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BS209: Molecular Biology > Chapter 2: Biological Molecules (Nucleic Acids & Proteins) > Flashcards

Chapter 2: Biological Molecules (Nucleic Acids & Proteins) Flashcards

1
Q

an atom is chemically reactive when ()

A

the shell is not full

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2
Q

an atom is most stable and chemically unreactive when ()

A

the outermost shell is filled

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3
Q

sharing of electrons forms ()

A

covalent bonds

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4
Q

when a double bond forms, rotation of atoms around the bond is (1), so other bonds are (2)

A
  1. restricted
  2. in a single plane
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5
Q

covalent bond that forms between 2 amino acids

A

peptide bonds

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6
Q

both the C-O and C-N bonds in peptide bonds have () character

A

partial double bond

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7
Q

radius of an imaginary hard sphere representing the distance of the closest approach for another atom

A

van der Waals radius

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8
Q

unequal sharing of electrons within a covalent bond

A

polar covalent bond

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9
Q

() bonds do not have any charge separation

A

non-polar bonds

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10
Q

separation of charge in polar bonds is called a ()

A

dipole

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11
Q

tendency of non-polar groups to associate with one another, driven by (), is a big contributor to the behavior of biomolecules, including protein structure

A

hydrophobic interactions

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12
Q

attraction between fully charged atoms

A

ionic interactions

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13
Q

ion product of water

A

10^-14 M

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14
Q

molecules that release H+ into solution are (1), those that accept H+ are (2)

A
  1. acids
  2. bases
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15
Q

weaker () can be formed and broken, allowing flexibility and dynamics in biomolecular structure

A

non-covalent bonds

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16
Q

non-covalent ionic interactions between charged atoms

A

salt bridges

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17
Q

non-covalent interactions between polar atoms with partial charges

A

hydrogen bonds

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18
Q

weak covalent interactions between atoms at a certain distance

A

van der Waals interactions

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19
Q

in salt bridges, the attraction between charged atoms is a function of the () only

A

distance between them

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20
Q

salt bridges in proteins are bonds between oppositely charged amino acid residues that are ()

A

sufficiently close to each other

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21
Q

the salt bridge most often arises from the anionic carboxylate of either (1) and the cationic ammonium from (2) or the guanidinium of (3)

A
  1. aspartic acid or glutamic acid
  2. lysine
  3. arginine
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22
Q

distance between the amino acid residues participating in the salt bridge should be less than ()

A

4 angstrom

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23
Q

hydrogen bond interactions are due to the ()

A

partial charge resulting from a polar covalent bond

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24
Q

hydrogen bonding results from the attractive force between a (1) and (2)

A
  1. hydrogen atom covalently bonded to a very electronegative atom (e.g. F, O, N)
  2. another very electronegative atom
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25
Q

the energy of a hydrogen bond is greatest when the 3 atoms involved are (

A

in a straight line

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26
Q

strength of a hydrogen bond interaction weakens with ()

A

increasing angles

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27
Q

the dependence of hydrogen bond strength on angle ensures () between hydrogen bond donor and acceptor

A

specificity

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28
Q

how do hydrogen bonds impose a high degree of specificity on the interactions between 2 binding partners

A

hydrogen bond donors and acceptors must line up at the binding interface s.t. the hydrogen bonds that form have the appropriate geometry and distance from one another

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29
Q

the van der Waals interaction arises when the close approach of 2 atoms causes each atom to induce ()

A

transient dipoles

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30
Q

() around atoms constantly create transient dipoles

A

electron movements

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31
Q

the aqueous environment affects:

A
  1. strength of the interactions
  2. types of interactions that occur
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32
Q

hydrophobic interactions drive ()

A

molecular folding

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33
Q

attractive energy of salt bridges is () by surrounding water molecules

A

reduced

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34
Q

ionic bonds are weakened by the () which interact with the charges

A

polar water molecules

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35
Q

preferential binding between certain molecules relative to others is directed by (1), a concept generally referred to as (2)

A
  1. relative binding strength
  2. specificity
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36
Q

strength of molecular interactions comes from the () formed between them

A

non-covalent interactions

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37
Q

it’s not the strength of a specific interaction, but rather the () that governs specificity

A

comparative strength of binding to the correct binding partner vs the incorrect partner

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38
Q

nucleotides comprise:

A
  1. base
  2. sugar
  3. phosphate
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39
Q

examples of additional biological functions of nucleotides

A

energy storage (in the form of ATP) and molecular transport

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40
Q

present in ribose but absent in deoxyribose

A

ribose has an additional 2’ oxygen atom

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41
Q

2 types of bases in RNA and DNA

A
  1. purines (adenine and guanine)
  2. pyrimidines (thymine, uracil, cytosine)
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42
Q

in simple terms, pKa is a number that shows how () an acid is

A

weak or strong

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43
Q

in DNA/RNA: base + sugar = ()

A

nucleoside

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44
Q

in nucleosides, each base is joined to a sugar by a ()

A

glycosidic bond

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45
Q

glycosidic bonds form between:

A
  1. C1’ of the sugar
  2. N1 of pyrimidine
  3. N9 of purine
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46
Q

in RNA/DNA: nucleoside + () = nucleotide

A

phosphate

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47
Q

phosphate groups are linked to the 3’ or 5’-OH of the sugar by ()

A

phosphate ester linkage

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48
Q

nucleotides are joined by ()

A

phosphodiester bonds

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49
Q

phosphodiester bonds form between the (1) of one sugar and the (2) of the next sugar

A
  1. 3’-OH
  2. phosphate attached to the 5’-OH
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50
Q

nucleic acid strands are directional and have distinct ends:

A

5’ end = 5’ phosphate
3’ end = 3’ hydroxyl

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51
Q

by convention, nucleic acid sequences are written in the () direction

A

5’ to 3’

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52
Q

in nucleic acids, the sugars and phosphates form a repeating unit called the ()

A

sugar-phosphate backbone

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53
Q

molecules in which a proton has migrated to a different place

A

tautomer

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54
Q

examples of tautomer pairs

A
  1. amino-imino tautomer
  2. keto-enol tautomer
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55
Q

the capacity to form (1) is a frequent source of errors during DNA replication, and can provide (2)

A
  1. alternative tautomers
  2. genetic variation
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56
Q

examples of nucleotide derivatives and their important role in cellular functions: carrier of chemical groups

A

SAM (s-adenosyl methionine)

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57
Q

examples of nucleotide derivatives and their important role in cellular functions: enzyme cofactors

A

NAD, FAD

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58
Q

examples of nucleotide derivatives and their important role in cellular functions: signal transduction

A

cAMP

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59
Q

in complementary base pairing, A pairs with T via (1), while C pairs with G via (2)

A
  1. 2 H-bonds
  2. 3 H-bonds
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60
Q

in DNA, the two strands are ()

A

antiparallel

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61
Q

most energetically favorable formation of double-stranded DNA

A

right-handed double helix

62
Q

the () arrangement is very energetically favorable, and in important for the stability of DNA

A

base-stacking

63
Q

predominant configuration of cellular DNA

A

B-DNA

64
Q

grooves in DNA arise from the ()

A

asymmetrical attachment of bases to the backbone sugars

65
Q

the structural features of the DNA helix, in particular, the () govern the way in which proteins can interact with DNA

A

atoms of the bases that are exposed in the grooves

66
Q

other conformations of DNA

A
  1. A-DNA
  2. Z-DNA
67
Q

regions rich in A-T pairing tend to be more ()

A

bendable

68
Q

DNA that is under torsional strain and thus twists in on itself to alleviate the strain

A

supercoiled DNA

69
Q

linear DNA can also be supercoiled if ()

A

the ends are immobilized and not free to rotate to release superhelical tension

70
Q

number of times one strand of DNA wraps around the other

A

linking number (Lk)

71
Q

Lk cannot change in (1) or (2)

A
  1. closed circular DNA
  2. constrained DNA
72
Q

the only way to change Lk is to introduce a ()

A

DNA strand break

73
Q

number of turns in a given fragment of DNA

A

Twist (Tw)

74
Q

if Tw > 0, DNA is a () helix

A

right-handed

75
Q

if Tw < 0, DNA is a () helix

A

left-handed

76
Q

number of superhelical turns

A

Writhe (Wr)

77
Q

if Wr > 0, supercoiled DNA is ()

A

positively coiled (left-handed turns)

78
Q

if Wr < 0, supercoiled DNA is ()

A

negatively coiled (right-handed turns)

79
Q

to maintain the Lk value, any change in Tw must be ()

A

balanced by an opposite change in the value of Wr

80
Q

negative supercoiling can occur when

A

right-handed DNA is underwound

81
Q

positive supercoiling can occur when:

A

right-handed DNA is overwound

82
Q

supercoiling can adopt either of 2 forms

A
  1. toroidal
  2. interwound
83
Q

why is negative supercoiling important in DNA

A

negative supercoiling balances the torsional strain of the DNA while it is being unwound for cellular processes

84
Q

introduce or remove supercoils from DNA in an energy-requiring process by temporarily breaking DNA and twisting it

A

topoisomerases

85
Q

(1) and (2) allow RNA to adopt diverse structures

A
  1. 2’ OH (hydroxyl) on ribose
  2. distinct chemical structure of uracil
86
Q

many RNA molecules (especially directly functional RNA rather than mRNA) require () to become fully functional

A

chemical modification after synthesis

87
Q

the position and nature of () in particular RNA are often conserved among species reflecting their crucial functional roles

A

nucleotide modifications

88
Q

chemical modifications of RNA are usually (1) and are (2)

A
  1. irreversible
  2. not regulatory
89
Q

the 2’ OH in RNA facilitates are reaction that ()

A

breaks phosphodiester bonds

90
Q

the 2’ OH in RNA means that RNA favors the () conformation

A

A-type helix

91
Q

the sugar part of nucleic acid molecules has buckled conformations, known as ()

A

sugar pucker

92
Q

in ribose, a formation called () is found, and favors the A-type helix

A

C3’ endo

93
Q

in deoxyribose, a formation called () is found, and favors the B-type helix

A

C2’ endo

94
Q

the C2’ OH also allows RNA to form () more extensively than DNA

A

hydrogen bonds

95
Q

structure of RNA: the RNA sequence, in 5’ to 3’ direction

A

primary structure

96
Q

structure of RNA: short double-helical regions

A

secondary structure

97
Q

structure of RNA: arrangement of the double helices and single-stranded regions in the final configuration of the RNA

A

tertiary structure

98
Q

the fundamental structural unit of folded RNA is the ()

A

RNA double helix

99
Q

if complementary sequences are close in primary RNA sequence, a () forms

A

hairpin structure

100
Q

in an RNA hairpin structure, the double-stranded part is the (1), and the unpaired section is the (2)

A
  1. stem
  2. loop
101
Q

what happens when complementary sequences are far in primary RNA sequence

A

RNA can still form double-helical structures, but lack hairpin structure

102
Q

the non-Watson-Crick base pairs in RNA molecules often feature ()

A

chemically modified bases (e.g. methylation)

103
Q

base pairing with modified bases in RNA can introduce ()

A

structural distortion

104
Q

() RNA structure is formed when short double-stranded helices interact with each other and with single-stranded regions

A

tertiary

105
Q

general features of tertiary RNA structure

A
  1. coaxial stacking
  2. hydrogen bonding interactions (particularly involving the 2’ OH)
106
Q

two Watson-Crick bases interacting with a third via an additional H-bond

A

base triple interaction

107
Q

() often stabilize a folded RNA structure

A

hydrogen bonding interactions

108
Q

an adenosine inserts into the minor groove of a double-helical region, and is stabilized by H-bonds (H bonds with 1 or 2 2’ OH groups and the bases)

A

A-minor motif

109
Q

main barrier to the folding of RNA into a compact 3D structure

A

electrostatic repulsion due to the high density of negative charge with the phosphodiester backbone

110
Q

RNA strategy to overcome barrier to folding into 3D structure

A

RNA molecules bind large numbers of cations to counteract electrostatic repulsion

111
Q

() is the comparison of characteristics among species

A

phylogenetic analysis

112
Q

phylogenetic analysis helps identify () as these are more likely to be conserved during evolution

A

true pairing regions

113
Q

differences that occur among species, yet conserve interactions, are known as (); sequences may change but base-pairing is conserved

A

covariations

114
Q

modern-day evidence to putative “RNA world”

A
  1. RNAs play diverse roles
  2. composition of many enzyme factors
  3. ability of RNA to fold in vitro and discovery of RNA switches
115
Q

() groups on cysteine can form covalent bonds with one another to make disulfide bridges

A

sulfhydryl (-SH) groups

116
Q

stereoisomer configuration often found in naturally occurring proteins

A

L-amino acids

117
Q

the pKa of () is close to the neutral pH of a cell, so it can act as H+ donor or acceptor during biological interactions

A

histidine

118
Q

bond between 2 amino acids

A

peptide bond

119
Q

a peptide bond between 2 amino acids results from a () between the carboxyl group of one amino acid and the amino group of another amino acid

A

condensation reaction

120
Q

distinct ends of proteins

A
  1. N-terminus
  2. C-terminus
121
Q

in proteins, a repeating series of C and N atoms forms the () with side chains protruding

A

peptide backbone

122
Q

peptide bonds are planar due to ()

A

resonance

123
Q

the () in peptide bonds prevents free rotation about the bonds, locking the atoms into a planar conformation

A

delocalization of electrons (between O, C, and N atoms)

124
Q

other parts of the polypeptide that can still rotate

A
  1. N-Calpha bond (rotation angle: phi)
  2. C-Calpha bond (rotation angle: psi)
125
Q

some angle combinations of phi and psi do not occur because ()

A

they cause collisions of side chains or the polypeptide backbone

126
Q

a () depicts the allowable combinations of phi and psi angles; depends on the amino acid residues of the polypeptide

A

Ramachandran plot

127
Q

due to the () side chain being small, it can tolerate many more angle combinations

A

glycine

128
Q

protein folding is driven by () of the atoms in the polypeptide

A

non-covalent interactions

129
Q

protein structure: sequence of amino acids in a protein chain

A

primary

130
Q

protein structure: regular and spatial organization of neighboring segments

A

secondary

131
Q

secondary protein structure is stabilized by ()

A

hydrogen bonds

132
Q

protein structure: final overall 3D shape of a protein molecule

A

tertiary

133
Q

tertiary protein structure depends on the interactions of amino side chains that are ()

A

far apart along the same backbone

134
Q

protein structure: overall structure of proteins composed of more than 1 polypeptide chain

A

quaternary

135
Q

common secondary protein structures are:

A
  1. alpha helices
  2. beta sheets
136
Q

protein folding forms structures that have cores filled with non-polar side chains that form ()

A

van der Waals interactions

137
Q

while protein folding occurs spontaneously in an aqueous environment, some proteins require the assistance of ()

A

chaperones

138
Q

comparing amino acid sequences: proteins with () the same amino acids are likely to have almost identical structures

A

50%

139
Q

() is a strong indicator of genes that have similar functions

A

conservation of important amino acids

140
Q

the arrangement of secondary structural elements in a protein

A

protein fold

141
Q

two proteins may have identical folds (even if they don’t appear to have identical structures) if they have essentially the same ()

A

secondary structural elements

142
Q

changes in the amino acid sequence that do not () may be tolerated

A

alter the protein’s fold

143
Q

pro of protein mutations: as a protein collects more mutations (also insertions or deletions), the protein may ()

A

evolve a new, useful function

144
Q

happens when proteins of different functions derive from a single ancestral protein

A

divergent evolution

145
Q

happens when proteins with similar functions evolve separately, from different ancestors

A

convergent evolution

146
Q

structurally distinct regions in polypeptides; is able to fold on its own

A

domains

147
Q

polypeptide domains can be thought of as “()”
that make up the whole protein

A

modules

148
Q

the pattern of functional groups exposed in the (1) of DNA is unique, while that of the (2) is less variable

A
  1. major groove
  2. minor groove
149
Q

DNA binding proteins recognize a specific base pair sequence by forming a () with the exposed groups of the DNA’s major group

A

chemically complementary set of non-covalent interactions

150
Q

to allow DNA-binding proteins to interact with the highly negatively charged sugar-phosphate backbone, residues facing the DNA helix are often:

A
  1. positively charged (e.g. lysine and arginine)
  2. have hydrogen bond donors, -OH groups (e.g. serine and tyrosine)
151
Q

proteins also interact extensively with RNAs via ()

A

specific RNA-binding domains

BS209: Molecular Biology (8 decks)

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