the average distance of the van der Waals interactions?
A
3-4 angstroms
21
Q
What type of bond shares a hydrogen atom/proton?
A
Hydrogen bonds
22
Q
What is the average distance of hydrogen bonds?
A
2.6-3.7 angstroms (between donor and acceptor)
23
Q
Water’s strange physical properties are explained by its _______ bonding ability.
A
Hydrogen
24
Q
Ice (solid) is less dense than liquid water, and the hydrogen bond distances are (GREATER/SMALLER) in the solid than in the liquid.
A
Greater
25
This is a measure of how highly packed atoms or molecules are.
Density
26
This is the amount of heat needed to change the temperature of 1 g of a given substance by plus or minus 1 degree Celsius.
Specific heat capacity
27
This is the amount of energy needed to change 1 g of a given substance from liquid to gas.
Heat of vaporization
28
Hydrogen bonds _____ energy to break and ______ energy when they form.
Take
| Release
29
The surface of water is strong. _______ is when water molecules attract each other (attraction to self). _______ is when water and other polar substances attract each other (attraction to other).
Cohesion
| Adhesion
30
Cohesion creates what?
Surface tension
31
Cohesion and adhesion work together to create ______ ______.
Capillary action
32
Water is the _______ solvent.
Universal
33
Charged/Polar molecules are (HYDROPHOBIC/HYDROPHILIC) and (DISSOLVE/SEPARATE).
Hydrophilic
| Dissolve
34
Nonpolar molecules are (HYDROPHOBIC/HYDROPHILIC) and (DISSOLVE/SEPARATE).
Hydrophobic
| Separate
35
_______ molecules have both hydrophilic and hydrophobic parts.
Amphipathic
36
Chemical _______ is making and/or breaking chemical bonds.
Reactions
37
Most reactions are ________.
Reversible
38
Equilibrium (DOES NOT/DOES) mean there are equal concentrations. There is no net formation or destruction.
Does not
39
A weak acid is a proton (ACCEPTOR/DONOR).
Donor
40
A conjugate base is a proton (ACCEPTOR/DONOR).
Acceptor
41
What is the dissociation constant?
Ka (or Kb)
**Means acid is "falling apart"
42
What is the dissociation constant equation (Ka)?
Ka = [H+] [A-]
------------
[HA]
**Products over reactants
43
Strong acids are always going to fall apart completely, so that means its Ka value will be (LARGER/SMALLER) and its pKa value will be (LARGER/SMALLER).
Larger
| Smaller
44
Little "p" means _____, so that means Ka and pKa will always be opposites (i.e., big/small).
-log
45
Weak acids kind of fall apart, so that means its Ka value will be (LARGER/SMALLER) and its pKa value will be (LARGER/SMALLER).
Smaller
| Larger
46
If it's a strong acid it will be easier to break apart, therefore requiring less energy. This means the energy required will be (MORE/LESS) negative.
Less
47
If it's a weak acid it will be more difficult to break apart, therefore requiring more energy. This means the energy required will be (MORE/LESS) negative.
More
48
A weak base is a proton (ACCEPTOR/DONOR).
Acceptor
49
A conjugate acid is a proton (ACCEPTOR/DONOR).
Donor
50
What is the equation for pKa?
pKa = -log Ka
** (or) pKb = -log Kb
51
What is the equation for the dissociation constant Kb?
***Remember for a BASE, the base itself is not dissociating, it is the WATER that is dissociating.
Kb = [BH+] [OH-]
-----------------
[B]
***Products over reactants
52
A strong base requires more energy because it's moving to an acid, therefore the required energy amount is (MORE/LESS) negative.
More
53
A weak base requires less energy moving to an acid, therefore the required energy amount is (MORE/LESS) negative.
Less
54
pKw = -log Kw = ????
14
55
pKw = pH + ????
pOH
56
pH = -log [???]
H+
57
What is the equation for Kw?
Kw = [H+] [OH-] = 10(-14) M
---------------
[H2O]
58
What is physiological pH?
7.4
59
This is the term for a weak acid or weak base that can stabilize pH (absorb protons).
Buffer
60
What is the Henderson-Hasselbach equation?
pH = pKa + log ( [A-] )
-------
( [HA] )
61
What is the alternate equation we are going to use for Henderson-Hasselbach?
[A-]
----- = 10(pH-pKa)
[HA]
62
If pH < pKa, then our exponent is going to be negative (in modified HH equation). This means our overall value is between 0 and 1 and that most of the molecules are _______ since [HA] > [A-].
Protonated
***Acid concentration is higher, that means there are more protons present (hence PROTONATED)***
63
If pH > pKa, then our exponent is going to be positive (in modified HH equation). This means our overall value is greater than 1 and that most of the molecules are _______ since [HA] < [A-].
Deprotonated
***Base concentration is higher, that means there are less protons present (hence DEPROTONATED)***
64
If pH = pKa, then our exponent is going to be 0 (in modified HH equation). This means our overall value is 1 and that the molecules are just as likely to be _______ or _______ since [HA] = [A-].
Protonated
| Deprotonated
65
In gel _________, the direction of migration is based on the net charge of the molecule (negative goes toward positive).
Electrophoresis
66
This is when the pH of ALL molecules of a given species in solution have an overall charge of 0.
Isoelectric Point (pI)
67
If pH < pI, that means the pH < pKa so the molecule is protonated. Thus, the molecule must have a (NEGATIVE/POSITIVE) charge.
Positive
68
If pH > pI, that means the pH > pKa so the molecule is deprotonated. Thus, the molecule must have a (NEGATIVE/POSITIVE) charge.
Negative
69
If pH = pI, then (by definition) the molecule no net ______.
Charge
70
The pI equations is an average of what two values?
pKa (+1) and pKa (-1)
***Anything beyond pKa (+1 or -1) we DO NOT CARE. Only can use these two pKa values for pI***
71
In this test, the pH changes over the length of the gel and proteins stop moving when they are uncharged (pH = pI).
Isoelectric focusing
72
If the pH > pI, then the protein is soluble (deprotonated). Most proteins are very soluble at high pH, where the molecules are (POSITIVELY/NEGATIVELY) charged and repel one another.
Negatively
73
If the pH < pI, then the protein is soluble (protonated). At low pH the proteins are soluble because of repulsions due to their (POSITIVE/NEGATIVE) charge.
Positive
74
When pH = pI then the protein has no net charge and the molecules retain regions of positive and negative charge on their surfaces. This results in an increased tendency the protein to _______ and _______ in solution.
Aggregate
| Precipitate
75
What is the first law of thermodynamics?
Energy is neither created nor destroyed in a closed system.
76
This type of energy deals with motion and performing work.
Kinetic energy
77
This type of energy deals with the position and the potential to do work.
Potential energy
78
________ energy is the potential energy within chemical bonds.
Chemical
79
At the atomic level, atoms are always in motion (______ energy) and the electric charges of protons and electrons in atoms constantly pull and push at each other (______ energy.
Kinetic
| Potential
80
In chemical energy and bonds, they are _______ energy to begin with but when we break the bonds they become more ______ energy because they can be used to do something else.
Potential
| Kinetic
81
In a(n) (OPEN/CLOSED) system, energy cannot leave the system.
Closed
**i.e., the universe
82
In a(n) (OPEN/CLOSED) system, energy can be exchanged between the system and its surroundings.
Open
**i.e., a cell
83
What is the second law of thermodynamics?
Disorder is increasing
84
This is the term used when small molecules are assembled into large ones and energy is required.
Anabolic
85
This is the term used when large molecules are broken down into small ones and energy is released.
Catabolic
86
Which type of metabolic reactions create more disorder, catabolic or anabolic?
Catabolic -- more pieces means more disorder
87
What is the Gibbs Free Energy Equation?
Delta G = Delta H - T (Delta S)
88
This is the change in available/usable energy (Gibbs free energy).
Delta G
89
This is the change in total energy (enthalpy) in the system.
Delta H
90
This is the change in disorder (entropy).
Delta S
91
Delta G, Delta H, and Delta S are all _____ _____, which means its value depends only on the initial and final values and not the pathway to get there.
State functions
92
Delta G is (POSITIVE/NEGATIVE) if free energy is released.
Negative
93
Delta G is (POSITIVE/NEGATIVE) if free energy is required.
Positive
94
If energy is released from the system, then Delta H is (POSITIVE/NEGATIVE).
Negative
95
In a closed system, Delta H should equal...
0
96
If disorder decreases, then Delta S is (POSITIVE/NEGATIVE).
Negative
97
If disorder increases, then Delta S is (POSITIVE/NEGATIVE).
Positive
98
When Delta G is negative and free energy is released, this is considered an (ENDERGONIC/EXERGONIC) reaction.
Exergonic
99
When Delta G is positive and free energy is required, this is considered an (ENDERGONIC/EXERGONIC) reaction.
Endergonic
100
When Delta G is positive and free energy is required, this is considered an unfavorable (SPONTANEOUS/DRIVEN) reaction.
Driven
101
When Delta G is negative and free energy is released, this is considered a favorable (SPONTANEOUS/DRIVEN) reaction.
Spontaneous
102
When Delta G equals 0, then the reaction is at _______.
Equilibrium
103
What 3 things make up a nucleotide?
Phosphate group
Sugar
Nitrogenous base
104
When a nucleic acid has no phosphate, it's called a...
Nucleoside
105
When a nucleic acid has a phosphate, it's called a...
Nucleotide
106
(DNA/RNA) has a hydrogen on the 2' carbon.
| (DNA/RNA) has a hydroxyl on the 2' carbon.
DNA
| RNA
107
The 1' carbon is where the base attaches, forming a _______ bond.
Glycosidic
108
The 3' and 5' carbons are where ________ bonds form.
Phosphodiester
109
The 4' carbon contains an _______ within the sugar ring.
Oxygen
110
In a sugar pucker, it can be either C-3'-endo or C-2'-endo. This means the _____ carbon sticks up slightly, or the _____ carbon sticks up slightly.
3'
| 2'
111
The nitrogenous bases can either be a ______ or ______.
Purine
| Pyrimidine
112
Purines have (ONE/TWO) rings, and pyrimidines have (ONE/TWO) rings.
Two
| One
113
Which nitrogenous bases are purines?
Adenine
Guanine
***PUre As Gold
114
Which nitrogenous bases are pyrimidines?
Cytosine
Thymine
Uracil
115
Uracil is only present in (RNA/DNA) and takes the place of (CYTOSINE/THYMINE).
RNA
| Thymine
116
In DNA, purines ALWAYS base-pair with pyrimidines. Which nitrogenous bases pair with which?
A - T
| G - C
117
How many hydrogen bonds are there between A - T?
| How many between G - C?
2 hydrogen bonds
| 3 hydrogen bonds
118
DNA is an _______ double helix running in the 5' to 3' direction.
Antiparallel
119
In vitro oligonucleotide synthesis proceeds in what direction?
3' to 5'
120
Whether a nitrogenous base is _____ or _____ means that is faces inward or outward.
Syn
| Anti
121
This double helix structure is right-handed, has a wide and deep major groove, and narrow and shallow minor groove.
B-form
122
The B-from helix has a ______ sugar pucker and _____ nitrogenous base orientation.
C2'-endo
| Anti
123
This double helix structure is right-handed, has a narrow and deep major groove, and wide and shallow minor groove.
A-form
124
The A-form helix has a ______ sugar pucker and ______ nitrogenous base orientation.
C3'-endo
| Anti
125
This double helix structure is left-handed, has a flat major groove, and a narrow and deep minor groove.
Z-form
126
The Z-form helix has a _____ (pur) and _____ (pyr) sugar pucker and _____ (pur) and _____ (pyr) nitrogenous base orientation.
C2'-exo
C2'-endo
Syn
Anti
127
What helical structure is the physiological DNA form?
B-form
128
What helical structure is primarily seen in RNA?
***RNA can be double stranded if it folds back on itself
A-form
129
What are the 3 possible models for DNA replication?
Conservative
Semi-conservative
Dispersive
130
Hairpins and cruciforms require a ________ sequence (inverted repeat).
Palindromic
131
Hairpins and cruciforms are created by superhelical _____.
Strain
132
A triplex is a 3-stranded DNA that may or may not occur in nature. It requires a ________-_______ duplex and uses Hoogsteen hydrogen bonds.
Homopurine
| Homopyrimidine
133
Quadriplexes are 4-stranded DNA that consist of _______ only.
Guanine
134
Quadriplexes occur at what 2 places?
Telomeres
| Promoters
135
The melting temperature (Tm) = temperature at which --
1. Delta G (ds -- ss) = 0 (at equilibrium)
2. Half of sample is ________ (ss)
Denatured
136
How does DNA go from 2 strands to 1?
Like a zipper
137
In tautomers, what is being moved?
Hydrogen
138
DNA has to be (SS/DS) to make tautomers/isomers.
SS
139
Other examples of isomers are the ______ and ______ conformation of nucleic acids.
Syn
| Anti
140
Do we prefer syn or anti?
Anti
***We don't like syn but it's better than having tautomer
141
How many chances do we have to make a syn/anti isomer?
One (Replication fork)
142
How many chances do we have to make a tautomer?
Two (Replication fork and mismatch repair)
143
What is a transition mutation?
Swapping a purine for purine OR pyrimidine for pyrimidine (Still Pur - Pyr pairing)
144
In a transition mutation, what must one of the BP have?
Unfavored tautomer conformation
145
What is a transversion mutation?
Swapping a pyrimidine for purine OR purine for pyrimidine (Now Pur - Pur or Pyr - Pyr)
146
In a transversion mutation, what do the BP look like?
1 is unfavored tautomer and the other is in syn conformation
147
What is the mutation rate for transitions without proofreading? With proofreading?
1x10(-4)
| 5x10(-9)
148
What is the mutation rate for transversions without proofreading? With proofreading?
2.5-5x10(-6)
| 1-2.5x10(-10)
149
What base pair changes to cause sickle cell?
A to T (Glu to Val)
150
Sickle cell is due to _________ of the A.
Self-depurination
151
In the Beta-Globin gene, the self-depurination occurs in codon ______.
6
152
This type of induced mutation, for example, can occur when BrdU pairs with either A or G depending on its chemical state.
Base analogs
153
This type of induced mutation includes mustard gases.
Alkylating agents
***Carbons and hydrogens (alkyne, alkene, etc.)
154
This type of induced mutation is when an agent inserts itself between base pairs in DNA and can cause frameshift mutations.
Intercalating agents
155
This type of induced mutation is when, often a carcinogen, bonds to the DNA through covalent bonds.
Adduct-forming agents
156
________ are intercalating agents that upon activation with UV light form adducts with neighboring pyrimidine residues.
Psoralens
157
Exposure to _______ forms T-T dimers (causes cancer).
UV light
158
In this type of induced mutation, its mutagenic properties are actually a secondary effect: betas, gammas, and x-rays cause electrons to be ejected from an atom, leaving a free radical (free radicals are harmful to the body).
Ionizing radiation
159
List the hydrophobic amino acids.
```
Valine
Alanine
Glycine
Leucine
Isoleucine
Proline
Methionine
Tryptophan
Phenylalanine
```
160
List the polar amino acids.
```
Cysteine
Serine
Tyrosine
Threonine
Asparagine
Glutamine
```
161
List the charged (-) amino acids.
Glutamate (Glutamic acid)
| Aspartate (Aspartic acid)
162
List the charged (+) amino acids.
Lysine
Arginine
Histidine
163
What amino acids are tiny?
AGCS
164
What amino acids are small?
PNTD
165
What amino acids are medium?
HEVQ
166
What amino acids are large?
MILRK
167
What amino acids are very large?
WFY
168
What amino acids are very large?
WFY
169
What are the essential amino acids (meaning humans cannot synthesize them)?
PVT TIM HALL
(FVW TIM HRKL)
***The other 10 humans can synthesize de novo (nonessential amino acids)***
170
_________ amino acids are incorporated into proteins during translation. It includes the 20 usual amino acids, plus 2 more we have to use stop codons to get.
Proteinogenic
171
What is the 21st amino acid and uses the UGA/opal codon?
Selenocysteine (Sec, U)
172
Selenoproteins are important for good health. They reduce ______ _____ in conjunction with Vitamin E. They are required in _______ neurons (growth and coordination), and they moderate _______ responses.
Oxidative stress
Cerebellum
Inflammatory
173
Selenium deficiency results in myopathies, including _______ disease (cardiomyopathy) and ______ intolerance (rhabdomyolysis).
Keshan
| Statin
174
If there is too much __________, then you can have hair and nail brittleness, "garlic breath", gastrointestinal/neurological lesions, myopathies, renal failure, and death.
Selenocysteine
175
What is the 22nd amino acid and uses the UAG/amber codon (present only in some prokaryotes)?
Pyrrolysine (Pyl, O)
176
Several members of the intestinal microbiome make/use _____, including types of Archaea and Eubacteria.
Pyl
177
__________ amino acids can be used during non-ribosomal protein synthesis (NRPS).
Nonproteinogenic
178
Nonproteinogenic amino acids can also be used for ________ (activate carboxyl), _______ (elongation intermediate), ________ (peptide bond formation), and ________ (release or cyclization).
Adenylation
Peptidyl Carrier Protein (Thiolation)
Condensation
Thioesterase
179
Nonproteinogenic amino acids can be used to _______ like penicillin or Odilorhabdins.
Antibiotics
180
Nonproteinogenic amino acids (ARE/ARE NOT) used to make proteins.
Are not
181
The _______ structure of proteins is a chain of amino acids.
Primary
182
The _______ structure of proteins is a local folding of the polypeptide chain.
Secondary
183
The _______ structure of proteins is folding of the secondary structure.
Tertiary
184
The _______ structure of proteins is the interaction of multiple peptides.
Quaternary
185
What is the bond name between proteins?
Peptide bonds
186
Is a peptide bond a single bond? Can it rotate?
Yes, it can rotate because of this
187
The peptide results in a ______ chain with side chains alternating up and down.
Planar
188
The ________ interaction is a major factor in the folding and stability of proteins.
Hydrophobic
189
Hydrogen bonds are (STRONGER/WEAKER) than covalent bonds and are somehow (LONGER/SHORTER) than covalent bonds. They have energies ranging from 1-5 kcal/mol.
Weaker
| Longer
190
What are possible secondary structures for proteins?
Alpha-helix
| Beta-sheet
191
A-helices are stabilized by hydrogen bonds between the ____ and ____ groups. This hydrogen bonds form four amino acid residues ahead in the sequence.
NH
| C=O
192
In an alpha-helix each aa residue is related to the next one by:
- A rise of ____ angstroms along the helix axis
- A ____ degree rotation
- A ____ aa residue per turn of helix
1.5
100
3.6
193
The screw sense of an alpha-helix can be _____-handed (clockwise) or _____-handed (counterclockwise).
Right
| Left
194
Alpha-helices found in proteins are (LEFT/RIGHT)-handed because they are energetically more favorable.
Right
195
Beta-sheets are composed of two or more polypeptide chains, called ______ ______.
Beta-strands
196
Beta-sheets are fully extended and the distance between adjacent amino acids along a Beta-strand is about ___ angstroms.
3.5
197
A Beta-sheet is formed by linking two or more Beta-strands via ________ bonds.
Hydrogen
198
Beta-sheets can run ________ or ________ directions.
Parallel
| Antiparallel
199
Most Beta-sheets are found in ________ proteins (i.e., hair).
Structural
200
Reversal directions provide compact and globular shapes for polypeptide chains. These are called...
Reverse turns
Beta-turns
Hairpin turns
201
In many reverse turns, _____ groups and ____ groups form hydrogen bonds for stability.
C=O
| N-H
202
Loops (i.e., Omega loops) do not have regular periodic structures. They are often well defined and rigid, and positioned on the surface of the protein. They participate in _______-______ interactions and interactions with other ________.
Protein-protein
| Molecules
203
An alpha-helical coiled coil is called a ________.
Superhelix
204
A superhelix provides proteins long fibers. They serve as a ________ role (i.e., alpha-keratin, collagen cell cytoskeleton, muscle proteins) and are involved in _________ functions (i.e., regulation of genes expression, oncoproteins).
Structural
| Biological
205
The two helices in alpha-keratin (superhelix) associate with each other by weak interactions such as...
Van der Waals forces
| Ionic interactions
206
A superhelix is characterized by a central region of _____ amino acids that contain heptad repeats. This provides two alpha-helices interact with one another.
300
207
Protein folding is a highly _________ process.
Cooperative
208
Bovine insulin consists of 2 chains (alpha-chain and beta-chain), linked by 2 interchain ______ bonds. The alpha-chain also has an intra-chain ______ bond.
Disulfide
| Disulfide
209
Extracellular proteins often have several _______ bonds.
| Intracellular proteins usually lack _______ bonds.
Disulfide
| Disulfide
210
The ______ ______ refers to --
1) Rapid formation of secondary structure
2) Formation of domains through cooperative aggregation
3) Formation of assembled domains ('molten globule')
4) Adjustment of conformation
5) More rigid structure
Folding funnel
211
Is the entropy higher at the denatured or native state of proteins?
Denatured
212
Is energy higher at the denatured or native state of proteins?
Denatured
213
There can be repeating motifs in a protein chain, an example being ________, a calcium sensor that contains four similar units in a single polypeptide chain.
Calmodulin
214
There can be alternative conformations of peptide sequence. Many sequences can adopt alternative conformations in different proteins. For example, the sequence VDLLKN could an _______ in one protein and a _______ in another.
Alpha-helix
| Beta-strand
215
________ exists in two conformations, which are in equilibrium (the Chemokine structure and the Glycosaminoglycan-binding structure).
Lymphotactin
216
The ______ ______ state is an intermediate conformational state between the native and the fully unfolded states of a globular protein.
Molten globule
217
Globular are more (ALPHA/BETA) and molten are more (ALPHA/BETA).
Alpha
| Beta
218
Molten globule state characteristics include:
1) The presence of a native-like content of _______ structure.
2) The absence of a specific _______ structure produced by the tight packing of amino acid side chains.
3) Compactness in the overall shape of the protein molecule, with a _______ 10 to 30% larger than that of the native state (not packed so tightly).
4) The presence of a loosely packed ________ core that increases the hydrophobic surface area accessible to solvent.
5) It is not specific and occurs in early stage of protein folding.
Secondary
Tertiary
Radius
Hydrophobic
219
The molten globule is a compact globule with a "molten" side-chain structure that is primarily stabilized by nonspecific ________ interactions.
Hydrophobic
220
What is the equation to calculate the frequency of aa residues in secondary structures?
f = aa in a-helix
-----------------
All aa
221
What is the equation for the propensity/natural inclination (P) to predict secondary structures in proteins?
P = f
----------
All aa
222
A ________ structure is the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide (S-S) bonds.
Tertiary
223
What is an example of a tertiary structure?
Myoglobin (heme group)
224
______ ______ ______ rearranges the polypeptide's non-native S-S bonds.
Protein disulfide isomerase (PDI)
225
Proteins can be can be denatured by several treatments to disrupt the tertiary structure. The protein folding and unfolding is an "________" process.
All-or-none
226
The molten globule stage is intermediate and very ______.
Short
227
A partial loss of folding ________ the remainder of the structure. The structural properties of proteins provide a clear rationale for the cooperative transition.
Destabilizes
228
A ________ structure is the spatial arrangement of subunits and nature of their interaction.
Quaternary
229
What is an example of a quaternary structure?
Hemoglobin (2 alpha-subunits, 2 beta-subunits)
230
This accessory protein interconverts cis and trans isomers of peptide bonds with the aa proline.
PPI (peptidyl prolyl cis-trans isomerases)
231
HSP 70 (HSP 40) are a type of _________ that are ATP-driven and function to reverse misfolds, check newly synthesized proteins, and unfold/refold trafficked proteins.
Chaperones
232
This type of accessory protein is a type of chaperone and provides favorable conditions for correct folding of proteins, a protein folding container.
Chaperonins
233
These were the 1st ever discovered chaperones in the nucleosome.
Nucleoplasmins
234
This type of chaperone is for signal transduction proteins.
HSP 90
235
Protein denaturation can be caused by certain conditions, including...
Heat
pH (extremes)
Agitation (forms precipitate)
236
Protein denaturation can be caused by certain chemicals, including...
Detergents (SDS) **Breaks disulfide bridges
Chaotropic agents (urea, guanidine hydrochloride **which disturbs hydrogen bonds)
Organic solvents (TCA) [Trichloroacetic acid] **Disturbs hydrogen bonds
237
What are 5 methods of analysis of protein denaturation?
```
Turbidity (cloudiness)
Circular Dichroism (CD)
UV absorption
Fluorescence
Biological activity (such as receptors, i.e., insulin)
```
238
This is a differential absorption of right-hand and left-hand circularly polarized light resulting from molecular asymmetry involving a chromophore group. It's used to study the conformation of proteins in solution.
Circular dichroism (CD)
239
Molecure _______ are essential proteins that bind to unfolded and partially folded polypeptide chains. They prevent the improper association of exposed hydrophobic segments. Non-native folding, polypeptide aggregation, and precipitation will not occur.
Chaperons
240
These allow misfolded proteins to refold into their native conformation.
Chaperons
241
There are 2 major classes of chaperons, which are...
Heat Shock Proteins (HSP)
| Chaperonins
242
This family of HSP coordinates cellular function by directing substrates for unfolding, disaggregation, refolding or degradation.
HSP 70
243
This family of HSP integrates signaling functions, acting at a late stage of folding of substrates.
HSP 90
244
These proteins are types of chaperonins (protein folding containers).
```
HSP 60 (GroEL)
HSP 10 (GroES) (co-chaperone)
```
245
Protein turnover is tightly regulated. They can either be stable (long life) like _______ (120 days) or be short-lived (participates in metabolic regulation) like ______ ______ (11 minutes).
Hemoglobin
| Ornithine carboxylase
246
Cells must remove aged proteins as well as damaged proteins. A number of pathological diseases are associated with protein ________.
Aggregation
247
This is a protein degradation machine, a large protease complex. It's part of the protein homeostasis system.
Proteasome
248
Proteasomes digest _________ proteins.
Ubiquinated
249
A _____ proteasome has 2 _____ regulatory unites and one _____ catalytic core.
26S
19S
20S
250
In the 26S proteasome, this part recognizes ubiquinated proteins. Isopeptidase cleaves off the ubiquitin, and it directs the protein into the catalytic core.
19S regulatory unit
251
In the 26S proteasome, this part is composed of 28 subunits. It is a catalytic core composed of a sealed barrel. Access is controlled by 19S.
20S catalytic core
252
The proteasome and other proteases generated _____ amino acids. Ubiquinated proteins are processed to peptide fragments. Peptide fragments are further digested to yield _____ amino acids. These can be used for biosynthetic reaction.
Free
| Free
253
The _______ method is an empirical technique for the prediction of secondary structures in proteins.
Chou-Fasman
254
Cellular quality control systems include...
Proteasomes
Autophagy
ERAD (ER-Associated Degradation)
255
Maintenance of protein homeostasis is _______.
Critical
256
This is what occurs when mutant CFTR (in cystic fibrosis) and Beta-glucosidase (in Gaucher's disease) are degraded through ERAD (endoplasmic reticulum associated degradation). These mutant proteins still retain partial functionality, which is still better than no protein at all. So the degradation is harmful.
Improper degradation
257
This is what occurs when AAT (alpha1-antitrypsin) does not fold properly. Normally, it is produced in the liver and gets transported to the lungs. When it is mutated the AAT is not transported to the lungs, causing the lungs to not do their job. This is called a ______ _____ ______. Since AAT cannot be moved to the lungs, it stays in the liver and aggregates. This is called a ______ _____ ______ _______.
Improper localization
Loss-of-function
Gain-of-function toxicity
258
This is a type of mutation that occurs when a mutant protein antagonizes the function of the WT protein. There is a loss of protein activity and the mutant protein presence interferes with the function of the WT protein at the cellular and structural levels. The examples used were keratin and p53. Each one have multiple subunits. If one subunit was mutated and the rest were normal, that mutant would take dominance and effect the whole structure.
Dominant Negative Mutations
259
This occurs when a protein conformational change can cause a dominant phenotype. Proteins become toxic. For example, APOE4 is a variant of APOE in Alzheimer's disease. This one change can cause mitochondrial disfunction and impair neurite outgrowth. Another example is Src kinases in cancer.
Gain-of-Toxic Function
260
These are insoluble protein aggregates.
Amyloid fibers
261
Amyloidogenic proteins have a _______ sequence, which can cause amyloid-related diseases.
VQIVY
262
Several amyloidogenic proteins form a pore-like structure and can disrupt the _____ _____ integrity.
Cell membrane
263
Misfiled forms of the protein are frequently observed in the elderly, as part of the natural aging process, and individuals with mutations in the protein early in life. A common result of amyloid fiber production are _______ in elderly (usually).
Cataracts
264
How does the amyloid progress to amyloid plaques?
Seeding (nucleation)
Fibril formation
Deposit
265
________ modifications enhances the formation of amyloid fibers.
Covalent
266
Understanding more about how misfolded proteins contribute to disease opens new avenues for drug discovery. For example, TTR (transthyretin protein) has four identical polypeptides. It is a primary carrier of hormone thyroxine and a retinol transporter, and is also amyloidogenic. We could block the aggregate formation by:
1) Using small molecules, such as ________
2) _____-_____ ______ (these recognized conformational changes and are sequence specific, such as VQIVY)
Stabilizer
| Site-specific antibodies
267
The organism maintains its capacity to grow and reproduce. Keystones for environmental stressors are...
To detect
To respond
To adopt
(DRA)
268
Intrinsic induction of stress defense programs and resulting adaptation can (INCREASE/DECREASE) life expectancy.
Increase
269
Applying moderate levels of stress could trigger beneficial and adaptive stress defense pathways, allowing a (LONGER/SHORTER) life.
Longer
270
_______ restriction prolongs the lifespan.
Caloric
271
This is the term used for the maintenance of "protein homeostasis".
Proteostasis
272
Cellular and organismal functionality requires protein protein _______, _______, and _______.
Production
Folding
Degradation
273
_____ _____ _____ are complex pathways to ensure proteostasis in different compartments such as the cytosol (HSR), the ER (UPRer), and mitochondria (UPRmt).
Unfolded protein responses (UPR)
274
Cellular proteins are folded by _______.
Chaperones
275
Membrane and secreted proteins fold and mature in the _____.
ER
276
A specific response helps to cope with misfolded protein accumulation. The _______ pathway is the last line of defense.
Apoptotic
277
This manages denatured proteins in the cytosol (HSF1).
Heat Shock Response (HSR)
278
This is the ER stress initiated signal pathway.
UPRer
279
This is the mitochondria initiated signal pathway.
UPRmt
280
If unfolded or misfolded proteins accumulate in the ER, it causes ER stress. ER stress imitates a signal pathway called unfolded protein response (UPR). This pathway is intended to save the cell. UPR tries to do this by:
1) Increase protein ________
2) Increase rate of ______
3) Decrease _______ production
4) ________ as a last resort when other methods of reducing ER stress fail
Chaperones
ERAD
Protein
Apoptosis
281
______ _____ _____ proteases are specific for each mitochondrial compartment. They recognize and degrade the proteins that don't fold and properly assemble. ______ sense the overload of this system's capacity and activates the transcription of nuclear encoded protective genes. This reestablishes the mitochondrial homeostasis.
Protein quality control (PQC)
| UPRmt
282
This is the term for an interdisciplinary field that set computational tools for understanding biological data. It combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret biological data.
Bioinformatics
283
This is the term for the study of proteins.
Proteomics
284
This is the term for the entire set of proteins produced by an organism.
Proteome
285
______ are two molecules that are derived from a common ancestor.
Homologs
286
______ are homologs present within one species that have a common origin (a duplication event) but may have evolved different functions.
Paralogs
287
______ are homologs that are present in different species and that have similar functions.
Orthologs
288
Sequence comparisons must rule out the possibility that the similarities are due to chance. Sequences are systematically aligned to search for similarities, a process called ______ ______. The similarity of alpha-hemoglobin and myoglobin can be compared.
Sequence alignment
289
Sequence identities can be established by sliding one sequence past the other and counting the number of ______. The two alignments with the largest number of matches are shown (slide 8). This plots the alignment with the greatest number of matches across all of the potential alignments.
Matches
290
Searching for sequence identities sometimes yields multiple alignments that display a large number of matches. Introduction of a _____ into one of the sequences may allow identities found in the different alignments to be represented in one alignment. However, the use of _____ may generate artificial similarities.
Gap
| Gaps
291
Scoring systems facilitate the use of gaps. For instance, 10 points are assigned for a match and 25 points are _______ for a gap.
Deducted
292
Myoglobin and alpha-hemoglobin are 25.9% identical with a score of 355. The score is (LOW/HIGH), this means we know their origin is similar.
High
293
The significance of an alignment can be assessed by randomly rearranging the sequence of one of the sequences being compared. The _______ sequences are used in the sequence alignment process and the alignment scores are determined. If the original score is not sufficiently different from the randomized score, the original alignment could be a result of ______.
Shuffled
| Chance
294
Alignment scores are calculated for many shuffled sequences, and the number of sequences generating a particular score is plotted agains the score. The resulting plot is a distribution of alignment scores occurring by chance. The alignment score for unshuffled alpha-hemoglobin and myoglobin is substantially greater than any of these scores, strongly suggesting that the sequence similarity (IS/IS NOT) significant.
Is
**See slide 12
295
A more sensitive scoring system takes into account the degree of similarity of amino acids. A ________ substitution replaces one amino acid with a similar one. A ________ substitution replaces one amino acid with one with different chemical properties.
Conservative
| Nonconservative
296
Amino acid substitutions can also be classified by the fewest number of ________ changes to achieve the amino acid substitution.
Nucleotide
297
A substitution matrix, such as _______, is a scoring system that awards points for substitutions that are commonly found in nature and subtracts points for substitutions that only rarely occur. The substitution matrix shows that many of the differences between alpha-hemoglobin and myoglobin are conservative.
Blosum-62 (Blocks Substitution Matrix)
298
Substitution matrices can reveal ________ not identified by sequence alignments only.
Homologies
299
The Blosum-62 indicates that a conservative substitution (i.e., lysine for arginine) receives a (POSITIVE/NEGATIVE) score, whereas a nonconservative substitution (i.e., lysine for tryptophan) is scored (POSITIVE/NEGATIVE).
Positive
| Negative
300
The use of Blosum-62 yields the alignment shown between human myoglobin and lupine leghemoglobin illustrating _______ and _______ substitutions. These sequences are 23% identical. Leghemoglobin is an oxygen carrier and hemoprotein found in the nitrogen-fixing root nodules of leguminous plants.
Identities
| Conservative
301
In order to detect sequence similarities between proteins or nucleic acids, ______ searches are performed. The sequence under investigation is entered into the database, and a ______ search yields a list of sequence alignments accompanied by an estimate that the alignments occurred by chance.
BLAST
BLAST
**(Basic Local Alignment Search Tool)
302
Tertiary structure is more closely associated with function than is primary structure. Plant leghemoglobin shows little sequence homology with other globins but is remarkably similar in ______.
Structure
303
On the basis of three-dimensional structure, actin and Hsp70, proteins with different biological functions, are _______.
Paralogs
304
Knowledge of 3D structures can aid in the evaluation of sequence alignments. A _______ _______, a map of conserved sequences that are structurally and functionally important and are common to a particular family of proteins, allows the detection of homologs that may not be apparent with other techniques.
Sequence template
305
T/F. Repeated motifs can be detected by aligning sequences with themselves. Many proteins have domains that are similar to one another. Such repeats are detected by performing sequence alignments with the protein itself.
True
306
_______ evolution is an example of proteins from different evolutionary pathways arriving at the same solution to a biochemical problem. Some proteins have common structural and functional features but do not share a common ancestor. An example of this evolution are serine proteases.
Convergent
307
Proteins derived from a common ancestor are a result of ________ evolution.
Divergent
308
Comparison of RNA sequences can be a source of insight into RNA ________ structures.
Secondary
309
The lengths of the branches of _______ ______ connecting two proteins are proportional to the number of differences in the amino acid sequences of the two proteins. For example, Hemoglobin form lamprey (whose ancestors diverged from bony fish approx. 400 million years ago) consists of only a single type of subunit.
Evolutionary trees
310
_____ _____ _____ is the exchange of DNA between species that confers selective advantage on the recipient. It is common among prokaryotes. This may explain unexpected branches of the evolutionary tree.
Horizontal gene transfer
311
The polymerase chain reaction and DNA sequencing technology make it possible to determine the sequence of _______ DNA. Comparison of DNA sequences revealed that neither Neanderthals nor Denisovans are on the line of direct descent leading to Homo sapiens but, instead, branched off earlier and then became extinct.
Ancient
312
The use of ________ chemistry makes it possible to observe molecular evolution in laboratory.
Combinatorial
313
Three criteria are required to mimic evolution --
1) A ______ population.
2) Selective pressure to allow ______ to be evident.
3) ________ that permits the enrichment of fit individual molecules.
Diverse
Fitness
Reproduction
314
This is an interdisciplinary field that uses computers and information technology to gain, store, analyze, communicate and display medical information and knowledge. This aids the understanding and evaluation of clinical information and improves accuracy, quickness and reliability of decision making. The main aims are to reduce medical risks, improve patient care and cut costs of treatment.
Medical bioinformatics
315
______ facilitates access to and communication about the relationships asserted between human variation and observed health status, and the history of that interpretation.
ClinVar
316
One component used to evaluate the potential significance of a nucleotide or amino acid variant is to examine its ________ over evolutionary history.
Conservation
317
______ extracts and prioritizes patient phenotypes directly from medical records to expedite genetic disease diagnosis.
ClinPhen
318
_____ _____ is a general term that implies the use of a computer to model intelligent behavior with minimal human intervention. In medicine, it has two main branches: ______ and _______.
Artificial intelligence (AI)
Virtual
Physical
319
The (PHYSICAL/VIRTUAL) branch of AI includes informatics approaches from deep learning information management to control of health management systems, including electronic health records, and active guidance of physicians in their treatment decisions.
Virtual
320
The (PHYSICAL/VIRTUAL) branch of AI is best represented by robots used to assist the elderly patient or the attending surgeon.
Physical
321
This type of enzyme moves electrons (redox reactions). Examples of activated carriers include: NADH, NADPH, FADH2, and FMNH2.
Oxidoreductases
322
This type of enzyme moves a functional group (group transfer). Activated carriers include: ATP, pyridoxal phosphate, SAM, Tetrahydrofolate, and 5'-deoxyadenosylcobalamin.
Transferases
**ATP and pyridoxal phosphate transfer phosphate groups
**SAM, Tetrahydrofolate, and 5'-deoxyadenosylcobalamin transfer methyl groups
323
This type of enzyme breaks a chemical bond by adding water across it (hydrolysis).
Hydrolases
324
This type of enzyme rearranges the order of atoms in a molecule (isomerization).
Isomerases
325
This type of enzyme breaks a chemical bond without using water.
Lyases
326
This type of enzyme pastes two pieces together (make a chemical bond), uses ATP.
Ligases
327
For ligases and lyases, TPP can be an activated carrier because it adds or subtracts an _______ group.
Aldehyde (-COH)
328
For ligases and lyases, CoASH and lipoamide can be activated carriers because they either add or subtract ______ groups.
Acyl (-COR)
329
For ligases and lyases, biotin can be an activated carrier because it adds or subtracts a _____ group.
CO2
330
In a nucleophilic substitution reaction we swap...
Functional groups
331
In a nucleophilic addition reaction we add...
Functional groups
332
In a carbonyl condensation reaction we change the number of...
Carbons
333
In an elimination reaction we increase the ______ order.
Bond
334
In an oxidation-reduction reaction we move...
Electrons
335
This is a site on a protein that is only a few residues. It is a 3D cleft/crevice/pocket, creating a unique environment. It determines substrate specificity by size and charge complementarity and contact with the substrate through non covalent interactions.
Active site
336
This type of binding does NOT occur at the binding site, but follows the same interaction rules. It involves a second substrate, which can be an activator or an inhibitor.
Allosteric binding
337
This type of inhibition occurs when an inhibitor binds to the active site, keeping the other substrates from getting to it.
Competitive inhibitor
338
This type of inhibition occurs when a substrate binds to another site on the enzyme, changing the shape of the active site. This now keeps the substrate from binding to the active site.
Allosteric inhibitor
339
This type of activator binds to another site on the enzyme, which causes the enzyme to change shape to fit the wanted substrate or become more desirable to that substrate.
Allosteric activator
340
T/F. Competitive activation exists.
False. Not a thing!
341
This type of enzyme is incomplete, inactive, and lacks a cofactor/coenzyme.
Apoenzymes
342
This type of enzyme is whole, active, and contains a cofactor/coenzyme. It requires allosteric activation!
Holoenzymes
343
If an enzyme has more than one binding site, the sites can be --
- _____ equivalent _____ independent
- _____ equivalent _____ independent
- _____ equivalent _____ independent
All; And
Either; Or
Neither; Nor
344
Kd is the dissociation constants for ExSn complexes. It is equal to the concentration of ligand where half the available binding sites are full OR you can say it is when the ______ is half-saturated.
Receptor
345
For n=1, when Y (fractional saturation) equals 0 that means No ligand is bound. When Y=1 it means the receptors is saturated. When Y=0.5 it means the receptor is _______.
Half-saturated
346
This is the term for when the binding of each subsequent ligand influences the affinity (strength of interaction) of the next ligand to bind an active site.
Cooperativity
347
In terms of cooperativity, we interpret Hill Coefficients in the following way:
- nH=1 means NO cooperativity (sites are independent)
- nH > 1 means (POSITIVE/NEGATIVE) cooperativity (affinity increases)
- 0 < nH < 1 means (POSITIVE/NEGATIVE) cooperativity (affinity decreases)
Positive
| Negative
348
The function of _______ are to transport oxygen from the lungs to the tissue. Hemoglobin occupies 33% of the volume of these.
Erythrocytes
349
65% of hemoglobin is synthesized before extrusion of the nucleus. _______ makes the remaining 35% of Hb required for the RBC.
Reticulocytes
350
There is a ______ phenomenon as to where red blood cells are made during development.
Switch
351
Hemoglobin is a multi-subunit protein (tetramer). It contains 2 _____ globin chains and 2 _____ globin chains.
Alpha
| Beta
352
There is one of these per subunit of hemoglobin. It has the iron atom that carries oxygen.
Heme
353
Hemoglobin also has four _________ IX rings.
Protoporphyrin
354
There are 3 types of hemoglobin in humans, including...
Embryonic
Fetal
Adult
355
There are 4 types of globin chains in the normal adult, including...
Alpha
Beta
Delta
Gamma
356
The predominant form of Hb in the human adult is _____ which has 2 alpha and 2 beta subunits.
HbA
357
In the adult about 97% is HbA, about 3% is another Hb called HbA2 composed of 2 _____ and 2 _____ subunits. Another 0.5% is fetal hemoglobin (HbF).
Alpha
| Delta
358
Fetal Hb is composed of 2 _____ and 2 _____ subunits.
Alpha
| Gamma
359
The globin proteins have alpha-like chains and beta-like chains. What falls under alpha-like chains? Beta-like chains?
Zeta (embryonic)
Alpha
Epsilon (embryonic)
Gamma (fetal)
Delta
Beta
360
Chromosome ____ has Beta globin genes (epsilon, gamma with glycine, gamma with alanine, delta, beta) and chromosome ____ has alpha globin genes (zeta, alpha 1, alpha 2).
11
| 16
361
Embryonic Hb is expressed in the ____ ____ but not after 8 weeks gestation. Embryonic Hb is 2 _____ and 2 _____ subunits.
Yolk sac
Zeta
Epsilon
362
Fetal Hb is made predominantly in the ______ (and ____ ____). In the fetus, HbF is 90-95% total Hb production until 34-36 weeks gestation.
Liver
| Bone marrow
363
After birth, adult Hb production starts. In a newborn 50-85% Hb is still HbF, and at _____ of life HbA reaches adult levels.
1 year
364
At amino acid position #6 in Beta globin there is a substitution of valine for glutamic acid, this is called ______. It causes polymerization of Hb.
HbS (sickle cell)
365
Research is ongoing to induce expression of ____ to help with sickle cell. We're currently using hydroxyurea to induce it and address inflammation but this is a chemotherapeutic agent.
HbF
366
Research is ongoing to induce expression of ____ to help with sickle cell. We're currently using hydroxyurea to induce it and address inflammation but this is a chemotherapeutic agent.
HbF
367
Globin genes are arranged in _______ fashion. Ordered in the 5' to 3' direction in the same sequence of activation and expression during embryonic, fetal and adult development.
Linear
368
In hemoglobin, this is a prosthetic group and non-amino acid group of a protein.
Heme
369
Heme gives blood its color, transports _______ and releases it where it is needed.
Oxygen
370
The heme is nestled in a _______ crevice of the protein chain.
Hydrophobic
371
75% of globin chain forms ______.
Alpha-helix
372
The heme group consists of an organic component and a central ______ atom.
Iron
373
The organic component of heme is called _________.
Protoporphyrin
374
Protoporphyrin is made up of four ________ rings.
Pyrrole
375
Pyrrole is characterized by a ring structure composed of four ______ atoms and one ______ atom.
Carbon
| Nitrogen
376
Four pyrrole rings form a _______ ring.
Tetrapyrrole
377
In heme, four ______ groups, two ______ groups, and two _______ side chains are attached. The iron atom lies in the center of the protoporphyrin, bonded to the four pyrrole nitrogen atoms.
Methyl
Vinyl
Propionate
378
There are 8 helical segments to a globin subunit and they are labeled ____ through ____.
A
| H
379
Amino acids are named according to the helical segment and # amino acid in that segment (i.e., F8 Histidine is the 8th residue in the F helix). What segment # is D in the globin subunit?
4th
380
The F8 Histidine is called the (PROXIMAL/DISTAL) histidine which is bound to the heme group (6th segment in globin chain).
Proximal
381
The E7 Histidine is called the (PROXIMAL/DISTAL) histidine and oxygen binds to the iron between the heme and distal histidine (5th segment in globin chain).
Distal
382
A ______ bond donated by the histidine E7 residue to the bound oxygen molecule helps stabilize oxyhemoglobin.
Hydrogen
383
In hemoglobin, oxygen binding changes the position of the ____ atom by 0.4 angstroms. This pulls the F8 proximal histidine which is attached to the globin chain and moves into the plane of the heme.
Iron
384
Upon _______, the iron atom moves into the plane of the heme and pulls the proximal F8 histidine residue of hemoglobin. This is incredibly important for the function of hemoglobin.
Oxygenation
385
Myoglobin is a _______ encoded by a different gene than the globin genes (Chr 22).
Monomer
386
Myoglobin has _____ heme-Fe2+ group.
One
387
Myoglobin is an oxygen (STORAGE/TRANSPORTER) protein and hemoglobin is an oxygen (STORAGE/TRANSPORTER) protein.
Storage
| Transporter
388
Myoglobin is very common in ______ cells. Its job is to store oxygen, for use when ______ are hard at work.
Muscle
| Muscles
389
Hb function is to transport oxygen from the ______ to the tissues via ______.
Lungs
| Blood
390
4 heme molecules can carry ______ O2 (oxygen).
4
391
Myoglobin has (LOW/HIGH) affinity for oxygen. It holds onto it tightly, hence why it's a storage protein.
High
392
T/F. The 0.4 angstrom change induced by binding of oxygen to Fe and pulling down of F8 histidine means little for myoglobin. It's important to hemoglobin.
True
393
Oxygen _______ ______ presents saturation of myoglobin with oxygen at different concentrations of oxygen (measured in Torr-mmHg)
Dissociation curve
394
Half the myoglobin molecules have bound oxygen when the oxygen partial pressure is ____ torr.
2
395
In RBC the Hb curve is shaped like an "S", or sigmoid shape. Hb switches between 2 states of affinity, _____ and _____.
High
| Low
396
Binding to oxygen must be _______. Hb is the ultimate "switch hitter", it can bind oxygen with high affinity and let go with low affinity.
Reversible
397
Hb picks up oxygen in the lungs at a pressure of 100 mmHg and is _____ saturated. Hb drops oxygen off in the tissues at about 10 to 20 mmHg and is only about _____ saturated. Sigmoidal shape is the result of interactions between the globin subunits.
100%
| 20%
398
Myoglobin has high affinity for oxygen and doesn't release oxygen until pressure in tissues is very (HIGH/LOW).
Low (close to 0 Torr)
399
P50 is the oxygen partial pressure at which molecule is half saturated with oxygen. P50 Myoglobin = ______ and P50 Hb = _____.
2.8 Torr
| 26 Torr
400
Hb binds oxygen in a _______ fashion, meaning as soon as one molecule of oxygen binds to one heme, it facilitates the binding of an oxygen to another heme.
Cooperative
401
T/F. Conformational change in one globin subunit induces a conformational change in another subunit in Hb. Hb's conformation, hence its oxygen affinity, changes as each successive molecule of oxygen is bound.
True
402
The binding of oxygen to iron of a globin subunit pulls the proximal F8 histidine. This pulls on the globin alpha-helix chain and changes the interaction with the other globin chains in Hb. This changes the organization of other globin chain and their affinity for oxygen. ________ occurs.
Cooperativity
403
Hypothetically if there was no cooperativity, Hb would not be a good _______ carrier.
Oxygen
404
T/F. As Hb loses oxygen in the tissue, the loss of an oxygen molecule by a globin subunit makes it more likely the next subunit will lose its oxygen molecule.
True
405
Hb is an allosteric protein. Structure and function are influenced by other molecules: ______, _____, (HbF).
2,3-BPG
| H+
406
A major modulator of Hb is 2,3-BPG. It is an intermediate by-product of glycolysis. In active tissues there is lots of 2,3-BPG made, it signals to Hb to let go of _______.
Oxygen
407
2,3-BPG is present in RBCs at approximately the same concentrations as Hb. Without 2,3-BPG, Hb would be an extremely inefficient ______ transporter.
Oxygen
408
Pure Hb (no 2,3-BPG) has a curve that is hyperbolic, like _______. Hb in RBCs with 2,3-BPG has a sigmoid curve that shifts to the right. At 20 Torr pure Hb only gives up 8% oxygen, but Hb gives up 66%.
Myoglobin
409
In active tissues there is lots of 2,3-BPG made, which signals to Hb to let go of oxygen. It reduces oxygen affinity so Hb gives up more oxygen to tissues. Cells actively perspiring are metabolizing _______ and will produce this molecule.
Glucose
410
In highly metabolizing tissue, you do not want Hb to hold onto oxygen, you want Hb to release oxygen. 2,3-BPG binds to the central pore of deoxyhemoglobin (interacts with 3 positively charged groups). NO 2,3-BPG (lungs) means (LOW/HIGH) affinity for oxygen. High 2,3-BPG (tissues) means (LOW/HIGH) affinity for oxygen.
High
| Low
411
The ______ or tight form of Hb means low affinity for oxygen.
Tense ("T")
412
The ______ form of Hb means high affinity for oxygen.
Relaxed ("R")
413
In non-oxygenated Hb, beta chains are farther apart. This is the (TENSE/RELAXED) form.
Tense
414
In oxygenated Hb, beta chains are closer together. This is the (TENSE/RELAXED) form.
Relaxed
415
High 2,3-BPG stabilizes the T form of Hb, (LOW/HIGH) affinity and releases oxygen.
Low
416
Low 2,3-BPG in lungs leads to R form, (LOW/HIGH) affinity for oxygen.
High
417
2,3-BPG is (HIGHER/LOWER) in smokers. Meaning oxygen carrying capacity is reduced in smokers.
Higher
418
The pH of actively respiring tissues is lower, it drops from pH of 7.4 to 7.2. The binding affinity of Hb for oxygen (INCREASES/DECREASES) as the pH decreases. An amino acid picks up H+ from tissue. It changes the conformation of Hb and favors the release of oxygen.
Decreases
419
The fetus needs Hb that has a (LOWER/HIGHER) affinity for oxygen than mother's Hb.
Higher
420
Oxygen flows from mother to fetus because HbF does not bind well to _______, therefore it has a higher affinity for oxygen.
2,3-BPG
421
HbF is mostly locked in the (TENSE/RELAXED) form because it does not bind well to 2,3-BPG. This signifies a high affinity of oxygen.
Relaxed
422
The _______ model of cooperativity is when each level of oxygen loading causes an adjacent globin chain to change from the T to R or vice versa state (One at a time).
Sequential
423
The _______ model is when ALL Hb tetramers exist in either the T state or R state (All or nothing).
Concerted
424
Carboxyhemoglobin occurs when heme is combined with ______ ______. The bond with this is 210 times stronger than the bond with oxygen. Transport of oxygen to tissues is impaired. Death can occur from overexposure (suffocation).
Carbon monoxide
425
______ occurs when a post translational modification of the N-terminus of the Beta-Globin chain occurs. This modification is glycosylation ( addition of glucose) that is irreversible. Usually there is 3% in a normal person but it varies with the level of blood glucose concentration to which RBCs have been exposed to in their 120 day lifespan. It is increased in diabetes by 2x to 3x (6% to 9%) and reflects the control of glucose levels for the last 120 days.
HbA1c
426
Hemoglobinopathies include two major types, which are...
Structural
| Quantitative
427
Structural hemoglobinopathies includes ______ ______ disease. There is a non-functioning globin protein and Beta globin chain defect.
Sickle cell
428
Quantitative hemoglobinopathies include ________. This occurs when insufficient globin chains are produced. There is an alpha and beta form, where alpha globin chains are affected or beta globin chains are affected.
Thalassemias
429
In alpha-Thalassemia, it involves both alpha globin genes. There is a deletion of 1, 2, 3, or 4 alpha globin genes. If only 1 is deleted then you are a _______. Deficiency of alpha globin chains affects Hb production in both fetal and adult life.
Carrier
| alpha+-Thalassemia
430
In fetal life, excess zeta globin chains (due to less alpha chains from thalassemia) form zeta 4 tetramers or Hb ______. This variant of Hb is so called as it was discovered at St. Bartholomew's Hospital in London.
In adults, excess Beta globin chains form Beta4 tetramers or _____. These tetramers precipitate slowly as red cells mature and age. Precipitate forms inclusion bodies (Heinz bodies) which lead to hemolytic anemia.
Bart's
| Hb H
431
Traits of alpha-thalassemia includes ________ (low MCV: mean cell volume) and _______ (low MCH: mean cell Hb), and normal percentages of HbA2 and HbF.
Microcytosis
Hypochromia
***Occurs when 2 genes are deleted
432
In alpha-thalassemia, _____ disease occurs when 3 alpha genes are affected. This disease is characterized by moderately severe anemia, microcytic, hyochromic hemolytic anemia, hepatosplenomegaly, mild jaundice.
Hb H
433
In alpha-thalassemia, _____ _____ with Hb Bart's occurs when all 4 alpha genes are completely inactivated. This is severe, stillborn or die few hours after birth. Few are saved by exchange transfusion. Fetal onset of generalized edema and severe hypochromic anemia.
Hydrops fetalis
434
Hb Bart's has high affinity for ______. It binds oxygen delivered by mother but releases almost none to fetal tissues. Severe hypoxia occurs and leads to profound edema (hydrops) due to congestive heart failure.
Oxygen
435
In beta-thalamessia causes reduced beta chain synthesis and excess alpha chains. These alpha chains precipitate as inclusions and cause damage to red cell precursors and red cells. Leads to profound _______.
Anemia
436
There are 2 main varieties of beta-thalamessia. Thalamessia ______ form has no beta-chain expression, severe homozygous condition. Thalamessia _____ form has partial deficiency beta-chains, heterozygous condition with milder anemia.
Major
| Minor
437
What do the cells look like with severe anemia?
Tear drops
| Targets
