Chapter 5b - The Central Dogma Revisited Flashcards
1
Q
DNA -> mRNA
A
transcription
2
Q
where does mRNA leave through
A
nuclear pores
3
Q
mRNA -> protein
A
translation
4
Q
used to synthesize proteins
A
ribosome
5
Q
model of DNA replication in humans
A
semiconservative
6
Q
direction of synthesis during DNA replication
A
5’ to 3’ direction
7
Q
needed for initiation
A
primer
8
Q
- enzymes and proteins needed in DNA replication
- large protein complex that carries out DNA replication, starting at the replication origin
A
replisome
9
Q
allows each strand of DNA to serve as a template for a new strand
A
base pairing
10
Q
- in DNA, adenine (A) forms a base pair with thymine (T) using two hydrogen bonds, and guanine (G) forms a base pair with cytosine (C) using three hydrogen bonds
- in RNA, thymine is replaced by uracil (U)
A
Watson–Crick base pairing
11
Q
- labeled “parent” nucleotides in DNA strands with heavy nitrogen = 15N
- label new nucleotides with lighter isotope = 14N
A
Meselson & Stahl
12
Q
Models of DNA replication
A
- conservative
- semiconservative
- dispersive
13
Q
parental double helix remains intact and all new copy is made
A
conservative
14
Q
two strands of the parental molecule separate, and each functions as a template for synthesis of a new complementary strand
A
semiconservative
14
Q
each strand of both daughter molecules contains a mixture of old and newly synthesized parts
A
dispersive
15
Q
how are base pairs bonded
A
hydrogen bonding
16
Q
the initiating point that generates a replication bubble
A
origin of replication
17
Q
unwound and open region of DNA where DNA replication occurs
A
replication bubble
18
Q
region where a cell’s DNA double helix has been unwound and separated to create an area where DNA polymerases and the other enzymes involved can use each strand as a template to synthesize a new double helix
A
replication fork
19
Q
formed at all potential origins of replication through the action of the origin recognition complex (ORC), Cdc6, Cdt1, and the Mcm2-7 complex
A
pre-replicative complex (pre-RC)
20
Q
powers nucleotide addition
A
pyrophosphate hydrolysis
21
Q
bond between two nucleotides (sugar-phosphate)
A
phosphodiester bond
22
Q
Different DNA Polymerases
A
- DNA polymerase I
- DNA polymerase II
- DNA polymerase III
23
Q
DNA polymerase I
A
- 5’-3’ polymerization
- 3’-5’ proofreading
- 5’-3’ exonuclease activity
24
DNA polymerase II
- DNA repair functions
- restarts replication after damaged DNA halts synthesis
25
DNA polymerase III
primary replication enzyme
26
DNA polymerase IV
- 5'-3' polymerase activity
- DNA repair
27
DNA polymerase V
- 5'-3' polymerase activity
- DNA repair
- translesion DNA synthesis
28
how are incorrect nucleotides removed
3'-5' proofreading
29
pair of abnormally chemically bonded adjacent thymine Bases in DNA, resulting from damage by ultra-violet irradiation
thymine dimer
30
cuts the damaged DNA strand at two points and the damaged section is removed
nuclease
31
repair synthesis and fills in missing nucleotides
DNA polymerase
32
seals the free end of the new DNA to the old DNA, making the strand complete
DNA ligase
33
unwinds parental double helix at replication forks
helicase
34
binds to and stabilizes single-stranded DNA until it can be used as a template
single-strand binding protein
35
corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands
topoisomerase
36
synthesizes a single RNA primer at the 5' end
primase
37
elongates strand, adding on to the primer
DNA polymerase III
38
removes primer from 5' end of strand and replaces it with DNA, adding on to the adjacent 3' end
DNA polymerase I
39
joins the nicks in DNA strand
DNA ligase
40
both daughter strands are laid down in the ___ direction
5' to 3'
41
transcribed DNA strand
template strand
42
untranscribed DNA strand
coding strand
43
untranscribed DNA strand = __ RNA
same sequence as RNA
44
- region containing the RNA polymerase, DNA, and the RNA product
- molecular structure formed during DNA transcription when a limited portion of the DNA double helix is unwound
- size ranges from 12 to 14 base pairs.
transcription bubble
45
enzyme used in making mRNA
RNA polymerase
46
Steps in Transcription
1. Initiation
2. Elongation
3. Termination
47
RNA polymerase binds to promoter sequence on DNA
Initiation
48
Role of promoter
1. starting point
2. template strand
3. direction on DNA
49
direction on DNA when transcribing
- always read DNA 3'-5'
- build RNA 5'-3'
50
Components of RNA polymerase holoenzyme
1. 2 αββ’ - core enzyme
2. (2 αββ’) δ - RNA polymerase holoenzyme
51
- these proteins bind to genes at sites known as enhancers
- help to determine which genes will be switched on, and they speed the rate of transcription
activators
52
site where activators bind to
enhancers
53
- these proteins bind to selected sets of genes at sites known as silencers
- interfere with the functioning of activators and thus slow transcription
repressors
54
sites where repressors bind to
silencers
55
these "adapter" molecules integrate signals from activators and perhaps repressors and relay the results to the basal factors
coactivators
56
in response to injunctions from activators, these factors position RNA polymerase at the start of the protein-coding region of a gene and send the enzyme on its way
basal factors
57
- define the direction of transcription and indicate which DNA strand will be transcribed;
- this strand is known as the sense strand
Promoter sequences
58
Promoter sequences are also known as __ __
sense strand
59
stop site of transcription
terminator
60
RNA polymerase copies DNA as it unwinds
elongation
61
how many base pairs are transcribed at a time
~20 base pairs
62
simple proofreading during elongation stage in transcription
- 1 error/10^5 bases
- make many mRNAs
- mRNA has short life
- not worth editing
63
direction of transcription
- "downstream"
- reads DNA 3'-5'
64
where does RNA polymerase stop
termination sequence
65
refers to two areas of a DNA strand whose base-pair sequences are inverted repeats of each other
Dyad symmetry
66
what is made when there is dyad symmetry in the DNA
hairpin turn
67
Different types of termination in transcription
1. Rho-independent termination
2. Rho-dependent termination
68
palindromic GC-rich region (hairpin loop) followed by a stretch of AAAAAAA in the DNA being transcribed
Rho-independent termination
69
- a hexamer which acts as a RNA-DNA helicase
- GC region slows down RNA pol and Rho factor catches up and dissociated RNA from transcription bubble
Rho-dependent termination
70
DNA __ leave nucleus
can't
71
where is DNA wound on
histone proteins
72
noncoding sequence of eukaryotic DNA
intron
73
coding sequence of eukaryotic DNA
exon
74
Transcription in Eukaryotes
1. RNA polymerase 1
2. RNA polymerase 2
3. RNA polymerase 3
75
- only transcribes rRNA genes
- makes ribosomes
RNA polymerase 1
76
transcribes genes into mRNA
RNA polymerase 2
77
only transcribes tRNA genes
RNA polymerase 3
78
each RNA polymerase has a __ __ __ it recognizes
specific promoter sequence
79
transcription factors bind to promoter region upstream of gene
initiation complex
80
turn on or off transcription
suite of proteins which bind to DNA
81
recognition site for transcription factors
TATA box binding site
82
what do the transcription factors trigger
binding of RNA polymerase to DNA
83
Eukaryotic Termination of Transcription
1. Poly-adenylation signal
2. Downstream Terminator Sequence
84
eukaryotic mRNA needs work after transcription
primary transcript (pre-mRNA)
85
edit out introns
mRNA spicing
86
what is made after mRNA processing
mature mRNA
87
what is added to protect mRNA from enzymes in cytoplasm
- 5' cap
- polyA tail
88
addition of methylated G nucleotide to the 5' end of the transcript
capping
89
when does capping occur
right after about 30 nucleotides RNA have been synthesized
90
purpose of capping
- protects growing RNA transcript from degradation
- ribosome recognition during translation
91
addition of 100-200 residues of poly A's to the 3' end even before termination of transcription has completed
tailing
92
where is the tail located
10-30 nucleotides upstream from site of cleavage
93
tailing signals __ _ __ to cleave a portion of the transcript before the poly A tail is synthesized
poly A polymerase
94
purpose of tailing
1. aids in export of mature mRNA from nucleus
2. prevents degradation from 3' end
3. serves as recognition signal for ribosome
95
intrns are cut out of immature RNA transcripts
splicing
96
splicing signals tell __ where to 'cut and paste' exons
spliceosomes
97
what do introns have that are recognized by spliceosomes
consensus sequence on 5' and 3' ends
98
key components of the spliceosome and are absolutely required for pre-mRNA splicing
Spliceosomal snRNPs
99
snRNPs
small nuclear RNA
100
discarded byproducts of RNA splicing, the process by which genetic instructions for making proteins are assembled
Lariats
101
ribonucleic acid (RNA) enzyme that catalyzes a chemical reaction
ribozyme
102
some mRNA can __ itself
splice
103
discovered that RNA actively aids chemical reactions in cells
- Sidney Altman
- Thomas R. Cech
104
cellular process in which exons from the same gene are joined in different combinations, leading to different, but related, mRNA transcripts
Alternative splicing
105
splicing must be __
accurate
106
a single base added or lost throws off the __ __
reading frame
107
Components of the Translation Machinery
1. ribosome
2. messenger RNA (mRNA)
3. transfer RNA (tRNA)
4. amino acyl synthetase
5. protein factors
6. peptidyl transferase
108
protein factory composed of aggregates of RNA and protein 70S in prokaryotes and 80S in eukaryotes
ribosome
109
protein __ in prokaryotes
70S
110
protein __ in eukaryotes
80S
111
what does ribosome facilitate
coupling of tRNA anticodon to mRNA codon
112
structure of ribosome
- large subunit
- small subunit
113
sites in ribosome
1. A site
2. P site
3. E site
114
holds tRNA carrying next amino acid to be added to chain
A site
115
A site
aminoacyl-tRNA site
116
holds tRNA carrying growing polypeptide chain
P site
117
P site
peptidyl-tRNA site
118
empty tRNA leaves ribosome
E site
119
E site
exit site
120
70S ribosome of prokaryotes
- 50S large subunit
- 30S small subunit
121
80S ribosome of eukaryotes
- 60S large subunit
- 40S small subunit
122
bears amino acid sequence
messenger RNA (mRNA)
123
prokaryotic mRNA
multiple translation start site
124
eukaryotic mRNA
single translation start site
125
start codon
AUG
126
carries the amino acids to the ribosomes
tRNA
127
three-nucleotide or triplet sequence found on mRNA that codes for a certain amino acid during translation
codon
128
three-nucleotide sequence found on tRNA that binds to the corresponding mRNA sequence
anticodon
129
structure of tRNA
"clover leaf" structure
130
where is the anticodon found
"clover leaf" end
131
where is amino acid found
3' end of tRNA
132
enzyme which bonds amino acid to tRNA
aminoacyl tRNA synthetase
133
bond requires energy (aminoacyl tRNA synthetase )
ATP -> AMP
134
energy stored in tRNA-amino acid bond
- unstable
- amino acid is released easily
135
Step 1 of binding amino acid with tRNA
AA + ATP --> AA-AMP + PPi
136
Step 2 of binding amino acid with tRNA
AA-AMP + tRNA --> AA-tRNA + AMP
137
for initiation, elongation and termination of translation
protein factors
138
catalyzes peptide bond formation
peptidyl transferase
139
determined 3-letter (triplet) codon system
Crick
140
- determined mRNA-amino acid match
- added fabricated mRNA to test tube of ribosomes, tRNA and amino acids
- Nirenberg
- Khorana
141
UUU
phenylalanine (phe)
142
point mutations
- silent mutations
- substitutions
143
frameshifts mutations
- insertions
- deletions
144
features of the genetic code
1. universal
2. triplet
3. non-overlapping
145
almost all organisms follow the same codon assignments
universal
146
three base code for one amino acid
triplet
147
start codon
- AUG
- methionine
148
stop codons
- UAA
- UAG
- UGA
149
the base at 5' end of the anticodon is not spatially confined as the other two bases allowing it to form hydrogen bonds with any of several bases located at the 3' end of a codon
wobble hypothesis
150
several codons code for one amino acid
redundant or degenerate
151
are represented by related codons
structurally similar amino acids
152
movement of ribosome
5' to 3'
153
translation in prokaryotes
simultaneous with transcription
154
time it takes from DNA to protein in eukaryote
~1 hour
155
Building of polypeptide
1. initiation
2. elongation
3. termination
156
brings together mRNA, ribosome subunits, initiator tRNA
initiation
157
adding amino acids based on codon sequence
elongation
158
end codon
termination
159
in prokaryotes, initiation requires the binding of rRNA to where?
Shine Dalgarno sequence (AGGA)
160
first amino acid in prokaryotes
fmet
161
eukaryotic inititaion of translation
starts with AUG nearest to 5' terminus of mRNA
162
- steps needed to release the completed polypeptide chain involves the dissociation of the ribosome
- very slow step
termination of translation
163
N-terminal sorting signal that targets the linked protein to the secretory pathway in eukaryotes and prokaryotes
signal peptides
164
possible destinations of proteins after synthesis
1. secretion
2. nucleus
3. mitochondria
4. chloroplasts
5. cell membrane
6. cytoplasm
