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molecular and cellular biomedicine (MCB) > module 1.1 > Flashcards

module 1.1 Flashcards

amino acids and protein structure

1
Q

what kind of reaction has a positive Gibbs free energy value?

A

spontaneous

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2
Q

what kind of reaction has a negative gibbs free energy vlue

A

xc

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3
Q

what is DELTA G

A

change in gibbs free energy

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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

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5
Q

what is the term given to a reaction that results in a decreased energy of a system

A

exergonic

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6
Q

what are the conditions of an exergonic reaction

A

favourable, spontaneous

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7
Q

what is the term given to a reaction that results in an increased energy of a system

A

endergonic

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8
Q

what are the conditions of an endergonic rection

A

unfavourable, non-spontaneous

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9
Q

what is the term given to a reaction where heat is released. what happens to the enthalpy value

A

exothermic, decreases

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10
Q

what is the term given to a reaction where heat is consumed? what happens to the enthalpy value

A

endothermic, increases

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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

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12
Q

the term given to the ratio of produce and reaction concentrations at equilibrium

A

thermodynamic equilibrium constant

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13
Q

what does Keq refer to

A

thermodynamic equilibrium constant

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14
Q

what does DELTA G’o refer to. which conditions does it rely on

A

standard free energy change, biochemical standard conditions

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15
Q

what are the requirements of bio and chem standard conditions?

A

298k, 101.3kPa, 1M concentration

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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

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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)

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18
Q

what is equal to 0 when a reaction is at equilibium? why?

A

Gibbs free energy change, no work to be done

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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

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20
Q

to be spontaneous, must the produce concentration be much MORE or much LESS than products

A

less

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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

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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

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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.

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24
Q
A
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25
Q

what are the three components of ATP? give both the biomolecule type and specific name/ amount

A

sugar (ribose), base (adenine), phosphate (3)

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26
Q

what does a nucleotide have that a nucleoside doesnt have

A

3 phosphates

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27
Q

at which carbon on the sugar is the base linked to in ATP?

A

1

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28
Q

at which carbon on the sugar is phosphate linked to?

A

4

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29
Q

what are the bonds linking phosphates called (specifically ATP)

A

phosphoanhydride bonds

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30
Q

what type of molecules do phosphoanhydride bonds link

A

phasphate

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31
Q

is ADP or ATP less stable?

A

ATP

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32
Q

why is phosphate very stable

A

resonance

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33
Q

does the hydrolysis of ATP to ADP have a negative or positive gibbs free energy?

A

negative

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34
Q

what makes the triphosphate structure of ATP less stable than the diphosphate structure of ADP

A

adjacent negative charges on Oxygen substituents

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35
Q

what is the term given to a linear heteropolymer of amino acids

A

polypeptide

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36
Q

all amino acids are chiral except..

A

glycine

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37
Q

what is the name given to an optical molecule that causes light to rotate clockwise?

A

dextrotatory

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38
Q

what is the name given to an optical molecule that causes light to rotate anticlockwise?

A

levorotatory

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39
Q

what is the molecule that all D amino acids are derived from and recieve their name?

A

D-glyceraldehyde

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40
Q

what is the molecule that all L amino acids are derived from and recieve their name?

A

L-glyceraldehyde

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41
Q

when determining L/D isomerism in amino acids the hydrogen points _____ the page. what groups do the lettern CORN refer to

A

out, carboxyl, r group, amine

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42
Q

what type of amino acid is found when the hydrogen is pointing out of the page and the CORN denotation is clockwise?

A

L

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43
Q

what type of amino acid is found when the hydrogen is pointing into the page and the CORN denotation is clockwise

A

D

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44
Q

what type of amino acid is found when the hydrogen is pointing out of the page and the CORN denotation is anticlockwise

A

D

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45
Q

what type of amino acid is found when the hydrogen is pointing into the page and the CORN denotation is anticlockwise

A

L

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46
Q

what are the non polar, alipathic amino acids?

A

Glycine, Alanine, Valine, Proline, Leucine, Isoleucine

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47
Q

what are the aromatic amino acids?

A

phenylalanine, tyrosine, tryptophan

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48
Q

what are the polar, uncharged amino acids?

A

serine, threonine, asparagine, glutamine

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49
Q

what are the positively charged amino acids?

A

lysine, arginine, histidine

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50
Q

what are the negatively charged amino acids

A

aspartic acid, glutamic acid

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51
Q

what are the amino acids containing sulfer

A

cysteine, methionine

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52
Q

what is the term given to the pH where an ionisable group is half protonated and half deprotonated

A

pKa

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53
Q

what is the deprontonation formula in acids

A

HA -> H+ + A-

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54
Q

what is the charge of a protonated acid

A

neutral

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55
Q

what is the charge of a deprotonated acid

A

negative

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56
Q

what is the deprotonation formula in bases

A

HB+ -> B + H+

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57
Q

what is the charge of a protonated base

A

positive

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58
Q

what is the charge of a deprotonated base

A

neutral

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59
Q

what unique feature can carboxylic acids do with metal ions

A

chelate

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60
Q

what type of acids are glutamic acid and aspartic acid

A

carboxylic acid

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61
Q

how many methylene groups precede the amine cap in lysine

A

4

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62
Q

how many methylene groups precede the guanidinium cap in arginine?

A

3

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63
Q

how many methylene groups precede the imidazole ring in histidine?

A

1

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64
Q

what is the pKa of histidine? what is the charge in biological contexts?

A

7, half molecules + and half molecules neutral

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65
Q

what kind of derivatives are asparagine and glutamine from their carboxylic acid predecessors

A

amide

66
Q

due to which substituent are serine and threonine both hydrogen donars and acceptors?

A

hydroxyl

67
Q

why is benzene so stable?

A

resonance of double bonds causing delocalisation

68
Q

what causes the flourescent and UV absorbant qualities of aromatic molecules?

A

altered e- excited state by conjugation

69
Q

what is the term given to the law that determines absorbancy

A

beer lambert law

70
Q

what is the beer lambert law equation

A

absorbance = extinction coefficient x concentration x path length

71
Q

what are the spectral properties exhibited by aromatic compounds?

A

UV absorbance and fluorescence

72
Q

following what process is a cysteine able to form disulfide bonds?

A

deprotonation

73
Q

what kind of bonds are disulfide bonds

A

covalent

74
Q

what are the two types of disulfide bonds?

A

intrachain, interchain

75
Q

whta property of dilsulfide bonds makes cysteine identifiable in experiments

A

UB absorbance

76
Q

by what reaction do two amino acids become linked

A

condensation polymerisation

77
Q

which bond in an amino acid has partial double bond features due to resonance? which neighbouring substituent gives it these features?

A

peptide bond, oxygen on carbonyl

78
Q

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?

A

steric hinderance

79
Q

why does an amino acid residue exist on a single plane (disregarding side chain)?

A

the partial double bond properties of the peptide linkage

80
Q

why are cis amino acids more favourable than trans amino acids

A

steric hinerance between adjacenet side chains

81
Q

why is the cis:trans ration of proline so small compared to other amino acids

A

the cyclical nature causes steric hinderance to adjacent side chain in both cis and trans forms

82
Q

what is the term given to the angle of the peptide bond in a polypeptide

A

omega

83
Q

what are the group of atoms called that define amino acid movement about a bond?

A

dihedral angles

84
Q

what are the possible angles of the omega dihedral angle?

A

-180, 0, 180

85
Q

what is the omega dihedral angle between 2 adjacent residues that are cis

A

0

86
Q

what are the possible omega dihedral angles between two trans adjacent residues

A

-180, 180

87
Q

which bond to you look along to determine the omega dihedral angle?

A

C-N

88
Q

which bonds in a residue have free rotation?

A

Ca-N and C-Ca

89
Q

what is the name of the dihedral angle along the C-Ca bond?

A

phi

90
Q

what is the name of the dihedral angle along the Ca-N bond?

A

Psi

91
Q

assuming all amino acids are trans, which dihedral acids determine rotation?

A

phi, psi

92
Q

when determining phi and psi angles, what does a clockwise rotation refer to?

A

positive angle

93
Q

when determining phi and psi angles, what does an anticlockwise rotation refer to?

A

negative angle

94
Q

what is the name given to the dihedral angles surrounding the bonds of side chains

A
95
Q

what are the four forces that make up protein folding

A

electrostatic, van der waals, hydrogen, hydrophobic

96
Q

what is the name given to the folded, correct orientation of a protein

A

native

97
Q

what is the name given to the unfolded orientation of a protein

A

non-native

98
Q

what is the name given to a chemical that is used to unfold a protein and expose all its side chains

A

denaturant

99
Q

what is the term given to the midpoint between a native and denatured protein

A

folding transition

100
Q

in a folding transition, can a proteins (without domains) exist as an intermission between folded and unfolded?

A

no

101
Q

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?

A

the cooperative nature of protein folding, denaturation

102
Q

who was the scientist that conducted the experiments expanding our understanding of protein denaturation and renaturation

A

christian anfinsen

103
Q

in christian anfinsens experiments, which molecules were used to denature and renature proteins? include concentrations

A

8M urea, b-mercaptoethanol

104
Q

in christian anfinsens experiments, what can be done to renature a protein that has been treated wrong? (there are two step)

A

add trace amounts of b-mercaptoethanol and air oxidise

105
Q

in christian anfinsens experiments, what is the order of treatment used to ensure renaturation?

A
  • add urea + mercaptoethanol,
  • remove urea,
  • remove mercaptoethanol
106
Q

do christian anfinsens experiments show that folding directs bond formation of the other way round?

A

folding directs bond formation

107
Q

do christian anfinsens experiments show that disulfide bonds reduce or increase the stability of a proteins folded state over unfolded state?

A

increase

108
Q

what kind of bonds do urea molecules cleave in proteins?

A

disulfide bonds

109
Q

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

A

chaperone

110
Q

what is the name of an environment with abundant biomolecular composition? why is this environment unfavourable to active chemical processes

A

molecular crowding, innapropriate reactions

111
Q

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?

A

HSP70, hydrolysis

112
Q

what are the two types of electrostatic forces

A

salt bridges, dipoles

113
Q

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?

A

salt bridge, electrostatic, distributed over several atoms

114
Q

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?

A

dipole, electrostatic

115
Q

what is the term given to a non directional and non specific interaction that naturally forms between two atoms?

A

van der waals interaction

116
Q

what is the term given to the interaction formed when two electronegative atoms compete for the same hydrogen?

A

hydrogen bond

117
Q

in a hydrogen bond, what is the charge of the hydrogen bond donar and how does it obtain this charge?

A

negative, dipole

118
Q

in a hydrogen bond, what is the charge of the hydrogen bond acceptor and how does it obtain this charge?

A

negative, full negative charge

119
Q

what properties do hydrogen bonds have

A

electrostatic and covalent

120
Q

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?

A

hydrophobic interactions, entropy, the entropy of the system increases

121
Q

what is the name of the top left quadrant of a ramachandran plot

A

beta

122
Q

what is on the x axis of a ramachandran plot?

A

phi angle

123
Q

what is on the y axis of a ramachandran plot?

A

psi angle

124
Q

why are there disallowed and highly unfavourable regions on a ramachandran plot?

A

steric crowding

125
Q

what is the bottom left quadrant of the ramachandran plot called?

A

alpha

126
Q

what is the top right quadrant of the ramachandran plot called? what amino acid mostly occupies it and why?

A

left handed turn, glycine, no steric hinderance allows positive phi

127
Q

what is the bottom right quadrant of the ramachandran plot?

A

disallowed

128
Q

what bond must all polar groups in a protein form

A

hydrogen bond

129
Q

how many residues is one turn in an alpha helix?

A

3.6

130
Q

how many degrees does a single residue occupy in an alpha helix

A

100

131
Q

in terms of secondary bonding, what is the benefit of the alpha helix formation?

A

maximises hydrogen bonding

132
Q

why are right handed alpha helices favourable to left handed alpha helices?

A

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
Q

what are the phi and psi angles in a perfect helix

A

phi: 57 psi: -47

134
Q

what is the term given to the phenomena where the dipoles of individual hydrogen bonds add in an alpha helix

A

macrodipole

135
Q

what are the three types of interactions between alpha helices and other secondary structures?

A

all a bundles, mixed ab, coiled coil

136
Q

what is the diameter of the inner alpha helixwithout side chains. is this big enough to fit water molecules?

A

4-5 angstroms, no

137
Q

what is the diameter of the alpha helix including side chains?

A

10-12 angstroms

138
Q

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

A

heptad repeat

139
Q

in a heptad repeat of an alpha helix, what is the alternating pattern of hydrophobic and hydrophilic residues?

A

1st and 4th hydrophobic

140
Q

which amino acids enhance alpha helix stability? why?

A

alanine, leucine, small hydrophobic side chains that pack together well

141
Q

why does proline greatly affect the stability of the alpha helix?

A

the amide of proline cannot be a hydrogen donor in hydrogen bonding due to its involvement with a cyclic side chain

142
Q

why does glycine greatly affect the stability of an alpha helix?

A

lack of side chain does not contribute to bonding

143
Q

what causes the hydrophobic and hydrophilic interface of a beta sheet?

A

alternating non polar and polar side chains faced alternating up and down.

144
Q

what are the phi and psi angles of an optimal beta sheet?

A

phi: -130 psi: 130

145
Q

why are antiparallel beta sheets more stable than parallel beta sheets?

A

antiparallel able to form colinear bonds. since parallel cannot, bond distance is longer, reducing stability

146
Q

what is the name of the structure where the polypeptide direction of a beta sheet is reversed 180 degrees?

A

reverse turn

147
Q

how many amino acids are involved in a reverse turn?

A

4

148
Q

what is the name of the reverse turn where the carbonyl group of residue i+1 is facing into the page?

A

type 1

149
Q

what is the name of the reverse turn where the carbonyl group of the reside i+1 is facing out of the page

A

type 2

150
Q

why is glycine typically found in residue i+2 of a reverse turn?

A

no side chain = no steric hinderance with reside i+1 carbonyl

151
Q

what are the regular secondary structures in proteins?

A

alpha helices, beta pleated sheets

152
Q

what are the irregular structures in proteins?

A

loops, reverse turns, random coils

153
Q

what features to regular secondary structures in proteins all share?

A

repeating phi and psi angles, repeating h bond polarity pattern

154
Q

what is the term given to the overall spacial arrangement of amino acids into an unbranched polypeptide chain

A

tertiary structure

155
Q

what are the types of tertiary bonding available to occur in a protein

A

hydrophobic, polar, disulfide bonds

156
Q

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?

A

domain, hydrophobic core

157
Q

what is the term given to the arrangement of secondary structure elements (a, b, random coil) relative to eachother

A

fold

158
Q

what is the aggregation of repeated domains called?

A

module

159
Q

what is a protein of two polypeptides with identical order, number, and amino acid sequenece called?

A

homodimer

160
Q

what is the term given to a grouping of two closely related yet non-identical polypeptides arranged in a quaternary structure?

A

dimer

161
Q

what is the smallest unit of a repeated pattern in a quaternary protein called

A

protomer

molecular and cellular biomedicine (MCB) (4 decks)

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