H2001 Midterm 1 Flashcards
(264 cards)
1
Q
Where is all the information required to fold a protein into its tertiary structure contained?
A
Primary sequence
2
Q
What do proteins need to include to bind oxygen?
A
A prosthetic group
3
Q
What is a crucial role of IDPs (2)
A
1) binding to multiple partners
2) high-specificity / low affinity interactions
4
Q
What is important to note about the hydrogen bond that stabilizes a-helices?
A
It STARTS from a carbonyl oxygen and GOES to the amino NH
5
Q
What groups are attached to the alpha carbon in an amino acid
A
alpha-carboxyl and alpha-amino
6
Q
Buffers
A
pH doesn’t change much as you add acid or base.
7
Q
p53
A
famous tumour suppressor protein with IDP regions
8
Q
What stabilizes the T state?
A
greater number of ionic interactions at the interfaces between subunits
9
Q
What happens if there are two deep wells in the E landscape? One corresponding to the right fold, and the other the wrong fold.
A
Mad cows disease
10
Q
What causes the twist in a coiled coil?
A
The two helices must twist around each other to match up their hydrophobic faces
11
Q
True or False: glycine does not have to be every third residue.
A
False
12
Q
How long are typical domains in terms of residues?
A
100-200 residues
13
Q
Polarity
A
distribution of e- clouds around covalent bond
14
Q
How are prions formed
A
PrP converted to an infectious, high B-sheet conformation called PrP^SC (scrapie); acts as a template to refold
15
Q
What conditions can denature proteins? (5)
A
1) High temperatures
2) extreme pH
3) Organic solvents
4) chemicals like urea and guanidinium hydrochloride
5) detergents like SDS
16
Q
Which point mutation listed below is least likely to wreck protein function?
Leu - Tyr
Leu - Ser
Leu - Phe
Leu - Trp
A
Leu - Phe
17
Q
List the cellular macromolecules and their building blocks
A
Proteins - amino acids
Sugars - polysaccharides
Fatty acids - lipids
Nucleic acids - nucleotides
18
Q
What does NOT stabilize silk fibroins?
A
Disfulfide bonds
19
Q
What are the names of the next 6 of the monomer naming convention?
A
dimer, trimer, tetramer, pentamer, hexamer
20
Q
Repeating unit of silk fibroin
A
G-S-G-A-G-A
21
Q
Cavity where BPG binds is lined with positive or negative amino acids that interact with the negative groups n BPG?
A
Positive
22
Q
Is CO2 soluble in aqueous solution?
A
Not very
23
Q
What special bonds can cysteine form?
A
Disulphide bonds
24
Q
Myoglobin History
A
binds O2; first atomic resolution protein structure ever solved with X-ray crystallography; earned nobel prize in 1962
25
What part of globular proteins allow them to carry out a wider range of biological functions than fibrous proteins?
Their tertiary structure
26
2 traditional methods to determine protein structures
1) X-Ray crystallography
2) Nuclear Magnetic Resonance (NMR)
27
When would a specific R group be negatively charged (general)?
pH > pKa
28
What do IDPs do to carry out their functions?
Fold
29
What side chain is likely to bind H+ in hemoglobin?
Histidine; forms ion pairs to asp that helps stabilize deoxyhemoglobin, which promotes deoxygenation by favouring transition to T state
30
When does enthalpy favour a process
when dH < 0
31
Review EDI info
32
At pH 7, what is the charge on this peptide:
AEGK
0
33
Dihedral Angles
Rotation can occur around the alpha carbons, only by two angles per residue
34
At neutral pH, do the charged on the C- and N- terminal groups of hemoglobin matter?
Yes, they help to form ionic interactions that stabilize deoxyhemoglobin
35
Review iClicker Qs in lecture 11
36
Apoprotein
protein without its prosthetic group
37
What stabilizes the structure of fibrous proteins? silk fibroin
Secondary: H bonds
Quaternary: van de waals
38
*Review how to explain the hydrophobic effect and hydrophobic interactions
39
Ionic interaction
attraction (or repulsion) of charged species (ions, dipoles, charged groups)
40
Allosteric activation
promotes O2 binding (CO)
41
Sickle-Cell Anemia is caused by mutation in B subunit of hemoglobin; glu6-val6.
a) hydrophobic residue - hydrophobic residue
b) charged residue - hydrophobic residue
c) hydrophobic - polar
B
42
2 major types of secondary structure
1) alpha-helices
2) beta-sheets
43
What are important buffer systems in biochem?
Phosphate (cytoplasm) and bicarbonate (blood plasma)
44
Which of the following is not a characteristic of peptide bonds?
a) Polar
b) planar
c) cis
d) formed by condensation of L amino acids
C
45
What is another type of secondary structure?
Beta Turns
46
Phi Dihedral Angle
toward N-terminus
47
Gibbs Free Energy Formula
dG = dH - TdS
48
Is myoglobin a tetramer like hemoglobin?
No, monomer
49
Why is the oxygen binding site buried deep in the protein?
When one O2 molecule reacts with 2 heme molecules, the result can be conversion of Fe2+ to Fe3+; burying the heme prevents this.
50
Carbon Monoxide poisoning
CO coordinates to heme
CO is colorless odorless, can build up in enclosed spaces, responsible for more than half of poisonings yearly.
250 fold greater affinity for hemoglobin than O2.
51
Bronsted Acid / Base Def
Acid: lose a proton
Base: gain a proton
52
What is another helix breaker and why?
Glycine; it has high conformational flexibility, making it entropically expensive to adopt the constrained a-helical structure
53
Intrinsically Disordered Proteins (IDPs)
lack stable tertiary and/or secondary structures under physiological conditions; exist as dynamic ensembles of interconverting structures
54
Endergonic
dG > 0
Will not occur spontaneously
55
Why do we need proteins for oxygen storage / transport?
O2 is poorly soluble in H2O; can't be carried in tissues. Also doesn't diffuse effectively
56
Hydrogen Bonding
occurs btwn an electronegative atom (O, N, F) and a H atom bonded to another electronegative atom
57
Are most a-helices right or left handed?
Right-handed
58
What stabilizes the structure of fibrous proteins? a-keratin
Secondary: H bonds
Quaternary: disulphide bonds
59
Enthalpy
changes are related to formation, breaking, or distortion of bonds (internal energy)
60
Where might proline fit well in a peptide?
In the first turn of an a-helix
61
Why do we use heme as opposed to free Fe as our binding group?
Free Fe is dangerous; promotes formation of highly reactive oxygen species that damage DNA (one of most common causes of death in children)
62
Why do cats spit up fur-balls?
a-keratin in fur is indigestible, insoluble due to S-S bonds
63
What range does a buffer work best for?
within +- 1 pH unit around the pKa value
64
Amyloids
misfolded proteins form insoluble fibrous protein aggregations formed largely of B-sheet structures
Amyloid plaques destroy nerve cells and lead to loss of thought and memory
65
Summary of collagen structure levels
Primary: Gly-Pro-Hyp-Gly-X-Y
Secondary: left-handed polypro helix
Tertiary: none
quaternary: right-handed triple helix, heterotrimer
66
Direction of collagen helix
left-handed
67
Summary of a-keratin structure levels
Secondary: a-helix
Tertiary: none
Quaternary: coiled coil
68
BPG
interacts with hemoglobin and modulates its O2 affinity
BPG binds at a site distant from O2 binding site, decreases the affinity of hemoglobin for O2
Allosteric inhibitor
69
Alpha-helix
secondary structure where the polypeptide chain winds tightly around; side chains stick out from the helical axis like branches
70
Carboxyl terminal residue
amino acid at the end with a free carboxyl group
71
Do we expect chunky sidechains to fit better with a-helices or b-sheets?
B-sheets
72
Fibrous proteins all possess structural features that give them:
a) frailty
b) delicacy
c) flimsiness
d) strength
d
73
What stereoisomer label is used for the only amino acids that occur in proteins?
L-amino acids (not D)
74
True or false: myoglobin and hemoglobin are conjugated proteins, but only myoglobin is a hemoprotein.
False; both are hemoproteins
75
Which amino acid sidechain is capable of participating in Hydrogen bonds?
Leucine
Tyrosine
Phenylalanine
Tyrosine
76
Phi values around -60 degrees and psi values around -50 degrees are in what handed helices?
Right-handed
77
dG vs. Keq formula
dG = - RT ln Keq
78
How does having small sidechains make silk fibroin strong?
close packing of B-sheets and an interlocking arrangement of R groups
79
Which of these point mutants (all n-p) is least likely to wreck a protein?
L - I
L - A
L - G
L - F
L - I
80
Tm - midpoint / inflection point
50% of protein is denatured
81
holoprotein
protein with its prosthetic group
82
True or False: H bonds are formed between two B-strands to make a B-sheet
True
83
Tertiary Structure
overall 3D arrangement of the atoms in a globular protein; how secondary structure pack together
84
Van der Waals
occur between transient partial charges / dipoles formed in e- clouds; weak
85
What holds helices together in coiled coils?
Hydrophobic interactions between hydrophobic residues
86
What orientation makes H bonding the strongest?
Linear
87
Thermodynamics
Tells you if a process is spontaneous or not
88
Tripeptide
3 amino acids, 2 peptide bonds
89
Review and draw / sketch a Ramachandram plot and indicate the regions for beta-sheets and right handed alpha helices
General: B-sheets above right-handed alpha-helices
90
What structural mechanisms are behind hemoglobin's sensitive response to O2?
Hemoglobin has 4 myoglobin-like chains; fewer than half amino acid residues are identical, although they fold similar to myoglobin
91
What direction is the helical path of the supertwists
Left-handed
92
Separation of Oil and Water is caused by changes in what?
Entropy
93
Quaternary structure
spacial arrangement of a protein's individual polypeptide chains; exhibited only by proteins which contain two or more polypeptide chains
94
What terminal end defines where peptides start being named?
The amino terminal, always placed at the left
95
Considering 3.6 residues per turn in an a-helix, which two residues in MEQALKRN would wind up on the same face of the helix?
M and A
96
What does the binding of O2 to one hemoglobin subunit in the T state trigger?
A change in conformation to the R state (high O2 affinity)
97
Chaperones
proteins present in cells that help other proteins fold
98
Would the presence of two Lys residues near the amino terminus stabilize or destabilize the a-helix?
Destabilize
99
A better view of protein folding
E landscape is funnel-shaped, so the protein is biased to fold towards the native state, with many different intermediate conformations leading to the same native state
100
In active tissues, there are more protons around, so the pH is _____ and hemoglobin has ____ affinity for O2 compared to in the lungs.
Lower, lower
101
What insect can eat wool and how?
Moths; they have high conc of mercaptans so they can reduce S-S bonds to eat wool from clothing
102
Entropy
Changes related to change in order or randomness of a system
103
At pH 1, what is the charge on this peptide:
AEGK
+2
104
2 major conformations of hemoglobin
"R State": relaxed; stabilized by O2 binding (oxyhemoglobin)
"T State": tense; more stable and dominant conformation if O2 isn't bound (deoxyhemoglobin)
105
106
Conjugated proteins
contain permanently associated chemical components (known as the prosthetic group) in addition to amino acids
107
What COHb levels does a healthy person have? What about a smoker / chain smoker?
1% or less
3-8% for smokers
15% chain smokers
108
How is the a-helix structure stabilized?
By H bonds forming between one alpha-carbonyl and the N-H group 4 residues further along the chain
109
What is the structure of alpha-keratin?
Built up from a-helices in a coiled coil; 2 helices wrap around each other to give a "supertwisted" coiled coil. Helices are parallel.
110
Are free amino and carboxyl groups ionizable?
Yes
111
Try to identify phi and psi from a drawing
112
What amino acids can bind oxygen?
None!
113
Zwitterion
spatially separated positive and negative charges; overall charge is 0.
114
Protein that prions are made from
PrP (Prion related protein), found in healthy people and animals
115
Protein Data Bank
contains all experimentally determined structures
116
Explain how entropy causes the separation of oil and water
lipid molecules become ordered around water; however when there are clusters of molecules, the entropy is increased
117
True or False? Multi-domain proteins have domains with all the same function.
False
118
Integrated transport by hemoglobin (Bohr effect)
Lungs carry O2 to tissues, tissues send H+ and CO2 back to lungs to increase affinity for O2 binding (?)
119
How many amino acids
20
120
What is tertiary structure stabilized by?
Many noncovalent interactions
121
What is likely to happen if we switch a polar amino acid for a non-polar one in a protein?
It will wreck the protein
122
How do proteins know what tertiary structure to fold into, and who discovered this?
Christian Anfinsen: started with ribonuclease, denatured by exposure to concentrated urea -- loss of all catalytic activity. He then removed urea, and ribonuclease regained its catalytic activity (refolded into native structure), all by itself (no cell components involved)
123
What do amino acid groups help us predict?
The consequences of mutations
124
Which is the strongest "weak" interaction in biomolecules?
Hydrogen bond
125
Secondary structure of collagen
stabilized by steric repulsion of Pro and hy-Pro rings
Not an a-helix, sometimes called the collagen helix
126
How many residues / turn in collagen helix
3
127
What stabilizes protofibril and protofilaments?
Disulfide bonds
128
In which direction does the dipole moment of an a-helix orient?
Large net dipole moment with - towards C-terminus, + toward N-term
129
Amino terminal residue
amino acid at the end with a free amino group
130
Globin fold
Myoglobin's domain fold
Typically 8 a-helices
stabilized by H bonds and non-covalent interactions btwn sidechains
131
What catalyzes the acid dissociation of CO2 in tissues?
Carbonic anhydrase
132
Protein Folding
conversion of an irregular, flexible arrangement of the protein chain to a regular, relatively rigid, well defined 3D structure
133
What enzyme is required for hydroxylation and what symptoms could arise from a lack of this?
Vit C
Scurvy
134
B-strands and B-sheets
Secondary structure with a much more extended conformation
135
Which type of forces are NOT responsible for stabilizing tertiary structure of globular proteins?
Peptide bonds
136
How many oxygen groups can hemoglobin bind?
4; 1 at each site
137
How does biochem explain changing hair from curly to straight or straight to curly?
Breaks the strong disulfide bonds with a reducing agent, put hair in the shape, then oxidize to re-form the disulfides
138
Which amino acid side chains are positively charged at pH 7?
Lys, Arg
139
Prions
proteins that can misfold and cause infectious disease.
The infectious agent is resistant to denaturation by protease, heat, and radiation.
The prions can refold abnormally into a structure which is able to convert normal molecules of the protein into a form that forms amyloid plaques.
140
Solution to Levinthal paradox, not supported by experimental evidence
A protein takes on specific intermediate conformations en route to the folded state
141
Second Law interpretation by VB
Systems tend to proceed from low entropy states to high entropy states
142
What is the central carbon in an amino acid called
Alpha carbon
143
As CO binds to one or two subunits of a hemoglobin tetrameter, the affinity for O2 is ____ , i.e. CO is an _____ of hemoglobin.
increased, allosteric activator
144
Would the interactions btwn neighboring D and R residues stabilize or destabilize an a-helix?
Stablize
145
What is protein primary structure?
Amino acid residues and peptide bonds
146
At pH 3, what is the charge on this peptide:
KITTEN
+1
147
Where does hair get its strength?
alpha-keratin
148
Would you expect glycines amino and carboxyl groups to be neutral or charged at pH 7?
Charged
149
Hair
an array of many a-keratin filaments
150
Protein misfolding diseases examples
Alzheimers, BSE/CJD, mad cows
151
True or false: subunits and domains are not the same thing.
True
152
Isoelectric point
pH at which a solute has no net electric charge ; pI
153
What happens to the pH as CO2 dissolves?
Decreases
154
Are most proteins globular or fibrous?
Globular
155
What are the approximate pKa values for the 5 main ionizable groups?
alpha carboxyl = 2
alpha amino = 9.5
asp, glu R groups = 4
lys, arg R groups = 11.5
Hist = 6 - 6.5
156
Residue
an amino acid unit within a protein / peptide
157
How to break a disulfide bond?
Use a reducing agent (such as mercaptoethanol)
158
Denatured state
the partially or completely unfolded form of a biological macromolecule; it is incapable of carrying out its functions
159
What is the fundamental units of tertiary structure?
Domains
160
Enzymes
protein catalysts that reduce the activation E and increase the rate of rxn
161
Collagen primary sequence
GXY repeats, usually with one of X or Y being Proline or hydroxyproline
No Cys, Trp, little Tyr
162
Post-translational modification
Chemical modification of protein after its translation
163
What do vdw forces depend on?
Size and shape of molecules interacting
164
When would a specific R group be positively charged (general)?
pH < pKa
165
Which of the following is false about IDP sequences?
a) IDPs have more hydrophobic amino acids than globular
b) IDPs have more polar/charged residues
c) IDPs have more glycine and proline residues
A
166
Protofilaments and protofibrils
Combined two-chain coiled coils in higher order structures
167
What does lower cysteine percentage correlate with practically?
Soft, stretchable and flexible materials; i.e. used for warmth, waterproofing
168
When does entropy favour a process
TdS > 0
169
T or F? At low pH, there is more H3O+ than OH-
T
170
Where might negatively charged ligands prefer to proteins (think of dipoles)?
The N-terminus
171
Which amino acids are prevalent in the regions of proteins that contact DNA (negatively charged)?
K, R
172
Do we expect long skinny sidechains to fit better with a-helices or b-sheets?
A-helices
173
Collagen
most abundant protein in the body (25%).
Bones, teeth, cartilage, tendons, cornea
GLue, gelatin
Insoluble, strong
30 different types
174
What does the sickle-cell anemia mutation cause?
Hydrophobic patch on surface of B-subunit, causes hemoglobin tetramers to polymerize long fibrils, distorting the shape of red blood cells. These don't fit through capillaries, block and interrupt delivery of O2 to tissues
175
How can you learn about the oligomeric structure of multisubunit proteins?
Treat them with B-mercaptoethanol (breaks disulfides) and/or urea (disrupts non-covalent interactions)
176
How many hydrogen bonds can water make?
4; donor of H to 2 and acceptor of H from 2
177
What is the difference between the N-terminus and the N-terminal residue?
The N-terminus is the amino terminal end (just the amino group), whereas the residue is the entire amino acid group at this end of the peptide
178
Why do hemoglobin and myoglobin differ in structure?
Because they differ in function
179
What are the dihedral angles expected in B-sheets?
Phi around -135 and psi around 135
180
True or False: there is no pH at which the alpha-amino and alpha-carboxyl groups of a free amino acid in an aqueous solution are both un-ionized.
True
181
Protein
Polymer of L-amino acids; capable of completing a variety of biological tasks
182
Protein Folding Energetics
difference in free E between folded and unfolded states is only about 10kcal/mol; proteins only barely fold
183
If you have a protein made up of D-amino acids instead of L, what do you think will happen if you treat it with a protease?
Nothing!
This is one strategy for stabilizing small protein drugs
184
Two types of common structural patterns in proteins (list ex of each)
1) Motifs: small; B-a-B loop
2) Domain folds: bigger; a/B Barrel
185
First Law Interpretation by VB
Energy can't be created or destroyed, but it can change form
186
What is the backbone of a peptide?
N-C-C-N-C-C-N-C-C
187
New Protein structure identification method
Cryoelectron microscopy and artificial intelligence (AlphaFold)
188
What is a second determinant to check if a point mutation will wreck a protien?
Size; if the size is very different it's more likely to wreck the protein
189
Does a-keratin have tertiary structure?
Not really; secondary structure is helix and quaternary structure is coiled coil
190
Native conformation (protein)
biologically relevant, folded protein conformation; denoted N
191
Shape of hemoglobin binding curve vs. myoglobin
Myoglobin: hyperbolic
Hemoglobin: sigmoidal (S shaped) because it permits a more sensitive response to ligand concentration
192
Energy landscapes
visual representations of E of protein conformations; the folded conformation is the minimum of E, the deep well
193
What happens to CO2?
some is carried away by hemoglobin, but most is hydrated to form bicarbonate
194
Which force is responsible for the slight spontaneity of protein folding, considering ionic, vdw, and hbond have dG values around 0?
Hydrophobic
195
Why is wool stretchier than silk?
Silk is stabilized by weak and numerous non-covalent interactions, whereas a-keratin is stabilized by strong but few covalent interactions (disulfide bonds), meaning silk cannot stretch, although it is flexible
196
Three major types of proteins
1) Globular
2) Fibrous
3) Integral membrane
197
What amino acid is the only case where the alpha carbon is not a chiral centre?
Glycine
198
Heme binds to Fe in what state? How many coordination bonds are possible?
Fe2+
6 coord bonds; 4 to N atoms in porphyrin ring and 2 perpendicular to porphyrin ring (one to N atom of the protein, other to O molecule)
199
What is the only interactions that favours folding
Hydrophobic
200
The overall 3D arrangement of secondary structure elements that characterizes a single domain is called a what?
Fold
201
True or False? there is a specific 3-base genetic code for the amino acid hydroxyproline so that it is incorporated into the protein during translation of mRNA
False
202
Peptide prefixes above tri
Tetra, penta, hexa, hepta, octa, nona, deca, oligo, poly
203
What prosthetic groups are good at binding oxygen?
Transition metals, including Fe and Cu
204
Why does binding of O2 make the affinity for O2 greater?
Causes the heme group to become planar, leading to a change in conformation of the whole protein
205
What type of reaction forms a protein?
Condensation reaction; endergonic
This means water is eliminated in formation
206
Allosteric protein
Conformation is changed when it binds a ligand; the new conformation changes the protein's ability to react to a second molecule
207
Where do peptide bonds form?
Between the amino group of one amino acid and the carboxyl group of another (both alpha)
208
Psi dihedral angle
toward C-terminus
209
Are van der Waals ever repulsive?
No, they always induce the opposite charge
210
Where does H bonding happen in quat structure of collagen?
from NH of Gly to carbonyl O of adjacent strand; no H bond for pro
211
Which of the following is true about protein domains?
a) a protein must have more than one domain to be functional.
b) protein domains lose their 3D structure when separated from the polypeptide chain.
c) protein domains lose their function when separated from the polypeptide chain.
d) protein domains often fold into stable globular units.
d
212
Henderson-Hasselbalch Equation
pH = pKa + log [conjugate base] / [conjugate acid]
213
What is protein secondary structure?
The local conformation of some part of the polypeptide
214
The protein folding problem / Levinthal paradox
many different conformations for proteins with many amino acids. A topic of active research.
215
List the 4 non-covalent, weak interactions
Ionic
Van der Waals
Hydrogen bonds
Hydrophobic
216
Dipeptide
2 amino acids, 1 peptide bond
217
Take some time to review the amino acids
218
Which amino acid can form disulfide bonds?
Cysteine
219
What are the 2 possible directions of B-sheets?
1) Antiparallel: N-term of one aligned with C-term of next
2) Parallel: N-terms of adjacent peptides aligned
220
How many residues are in each turn in an alpha-helix?
3.6
221
What does higher cysteine percentage correlate with practically?
Harder, rigid, and inflexible materials; i.e. used for protection and defense
222
What is the primary sequence of a-keratin?
A repeat of 7 residues (abcdefg) with hydrophobic residues at positions a and d, on the same face
223
Fetal Hemoglobin
a fetus must extract O2 from its mothers blood, so fetal hemoglobin must have higher affinity for O2 than the mother does.
224
The amino acid composition of spider silk (more flexible) and silk from cocoons (less flexible) is different. Which combo belongs to spiders?
A) 45% G
30% A
12% S
no C
B) 37% G
21% A
4.5% S
no C
B
225
What amino acid is called a helix-breaker and why?
Proline, because it has no backbone NH to participate in H bonds
226
Domain Fold
the particular topographical arrangement of secondary structure elements that characterizes a single domain
227
Allosteric inhibition
inhibits O2 binding (H+ and CO2)
228
What type of mer is hemoglobin?
Heterotetramer
229
Standard Conditions in Biochemistry
[H+] = 10^-7M (pH 7)
230
How strong are disulfide bonds?
About 100 times stronger than H bonds
231
Unfolded conformation (protein)
denoted U
232
Polypeptide
2 or more amino acids joined by peptide bonds
233
Silk fibroin
Protein produced by spiders and insects; very strong and waterproof
234
What determines a protein's function?
Its structure!
235
Hydrophobic Effect
The only of the forces due to entropy.
236
Cooperative binding
A little bit of binding initially leads to a lot more binding; gives sigmoidal shaped binding curves
237
Summary of fibroin structure levels
Secondary: antiparallel B-strands
Tertiary: none
Quaternary: stacked B-strands
238
Do parallel or anti-parallel B-sheets have stronger H bonds?
Antiparallel, because the bonds are linear
239
At low pH, things will tend to be more or less protonated than at high pH?
More
240
Metamorphic proteins
2 conformations in equilibrium with different activity for each conformation
241
What are Beta turns?
found in regions where polypeptide chain reverses direction, within a span of 4 residues, stabilized by H bonds between first and fourth resiudes
242
General rule for globular protein organization
Most hydrophobic residues are on the inside, most hydrophilic residues are on the outside
243
What differences in amino acid composition make IDPs less structured than globular proteins?
Less hydrophobic core
244
Are the CO and NH groups that connect one amino acid to the next ionizable in a peptide?
No
245
What is fetal hemoglobin composed of?
Gamma subunits (not as many K/R residues) instead of B subunits; this has a lower affinity for BPG = higher affinity for O2
246
What is dG at eq
0
247
Exergonic
dG < 0
Occurs Spontaneously
248
Domain
a compact unit of protein structure that is usually capable of folding stably as an independent entity in solution
249
How does oxygen get to the buried binding site?
Dynamics; the proteins are always rearranging and are only marginally stable. This opens cavities that momentarily open / close, big enough to hold O2
250
What holds the quaternary structure of hemoglobin together?
Hydrophobic and ionic interactions
251
Ramachandran plot
plot of psi vs. phi; blue areas show 'allowed' options
252
What is responsible for biological function of a protein?
Folded structure
253
What does BPG play an important role in?
Physiological adaptation to high altitude and the reduced O2 available there
BPG conc in blood rises, leading to more O2 being released into tissues
254
Monomor / subunit
one polypeptide chain in a protein with more than 1 chain
255
Can hemoglobin bind to H+?
Yes, but at a different site from O2 binding site
256
What is the function of fibrous proteins?
Structural support
257
Myoglobin and hemoglobin
related proteins that store and transport oxygen
258
What is the secondary structure of silk fibroin?
Antiparallel B-pleated sheet, stabilized by H bonding. Sheets stack with glycines facing each other, and ala/ser facing each other, stabilized by noncovalent interactions
259
3 characteristics of the peptide bond
1) Planar
2) Polar
3) Trans
260
How do disulfides form properly in tertiary structure?
Non-covalent interactions ensure that cysteines are positioned to form disulfide bonds correctly
261
Which of the 20 amino acids have ionizable sidechains? (5)
R, K, E, D, H
262
Collagen quaternary structure
heterotrimer, right-handed triple helix, glycine residues in the centre, R groups face out, sided gelix
263
Coupled Process
an unfavourable process can be coupled with a highly favourable one to drive the overall process
264
What is one of the biggest things to remember when finding pH of peptides?
Don't forget to account for the charge of the terminal groups
