lecture 6 Flashcards
(141 cards)
1
Q
What does the transfer of genetic information require?
A
-replication of genetic information, complex machinery
-replication is where both strands are templates for dna synthesis
-segregation of genetic material
2
Q
What is segregation followed by and what happens during it?
A
-followed by cell division
-one copy of genome goes to each cell
3
Q
What is the central dogma of biology?
A
dna to rna to protein
4
Q
What processes are involved in the flow of genetic information?
A
-transcription and translation
5
Q
basic steps of transcription?
A
-dna transcribed to rna
-rna polymerase
-template for rna synthesis
6
Q
basic steps of translation?
A
-rna translated to protein
-ribosomes
-messenger rna is template for protein synthesis
7
Q
What type of gene expression is common in prokaryotes but rare in eukaryotes?
A
-polycistronic messages
8
Q
what type of gene expression is common in eukaryotes but rare in prokaryotes?
A
-non-coding sequence in ORF
9
Q
difference between orf process in eukaryotes and prokaryotes?
A
-extensive mrna prcoessing for eukaryotes
-majority of prokaryote orf’s don’t require processing
10
Q
Where does processing occur? for eukaryote and prokaryote transcriptions
A
-processing at 5 prime and 3 prime ends of mrna
11
Q
where does base pairing occur?
A
-between purine and pyrimidine
12
Q
guanine pairs with
A
cytosine - 3 hydrogen bonds
13
Q
adenine pairs with
A
thymine or uracil - 2 hydrogen bonds
14
Q
g-c rich sequences have high
A
-melting points
15
Q
a-t rich sequences have low
A
-melting points
16
Q
a-u base pair is
A
-weakest of all interactions, it is important for termination of transcription
17
Q
what type of ends does dna have?
A
5 prime and 3 prime
18
Q
what do dna strands have on the 5 prime end?
A
-a phosphate
-attached to 5 prime carbon of deoxyribose
19
Q
what do dna strands have on the 3 prime end and what is its signifigance?
A
-oh group
-oh attached to 3 prime carbon
-is attachment point for nucleotide of growing dna chain
20
Q
the 2 strands of dna are ___ with respect to ___
A
antiparallel, orientation ends
21
Q
what does base pairing give dna?
A
-it gives it structure, the double helix
22
Q
dna strands are
A
-antiparallel and complementary
23
Q
what is the helical rise?
A
3.4 nm/turn
24
Q
how many nucleotides per turn?
A
10.5
25
what does the major groove do?
-has significant information
-has sequence specific binding
26
What does minor groove do?
-little information, non specific binding
27
what do inverted repeats allow?
-formation of specific structures
28
what is possible for double stranded sequences?
-cruciform structures
29
what is possible for single stranded sequences?
-stem loop structure
30
what does the nitrogenous base component do?
-absorb uv radiation and it has an aromatic ring
31
what is nucleic acid absorbance maxima?
-260 nm,, quenched for double stranded nucleic acids
32
what happens when nitrogenous bases stack on each other?
-they shield each other
33
what does melting result in?
-increased absorbance and relief in stacked nitrogen bases and hyperchromatic shift
34
what do prokaryotes lack?
-well defined organizational units
35
what appears as a dense region occupying 1/3 of the cell?
-nucleioid
36
what is the extent of packaging evident upon?
-lysis
37
does an extruded chromosome occupy greater area than cell mass?
yah
38
is the bacterial chromosome fully extended?
no but it has multiple loops and proteins still associated
39
bacterial chromosome is many times longer than what?
the cell
40
how much more volume does the bacterial chromosome occupy when it is in its packaged form?
10% of cellular volume
41
how is the bacterial chromosome packaged?
through super coiling
42
what enzyme induces super coiling?
DNA gyrase
43
break sealed after ___ strand is pulled through
intact
44
what does a packaged bacterial chromosome form?
1 supercoil
45
how is the chromosome organized?
in a series of loops
46
what is the measurement of the loops?
40 kb/loop
47
what is at the base of the loop?
an unkown anchor
48
what evidence does the model support?
structure
49
the isolated nucleoid is
super coiled
50
intercalating agents measure what
extent of super coiling
51
if multiple loops structures did not exist, would the single nick relieve all supercoiling?
no
52
is the bacterial chromosome extremely long?
yes
53
how many times longer is the chromosome than bacteria?
1000 times longer
54
in the chromosome, what occurs w the proteins?
proteins bind and fold
55
how much volume does the chromosome occupy of the cell?
10% of cell volume
56
are bacterial chromosomes circular?
yes
57
in the bacterial chromosome, the e coli genes have assigned what
positions
58
how are the positions of e coli genes given?
in minutes
59
e coli gene positions are based on what
elegant conjugation experiments
60
what are plasmids?
autonomously replicating small circular dna
61
what do plasmids possess?
origin of replication
62
what purposes do plasmids serve?
selective advantage, antibiotic resistance, and alternative carbon sources
63
plasmids are artificially manipulated to allow what
recombinant dna technology
64
are plasmids critical for genetic engineering in the biotechnology sector?
u bet ur ass it does
65
synthesis of dna requires
sequence of events
66
each event in dna synthesis requires
a specific enzyme
67
during dna synthesis, dna must be melted by what enzymes
helicase, topisomerase
68
rna ___ must be made during dna synthesis and made by what enzyme
primer, which is done by primase
69
dna segments must be __ by what enzyme
joined by DNA ligase
70
does the synthesis of dna require coordination
yuh
71
DnaB provides what enzyme activity
helicase activity
72
dna replication is a ___ requiring process
energy
73
where is energy obtained during dna replication/helicase activity?
ATP hydrolysis
74
during helicase activity, what does it create a region of
region of single stranded DNA, that serves as a template, bound by ssDNAbp
75
___ binds single stranded regions and prevents hybridization
SSB
76
DnaB activates
DnaG
77
what is DnaG
primase - synthesizes RNA
78
what ensues during dna replication?
dna synthesis
79
dna synthesis only occurs in what direction
5' - 3'
80
opposite strans on replicaition fork possess
opposite polarities
81
what does one strand provide for synthesis in 5' - 3' direction
provides the template
82
what does one strand provide in the 3' - 5' diretion
another template lol
83
synthesis on one strand is continuous
leading strand
84
synthesis on opposite strand is discontinuous
lagging strand
85
dna polymerase has third activity 5' - 3' (an enzyme)
exonuclease
86
exonuclease is capable of excising what as it encounters during synthesis
nucleotides
87
the rna primers encountered are
degraded and replaced with dna
88
what is left after degrading RNA and it is sealeed by wat
nicks is left, sealed by dna ligase
89
what enzyme complex is used to catalyze the formation of phosphodiester bond
amp enzyme complex
90
amp is attached to
5 phosphate
91
what forms after amp attaches to 5 phosphate
phosphodiester bond
92
what shape is the bacterial chromosome
circular
93
where direction does replication occur for bacterial chromosome
bidrectionally
94
during replication of bacterial chromosome what is generated
theta from dna
95
when does replication terminate during replication of bacterial chromosome
when 2 polymerases meet
96
due to circular chromosome, how many origins of replicationon are needed
1
97
during termination of dna synthesis, what factor is required
cis-acting factor - ter
98
dna sequences have how many base pairs
23
99
termination of dna synthesis has what sequence
consensus
100
ter sites serve as
binding site for trans-acting factor - tus gene product
101
what do ter sites bind and what does binding prohibit
binds DNA and prohibits unwinding of double helix
102
ter sites inactivate
DnaB function
103
ter sites stop what process
replication
104
what do proteins recognize and what is this called
specific sequences of DNA, inverted repeats
105
what do inverted repeats create and generate
staggered cut generating sticky end
106
what can the sticky end do
hybridize another piece of dna THAT HAS BEEN CUT WITH THE SAME OR COMPATIABLE ENZYME
107
what can the sticky end join
covalently joined with dna ligase
108
when sticky end joins with dna ligase, what forms
catalyzes formation of phosphodiester bond
109
after sticky end joins with ligase, forms phosphodiester bond, what do we have now
recombinant plasmid
110
the discovery of restriction enzymes was __ thru a series of __ __
serendipitous thru a series of phage studies
111
for restriction enyymes, the phage effectively did what to one strain of e coli but not another
the phage effectively infected one strain
112
restriction enzyme
the few phage plaque that formed from resistant e coli could now form what
plaques readily in the resistant strain but not in the original strain
113
restriction enzyme
after phage plaque formed in the resistant strain, what happens to the cycle
repeats itself reproducibly
114
restriction enzyme process had to do with
restriction/methylation systems
115
what do restriction enzymes cut at specific sequences?
DNA
116
what do bacteria need to prevent?
cutting over their own DNA
117
How do endogenous enzymes modify their cut site
they use methylases
118
can methylated restriction sites be cut
no
119
methylated restriction sites are an effective defense against
viral attacks
120
if a virus was produced by strain with different restriction/methylation system
DNA will be degraded
121
can a viral genome be modified prior to digestion?
yas
122
both dna and rna have
uniform charge to mass ratio
123
due to nucleic acids phosphate back bone, they have a
strong negative charge
124
the phosphate back bone causes
nucleic acid to migrate towards (+) electrode
125
nucleic acids need a method to
retard movement of fragments based on size
126
what does agarose form and create
porous gel - creates obstacle course that fragments must naviate
127
how do smaller fragments move
quickly
128
how do larger fragments move
slowly
129
what does the electrophoresis of nucleic acids allow
separation based on size, which is an inverse relationship
130
what does the southern blotting method digest
dna
131
what does the southern blotting method separate
fragments on gel
132
what does the souther blotting method denature
fragments in gel
133
what does southern blotting method transfer
transfers fragments to membrane
134
what does southern blotting method probe
probes membrane with radio labeled gene of interest
135
what does the southern blotting method wash
washes off unbound probe
136
what does southern blotting method expose
exposes x-ray to film
137
dna synthesis rxns alone cannot
yield sequence information
138
for dna sequencing, what is required to stop dna synthesis
special nucleotide derivatives
139
what are the special nucleotide derivatives that stops dna synthesis called?
dideoxynucleotides
-check slide 26 but it exists for all 4, label each with fluorophore
140
dideoxynucleotides stop dna synthesis when
incorporated into growing nucleotide strand
141
the ratio of dideoxynucleotide to what is critical
ratio of dideoxynucletoide to dideoxynucleotide
