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Biochemistry > Week 10: Transcription > Flashcards

Week 10: Transcription Flashcards

1
Q

What are the components of the central dogma?

A

DNA replication →Transcription RNA → Translation Protein

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2
Q

How much of genomes in the body code for proteins?

A

1.5%

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3
Q

In what ways does the biological significance of noncoding sequences remain unclear?

A
  1. Some DNA regions directly participate in the regulation of gene expression
  2. Some DNA encodes for small regulatory RNA (poorly understood)
  3. Some DNA may be junk
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4
Q

What are exons?

A

Expressed sequences that are translated into amino acid sequence

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5
Q

How much of DNA is exons?

A

1.5%

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6
Q

What are introns?

A

Regions of genes that are transcribed but not translated

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7
Q

What is a mature transcript?

A

Introns are removed after transcription and the exon nRNA sequences are spliced together

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8
Q

What are centromeres?

A

Region where 2 daughter chromosomes are held together during mitosis

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9
Q

What is the purpose of centromeres?

A

Essential for equal distribution of chromosomes sets to daughter cells

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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

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11
Q

How are telomeres associated with cellular aging?

A

Telomeres shorten after each round of replication

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12
Q

What are components of a nucleoside?

A

Phosphate Base + Riboseugar

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13
Q

What are the components of a nucleotide?

A

Nucleoside + 3 phosphates

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14
Q

What is a oligonucleotide?

A

Polymers of nucleotides that lose 2 phosphates

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15
Q

What is a dsDNA chain?

A

Two complete chains H-bond in antiparallel orientation

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16
Q

What is a ds helix?

A

Coiling of ds chain

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17
Q

What is a chromatin?

A

Ds helix wraps around histone

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18
Q

What is a nucleosome?

A

Ds helix wrapped around an octane of histones

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19
Q

What is at chromosome?

A

Packed nucleosomes is condensed into chromosome during mitosis

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20
Q

What are the cell cycle phases?

A
  1. G0
  2. G1
  3. S phase
  4. G2
  5. M
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21
Q

What occurs during Go phase?

A

Gap phase for cells who do not divide often or ever

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22
Q

What is the pre synaptic gap?

A

G1

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23
Q

What is the G1 phase?

A

Cells create organelles for energy and protein production and cells double in size

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24
Q

What is the synthesis phase?

A

S

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25
Q

What is the S phase?

A

Cell synthesizes its genetic material so the daughter cell will have identical copies

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26
Q

What is the post synaptic gap?

A

G2

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27
Q

What occurs in the G2 phase?

A

Final stage before cell division used to make sure all components of the cell are present

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28
Q

What occurs during the M phase?

A

Mitosis and cell division

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29
Q

What is synthesized during the S phase?

A
  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
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30
Q

What is the structure of DNA?

A
  1. 2 long polynucleotide chains
  2. 4 types of nucleoside subunits
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31
Q

What are nucleotides?

A

The building blocks of DNA and RNA

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32
Q

What are the components of a nucleotide?

A
  1. 5 Carbon sugar (deoxyribose or ribose)
  2. Phosphate group attached to C-5
  3. Nitrogenous base (Pyrimidine or purine)
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33
Q

What links several pentose sugars together creating a linear polymer?

A

Phosphate group

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34
Q

What are the types of nitrogenous bases?

A

Purines and pyrimidines

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35
Q

What are the purines?

A

Adenine
Guanine

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36
Q

What are the pyrimidines?

A

Cytosine
Uracil
Thymine

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37
Q

What nitrogenous base is only found in DNA?

A

Thymine

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38
Q

What nitrogenous base is found only in RNA?

A

Uracil

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39
Q

Describe the general structure of nitrogenous bases?

A
  1. Nitrogen containing heteroaromatic molecules
  2. Planar or almost planar structures
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40
Q

Describe the properties of nitrogenous bases?

A
  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
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41
Q

How does the pentose ring attach to the nitrogenous base?

A

N-glycosidic bond

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42
Q

Where is the N-glycosidic bond formed?

A

The anomeric carbon of the sugar in beta configuration

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43
Q

Where is the N-glycosidic bond formed?

A
  1. To position N1 in pyrimidines
  2. To position N9 in purines
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44
Q

What kind of bond is N-glycosidic bond?

A

Phosphodiester bond

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45
Q

What is a nucleic acid?

A

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

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46
Q

What occurs during a phosphodiester linkage?

A

The formation of 2 ester bonds by phosphoric acid

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47
Q

What does it mean when the nucleic acid has directionality?

A
  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
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48
Q

What is the primary structure of a nucleic acid?

A

Sequence of bases along the pentose phosphodiester backbone of a DNA molecule

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49
Q

What is the secondary structure of nucleic acid?

A

Base pairing

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50
Q

What is base pairing?

A

Each DNA molecule consists of 2 polypeptide chains joined by H-bonds between the bases forming base pairs

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51
Q

What is coupled during a base pair?

A

Purine h-bonded to a pyrimidine

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52
Q

How many H-bonds is between Adenine and Thymine?

A

2

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53
Q

How many H-bonds are between Cytosine and Guanine?

A

3

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54
Q

What is the purpose of base pairing?

A

Allows a strand of DNA to serve as a template for the synthesis of a complementary strand of RNA

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55
Q

What is the 3-D structure of DNA?

A

Double helix

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56
Q

What is the hydrophilic portion of a double helix?

A
  1. Sugar-phosphate backbones are solvent exposed (hydrophilic)
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57
Q

What is the hydrophobic portion of the double helix?

A

Bases pairs being perpendicular to backbone causing stacking to minimize solvent exposure

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58
Q

Describe the layout of a double helix?

A
  1. 2 chains differ in sequence
  2. Chains are complementary
  3. Complementary strands run antiparallel
  4. 2 Strands twist to form a double helix
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59
Q

What is the normal physiological form of the double helix?

A

B-form

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60
Q

How many base pairs make a complete turn of DNA?

A

10

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61
Q

What stabilizes the helix?

A

The electrons of the base pairs interact generate hydrophobic stacking forces

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62
Q

What generates hydrophobic stacking forces of DNA?

A

Van der Waals interactions of pi-cloud electrons

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63
Q

What are helical grooves?

A

Where bases interact with proteins and other molecules

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64
Q

What make RNA different from DNA?

A
  1. Single-stranded
  2. Long, unbranched chains of nucleotides joined by phosphodiester bonds
  3. b-D-ribose
  4. Uracil
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65
Q

How many types of RNA are there?

A

6

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66
Q

What is a mRNA?

A

Carries and encode genetic messages from the cytoplasm from the nucleus

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67
Q

What does sequence of bases in DNA encode?

A

Genetic information

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68
Q

What occurs during replication?

A

Process of duplicating DNA where 1 parent strand is converted in the new DNA molecule

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69
Q

What occurs during transcription?

A

Process of forming RNA on a DNA template where base sequence of DNA is reflected in the base sequence of RNA

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70
Q

What occurs during translation?

A

Process of protein synthesis where amino acid sequence of the protein reflects the sequence go bases in the gene that codes for the protein

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71
Q

What is a genome?

A

Complete cell DNA sequence

72
Q

What is semiconservative replication?

A

The replication that occurs when 2 daughter helices have one parent strand and one newly synthesized strand

73
Q

What catalyzes DNA synthesis

A

DNA polymerase

74
Q

What are the components of a new DNA molecule?

A
  1. A Daughter strand
  2. A parent strand
75
Q

What happens to the DNA when it is not being replicated?

A

It is tightly coiled and must be uncoiled and separated into 2 singe strands (supercoiling)

76
Q

What is the origin of replication?

A

The site in which the DNA is unwound

77
Q

How many origin of replications does a prokaryote have?

A

1

78
Q

How many origin of replications does an eukaryote have?

A

several

79
Q

What occurs at the origin of replication?

A

Generation of new DNA proceeds in both direction creating replications forks

80
Q

What is the purpose of helicase?

A

Unwinds the helix generating singe-stranded regions of DNA

81
Q

What is the function of SSB proteins?

A

Keeps the strands from reassociating and binds to ssDNA to stabilize it

82
Q

What does topoisomerase II achieve?

A

Relieves the strain on the DNA helix by making a double strand break using ATP hydrolysis

83
Q

How is the DNA unzipped?

A

Opposing directions, both toward and away from the replication fork

84
Q

What is the difference between leading and lagging strand?

A

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
Q

What is DNA polymerase responsible for?

A

Adding individual nucleotides to the growing strand required by a RNA primer

86
Q

What is a primase?

A

Generates the RNA primer needed to generate the new strand

87
Q

What replaces RNA primers?

A

DNA

88
Q

In what direction does DNA synthesis proceed?

A

5’ -> 3’

89
Q

What binds Okazaki fragments?

A

DNA ligase

90
Q

What are the disadvantages of the lagging strand?

A

More subject to errors

91
Q

Because DNA polymerase can’t initiate synthesis of complementary strand, what does it require for activation?

A
  1. RNA primer (4 ribonucleoside triphosphates)
  2. All 4 deoxyribonucleoside triphosphate
  3. Mg2+
  4. DNA template
92
Q

What are the ribonucleoside triphosphates?

A

ATP, UTP, GTP, CTP

93
Q

What are the deoxyribonucleoside triphosphates?

A

dTTP, dATP, dGTP, dCTP

94
Q

What does an RNA primer consist of?

A

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
Q

What is proofreading?

A

Removing incorrect nucleotides during DNA replication

96
Q

What is repair?

A

Removing incorrect nucleotides from DNA and replacing them with correct ones

97
Q

What occurs during the packaging of DNA?

A
  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
Q

What direction does polymerization occurs?

A
  1. Daughter strand 5’ to 3’ direction
  2. Strands are antiparallel
  3. Template strand is 3’ -> 5’
99
Q

Why does DNA polymerase require a template?

A

DNA cannot be made from scratch

100
Q

Why does DNA polymerase require a primer

A
  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
Q

What is a mutation?

A

The alteration of a cell’s DNA

102
Q

What happens to badly damaged DNA?

A

Apoptosis

103
Q

What is a lesion

A

Errors in DNA synthesis and if the damage can’t be repaired, it leads to a permanent change

104
Q

What is a point mutation?

A

Single nucleotide substitution

105
Q

What is the difference between transition and transversion?

A

Transition: purine changed to another purine or pyrimidine changed to another pyrimidine
Transversion: Purine changed to a pyrimidine (vice versa)

106
Q

What are examples of point mutation?

A

Transition and transversion

107
Q

What is a frameshift mutation?

A

Alters the codon translation reading frame

108
Q

What are examples of frameshift mutation?

A

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
Q

What is deletion?

A

Deletion of at least 1 nucleotide

Base or number of bases are removed from DNA (protein has fewer aa than normal)

110
Q

What is insertion?

A

Insertion of at least 1 nucleotide

When a base or number of bases are added to DNA (protein with more aa than normal)

111
Q

What arises from occasional incorporation of incorrect nucleotides due to mistakes by DNA polymerase?

A

Mismatched bases

112
Q

What is a silent mutation?

A

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
Q

What are mutation hot spots?

A

Have higher mutation rate than most DNA

114
Q

What is a spontaneous deprivation?

A

Glycosidic bond connecting base to ribose sugar is broken

115
Q

What is spontaneous deamination?

A
  1. Removal of an amine group
  2. Cytosine can deaminated to uracil
  3. Methylated cytosine can deaminated to thymine
116
Q

How spontaneous is depurination?

A

18,000 times/day

117
Q

How spontaneous is deamination?

A

500 times/day

118
Q

What are examples of chemical agents?

A

Abnormal bases arise from spontaneous deamination, chemical alkylation, or exposure to free radicals

119
Q

What can cause changes in DNA and gene expression?

A

Environmental mutagens

120
Q

What are examples of physical agents?

A
  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
Q

What are the types of DNA repair mechanisms?

A
  1. Nucleotide excision repair
  2. Base excision repair
  3. Mismatch repair
122
Q

What is nucleotide excision repair?

A
  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
Q

What is base excision repair?

A
  1. Used to repair damage to single base
  2. Removes abnormally modified bases by glycosylases and replaces them with appropriate bases
124
Q

What is mismatch repair?

A
  1. Fixes errors that escape proofreading
  2. Involves both base-excision and nucleotide excision repair mechanisms
125
Q

What is gene expression?

A

The process where information contained on the gene has effects in the cell

126
Q

What is transcription?

A

The synthesis of RNA using DNA as a template

127
Q

What must happen for gene expression to occur?

A

Genetic information must be transcribed from DNA to RNA and then be expressed as protein

128
Q

Which nucleic acid is less stable?

A

RNA

129
Q

What is tRNA?

A

Carries amino acids from cytoplasm to the ribosome to the growing protein

130
Q

What is rRNA?

A

Produced in the nucleus and is used for protein assembly in the cytoplasm

131
Q

How is mRNA created

A

Transcription from DNA

132
Q

What is a manocistronic?

A

1 gene, 1 product

Eukaryotic mRNA

133
Q

Once transcripted where does mRNA go?

A

From the nucleus to the cytoplasm for translation into proteins

134
Q

What are the 3 stages of transcription?

A
  1. Initiation
  2. Elongation
  3. Termination
135
Q

How does RNA polymerase differ from DNA polymerase?

A
  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
Q

What happens at initiation of transcription?

A
  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
Q

What are the steps of initiation?

A
  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
Q

What occurs during the elongation of transcription?

A
  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
Q

What occurs during termination of transcription?

A
  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
Q

What happens in post-transcriptional processing of mRNA?

A
  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
Q

What doesn’t appear in the final sequences of mRNA of the gene product?

A

intervening base sequences of eukaryotic genes

142
Q

What are exons?

A

DNA sequences that expressed in the mRNA sequence

143
Q

What are introns?

A

Intervening DNA sequences that are not expressed in the final mRNA sequence

144
Q

How are introns removed?

A
  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
Q

What is alternative splicing?

A

Gene expression can be controlled at the level of RNA splicing

146
Q

What are isoforms?

A

Different forms of a protein produced by alternative splicing reactions

147
Q

What are the different peptides a single gene can yield from RNA processing?

A
  1. Isoforms
  2. Two forms of the mRNA in the same cell
  3. One form in one tissue, but a different in another
148
Q

What percent of human genes are alternatively spliced?

A

50%

149
Q

What are transcription factors?

A

The control for activation or inhibition of DNA polymerase for the expression of individual genes

150
Q

What is a regulatory factor?

A

Can bind to distant sites from the promoter to turn transcription on or off

151
Q

What influences the rate of transcription initiation?

A

RNA pol-promoter

152
Q

What are regulatory proteins?

A

Work to enhance or inhibit RNA pol-DNA promoter interaction

153
Q

What is a codon?

A

A triplet of 3 nucleotides specifying an amino acid

154
Q

How do you translate the language of RNA to proteins?

A

Codons are read as the sequence of mRNA and translated into protein sequences

155
Q

How many words are in a genetic code?

A

64

156
Q

What causes redundancy in genetic code?

A

Excess of codons

157
Q

What is the start codon?

A

AUG

158
Q

What are the stop codons?

A

UAA, UAG, UGA

159
Q

What are the the most common amino acids coded by codons?

A

Leu and Gly

160
Q

When can translation begin?

A

Once mRNA is in the cytoplasm

161
Q

What is required for translation?

A
  1. mRNA transcript
  2. tRNA
  3. Amino acids
  4. Ribosome
  5. Energy
162
Q

What are the steps of translation?

A
  1. Initiation
  2. Elongation
  3. Termination
163
Q

What is carried by a tRNA?

A

Anticodon

164
Q

What is an anticodon?

A

A sequence of ribonucleotides that is complementary to the codon the tRNA translates

165
Q

What is the key step in translation?

A

The specific base pairing between the tRNA anticodon and the mRNA codon

166
Q

Where does the amino acid attaches to the tRNA?

A

Amino acid acceptor site in the tRNA

167
Q

What is the purpose of aminoacyl-tRNA complex?

A

Occurs when the amino acid is attached to the tRNA by tRNA synthetase generating a charged tRNA

168
Q

What are the components of a ribosome?

A
  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
Q

What do ribosomes bind to?

A
  1. mRNA
  2. tRNA (A, P, and E sites)
170
Q

What is the A site?

A

Where tRNA delivers aa

171
Q

What is the P site?

A

Where the growing polypeptide chain still attached to a tRNA

172
Q

What is the E site?

A

Exit that contains the empty tRNA

173
Q

Describe the initiation of translation

A
  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
Q

Describe elongation of translation?

A
  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
Q

Describe termination of translation

A
  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
Q

What is a nonsense mutation?

A

Change a codon specifying an amino acid to a stop codon which terminates translation and causes the production of a truncated protein

177
Q

What is a missense mutation?

A

Changes in the codon specificity from 1 amino acid to another, altering protein sequence affecting function (sickle cell)

Biochemistry (16 decks)

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