module 1.1 Flashcards
amino acids and protein structure
1
Q
what kind of reaction has a positive Gibbs free energy value?
A
spontaneous
2
Q
what kind of reaction has a negative gibbs free energy vlue
A
xc
3
Q
what is DELTA G
A
change in gibbs free energy
4
Q
what is the equation links free energy to enthalpy and entropy
A
change in free energy = change in enthalpy - temp (K) x change in entropy
5
Q
what is the term given to a reaction that results in a decreased energy of a system
A
exergonic
6
Q
what are the conditions of an exergonic reaction
A
favourable, spontaneous
7
Q
what is the term given to a reaction that results in an increased energy of a system
A
endergonic
8
Q
what are the conditions of an endergonic rection
A
unfavourable, non-spontaneous
9
Q
what is the term given to a reaction where heat is released. what happens to the enthalpy value
A
exothermic, decreases
10
Q
what is the term given to a reaction where heat is consumed? what happens to the enthalpy value
A
endothermic, increases
11
Q
which term accurately defines spontenity of a reaction (gibbs / enthalpy)? which factor is disregarded by the other that makes determining spontenity unreliable?
A
gibbs free energy, entropy
12
Q
the term given to the ratio of produce and reaction concentrations at equilibrium
A
thermodynamic equilibrium constant
13
Q
what does Keq refer to
A
thermodynamic equilibrium constant
14
Q
what does DELTA G’o refer to. which conditions does it rely on
A
standard free energy change, biochemical standard conditions
15
Q
what are the requirements of bio and chem standard conditions?
A
298k, 101.3kPa, 1M concentration
16
Q
what are the requirements of biochemical standard conditions.
A
298k, 101.3kPa, 1M concentration of all agents except:
- [H+]=10^-7
- Mg2+ = 1mM
17
Q
what is the equation linking free energy to reactant concentration
A
change in gibbs free energy = standard free enthalpy change + gas constant x temp(k) x in(K)
18
Q
what is equal to 0 when a reaction is at equilibium? why?
A
Gibbs free energy change, no work to be done
19
Q
what range of numbers must K be to produce a negative gibbs free energy change. what does this make the reaction?
A
above, spontaneous
20
Q
to be spontaneous, must the produce concentration be much MORE or much LESS than products
A
less
21
Q
what is the first method of making reactions favourable. what type of chemical driving does it employ
A
remove product at faster rate than reactant. kinetic
22
Q
what is the second method of making reactions favourable? what type of chemical driving does it employ?
A
adding reactant at a faster rate than consumption. kinetic
23
Q
what is the third method of making reactions favourable? what type of chemical driving does it employ?
A
mixing an unfavourable reaction with a highly favourable reaction that shares products and reactants. thermodynamically driven.
24
Q
A
25
what are the three components of ATP? give both the biomolecule type and specific name/ amount
sugar (ribose), base (adenine), phosphate (3)
26
what does a nucleotide have that a nucleoside doesnt have
3 phosphates
27
at which carbon on the sugar is the base linked to in ATP?
1
28
at which carbon on the sugar is phosphate linked to?
4
29
what are the bonds linking phosphates called (specifically ATP)
phosphoanhydride bonds
30
what type of molecules do phosphoanhydride bonds link
phasphate
31
is ADP or ATP less stable?
ATP
32
why is phosphate very stable
resonance
33
does the hydrolysis of ATP to ADP have a negative or positive gibbs free energy?
negative
34
what makes the triphosphate structure of ATP less stable than the diphosphate structure of ADP
adjacent negative charges on Oxygen substituents
35
what is the term given to a linear heteropolymer of amino acids
polypeptide
36
all amino acids are chiral except..
glycine
37
what is the name given to an optical molecule that causes light to rotate clockwise?
dextrotatory
38
what is the name given to an optical molecule that causes light to rotate anticlockwise?
levorotatory
39
what is the molecule that all D amino acids are derived from and recieve their name?
D-glyceraldehyde
40
what is the molecule that all L amino acids are derived from and recieve their name?
L-glyceraldehyde
41
when determining L/D isomerism in amino acids the hydrogen points _____ the page. what groups do the lettern CORN refer to
out, carboxyl, r group, amine
42
what type of amino acid is found when the hydrogen is pointing out of the page and the CORN denotation is clockwise?
L
43
what type of amino acid is found when the hydrogen is pointing into the page and the CORN denotation is clockwise
D
44
what type of amino acid is found when the hydrogen is pointing out of the page and the CORN denotation is anticlockwise
D
45
what type of amino acid is found when the hydrogen is pointing into the page and the CORN denotation is anticlockwise
L
46
what are the non polar, alipathic amino acids?
Glycine, Alanine, Valine, Proline, Leucine, Isoleucine
47
what are the aromatic amino acids?
phenylalanine, tyrosine, tryptophan
48
what are the polar, uncharged amino acids?
serine, threonine, asparagine, glutamine
49
what are the positively charged amino acids?
lysine, arginine, histidine
50
what are the negatively charged amino acids
aspartic acid, glutamic acid
51
what are the amino acids containing sulfer
cysteine, methionine
52
what is the term given to the pH where an ionisable group is half protonated and half deprotonated
pKa
53
what is the deprontonation formula in acids
HA -> H+ + A-
54
what is the charge of a protonated acid
neutral
55
what is the charge of a deprotonated acid
negative
56
what is the deprotonation formula in bases
HB+ -> B + H+
57
what is the charge of a protonated base
positive
58
what is the charge of a deprotonated base
neutral
59
what unique feature can carboxylic acids do with metal ions
chelate
60
what type of acids are glutamic acid and aspartic acid
carboxylic acid
61
how many methylene groups precede the amine cap in lysine
4
62
how many methylene groups precede the guanidinium cap in arginine?
3
63
how many methylene groups precede the imidazole ring in histidine?
1
64
what is the pKa of histidine? what is the charge in biological contexts?
7, half molecules + and half molecules neutral
65
what kind of derivatives are asparagine and glutamine from their carboxylic acid predecessors
amide
66
due to which substituent are serine and threonine both hydrogen donars and acceptors?
hydroxyl
67
why is benzene so stable?
resonance of double bonds causing delocalisation
68
what causes the flourescent and UV absorbant qualities of aromatic molecules?
altered e- excited state by conjugation
69
what is the term given to the law that determines absorbancy
beer lambert law
70
what is the beer lambert law equation
absorbance = extinction coefficient x concentration x path length
71
what are the spectral properties exhibited by aromatic compounds?
UV absorbance and fluorescence
72
following what process is a cysteine able to form disulfide bonds?
deprotonation
73
what kind of bonds are disulfide bonds
covalent
74
what are the two types of disulfide bonds?
intrachain, interchain
75
whta property of dilsulfide bonds makes cysteine identifiable in experiments
UB absorbance
76
by what reaction do two amino acids become linked
condensation polymerisation
77
which bond in an amino acid has partial double bond features due to resonance? which neighbouring substituent gives it these features?
peptide bond, oxygen on carbonyl
78
what is the term given to the phenomena where unfavourable, bulky, or charged interactions between atoms in molecules reduce the rate of a chemical reaction?
steric hinderance
79
why does an amino acid residue exist on a single plane (disregarding side chain)?
the partial double bond properties of the peptide linkage
80
why are cis amino acids more favourable than trans amino acids
steric hinerance between adjacenet side chains
81
why is the cis:trans ration of proline so small compared to other amino acids
the cyclical nature causes steric hinderance to adjacent side chain in both cis and trans forms
82
what is the term given to the angle of the peptide bond in a polypeptide
omega
83
what are the group of atoms called that define amino acid movement about a bond?
dihedral angles
84
what are the possible angles of the omega dihedral angle?
-180, 0, 180
85
what is the omega dihedral angle between 2 adjacent residues that are cis
0
86
what are the possible omega dihedral angles between two trans adjacent residues
-180, 180
87
which bond to you look along to determine the omega dihedral angle?
C-N
88
which bonds in a residue have free rotation?
Ca-N and C-Ca
89
what is the name of the dihedral angle along the C-Ca bond?
phi
90
what is the name of the dihedral angle along the Ca-N bond?
Psi
91
assuming all amino acids are trans, which dihedral acids determine rotation?
phi, psi
92
when determining phi and psi angles, what does a clockwise rotation refer to?
positive angle
93
when determining phi and psi angles, what does an anticlockwise rotation refer to?
negative angle
94
what is the name given to the dihedral angles surrounding the bonds of side chains
95
what are the four forces that make up protein folding
electrostatic, van der waals, hydrogen, hydrophobic
96
what is the name given to the folded, correct orientation of a protein
native
97
what is the name given to the unfolded orientation of a protein
non-native
98
what is the name given to a chemical that is used to unfold a protein and expose all its side chains
denaturant
99
what is the term given to the midpoint between a native and denatured protein
folding transition
100
in a folding transition, can a proteins (without domains) exist as an intermission between folded and unfolded?
no
101
what is the law that states if any part of protein (without multiple domains) folding is disrupted, the function and folding of the entire protein is disrupted. what does this cause?
the cooperative nature of protein folding, denaturation
102
who was the scientist that conducted the experiments expanding our understanding of protein denaturation and renaturation
christian anfinsen
103
in christian anfinsens experiments, which molecules were used to denature and renature proteins? include concentrations
8M urea, b-mercaptoethanol
104
in christian anfinsens experiments, what can be done to renature a protein that has been treated wrong? (there are two step)
add trace amounts of b-mercaptoethanol and air oxidise
105
in christian anfinsens experiments, what is the order of treatment used to ensure renaturation?
- add urea + mercaptoethanol,
- remove urea,
- remove mercaptoethanol
106
do christian anfinsens experiments show that folding directs bond formation of the other way round?
folding directs bond formation
107
do christian anfinsens experiments show that disulfide bonds reduce or increase the stability of a proteins folded state over unfolded state?
increase
108
what kind of bonds do urea molecules cleave in proteins?
disulfide bonds
109
what is the term given to an assisting molecule that helps avoid protein folding, particularly by binding to a side chain to prevent inappropriate interactions from forming
chaperone
110
what is the name of an environment with abundant biomolecular composition? why is this environment unfavourable to active chemical processes
molecular crowding, innapropriate reactions
111
what is the name of the chaperone produced at high excess in heat? what bond does it do with hydrophobic regions to prevent the forming of innapropriate interactions?
HSP70, hydrolysis
112
what are the two types of electrostatic forces
salt bridges, dipoles
113
what is the term and category given to an ionic interaction between oppositely charged groups (particulary in proteins)? is this reaction confined to a single atom pair of can it be distributed over several atoms?
salt bridge, electrostatic, distributed over several atoms
114
what is the term and category given to the interaction between two atoms with no net charge, but a partial charge produced by electron delocalisation due to resonance?
dipole, electrostatic
115
what is the term given to a non directional and non specific interaction that naturally forms between two atoms?
van der waals interaction
116
what is the term given to the interaction formed when two electronegative atoms compete for the same hydrogen?
hydrogen bond
117
in a hydrogen bond, what is the charge of the hydrogen bond donar and how does it obtain this charge?
negative, dipole
118
in a hydrogen bond, what is the charge of the hydrogen bond acceptor and how does it obtain this charge?
negative, full negative charge
119
what properties do hydrogen bonds have
electrostatic and covalent
120
what is the term given to the phenomena where the hydrophobic regions of a proteins are more stable when they exclude water molecules from their surface? what property facilitates this stability and how does it change when water is removed?
hydrophobic interactions, entropy, the entropy of the system increases
121
what is the name of the top left quadrant of a ramachandran plot
beta
122
what is on the x axis of a ramachandran plot?
phi angle
123
what is on the y axis of a ramachandran plot?
psi angle
124
why are there disallowed and highly unfavourable regions on a ramachandran plot?
steric crowding
125
what is the bottom left quadrant of the ramachandran plot called?
alpha
126
what is the top right quadrant of the ramachandran plot called? what amino acid mostly occupies it and why?
left handed turn, glycine, no steric hinderance allows positive phi
127
what is the bottom right quadrant of the ramachandran plot?
disallowed
128
what bond must all polar groups in a protein form
hydrogen bond
129
how many residues is one turn in an alpha helix?
3.6
130
how many degrees does a single residue occupy in an alpha helix
100
131
in terms of secondary bonding, what is the benefit of the alpha helix formation?
maximises hydrogen bonding
132
why are right handed alpha helices favourable to left handed alpha helices?
if all amino acids are L configuration, right handed has side chains projecting outward while left handed has side chains projecting inwards. steric hinderance reduces stability of left handed
133
what are the phi and psi angles in a perfect helix
phi: 57 psi: -47
134
what is the term given to the phenomena where the dipoles of individual hydrogen bonds add in an alpha helix
macrodipole
135
what are the three types of interactions between alpha helices and other secondary structures?
all a bundles, mixed ab, coiled coil
136
what is the diameter of the inner alpha helixwithout side chains. is this big enough to fit water molecules?
4-5 angstroms, no
137
what is the diameter of the alpha helix including side chains?
10-12 angstroms
138
what is the name of the phenomena that suggests that two rotations of an alpha helix is roughly seven residues. Meaning, by having an specific repeating pattern of hydrophobic and hydrophilic amino acids, a hydrophobic interface can be devised
heptad repeat
139
in a heptad repeat of an alpha helix, what is the alternating pattern of hydrophobic and hydrophilic residues?
1st and 4th hydrophobic
140
which amino acids enhance alpha helix stability? why?
alanine, leucine, small hydrophobic side chains that pack together well
141
why does proline greatly affect the stability of the alpha helix?
the amide of proline cannot be a hydrogen donor in hydrogen bonding due to its involvement with a cyclic side chain
142
why does glycine greatly affect the stability of an alpha helix?
lack of side chain does not contribute to bonding
143
what causes the hydrophobic and hydrophilic interface of a beta sheet?
alternating non polar and polar side chains faced alternating up and down.
144
what are the phi and psi angles of an optimal beta sheet?
phi: -130 psi: 130
145
why are antiparallel beta sheets more stable than parallel beta sheets?
antiparallel able to form colinear bonds. since parallel cannot, bond distance is longer, reducing stability
146
what is the name of the structure where the polypeptide direction of a beta sheet is reversed 180 degrees?
reverse turn
147
how many amino acids are involved in a reverse turn?
4
148
what is the name of the reverse turn where the carbonyl group of residue i+1 is facing into the page?
type 1
149
what is the name of the reverse turn where the carbonyl group of the reside i+1 is facing out of the page
type 2
150
why is glycine typically found in residue i+2 of a reverse turn?
no side chain = no steric hinderance with reside i+1 carbonyl
151
what are the regular secondary structures in proteins?
alpha helices, beta pleated sheets
152
what are the irregular structures in proteins?
loops, reverse turns, random coils
153
what features to regular secondary structures in proteins all share?
repeating phi and psi angles, repeating h bond polarity pattern
154
what is the term given to the overall spacial arrangement of amino acids into an unbranched polypeptide chain
tertiary structure
155
what are the types of tertiary bonding available to occur in a protein
hydrophobic, polar, disulfide bonds
156
what is the term given to a region of a protein that forms independent folding to the rest of the protein. what do these regions have contained in their own space?
domain, hydrophobic core
157
what is the term given to the arrangement of secondary structure elements (a, b, random coil) relative to eachother
fold
158
what is the aggregation of repeated domains called?
module
159
what is a protein of two polypeptides with identical order, number, and amino acid sequenece called?
homodimer
160
what is the term given to a grouping of two closely related yet non-identical polypeptides arranged in a quaternary structure?
dimer
161
what is the smallest unit of a repeated pattern in a quaternary protein called
protomer
