Chapter 7 Flashcards
(170 cards)
1
Q
complete set of genetic information
A
genome
2
Q
what are in chromosome
A
plasmids + chloroplast + mitochondria
3
Q
Functional unit is
A
gene
4
Q
Study of nucleotide sequence is
A
genomics
5
Q
Cells must accomplish two tasks to multiply / divide which are
A
- DNA replication
- Gene expression
6
Q
(DNA and RNA) carry genetic
information in sequence of nucleotides
A
Nucleic acids
7
Q
Nucleic acids (DNA and RNA) carry genetic information in sequence of
A
nucleotides
8
Q
Nucleotides have
three parts which are
A
- Deoxyribose
- Phosphate group
- Nucleobase (= nitrogenous base
or base)
9
Q
Nucleobase with Two fused rings
A
adenine (A), guanine (G)
“pure As Gold”
10
Q
Nucleobase with single fused rings
A
cytosine (C),
thymine (T), [uracil (U) only in RNA)
11
Q
linear chains of nucleotides
A
Nucleic acids
12
Q
Nucleotides joined between
A
5’ PO4 and 3’ OH
13
Q
what kind of backbone does DNA have
A
sugar-phosphate
14
Q
what ends does DNA have
A
5′ end and 3′ end
15
Q
DNA Base-pairing
A
Adenine (A) to thymine (T) (two hydrogen bonds)
Cytosine (C) to guanine (G) (three hydrogen bonds)
16
Q
Separating strands called
A
melting or denaturing
17
Q
what does RNA consist of
A
ribonucleic acid
18
Q
what takes place of thymine
A
Uracil
19
Q
Usually shorter single strand
A
RNA (ribonucleic acid)
20
Q
Synthesized from DNA template strand
A
RNA (ribonucleic acid)
21
Q
RNA molecule is a what
A
transcript
22
Q
Three types of RNA required for gene expression
A
- Messenger RNA (mRNA)
- Ribosomal RNA (rRNA)
- Transfer RNA (tRNA)
23
Q
(mRNA)
A
- Messenger RNA
24
Q
(rRNA)
A
- Ribosomal RNA
25
(tRNA)
* Transfer RNA
26
is DNA replication bidirectional or single directional
bidirectional
27
meet at terminating site when process complete
Two replication forks
28
how many replication forks does DNA replication make
two
29
is replication conservative or semiconservative?
semiconservative
30
how is dna replication semiconservative
DNA contains one original, one newly synthesized strand
31
Replication begins at
origin of replication (initiation
site).
32
temporarily breaks the strand of DNA
DNA gyrase
33
temporarily unwind the DNA helix
DNA helicase
34
synthesize short stretches of complementary RNA
Primases
35
short stretches of complementary RNA
primers
36
complex of enzymes and other proteins that synthesize DNA
Replisomes
37
DNA polymerases synthesize in what direction
5′ to 3′ direction
38
Adds nucleotide to which end of the new strand
3’ end
39
Hydrolysis of high-energy phosphate bond
powers
40
DNA polymerase can only add nucleotides to
existing strand
41
“unzip” DNA strands
helicases
42
synthesized continuously
Leading strand
43
synthesized discontinuously
Lagging strand
44
DNA polymerases can only add
nucleotides to what end
3'
45
seals gaps between
fragments
ligase
46
Replication produces what
two complete copies of DNA
47
when can cell initiate another round of replication
before previous round is complete
48
Each daughter cell inherits what
one complete chromosome
already undergoing replication
49
what does Transcription do?
DNA → RNA
50
synthesizes single-stranded RNA using DNA as a template
RNA polymerase
51
RNA polymerase binds to sequence called a
promoter
52
can RNA poly initiate without primer
yes
53
Transcription ends where
Stops at terminator
54
what is RNA sequence in regards to DNA template strand
RNA sequence is complementary, antiparallel to DNA template strand
55
DNA template is charged how
-
56
RNA sequence is charged how
+
57
Monocistronic
one gene
58
Polycistronic
multiple genes
59
recognizes promoter
Sigma (σ) factor
60
controls transcription of sets of
genes
Synthesis of sigma factors
61
recognizes promoters
transcription factors
62
orients direction of transcription
Promoter
63
Once RNA polymerase has moved past, another what can bind
RNA polymerase
64
moves along DNA
RNA polymerase
65
what does RNA polymerase use as a template
(−) strand
66
Nucleotides are added only to the what end by RNA poly
3′ end
67
When RNA polymerase advances what happens
➢ It denatures a new stretch of DNA
➢ A new region of the template is exposed
➢ The previous portion renatures
68
When RNA polymerase encounters a sequence
called a terminator what happens
it falls off the DNA template
and releases the newly synthesized RNA.
69
Genetic code: three nucleotides =
codons
70
Stop Codons
UGA, UAA, and UAG
"U Go Away, U Are Away, U
Are Gone!"
71
serve as translation “machines”
Ribosomes
72
In prokaryotes, the ribosome will begin to assemble at a
sequence in mRNA called
the ribosome-binding site
73
start codons
AUG
74
Translation ends at a
stop codon
75
deliver correct amino acid
Transfer RNAs (tRNAs)
76
a sequence of three nucleotides forming a unit of genetic code in a transfer RNA molecule, corresponding to a complementary codon in messenger RNA.
anticodon
77
steps of Initiation of Translation
* Part of ribosome binds to ribosome-binding site
* First AUG after that site serves as start codon
* Initiating tRNA brings altered form of methionine to P-site
* P-site occupied by tRNA carrying methionine
* Another tRNA recognizes codon in empty A-site
* Enzyme creates peptide bond between amino acids
* tRNA in A-site carries both amino acids
78
Initiating tRNA brings altered form of methionine to
P-site
79
Another tRNA recognizes codon in empty
A-site
80
Enzyme creates peptide bond between
amino acids
81
what in A-site carries both amino acids
tRNA
82
steps of Elongation of Polypeptide Chain
- Ribosome advances along mRNA in 5′ to 3′ direction
- Initiating tRNA exits through E-site
- Remaining tRNA carrying both amino acids occupies P-site
- A-site transiently empty
- a tRNA that recognizes codon in A-site quickly attaches
- Peptide bond formed between amino acids
- Ribosome advances one codon on mRNA
- Process repeats
- Once ribosome clears initiating sequences, another ribosome can bind
83
Ribosome advances along mRNA in what direction
5′ to 3′ direction
84
Initiating tRNA exits through
E-site
85
Remaining tRNA carrying both amino acids occupies
P-site
86
transiently empty
A-site
87
A tRNA that recognizes codon in A-site quickly what
attaches
88
formed between amino acids
Peptide bond
89
multiple ribosome on same mRNA
polysome
90
Once ribosome clears initiating sequences, another ribosome can bind
polyribosome or polysome
91
steps of termination
- Elongation continues until
ribosome reaches stop codon
- Enzymes break covalent bond joining polypeptide to tRNA
- Freed ribosome falls off mRNA
- Disassociates into component subunits (30S and 50S)
- Subunits can be reused to initiate translation at other sites
92
Elongation continues until ribosome reaches
stop codon
93
Enzymes break covalent bond joining
polypeptide to tRNA
94
what happens to Freed ribosome
falls off mRNA
95
can be reused to initiate translation at other sites
Subunits
96
what is the mRNA synthesized in precursor form for eukaryotic
pre-mRNA
97
when must pre-mRNA be processed in Eukaryotic transcription
during and after transcription
98
what happens with 5′ end in Eukaryotic transcription
it is capped with methylated guanine derivative
99
what happens with 3′ end in Eukaryotic transcription
modified via polyadenylation
100
stabilizes transcript, enhances translation in Eukaryotic transcription
Poly A tail
101
splicing removes what in Eukaryotic transcription
introns
102
are expressed regions
Exons
103
mRNA transported to
cytoplasm
104
refers to a type of messenger RNA (mRNA) that encodes a single protein.
monocistronic
105
Microorganisms constantly face changing what
environment
106
cell signaling
Signal Transduction
107
transmits information from outside cell to inside
Signal Transduction
108
Allow cell to monitor and react to environmental conditions
Signal Transduction
109
“Sense” density of cells of their own population
Quorum Sensing
110
Cells activate genes useful only when expressed by a critical
mass producing a signaling molecule
Quorum Sensing
111
Two-Component Regulatory Systems
1) Membrane-spanning sensor
2) Response regulator
112
* To change expression of genes (depending on outside conditions)
* Consists of 2 different proteins
Two-Component Regulatory Systems
113
* Modifies internal region in response to specific environmental variations
* Phosphorylates amino acid
Membrane-spanning sensor
114
* Phosphate group transferred from sensor
* Turns genes on or off in response
Response regulator
115
how can Natural selection play role in gene expression
* Expression of some genes changes randomly in cells
* Enhances survival of at least part of population
116
change in some characteristics of
surface proteins (helps evade host defenses)
Antigenic variation
117
* Only expresses the gene in expression locus
* Randomly moves genes in and out of expression locus
* Immune system responds initially to dominant pilin type
* Bacteria that have “switched” type survive
Antigenic variation
118
switching genes on and off
Phase variation
119
* Allows E. coli to attach via pili, detach by turning off
* E. coli colonize epithelial cells somewhere else
* Part of the E. coli population is ready for change
Phase variation
120
a set of regulated genes transcribed as single
mRNA along with its control sequences
Operon
121
Separate operons controlled by single regulatory mechanism
Regulon
122
is simultaneous regulation of numerous genes
Global control
123
Enzymes can be grouped by type of regulation
- Constitutive enzymes
- Inducible enzymes
- Repressible enzymes
124
synthesized constantly
[Typically in central metabolism]
Constitutive enzymes
125
not routinely produced
[Synthesized only when needed]
Inducible enzymes
126
enzymes produced routinely
[Turned off when not required]
Repressible enzymes
127
two most common Mechanisms to Control Transcription
* Alternative sigma factors
* DNA-binding proteins
128
what must Mechanisms to Control Transcription be able to do
Must be readily reversible and allow cells to control relative
number of transcripts produced
129
types of Alternative sigma factors
* Standard sigma factors:
* Alternative sigma factors: r
130
loose components of RNA
polymerase that recognizes specific promoters for genes
expressed during routine growth conditions
Standard sigma factors
131
recognize different sets of
promoters to control expression of specific groups of genes
Alternative sigma factors
132
DNA-binding proteins can act as what or what
repressors or activators
133
blocks transcription (negative regulation)
Repressor
134
a site downstream of the promoter)
operator
135
Binds to operator (a site downstream of the promoter) and stops RNA polymerase
Repressor
136
have binding site that alters ability to bind to DNA
allosteric:
137
two general mechanisms of
transcriptional regulatory systems
induction and repression
138
The repressor is a form that binds the operator and
blocks transcription
Induction
139
When what attaches to repressor, repressor
unable to bind
inducer
140
is a form that cannot binds the operator and does not block transcription
Repression
141
When what attaches to repressor, complex
now binds to DNA and blocks transcription
corepressor
142
facilitates transcription (positive regulation)
Activator
143
(upstream of ineffective promoter)
Activator-binding site
144
binding to activator allows binding to DNA
Inducer
145
Binding of activator allows RNA polymerase at
promoter
146
Encodes proteins involved with transport and degradation
of lactose
The lac Operon
147
when is The lac Operon on/off
Turned on when glucose is not available, but lactose is
Turned off when glucose is available
148
what happens when No lactose available
repressor prevents transcription
149
what happens when Lactose is present
some converted to inducer allolactose
* Binds to repressor
* Repressor releases
operator
* RNA polymerase
transcribes operon
150
what happens when both glucose and lactose are present
Carbon catabolite repression (CCR) mechanism
151
mechanism prevents
expression of genes that metabolize lactose in presence of
glucose
Carbon catabolite repression (CCR)
152
When glucose is present, lac
operon is
repressed
153
The lac operon has an activator called
CAP (catabolite
activator protein)
154
CAP binds to the activator-binding site and is required for
transcription
155
CAP is functional only when bound by inducer
cAMP
156
made when glucose low
cAMP
157
Another mechanism of
regulation:
Inducer exclusion
158
– Glucose transporter
component binds to
lactose transporter
(permease)
– Lactose transporter is
temporaily blocked during
glucose transport
Inducer exclusion
159
Glucose transporter
component binds to
lactose transporter
(permease)
160
is temporaily blocked during
glucose transport
Lactose transporter
161
Eukaryotic Gene Regulation
* Modification of chromosome structure
* Regulation of initiation of transcription
* Altering pre-mRNA processing and modification
* RNA interference (RNAi) process
162
Short RNA strand + multi-protein unit
RNA-induced
silencing complex (RISC)
163
RNA strand serves as probe for binding to
mRNA
164
Tags mRNA for destruction
RNA interference (RNAi)
165
Two types of RNA molecules:
– microRNA (miRNA)
– short interfering RNA (siRNA)
166
Data interpretation complex:
* Promoter orientation
* Which DNA strand is template
* Reading frame
167
used to represent sequence of RNA transcript
(+) strand
168
Computers search for
open reading frames (ORFs)
169
Analysis of total microbial genomes in environment
Metagenomics
170
Can study all microorganisms and viruses in community
Metagenomics
