midterm Flashcards
1
Q
what are the 4 classes of biomolecules?
A
amino acids, carbohydrates, nucleotides, lipids
2
Q
what does the spacefilling model do?
A
gives idea about the shape, but loses information about connectivity
3
Q
what do amino acids make and with what bond?
A
proteins with peptide bonds
4
Q
what do nucleotides make and with what bond?
A
nucleic acids with phosphodiester bonds
5
Q
what do monosaccharides make and with what bond?
A
polysaccharides with glycosidic (ether) bonds
6
Q
what is the bond angle for water
A
104.5
7
Q
structural difference between water and ice?
A
ice is a regular lattice of H bonds, water is a fluctuating H bond structure
8
Q
approximately how many hydrogen bonds per water molecule?
A
3
9
Q
what are the 3 types of electrostatic forces
A
ionic interactions, hydrogen bonds, van der waals forces
10
Q
what are hydrophobic effects determined by?
A
the solvent
11
Q
what are the 2 types of van der waals interactions?
A
dipole-dipole, london dispersion
12
Q
dipole dipole interactions
A
between two polar non charged groups, weaker than h bonds
13
Q
london dispersion interactions
A
b/w non polar molecules, weaker than dipole-dipole
14
Q
what is the hydrophobic effect?
A
when nonpolar molecules clump together they reduce their effective surface area which leads to a higher entropy (disorder) for the solvent. entropically favorable.
15
Q
generalized structure of amino acids
A
amino group, carboxyl group, variable side chain
16
Q
what is the ratio of CHO in carbohydrates
A
1:2:1
17
Q
generalized structure of nucleotides
A
carbohydrate, nitrogen containing base, phosphate group
18
Q
what is a key feature in lipids?
A
presence of long, hydrophobic fatty acid chains
19
Q
what are nucleotides used for?
A
incorporations into nucleic acids, and used as high energy molecules (NTP’S)
20
Q
what is a nucleoside?
A
nitrogen containing base and a sugar. differentiated by the absence of a phosphate
21
Q
what does a hydrogen bond acceptor have?
A
lone pairs
22
Q
what does a hydrogen bond donator have?
A
a proton
23
Q
what hydroxyl is DNA missing
A
2’ hydroxyl
24
Q
how is a nucleoside formed?
A
purines and pyrimidine bases are linked to a 5 carbon sugar
25
what is the linkage of a pyrimidine in a nucleoside or nucleotide?
n1 to c1
26
what is the linkage of a purine in a nucleoside or nucleotide?
n9 to c1
27
what does the lack of c2' OH do in DNA?
reduces the amount of hydrogen bonds
28
when naming nucleosides, what do purines end with?
-ine to -osine
29
when naming nucleosides, what do pyrimidines end with?
-idine
30
which bases are pyrimidines?
U, T, C
31
which bases are purines?
A, G
32
how are nucleic acids formed?
polymers of nucleotides linked by 3'-5' phosphodiester bonds
33
by convention, which way are nucleotide sequences written?
5' to 3'
34
what is the backbone of nucleic acids?
the sugar and the phosphate. the nucleic acids are not considered part of the backbone
35
examples of mononucleotides
ATP, ADP, FMN
36
does hydrolysis of phosphodiester bonds happen in DNA? why or why not?
it doesnt happen in DNA because there is no 2' OH which doesnt allow for a intermediate linkage
37
in what conditions does hydrolysis of phosphodiester bonds happen? what does this mean about RNA and DNA?
high ph. makes DNA more stable in basic conditions, and spontaneous alkaline hydrolysis of RNA
38
spontaneous deamination
spontaneous reaction that converts C to U
39
sugar phosphate backbone is polar or nonpolar?
polar
40
what are the properties of bases?
heterocyclic, aromatic, basically planar (slightly pucker in purine bases), poorly soluble in water, hydrophobic
41
how do you measure the purity of DNA?
A260/ A280
42
what is the A 260/ A 280 for pure dna?
1.95
43
what is A280?
protein absorption maximum, dna absorption is decreased by approximately 50% at 280
44
what happens when dna is contaminated with protein?
the ratio of A260/A280 will go down
45
what is A260 used for? what is the relationship?
to measure the concentration of nucleic acids in solution. linear relationship
46
what is the primary structure of DNA
sequence of nucleotide residues
47
what is the secondary structure of DNA
3d shape
48
how is a double helix formed?
hydrogen bonds between the bases
49
what did erwin chargaff do?
base composition varies from organism to organism, helped watson and crick deduce the double helix sturcutre
50
what happens to hydrogen bonds in solution?
when they break, they can form new interactions with water. isolation from solvent strengthens the H bond interactions
51
what is base stacking and what does it involve and do?
DNA is stabilized by base stacking interactions and hydrogen bonds. base stacking is the primary stabilizing force, involves primarily van der waals forces, but also hydrophobic forces
52
major groove
wide enough to accomadate protein-DNA interactions
53
what is the core in b-DNA
hydrophobic core
54
what is the exterior in b-DNA
polar exterior
55
are the bases surrounded or excluded from water? why?
bases are largely excluded from water, this stabilizes the hydrogen bonds
56
which parts of b-DNA are exposed to water?
ribose/deoxyribose and phosphates
57
how many bp per turn in b-DNA?
10
58
what is chargaff's rule?
a+g=c+t
59
what does denaturation disrupt?
non-covalent forces. effects base stacking and hydrogen bonding
60
what does denaturation cause a change in?
increase in absorption at 260nm as strands separate
61
what is tm and how does it vary?
tm is the midpoint of melting of DNA, varies by base composition. also depends on solution
62
what kind of process is DNA melting and why?
cooperative process, once it beings its easy to continue
63
single stranded dna has higher or lower absorbance at 260 compared to ds?
higher absorbance
64
what does ss dna have?
hyperchromicity, relatively high absorbance (dna has hypochromocity)
65
renaturation
reformation of dsDNA so it regains its native conformation
66
what does a base pair of a higher GC concentration mean? why?
higher tm. because of base stacking, but you can remember in terms of hydrogen bonds (GC has 3 h bonds), but it is NOT because of hydrogen bonding
67
what is the relationship between GC and Tm
linear relationship
68
what portion of DNA denatures first?
those rich in AT regions. become nucleation sites for strand separation
69
how does changing pH effect Tm
affects protonation state of DNA
70
describe how changing salt concentrations effects Tm
ion concentration shields the negative charges on the phosphate backbone of dna, which stabilizes the structure, therefore increasing Tm. If there is low salt concentration, the double helix will be destabilized and will have a lower Tm
71
how does hybridization effect Tm?
the better the match between the two strands, the higher the Tm
72
how is RNA stabilized?
base stacking and h bonds
73
what is different about RNA vs DNA in terms of their base pairing
RNA has intrastand base pairing, DNA has interstrand base pairing
74
what is a wobble pair and where is it found
in RNA, when a G binds to a U. not a watson and crick bond
75
what kind of forces stabilize RNA secondary structure?
the same as DNA. includes hydrogen bonding and base stacking
76
is rna single stranded or double?
can be a mixture of both
77
what is the 260/280 ration in RNA
2.1
78
What is B-DNA?
regular dna
79
can DNA and complementary RNA form double stranded helix?
yeah, the structure is not as high order, and is somewhat disordered. it is right handed, and the predominant stabilizing form is base stacking interactions
80
what is different about the melting curve for rna?
RNA goes from partially ss to fully ss, while dna goes from fully ds to fully ss
81
where is it the essence of a protein's function?
its interactions with other molecules
82
what is a protein's function determined by?
its structure
83
what is a zwitterion?
overall neutral ion with both positive and negative charges
84
what is included in a general amino acid?
amino group, carboxylate group, variable side chain, alpha carbon
85
what happens to the value of ka as dissociation is favored?
value of ka gets larger
86
what happens when the ph is smaller than the pka
[acid] > [base]. protons are added, shift to acid
87
ph > pka
[base] > [acid]. protons are removed. shifts to base.
88
what is the pka of the carboxylic acid
2
89
what is the pka of the amino group
9.5
90
are amino acids chiral? what does this mean?
they are chiral, their mirror images cant be superimposed
91
how are the common 20 amino acids classified?
by the overall chemical properties of their side chains
92
what 3 groups are the side chains grouped in?
nonpolar (hydrophobic), polar, charged
93
what amino group has a secondary amino group and what is it referred to as?
proline (pro), imino group
94
what do polar amino acids contain?
side chains that contain an electronegative atom
95
what do hydrophobic side chains contain?
lack reactive functional groups have mainly hydrocarbons
96
what is the one achiral amino acid?
glycine
97
where is glycine found?
in flexible regions because it is so small
98
pka of tyrosine
10.5
99
pka cysteine
8.5
100
what is a cystine and how they formed
2 cys that are covalently attached to each other. when cysteine residues undergo oxidation
101
pka of histidine
6
102
is histidine an acid or a base? what is it involved in?
can act as either. involved in enzymatic reactions
103
what 4 amino acids have a charge at neutral ph?
aspartate, glutamate, lysine, arginine
104
pka of aspartate?
4
105
what is aspartate called at ph 1?
aspartic acid
106
charge of aspartate at ph 7?
negative
107
charge of glutamate at ph7?
negative
108
pka of glutamate?
4
109
what is glutamate called at ph1?
glutamic acid
110
charge of lysine at ph 7?
positive
111
pka of lysine?
10
112
charge of arginine at ph 7?
positive
113
pka of arginine?
too high
114
3 letter code for asparagine
asn
115
3 letter code for glutamine
gln
116
3 letter code for isoleucine
ile
117
tryptophan
trp
118
where are polar side chains (uncharged) found?
usually on surface of proteins, but may be in the middle
119
where are polar charged side chains found?
usually located on the surface of proteins
120
charge on the n term?
positive one
121
charge on c term?
negative one
122
what is a dipeptide?
two amino acids joined by one peptide
123
peptides/oligopeptides
general term for a larger number of amino acids, often refers to synthetic peptides.
124
polypeptides
long chains of amino acids, usually produced naturally
125
protein
large polypeptide (or >1 polypeptide) with a biological function
126
what keeps their charge during a peptide bond formation?
only the terminal amino and carboxylate groups maintain charge. side chains retain charge if they had one.
127
characteristics of peptide bonds
rigid, planar
128
how are the electrons distributed in a peptide bond and what does this mean?
the electrons in peptide bonds are somewhat delocalized, meaning that they exhibit partial double-bond characteristics, and no rotation around the C-N bond
129
are the folding conformations in polypeptides limited? why?
yes they are, because the rotation of the backbone is limited
130
can the polypeptide backbone contribute to hydrogen bonding?
yes. the chemical groups in the backbone are polar. the carbonyl group can act as a h bond acceptor, and the nh group can act as a donor
131
what is the secondary structure of a polypeptide?
local folding of the polypeptide backbone, allows for hydrogen bonding of the backbone.
132
what is a regular secondary structure in polypeptides?
occurs when each amino acid adopts the same geometry
133
what are two forms of secondary structures?
alpha helix, beta sheet
134
how is an alpha helix formed?
carbonyl oxygen of each residue forms a Hbond with the backbone NH group four residues downstream
135
why is proline not common in the middle of an alpha helix?
the nitrogen cant act as a Hbond donator
136
how are b sheets organized?
parallel or antiparallel
137
what the h bonds like in a parallel b sheet?
diagonal
138
which is more stable? alpha or beta?
neither
139
which way do the arrows point in a b sheet?
from the n term to the c term
140
where are side chains located in strands of b sheets?
side chains are located above and below the plane of the sheet
141
what force stabilizes alpha helices?
h bonds between the backbone CO and NH groups in the same helices
142
what force stabilizes beta sheets?
h bonds between backbone CO and NH groups of neighbouring strands
143
what types of secondary structures are alpha helix and beta sheets? what does this mean?
regular secondary structures, the peptide backbone has the same configuration regardless of the amino acid composition
144
how are irregular structures made?
distinct elements of regular secondary structure are linked together by polypeptide loops of various sizes
145
what is the tertiary structure of proteins?
arrangement of all atoms in a single polypeptide: arrangement of secondary structures in relation to one another, positions of amino acid sidechains, prosthetic groups
146
what are the two ways tertiary structures can be classified?
fibrous (elongated), and globular (compact)
147
characteristics of fibrous proteins?
insoluble in aqueous solutions, form long protein filaments, usually structural or connective proteins
148
characteristics of globular proteins?
basically soluble in aqueous solutions, fold into compact structures with nonpolar cores and polar surfaces
149
what is found in the interior folding or proteins?
regular secondary structure
150
what is the hydrophobic effect in protein folding?
the "driving force" via which globular proteins adopt/maintain their tertiary structure
151
what does the shape of globular proteins depend on?
depends on the relative position of hydrophobic amino acids in the proteins primary sequence
152
what do ion pairs and salt bridges do?
as with h bonds, they help to fine tune and stabilize the tertiary structure of proteins
153
what are ion pairs?
electrostatic interactions
154
what is a disulphide bridge?
covalent bond, overall RSSR
155
what is a domain in protein structure?
polypeptide segment that has folded into a single structural unit with a hydrophobic core. proteins may contain one or more domain. can also be associated with function
156
what is a motif in protein structure?
a short region of polypeptide with recognizable 3d shape, example zinc fingers. smaller than domain, but still recognizable pattern.
157
what is a prosthetic group?
a non peptide component that is permanently incorporated into a protein. they provide structure and reactive groups
158
what is the prosthetic group in hemoglobin?
heme
159
in what phase are prosthetic groups incorporated?
part of the tertiary structure. without these groups the tertiary structure isnt properly formed
160
why are globular proteins denatured easily?
they are stabilized by weak non covalent forces and are easily unfolded
161
when denaturing a protein, what does changing heat do?
effects hydrogen bonds, and hydropphobic interactions
162
when denaturing a protein, what does changing ph?
salt bridges, h bonds
163
when denaturing a protein, what does changing salt concentration do?
salt bridges, ion pairs
164
when denaturing a protein, what does adding a detergent do?
hydorphobic interactions
165
how do you break a disulphide bond?
add a reducing agent (DTT)
166
what is a quaternary structure of proteins?
proteins composed of more than one polypeptide chain. each polypeptide is called a subunit
167
in quaternary structure, what are 2 identical subunits called? two non identical subunits?
homodimer, and heterodimer
168
what are quaternary structure stabilized by?
same as tertiary structures. hydrophobic interactions, h bonds, ion pairs "fine tune"
169
what is the tertiary structure of proteins determined by?
the primary
170
what kind of structure does myoglobin have?
monomer, no quaternary structure
171
what kind of structure does hemoglobin have?
oligomer, quaternary structure
172
hemoglobin
in red blood cells, binds o2 in the lungs and releases it in the tissues
173
myoglobin
binds o2 in muscle cells, acts as a local reserve of o2 during intense exercise, stores o2 in aquatic animals
174
similarities and differences of myoglobin and hemoglobin?
both bind oxygen reversibly, but bind with different affinities and in different conditions
175
what does the function of many proteins depend on?
their ability to bind other small molecules (ligands) reversibly
176
what does a greater affinity between ligand and protein mean about the dissociation constant?
the kd would be smaller with greater affinity
177
what does the value of kd equal?
50% saturation when the concentration ligand equals the value of kd
178
where is the heme prosthetic group in myoglobin?
between helix E and F. relatively hydrophobic (hydrophobic pocket)
179
what is the structure of heme
circular and planar
180
is heme hydrophobic or hydrophilic?
hydrophobic (core) except for two groups that contain carboxylate
181
what is the functional state of iron in heme?
2+
182
what position in heme does oxygen bond?
6th coordination position
183
where does the polypeptide bind in heme?
5th coordination position (his f8)
184
how is the structure of myoglobin maintained?
ring held in place by hydrophobic interactions, and by coordination bond between fe2+ and histidine HIS F8 (proximal)
185
proximal histidine?
histidine f8
186
distal histidine
histidine e7
187
what does the distal histidine do?
increases affinity for o2. decreases affinity for co2. "specificity"
188
how does the distal histidine effect the affinity of co and o2?
distal histidine causes direct steric conflict with CO, unfavourable position. affinity for o2 is enhanced by structure of oxygen binding site
189
what is the quaternary structure of hemoglobin?
tetramer (4 polypeptide chains) with two types of globin. 2 alpha subunits, 2 beta subunits. each has one heme, so each hemoglobin can bind 4 oxygen molecules
190
how many o2 can myoglobin bind?
it only has one polypeptide chain, so one heme, and only one oxygen molecule
191
what is similar about the alpha globin, the beta globin, and myoglobin? what is this called?
all compromise from 8 alpha helices with a heme between E and F. are homologous proteins
192
what critical residues in the oxygen binding sites are invariant?
his F8, his E7
193
what does a hyperbolic curve indicate and what is an example?
indicates constant affinity (ligand affinity/kd does not change). myoglobin
194
what does a sigmoidal curve indicate and what is an example? why is it necessary?
indicates cooperative binding affinity (ligand affinity changes as more ligand binds). hemoglobin. necessary for efficient o2 delivery.
195
what is kd called in a hemoglobin binding curve?
k0.5
196
what are the two structures for hemoglobin? which has high affinity?
tense sate (t), relaxed state (r). relaxed state has high affinity.
197
how does hb change its affinity for o2?
conformational change in hb structure. central cavity changes shape and size.
198
describe the t state. what is it represented as?
low affinity for o2, deoxy hb. larger central cavity, allows for binding of larger molecules that arent oxygen. represented by a square box.
199
describe the r state. what is it represented as?
high affinity for o2. oxy hb. smaller central cavity. represented by circles.
200
what are effectors and what are the 4 kind?
compounds which, upon binding, alter affinity at other binding site. homoallosteric, heterallosteric, activators, inhibitors.
201
homoallosteric
binding of the effector affects further binding of the same compound
202
heterallosteric
binding of the effector affects further binding of a different compound
203
activators
increasing binding affinity
204
inhibitors
decrease binding affinity
205
what is o2 for hb (in terms of effector)
homoallesteric activator
206
list events starting with o2 binding to hb
o2 binds to a subunit. iron moves into the plane of heme and oxygen can bind. when the iron moves, the proximal histine (helix f) also moves and causes a conformational change. this subunit interface change affects other subunits. oxygen binding site becomes high affinity (R)
207
what is bpg (in terms of effector)? h+?
both heteroallesteric inhibitors (for o2)
208
what is bpg essential for? how does it work? why does it not work in r state?
formation of t state of hb. binds to the central cavity of deoxy hb (t state). negative charges on BPG interacts with positive charges in cavity. r state central cavity is too small for bpg
209
what is the bohr effect? describe the process
decrease o2 binding with decrease ph relationship. happens because lowering ph protinates side chains. groups associated with bpg binding become protinated, and bpg binding becomes enhanced, leads to T state, subunit interface changing, and reduced o2 binding.
210
bohr effect and physiological significance
ph of blood in skeletal muscles is lower than ph of blood in lungs. so lungs have enhanced o2 binding, while the tissues have enhanced release of o2 in skeletal muscles
