FINAL EXAM Flashcards
1
Q
Who is Chargaff?
A
- Determined that in a DNA molecule the amounts of purines were present in equal amounts to pyrimidines
2
Q
What are purines
A
- Adenine and Guanine (A + G)
3
Q
What are pyrimidines
A
- Thymine and Cytosine (C + T)
4
Q
What is equal to A
A
T
5
Q
What is equal to G
A
C
6
Q
A+G=?
A
C+T
7
Q
How many H bonds between T & A
A
2 H-Bonds
8
Q
How many Hydrogen bonds between C & G
A
3
9
Q
What are the two grooves of DNA called
A
- Major groove
- Minor groove
10
Q
How is the polarity of the antiparallel strand determined?
A
- By sugar-phosphate bonds
11
Q
What is the 3’ end attached to
A
free 3’ hydrixyl group end
12
Q
What is the 5’ end attach to
A
free 5’ phosphate group
13
Q
What way is the DNA secqunce written
A
5’ to 3’
14
Q
What do phosphate groups do
A
- Connect the 3’ C of one sugar and the 5’ C of the next sugar
15
Q
Explain why base pairing in DNA is complementary
A
- Nitrogenous bases in DNA always pair in a specific way due to their chemical structure and hydrogen bonding rules
*A & T = 2 H bonds
* C & G = 3 H bonds
16
Q
What kind of strands if DNA made up of?
A
- Antiparallel strands
17
Q
Do the 5’ to 3’ ends if the helix have the same polarity?
A
- No, they have opposite chemical polarity
18
Q
What is gel electrophoresis used for?
A
- Used to separate & analyze DNA samples
19
Q
Explain the steps of gel electrophoresis
A
- DNA samples are loaded into cells
- Machine turns on, DNA fragments migrate through gel
- DNA fragments are separated by size
20
Q
What are restriction enzymes? (RE)
A
- A group of endonucleases produced in bacteria as a means of destroying foreign DNA
21
Q
- How do restriction enzymes function?
A
- They function by cleaving DNA at specific double-stranded sequences known as restriction sites
22
Q
What are restriction sites?
A
- typically 4-8 bp in length are often palindromic
- occur randomly all throughput genome
23
Q
Palindromic meaning
A
- a region where the sequence of bases reads the same on both strands when read in the 5’ to 3’ direction on one strand and the 3’ to 5’ direction on the complementary strand.
ex.
5’ - GAATTC - 3’
3’ - CTTAAG - 5’
24
Q
How can restriction enzymes use restriction sites?
A
- RE can be used as a tool to target and cleave DNA at particular locations where a restriction site occurs
25
Explain PCR
- Builds on the natural process of DNA replication as well as DNA hybridization to target & replicate specific DNA sequences, producing large quantities of target DNA
26
Why is PCR a powerful and valuable tool in molecular biology?
- Process is quick
- Inexpensive
- Highly versatile and requires little starting material
27
Explain the steps of PCR of 1 cycle how how many copies after 1 cycle
1. Denaturalization (95° C)
2. Primer Annealing (52 °C)
3. Elongation (72 °C)
- After every cycle 2 new copies get added--> 2^n
- n= # of cycles
28
Explain steps of PCR in a tube (PCR thermal cycle)
1. Denaturation (90°C - 95°C)
2. Annealing (primer temp)
3. Extension (72°C)
29
What are the PCR ingredients
1. DNA template
2. Primers
3. dNTPS (dATP, dTTP, dCTP, dGTP)
4. DNA polymerase
5. Salts & a buffer
30
What are primers used for in PCR?
- Always necessary for targeting specific DNA or RNA sequences
31
What are the steps in primers?
1. Strands separate
2. Primers anneal
3. Strands elongate
32
What is a forward primer
- Anneals to the bottom strand and has the same sequence as the top strand
33
What are the two types of primers
- Forward primer
- Reverse Primer
34
What is a reverse primer
- Anneals to the top strand and has the identical sequences as the bottom strand
35
How is bacteria chromosome formed?
- Circular unfolded
- supercoiled & folded
- DNA supercoiling is the second way to compact the bacterial chromosome
36
Explain the chromosome structure in Eukaryotes
- Diploid: 2 sets of genes, 2 sets of chromosomes
- haploid: 23 chromosomes
- total length of diploid genomes: ~2meters
- human nucleus: 5-10 um (diameter)
37
How must human DNA be?
- Must be tightly packed into multiple chromosomes
38
What does each Eukaryotic chromosome consist of
- one large linear molecule of DNA
- Large amounts of two types of proteins
1. Histones
2. A divergent group of non-histone proteins
- chromoatin
39
what does chromatin
- DNA + Histones + Proteins
40
What are histones
- High positive charged polypeptides
41
What are the three levels of DNA packaging in chromatin
1. First level: Nucleosomes
2. Second level: 30 nm chromatin fiber
3. Third level: Inter-phase chromosomes
42
What do nucleosomes consist of
- Nucleosome core: consists of 2 molecules of each of 4 histones
- Complete nucleosome: consists of Histone H1
43
During mitosis what stage does the chromosomes undergo another stage of packaging?
- The metaphase chromosome
44
Where is the DNA present in eukaryotic cells
- In the cell nucleus and in the chromosomes
45
Where does DNA double in eukaryotes cell divison
- S phase of cell cycle
46
Is there twice as much DNA in diploid cells or haploid cells?
Haploid cells
47
How many pairs of homologous chromosomes prior to S phase?
1 pair
48
How many pairs of replicated homologous chromosomes are there following the S phase
1 pair
49
How many daughter cells are there in the divison of mitosis and are they identical?
- 2 identical daughter cells
50
Why does DNA replication have to be fast?
- It has to be fast for cell divison
51
What has to happen for DNA replication to be perfect
- Genetic information must be accurately copied everytime a cell divides
52
What are the three models of DNA replication
1. semi-conservative
2. Conservative
3. Dispersive
53
What is semi-constructive
- a type of DNA replication
- each parental strand is a template for a new strand
54
What is conservative
- A type of DNA replication
-two parental strands remain together in one daughter molecule while serving as a template for another daughter molecule
55
What is dispersive
- A type of model of DNA replication
- Parent molecule is dispersed among both strands in the two daughter molecules
56
What was the hypothesis of the Meselson-Stahl Experiment
- DNA replicates semiconservatievly
57
What were the results of the Meselson-Stahl Experiment
- After one round of DNA replication, DNA had an intermediate weight; after subsequent rounds of DNA appeared with intermediate weight DNA
58
What model suggested a possible semi-conservative coping mechanism
- The Watson-crick
59
What are the results of the Watson-crick mechanism?
- after one round of replication, each DNA contains 1 parental and 1 newly-synthesized strand
60
Explain DNA replication
- DNA replicates through a semi-conservative mechanism that involves many proteins
61
What are the modes of replication?
1. Theta Replication
2. Rolling circle replication
3. Linear chromosome replication
62
Explain Theta replication model
- Replication that occurs in most circular DNA (e.g. bacteria)
- DNA template: circular
- No breakage of nucleotide strand
- 1 replicons
- can be unidirectional or bidirectional
- products is two circular molecules
63
Explain rolling circle replication
- Specialized form of replication that occurs in the F factor and some viruses (only one origin of replication)
- DNA template is circular
- There is breakage of the nucleotide strand
- 1 number of replicons
- Is unidirectional
- One circular molecule & one linear molecule that may circulate
64
Explain Linear chromosome replication
- Occurs in the linear chromosomes of eukaryotic cells
- DNA template is linear
- No breakage of nucleotide strand
- There are many # of replicons
- Is bidirectional
- Product: Two linear molecule
65
What are the features of DNA replication?
- DNA-dependent DNA polymerase
- Four deoxyribonucleotide triphosphates (dNTPS)
- A single-stranded template of DNA to be copied
- An RNA primer (provides the 3' - OH end to initiate DNA synthesis by DNA polymerase)
- DNA is continuously synthesized in the 5' to 3' direction (unidirectional)
- Newly-synthesised DNA strand is complementary and antiparallel to the parent strand
- DNA strands are held together by hydrogen bonds between complementary bases
66
What are the ingredients for PCR?
- Nucleotides
- Primers - buffer
- DNA you extracted
- DNA polymerase
67
How is DNA replication in a cell?
1. Initiation: Unwinding (denaturing) the DNA double helix and synthesizing RNA primers
2. Elongation: Synthesizing new strands of DNA using each of the parental strands as templates
3. Termination: Synthesis ends
68
During Initiation what do the strands want to do when they separate?
- They want to come back together to their stable base-paired form
69
How are the strands in initiation kept separate
- by proteins which bind to the single-stranded portions of the DNA molecule by single-stranded binding proteins - SSBs
70
In the initiation step does DNA polymerase start adding nucleotides?
- No, it needs a starter
71
What is the starter provided in the initiation
+1 purine downstream 5-9 base pairs from -10
72
What is the first step of initiation?
- DNA strands must be separated --> done by an enzyme called DNA helicase
73
What is and what does DNA helicase do
- an enzyme
- separates the two strands so the nucleotides are no longer based paired in the initiation step of DNA replication
74
What is Topoisomerase
- A protein
- As strands separate topoisomerase protects the res of the DNA molecule from being wound tighter
75
What is primase
- is a enzyme starter
- it connects a few complementary RNA bases to the template strand
76
What is the part on the template strand where primases attach to in the initatiation stage
- RNA primer
77
What is the first step in the elongation process in DNA replication
- DNA polymerase adds bases to the RNA primer, copying the template strand in the 5' to 3' direction
78
What direction does the DNA polymerase work in?
- one direction: 5' to 3'
- adds nucleotides to the 3' end of the RNA primer
79
In what way does copying proceed in the DNA molecule and why?
- DNA is composed of anti-parallel strands copying also proceeds in opposite directions
- DNA polymerase only works 5' to 3' of the newly synthesized strand
80
When does the new DNA synthesis stop?
- Stops when the polymerase reaches the 5' end of the previously synthesized Okazaki fragment
81
What does the exonuclease activity do
- DNA polymerase removes the RNA primer of the previously synthesized Okazaki fragment one nucleotide at a time using its 5' to 3' exonuclease activity
- Replaces the RNA nucleotides with the polymerizing activity
82
When does the enzyme leave the template?
- when RNA primer is removed
- when RNA nucleotides are replaced with DNA nucleotides
83
What seals the nick between the two lagging strands?
DNA ligase
84
How is DNA replicated?
- through the replication fork
85
What is the replication fork?
- the site where DNA unwinds to expose bases
- One new strand, the leading strand, can grow continuously at its 3' end as the fork opens
- the other stand cannot be made that way (no 3' to 5' synthesis allowed)
* the other strand is made in small pieces (Okazaki fragments) in the 5' to 3' direction
* cannot begin until the fork has advanced a little ways - is called the lagging strand
* Is oriented so that its exposed 3' end gets farther from the fork
86
where does DNA replication begin?
- begins with a short primer
- a starter strand of RNA complementary to the DNA template
- required for leading strand and each Okazaki fragment
87
What is DNA polymerase?
- Processive
- catalyzes many polymerizations each time they bind to DNA; very rapid
88
In the elongation step of DNA replication when does synthesis occur?
- Synthesis occurs discontinuously in a series of fragments called Okazaki fragments
89
In the elongation step of DNA replication what happens on the lagging strand of DNA synthesis
- on the lagging strand, synthesis is in the opposite direction to fork movement and requires constant re-priming
90
In DNA replication what replaces the primers with DNA
- A different DNA polymerase
91
What is the step in DNA replication called termination?
- in eukaryotic occurs when the two replication forks meet
92
What is end-replication problem?
- When the last primer is removed from the lagging strand, no DNA synthesis occurs because there is no 3' end to extend a single strand bit of DNA is left at each end
93
What is the result of the end-replication problem
- the new chromosomes has a short region of single-stranded DNA overhang at one end
- Then chromosomes become shorter, and this is a serious problem
- Every time the cell undergoes cell division, linear chromosomes get shorter
94
What will fix the end replication problem and how?
- Telomeres: are repetitive sequences (TTAGGG) at the ends of eukaryotic chromosomes. Telomeres are DNA sequnces that do not encode proteins
95
What are the functions of telomeres
- Protect the important protein-coding DNA in the chromosome from being lost
- Telomeres extend the chromosome and prevent coding regions of DNA from being cut off
- prevent DNA repair mechanisms from mistakenly joining chromosome ends
96
What is telomerase?
- adds telomeres back onto the end of the chromosome
- some cells (bone marrow stem cells, cancer cells) have telomerase
97
What does telomerase contain
- Has RNA template that base-pairs with the single-strand overhang
- Telomerase works as a DNA polymerase to synthesize new DNA
98
What happens if too many telomeres are lost?
- The cell will undergo apoptosis
99
What are the proteins involved in prokaryotic DNA replication
- DNA helicase
- DnaA
-DNA gyrase
- Single stranded DNA
- Primase
100
Explain DNA helicase in prokaryotes
- Helicase only binds to single-stranded DNA (unique prokaryotic) between complementary base pairs
- unwinds the DNA in the 5' to 3' direction:L it travels only on the lagging strand ahead of the replication machinery
101
Does DNA polymerization require a primer to initiate synthesis?
Yes
102
Does RNA polymerase require a primer to initiate synthesis?
No
103
What does the protein DnaA initator proteins do in prokaryotic DNA replication?
- bind to oriC and opens up the DNA
104
What does DNA gyrase do
- prokaryotic DNA replication
- Binds upstream of the unwinding fork to prevent torsion
105
What does the single-stranded DNA proteins do?
- Prokaryotic DNA replication
- Bind to keep DNA single stranded
106
What does primase (RNA polymerase) do in prokaryotic DNA replication
- Synthesizes a short RNA primer (10-12 nt) that provides the 3' OH end for DNA polymerase to begin DNA synthesis
107
What does DNA polymerase do in prokaryotic DNA replication?
- Enlongate the new polynucleotide strand by catalyzing DNA polymerization. Requires a primer
108
What does DNA polymjerase I do in prokaryotic DNA replication?
- Similar to DNA poly III but also has 5' to 3' exonuclease activity meaning it can remove the RNA primer and replace it with DNA
109
What does DNA polymerase III do in prokaryotic DNA replication?
- Main DNA polymerase
- Has 5' to 3' polymerase activity
- Has 3' to 5' exonuclease activity
- This means that dNTP on the 3' end but can also back up to remove a nucleotide that has been mis-incorporated
110
Does the lagging strand DNA synthesis by polymerase III occur in sections, if so, why? - prokaryotic DNA replication
- yes, due to unwinding
- it is discontinuous
110
What happens on the lagging strand
- When DNA synthesis by pol.III reaches the 5' end of the RNA primer, pol III is "swapped" for Pol I
- DNA polymerase I (with its 5' to 3' exonuclease activity) removes the RNA primer and re-synthesizes a short tract of DNA
- DNA ligase makes a phosphodiester bond between the 5' phosphate and the 3' OH group
- Okazaki fragments are thus joined together to make one continuous length of DNA
110
During prokaryotic DNA replication what is happening on the leading strand?
- DNA synthesis by polymerase III is continuous, making a completely new DNA strand
111
What does the initiator protein do
- Binds to the origin and separates strands of DNA to initiate replication
112
Where does Eukaryotic chromosome replication begin?
- Replication begins at autonomously replicating sequences
113
In eukaryotic chromosome replication, where does the helicase bind?
- binds to the initiator protein on double-stranded DNA
- Involves the MCM complex of proteins
114
What are the RNA primers and Okazaki fragments like in eukaryotic chromosome?
- Shorter RNA primers and shorter Okazaki fragments
115
When does DNA replication occur in eukaryotes?
- Only occurs during the S phase
116
How many DNA polymerases in Eukaryotic chromosome replication
- Multiple (up to 15)
117
What does Polymerase alpha do
- Has primase activity (generates the RNA primer)
118
What does polymerase epsilon do
- Performs leading strand replication
119
What does polymerase delta do
- Performs lagging strand replication
120
What does telomeres do in eukaryotic DNA replication
- Shorten at each round of eukaryotic replication
121
what nucleosomes need to do in eukaryotic DNA replication and how many of each histones are there
- two of each histosome
- they need to be removed from parental DNA and properly re-assembled on newly-synthesized DNA
122
What kind of replication on each chromosome in Eukaryotic chromonosome replcaition
- Bidirectional replication from multiple origins of replication on each chromosome
123
What happens in G1 phase of eukarotic chromosome replication
- Eukaryotic origins are "prepared" for replication in G1 phase (called "origin licensing")
- Replication licensing factors attach to each origin of replication during G1 phase
- Mechanisms are in place to prevent re-initiation of replication
- Allows replication of the entire genome once and only once
124
What is Eukaryotic DNA like
- complexed with nucleosomes (histone proteins) that are modified to affect the stability, packaging and accessibility of DNA
125
What happens when DNA is doubled in eukaryotes
- Histones also need to be doubled, and the modifications on them need to be replicated
126
Explain telomerase in eukaryotes
- can extend the 3' end of the chromosome without the use of a complementary DNA template
- gap remains, but this does not matter because the end of the chromosome is extended at each replication
- Chromosome does not become shorter overall
127
Where is telomerase highly present in eukaryotes?
- Telomerase present in highly dividing somatic and germ cells
- In slowly dividing cells, lack of telomerase will result in the shortening of telomeres over time
128
How does gene expression to form a specific polypeptide occur?
Process called the central dogma: DNA to RNA to polypeptide (protein)
1. Transcription
2. Translation
129
What is transcription
- copies of information from a DNA sequence (a gene) to a complementary RNA sequnce
130
What is Translation?
- Converts RNA sequence to amino acid sequence of a polypeptide
131
Explain the process gene to protein process in eukaryotes
- The nuclear envelope separates transcription & translation
- DNA in the nucleus, site of transcription
- Ribosomes in cytoplasm (ER), site of translation
- mRNA is the intermediate messenger
132
Explain the process of gene to protein in prokaryotes
- Translation occurs on growing mRNA
133
How does RNA (ribonucleic acid) differ from DNA
- Usually, a single polynucleotide strand
- The sugar is ribo
- Contains uracil (U) instead of thymine (T)
134
Explain RNAs structure
- Single strand
- Can fold in different ways and even more than DNA
- Is similar to proteins making secondary, tertiary and quandary structures
135
Explain the transfer of RNA
- CCA is a sepcific sequence of three nucleotides that appears on the 3' end of transfer RNA (tRNA molecules)
- It’s not encoded in most tRNA genes — it's added enzymatically after transcription by an enzyme called tRNA nucleotidyltransferase
- CCA is the attachment site for amino acids
136
Why is RNA less stable than DNA
- The presence of the unique 2'OH group in ribose causes it to react intramolecularly with the 3'OH site, resulting in phosphate bond breakage
137
Why is RNA used
- RNA evolved first
- RNA can form many tertiary structures allowing it to have different conformations for different functions, whereas DNA is generally only double-stranded
- Partly because temporary and degraded molecule offers a way of controlling its level (for example, shutting off expression)
138
What type of sugar does DNA consist of
- Deoxyribose
139
Is there a presence of 2'OH group in DNA
No
140
Is there a presence of 2'OH group in RNA
Yes
141
Bases in DNA
A,G,C,T
142
Bases in RNA
A,G,C,U
143
Is RNA double-stranded or single
- single
144
secondary structure of DNA
- double helix
145
Is DNA stable
Yes
146
Is RNA stable?
- Easily degraded
147
Explain the process of gene expression of RNA
- Transcription: Synthesis of RNA from DNA templates
- All cellular RNAs are synthesized from DNA template
148
What is mRNA
- a messenger RNA
- a protein
149
What happens with RNA gene expression in prokaryotes
- Coding region is often a single, continuous unit
- Transcription and Translation occur at the same time (they are coupled)
150
In what way is RNA synthesized in gene expression
- RNA is synthesized in the 5' to 3' direction using the 3' to 5' template strand
- RNA synthesis is complementary and ant-parallel to the DNA template strand
151
In RNA gene expression, where is each gene transcribed from?
- Each gene is transcribed from a single DNA strand (the 3' to 5' template strand)
- There are multiple genes on chromosomes and they can be located on either DNA strand
- Therefore, transcription can utilize either DNA strands as the 3' to 5' template, but transcription ALWAYS occurs in the 5' to 3' direction
152
What decides which way the transcription goes?
- Promotor
153
What are the general features of RNA synthesis?
- Similar to DNA synthesis except for:
* The precursors are ribonucleoside triphosphates (rNTPS)
* Only one strand of DNA is used as the template (the 3' to 5' strand)
* RNA chains can be initiated de novo (no primer required)
- The 5' to 3' RNA molecule will be complemntry to the DNA template 3' to 5' strand (also known as the DNA anti-sense strand)
- The 5' to 3' RNA molecule will be similar (except U replaces T) to the DNA non-template 5' to 3' strand aka DNA sense
- RNA synthesis is catalyzed by RNA polymerases and ALWAYS proceed in 5' to 3' direction
154
How is the info content in DNA transcribed to produce RNA to RNA polymerase
- RNA polymerases catalyze synthesis of RNA from a DNA template
- RNA polymerases are processive: a single enzyme-template binding results in polymerization of hundreds of RNA bases (LIKE DNA PLOYMERASES)
- RNA polymerases can only add new nucleotides to the 3' end of a growing strand (synthesis is 5' to 3')
155
What are some features of RNA polymerase
- RNA polymerases catalyze synthesis of RNA from a DNA template
- RNA polymerases can initate synthesis without an existing 3'-OH group, so do not need primers (UNLIKE RNA POLYMERASES)
- RNA polymerases lack a proofreading function
- RNA poly can unwind and rewind DNA
156
Explain the components of the transcription of DNA to RNA
- DNA template for base pairings- one of the two strands of DNA
- Nucleoside triphosphates (ATP, GTP, CTP,UTP) as substrates
- An RNA polymerase enzyme
157
What are the three phases of transcription of DNA to RNA
1. Initiation
2. Elongation
3. Termination
158
What are the subunits of RNA polymerase in prokaryotes
- alpha
-beta
-beta-prime
-omega
-sigma: binds to the RNA polymerase tetrameric core and assists in the correct initiation of transcription, specifically at the promoter region of the prokaryotic gene
- important for polymerase to bind to protein
159
What does the sigma factor do in prokaryotes
- recognizes and binds to the -35 and -10 consensus sequences in the promotor region, correctly positioning the RNA polymerase to begin transcription
160
What are the base sequences in the promoter region for -35 sequence
TTGACA
161
What are the base sequences in the promoter region for -10 sequence
TATAAT
162
Is the -10 consensus sequence prone to unwinding, and if so why?
- it is prone to unwinding due to its AT rich content
163
Where is the TTGACA and TATAAT box located?
- Promoter region
- on the non-template strand (5' to 3')
164
What does the TTGACA promoter region do?
- Binding
- The sigma subunit of the RNA polymerase holoenzyme binds the - 35 sequnce
165
What does the TATAAT promoter region do?
- Unwinding
- The AT-rich -10 sequence enables localized DNA strand separation to form the transcription bubble
166
What are the core promoters of Eukaryotes
- G/CG/CG/CCGCC. -35
- TATAAA -25
- Does not use sigma factors
167
What does the TATA box in eukaryotes do?
- Binding site of the first general transcription factor (TF IID complex which contains TATA-binding protein) to the TATA box
168
What is the first step of initiation of transcription steps
1. Initiation requires a promoter - which is a unique sequence of DNA
- RNA polymerase binds to the promotor
- Promotor directs RNA polymerase where to start and which direction to transcribe
- Part of each promoter is the initiation site of transcription
169
In the initiation step of transcription in prokaryotes, how does the strand determine which strand will be the template for transcription and the direction?
- The orientation and spacing of consensus sequences on a DNA strand determine which strand will be the template for transcription and thereby determine the direction of transcription
170
In transcription in prokaryotes in the initiation step what does the RNA polymerase do?
- RNA polymerase binds, unwinds and joins the first two nucleotides
- Initiation of RNA synthesis DOES NOT REQUIRE a primer
171
What is the second step of transcription in prokaryotes?
2. Elongation
172
When does elongation occur in transcription in prokaryotes?
- occurs when sigma factor is released, and RNA polymerase begins to move along the 3' to 5' template strand
173
What happens in the elongation step of transcription in prokaryotes?
- complementary nucleotides continue to be added during the elongation process
- Localized DNA unwinding ahead of RNA polymerase generates a "transcription bubble"
- Transcription bubble moves with the RNA polymerase and the unwound DNA rewinds behind it. RNA polymerase has both helix unwinding and rewinding activities
174
What is the last step in the transcription of prokaryotes?
Termination
175
Explain termination in transcription in prokaryotes
- Stops when RNA polymerase reaches the "terminator" region of the gene
- Occurs upstream of where the actual termination will take place
- The newly-synthesized RNA together with the RNA polymerase are released
- Bacterial cells possess two major types of terminators Rho-dependent (requires Rho factor) and Rho-independent (aka intrinsic terminator)
176
What direction does the template strand read in elongation of the transcription of DNA to RNA
- RNA polymerase unwinds DNA about 10-18 base pairs at a time
- Reads template in 3' to 5' direction
177
Do RNA polymerases proof read and correct mistakes?
- No
178
How is the info content in DNA transcribed to produce RNA?
- Elongation: RNA polymerase unwinds DNA about 10 base pairs at a time; reads template in 3' to 5' direction
- Termination: Is specified by a specified by a specific DNA base sequence that destabilizes the transcription complex
- for some genes the transcript falls away from the DNA template and RNA polymerase
- For other genes a helper protein pulls it away
179
Explain Rho-dependent termination and what is it like?
- Like sigma
- DNA sequnce of terminator site causes polymerase to pause
- DNA sequnce upstream of terminator encodes a strech of RNA that is C rich and devoid of secondary structure
a) called the rho utilization (rut) site
b) Rho binds to rut site
180
What does the Rho-dependent termination do?
- Rho moves along RNA towards paused polymerase
- Rho factor has helicase activity
- Unwinds the RNA-DNA hybrid
- Brings transcription to an end
181
How many RNA polymerases do eukaryotes have during transcription
- Have at least three RNA polymerases
182
What does the RNA polymerase I do?
- present in all eukaryotes
- Transcribes large rRNAs
183
What does the RNA polymerase II do?
- Present in all eukaryotes
- Transcribes: Pre-mRNA, some snRNAs,snoRNA, some miRNAs
184
What does the RNA polymerase III do?
- Present in all eukaryotes
- Transcribes: tRNAs, small rRNAS, some snRNAs, some miRNAs
185
Are all RNAs are translated to proteins?
- NO
186
What strand of DNA are the -35 and -10 on ALWAYS
- Non-template strand
187
are there specific promoter sequences for genes being transcribed by RNA polymerases I, II, III?
- Yes, pol I, II and III are only recruited to their promoter-specific accessory proteins
188
Explain the process
