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Biochem 2 > Exam 1 > Flashcards

Exam 1 Flashcards

0
Q

Major types of nucleic acids

A

DNA - deoxyribonucleic acid

RNA - ribonucleic acid

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1
Q

Fourth group of macromolecules

A

Nucleic Acids

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2
Q

Nucleotides are composed of

A

Sugar (pentose - ribose or deoxyribose)
Nitrogenous bases
Phosphate

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3
Q

A phosphate without a phosphate group

A

Nucleoside

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4
Q

Consists of a nitrogenous base covalently attached to a sugar but without a phosphate group

A

Nucleoside

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5
Q

Adenine nucleoside names and nucleic acids

A

Adenosine —- RNA

Deoxyadenosine—- DNA

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6
Q

Adenine nucleotide names

A

Adenylate —- RNA

Deoxyadenylate —- DNA

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7
Q

Guanine nucleoside names

A

Guanosine —- RNA

Deoxyguanosine —- DNA

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8
Q

Purines

A

Adenine and guanine

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9
Q

Guanine nucleotide names

A

Guanylate — RNA

Deoxyguanylate — DNA

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10
Q

Pyrimidines

A

Cytosine, thymine, uracil

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11
Q

Cytosine nucleoside names

A

Cytidine —- RNA

Deoxycytidine —- DNA

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12
Q

Cytosine nucleotide names

A

Cytidylate —- RNA

Deoxycytidylate —- DNA

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13
Q

Thymine nucleoside names

A

Thymidine —- DNA

Deoxythymidine —– DNA

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14
Q

Thymine nucleotide names and nucleic acids

A

Thymidylate —- DNA

Deoxythymidylate —- DNA

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15
Q

Uracil nucleoside names and nucleic acid

A

Uridine — RNA

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16
Q

Uracil nucleotide names and nucleic acid

A

Uridylate —- RNA

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17
Q

DNA nitrogenous bases

A

Adenine - thymine

Guanine - cytosine

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18
Q

RNA nitrogenous bases

A

Adenine - uracil

Guanine - cytosine

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19
Q

Mono ribonucleoside abbreviations (RNA)

A

AMP
GMP
CMP
UMP

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20
Q

Di ribonucleoside abbreviations

A

ADP
GDP
CDP
UDP

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21
Q

Tri ribonucleoside abbreviations

A

ATP
GTP
CTP
UTP

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22
Q

Mono deoxyribonucleoside abbreviations

A

dAMP
dGMP
dCMP
dTMP

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23
Q

Di deoxyribonucleoside abbreviations

A

dADP
dGDP
dCDP
dTMP

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24
Q

Tri deoxyribonucleoside abbreviations

A

dATP
dGTP
dCTP
dTTP

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25
Q

NMP

A

One phosphate group attached to sugar and nitrogenous base

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26
Q

NDP

A

Two phosphate group attached to sugar and nitrogenous base

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27
Q

NTP

A

Three phosphate group attached to sugar and nitrogenous base

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28
Q

Nucleotides are linked covalently to each other by

A

Phosphodiester bonds

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29
Q

Base pair means we have 2 complimentary bases paired with

A

Hydrogen bonds

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30
Q

Nucleotide polymers (I.e. DNA or RNA) exhibit

A

Directionality

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31
Q

Nucleotide polymers also exhibit

A

Individuality due to the sequences of the bases

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32
Q

Phosphodiester bonds are

A

Very stable

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33
Q

Breaks phosphodiester bonds

A

Nucleases (endo and exo)
RNA - ribonuclease
DNA - deoxyribonuclease

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34
Q

Within molecule clipping

A

Endo

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35
Q

Clips only end nucleotides

A

Exo

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36
Q

RNA is _______ hydrolyzed under alkaline conditions but ______ is not

A

Rapidly

DNA

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37
Q

DNA is most often found as a ________ _______ molecule, twisted into a ________

A

Double stranded

Helical

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38
Q

The DNA strands are

A

Anti parallel

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39
Q

The two DNA strands that make up dsDNA are

A

Complimentary

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40
Q

The c-g and a-t base pairing allows for

A

DNA self replication

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41
Q

Palindrome

A

Same at the four corners of two DNA strands

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42
Q

Mirror repeat

A

Mirrored in the same line

First half mirrors second half

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43
Q

Hairpin

A

Middle four base pairs at the top curve, the rest down the sides

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44
Q

Play an important role in transcription and translation

A

Hairpin

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45
Q

Cruciform

A

2 hairpins

Looks like a cross

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46
Q

Knot like structures in rubber band example

A

Supercoiling (not sequence dependent)

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47
Q

Supercoiling

A

Happens in DNA when it splits to replicate

Mechanical stress can break phosphodiester bonds

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48
Q

What is transcription?

A

The synthesis of RNA from DNA template

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49
Q

2 daughter cells form __________ at the end of replication

A

Catenane

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50
Q

Catenane

A

Formed by 2 daughter cells at the end of replication

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51
Q

Old central dogma

A

DNA–> more DNA –> RNA –> Protein

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52
Q

New Central Dogma

A

DNA –> more DNA –> RNA –> DNA (reverse transcription)

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53
Q

HIV is

A

reverse transcriptase virus

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54
Q

Information RNA

A

mRNA

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55
Q

Structure RNA

A

rRNA (makes ribosomes)

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56
Q

Adapter RNA

A

tRNA (covalently linked to one of 20 standard amino acids, 3 base anti-codon, 3 base codon in mRNA)

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57
Q

Degeneracy

A

Different codon sequences code for the same amino acid

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58
Q

Sense

A

The coding strand of DNA but this is not the strand from which RNA is made including mRNA because you want RNA to be a sense strand

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59
Q

___________ regions in DNA signal RNA Pol where to bind, how tightly to bind, and how frequently to transcribe an RNA chain

A

Promoter (can be weak or strong; long or short)

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60
Q

_____________ regions in DNA signal RNA Pol to stop transcribing

A

Terminator

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61
Q

Transcription is catalyzed by

A

RNA polymerase

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62
Q

Composed of beta prime, beta, alpha, and sigma units

A

RNA Pol

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63
Q

Functions in promoter recognition and initiation

A

Sigma

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64
Q

Regulatory factors associated with RNA Pol include

A

P (rho), nusA, Tau (all of these function in termination of transcription)

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65
Q

When all the subunits of a multi-subunit enzyme associate with each other

A

Holoenzyme

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66
Q

Holoenzyme

A

When all the subunits of a multi-subunit enzyme associate with each other

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67
Q

When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other

A

Core Polymerase RNA : no sigma: the assembly is referred to as the core enzyme or polymerase

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68
Q

Core Polymerase RNA

A

When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other

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69
Q

RNA Pol I

A

Located in nucleolus and produces pre rRNA

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70
Q

RNA Pol II

A

Located in nucleoplasm and produces mRNA, hnRNA (heterogenous nuclear)

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71
Q

RNA Pol III

A

Located in nuceoplasm and produces pre tRNA, 5S RNA

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72
Q

There is only 1 ____ ________ ________ in prokaryotes

A

RNA Pol Holoenzymes

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73
Q

Many but NOT ALL eukaryote genes have the common sequence___________ located about ___ to _____ bases before the transcription site

A

TaTAAATA
25 to 30
TATA BOX

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74
Q

TATA is

A

a subunit of promoter

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75
Q

Certain boxes binds selectively to

A

the TATA sequence

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76
Q

Proteins needed to initiate transcription

A

TATA box

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77
Q

CAAT Box

A

GGCCAATCT or GGTCAATC: Common sequence located 60 - 80 bases upstream from the transcription start site

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78
Q

Transcription and translation occur simultaneously in prokaryotes in the

A

Cytoplasm of the bacterium

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79
Q

Transcription in euk. occurs in the

A

Nucleus

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80
Q

Translation in euk. occurs in the

A

Cytoplasm (on ribosomes)

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81
Q

Large mRNA precursor molecules are synthesized in the

A

Nucleus

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82
Q

Form ribonucleoprotein particles

A

Large mRNA precursor molecules: these are transported from the nucleus to the cytoplasm

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83
Q

Modification

A

Addition or alteration of existing bases or sugars in RNA

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84
Q

Sometimes involves the addition of 1 or more nucleotides

A

Modification

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85
Q

Processing

A

Phosphodiester bond cleavage and loss of certain nucleotides

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86
Q

Examples of post-transcriptional modifications

A

Capping

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87
Q

Capping

A

During transcription a GMP is added to the 5’ end of mRNA, G is methylated at position N-7 followed by methylation of the 1st nucleotide in the initial transcription at the O2 on ribose

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88
Q

Facilitates the binding of ribosomes to the mRNA

A

Capping

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89
Q

Has reduced half-life compared to capped mRNA

A

Uncapped mRNA (prevents exonucleases)

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90
Q

Most euk. mRNA associated with a ribosome contain _______ adenine nucleotides on 3’ end

A

50 - 150

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91
Q

Not coded for by the DNA template

A

PolyA tail

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92
Q

PolyA tail is added post-transcriptionally by

A

PolyA polymerase

93
Q

Translation

A

synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA

94
Q

Synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA

A

Translation

95
Q

Translation requires

A

mRNA, tRNA, amino acids, and ribosomes

96
Q

Translation occurs in the _________ direction along the mRNA

A

5’ to 3’

The resulting polypeptide is assembled N-terminus to C-terminus

97
Q

Start codons

A

AUG

fMet or Met???

98
Q

Stop codons

A

UAA, UAG, UGA

99
Q

Bacteria ribosomes

A

50S + 30S = 70S

100
Q

Euk. ribosomes

A

60S + 40S = 80S

101
Q

Determined by the speed particles traveling through G force like centrifugation

A

Sedimentation coefficients

102
Q

Ribosome

A

Ribonucleoprotein (rRNA + protein)
Pro. less proteins
Euk. More proteins

103
Q

The nucleotide at the Wobble position

A

Does NOT base pair strongly at 5’ on anticodon

104
Q

Wobble position

A

Anticodon Arm

105
Q

Contains 2 or 3 D residues at different positions

A

D arm

106
Q

Anticodon arm

A

wobble position

107
Q

Variable in size, not present in all tRNA

A

Extra arm

108
Q

Arms starting left going right

A

D arm, Wobble Position, Anti-codon arm, Extra arm (not always present), TUC (trident= Pseudouridine) arm, Amino acid arm (at top)

109
Q

Specialized base pair called ___________ which pair WEAKLY with all base pairs

A

Inosinate —— WEAKLY

110
Q

Activation of Amino Acids

A

20 AA, 20 aminoacyl-tRNA synthetases, 32 or more tRNA, APT, Mg 2+

111
Q

Initiation

A

mRNA, N-fMet-tRNA (N-formalmethionyl-tRNA), 30S ribosomal unit, 50S ribosomal unit, initiation factors IF-1, IF-2, IF-3, GTP, Mg 2+

112
Q

Elongation

A

Functional 70S ribosome (initiation complex), aminoacyl-tRNA sepcified by codons, elongation factors EF-Tu, EF-Ts, EF-G, GTP, Mg 2+

113
Q

Termination and Release

A

Termination codon in mRNA, release factors RF-1, RF-2. RF-3

114
Q

Folding and Post-translation processing

A

Specific enzymes, cofactors, and other components for removal of initiating residues and signal sequences, additional proteolytic processing, modification of terminal residues, and attachment of phosphate, methyl, carboxyl, carbohydrate, or prosthetic groups

115
Q

Translation Step 1:

A

Coupling of tRNA to amino acids/amino acids activation

116
Q

Amino acids are covalently attached to tRNAs by the enzyme

A

Aminoacyl-tRNA synthetase

117
Q

Synthetase

A

catalyzes a reaction with ATP involved

118
Q

Synthase

A

catalyzes a reaction without ATP

119
Q

E. Coli has 20 different aminoacyl-tRNa synthetases, one for each of the standard amino acids, that

A

improves reaction efficiency linking correct amino acids

120
Q

2 steps in activation of amino acids

A
  1. The amino acid is activated by ATP to form aminoacyl adenlyate = aminoacyl AMP
  2. While the aminoacyl adenylate intermediate is bound to the sythetase it reacts with the correct tRNA to form a covalent linkage with it, AMP is released
121
Q

The amino acid is activated by ATP to form

A

Aminoacyl adenylate = aminoacyl AMP

122
Q

The synthestase _______ choose the correct tRNA based on the anticodon sequence

A

DOES NOT

123
Q

Critical determinant of choosing the correct tRNA

A

The sequence in the ACCEPTOR STEM

124
Q

Once tRNA is linked to amino acid, the tRNA is said to be

A

Charged (not + or -)

125
Q

Process of translation

A

Ribosome starts process
AUG binds on top of P site
UAC always carries modified methiamine
Once methiamine is in place GTP kicks off initiating factors and allows large subunit to join small
Large and small subunit and fMet carrying incoming tRNAs associate with EF-Tu
The peptidyl transferase activity of large subunit catalyzes between amino acids
Dipeptidyl tRNA forms at the A site
Deacylated tRNA
Translocation occurs
UAG–> Stop codon –>A site
RF binds and triggers disassembly of everything and large and subunits separate and empty tRNA is released
Cylce repeats

126
Q

Ribosome Cycling

A

two subunits join and separate repeatedly

127
Q

Helps guide tRNA into ribosome

A

Elongation factor Tu (EF-Tu)

128
Q

Translocation

A

Forced movement of mRNA inside ribosome

Can be promoted by GTP

129
Q

Translation occurs on free ribosomes in the cytosol or on ribosomes bound to the ER (rough) in

A

Eukaryotes

130
Q

Tend to remain cytosolic (water soluble)

A

Proteins made on free ribosomes

131
Q

Proteins made on rought ER

A

hydrophobic

132
Q

Protein targeting

A

The general mechanism for the sorting and transport of proteins to their proper subcellular location

133
Q

Signal sequence

A

A short amino acid sequence (23-36 AA long) at the N-terminus of newly made polypeptide
It is important in targeting

134
Q

One protein being made at N-terminus end (5’end)

A

Signal sequence

135
Q

Signal Recognition Particle

A

Large protein complex that directs the forming polypeptide into the lumen of the ER for processing

136
Q

Purpose of the signal sequence

A

Direct a free ribosome to ER where signal sequence and ribosome are bound by SRP

137
Q

What is transcription?

A

The synthesis of RNA from DNA template

138
Q

2 daughter cells form __________ at the end of replication

A

Catenane

139
Q

Catenane

A

Formed by 2 daughter cells at the end of replication

140
Q

Old central dogma

A

DNA–> more DNA –> RNA –> Protein

141
Q

New Central Dogma

A

DNA –> more DNA –> RNA –> DNA (reverse transcription)

142
Q

HIV is

A

reverse transcriptase virus

143
Q

Information RNA

A

mRNA

144
Q

Structure RNA

A

rRNA (makes ribosomes)

145
Q

Adapter RNA

A

tRNA (covalently linked to one of 20 standard amino acids, 3 base anti-codon, 3 base codon in mRNA)

146
Q

Degeneracy

A

Different codon sequences code for the same amino acid

147
Q

Sense

A

The coding strand of DNA but this is not the strand from which RNA is made including mRNA because you want RNA to be a sense strand

148
Q

___________ regions in DNA signal RNA Pol where to bind, how tightly to bind, and how frequently to transcribe an RNA chain

A

Promoter (can be weak or strong; long or short)

149
Q

_____________ regions in DNA signal RNA Pol to stop transcribing

A

Terminator

150
Q

Transcription is catalyzed by

A

RNA polymerase

151
Q

Composed of beta prime, beta, alpha, and sigma units

A

RNA Pol

152
Q

Functions in promoter recognition and initiation

A

Sigma

153
Q

Regulatory factors associated with RNA Pol include

A

P (rho), nusA, Tau (all of these function in termination of transcription)

154
Q

When all the subunits of a multi-subunit enzyme associate with each other

A

Holoenzyme

155
Q

Holoenzyme

A

When all the subunits of a multi-subunit enzyme associate with each other

156
Q

When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other

A

Core Polymerase RNA : no sigma: the assembly is referred to as the core enzyme or polymerase

157
Q

Core Polymerase RNA

A

When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other

158
Q

RNA Pol I

A

Located in nucleolus and produces pre rRNA

159
Q

RNA Pol II

A

Located in nucleoplasm and produces mRNA, hnRNA (heterogenous nuclear)

160
Q

RNA Pol III

A

Located in nuceoplasm and produces pre tRNA, 5S RNA

161
Q

There is only 1 ____ ________ ________ in prokaryotes

A

RNA Pol Holoenzymes

162
Q

Many but NOT ALL eukaryote genes have the common sequence___________ located about ___ to _____ bases before the transcription site

A

TaTAAATA
25 to 30
TATA BOX

163
Q

TATA is

A

a subunit of promoter

164
Q

Certain boxes binds selectively to

A

the TATA sequence

165
Q

Proteins needed to initiate transcription

A

TATA box

166
Q

CAAT Box

A

GGCCAATCT or GGTCAATC: Common sequence located 60 - 80 bases upstream from the transcription start site

167
Q

Transcription and translation occur simultaneously in prokaryotes in the

A

Cytoplasm of the bacterium

168
Q

Transcription in euk. occurs in the

A

Nucleus

169
Q

Translation in euk. occurs in the

A

Cytoplasm (on ribosomes)

170
Q

Large mRNA precursor molecules are synthesized in the

A

Nucleus

171
Q

Form ribonucleoprotein particles

A

Large mRNA precursor molecules: these are transported from the nucleus to the cytoplasm

172
Q

Modification

A

Addition or alteration of existing bases or sugars in RNA

173
Q

Sometimes involves the addition of 1 or more nucleotides

A

Modification

174
Q

Processing

A

Phosphodiester bond cleavage and loss of certain nucleotides

175
Q

Examples of post-transcriptional modifications

A

Capping

176
Q

Capping

A

During transcription a GMP is added to the 5’ end of mRNA, G is methylated at position N-7 followed by methylation of the 1st nucleotide in the initial transcription at the O2 on ribose

177
Q

Facilitates the binding of ribosomes to the mRNA

A

Capping

178
Q

Has reduced half-life compared to capped mRNA

A

Uncapped mRNA (prevents exonucleases)

179
Q

Most euk. mRNA associated with a ribosome contain _______ adenine nucleotides on 3’ end

A

50 - 150

180
Q

Not coded for by the DNA template

A

PolyA tail

181
Q

PolyA tail is added post-transcriptionally by

A

PolyA polymerase

182
Q

Translation

A

synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA

183
Q

Synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA

A

Translation

184
Q

Translation requires

A

mRNA, tRNA, amino acids, and ribosomes

185
Q

Translation occurs in the _________ direction along the mRNA

A

5’ to 3’

The resulting polypeptide is assembled N-terminus to C-terminus

186
Q

Start codons

A

AUG

fMet or Met???

187
Q

Stop codons

A

UAA, UAG, UGA

188
Q

Bacteria ribosomes

A

50S + 30S = 70S

189
Q

Euk. ribosomes

A

60S + 40S = 80S

190
Q

Determined by the speed particles traveling through G force like centrifugation

A

Sedimentation coefficients

191
Q

Ribosome

A

Ribonucleoprotein (rRNA + protein)
Pro. less proteins
Euk. More proteins

192
Q

The nucleotide at the Wobble position

A

Does NOT base pair strongly at 5’ on anticodon

193
Q

Wobble position

A

Anticodon Arm

194
Q

Contains 2 or 3 D residues at different positions

A

D arm

195
Q

Anticodon arm

A

wobble position

196
Q

Variable in size, not present in all tRNA

A

Extra arm

197
Q

Arms starting left going right

A

D arm, Wobble Position, Anti-codon arm, Extra arm (not always present), TUC (trident= Pseudouridine) arm, Amino acid arm (at top)

198
Q

Specialized base pair called ___________ which pair WEAKLY with all base pairs

A

Inosinate —— WEAKLY

199
Q

Activation of Amino Acids

A

20 AA, 20 aminoacyl-tRNA synthetases, 32 or more tRNA, APT, Mg 2+

200
Q

Initiation

A

mRNA, N-fMet-tRNA (N-formalmethionyl-tRNA), 30S ribosomal unit, 50S ribosomal unit, initiation factors IF-1, IF-2, IF-3, GTP, Mg 2+

201
Q

Elongation

A

Functional 70S ribosome (initiation complex), aminoacyl-tRNA sepcified by codons, elongation factors EF-Tu, EF-Ts, EF-G, GTP, Mg 2+

202
Q

Termination and Release

A

Termination codon in mRNA, release factors RF-1, RF-2. RF-3

203
Q

Folding and Post-translation processing

A

Specific enzymes, cofactors, and other components for removal of initiating residues and signal sequences, additional proteolytic processing, modification of terminal residues, and attachment of phosphate, methyl, carboxyl, carbohydrate, or prosthetic groups

204
Q

Translation Step 1:

A

Coupling of tRNA to amino acids/amino acids activation

205
Q

Amino acids are covalently attached to tRNAs by the enzyme

A

Aminoacyl-tRNA synthetase

206
Q

Synthetase

A

catalyzes a reaction with ATP involved

207
Q

Synthase

A

catalyzes a reaction without ATP

208
Q

E. Coli has 20 different aminoacyl-tRNa synthetases, one for each of the standard amino acids, that

A

improves reaction efficiency linking correct amino acids

209
Q

2 steps in activation of amino acids

A
  1. The amino acid is activated by ATP to form aminoacyl adenlyate = aminoacyl AMP
  2. While the aminoacyl adenylate intermediate is bound to the sythetase it reacts with the correct tRNA to form a covalent linkage with it, AMP is released
210
Q

The amino acid is activated by ATP to form

A

Aminoacyl adenylate = aminoacyl AMP

211
Q

The synthestase _______ choose the correct tRNA based on the anticodon sequence

A

DOES NOT

212
Q

Critical determinant of choosing the correct tRNA

A

The sequence in the ACCEPTOR STEM

213
Q

Once tRNA is linked to amino acid, the tRNA is said to be

A

Charged (not + or -)

214
Q

Process of translation

A

Ribosome starts process
AUG binds on top of P site
UAC always carries modified methiamine
Once methiamine is in place GTP kicks off initiating factors and allows large subunit to join small
Large and small subunit and fMet carrying incoming tRNAs associate with EF-Tu
The peptidyl transferase activity of large subunit catalyzes between amino acids
Dipeptidyl tRNA forms at the A site
Deacylated tRNA
Translocation occurs
UAG–> Stop codon –>A site
RF binds and triggers disassembly of everything and large and subunits separate and empty tRNA is released
Cylce repeats

215
Q

Ribosome Cycling

A

two subunits join and separate repeatedly

216
Q

Helps guide tRNA into ribosome

A

Elongation factor Tu (EF-Tu)

217
Q

Translocation

A

Forced movement of mRNA inside ribosome

Can be promoted by GTP

218
Q

Translation occurs on free ribosomes in the cytosol or on ribosomes bound to the ER (rough) in

A

Eukaryotes

219
Q

Tend to remain cytosolic (water soluble)

A

Proteins made on free ribosomes

220
Q

Proteins made on rought ER

A

hydrophobic

221
Q

Protein targeting

A

The general mechanism for the sorting and transport of proteins to their proper subcellular location

222
Q

Signal sequence

A

A short amino acid sequence (23-36 AA long) at the N-terminus of newly made polypeptide
It is important in targeting

223
Q

One protein being made at N-terminus end (5’end)

A

Signal sequence

224
Q

Signal Recognition Particle

A

Large protein complex that directs the forming polypeptide into the lumen of the ER for processing

225
Q

Purpose of the signal sequence

A

Direct a free ribosome to ER where signal sequence and ribosome are bound by SRP

226
Q

Tm

A

Temperature at which a molecule of DNA is 50% denatured.

Dependent on base composition of DNA

227
Q

Nick

A

A missing phosphodiester bond. Sealed by DNA ligase

228
Q

Tm

A

The point at which a molecule is 50% denatured

229
Q

Tm

A

The point at which a molecule is 50% denatured

Biochem 2 (3 decks)

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