Week 10: Transcription Flashcards
(177 cards)
1
Q
What are the components of the central dogma?
A
DNA replication →Transcription RNA → Translation Protein
2
Q
How much of genomes in the body code for proteins?
A
1.5%
3
Q
In what ways does the biological significance of noncoding sequences remain unclear?
A
- Some DNA regions directly participate in the regulation of gene expression
- Some DNA encodes for small regulatory RNA (poorly understood)
- Some DNA may be junk
4
Q
What are exons?
A
Expressed sequences that are translated into amino acid sequence
5
Q
How much of DNA is exons?
A
1.5%
6
Q
What are introns?
A
Regions of genes that are transcribed but not translated
7
Q
What is a mature transcript?
A
Introns are removed after transcription and the exon nRNA sequences are spliced together
8
Q
What are centromeres?
A
Region where 2 daughter chromosomes are held together during mitosis
9
Q
What is the purpose of centromeres?
A
Essential for equal distribution of chromosomes sets to daughter cells
10
Q
What are telomere sequences?
A
Repetitive nucleotide sequence at the ends of liner chromosomes that protect the ends for deterioration during DNA replication
11
Q
How are telomeres associated with cellular aging?
A
Telomeres shorten after each round of replication
12
Q
What are components of a nucleoside?
A
Phosphate Base + Riboseugar
13
Q
What are the components of a nucleotide?
A
Nucleoside + 3 phosphates
14
Q
What is a oligonucleotide?
A
Polymers of nucleotides that lose 2 phosphates
15
Q
What is a dsDNA chain?
A
Two complete chains H-bond in antiparallel orientation
16
Q
What is a ds helix?
A
Coiling of ds chain
17
Q
What is a chromatin?
A
Ds helix wraps around histone
18
Q
What is a nucleosome?
A
Ds helix wrapped around an octane of histones
19
Q
What is at chromosome?
A
Packed nucleosomes is condensed into chromosome during mitosis
20
Q
What are the cell cycle phases?
A
- G0
- G1
- S phase
- G2
- M
21
Q
What occurs during Go phase?
A
Gap phase for cells who do not divide often or ever
22
Q
What is the pre synaptic gap?
A
G1
23
Q
What is the G1 phase?
A
Cells create organelles for energy and protein production and cells double in size
24
Q
What is the synthesis phase?
A
S
25
What is the S phase?
Cell synthesizes its genetic material so the daughter cell will have identical copies
26
What is the post synaptic gap?
G2
27
What occurs in the G2 phase?
Final stage before cell division used to make sure all components of the cell are present
28
What occurs during the M phase?
Mitosis and cell division
29
What is synthesized during the S phase?
1. DNA is replicated
2. Nucleosomes disassemble and replication begins
3. Histones and other proteins form
4. DNA and histone both double as chromosomes duplicate
5. Histone complex with DNA and nucleosomes are rapidly formed behind the the replication
30
What is the structure of DNA?
1. 2 long polynucleotide chains
2. 4 types of nucleoside subunits
31
What are nucleotides?
The building blocks of DNA and RNA
32
What are the components of a nucleotide?
1. 5 Carbon sugar (deoxyribose or ribose)
2. Phosphate group attached to C-5
3. Nitrogenous base (Pyrimidine or purine)
33
What links several pentose sugars together creating a linear polymer?
Phosphate group
34
What are the types of nitrogenous bases?
Purines and pyrimidines
35
What are the purines?
Adenine
Guanine
36
What are the pyrimidines?
Cytosine
Uracil
Thymine
37
What nitrogenous base is only found in DNA?
Thymine
38
What nitrogenous base is found only in RNA?
Uracil
39
Describe the general structure of nitrogenous bases?
1. Nitrogen containing heteroaromatic molecules
2. Planar or almost planar structures
40
Describe the properties of nitrogenous bases?
1. All bases are good H-bond donors and acceptors
2. Neutral molecule at pH 7
3. Carbon and nitrogen atoms of base are numbered in cyclic normal
41
How does the pentose ring attach to the nitrogenous base?
N-glycosidic bond
42
Where is the N-glycosidic bond formed?
The anomeric carbon of the sugar in beta configuration
43
Where is the N-glycosidic bond formed?
1. To position N1 in pyrimidines
2. To position N9 in purines
44
What kind of bond is N-glycosidic bond?
Phosphodiester bond
45
What is a nucleic acid?
The backbone of DNA and RNA consisting of sugars linked by phosphodiester bonds between 3' hydroxyl of one sugar and 5' hydroxyl of an adjacent sugar
46
What occurs during a phosphodiester linkage?
The formation of 2 ester bonds by phosphoric acid
47
What does it mean when the nucleic acid has directionality?
1. A phosphorylation group attached to the 5' carbon atom of the sugar
2. 3' carbon of the sugar has a free hydroxyl
3. Nucleic acid sequences are written in the 5' to 3' direction
48
What is the primary structure of a nucleic acid?
Sequence of bases along the pentose phosphodiester backbone of a DNA molecule
49
What is the secondary structure of nucleic acid?
Base pairing
50
What is base pairing?
Each DNA molecule consists of 2 polypeptide chains joined by H-bonds between the bases forming base pairs
51
What is coupled during a base pair?
Purine h-bonded to a pyrimidine
52
How many H-bonds is between Adenine and Thymine?
2
53
How many H-bonds are between Cytosine and Guanine?
3
54
What is the purpose of base pairing?
Allows a strand of DNA to serve as a template for the synthesis of a complementary strand of RNA
55
What is the 3-D structure of DNA?
Double helix
56
What is the hydrophilic portion of a double helix?
1. Sugar-phosphate backbones are solvent exposed (hydrophilic)
57
What is the hydrophobic portion of the double helix?
Bases pairs being perpendicular to backbone causing stacking to minimize solvent exposure
58
Describe the layout of a double helix?
1. 2 chains differ in sequence
2. Chains are complementary
3. Complementary strands run antiparallel
4. 2 Strands twist to form a double helix
59
What is the normal physiological form of the double helix?
B-form
60
How many base pairs make a complete turn of DNA?
10
61
What stabilizes the helix?
The electrons of the base pairs interact generate hydrophobic stacking forces
62
What generates hydrophobic stacking forces of DNA?
Van der Waals interactions of pi-cloud electrons
63
What are helical grooves?
Where bases interact with proteins and other molecules
64
What make RNA different from DNA?
1. Single-stranded
2. Long, unbranched chains of nucleotides joined by phosphodiester bonds
3. b-D-ribose
4. Uracil
65
How many types of RNA are there?
6
66
What is a mRNA?
Carries and encode genetic messages from the cytoplasm from the nucleus
67
What does sequence of bases in DNA encode?
Genetic information
68
What occurs during replication?
Process of duplicating DNA where 1 parent strand is converted in the new DNA molecule
69
What occurs during transcription?
Process of forming RNA on a DNA template where base sequence of DNA is reflected in the base sequence of RNA
70
What occurs during translation?
Process of protein synthesis where amino acid sequence of the protein reflects the sequence go bases in the gene that codes for the protein
71
What is a genome?
Complete cell DNA sequence
72
What is semiconservative replication?
The replication that occurs when 2 daughter helices have one parent strand and one newly synthesized strand
73
What catalyzes DNA synthesis
DNA polymerase
74
What are the components of a new DNA molecule?
1. A Daughter strand
2. A parent strand
75
What happens to the DNA when it is not being replicated?
It is tightly coiled and must be uncoiled and separated into 2 singe strands (supercoiling)
76
What is the origin of replication?
The site in which the DNA is unwound
77
How many origin of replications does a prokaryote have?
1
78
How many origin of replications does an eukaryote have?
several
79
What occurs at the origin of replication?
Generation of new DNA proceeds in both direction creating replications forks
80
What is the purpose of helicase?
Unwinds the helix generating singe-stranded regions of DNA
81
What is the function of SSB proteins?
Keeps the strands from reassociating and binds to ssDNA to stabilize it
82
What does topoisomerase II achieve?
Relieves the strain on the DNA helix by making a double strand break using ATP hydrolysis
83
How is the DNA unzipped?
Opposing directions, both toward and away from the replication fork
84
What is the difference between leading and lagging strand?
Leading: made continuously as the replication fork advances
Lagging: Copied in the direction away from the replication fork, made discontinuously in short pieces (okazaki fragments) that are joined together to make a continuous strand
85
What is DNA polymerase responsible for?
Adding individual nucleotides to the growing strand required by a RNA primer
86
What is a primase?
Generates the RNA primer needed to generate the new strand
87
What replaces RNA primers?
DNA
88
In what direction does DNA synthesis proceed?
5' -> 3'
89
What binds Okazaki fragments?
DNA ligase
90
What are the disadvantages of the lagging strand?
More subject to errors
91
Because DNA polymerase can't initiate synthesis of complementary strand, what does it require for activation?
1. RNA primer (4 ribonucleoside triphosphates)
2. All 4 deoxyribonucleoside triphosphate
3. Mg2+
4. DNA template
92
What are the ribonucleoside triphosphates?
ATP, UTP, GTP, CTP
93
What are the deoxyribonucleoside triphosphates?
dTTP, dATP, dGTP, dCTP
94
What does an RNA primer consist of?
A short stretch of RNA H-bonded to the template DNA with a free 3 OH group serving as the first acceptor of a DNA nucleotide by DNA polymerase
95
What is proofreading?
Removing incorrect nucleotides during DNA replication
96
What is repair?
Removing incorrect nucleotides from DNA and replacing them with correct ones
97
What occurs during the packaging of DNA?
1. DNA molecule could around itself into a supercoil
2. DNA wraps around histone forming chromatin
3. Chromatin packs together into nucleosomes
4. Nucleosomes are condensed into chromosomes
98
What direction does polymerization occurs?
1. Daughter strand 5' to 3' direction
2. Strands are antiparallel
3. Template strand is 3' -> 5'
99
Why does DNA polymerase require a template?
DNA cannot be made from scratch
100
Why does DNA polymerase require a primer
1. Can only add nucleotides to an existing chain
2. Primase begins replication by creating the small RNA primer needed by DNA pol
3. RNA primer is later replaced by DNA
101
What is a mutation?
The alteration of a cell's DNA
102
What happens to badly damaged DNA?
Apoptosis
103
What is a lesion
Errors in DNA synthesis and if the damage can't be repaired, it leads to a permanent change
104
What is a point mutation?
Single nucleotide substitution
105
What is the difference between transition and transversion?
Transition: purine changed to another purine or pyrimidine changed to another pyrimidine
Transversion: Purine changed to a pyrimidine (vice versa)
106
What are examples of point mutation?
Transition and transversion
107
What is a frameshift mutation?
Alters the codon translation reading frame
108
What are examples of frameshift mutation?
Deletion and insertion
When the number of bases added or deleted is not a multiple of 3
Shifts the reading frame so that completely different sets of codons are read from the point where the mutation started
109
What is deletion?
Deletion of at least 1 nucleotide
Base or number of bases are removed from DNA (protein has fewer aa than normal)
110
What is insertion?
Insertion of at least 1 nucleotide
When a base or number of bases are added to DNA (protein with more aa than normal)
111
What arises from occasional incorporation of incorrect nucleotides due to mistakes by DNA polymerase?
Mismatched bases
112
What is a silent mutation?
Base substitutions that do not alter the amino acid sequence encoded by the gene
3rd base of a codon and don't alter codon specificity, no effect of the protein sequence
113
What are mutation hot spots?
Have higher mutation rate than most DNA
114
What is a spontaneous deprivation?
Glycosidic bond connecting base to ribose sugar is broken
115
What is spontaneous deamination?
1. Removal of an amine group
2. Cytosine can deaminated to uracil
3. Methylated cytosine can deaminated to thymine
116
How spontaneous is depurination?
18,000 times/day
117
How spontaneous is deamination?
500 times/day
118
What are examples of chemical agents?
Abnormal bases arise from spontaneous deamination, chemical alkylation, or exposure to free radicals
119
What can cause changes in DNA and gene expression?
Environmental mutagens
120
What are examples of physical agents?
1. Pyrimidine dimers form when DNA is exposed to UV light
2. Backbone lesions occur from exposure to ionizing radiation and free radicals causing dsDNA breaks and cross-links
121
What are the types of DNA repair mechanisms?
1. Nucleotide excision repair
2. Base excision repair
3. Mismatch repair
122
What is nucleotide excision repair?
1. Used to repair mismatched base or bulky adducts
2. Removes the region around modified base or single-strand break by cutting the DNA strand on either side of the lesion and filling the resulting gap
123
What is base excision repair?
1. Used to repair damage to single base
2. Removes abnormally modified bases by glycosylases and replaces them with appropriate bases
124
What is mismatch repair?
1. Fixes errors that escape proofreading
2. Involves both base-excision and nucleotide excision repair mechanisms
125
What is gene expression?
The process where information contained on the gene has effects in the cell
126
What is transcription?
The synthesis of RNA using DNA as a template
127
What must happen for gene expression to occur?
Genetic information must be transcribed from DNA to RNA and then be expressed as protein
128
Which nucleic acid is less stable?
RNA
129
What is tRNA?
Carries amino acids from cytoplasm to the ribosome to the growing protein
130
What is rRNA?
Produced in the nucleus and is used for protein assembly in the cytoplasm
131
How is mRNA created
Transcription from DNA
132
What is a manocistronic?
1 gene, 1 product
Eukaryotic mRNA
133
Once transcripted where does mRNA go?
From the nucleus to the cytoplasm for translation into proteins
134
What are the 3 stages of transcription?
1. Initiation
2. Elongation
3. Termination
135
How does RNA polymerase differ from DNA polymerase?
1. 6 subunits
2. Requires no primer
3. No proofreading capability
4. Lacks 3' to 5' exonuclease
5. Has a high error rate
6. Binds to promoter regions to initiate transcription
136
What happens at initiation of transcription?
1. DNA is unwound to access the gene of interest
2. Transcription occurs only 5' to 3'
3. Catalyzed by RNA polymerase
4. Begins at the promoter site and ends at termination sequence
137
What are the steps of initiation?
1. RNA polymerase II binds and scans along the DNA searching for appropriate promoter
2. Binds to TATA box within the promoter region
3. RNA pol II unwinds 17 base pairs of DNA to form transcription bubble
4. RNA pol II forms the first phosphodiester bond between ribonucleotides to initiate new chain
138
What occurs during the elongation of transcription?
1. Transcript elongates by incorporating ribonucleotides to create a RNA complement of DNA template
2. RNA pol unwinds the DNA and transcription bubble forms
3. Ribonucleotides are added4. DNA topoisomerase prevent supercoiling ahead and behind the moving transcription bubble
139
What occurs during termination of transcription?
1. RNA polymerase reaches a termination sequence, the RNA polymerase dissociates from DNA
2. Transcription is terminated
3. DNA helix reforms and the newly formed RNA is pre-mRNA
140
What happens in post-transcriptional processing of mRNA?
1. pre-mRNA must undergo 3 processes to become mRNA that can interact with the ribosome in the cytoplasm and before it can leave the nucleus
2. A 5'guanosyl cap is added to stabilize the end
3. Poly A tail is added to protect 3' end
4. Removal of introns and splicing the coding region (exons) together
141
What doesn't appear in the final sequences of mRNA of the gene product?
intervening base sequences of eukaryotic genes
142
What are exons?
DNA sequences that expressed in the mRNA sequence
143
What are introns?
Intervening DNA sequences that are not expressed in the final mRNA sequence
144
How are introns removed?
1. Removal of introns happen in the nucleus
2. Spliceosomes coordinate the cleavage at the 5' and 3' end of the introns and the joining of the 2 ends of the extrons
145
What is alternative splicing?
Gene expression can be controlled at the level of RNA splicing
146
What are isoforms?
Different forms of a protein produced by alternative splicing reactions
147
What are the different peptides a single gene can yield from RNA processing?
1. Isoforms
2. Two forms of the mRNA in the same cell
3. One form in one tissue, but a different in another
148
What percent of human genes are alternatively spliced?
50%
149
What are transcription factors?
The control for activation or inhibition of DNA polymerase for the expression of individual genes
150
What is a regulatory factor?
Can bind to distant sites from the promoter to turn transcription on or off
151
What influences the rate of transcription initiation?
RNA pol-promoter
152
What are regulatory proteins?
Work to enhance or inhibit RNA pol-DNA promoter interaction
153
What is a codon?
A triplet of 3 nucleotides specifying an amino acid
154
How do you translate the language of RNA to proteins?
Codons are read as the sequence of mRNA and translated into protein sequences
155
How many words are in a genetic code?
64
156
What causes redundancy in genetic code?
Excess of codons
157
What is the start codon?
AUG
158
What are the stop codons?
UAA, UAG, UGA
159
What are the the most common amino acids coded by codons?
Leu and Gly
160
When can translation begin?
Once mRNA is in the cytoplasm
161
What is required for translation?
1. mRNA transcript
2. tRNA
3. Amino acids
4. Ribosome
5. Energy
162
What are the steps of translation?
1. Initiation
2. Elongation
3. Termination
163
What is carried by a tRNA?
Anticodon
164
What is an anticodon?
A sequence of ribonucleotides that is complementary to the codon the tRNA translates
165
What is the key step in translation?
The specific base pairing between the tRNA anticodon and the mRNA codon
166
Where does the amino acid attaches to the tRNA?
Amino acid acceptor site in the tRNA
167
What is the purpose of aminoacyl-tRNA complex?
Occurs when the amino acid is attached to the tRNA by tRNA synthetase generating a charged tRNA
168
What are the components of a ribosome?
1. Macromolecule consisting of protein and rRNA
2. A small and large subunit
3. Brings together the aminoacyl-tRNA complex and the mRNA to generate protein
169
What do ribosomes bind to?
1. mRNA
2. tRNA (A, P, and E sites)
170
What is the A site?
Where tRNA delivers aa
171
What is the P site?
Where the growing polypeptide chain still attached to a tRNA
172
What is the E site?
Exit that contains the empty tRNA
173
Describe the initiation of translation
1. mRNA binds to active site of small ribosomal subunit
2. Small ribosome slides along the mRNA until it reaches the start codon (5' to 3')
3. Initiation aminoacyl-tRNA complex base pairs with start codon
4. ATP provides the energy for this process
5. Large subunit joins the complex completing the ribosome
6. tRNA is in the P site
174
Describe elongation of translation?
1. Ribosome slides along the mRNA adding new aa
2. H bonds form between mRNA codon in the A site and the tRNA anticodon
3. A and P sites are charged with aminoacyl-tRNA
4. Peptidyl transferase forms peptide bonds between aa from tRNA in P site to A site
5. Empty tRNA is released form E site
6. Ribosome shifts from 5' to 3' to next codon
175
Describe termination of translation
1. tRNA with growing polypeptide chain is now in the P site
2. A newly charged aminoacyl-tRNA with correct anticodon moves to A site
3. Continues until stop codon
4. A release factor binds to the termination codon and the polypeptide chain is released from P site and 2 ribosomal subunits dissociates
176
What is a nonsense mutation?
Change a codon specifying an amino acid to a stop codon which terminates translation and causes the production of a truncated protein
177
What is a missense mutation?
Changes in the codon specificity from 1 amino acid to another, altering protein sequence affecting function (sickle cell)
