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biochem 200 > midterm > Flashcards

midterm Flashcards

1
Q

what are the 4 classes of biomolecules?

A

amino acids, carbohydrates, nucleotides, lipids

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2
Q

what does the spacefilling model do?

A

gives idea about the shape, but loses information about connectivity

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3
Q

what do amino acids make and with what bond?

A

proteins with peptide bonds

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4
Q

what do nucleotides make and with what bond?

A

nucleic acids with phosphodiester bonds

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5
Q

what do monosaccharides make and with what bond?

A

polysaccharides with glycosidic (ether) bonds

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6
Q

what is the bond angle for water

A

104.5

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7
Q

structural difference between water and ice?

A

ice is a regular lattice of H bonds, water is a fluctuating H bond structure

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8
Q

approximately how many hydrogen bonds per water molecule?

A

3

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9
Q

what are the 3 types of electrostatic forces

A

ionic interactions, hydrogen bonds, van der waals forces

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10
Q

what are hydrophobic effects determined by?

A

the solvent

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11
Q

what are the 2 types of van der waals interactions?

A

dipole-dipole, london dispersion

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12
Q

dipole dipole interactions

A

between two polar non charged groups, weaker than h bonds

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13
Q

london dispersion interactions

A

b/w non polar molecules, weaker than dipole-dipole

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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.

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15
Q

generalized structure of amino acids

A

amino group, carboxyl group, variable side chain

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16
Q

what is the ratio of CHO in carbohydrates

A

1:2:1

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17
Q

generalized structure of nucleotides

A

carbohydrate, nitrogen containing base, phosphate group

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18
Q

what is a key feature in lipids?

A

presence of long, hydrophobic fatty acid chains

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19
Q

what are nucleotides used for?

A

incorporations into nucleic acids, and used as high energy molecules (NTP’S)

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20
Q

what is a nucleoside?

A

nitrogen containing base and a sugar. differentiated by the absence of a phosphate

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21
Q

what does a hydrogen bond acceptor have?

A

lone pairs

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22
Q

what does a hydrogen bond donator have?

A

a proton

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23
Q

what hydroxyl is DNA missing

A

2’ hydroxyl

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24
Q

how is a nucleoside formed?

A

purines and pyrimidine bases are linked to a 5 carbon sugar

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25
Q

what is the linkage of a pyrimidine in a nucleoside or nucleotide?

A

n1 to c1

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26
Q

what is the linkage of a purine in a nucleoside or nucleotide?

A

n9 to c1

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27
Q

what does the lack of c2’ OH do in DNA?

A

reduces the amount of hydrogen bonds

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28
Q

when naming nucleosides, what do purines end with?

A

-ine to -osine

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29
Q

when naming nucleosides, what do pyrimidines end with?

A

-idine

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30
Q

which bases are pyrimidines?

A

U, T, C

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31
Q

which bases are purines?

A

A, G

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32
Q

how are nucleic acids formed?

A

polymers of nucleotides linked by 3’-5’ phosphodiester bonds

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33
Q

by convention, which way are nucleotide sequences written?

A

5’ to 3’

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34
Q

what is the backbone of nucleic acids?

A

the sugar and the phosphate. the nucleic acids are not considered part of the backbone

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35
Q

examples of mononucleotides

A

ATP, ADP, FMN

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36
Q

does hydrolysis of phosphodiester bonds happen in DNA? why or why not?

A

it doesnt happen in DNA because there is no 2’ OH which doesnt allow for a intermediate linkage

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37
Q

in what conditions does hydrolysis of phosphodiester bonds happen? what does this mean about RNA and DNA?

A

high ph. makes DNA more stable in basic conditions, and spontaneous alkaline hydrolysis of RNA

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38
Q

spontaneous deamination

A

spontaneous reaction that converts C to U

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39
Q

sugar phosphate backbone is polar or nonpolar?

A

polar

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40
Q

what are the properties of bases?

A

heterocyclic, aromatic, basically planar (slightly pucker in purine bases), poorly soluble in water, hydrophobic

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41
Q

how do you measure the purity of DNA?

A

A260/ A280

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42
Q

what is the A 260/ A 280 for pure dna?

A

1.95

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43
Q

what is A280?

A

protein absorption maximum, dna absorption is decreased by approximately 50% at 280

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44
Q

what happens when dna is contaminated with protein?

A

the ratio of A260/A280 will go down

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45
Q

what is A260 used for? what is the relationship?

A

to measure the concentration of nucleic acids in solution. linear relationship

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46
Q

what is the primary structure of DNA

A

sequence of nucleotide residues

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47
Q

what is the secondary structure of DNA

A

3d shape

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48
Q

how is a double helix formed?

A

hydrogen bonds between the bases

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49
Q

what did erwin chargaff do?

A

base composition varies from organism to organism, helped watson and crick deduce the double helix sturcutre

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50
Q

what happens to hydrogen bonds in solution?

A

when they break, they can form new interactions with water. isolation from solvent strengthens the H bond interactions

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51
Q

what is base stacking and what does it involve and do?

A

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

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52
Q

major groove

A

wide enough to accomadate protein-DNA interactions

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53
Q

what is the core in b-DNA

A

hydrophobic core

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54
Q

what is the exterior in b-DNA

A

polar exterior

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55
Q

are the bases surrounded or excluded from water? why?

A

bases are largely excluded from water, this stabilizes the hydrogen bonds

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56
Q

which parts of b-DNA are exposed to water?

A

ribose/deoxyribose and phosphates

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57
Q

how many bp per turn in b-DNA?

A

10

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58
Q

what is chargaff’s rule?

A

a+g=c+t

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59
Q

what does denaturation disrupt?

A

non-covalent forces. effects base stacking and hydrogen bonding

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60
Q

what does denaturation cause a change in?

A

increase in absorption at 260nm as strands separate

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61
Q

what is tm and how does it vary?

A

tm is the midpoint of melting of DNA, varies by base composition. also depends on solution

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62
Q

what kind of process is DNA melting and why?

A

cooperative process, once it beings its easy to continue

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63
Q

single stranded dna has higher or lower absorbance at 260 compared to ds?

A

higher absorbance

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64
Q

what does ss dna have?

A

hyperchromicity, relatively high absorbance (dna has hypochromocity)

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65
Q

renaturation

A

reformation of dsDNA so it regains its native conformation

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66
Q

what does a base pair of a higher GC concentration mean? why?

A

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

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67
Q

what is the relationship between GC and Tm

A

linear relationship

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68
Q

what portion of DNA denatures first?

A

those rich in AT regions. become nucleation sites for strand separation

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69
Q

how does changing pH effect Tm

A

affects protonation state of DNA

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70
Q

describe how changing salt concentrations effects Tm

A

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

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71
Q

how does hybridization effect Tm?

A

the better the match between the two strands, the higher the Tm

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72
Q

how is RNA stabilized?

A

base stacking and h bonds

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73
Q

what is different about RNA vs DNA in terms of their base pairing

A

RNA has intrastand base pairing, DNA has interstrand base pairing

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74
Q

what is a wobble pair and where is it found

A

in RNA, when a G binds to a U. not a watson and crick bond

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75
Q

what kind of forces stabilize RNA secondary structure?

A

the same as DNA. includes hydrogen bonding and base stacking

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76
Q

is rna single stranded or double?

A

can be a mixture of both

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77
Q

what is the 260/280 ration in RNA

A

2.1

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78
Q

What is B-DNA?

A

regular dna

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79
Q

can DNA and complementary RNA form double stranded helix?

A

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

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80
Q

what is different about the melting curve for rna?

A

RNA goes from partially ss to fully ss, while dna goes from fully ds to fully ss

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81
Q

where is it the essence of a protein’s function?

A

its interactions with other molecules

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82
Q

what is a protein’s function determined by?

A

its structure

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83
Q

what is a zwitterion?

A

overall neutral ion with both positive and negative charges

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84
Q

what is included in a general amino acid?

A

amino group, carboxylate group, variable side chain, alpha carbon

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85
Q

what happens to the value of ka as dissociation is favored?

A

value of ka gets larger

86
Q

what happens when the ph is smaller than the pka

A

[acid] > [base]. protons are added, shift to acid

87
Q

ph > pka

A

[base] > [acid]. protons are removed. shifts to base.

88
Q

what is the pka of the carboxylic acid

A

2

89
Q

what is the pka of the amino group

A

9.5

90
Q

are amino acids chiral? what does this mean?

A

they are chiral, their mirror images cant be superimposed

91
Q

how are the common 20 amino acids classified?

A

by the overall chemical properties of their side chains

92
Q

what 3 groups are the side chains grouped in?

A

nonpolar (hydrophobic), polar, charged

93
Q

what amino group has a secondary amino group and what is it referred to as?

A

proline (pro), imino group

94
Q

what do polar amino acids contain?

A

side chains that contain an electronegative atom

95
Q

what do hydrophobic side chains contain?

A

lack reactive functional groups have mainly hydrocarbons

96
Q

what is the one achiral amino acid?

A

glycine

97
Q

where is glycine found?

A

in flexible regions because it is so small

98
Q

pka of tyrosine

A

10.5

99
Q

pka cysteine

A

8.5

100
Q

what is a cystine and how they formed

A

2 cys that are covalently attached to each other. when cysteine residues undergo oxidation

101
Q

pka of histidine

A

6

102
Q

is histidine an acid or a base? what is it involved in?

A

can act as either. involved in enzymatic reactions

103
Q

what 4 amino acids have a charge at neutral ph?

A

aspartate, glutamate, lysine, arginine

104
Q

pka of aspartate?

A

4

105
Q

what is aspartate called at ph 1?

A

aspartic acid

106
Q

charge of aspartate at ph 7?

A

negative

107
Q

charge of glutamate at ph7?

A

negative

108
Q

pka of glutamate?

A

4

109
Q

what is glutamate called at ph1?

A

glutamic acid

110
Q

charge of lysine at ph 7?

A

positive

111
Q

pka of lysine?

A

10

112
Q

charge of arginine at ph 7?

A

positive

113
Q

pka of arginine?

A

too high

114
Q

3 letter code for asparagine

A

asn

115
Q

3 letter code for glutamine

A

gln

116
Q

3 letter code for isoleucine

A

ile

117
Q

tryptophan

A

trp

118
Q

where are polar side chains (uncharged) found?

A

usually on surface of proteins, but may be in the middle

119
Q

where are polar charged side chains found?

A

usually located on the surface of proteins

120
Q

charge on the n term?

A

positive one

121
Q

charge on c term?

A

negative one

122
Q

what is a dipeptide?

A

two amino acids joined by one peptide

123
Q

peptides/oligopeptides

A

general term for a larger number of amino acids, often refers to synthetic peptides.

124
Q

polypeptides

A

long chains of amino acids, usually produced naturally

125
Q

protein

A

large polypeptide (or >1 polypeptide) with a biological function

126
Q

what keeps their charge during a peptide bond formation?

A

only the terminal amino and carboxylate groups maintain charge. side chains retain charge if they had one.

127
Q

characteristics of peptide bonds

A

rigid, planar

128
Q

how are the electrons distributed in a peptide bond and what does this mean?

A

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
Q

are the folding conformations in polypeptides limited? why?

A

yes they are, because the rotation of the backbone is limited

130
Q

can the polypeptide backbone contribute to hydrogen bonding?

A

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
Q

what is the secondary structure of a polypeptide?

A

local folding of the polypeptide backbone, allows for hydrogen bonding of the backbone.

132
Q

what is a regular secondary structure in polypeptides?

A

occurs when each amino acid adopts the same geometry

133
Q

what are two forms of secondary structures?

A

alpha helix, beta sheet

134
Q

how is an alpha helix formed?

A

carbonyl oxygen of each residue forms a Hbond with the backbone NH group four residues downstream

135
Q

why is proline not common in the middle of an alpha helix?

A

the nitrogen cant act as a Hbond donator

136
Q

how are b sheets organized?

A

parallel or antiparallel

137
Q

what the h bonds like in a parallel b sheet?

A

diagonal

138
Q

which is more stable? alpha or beta?

A

neither

139
Q

which way do the arrows point in a b sheet?

A

from the n term to the c term

140
Q

where are side chains located in strands of b sheets?

A

side chains are located above and below the plane of the sheet

141
Q

what force stabilizes alpha helices?

A

h bonds between the backbone CO and NH groups in the same helices

142
Q

what force stabilizes beta sheets?

A

h bonds between backbone CO and NH groups of neighbouring strands

143
Q

what types of secondary structures are alpha helix and beta sheets? what does this mean?

A

regular secondary structures, the peptide backbone has the same configuration regardless of the amino acid composition

144
Q

how are irregular structures made?

A

distinct elements of regular secondary structure are linked together by polypeptide loops of various sizes

145
Q

what is the tertiary structure of proteins?

A

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
Q

what are the two ways tertiary structures can be classified?

A

fibrous (elongated), and globular (compact)

147
Q

characteristics of fibrous proteins?

A

insoluble in aqueous solutions, form long protein filaments, usually structural or connective proteins

148
Q

characteristics of globular proteins?

A

basically soluble in aqueous solutions, fold into compact structures with nonpolar cores and polar surfaces

149
Q

what is found in the interior folding or proteins?

A

regular secondary structure

150
Q

what is the hydrophobic effect in protein folding?

A

the “driving force” via which globular proteins adopt/maintain their tertiary structure

151
Q

what does the shape of globular proteins depend on?

A

depends on the relative position of hydrophobic amino acids in the proteins primary sequence

152
Q

what do ion pairs and salt bridges do?

A

as with h bonds, they help to fine tune and stabilize the tertiary structure of proteins

153
Q

what are ion pairs?

A

electrostatic interactions

154
Q

what is a disulphide bridge?

A

covalent bond, overall RSSR

155
Q

what is a domain in protein structure?

A

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
Q

what is a motif in protein structure?

A

a short region of polypeptide with recognizable 3d shape, example zinc fingers. smaller than domain, but still recognizable pattern.

157
Q

what is a prosthetic group?

A

a non peptide component that is permanently incorporated into a protein. they provide structure and reactive groups

158
Q

what is the prosthetic group in hemoglobin?

A

heme

159
Q

in what phase are prosthetic groups incorporated?

A

part of the tertiary structure. without these groups the tertiary structure isnt properly formed

160
Q

why are globular proteins denatured easily?

A

they are stabilized by weak non covalent forces and are easily unfolded

161
Q

when denaturing a protein, what does changing heat do?

A

effects hydrogen bonds, and hydropphobic interactions

162
Q

when denaturing a protein, what does changing ph?

A

salt bridges, h bonds

163
Q

when denaturing a protein, what does changing salt concentration do?

A

salt bridges, ion pairs

164
Q

when denaturing a protein, what does adding a detergent do?

A

hydorphobic interactions

165
Q

how do you break a disulphide bond?

A

add a reducing agent (DTT)

166
Q

what is a quaternary structure of proteins?

A

proteins composed of more than one polypeptide chain. each polypeptide is called a subunit

167
Q

in quaternary structure, what are 2 identical subunits called? two non identical subunits?

A

homodimer, and heterodimer

168
Q

what are quaternary structure stabilized by?

A

same as tertiary structures. hydrophobic interactions, h bonds, ion pairs “fine tune”

169
Q

what is the tertiary structure of proteins determined by?

A

the primary

170
Q

what kind of structure does myoglobin have?

A

monomer, no quaternary structure

171
Q

what kind of structure does hemoglobin have?

A

oligomer, quaternary structure

172
Q

hemoglobin

A

in red blood cells, binds o2 in the lungs and releases it in the tissues

173
Q

myoglobin

A

binds o2 in muscle cells, acts as a local reserve of o2 during intense exercise, stores o2 in aquatic animals

174
Q

similarities and differences of myoglobin and hemoglobin?

A

both bind oxygen reversibly, but bind with different affinities and in different conditions

175
Q

what does the function of many proteins depend on?

A

their ability to bind other small molecules (ligands) reversibly

176
Q

what does a greater affinity between ligand and protein mean about the dissociation constant?

A

the kd would be smaller with greater affinity

177
Q

what does the value of kd equal?

A

50% saturation when the concentration ligand equals the value of kd

178
Q

where is the heme prosthetic group in myoglobin?

A

between helix E and F. relatively hydrophobic (hydrophobic pocket)

179
Q

what is the structure of heme

A

circular and planar

180
Q

is heme hydrophobic or hydrophilic?

A

hydrophobic (core) except for two groups that contain carboxylate

181
Q

what is the functional state of iron in heme?

A

2+

182
Q

what position in heme does oxygen bond?

A

6th coordination position

183
Q

where does the polypeptide bind in heme?

A

5th coordination position (his f8)

184
Q

how is the structure of myoglobin maintained?

A

ring held in place by hydrophobic interactions, and by coordination bond between fe2+ and histidine HIS F8 (proximal)

185
Q

proximal histidine?

A

histidine f8

186
Q

distal histidine

A

histidine e7

187
Q

what does the distal histidine do?

A

increases affinity for o2. decreases affinity for co2. “specificity”

188
Q

how does the distal histidine effect the affinity of co and o2?

A

distal histidine causes direct steric conflict with CO, unfavourable position. affinity for o2 is enhanced by structure of oxygen binding site

189
Q

what is the quaternary structure of hemoglobin?

A

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
Q

how many o2 can myoglobin bind?

A

it only has one polypeptide chain, so one heme, and only one oxygen molecule

191
Q

what is similar about the alpha globin, the beta globin, and myoglobin? what is this called?

A

all compromise from 8 alpha helices with a heme between E and F. are homologous proteins

192
Q

what critical residues in the oxygen binding sites are invariant?

A

his F8, his E7

193
Q

what does a hyperbolic curve indicate and what is an example?

A

indicates constant affinity (ligand affinity/kd does not change). myoglobin

194
Q

what does a sigmoidal curve indicate and what is an example? why is it necessary?

A

indicates cooperative binding affinity (ligand affinity changes as more ligand binds). hemoglobin. necessary for efficient o2 delivery.

195
Q

what is kd called in a hemoglobin binding curve?

A

k0.5

196
Q

what are the two structures for hemoglobin? which has high affinity?

A

tense sate (t), relaxed state (r). relaxed state has high affinity.

197
Q

how does hb change its affinity for o2?

A

conformational change in hb structure. central cavity changes shape and size.

198
Q

describe the t state. what is it represented as?

A

low affinity for o2, deoxy hb. larger central cavity, allows for binding of larger molecules that arent oxygen. represented by a square box.

199
Q

describe the r state. what is it represented as?

A

high affinity for o2. oxy hb. smaller central cavity. represented by circles.

200
Q

what are effectors and what are the 4 kind?

A

compounds which, upon binding, alter affinity at other binding site. homoallosteric, heterallosteric, activators, inhibitors.

201
Q

homoallosteric

A

binding of the effector affects further binding of the same compound

202
Q

heterallosteric

A

binding of the effector affects further binding of a different compound

203
Q

activators

A

increasing binding affinity

204
Q

inhibitors

A

decrease binding affinity

205
Q

what is o2 for hb (in terms of effector)

A

homoallesteric activator

206
Q

list events starting with o2 binding to hb

A

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
Q

what is bpg (in terms of effector)? h+?

A

both heteroallesteric inhibitors (for o2)

208
Q

what is bpg essential for? how does it work? why does it not work in r state?

A

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
Q

what is the bohr effect? describe the process

A

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
Q

bohr effect and physiological significance

A

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

biochem 200 (1 decks)

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