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BIO 220 > Chapter 6 > Flashcards

Chapter 6 Flashcards

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1
Q

When a cell needs a particular protein, appropriate portion is first copied into RNA through a process called

A

Transcription

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2
Q

RNA copies are used directly as templates to direct the synthesis of the protein in a process called

A

Translation

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3
Q

What is the central dogma of molecular biology?

A

The flow of genetic information in cells from DNA to RNA to protein

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4
Q

What type of bonds link RNA nucleotide subunits

A

Phosphodiester

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5
Q

What are the chemical differences between RNA and DNA

A
  1. The nucleotides in RNA are ribonucleotides containing the sugar ribose
  2. RNA contains uracil instead of thymine
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6
Q

Stages of transcription: initiation

A

RNA polymerase binds to a promoter, where the helix unwinds and transcription starts

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7
Q

Stages of transcription: elongation

A

RNA nucleotides are added to the chain

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8
Q

Stages of transcription: termination

A

RNA polymerase reaches a terminator sequence and detaches from the template

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9
Q

Enzyme that performs transcription

A

RNA polymerase

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10
Q

What enzyme catalyzes the formation of the phosphodiester bonds that link the nudeotides together to form a linear chain

A

RNA polymerase

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11
Q

What allows many RNA copies to be made from the same gene in a short amount of time?

A

Immediate release of the RNA strand from DNA as it is synthesized

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12
Q

Unlike DNA, RNA does not…

A

Permanently store genetic information in cells

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13
Q

After catalyzing the links of ribonucleotides, RNA polymerase can

A

Start an RNA chain without a primer

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14
Q

Are DNA and RNA polymerases structurally related?

A

No, other than containing Mg^2+ ion at the catalytic site, they are unrelated

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15
Q

Inorganic enzymes

A

Cofactor

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16
Q

Organic enzymes

A

Co-enzymes

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17
Q

RNA molecules that are copied from genes

A

Messenger RNA (mRNA)

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18
Q

Molecules that direct the splicing of pre-mRNA to form mRNA removing noncoded sections and joining coded ones

A

Small nuclear RNA (snRNA)

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19
Q

Molecules that serve as key regulators of eucaryotic gene expression

A

MicroRNA (miRNA) and small interfering RNA (siRNA)

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20
Q

Each transcribed segment of DNA is called

A

Transcription Unit

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21
Q

Carries the information of just one gene, and codes for either a single RNA molecule or a single protein

A

Transcription unit

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22
Q

What detachable subunit associates with the core enzyme and assists it in reading the signals in the DNA that tell it where to begin transcribing

A

Sigma factor

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23
Q

Together, sigmas factor and core enzyme are known as

A

RNA polymerase holoenzyme

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24
Q

Adheres only weakly to bacterial DNA when the two collide and slides rapidly along the long DNA molecule until it dissociates again

A

RNA polymerase holoenzyme

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25
Q

A special sequence of nucleotides indicating the starting point for RNA synthesis

A

Promoter

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26
Q

When the polymerase holoenzyme slides into a promoter polymerase binds

A

Tightly to this DNA

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27
Q

After DNA polymerase holoenzyme binds to promoter DNA it

A

Opens up the double helix to expose a short stretch of nucleotides on each strand

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28
Q

What happens afthe the first ten nucleotides of RNA have been synthesized?

A
  1. Core enzyme breaks it interactions with promoter DNA

2. Weakens its interactions with sigma factor and begins to moved down the DNA

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29
Q

Chain elongation continues until the enzyme encounters a second signal in the DNA called

A

Terminator

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30
Q

What causes the polymerase to halt and release the new RNA chain and DNA template

A

Terminator

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31
Q

How do the termination signals in the DNA stop the elongating polymerase?

A

For most bacterial genes a termination signal consists of a string of A-T nucleotide pairs followed by a two-fold symmetric (hairpin) DNA sequence CG area

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32
Q

The formation of the hair pin may help

A

To “pull” the RNA transcript from the active site

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33
Q

Transcription initiation difference between eukaryotes and bacteria

A

Bacteria has RNA polymerase

Eukaryotes have RNA polymerase I, RNA polymerase II, and RNA polymerase III

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34
Q

Centrifugation measures

A

RNA’s sedimentation coefficient

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35
Q

Transcribes the genes encoding transfer RNA, ribosomal RNA, and various small RNAs

A

RNA polymerases I and III

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36
Q

Transcribes most genes, including all those that encode proteins

A

RNA polymerase II

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37
Q

Helps to

  • position eukaryotic RNA polymerase correctly at the promoter
  • aid in pulling apart the two strands of DNA to allow transcription to begin
  • release RNA polymerase from the promoter into the elongation mode once transcription has begun
A

General transcription factors that RNA polymerase II requires

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38
Q

General transcription factors carry out functions equivalent to

A

Sigma factor in bacteria

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39
Q

TFII

A

Transcription factor for polymerase II

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40
Q

TBP

A

TATA box binding protein

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41
Q

Subunit of TFII

A

TBP

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42
Q

Short DNA sequence primarily composed of T and A nucleotides

A

TATA box

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43
Q

Where is the TATA box located and what does it allow for

A

25 nucleotides upstream from transcription start site allowing for subsequent protein assembly steps

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44
Q

Other factors assemble along with RNA polymerase II to form a complete

A

Transcription initiation complex

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45
Q

Most complicated of the general transcription factors is and why

A

TFIIH - consists of 9 subunits, as large as RNA polymerase II, and performs several enzymatic steps needed for the initiation of transcription

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46
Q

How does polymerase II gain access to the template strand at the transcription start point?

A

TFIIH which contains DNA helicase as a subunit hydrolyzes ATP and unwinds the DNA. Then, at the promoter, RNA polymerase II synthesizes short lengths of RNA until it undergoes a series of conformational changes that allow it to move away from promoter

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47
Q

Where are phosphate groups added to on the RNA polymerase

A

The tail or C-terminal

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48
Q

In humans, the CTD consists of

A

52 tandem repeats of a seven-amino-acid sequence

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49
Q

When are most of the general transcription factors released from DNA

A

Once the polymerase II has begun elongating the RNA transcript

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50
Q

Gene regulatory proteins

A

Transcriptional activators

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51
Q

Protein complex that allows the activator proteins to communicate properly with the polymerase II and general transcription factors

A

Mediator

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52
Q

Transcription initiation requires the local recruitment of

A

Chromatin-modifying enzymes

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53
Q

Proteins that decrease the likelihood that RNA polymerase will dissociate before it reaches the end of a gene

A

Elongation factors

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54
Q

Help polymerases to move through the wide variety of different DNA sequences that are found in genes

A

Elongation factors

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55
Q

What happens once RNA polymerase II has produced 25 nucleotides of RNA

A

A cap that consists of a modified guanine nucleotide is added to the 5’ end

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56
Q

What 3 enzymes perform the capping reaction

A

Phosphatase, guanyl transferase, methyl transferase

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57
Q

Enzyme that removes a phosphate from the 5’ end of the developing RNA

A

Phosphatase

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58
Q

What enzyme adds a GMP in a reverse linkage (5’ to 5’ instead of 5’ to 3’)

A

Guanyl transferase

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59
Q

What enzyme adds a methyl group to the guanosine

A

Methyl transferase

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60
Q

What helps the cell to distinguish mRNAs from other types of RNA molecules present

A

5’ cap

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61
Q

Noncoding intervening sequences

A

Introns

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62
Q

Expressed sequences

A

Exons

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63
Q

Which sequences are longer, introns or exons?

A

Introns

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64
Q

Intron sequences are removed from the newly synthesized RNA through the process of

A

RNA splicing

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65
Q

The majority of RNA splicing focuses on

A

Precursor-mRNA or pre-mRNA splicing

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66
Q

Describe a splicing event

A
  1. Cuts the intron on the 5’ side
  2. 5’ end of intron covalently links to the adenine nucleotide creating a loop
  3. Exon end reacts with start of other exon joining them together
  4. Intron sequence is released in the shape of a lariat
  5. Two exon sequences become joined
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67
Q

Phosphoryl- transfer reactions when splicing

A

Transesterifications

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68
Q

Why does pre-mRNA splicing occur

A

Introns in DNA allows genetic recombination, enabling genes for new proteins to evolve more easily by the combination of parts of preexisting genes

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69
Q

Benefit of alternative splicing

A

Allows the same gene to produce a corresponding set of different proteins

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70
Q

What signals where splicing occurs

A

Nucleotide sequences

71
Q

What 3 portions of the precursor RNA molecule must be recognized by splicing machinery

A
  1. 5’ splice site
  2. 3’ splice site
  3. Branch point in the intron sequence that forms the base of the excised lariat
72
Q

RNA splicing is performed by

A

Sliceosome

73
Q

Where is a spliceosome found

A

Within the splicing speckles of the cell nucleus of eukaryotic cells

74
Q

What forms a spliceosome and what is it assembled from?

A

Assembled from snRNAs (small nuclear RNAs) with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome.

75
Q

What snRNAs male up the major spliceosome

A

U1, U2, U4, U5 U6

76
Q

Removes introns from a transcribed pre-mRNA, a type of primary transcript

A

Spliceosome

77
Q

During splicing, recognition of the 5’ splice site, the branch-point site, and 3’ splice site is performed largely through base-pairing between

A

snRNAs and RNA sequences in the pre-mRNA substrate

78
Q

Two multisubunit proteins important for 3’ end of each mRNA molecule

A
  • CstF

- CPSF

79
Q

CstF

A

Cleavage stimulation factor

80
Q

CPSF

A

Cleavage and polyadenylation specificity factor

81
Q

What is transferred from the RNA polymerase tail to the 3’ end processing sequence on an RNA molecule as it emerges from the RNA polymerase

A

CstF and CPSF

82
Q

What happens after RNA is cleaved

A

Poly-A polymerase (PAP) enzyme one at a time adds 200 A nucleotides to the 3’ end

83
Q

As the poly-A tail is synthesized what proteins assemble onto it

A

Poly-A-binding proteins

84
Q

What does the newly synthesized RNA that has emerged lack after 3’ end cleavage has occurred?

A

A 5’ cap

85
Q

How does the cell distinguish between mature mRNA molecules and debris from RNA processing (excised introns, broken RNAs)?

A

As an RNA molecule is processed, it loses certain proteins and acquires others, thereby signifying the successful completion of each of the different steps

86
Q

A properly completed mRNA molecule is distinguished by

A

The protein it lacks

87
Q

The presence of snRNP on a mRNA molecule signifies

A

Incomplete or abnormal splicing

88
Q

Improperly processed mRNAs and other RNA debris are retained in the nucleus where they are degraded by

A

Nuclear exosome rich in 3’-to-5’ RNA exonucleases

89
Q

hnRNP

A

Heterogeneous nuclear ribonuclear proteins

90
Q

Proteins that assemble on pre-mRNA molecules that unwind the hairpin helices so that splicing and other signals can be read more easily

A

hnRNPs (heterogeneous nuclear ribonuclear proteins)

91
Q

Successfully processed mRNAs are guided through

A

Nuclear pore complexes (NPCs)

92
Q

Macromolecules are moved through nuclear pore complexes by

A

Nuclear transport receptors

93
Q

Dissociates from the mRNA after transport, re-enters the nucleus, and exports a new mRNA molecule

A

Nuclear transport receptors

94
Q

As genes are transcribed, the newly formed RNA is seen to be packaged by what proteins?

A

hnRNPs, SR proteins, components of the spliceosome

95
Q

Structures that gain and lose numerous specific proteins during RNA synthesis, processing, and export

A

Pre-mRNA-protein and mRNA-protein

96
Q

Polymerase dedicated to producing rRNAs

A

RNA polymerase I

97
Q

Reason why polymerase I’s transcripts are neither capped nor polyadenylated

A

Absence of a C-terminal tail

98
Q

One copy per ribosome, what are the four types of eukaryotic rRNAs

A

18S, 5.8S, 28S, 5SRNA

99
Q

Which 3 eukaryotic rRNAs are made by chemically modifying and cleaving a single large precursor rRNA

A

18S, 5.8S, 28S

100
Q

Which eukaryotic rRNA is synthesized from a separate cluster of genes by a different polymerase, RNA polymerase III, and does not require chemical modification

A

5SRNA

101
Q

A large class of RNAs that perform their functions in a subcompartment of the nucleus called the nucleolus and are synthesized by RNA polymerase II

A

Small nucleolar RNAs (snoRNAs)

102
Q

The site for the processing of rRNAs and their assembly into ribosome subunits. Not bound by a membrane

A

Nucleolus

103
Q

The nucleolus is a large aggregate of macromolecules including:

A
  • The rRNA genes themselves
  • precursor rRNAs
  • mature rRNAs
  • rRNA-processing enzymes
  • snoRNPs (small nuclear ribonuclear proteins)
  • ribosomal proteins
  • partly assembled ribosomes
104
Q

Site where other RNAs are produced and other RNA-protein complexes are assembled

A

Nucleolus

105
Q

The nucleotide sequence of a gene, through the intermediary of mRNA, is translated into the amino acid sequence of a protein by rules that are known as

A

The genetic code

106
Q

How many different amino acids are commonly found in proteins

A

20

107
Q

Group of three consecutive nucleotides in RNA

A

Codon

108
Q

Each codon specifies

A

Either one amino acid or a stop to the translation process

109
Q

Adaptors that consist of a set of small RNA molecules that translate mRNA into protein and can recognize and bind both to the codon

A

Transfer RNAs (tRNAs)

110
Q

What are the two regions of unpaired nucleotides situated at either end of the L-shaped molecule that are important to the function of tRNA in protein synthesis

A
  1. Anticodon- set of 3 consecutive nucleotides that pair with the complementary code in an mRNA molecule
  2. Short single-stranded region at the 3’ end where the amino acid that matches the codon is attached to the tRNA
111
Q

What are the 2 possible explanations why several different codons can specify a single amino acid

A
  1. There is more than one tRNA for many of the amino acids

2. Some tRNA molecules can base-pair with more than one codon

112
Q

Accurate base-pairing for first 2 positions of the codon but tolerable mismatch for third

A

Wobble

113
Q

Eukaryotic tRNAs are synthesized by

A

RNA polymerase III

114
Q

How do pre-mRNA splicing and tRNA splicing differ?

A

Pre-mRNA splicing generates a lariat intermediate

tRNA splicing uses a cut-and-paste mechanism catalyzed by proteins

115
Q

What are 4 examples of tRNA modifications

A
  1. Addition of 2 methyl groups to G
  2. Addition of 2 hydrogens to U
  3. Sulfur replaces oxygen in U
  4. Deamination of A (replace amino group with oxygen)
116
Q

Enzyme that covalently couples each amino acid to its appropriate set of tRNA molecules

A

Aminoacyl-tRNA synthetases

117
Q

For each amino acid most cells have

A

A different synthetase enzyme

118
Q

First step in selecting correct amino acid for tRNA

A

The correct amino acid has the highest affinity for the active-site pocket of its synthetase

119
Q

Problem with first step in selecting correct amino acid for tRNA

A

Two similar amino acids

120
Q

Second step in selecting the correct amino acid for tRNA

A

Once amino acid enter an editing pocket, it is hydrolyzed from the AMP (or from tRNA) and is released from the enzyme. This hydrolytic editing is analogous to the exonucluolytic proofreading by DNA polymerases

121
Q

The tRNA syntheses must also recognize

A

The correct set of tRNAs

122
Q

What is the fundamental reaction of protein synthesis

A

The formation of a peptide bond between the carboxyl group and a free amino group on an incoming amino acid

123
Q

What is the general structure of an amino acid?

A
124
Q

What kind of reaction forms a peptide bond

A

Dehydration

125
Q

How is a peptide bond formed?

A

The C-terminal of one amino acid loses its OH and the N-terminal of the other amino acid loses a H to bind C to N

126
Q

To maintain the correct reading frame and to ensure accuracy, protein synthesis is performed in the

A

Ribosome

127
Q

A complex catalytic machine made from more than 50 different proteins (the ribosomal proteins) and several RNA molecules

A

Ribosomal RNAs (rRNAs)

128
Q

Where are eukaryotic ribosome subunits assembled

A

Nucleolus

129
Q

How are proteins synthesized

A

Protein part is transported into the nucleus after synthesis in the cytoplasm. The two ribosomal subunits are then exported to the cytoplasm, where they join together

130
Q

What is the design of eukaryotic and prokaryotic ribosomes

A

Both are composed of one large and one small subunit that fit together to form a complete ribosome with a mass of several million daltons

131
Q

What are the functions of eukaryotic and prokaryotic ribosomes

A

The small subunit provides the framework on which the tRNAs can be accurately matched to the codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that link the amino acids together into a polypeptide chain

132
Q

How is the mRNA nucleotide sequence translated into an amino acid sequence

A

The tRNAs are used as adaptors to add each amino acid in the correct sequence

133
Q

Central reaction of protein synthesis is catalyzed by what enzyme contained in the large ribosomal subunit?

A

Peptidyl transferase

134
Q

E-site

A

Exit site: left side

135
Q

P-site

A

Peptidyl-site: middle

136
Q

A-site

A

Aminoacyl-site: right side

137
Q

The ribosome is a large complex composed of

A
  • Two-thirds RNA

- one-third protein

138
Q

RNA molecules that possess catalytic activity

A

Ribozymes

139
Q

What is responsible for the ribosome’s overall structure, its ability to position tRNAs on the mRNA, and its catalytic activity in forming covalent peptide bonds

A

rRNAs

140
Q

What is the main role of the ribosomal proteins and what do they aid in?

A

Stabilize the RNA core while permitting the changes in rRNA conformation necessary for RNA to catalyze efficient protein synthesis. They aid in the initial assembly of the rRNAs that make up the core

141
Q

What codon begins translation of an mRNA

A

AUG

142
Q

What always carries the amino acid methionine

A

Initiator tRNA

143
Q

The mitiater tRNA-methionine complex is first loaded into the small ribosomal subunit along with what proteins

A

Eukaryotic initiation factors (eIFs)

144
Q

How does the small ribosomal subunit know where to bind?

A

It recognizes the 5’ end by its 5’ cap and its two bound initiation factors, eIF4E (which directly birds the cap) and eIF4G

145
Q

What does this image show

A

An “export-ready” mRNA molecule and its transport through the nuclear pore

146
Q

Where does the initiator tRNA bind?

A

P-site

147
Q

How do we know protein synthesis is ready to begin?

A
  1. Small ribosomal submit moves forward 5’ to 3’ looking for AUG
  2. Initiation factors dissociate
  3. Large ribosomal subunit assembles
  4. Initiator tRNA still bound to P-site leaving A-site vacant
148
Q

Why would scanning ribosomal subunits sometimes ignore the first AUG codon in mRNA

A

The recognition site differs substantially from the consensus recognition sequence

149
Q

The process of ignoring the first or second AUG codon is known as

A

Leaky scanning

150
Q

Bacterial mRNAs lack what to signal the beginning of translation?

A

5’ caps

151
Q

What is the name of the binding site that bacterial mRNA contains to begin translation

A

Shine - dalgarno sequence

152
Q

Bacterial mRNAs are what since they encode several different proteins, each of which is translated from the same mRNA molecule

A

Polycistronic or polygenic

153
Q

A eukaryotic mRNA encodes how many proteins

A

One

154
Q

Prokaryotic mRNA molecules contain multiple what?

A

Open reading frames (ORFs)

155
Q

Three stop codons

A

UAA, UAG, UGA

156
Q

What proteins bind to any ribosome with a stop codon positioned in the A-site forcing peptidyl transferase to catalyze the addition of a water molecule

A

Release factors

157
Q

Where does the protein chain go once completed?

A

The cytoplasm

158
Q

What does the ribosome do once the protein chain is released

A

Release the mRNA and separates into the large and small subunits which can assemble on this or another mRNA molecule to begin a new round of protein synthesis

159
Q

When one type of macromolecule resembles the shape of a chemically unrelated molecule. Release factors are an example of

A

Molecular mimicry

160
Q

Large cytoplasmic assembly made up of several ribosomes spaced as close as 80 nucteotides apart along a single mRNA molecule. Proteins are made on these

A

Polyribosomes or polysomes

161
Q

Allows more than one protein to be synthesized from a single mRNA

A

Translational frameshifting

162
Q

Members of a large group of eukaryotic-infecting pathogens that use translational frameshifting

A

Retroviruses

163
Q

Translational frameshifting occurs at a particular codon in the mRNA and requires a specific

A

Recoding signal

164
Q

Who discovered penicillin and how

A

Sir Alexander Fleming noticed that colonies of bacteria were being lysed by a fungal contaminant

165
Q

To be useful to the cell, the new polypeptide chain must

A
  • Fold into its three-dimensional conformation
  • bind any requiring small-molecule cofactors
  • be appropriately modified by protein kinases or other protein-modifying enzymes
  • assemble correctly with other protein subunits
166
Q

The information needed for a polypeptide chain to be useful is contained where

A

The sequence of linked amino acids

167
Q

Dynamic and flexible state for protein domains

A

Molten globule

168
Q

Helps convert unfolded or partially folded proteins to their final compact conformation

A

Molecular chaperones

169
Q

What are molecular chaperones called because they are synthesized in increased amounts after brief exposure to an elevated temperature

A

Heat-shock proteins (Hsp)

170
Q

What helps to fold proteins in the endoplasmic reticulum

A

A special Hsp70 called BIP

171
Q

How does Hsp70 function?

A

Acts early in the life of proteins, binding to about seven hydrophobic amino acids before the protein leaves the ribosome

172
Q

How does Hsp60 function?

A

Form a large barrel shaped structure that acts after a protein has been fully synthesized

173
Q

When misfolded proteins are fed, preventing their aggregation and providing them with a favorable environment to attempt to refold it forms

A

An isolation chamber

174
Q

Chaperones use many cycles of what to fold a polypeptide chain correctly

A

ATP hydrolysis

BIO 220 (5 decks)

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