Chapter 6 Flashcards
1
Q
When a cell needs a particular protein, appropriate portion is first copied into RNA through a process called
A
Transcription
2
Q
RNA copies are used directly as templates to direct the synthesis of the protein in a process called
A
Translation
3
Q
What is the central dogma of molecular biology?
A
The flow of genetic information in cells from DNA to RNA to protein
4
Q
What type of bonds link RNA nucleotide subunits
A
Phosphodiester
5
Q
What are the chemical differences between RNA and DNA
A
- The nucleotides in RNA are ribonucleotides containing the sugar ribose
- RNA contains uracil instead of thymine
6
Q
Stages of transcription: initiation
A
RNA polymerase binds to a promoter, where the helix unwinds and transcription starts
7
Q
Stages of transcription: elongation
A
RNA nucleotides are added to the chain
8
Q
Stages of transcription: termination
A
RNA polymerase reaches a terminator sequence and detaches from the template
9
Q
Enzyme that performs transcription
A
RNA polymerase
10
Q
What enzyme catalyzes the formation of the phosphodiester bonds that link the nudeotides together to form a linear chain
A
RNA polymerase
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
12
Q
Unlike DNA, RNA does not…
A
Permanently store genetic information in cells
13
Q
After catalyzing the links of ribonucleotides, RNA polymerase can
A
Start an RNA chain without a primer
14
Q
Are DNA and RNA polymerases structurally related?
A
No, other than containing Mg^2+ ion at the catalytic site, they are unrelated
15
Q
Inorganic enzymes
A
Cofactor
16
Q
Organic enzymes
A
Co-enzymes
17
Q
RNA molecules that are copied from genes
A
Messenger RNA (mRNA)
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)
19
Q
Molecules that serve as key regulators of eucaryotic gene expression
A
MicroRNA (miRNA) and small interfering RNA (siRNA)
20
Q
Each transcribed segment of DNA is called
A
Transcription Unit
21
Q
Carries the information of just one gene, and codes for either a single RNA molecule or a single protein
A
Transcription unit
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
23
Q
Together, sigmas factor and core enzyme are known as
A
RNA polymerase holoenzyme
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
25
A special sequence of nucleotides indicating the starting point for RNA synthesis
Promoter
26
When the polymerase holoenzyme slides into a promoter polymerase binds
Tightly to this DNA
27
After DNA polymerase holoenzyme binds to promoter DNA it
Opens up the double helix to expose a short stretch of nucleotides on each strand
28
What happens afthe the first ten nucleotides of RNA have been synthesized?
1. Core enzyme breaks it interactions with promoter DNA
| 2. Weakens its interactions with sigma factor and begins to moved down the DNA
29
Chain elongation continues until the enzyme encounters a second signal in the DNA called
Terminator
30
What causes the polymerase to halt and release the new RNA chain and DNA template
Terminator
31
How do the termination signals in the DNA stop the elongating polymerase?
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
32
The formation of the hair pin may help
To “pull” the RNA transcript from the active site
33
Transcription initiation difference between eukaryotes and bacteria
Bacteria has RNA polymerase
| Eukaryotes have RNA polymerase I, RNA polymerase II, and RNA polymerase III
34
Centrifugation measures
RNA's sedimentation coefficient
35
Transcribes the genes encoding transfer RNA, ribosomal RNA, and various small RNAs
RNA polymerases I and III
36
Transcribes most genes, including all those that encode proteins
RNA polymerase II
37
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
General transcription factors that RNA polymerase II requires
38
General transcription factors carry out functions equivalent to
Sigma factor in bacteria
39
TFII
Transcription factor for polymerase II
40
TBP
TATA box binding protein
41
Subunit of TFII
TBP
42
Short DNA sequence primarily composed of T and A nucleotides
TATA box
43
Where is the TATA box located and what does it allow for
25 nucleotides upstream from transcription start site allowing for subsequent protein assembly steps
44
Other factors assemble along with RNA polymerase II to form a complete
Transcription initiation complex
45
Most complicated of the general transcription factors is and why
TFIIH - consists of 9 subunits, as large as RNA polymerase II, and performs several enzymatic steps needed for the initiation of transcription
46
How does polymerase II gain access to the template strand at the transcription start point?
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
47
Where are phosphate groups added to on the RNA polymerase
The tail or C-terminal
48
In humans, the CTD consists of
52 tandem repeats of a seven-amino-acid sequence
49
When are most of the general transcription factors released from DNA
Once the polymerase II has begun elongating the RNA transcript
50
Gene regulatory proteins
Transcriptional activators
51
Protein complex that allows the activator proteins to communicate properly with the polymerase II and general transcription factors
Mediator
52
Transcription initiation requires the local recruitment of
Chromatin-modifying enzymes
53
Proteins that decrease the likelihood that RNA polymerase will dissociate before it reaches the end of a gene
Elongation factors
54
Help polymerases to move through the wide variety of different DNA sequences that are found in genes
Elongation factors
55
What happens once RNA polymerase II has produced 25 nucleotides of RNA
A cap that consists of a modified guanine nucleotide is added to the 5’ end
56
What 3 enzymes perform the capping reaction
Phosphatase, guanyl transferase, methyl transferase
57
Enzyme that removes a phosphate from the 5’ end of the developing RNA
Phosphatase
58
What enzyme adds a GMP in a reverse linkage (5’ to 5’ instead of 5’ to 3’)
Guanyl transferase
59
What enzyme adds a methyl group to the guanosine
Methyl transferase
60
What helps the cell to distinguish mRNAs from other types of RNA molecules present
5’ cap
61
Noncoding intervening sequences
Introns
62
Expressed sequences
Exons
63
Which sequences are longer, introns or exons?
Introns
64
Intron sequences are removed from the newly synthesized RNA through the process of
RNA splicing
65
The majority of RNA splicing focuses on
Precursor-mRNA or pre-mRNA splicing
66
Describe a splicing event
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
67
Phosphoryl- transfer reactions when splicing
Transesterifications
68
Why does pre-mRNA splicing occur
Introns in DNA allows genetic recombination, enabling genes for new proteins to evolve more easily by the combination of parts of preexisting genes
69
Benefit of alternative splicing
Allows the same gene to produce a corresponding set of different proteins
70
What signals where splicing occurs
Nucleotide sequences
71
What 3 portions of the precursor RNA molecule must be recognized by splicing machinery
1. 5’ splice site
2. 3’ splice site
3. Branch point in the intron sequence that forms the base of the excised lariat
72
RNA splicing is performed by
Sliceosome
73
Where is a spliceosome found
Within the splicing speckles of the cell nucleus of eukaryotic cells
74
What forms a spliceosome and what is it assembled from?
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
What snRNAs male up the major spliceosome
U1, U2, U4, U5 U6
76
Removes introns from a transcribed pre-mRNA, a type of primary transcript
Spliceosome
77
During splicing, recognition of the 5’ splice site, the branch-point site, and 3’ splice site is performed largely through base-pairing between
snRNAs and RNA sequences in the pre-mRNA substrate
78
Two multisubunit proteins important for 3' end of each mRNA molecule
- CstF
| - CPSF
79
CstF
Cleavage stimulation factor
80
CPSF
Cleavage and polyadenylation specificity factor
81
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
CstF and CPSF
82
What happens after RNA is cleaved
Poly-A polymerase (PAP) enzyme one at a time adds 200 A nucleotides to the 3' end
83
As the poly-A tail is synthesized what proteins assemble onto it
Poly-A-binding proteins
84
What does the newly synthesized RNA that has emerged lack after 3' end cleavage has occurred?
A 5' cap
85
How does the cell distinguish between mature mRNA molecules and debris from RNA processing (excised introns, broken RNAs)?
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
A properly completed mRNA molecule is distinguished by
The protein it lacks
87
The presence of snRNP on a mRNA molecule signifies
Incomplete or abnormal splicing
88
Improperly processed mRNAs and other RNA debris are retained in the nucleus where they are degraded by
Nuclear exosome rich in 3’-to-5’ RNA exonucleases
89
hnRNP
Heterogeneous nuclear ribonuclear proteins
90
Proteins that assemble on pre-mRNA molecules that unwind the hairpin helices so that splicing and other signals can be read more easily
hnRNPs (heterogeneous nuclear ribonuclear proteins)
91
Successfully processed mRNAs are guided through
Nuclear pore complexes (NPCs)
92
Macromolecules are moved through nuclear pore complexes by
Nuclear transport receptors
93
Dissociates from the mRNA after transport, re-enters the nucleus, and exports a new mRNA molecule
Nuclear transport receptors
94
As genes are transcribed, the newly formed RNA is seen to be packaged by what proteins?
hnRNPs, SR proteins, components of the spliceosome
95
Structures that gain and lose numerous specific proteins during RNA synthesis, processing, and export
Pre-mRNA-protein and mRNA-protein
96
Polymerase dedicated to producing rRNAs
RNA polymerase I
97
Reason why polymerase I’s transcripts are neither capped nor polyadenylated
Absence of a C-terminal tail
98
One copy per ribosome, what are the four types of eukaryotic rRNAs
18S, 5.8S, 28S, 5SRNA
99
Which 3 eukaryotic rRNAs are made by chemically modifying and cleaving a single large precursor rRNA
18S, 5.8S, 28S
100
Which eukaryotic rRNA is synthesized from a separate cluster of genes by a different polymerase, RNA polymerase III, and does not require chemical modification
5SRNA
101
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
Small nucleolar RNAs (snoRNAs)
102
The site for the processing of rRNAs and their assembly into ribosome subunits. Not bound by a membrane
Nucleolus
103
The nucleolus is a large aggregate of macromolecules including:
- The rRNA genes themselves
- precursor rRNAs
- mature rRNAs
- rRNA-processing enzymes
- snoRNPs (small nuclear ribonuclear proteins)
- ribosomal proteins
- partly assembled ribosomes
104
Site where other RNAs are produced and other RNA-protein complexes are assembled
Nucleolus
105
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
The genetic code
106
How many different amino acids are commonly found in proteins
20
107
Group of three consecutive nucleotides in RNA
Codon
108
Each codon specifies
Either one amino acid or a stop to the translation process
109
Adaptors that consist of a set of small RNA molecules that translate mRNA into protein and can recognize and bind both to the codon
Transfer RNAs (tRNAs)
110
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
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
What are the 2 possible explanations why several different codons can specify a single amino acid
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
Accurate base-pairing for first 2 positions of the codon but tolerable mismatch for third
Wobble
113
Eukaryotic tRNAs are synthesized by
RNA polymerase III
114
How do pre-mRNA splicing and tRNA splicing differ?
Pre-mRNA splicing generates a lariat intermediate
| tRNA splicing uses a cut-and-paste mechanism catalyzed by proteins
115
What are 4 examples of tRNA modifications
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
Enzyme that covalently couples each amino acid to its appropriate set of tRNA molecules
Aminoacyl-tRNA synthetases
117
For each amino acid most cells have
A different synthetase enzyme
118
First step in selecting correct amino acid for tRNA
The correct amino acid has the highest affinity for the active-site pocket of its synthetase
119
Problem with first step in selecting correct amino acid for tRNA
Two similar amino acids
120
Second step in selecting the correct amino acid for tRNA
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
The tRNA syntheses must also recognize
The correct set of tRNAs
122
What is the fundamental reaction of protein synthesis
The formation of a peptide bond between the carboxyl group and a free amino group on an incoming amino acid
123
What is the general structure of an amino acid?
124
What kind of reaction forms a peptide bond
Dehydration
125
How is a peptide bond formed?
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
To maintain the correct reading frame and to ensure accuracy, protein synthesis is performed in the
Ribosome
127
A complex catalytic machine made from more than 50 different proteins (the ribosomal proteins) and several RNA molecules
Ribosomal RNAs (rRNAs)
128
Where are eukaryotic ribosome subunits assembled
Nucleolus
129
How are proteins synthesized
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
What is the design of eukaryotic and prokaryotic ribosomes
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
What are the functions of eukaryotic and prokaryotic ribosomes
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
How is the mRNA nucleotide sequence translated into an amino acid sequence
The tRNAs are used as adaptors to add each amino acid in the correct sequence
133
Central reaction of protein synthesis is catalyzed by what enzyme contained in the large ribosomal subunit?
Peptidyl transferase
134
E-site
Exit site: left side
135
P-site
Peptidyl-site: middle
136
A-site
Aminoacyl-site: right side
137
The ribosome is a large complex composed of
- Two-thirds RNA
| - one-third protein
138
RNA molecules that possess catalytic activity
Ribozymes
139
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
rRNAs
140
What is the main role of the ribosomal proteins and what do they aid in?
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
What codon begins translation of an mRNA
AUG
142
What always carries the amino acid methionine
Initiator tRNA
143
The mitiater tRNA-methionine complex is first loaded into the small ribosomal subunit along with what proteins
Eukaryotic initiation factors (eIFs)
144
How does the small ribosomal subunit know where to bind?
It recognizes the 5' end by its 5' cap and its two bound initiation factors, eIF4E (which directly birds the cap) and eIF4G
145
What does this image show
An "export-ready" mRNA molecule and its transport through the nuclear pore
146
Where does the initiator tRNA bind?
P-site
147
How do we know protein synthesis is ready to begin?
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
Why would scanning ribosomal subunits sometimes ignore the first AUG codon in mRNA
The recognition site differs substantially from the consensus recognition sequence
149
The process of ignoring the first or second AUG codon is known as
Leaky scanning
150
Bacterial mRNAs lack what to signal the beginning of translation?
5' caps
151
What is the name of the binding site that bacterial mRNA contains to begin translation
Shine - dalgarno sequence
152
Bacterial mRNAs are what since they encode several different proteins, each of which is translated from the same mRNA molecule
Polycistronic or polygenic
153
A eukaryotic mRNA encodes how many proteins
One
154
Prokaryotic mRNA molecules contain multiple what?
Open reading frames (ORFs)
155
Three stop codons
UAA, UAG, UGA
156
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
Release factors
157
Where does the protein chain go once completed?
The cytoplasm
158
What does the ribosome do once the protein chain is released
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
When one type of macromolecule resembles the shape of a chemically unrelated molecule. Release factors are an example of
Molecular mimicry
160
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
Polyribosomes or polysomes
161
Allows more than one protein to be synthesized from a single mRNA
Translational frameshifting
162
Members of a large group of eukaryotic-infecting pathogens that use translational frameshifting
Retroviruses
163
Translational frameshifting occurs at a particular codon in the mRNA and requires a specific
Recoding signal
164
Who discovered penicillin and how
Sir Alexander Fleming noticed that colonies of bacteria were being lysed by a fungal contaminant
165
To be useful to the cell, the new polypeptide chain must
- 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
The information needed for a polypeptide chain to be useful is contained where
The sequence of linked amino acids
167
Dynamic and flexible state for protein domains
Molten globule
168
Helps convert unfolded or partially folded proteins to their final compact conformation
Molecular chaperones
169
What are molecular chaperones called because they are synthesized in increased amounts after brief exposure to an elevated temperature
Heat-shock proteins (Hsp)
170
What helps to fold proteins in the endoplasmic reticulum
A special Hsp70 called BIP
171
How does Hsp70 function?
Acts early in the life of proteins, binding to about seven hydrophobic amino acids before the protein leaves the ribosome
172
How does Hsp60 function?
Form a large barrel shaped structure that acts after a protein has been fully synthesized
173
When misfolded proteins are fed, preventing their aggregation and providing them with a favorable environment to attempt to refold it forms
An isolation chamber
174
Chaperones use many cycles of what to fold a polypeptide chain correctly
ATP hydrolysis
