eczema 2 Flashcards
1
Q
Nucleotides are the subunits of _____ & ______
A
DNA & RNA
2
Q
What did Hershey and Chase do
A
They used radioactive labeling to prove that DNA is responsible for heredity
3
Q
What did Watson & Crick do
A
They proposed the double helix structure of DNA
4
Q
Before we know the structure of DNA we thought Chromosomes contain ____ & _____
A
Dna & protein
5
Q
Before we new the structure of DNA we knew:DNA had a _______backbone and DNA had _____________ attached to each sugar
A
sugar phosphate ; nitrogenous bases
6
Q
The double helix model with the Xray diffraction pattern was generated by who? And what did it reveal?
A
Rosalind Franklin; revealed that DNA was a long thin helical molecule
7
Q
The Watson and Crick Model said what 4 things
A
sugar phosphate backbone is on the outside
Bases are on the inside
Strands run antiparallel to each other
10 Nucleotide pairs per complete turn
8
Q
Watson and Crick model was supported by what
A
Chargaff’s rules A=T and G=C
9
Q
Nucleotides have chemically distinct ____
A
sides
10
Q
What are the 4 nucleotide building blocks of DNA and what are the Purines, what are the pyrimadines?
A
A,T,G,C
PURINES: A, G
PYRIMADINES: T, C
11
Q
What links nucleotide subunits within the DNA strand?
A
Phosphodiester bonds
12
Q
5’ carbon of the sugar has a _________
A
phosphate group
13
Q
3’ Carbon of sugar has a ______
A
OH
14
Q
What holds the strands of the double helix together
A
hydrogen bonds
15
Q
What forms as DNA strands twist around each other
A
major and minor grooves
16
Q
The structure of DNA provides a machanism for _______
A
heredity
17
Q
Segment of DNA that directs the production of a particular protein or functional RNA molecule
A
Gene
18
Q
DNA is packaged into
A
chromosomes
19
Q
DNA bound to protein
A
Chromatin
20
Q
Condensed chromatin fibers
A
Chromosome
21
Q
How are abnormal chromosomes detected
A
karyotyping
22
Q
Organize and carry genetic info
A
chromosomes
23
Q
The total genetic information carried by all the chromosomes of a cell or organism
A
Genome
24
Q
T/F: The total genetic information carried by all the chromosomes of a cell or organism is called the genome
A
true
25
T/F: If the genome sizes are similar (between 2 species), their chromosome numbers must be similar
false
26
The ordered series of events by which a cell duplicates its contents and divides into two
cell cyle
27
Specialized DNA sequences are required for _________ & ___________
DNA replication; Chromosome segregation
28
The site where DNA replication begins
Replication origin
29
T/F: There is 1 replication origin in eukaryotic cells
False, there are multiple
30
The ends of a chromosome are called what
Telomeres
31
Telomeres contain _______________ & ___________
repeated nucleotide sequences; protective caps
32
What allows the duplicated chromosomes to be separated?
the centromere
33
The identical duplicated DNA molecule is called what
chromatid
34
The process where chromosomes are replicated, seperated and then partitioned into 2 daughter cells
cell cycle
35
Describe the chromosomes in interphase
they're long and thin. They are organized within the nucleus in chromosome regions/territories which keeps the strands from getting tangled
36
Chromosome regions attach to sites on the________. Which is formed as a network of __________ made from ___________
nuclear envelope/ nuclear lamina; intermediate filaments; nuclear lamins
37
The large structure within the nucleus is called what
nucleolus
38
The nucleolus is the site of ______________ and ___________ assembly.
Ribosomal RNA transcription; ribosomal unit assembly
39
What can produce large biochemical subcompartments in cells?
weak interactions between macromolecules
40
What can produce large biochemical subcompartments in cells
weak interactions between macromolecules
41
For eukaryotes DNA must fit in the ______
nucleus
42
The levels of chromosome condensation depend on 3 things
stage of the cell cycle
whether active/ inactive gene
proteins the coil and fold DNA (like histones)
43
The complex of DNA and proteins that make up the chromosomes in a eukaryotic cell
chromatin
44
The structural unit of the eukaryotic chromosome. It's composed of short length of DNA wrapped around an octameric core of histone proteins.
Nucleosome
45
The basic unit of eukaryotic chromatin structure
nucleosome
46
What is a nucleosome made of (2 general things)
Core particle (histone octamers)
Linker DNA
47
The small basic proteins with high proportion of positively charged amino acids (lysine and arginine)
Histones
48
_______ has N-terminal tails that can be modified. They package/condense DNA
histones
49
How many main types of histones are there
5
50
What does the positive charge of the Histone's amino acids help do
bind to negatively charged DNA
51
Which of the 5 types of histone helps pull adjacent nucleosomes together?
H1
52
Chromatin loops are established by what
nonhistone proteins
53
Changes in nucleosome structure allows access to
DNA
54
___________DNA is less tightly packaged than inactive DNA
Transcriptionally active (Euchromatin)
55
Chromatin remodeling complexes interact with _______ & ______
histones; DNA
56
T/F: Chromatin remodeling complexes are highly regulated
true
57
ATP dependent enzymes that change the position of DNA wrapped around nucelosomes
chromatin remodeling complexes
58
Uses the energy of ATP hydrolysis to move nucleosomes to hence allow access to the tightly bound chromosome
chromatin remodeling complexes
59
Whats is another word for active (turned on) Chromatin?
Euchromatin (transcriptionally active, and hence looser)
60
What is another word for inactive (turned off) Chromatin? What process does this inhibit?
Heterochromatin (transcriptionally inactive, and hence densely coiled);
prevents transcription
61
In its default state, the tight coiling that characterizes chromatin structure limits the access of RNA polymerase and ___________ to eukaryotic DNA. Therefore, a cell's chromatin must "open" in order for gene expression to take place. This process of "opening" is called __________, and it's vital for the proper functioning of eukaryotic cells.
transcription factors; chromatin remodeling
62
A open/active chromatin (genes are switched on) has what kind of histones?
acetylated histones
63
A closed/inactive chromatin (genes are switched off) has what kind of histones?
deacytlated histones
64
What does histone modification do?
regulates transcriptional activity
65
Histone tail can be modified by the addition or removal of (list 3)
methyl, acetyl, phosphate, or other groups
66
T/F: Histone tail modification is irreversible
False, its reversible
67
Histone methylation leads to ________
tighter packing (gene repressed)
68
Histone acetylation leads to ________
looser packing (leads to gene expression)
69
T/F: Interphase chromosomes are uniformly packed
False, they contain both highly condensed and more extended forms of chromatin
70
Highly compacted chromatin
heterochromatin
71
more loosely packed, diffused chromatin
Euchromatin
72
What is the purpose of different cell types having different regions of chromosomes be more condensed or more extended?
it allows Cell type specific gene expression
73
T/F: During cell division ALL the chromatin becomes highly compacted
true
74
A chromosome is made of 2 identical sister ________
chromatids
75
What are the 2 types of heterochromatin?
Facultative & constitutive
76
Whats the difference between Facultative Heterochromatin and Constitutive Heterochromatin?
Facultative Heterochromatin can be converted to euchromatin
Constitutive Heterochromatin is permanently compact.
77
Constitutive Heterochromatin serves ________ functions within chromosomes and does NOT contain _______.
structural; genes
78
!What allows heterochromatin to form and spread? When does the spread stop?
Heterochromatin specific histone modifications
Ex. methylation of lysine 9 in H3 tail;
Stops once it reaches the Barrier DNA sequence
79
Barrier DNA sequence may contain ____________ for histone acetyltransferases
binding sites
80
!Sometimes genes located near ________ chromatin can get accidentally packaged into ________chromatin which prevents ____________. Ex) B-globin gene
Constitutive chromatin; Heterochromatin ;gene expression
81
!One of the 2 X chromosomes is inactivated by ________________ in the cells of mammalian females.
heterochromatin formation
82
!What are 2 types of Constitutive heterochromatin?
Centromeres and Telomeres
83
The centromere is bound by a complex of proteins called the what
kinetochore
84
What is the function of the centromere?
maintains sister chromatid cohesion during mitosis and meiosis
85
What protects chromosome ends from degradation during each round of DNA replication?
telomeres
86
What are the 2 purines and what are the 2 pyrimidines?
Purines- A & G
Pyrimidines- CUT cytosine, uracil thymine
87
T/F: Which of the following is NOT true of the N-terminal “tail” of histones binds to DNA in a sequence-specific manner
XXXXX ignore this Qxxxxxxx
false
88
The core histones' long, extended tail at the N-terminus can be modified, it also helps DNA pack tightly and it extends
out of the _____________.
out of the nucleosome core.
89
Stepwise condensation of linear DNA happens in five different packing processes. Which process has a direct requirement for histone H1?
formation of the 30-nm fiber
90
T/F: Histones are highly evolutionarily conserved
true
91
Genes that are being transcribed are thought to be packaged in a _________ (more/less) condensed type of euchromatin.
less
92
Nucleosome core particles are separated from each other by stretches of ________ DNA.
linker
93
A string of nucleosomes coils up with the help of
_________ to form the more compact structure of the 30-nm fiber. A zigzag model describes the structure of the 30-
nm fiber. The 30-nm chromatin fiber is further compacted by the formation of ______that emanate from a central axis
histone H1; loops
94
Heterochromatin is highly ________.
Constitutive heterochromatin plays a(n) ________ role and Facultative heterochromatin functions in ________.
compact; structural; regulating gene expression
95
Cells must be able to _________ reproduce, or replicate, their genetic material at each cell division.
accurately
96
What enables DNA replication
base pairing
97
The cluster of proteins involved in DNA replication
Replication machine
98
The nucleotide sequence at which DNA replication is initiated. It attracts initiator proteins that pry DNA apart.
Replication Origin
99
Replication origin is rich with what bases
A and T
100
How many replication forks form at the replication origin?
2
101
The group of proteins that carry out replication. They're attracted to origin of replication by initiator proteins.
Replication machine
102
This complex sits on the origin of replication throughout cell cycle
origin recognition complex
103
Replication machines (rapid) assemble at each replication fork. They replicate in which direction(s)
bidirectionally
104
What important enzyme does the Replication machine contain?
DNA polymerase
105
DNA polymerase can copy DNA molecules. Incoming nucleotides are added to the ________ end of the growing DNA chain. Therefore, elongation occurs in the __________ direction.
3′ hydroxyl; 5′ to 3′ direction
106
DNA Polymerase synthesizes DNA using the _______ strand as a template.
parental
107
What 3 things does DNA polymerase need?
1. Template DNA
2. Primer
3. Deoxyribonucleoside Triphosphate (dNTP) bases
108
Due to complimentary base pairing, the incoming dNTP depends on the ______ in the template strand
base
109
Name the 4 dNTP bases
dATP, dTTP, dGTP, dCTP
110
What bond is formed between the *phosphate group on the 5’-carbon* of the incoming dNTP and the *hydroxyl group of the 3’-carbon* of the nucleotide on the growing chain?
The energy for this reaction comes from removing a what?
phosphodiester bond;
pyrophosphate
111
What is DNA polymerase's role during the linking of the incoming 5′ phosphate with the 3′ hydroxyl group of the end nucleotide?
it catalyzes the reaction, it guides and positions the incoming nucleoside triphosphate to the template strand
112
The replication fork is _____________(symmetrical/asymetrical)
asymetrical
113
T/F: Only one parental strand needs to be replicated
Do Parental strands run in opposite directions (antiparallel)?
false; yes
114
The “_______strand” is synthesized continuously toward the replication fork. The “_______strand” is synthesized in the direction away from the replication fork.
leading ; lagging
115
Overall DNA is synthesized as _________ segments
discontinuous
116
Although mistakes are rare, DNA polymerase is able to _____________
self correct/ proofread
117
If the DNA polymerase added the wrong nucleotide during replication how does it correct the mismatch?
The new strand is moved to the editing (E) site. The mismatched nucleotide is cut from the new strand and replaced with the correct match.
118
T/F: DNA polymerase undergoes small structural rearrangement that allows it to catalyze the reaction.
true
119
The energy required for DNA polymerase's proofreading comes from the hydrolysis of what?
of dNTP's high-energy bond
120
T/F: If strands grew in the 3’-to-5’ direction, DNA polymerase's removal of an incorrect nucleotide leaves the new stand without a high-energy bond to fuel the reaction
true
121
DNA polymerase can add nucleotides only to the ___ end of an existing nucleotide chain
3′
122
Short lengths of RNA act as _____ for DNA synthesis
primers
123
RNA primers are synthesized by _______ using a single DNA strand as the template
primase
124
Primase uses ________________ rather than deoxyribonucleoside triphosphate
ribonucleoside triphosphate
125
What starts the leading & lagging strand's synthesis?
How many primers does leading strand synthesis need and how many does lagging strand synthesis need?
DNA polymerase;
Leading strand needs 1 primer
Lagging strand requires multiple primers
126
Why does the lagging strand require multiple primers?
since DNA polymerase is making Okazaki fragments, so at the start of each, there needs to be a primer
127
They keep polymerase attached to template DNA
Sliding clamp proteins
128
They hydrolysis the ATP to get the sliding clamp around the DNA
Clamp loaders
129
What does primase add
an RNA primer
130
What do DNA helicases do and what do they require to carry out their function?
they unwind DNA, and break hydrogen bonds
Helicase requires ATP
131
They bind single stranded DNA to prevent it from closing back up after its been unzipped
Single-stranded binding proteins
132
What relaxes the DNA's supercoiling by creating ticks? Without it, the DNA can not rapidly rotate
Topoisomerases
133
T/F: Circular DNA molecules have a problem in completing DNA replication on the lagging strand because primers are required. Each replication would result in some nucelotides lost
False, linear DNA does
134
_________ DNA molecules have a problem in completing DNA replication on the lagging strand because primers are required. Each replication would result in some nucleotides lost at the ends
How is this problem solved?
Linear;
Eukaryotes solve this problem with telomeres. They attract the enzyme telomerase. Telomerase replicates the ends of eukaryotic chromosomes
135
Telomerase is composed of protein and ______. Telomerase adds nucleotides to __________. Telomerase's ______________ acts as a template for adding the DNA repeat sequence to the telomere ends
RNA; telomere ends; enzyme-bound RNA
136
T/F: DNA damage occurs continually in cells
true
137
T/F: Mutations are spontaneous damage
true
138
DNA damage can be induced by radiation and chemicals
just know that
139
One example of spontaneous damage to DNA is Depurination, what is that?
loss of purine base A or G
140
One example of spontaneous damage to DNA is Deamination, what is that?
loss of an amine group from Adenine, Cytosine, and Guanine
Fun fact: A human cell may undergo about 100 deaminations each day
141
T/F: Depurination and deamination break the phosphodiester backbone
false, neither do
142
If left unrepaired, chemical modifications of nucleotides leads to what? Ex. if unrepaired, depurination can lead to the loss of a nucleotide pair
mutations
143
The major type of deamination reaction converts ________ to _________ and takes place on double helical DNA.
cytosine; uracil
144
DNA damage from radiation causes two adjacent _______ bases to become covalently attached to each other. This leads to the formation of _____________.
thymine; thymine dimers
145
DNA damage from chemicals can add bulky side groups to the bases and result in improper ____ pairing.
base
146
Most DNA damage is __________ (permanent/ temporary). However, mutations are ____________(permanent/ temporary).
temporary; permanent
147
What are the 3 steps in basic DNA repair
Excision
Resynthesis
Ligation
148
Which step of the DNA repair process does this describe:
The damage is cut out by a nuclease. Each nuclease is specialized for a certain type of DNA damage.
step 1, Excision
149
Which step of the DNA repair process does this describe:
A Repair DNA polymerase inserts the correct DNA sequence
step 2, Resynthesis
150
Which step of the DNA repair process does this describe:
DNA ligase closes the nick left in the sugar-phosphate backbone of the newly repaired strand
step 3, Ligation
151
What process removes replication errors that were missed during proofreading?
DNA mismatch repair system
152
What process corrects singular damaged bases?
Base excision repair
153
During base excision repair, a ________ removes the base by cleaving the bond between the base and the sugar. Then the Repair enzyme cleaves the backbone and removes the sugar.
_______________ synthesizes the correct new base. Finally,
______________ seals the nick in the DNA.
nuclease; DNA polymerase; DNA ligase
154
Uracil DNA glycosyla detects what
Uracil in DNA
155
Mismatch repair and Base excision repair are very similar. What is the main difference between the two?
Base excision repair corrects singular bases (think excision--> precise), whereas Mismatch repair takes out a whole chunk of bases
156
When *both* strands of the DNA break, what are the 2 options for repair?
Nonhomologous end-joining
Homologous recombination
157
Describe nonhomologous end joining
====== ====== We have broken double strands
======0 0====== Proteins attach at the ends
====0 0==== Protein (nuclease) munches off some
nucleotides at these ends
=======L======= DNA ligase seals the gap up
=============== yayyy DNA is repaired :D
158
Describe homologous recombination
- Nuclease chews back 5’ end on both broken strands.
-Then one broken end ‘invades‘ the unbroken homologue (assisted by specialized enzymes)
- Complementary base pairing occurs
- DNA polymerase elongates the broken strand
- Elongated strand is released from homologue and joins original (also broken) partner
- Additional DNA synthesis occurs to fill in gaps on other broken strand
- DNA ligase seals the breaks
159
This process can flawlessly repair DNA double-strand breaks as well as other forms of DNA damage. It involves the process of crossing over
homologous recombination
160
DNA sequence comparison between humans and chimps shows the sequences are _____% identical
98%
161
The enzyme DNA ligase is required continuously during DNA replication in order for fragments of the ___________(lagging/leading) strand to be joined together.
lagging
162
The first repair of mistakes during DNA replication is made by
DNA polymerase
163
!Within a double-stranded DNA molecule, an A on one strand is paired with a G on the other. Which DNA repair
system would most likely fix this error?
mismatch repair
164
!RNA primers are necessary in DNA synthesis because the DNA polymerase enzyme requires the ________ end of an existing strand to catalyze the addition of
deoxyribonucleotides.
3ʹ hydroxyl
165
In DNA replication, nucleotides are added to the growing new strand at the _______ end, the end at which the DNA strand has a free _______ group.
3'; hydroxyl
166
T/F: In the leading strand, DNA replication progresses in the direction of the acting helicase
true
167
If the cytosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication?
TTAT
168
If the adenosine in the sequence TCAT is deaminated and not repaired, which of the following is the point mutation you would observe after this segment has undergone two rounds of DNA replication?
TCT
169
Nonhomologous end joining is a process by which a double-stranded DNA end is joined to the nearest available.....
nearest available double-stranded DNA end
170
!The nucleotide sequence of one DNA strand in a DNA double helix is 5'-CATTGCCAGAAAAAT-3'. What is the sequence of the complementary strand produced during replication?
5' ATTTTTCTGGCAATG 3'
The complementary strand is always written 5'-3' so the sequence is going to be backwards (the 5' end of the of strand and the 3' have to be across from one another)
171
T/F: A single DNA strand can serve as a template for both leading and lagging DNA strands during the synthesis of
double-stranded DNA.
True, for all types of DNA
172
T/F: A newly synthesized RNA strand is not identical to the template strand, its complementary to it
true
173
What happens after the DNA polymerase on the lagging-strand template completes an Okazaki fragment?
The sliding clamp attached to the polymerase dissociates from the DNA, and the polymerase temporarily releases the lagging-strand template.
174
An mRNA sequence is 5' AUGAAAUCCUAG 3' what is the DNA sequence?
5’ CTAGGATTTCAT 3’
175
The **coding** DNA sequence is 5' GTCTATGCATTA 3' what is the RNA sequence?
5' CAGAUACGUAAU 3'
176
What bond links RNA nucleotides
Phosphodiester (down the single strand)
177
In an RNA strand, what are the 2 types of base pairing
conventional and nonconventional
178
T/F: The DNA coding strand and template strand are the same thing
False
179
During Transcription, Ribonucleoside Triphosphates base pair with __________ on DNA. The reaction is catalyzed by ____________
nucleotides; RNA polymerase
180
RNA molecule ________ (will/wont) stay bound to template DNA
wont
181
T/F: During Transcription, limited regions of DNA are copied
true
182
During Transcription, what unwinds DNA?
RNA polymerase
183
Does RNA polymerase need a primer? Does it proofread?
no; no
184
What direction is RNA synthesized in?
5'- 3'
185
In DNA replication the energy needed comes from incoming dNTPs, however, in RNA synthesis, energy comes from what?
incoming ATP, CTP, UTP or GTP
186
Release of RNA from template allows for _____ (slower/ quicker) production of many RNA molecules
quicker
187
This codes for proteins
mRNA
188
These form the core of the ribosome's structure and catalyze protein synthesis
rRNAs
189
This type of RNA regulates gene expression
miRNAs
190
These serve as adaptor between mRNA and amino acids during protein synthesis
tRNAs
191
This type of RNA is used in RNA splicing, gene regulation, telomere maintenance and many other processes
other noncoding RNAs
192
Signals in the ______ tell RNA polymerase where to start and stop transcription
DNA
193
In bacterial cells:
During the initiation of transcription, how would you describe the way RNA polymerase associates with DNA?
randomly and loosely
194
In bacterial cells:
(Initiation step) Transcription begins when RNA polymerase binds to a __________ sequence. This triggers the unwinding of the DNA double helix.
Promoter
195
In bacterial cells:
The promoter sequence is found _______(upstream/downstream) of the start site
upstream
196
In bacterial cells:
This recognizes transcription start site and releases once transcription starts
sigma factor
197
In bacterial cells:
What step is it when RNA polymerase moves along the DNA template, unwinding the helix and elongation the RNA?
elongation
198
In bacterial cells:
During elongation, RNA polymerase catalyzes the formation of a ____________ bond between incoming ribonucleoside triphosphate molecules (NTPs)
phosphodiester
199
In bacterial cells:
In elongation, RNA polymerase continues along the gene until it hits the ___________ sequence. This triggers the next step of the process called ______________.
terminator; Termination
200
In bacterial cells:
During this step, RNA polymerase dissociates from the DNA template, hence terminating synthesis and releasing the RNA molecule.
Termination
201
DNA to RNA is called what?
RNA to protein is called what?
Transcription; translation
202
During Termination, the interaction of 3’ terminator sequence with polymerase causes the _________
release
203
RNA polymerase always moves in the __________ direction with respect to the template DNA strand
3' to 5'
204
The ________ of the promoter sequences determines which strand will serve as the template
All bacterial promoters contain DNA sequences at –10 and _____.
Polarity; –35
205
Eukaryotic transcription uses multiple RNA polymerases name the 3.
RNA polymerase 1,2,3
206
Which of the 3 RNA polymerases transcribes most rRNA genes?
1
207
Which of the 3 RNA polymerases transcribes tRNA genes and many other small RNAs?
3
208
Which of the 3 RNA polymerases transcribes mRNA and ALL protein-coding genes?
2
209
Where is RNA polymerase 1 found?
Where is RNA polymerase 2 found?
Where is RNA polymerase 3 found?
nucleolus
nucleoplasm
nucleoplasm
210
RNA polymerases in eukaryotes require additional proteins called _____________
transcription factors (TF)
211
T/F: In Eukaryotes, some transcription factors must bind *before* the RNA polymerase can bind.
true
212
T/F: Protein-protein interactions play a minor role in eukaryotic transcription
False, p-p interactions play a prominent role in euk transcription
213
!T/F:In eukaryotes, A general transcription factor (TF) is *always* required for RNA polymerase binding to promoters
true
214
Transcription factors bind to the promoter in a defined order starting with _______. Eventually, a large complex of proteins forms a _____________________ on the promoter
TFIID; transcription initiation complex
215
DNA sequence found in most eukaryotic promotors. Its recognized by a subunit of TFIID.
TATA box
216
______ recognizes and binds DNA because of its TATA- binding protein (TBP) subunit.
TFIID
217
The binding of TFIID enables the adjacent binding of ______. The rest of the general transcription factors, including RNA polymerase, then assemble at the promoter.
TFIIB
218
!This transcription factor unwinds DNA and phosphorylates the RNA polymerase 2 C-terminal tail so that it can begin RNA synthesis (initiation step)
TFIIH
219
T/F: The acetylation of RNA polymerase II releases it from the transcription factors so it can begin RNA synthesis
False, it should be the Phosphorylation
220
Eukaryotic promoters contain sequences that promote the binding of the __________ factors
general transcription
221
T/F: Theres 1 promoter in eukaryotic cells
False, there's various
222
Promoters can be located _________ (upstream/downstream/both) of the gene
both
223
Eukaryotic mRNAs Are Processed in the ______. And then must be exported to the cytosol via pores in the nuclear envelope.
Nucleus
224
Additional _____________(methylation/phosphorylation/acetylation) of the tail of RNA polymerase II allows RNA-processing proteins to assemble on the tail
phosphorylation
225
A newly produced RNA molecule is called the __________ transcript. It must undergo RNA processing (modification) before it can function in the cell. ALL eukaryotic RNA undergoes some form of processing.
primary
226
What 3 things does mRNA processing in eukaryotes do to change it from premRNA to mature mRNA?
adding 5' cap
adding 3' Poly(A) tail
splicing of Introns
227
What 3 things does mRNA processing in eukaryotes do to change it from premRNA to mature mRNA?
adding 5' cap
adding 3' Poly(A) tail
splicing of Introns
228
What is a UTR?
untranslated region (in mature mRNA)
229
In Eukaryotic mRNA modification:
The 5′ cap is guanosine that is _________ (acetylated/ methylated/ phosphorylated) at position 7 of the purine ring.
It is bound to the RNA molecule by an unusual ________ linkage rather than the usual 3′→5′ bond
Methylated; 5′→5′
230
!In Eukaryotic mRNA modification:
What does the added 5' guanosine triphosphate (GTP) cap help mRNA do?
facilitates the binding of mRNA to ribosomes
231
What does the mRNA's 5' cap addition contribute to the mRNA?
stability and positioning the RNA on the ribosome.
Required for exporting the transcript to the cytoplasm (swimming!)
232
What enzyme adds mRNA's poly(A) tail?
poly(A) polymerase
233
In eukaryotes, protein-coding genes are interrupted by ________ sequences
noncoding
234
What are the coding regions usually translated into amino acid sequences called?
What about the noncoding regions?
Expressed sequences (exons)
Intervening sequences (introns)
235
T/F: Different genes have different numbers of exons
true
236
What are the stages of transcription?
Binding
Initiation
Elongation
Termination
237
In transcription, the first step is Binding. What's helping the RNA polymerase bind in prokaryotes vs eukaryotes?
In prokaryotes, polymerase binds with the help of the sigma factor
In eukaryotes, polymerase binds with the help of general TFs
238
What 4 steps occur in tRNA processing in eukaryotes to change it from pre-tRNA to mature tRNA?
Removal
Replacement
Chemical Modification
Excision
239
Special __________ sequences in a pre-mRNA transcript signal the beginning and the end of an intron.
nucleotide
240
______, (a type of RNA-protein complex) recognizes the sequences marking the beginning and end of an intron. They then direct the cleavage of the RNA at the intron-exon borders
snRNPs
241
During splicing of a premRNA, which nucleotide base attacks the 5’ splice site, cutting the sugar-phosphate backbone.
A
242
The RNA portion of the snRNP recognizes and base pairs with the intron splicing sequence. snRNPs assemble into a _________ (a large assembly of RNA and protein) in a stepwise manner.
spliceosome
243
During mRNA splicing, the splice site junction is marked by the ______ Junction Complex.
Exon
244
What enzyme joins exon ends after splicing?
RNA ligase
245
The presence of introns allows each gene’s pre-mRNA molecule to be spliced in multiple ways
This can lead to the production of multiple protein products. What do we call this?
alternative splicing
246
RNA synthesis and processing takes place in “factories” within the _______
nucleus
247
A specialized set of RNA-binding proteins mark mRNA as completed and ready for export out of the ________. A nuclear transport receptor associates with the mRNA and guides it through the nuclear pore
nucleus
248
mRNA molecules are eventually degraded in the _______
cytosol
249
The set of rules by which the information contained in the nucleotide sequence of a gene and its corresponding RNA molecule is translated into the amino acid sequence of a protein
Genetic Code
250
In translation:
______ molecules encode the amino acid sequence information.
______ molecules align the amino acids in the correct order.
_____________ attach amino acids to their appropriate tRNA molecules.
________ carry out the process of polypeptide synthesis.
mRNA; tRNA; Aminoacyl-tRNA synthetases; Ribosomes
251
What is translation?
making a polypeptide (mRNA is used to build a protein)
252
During ______ mRNAs encode instructions for polypeptide.
translation
253
In translation, an mRNA sequence is decoded in sets of _____ nucleotides (codons).
three
254
What does the genetic code is "redundant" mean?
sometimes more than 1 codon (ex. GAG and GAA) can code for the same amino acid
(ex. both GAG and GAA code for Glycine)
255
One of the three possible ways in which a set of successive nucleotide triplets can be translated into protein. It depends on which nucleotide serves as the starting point.
Reading Frame
256
!During translation, the _______ molecule serves as the adaptor molecule.
It translates the three-nucleotide codon sequence in the mRNA into the amino acid of that codon.
tRNA
257
The 3 nucleotide sequence in tRNA that corresponds to a complementary codon in messenger RNA.
Anticodon
258
_______ phenomena base pairing lets the same tRNA recognize multiple codons for the amino acid it carries. Ex. Glycine can be coded for by TTA & ATA)
The 3′ end of the codon shows the most redundancy.
Wobble
259
What is the charged tRNA molecule called?
Hint: its a tRNA with amino acid attached
Aminoacyl tRNA
260
Specific enzymes called ___________________ couple tRNAs to the correct amino acid.
Aminoacyl-tRNA Synthetases
261
The mRNA message is decoded on _________. But mRNA must first be exported from the nucleus to the cytoplasm.
ribosomes
262
T/F: The sequence of codons in mRNA directs the order of amino acids in the polypeptide.
true
263
Particles made of rRNA and protein. they have a large and small sub unit.
ribosomes
264
Ribosomes are ______(free/bound) in the cytoplasm but _______(free/bound) in theER
Ribosomes are also found in Mitochondrial matrix and Chloroplast stroma.
free; bound
265
Ribosomes carry out polypeptide synthesis.
A ribosome has three binding sites for tRNA, what are they?
E – exit site
P - peptidyl-tRNA site
A - aminoacyl-tRNA site
266
During polypeptide synthesis in a ribosome:
Which site corresponds to each description
This site holds the tRNA that carries the growing polypeptide chain.
This site holds the tRNA that carries the next amino
This site is the exit site, where discharged tRNAs leave the ribosome
p; a; e
267
What is the DNA coding strand identical to?
(except for thymine being replaced with uracil)
the RNA strand
268
4 steps of Translation
Step 1
Step 2
Step 3
Step 4
Charged tRNA carrying the next amino acid (aa#4) binds to the vacant A site on the ribosome. tRNA forms base pairs with the mRNA codon that is exposed.
Carboxyl end of the polypeptide chain (aa#3) is uncoupled from the tRNA at the P site
aa #3 is joined by a peptide bond to the free amino group of the amino acid linked to the tRNA at the A site.
This reaction is carried out by a catalytic site in the large subunit
A shift of the large subunit relative to the small subunit moves the two bound tRNAs into the E and P sites of the large subunit.
The small subunit moves exactly three nucleotides along the mRNA molecule. This movement ejects the spent tRNA and resets the ribosome with an empty A site so that the next charged tRNA molecule can bind
269
T/F: The ribosome is a ribozyme
true
270
Which terminal end of a protein is made first?
N-terminal
271
A series of ribosomes that can simultaneously translate the same mRNA molecule
Polyribosomes (Polysomes)
272
T/F: Many antibiotics are inhibitors of prokaryotic protein synthesis
true
273
Proteins are degraded by the __________. It target proteins are marked for destruction primarily by the attachment of ubiquitin/polyubiquitin
proteasome
274
Proteins marked by a _________ are degraded by the proteasome
polyubiquitin
275
What are some examples of Post translation modifications
Phosphorylation
Glycosylation
Methylation
Acetylation
276
T/F: !RNA is thought to predate DNA in evolution
true
277
A cell capable of giving rise to any type of cell or tissue
pluripotent cell
278
The process by which a pluripotent cell undergoes a progressive coordinated change to a more specialized cell type
Brought about by *large scale change in gene expression*
differentiation
279
T/F: The different cell types of a multicellular organism contain the same DNA
true
280
Different cell types produce different sets of proteins. What are the 2 main proteins?
1. Housekeeping proteins (EXPRESSED IN ALL CELLS, BASIC FUNCTIONS)
2. Specialized proteins (for particular functions, Ex. Hemoglobin, insulin)
281
A cell can change the expression of its genes in response to _______ signals. (cortisol and liver cells prove this)
external
282
!!Transcription regulators bind to regulatory DNA sequences.
List the 3 DNA sequences that control gene transcription. (hint- one is in the question)
Promoter region, Transcription initiation sites, Regulatory DNA Sequence
283
Regulatory DNA Sequence- where transcription regulators bind. this will determine when, where and how much of a gene is to be transcribed into ___
RNA
284
Transcription Regulators bind to a regulatory DNA sequence.
The binding of a regulator to the regulatory DNA sequence acts as a switch.
There are 2 kinds of Transcriptional Regulators: Transcriptional Activator (On switch)
Transcriptional Repressor (Off switch)
What do each of them do?
Transcriptional Activator (On switch)- stimulates transcription of an adjacent gene
Transcriptional Repressor (Off switch)-prevents transcription of an adjacent gene
285
T/F: Protein-DNA interactions are specific and strong
true
286
Many Transcription Regulators bind as dimers, why?
It increases contact area between regulatory proteins and DNA. Dimerization increases the strength and specificity of interaction
287
A cluster of genes with similar functions that are under the control of a single operator and promoter (common in bacteria, rare in eukaryotes).
Allows for transcription of these genes to be turned on or off together
Operon
288
Just know Trp operon has to do with synthesis of tryptophan
289
!!Ribozymes are known to catalyze which of the following reactions in cells?
A. DNA synthesis
B. transcription
C. RNA splicing
C. rna splicing
290
10. In eukaryotes, but not in prokaryotes, ribosomes find the start site of translation by
A. binding directly to a ribosome-binding site preceding the initiation codon.
B. scanning along the mRNA from the 5′ end.
C. recognizing an AUG codon as the start of translation.
D. binding an initiator tRNA.
B. scanning along the mRNA from the 5′ end.
291
In eukaryotic cells, translation occurs in the _______ and transcription occurs _______.
A. cytoplasm; in the nucleus
B. nucleus; in the nucleus
C. nucleus; in the cytoplasm
D. nucleus; outside of the cell
A
292
Which of these is not required for transcription?
A. DNA template
B. primer
C. Ribonucleoside triphosphate
D. RNA polymerase
E. Helicase
primer (used in DNA replication)
293
In prokaryotes, the region of DNA to which RNA polymerase binds most tightly is the
A. promoter.
B. poly C center.
C. enhancer.
D. operator site.
E. minor groove.
a. promoter
294
DNA is composed of two strands, only one of which is typically used as a template for RNA synthesis. By what
mechanism is the correct strand chosen?
A. The promoter acts to direct the RNA polymerase.
B. Only one strand has a start codon.
C. Both strands are tried, and the one that works is remembered.
D. An initiation factor informs the system about which strand to use.
E. The strand chosen randomly.
A. promotor directs the RNA polymerase
to the correct strand
295
Whats the total number of different possible codons?
64
296
Aside from using T instead of U, the coding strand of DNA is _______ to the mRNA.
identical (its not even antiparallel)
297
How is it possible for single-stranded RNA to fold into complex shapes?
A. Phosphodiester linkages form between the phosphate and the sugar ribose.
B. Internal base pairings occur—adenine with uracil, and cytosine with guanine.
C. Uracil’s methyl group binds to adenine, coiling the molecule.
D. The single strand “twists” around itself.
B. Internal base pairings occur—adenine with uracil, and cytosine with guanine.
298
The anticodon 3′-UAC-5′ will bind to which of the following codons?
A. 5′-ATC-3′
B. 5′-AUC-3′
C. 5′-AUG-3′
D. 5′-TAG-3′
E. 3′-AUG-5′
C. 5'- AUG- 3'
remember mRNA has U replaced for A.
mRNA binds to tRNA (this is the anticodon) and A binds to U.
299
The wobble phenomenon occurs at _______end of the anticodon and helps explain why the _______ end of the
codon shows the most redundancy.
5' ; 3'
300
!Translation of messenger RNA into protein occurs in mRNA in a _______ direction, and the protein is built from _______ terminus to _______ terminus.
5’-to-3’; N; C
301
1. Which of the following statements about transcriptional regulators is FALSE?
A. Transcription regulators interact only with the sugar–phosphate backbone on the outside of the double
helix to determine where to bind on the DNA helix.
B. Transcription regulators will form hydrogen bonds, ionic bonds, and hydrophobic interactions with DNA.
C. The DNA-binding motifs of transcription regulators usually bind in the major groove of the DNA helix.
D. The binding of transcription regulators generally does not disrupt the hydrogen bonds that hold the
double helix together
A. Transcription regulators interact only with the sugar–phosphate backbone on the outside of the double
helix to determine where to bind on the DNA helix.
302
T/F: DNA methylation involves a covalent modification of cytosine bases.
true
303
Which event would lead to a reduction in gene expression?
A. Mutation of the DNA-binding domain of an activator, changing its shape
B. Mutation of the binding site of a co-repressor molecule within a repressor protein
C. Removal of all methylation marks from a region of DNA
D. Remodeling of the chromatin environment, resulting in removal of histone octamers from a gene’s
promoter region
A. Mutation of the DNA-binding domain of an activator, changing its shape
304
It binds tryptophan, binds to operator and blocks RNA polymerase from binding to promoter, hence blocking transcription.
Trp repressor (regulator)-
305
Repressors turn genes ____, and activators turn them ___
off; on
306
They work with inefficient promotors, Bind to regulatory sequences, interact with RNA pol, AND help initiate transcription
Activators
307
It encodes the proteins required to import and digest lactose. It's turned on when there's no glucose (not provided by CAP activator) and there's lactose.
And it's turned off by Lac repressor, unless lactose is present.
Lac Operon
308
Lac Operon turned ON when two conditions are met, what are they?
NO: glucose, YES: lactose
309
**Eukaryotic transcription regulators**- control gene expression ________(nearby/ from a distance) .
**Enhancers**- regulatory DNA sequences, they bind activators AND INCREASE TRANSCRIPTION RATES.
In eukaryotes, _______ can bind far away (upstream or downstream) from the promoter
from a distance;
activators
310
One or more of the activator proteins cause the DNA to form a loop that brings the _______ close to the promoter.
enhancer
311
This acts as a bridge between the activator, which is associated with enhancers, and the general transcription factors. Binds to RNA polymerase
Mediator
312
The arrangement of chromosomes into ________ keeps enhancers in check
looped domains
313
Triggers differentiation of all specialized cells types in organ
Master regulators
314
If the gene encoding the lac repressor is mutated such that the repressor can no longer bind the operator, will
transcription of that operon occur?
A. Yes, because the repressor transcriptionally activates the lac genes.
B. Yes, but only when lactose is present.
C. No, because RNA polymerase is needed to transcribe the genes.
D. Yes, because RNA polymerase will be able to bind the promoter and transcribe the operon.
E. No, because cAMP levels are low when the repressor is nonfunctional
D. Yes, because RNA polymerase will be able to bind the promoter and transcribe the operon.
315
When an enhancer is bound, it
A. increases the stability of a specific mRNA.
B. stimulates transcription of a specific gene.
C. stimulates transcription of nearly all genes.
D. stimulates splicing of a specific mRNA.
E. stimulates splicing of nearly all mRNAs.
B. stimulates transcription of a specific gene.
316
Which is an example of regulation of eukaryotic transcription?
A. Iron binding the repressor protein for the ferritin mRNA and increasing ferritin expression
B. Proteasome breakdown of protein–polyubiquitin complexes
C. MicroRNAs binding their target mRNA and causing its degradation
D. Alternative splicing of an mRNA transcript
E. Activator proteins binding an enhancer
E. Activator proteins binding an enhancer (increases transcription rate)
317
These are all examples of things that would effect _____ expression
A. Deletion of a promoter
B. Deletion of an enhancer
C. Lack of modification of the cap structure on mRNA
D. Inability of a transcription factor to bind the promoter
gene
318
Methylation most often occurs to _______ that are next to _______.
A. adenines; cytosines
B. adenines; guanines
C. cytosines; adenines
D. cytosines; guanines
E. guanines; adenines
D. cytosines; guanines
319
In eukaryotic cells, a positive regulator or enhancer
A. binds to the enhancer region to block transcription.
B. is made of RNA.
C. binds to transcription factors to increase transcription rates.
D. is a carbohydrate.
E. is an enzyme
C. binds to transcription factors to increase transcription rates.
320
All cells in a given mammal carry the same genome, yet certain genes are expressed only in a particular tissue,
such as in the eye, and not expressed in other tissues, such as in the liver. How is this specificity of gene
expression for a particular tissue achieved?
A. Different tissues inactivate whole swaths of the genome, like a Barr body, thereby achieving tissuespecific gene expression.
B. Different tissues express unique transcription factors that are bound to tissue-specific enhancer elements, thereby achieving tissue-specific gene expression.
C. All different cell types in the organism express all proteins equally and degrade the proteins that they don’t need.
D. Certain organ and tissue systems, such as the nervous system, form relatively early in the organism’s embryonic life, as compared to the epidermis; it is this relative age of the tissue lineage that determines which tissue-specific genes are expressed.
B. Different tissues express unique transcription factors that are bound to tissue-specific enhancer elements, thereby achieving tissue-specific gene expression.
321
A mutation causes an increase in the production of DNA demethylase. The expected effect would be _______ in
the amount of overall methylation and a consequential _______ in overall gene expression.
A. an increase; increase
B. an increase; decrease
C. no change; increase
D. a decrease; increase
E. a decrease; decrease
D. a decrease; increase
322
Combinatorial control of gene expression
A. involves every gene using a different combination of transcriptional regulators for its proper expression.
B. involves groups of transcription regulators working together to determine the expression of a gene.
C. involves only the use of gene activators used together to regulate genes appropriately.
D. is seen only when genes are arranged in operons.
A. involves every gene using a different combination of transcriptional regulators for its proper expression.
