Nucleic acids! Flashcards
(198 cards)
1
Q
What are the full names of the 2 kinds of nucleic acids?
A
Deoxyribonucleic acid
Ribonucleic acid
2
Q
What 3 structures make up a nucleotide?
A
- a five carbon sugar.
- a nitrogenous base.
- a phosphate group
3
Q
What are the purines? How many rings do they have?
A
Guanine and adenine
2 rings
4
Q
What are the pyrimidines? How many rings do they have?
A
Cytosine and thymine (and uracil)
1 ring
5
Q
What is a nucleoside composed of?
A
A nitrogenous base and a sugar - NOT a phosphate group
6
Q
What are the names of the 4 nucleosides?
A
Deoxyadenosine
Deoxycitidine
Deoxyguanosine
Deoxythymidine
7
Q
What are the names of the 4 nucleotides found in DNA?
A
Deoxyadenosine monophosphate
Deoxycitidine monophosphate
Deoxyguanosine monophosphate
Deoxythymidine monophosphate
8
Q
What kind of bond are nucleotides joined with?
A
Phosphodiester bonds
9
Q
How many hydrogen bonds do cytosine and guanine form?
A
3
10
Q
How many hydrogen bonds go adenine and thymine form?
A
2
11
Q
What does Chargaff’s rule state?
A
In double stranded DNA, %A = %T and %G = %C
12
Q
Is DNA right handed or left handed?
A
Right handed
13
Q
State the approximate diameter and height of DNA
A
Diameter 2 nm
6. Height 3.4 nm per turn
14
Q
How many base pairs are there per turn of DNA?
A
10
15
Q
What are the 3 alternate DNA conformations? Describe them
A
- B-DNA - the common form
- A-DNA - 11bp/turn, right-handed, slanted base-pairs.
- Z-DNA - 12bp/turn, left-handed. Zig-zag backbone.
16
Q
Why might Z-DNA form?
A
If DNA contains long runs of alternating G and C
17
Q
Why might A-DNA form?
A
If DNA is dehydrated
18
Q
What is the most common configuration of DNA?
A
B-DNA
19
Q
What does underwinding of DNA form?
A
Negative supercoils
20
Q
What does overwinding of DNA form?
A
Positive supercoils - more turns than in the relaxed state
21
Q
Unwinding a DNA molecule with fixed ends introduces what kind of supercoils?
A
Positive
22
Q
What kind of enzyme manages supercoiling?
A
Topoisomerases
23
Q
What is the hyperchromic shift?
A
The increase in UV absorbance (especially at 260 nm) that occurs when double-stranded DNA is denatured into single strands
24
Q
How does the OH on C2 change the properties of RNA?
A
Makes it denser, and more reactive
(less stable) and versatile than DNA
25
What nucleotide changes in RNA compared to DNA?
RNA has uracil, DNA has thymine
26
What is the full uracil nucleotide name?
Uridine monophosphate
27
How does transfer RNA form?
RNA molecules fold back on themselves to form complex secondary structures with intramolecular base-pairing
28
List the 4 functions of RNA
1. Carry information (messenger RNA).
2. Act as a transporter (transfer RNA).
3. Act structurally or catalytically (e.g. ribosomal RNA).
4. Act as a regulator of gene expression (e.g. micro RNAs)
29
Define chromosome
A single long molecule of DNA that includes numerous genes. The DNA of a chromosome is usually associated with proteins.
30
Define chromatin
The DNA-protein complex present in the nuclei of eukaryotic cells during interphase
31
What are the three components of a nucleotide?
A five-carbon sugar, a phosphate group, and a nitrogenous base
32
What is the difference between a nucleotide and a nucleoside?
A nucleotide has a phosphate group; a nucleoside does not
33
What type of bond connects nucleotides in nucleic acids? Where?
Phosphodiester bonds between the 5′ and 3′ carbon atoms
34
What is the charge of nucleic acids and why?
Negative, due to the phosphate groups
35
What type of bonds form between DNA base pairs?
Hydrogen bonds — 2 between A-T, 3 between G-C
36
What stabilizes the DNA double helix besides hydrogen bonding?
Base-stacking interactions (hydrophobic interactions between adjacent bases)
37
What is the diameter of the DNA double helix?
2 nanometers (nm)
38
How many base pairs per helical turn in DNA?
10 base pairs
39
What is the height of one helical turn in DNA?
3.4 nanometers (nm)
40
What structural feature of DNA allows protein interactions?
Major and minor grooves
41
What is the sugar found in RNA?
Ribose
42
What kind of supercoils are generated by overwinding?
Positive supercoils
43
What happens when DNA with fixed ends is unwound?
Positive supercoils are introduced
44
At what temperatures does DNA typically denature?
Between 70–110°C
45
What is Tₘ (melting temperature) in DNA?
The temperature at which 50% of DNA strands are denatured
46
What factors increase DNA’s melting temperature?
Higher GC content and presence of cations like Na⁺
47
How does denaturation affect UV absorbance of DNA?
Absorbance increases (hyperchromic shift) as DNA becomes single-stranded
48
Why is RNA more reactive and less stable than DNA?
Because RNA has a hydroxyl group (-OH) on the 2′ carbon of ribose
49
What type of secondary structures can RNA form?
Stem-loops, hairpins, and complex folds via intramolecular base pairing
50
What type of double helix does double-stranded RNA resemble?
A-DNA
51
How does DNA compact inside prokaryotic cells?
It binds to proteins forming the nucleoid structure
52
How many copies of a plasmid can exist in a single cell?
Between 1 and 200 copies
53
What is the typical size range of plasmids?
1 kb to 400 kb
54
What do plasmids require to replicate?
An origin of replication
55
What do over 85% of bacterial genomes consist of?
Coding DNA (genes)
56
What happens when denatured DNA cools slowly?
The strands re-anneal (reform the double helix)
57
What is the size of mitochondrial DNA in humans?
About 16,500 base pairs (bp)
58
How many genes are found in human mitochondrial DNA?
37 genes
59
During which phase are chromosomes visible under a microscope?
Mitosis or meiosis
60
What are eukaryotic mitotic chromosomes composed of by mass?
Equal parts DNA and protein (including histones and non-histone proteins)
61
What is a sister chromatid?
One of two identical copies of a chromosome joined at the centromere
62
What are the five types of histone proteins?
H1, H2A, H2B, H3, and H4
63
What is a nucleosome?
A unit of DNA packaging with 146 bp of DNA wrapped around a core of histone proteins
64
Which histones are in the nucleosome core?
2 each of H2A, H2B, H3, and H4
65
What is the role of histone H1?
It binds to DNA outside the core, sealing it to the nucleosome
66
What is chromatin?
DNA packaged with proteins into a fiber; consists of chains of nucleosomes
67
What is the '10 nm filament'?
The 'beads on a string' structure of nucleosomes seen in interphase chromatin
68
What anchors long loops of nucleosomes in mitotic chromosomes?
A scaffold of non-histone proteins (e.g., condensins, topoisomerase II)
69
What does condensin do?
Forms a ring structure that anchors DNA loops during chromosome condensation
70
What does topoisomerase II do?
Removes or adds supercoils to DNA to help with compaction
71
What effect does histone acetylation have on gene expression? Adding an acetyl group
It makes DNA less tightly bound, increasing accessibility and transcription - this is because it removes the positive charge on the side chain, so it is less attracted to negative DNA
72
What enzyme removes acetyl groups from histones?
Histone deacetylase
73
Which experiment confirmed DNA replicates semi-conservatively?
The Meselson-Stahl experiment (1958)
74
How did Meselson and Stahl label DNA to measure its replication?
By growing E. coli in heavy nitrogen (¹⁵N), then switching to light nitrogen (¹⁴N)
75
How is DNA density measured in the Meselson-Stahl experiment?
By ultracentrifugation in a cesium chloride (CsCl) gradient
76
What was the key result of the Meselson-Stahl experiment?
All DNA had intermediate density after one replication cycle, proving semi-conservative replication
77
How do nucleosomes affect transcription?
They can block access to DNA unless histones are modified (e.g., by acetylation)
78
What is a promoter?
A DNA sequence where RNA polymerase binds to initiate transcription
79
Where does splicing occur in genes?
At the 5′ (GT) and 3′ (AG) splice sites between exons and introns
80
What is the role of enhancers?
DNA elements that increase transcription of a gene, often located far from the promoter
81
What are the key structural levels from DNA to chromosome?
DNA → Nucleosomes → Chromatin → Chromosome loops → Mitotic chromosome scaffold
82
What is the direction of DNA synthesis by DNA polymerases?
5′ → 3′ direction
83
Where does DNA replication begin in E. coli?
At a single origin of replication
84
Is replication in E. coli unidirectional or bidirectional?
Bidirectional — two replication forks form at the origin
85
What substrates do DNA polymerases require to function?
1. All four deoxynucleoside triphosphates (dATP, dTTP, dGTP, dCTP)
2. A single-stranded DNA template
3. A primer with a free 3′-OH group
86
What is the function of a primer in DNA replication?
It provides a 3′-OH group to start DNA synthesis
87
What are the two key DNA polymerases in E. coli?
DNA polymerase I and DNA polymerase III
88
What is the main role of DNA polymerase III?
Synthesizing most of the new DNA during replication due to its high speed and processivity
89
What is the main role of DNA polymerase I?
Replacing RNA primers with DNA and proofreading
90
What additional enzymatic activities does DNA polymerase I have?
3′→5′ exonuclease for proofreading and
5′→3′ exonuclease for primer removal and nick translation
91
What are Okazaki fragments?
Short DNA fragments synthesized on the lagging strand during replication
92
Why is lagging strand synthesis discontinuous?
Because DNA polymerase only synthesizes 5′→3′, so the lagging strand must be made in fragments moving away from the fork
93
What synthesizes the RNA primers in E. coli?
Primase
94
What enzyme unwinds the DNA double helix at the replication fork?
Helicase
95
What protein stabilizes single-stranded DNA during replication?
Single-stranded binding proteins (SSBs)
96
What enzyme removes positive supercoils ahead of the replication fork?
DNA gyrase (a type II topoisomerase)
97
What replaces the RNA primers with DNA?
DNA polymerase I (via nick translation)
98
What seals the nicks between Okazaki fragments?
DNA ligase
99
What is nick translation?
A process by which DNA polymerase I removes RNA primers and replaces them with DNA
100
What is the role of DNA ligase?
It forms phosphodiester bonds to seal gaps between Okazaki fragments
101
Is DNA replication in all organisms semi-conservative?
Yes, all known species use semi-conservative replication
102
How many replication forks form from one origin?
Two — one in each direction (bidirectional replication)
103
How does DNA gyrase relieve supercoiling?
It cuts both DNA strands, passes another segment through, and reseals the cut
104
How does eukaryotic DNA replication differ from prokaryotic?
Eukaryotes have slower polymerases but multiple origins of replication, so overall replication is faster
105
What ensures high fidelity during DNA replication?
Proofreading by the 3′→5′ exonuclease activity of DNA polymerases
106
What might be a challenge in replicating linear chromosomes?
Replicating the very ends (telomeres) — this is known as the end-replication problem
107
What helps the replication fork progress smoothly in bacteria?
A coordinated complex of enzymes including helicase, SSBs, primase, polymerase III, DNA gyrase, and DNA ligase
108
What enzyme carries out transcription?
RNA polymerase
109
What are the three main stages of transcription?
Initiation, Elongation, and Termination
110
What is the coding strand in transcription?
The DNA strand with the same base sequence as the RNA (except T is replaced with U)
111
What is the template strand in transcription?
The DNA strand that is complementary to the RNA being synthesized ANTISENSE, NON-CODING
112
Does RNA polymerase require a primer?
No
113
What is a terminator?
A DNA sequence that signals the end of transcription
114
In E. coli, what is the sigma (σ) subunit?
A protein required for promoter recognition and initiation of transcription
115
What happens to the sigma subunit after initiation?
It dissociates, leaving the core enzyme to carry out elongation
116
What is the difference between the RNA polymerase core enzyme and holoenzyme in E. coli?
The holoenzyme includes the sigma subunit and initiates transcription; the core enzyme lacks sigma and performs elongation
Holoenzyme is hexamer a2BB'wo
Core enzyme is pentamer a2BB'w
117
How many types of RNA polymerase does E. coli have?
One type that synthesizes all RNAs
118
How many types of RNA polymerase do eukaryotes have?
Three:
- RNA polymerase I (rRNA)
- RNA polymerase II (mRNA)
- RNA polymerase III (tRNA)
119
What is the pre-mRNA or 1° transcript?
The initial RNA transcript made in eukaryotes before processing
120
What are the three main RNA processing steps in eukaryotes?
1. 5′ capping
2. 3′ polyadenylation
3. RNA splicing
121
What is added during 5′ capping?
A methylated guanine cap
122
What is added during 3′ polyadenylation?
A poly-A tail (~250 adenine residues)
123
What is the TATA box?
A common core promoter element recognized by transcription factors in eukaryotes
124
What are proximal promoter elements?
Short sequences near the core promoter that regulate gene expression (e.g., CCAAT box)
125
What are enhancers?
Distant DNA sequences that increase transcription efficiency by interacting with transcription factors
126
What are general transcription factors?
Proteins required for RNA polymerase II to bind to the promoter and initiate transcription
127
What is the pre-initiation complex?
The assembly of RNA polymerase II and general transcription factors at the promoter
128
How does transcription differ between prokaryotes and eukaryotes?
Prokaryotes use one RNA polymerase and no RNA processing; eukaryotes use multiple polymerases and process pre-mRNA
129
Which RNA polymerase transcribes mRNA in eukaryotes?
RNA polymerase II
130
What is the role of RNA polymerase I?
Synthesizes ribosomal RNA (rRNA)
131
What is the role of RNA polymerase III?
Synthesizes transfer RNA (tRNA)
132
What does the Pribnow box refer to?
A conserved sequence (~TATAAT) in bacterial promoters, located around the -10 position
133
What does the -35 hexamer refer to?
A conserved bacterial promoter sequence around 35 bases upstream of the transcription start site
134
How many base pairs of DNA are typically unwound during transcription?
15–17 base pairs
135
What regulates when and where a eukaryotic gene is expressed?
The binding of transcription factors to enhancers and promoter elements
136
What is the function of a 5′ cap on eukaryotic mRNA?
Stabilizes the transcript and is required for translation
137
What is the function of the 3′ poly-A tail?
Stabilizes mRNA and enhances translation efficiency
138
What is a consensus sequence?
An average sequence derived from aligning many similar promoter sequences
139
What is a cis-acting element?
A DNA sequence that affects gene expression on the same DNA molecule
140
In eukaryotes, what does RNA polymerase I require to bind to the promoter?
Other transcription factors
141
Who cracked the genetic code?
Marshall Nirenberg in 1961 using synthetic RNA
## Footnote
e.g., UUU for phenylalanine
142
What does it mean that the genetic code is degenerate?
Most amino acids are encoded by more than one codon
143
Which two amino acids are encoded by only one codon?
Methionine (AUG) and Tryptophan (UGG)
144
What codons signal termination of translation?
UGA, UAG, UAA
145
How many possible reading frames does a sequence have?
Three
146
What are unusual bases found in tRNA?
Dihydrouracil, pseudouracil, thymine (modified U), methylguanine
147
What is always found at the 3′ end of a tRNA?
The unpaired sequence CCA, which binds to the amino acid
148
What is the secondary structure of tRNA?
A cloverleaf with 3 (or 4) loops and 4 double-stranded stems
149
What is the tertiary structure of tRNA?
An inverted L-shape formed by folding the cloverleaf structure
150
What is an aminoacyl tRNA?
A tRNA linked to its corresponding amino acid — also called a charged tRNA
151
What is gly-tRNAᵍˡʸ?
The charged tRNA for glycine (glycine attached to tRNAᵍˡʸ)
152
What is base wobble?
The ability of some anticodon bases to pair with more than one codon due to flexible pairing at the third position
153
Which base pairings are possible due to wobble?
G–U, U–G, G–C, C–G, A–U, U–A
154
Why is wobble important?
It allows fewer tRNAs to cover all 61 codons that encode amino acids
155
What ensures that each codon is matched with the correct amino acid?
Aminoacyl-tRNA synthetases
156
What are aminoacyl-tRNA synthetases?
Enzymes that link each amino acid to its correct tRNA
157
What are the two steps in the aminoacylation reaction?
1. Amino acid + ATP → aminoacyl-AMP
2. Aminoacyl-AMP + tRNA → aminoacyl-tRNA + AMP
158
What is an intermediate in the aminoacylation reaction?
Aminoacyl-AMP
159
What would happen if a tRNA were incorrectly charged?
It would deliver the wrong amino acid, potentially producing a faulty protein
160
How does mitochondrial genetic code differ from standard?
UGA codes for tryptophan in mitochondria (instead of acting as a stop codon)
161
What region of mRNA is not translated but affects regulation?
The 5′ and 3′ untranslated regions (UTRs)
162
What is the purpose of the CCA tail at the 3′ end of tRNA?
It binds the amino acid via its 3′-OH group
163
What are the three tRNA binding sites on the ribosome?
A (aminoacyl), P (peptidyl), E (exit).
164
What are ribosomes made of?
Protein and ribosomal RNA (rRNA).
165
How are ribosome sizes measured?
In Svedberg units (S), based on sedimentation rate.
166
What is the size of the E. coli ribosome?
70S (30S small + 50S large subunit).
167
What is the size of a eukaryotic cytoplasmic ribosome?
80S (40S small + 60S large subunit).
168
Where is peptidyl transferase activity located?
In the 23S rRNA of the large subunit (it's an rRNA-based enzyme).
169
What is the first amino acid in prokaryotic translation?
N-formyl-methionine (fMet).
170
What signals initiation in prokaryotic translation?
Base pairing between the 16S rRNA and the ribosome binding site (Shine-Dalgarno sequence).
171
What signals initiation in eukaryotic translation?
Recognition of the 5′ cap on mRNA by the 40S subunit.
172
What happens during translation elongation?
Aminoacyl-tRNA binding, peptide bond formation, translocation of the ribosome.
173
What molecule provides energy for translocation?
GTP.
174
What delivers aminoacyl-tRNA to the ribosome?
EF-Tu in prokaryotes; EF-1α in eukaryotes.
175
What moves the ribosome during translocation?
EF-G in prokaryotes; EF-2 in eukaryotes.
176
How many high-energy bonds are used per amino acid during translation?
Three: 1 ATP (tRNA charging), 2 GTP (tRNA delivery + translocation).
177
Which antibiotics target prokaryotic ribosomes?
Erythromycin, clarithromycin, chloramphenicol.
178
Which toxin targets eukaryotic ribosomes?
Ricin – cleaves a base from 28S rRNA in the 60S subunit.
179
What are housekeeping genes?
Genes expressed constantly in all tissues to perform essential cellular functions.
180
Describe the complete process of translation initiation in E. coli.
1. The 30S small subunit binds the Shine-Dalgarno sequence on the mRNA via base pairing with the 16S rRNA.
2. fMet-tRNAᶠᴹᵉᵗ binds to the start codon (AUG).
3. The 50S large subunit joins to form the functional 70S ribosome with fMet-tRNA in the P site.
181
How does translation initiation differ between prokaryotes and eukaryotes?
Prokaryotes use base pairing between 16S rRNA and the Shine-Dalgarno sequence; eukaryotes rely on recognition of the 5′ cap by the 40S subunit. The 40S subunit scans the mRNA for the first AUG, after which the 60S subunit binds to complete the ribosome.
182
What is the function of EF-Tu (or EF-1α in eukaryotes)?
It binds aminoacyl-tRNAs and delivers them to the A site of the ribosome during elongation. This step requires GTP hydrolysis for accurate codon-anticodon pairing.
183
What is the role of EF-G (EF-2 in eukaryotes)?
It promotes ribosomal translocation — the movement of the ribosome one codon downstream along the mRNA. This process requires GTP hydrolysis.
184
How does peptide bond formation occur on the ribosome?
The amino group of the aminoacyl-tRNA in the A site attacks the carboxyl end of the polypeptide in the P site. This reaction is catalyzed by the 23S rRNA in the large subunit, not by protein enzymes.
185
Why is peptide bond formation considered ribozyme activity?
Because it is catalyzed by ribosomal RNA (specifically 23S rRNA), not a protein — making the ribosome a ribozyme.
186
What is the energy cost of adding one amino acid to a growing polypeptide chain?
~3 high-energy phosphate bonds are used: 1 ATP to charge the tRNA, 1 GTP for aminoacyl-tRNA delivery, and 1 GTP for ribosome translocation.
187
What is catabolite repression in the context of the lac operon?
A regulatory mechanism where the presence of glucose inhibits transcription of the lac operon. High glucose = low cAMP = no CAP-cAMP complex = weak transcription even if lactose is present.
188
Explain how the lac operon is induced.
When lactose is present, some is converted to allolactose, which binds to the lac repressor, altering its shape so it can't bind to the operator. This allows RNA polymerase to transcribe the lacZYA genes, albeit weakly without CAP-cAMP.
189
How does the CAP-cAMP complex enhance transcription of the lac operon?
When glucose is low, cAMP increases and binds to CAP. The CAP-cAMP complex binds near the promoter and enhances RNA polymerase binding, leading to strong transcription if lactose is also present.
190
How does the lac repressor inhibit transcription in the absence of lactose?
It binds to the operator sequence, physically blocking RNA polymerase from accessing the promoter, thereby preventing transcription.
191
What is an operon and how is it transcribed?
An operon is a cluster of genes under control of a single promoter and transcribed into one polycistronic mRNA. The lac operon includes lacZ, lacY, and lacA, all expressed together.
192
How is gene expression controlled in eukaryotes at the transcriptional level?
By the binding of transcription factors to core promoters (e.g., TATA box), proximal promoter elements (e.g., CCAAT box), and enhancers. These regulate the formation of the pre-initiation complex and chromatin accessibility.
193
Describe the role of MyoD in gene expression.
MyoD is a muscle-specific transcription factor that binds E-box sequences (CANNTG) in PPEs of muscle genes like α-actin and myosin. It activates transcription in muscle cells, contributing to muscle-specific gene expression.
194
What makes the lac promoter inherently weak?
Its sequence diverges from the consensus −10 (Pribnow box) and −35 elements, resulting in lower affinity for RNA polymerase binding unless enhanced by the CAP-cAMP complex.
195
What kind of supercoiled is DNA in vivo?
Negative
196
When determining structure of eukaryotic chromosomes during mitosis, how do you find the packing ratio?
197
This is just a fat DNA synthesis figure
198
What 4 channels does RNA polymerase have and what are they for?
DNA entry channel
DNA exit channel
RNA exit channel
rNTP entry channel
