microbio lecture 6 chapter 7 Flashcards
(228 cards)
1
Q
DNA: Blueprint of Life
A
Incredible diversity of life dictated by information within DNA
2
Q
what are the composed nucleotides?
A
Adenine (A), Thymine (T), Cytosine (C), Guanine (G)
3
Q
What does each nucleotide contain?
A
a nucleobase
4
Q
How many nucleotides encode a specific amino acid?
A
3
5
Q
What makes up protein?
A
Amino acids
6
Q
What determines the structure and function of protein?
A
The sequence of amino acids
7
Q
proteins serve as
A
structural components of cells
8
Q
enzymes…
A
direct cellular activities (biosynthesis+energy conversion)
9
Q
genome
A
complete set of genetic information
10
Q
the genome consists of
A
chromosome plus (technically) plasmids
11
Q
all cells have…
A
DNA genome
12
Q
viruses may have…
A
RNA genome
13
Q
gene
A
functional unit; encodes a gene product
14
Q
gene
A
usually a protein
15
Q
genomics
A
study of nucleotide sequence of DNA
16
Q
cells must accomplish two tasks to multiply
A
DNA replication & Gene expression
17
Q
Gene expression
A
DNA is decoded so cell can synthesize gene products
18
Q
transcription
A
information in DNA is copied into RNA
19
Q
translation
A
RNA used to synthesize encoded protein
20
Q
(central dogma of molecular biology) information flows from…
A
DNA –> RNA –> protein
21
Q
DNA forms…
A
double-stranded helix
22
Q
carbon atoms of pentose sugar are
A
numbered
23
Q
nucleotides joined between
A
5’PO4 and 3’OH
24
Q
joining of the nucleotides alternating sugar and phosphate forms
A
sugar-phosphate backbone
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single DNA strand will have a
5' end and 3'end
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strands are ______, held together by ______
_______ between nucleobases
complementary; hydrogen bonds
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base pairing
Adenine (A) to thymine (T) (two hydrogen bonds)
Cytosine (C) to guanine (G) (three hydrogen bonds)
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strands are
anti-parallel; oriented in opposite directions
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characteristics of RNA (ribonucleic acid)
Ribose instead of deoxyribose
Usually shorter single strand
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(in RNA) ___________ in place of thymine
uracil
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RNA is synthesized from...
DNA template strand
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RNA molecule is ______
transcript
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for RNA, base-pairing rules apply except
uracil pairds with adenine
34
transcript ___________ separates from DNA
quickly
35
what are the three types of RNA (ribonucleic acid)?
Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
36
cells ________ expression of certain genes
regulate
37
within minutes of being produced, mRNA transcripts undergo
rapid degradation
38
DNA replication usually __________ from origin of replication
bidirectional
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two replication forks....
meet at terminating site when process complete
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replication is _______________
semiconservative
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semiconservative
DNA contains one original, one newly synthesized strand
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initiation of DNA replication ->
enzymes need to get started
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DNA ________ and ___________ bind to origin of replication
gyrase; helicase
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functions of DNA gyrase and helicases
Break and unwind DNA helix and expose single-stranded region that can act as a template
45
Primase (an RNA polymerase) function
synthesizes short regions of RNA called
primers
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DNA replication is complicated and requires....
coordinated action of many enzymes and other components
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Many of the enzymes form "assembly lines" called...
replisomes
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___________ is absolutely needed for DNA synthesis
Primase RNA polymerase
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The DNA Polymerase (replicase) is unable to
initiate strand synthesis de novo.
50
dna polymerase requires a
3’-OH Group to attach to.
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RNA polymerase CAN initiate
stand synthesize de novo, giving the -OH group need by DNA pol-ase
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DNA polymerases synthesize in the _______ direction
5' to 3'
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DNA polymerase powers reaction with
Hydrolysis of high-energy phosphate bond powers
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DNA polymerase can only _____ nucleotides, not initiate
add
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since DNA pol-ase cannot initiate synthesis, they require....
primers at origin of replication
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helicases _____ DNA strands
unzip
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helicases reveal
template sequences
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leading strand
synthesized continuously
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lagging strand
synthesized discontinuously
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DNA polymerases can only add nucleotides to
3' end
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discontinuous synthesis produces
Okazaki fragments
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different DNA polymerase
replaces primers
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DNA ligase forms
covalent bond between adjacent nucleotides
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DNA gyrase
Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix.
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DNA ligase
Enzyme that joins two DNA fragments together by forming a covalent bond between the sugar and phosphate residues of
adjacent nucleotides.
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DNA polymerases
Enzymes that synthesize DNA; they use one strand of DNA as a template to make the complementary strand. Nucleotides can be
added only to the 3′ end of an existing fragment—therefore, synthesis always occurs in the 5′ to 3′ direction.
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Helicases
Enzymes that unwind the DNA helix at the replication fork.
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Okazaki fragment
Nucleic acid fragment produced during discontinuous synthesis of the lagging strand of DNA.
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Origin of replication
Distinct region of a DNA molecule at which replication is initiated.
70
Primase
Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis.
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Primer
Fragment of nucleic acid to which DNA polymerase can add nucleotides (the enzyme can add nucleotides only to an existing
fragment).
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Replisome
The complex of enzymes and other proteins that synthesize DNA.
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Replication produces _____ complete copies of DNA
2
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how many copies of DNA does each daughter cell receive?
one
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replication of E.coli chromosome takes approx.
40 minutes
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optimal generation time of E. coli
20 minutes
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before previous round of replication is complete, cell can
initiate another round of replication
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each daughter cell inherits
one complete chromosome already undergoing replication
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transcription
RNA polymerase synthesizes single-stranded RNA (mRNA/messenger RNA) from DNA template
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RNA polymerase binds to sequence called a
promoter
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RNA polymerase synthesize in _______ direction
5' to 3' direction (orientation of newly synthesized strand)
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RNA polymerase can ____________ without a primer
initiate mRNA synthesis
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transcription stops at sequence called a
terminator
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RNA sequence is _______ AND ________ to DNA template strand
complementary; antiparallel
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DNA template is ______ strand
minus (-)
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Complement is ______ strand
plus (+)
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RNA has same sequence as __________ strand except Uracil instead of Thymine
(+) DNA strand
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prokaryotic mRNA transcripts
Monocistronic
Polycistronic
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monocistronic
one gene
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polycistronic
multiple genes
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proteins encoded on polycistronic message...
generally have related functions
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promoter orients
direction of transcription
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promoter is found
upstream of gene it controls
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Once RNA polymerase has moved beyond promoter ___________, allowing rapid and repeated transcription of single gene
another RNA polymerase can bind
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initiation of RNA synthesis (Role of Sigma factors)
Sigma factor recognizes promoter
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various types of sigma factors...
recognize different promoters
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synthesis of sigma factors controls
transcription of sets of genes
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eukaryotic cells and archaea
use transcription factors to recognize promoters
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(−) strand of DNA
Strand of DNA that serves as the template for RNA synthesis;
the resulting RNA molecule is complementary to this strand.
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(+) strand of DNA
Strand of DNA complementary to the one that serves as the template for RNA synthesis; the nucleotide sequence of the RNA molecule is the same as this strand, except it has uracil
rather than thymine.
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Promoter
Nucleotide sequence to which RNA polymerase binds to initiate transcription.
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RNA polymerase
Enzyme that synthesizes RNA using one strand of DNA as a template; synthesis always occurs in the 5′ to 3′ direction
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Sigma factor
Component of RNA polymerase that recognizes the promoter regions. A cell can have different types of σ factors that recognize different promoters, allowing the cell to transcribe
specialized sets of genes as needed.
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Terminator
Nucleotide sequence at which RNA synthesis stops; the RNA polymerase falls off the DNA template and releases the newly
synthesized RNA.
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translation
process of decoding information in mRNA
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translation is...
The process of protein synthesis
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major components of translation are
mRNA, ribosomes (contain rRNA), tRNAs, and accessory proteins
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mRNA is
temporary copy of genetic information
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Cell must decode the information imbedded in ....; translating them into the amino acid sequence contained in a protein
linear array of the mRNA nucleotide sequence
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Genetic code =
three nucleotides
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three nucleotides =
a codon = one amino acid
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more than one codon can specify
a specific amino acid; code is degenerate
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the genetic code is practically
universal; w/ minor exceptions, it is used by all living things
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stop codes
UAA, UAG, UGA
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start code
AUG
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nucleotide sequence defines
coding region
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sequences
designates beginning, end of region to be translated
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ribosomes serve as
translation "machines"
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the ribosome aligns
and forms peptide bonds between amino acids
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ribosomes locate punctuation sequences
on mRNA molecules
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the ribosome begins at
start site, moving along in 5' to 3' direction
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any given sequence has 3 different reading frames, which ribosomes
maintain in correct frame
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Prokaryotic ribosomes are comprised of______, each made of protein and ribosomal RNA (rRNA)
30s and 50s subunits
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three reading frames possible, or ways in which
triplets of nucleotides can be grouped
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if translation begins at wrong spot, or in "wrong reading frame", a very...
different, and likely nonfunctional protein or a premature termination will result
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transfer RNAS (tRNAS) deliver
correct amino acids
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each tRNA has
specific anticodon sequence; base-pairs with codon
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each TRNA carries appropriate
amino acids specified by codon
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after delivering amino acid,
tRNA can be recycled
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initiation of translation: part of ribosome binds to mRNA sequence called
the ribosome binding site
131
the ribosome binding site is _________ of the start codon
upstream
132
first AUG after that site serves as _________, where complete ribosome assemble
start codon
133
initiating tRNA brings _______ ________ of methionine
tRNA --> occupies P-site
134
elongation of polypeptide chain
ribosome has two sites to which tRNAs can bind
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tRNA recognizes that next codon occupies __________, brings correct amino acid
empty A-site
136
A-site and P-site now occupied
by correct tRNAs
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rRNA creates _______ between their amino acids
peptide bond
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Amino acid from tRNA in P-site added to
amino acid carried by tRNA in A-site
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Ribosome advances along mRNA in _________ direction
5' to 3'
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process of elongation of polypeptide chain 1
* Initiating tRNA exits through E-site
* Remaining tRNA carrying both amino acids occupies P-site
* A-site temporarily empty
* A tRNA that recognizes codon in A-site quickly attaches
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* Peptide bond formed between amino acids
* Ribosome advances one codon on mRNA
* tRNA exits E-site
* tRNA with growing protein occupies P site
* new tRNA occupies A-site
* The process repeats
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Termination
Elongation continues until ribosomes reaches a stop codon
143
in termination, enzymes break covalent bond
joining polypeptide to tRNA
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in termination, ribosome falls off
mRNA
145
after falling off, mRNA disassociates into
component subunits (30s and 50s)
146
subunits can be reused to
initiate translation at other sites
147
translation in prokaryotes begins before
transcription is complete
148
transcription and translation are
linked in prokaryotes
149
once a ribosome clears initiating sequences, another ribosome can bind, forming...
polyribosome or polysome
150
Anticodon
Sequence of three nucleotides in a tRNA molecule that is complementary to a particular
codon in mRNA. The anticodon allows the tRNA to recognize and bind to the appropriate
codon.
151
mRNA Polyribosome (polysome) Reading frame
Type of RNA molecule that contains the genetic information decoded during translation.
Multiple ribosomes attached to a single mRNA molecule.
Grouping of a stretch of nucleotides into sequential triplets that code for amino acids; an mRNA molecule has three potential reading frames, but only one is typically used in
translation.
152
Ribosome
Structure that facilitates the joining of amino acids during the process of translation;
composed of protein and ribosomal RNA. The prokaryotic ribosome (70S) consists of a
30S and a 50S subunit.
153
Ribosome-binding site
Sequence of nucleotides in mRNA to which a ribosome binds; the first time the codon for
methionine (AUG) appears after that site, translation generally begins.
154
rRNA
start codon
Type of RNA molecule present in ribosomes.
Codon at which translation is initiated; it is typically the first AUG after a ribosome-
binding site.
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Stop codon
Codon that terminates translation, signaling the end of the protein; there are three stop
codons.
156
tRNA
Type of RNA molecule involved in interpreting the genetic code; each tRNA molecule
carries a specific amino acid dictated by its anticodon.
157
Eukaryotic mRNA synthesized in precursor form:
pre-mRNA
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pre-mRNA
must be processed during and after transcription
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Capping adds methylated
guanine derivative to 5' end
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Capping binds
specific proteins: stabilize, enhance translation
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3' end modified via
polyadenylation
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polyadenylatoin
adds approx 200 adenine derivatives to new 3' end
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polyadenylations creates a poly A tail that
stabilizes transcript, enhances translation
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splicing
removes segments of eukaryotic transcript
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introns
non-codings intervening sequences that are removed
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exons
expressed regions that remain
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eukaryotic mRNA produced within membrane-bound nucleus and must be transported to cytoplasm:
* Translation cannot begin during transcription
* mRNA typically monocistronic
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in eukaryotic mRNA,
translation begins at first AUG and ribosomes are composed of 40s and 60s subunits
169
differences from prokaryotic ribosomes important in
targeting antibiotics
170
Prokaryotes
- mRNA does not have a cap or a poly A
tail.
- Transcript (mRNA) does not contain
introns.
- Translation of mRNA begins as it is
being transcribed.
- mRNA is often polycistronic;
translation usually begins at the first
AUG codon that follows a ribosome-
binding site.
171
Eukaryotes
- Processing of the transcript (pre-mRNA) results in mRNA with a cap at the 5′ end and a poly A tail at the 3′ end.
- Transcript (pre-mRNA) contains introns, which are removed by splicing.
- mRNA is transported out of the nucleus so that it can be translated in the cytoplasm.
- mRNA is monocistronic; translation begins at the first AUG.
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genes can be routinely
expressed or regulated
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operon
A set of regulated genes transcribed as single mRNA along with its
control sequences
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lac operon
lactose metabolism
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regulon
Separate operons controlled by single regulatory mechanism
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global control
is simultaneous regulation of numerous genes
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enzymes can be grouped by
type of regulation
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constitutive enzymes synthesized constantly
* Typically indispensable roles in central metabolism (for example, enzymes of glycolysis)
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Inducible enzymes synthesized only when needed
Avoids waste of resources
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example of inducible enzymes
for example, B-galactosidase turned on only when lactose present)
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Repressible enzymes are
produced routinely, but are turned off when not needed
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mechanisms to control transcription
Must be readily reversible, allow cells to control relative number of transcripts produced
183
two most common regulatory mechanisms are
alternative sigma factors and DNA-binding proteins
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Standard sigma factor is loose component of RNA polymerase
recognizes promoters for genes expressed during routine growth conditions
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Alternative sigma factors recognize
different sets of promoters to control expression of specific groups of genes
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example of alternative sigma factors
sporulation in Bacillus subtilis controlled by multiple different alternative sigma factors
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DNA-binding proteins can act
as repressors
188
Repressor
blocks transcription (negative regulation)
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Represser binds to operator, stops
RNA polymerase
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Repressors are _______, having binding site that alters ability to bind to DNA
allosteric
191
Two general mechanisms of repressors
induction and repression
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induction
repressor binds to operator, blocks transcription
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inducer
binds to repressor, repressor unable to bind
194
Repression
repressor cannot bind to operator
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Corepressor attaches to the repressor, complex now..
binds to operator and blocks transcription
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transcriptional regulation by
induction and repression
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DNA-binding proteins
can act as activators
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activator facilitates
transcription(positive regulation)
199
Ineffective promoter preceded by
activator-binding site
200
The binding of the activator enhances the ability of
RNA polymerase to initiate transcription at promoter
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Inducer binding to the activator allows
binding to DNA, and may also interfere with repressor
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the lac operon
Encodes proteins involved with transport and degradation of lactose
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lac operon turned on when
glucose is not available, but lactose is
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lac operon turned off when
glucose is available (cell uses most efficiently metabolized carbon source)
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when lactose is not available
Repressor prevents transcription; binds operator
206
When lactose is present
* Some converted to inducer
allolactose; binds repressor
* Repressor releases
operator
* RNA polymerase transcribes
operon
* Only occurs when glucose is
not available
207
When both glucose and lactose are present
Carbon catabolite repression (CCR)
208
Carbon catabolite repression (CCR)
prevents expression of genes that metabolize lactose in presence of glucose
209
CCR prioritize
carbon/energy sources; yields diauxic growth
210
glucose transport system senses
glucose
211
catabolite activator protein (CAP)
required for transcription of lac operon
212
CAP functional only when
bound by inducer called cAMP
213
cAMP made only when
glucose level is low
214
enzymes that make cAMP
activated by idle form of glucose transporter
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inducer exclusion
lactose transporter blocked during glucose transport by active glucose transporter
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In the initiation stage of transcription,
RNA polymerase binds to the promoter and melts a short stretch of DNA. In the elongation stage, sigma factor often dissociates from DNA polymerase, leaving the core enzyme to complete transcription. RNA is synthesized in the 5′ to 3′ direction as the enzyme adds
nucleotides to the 3′ end of the growing chain. In the termination stage, RNA polymerase encounters a terminator, falls off the template, and releases the newly synthesized RNA.
217
When few cells are present,
the concentration of the signaling molecule is low.
218
When many cells are present,
the signaling molecule reaches a concentration high enough to induce the expression of certain genes.
219
The sensor protein spans the
cytoplasmic membrane
220
The response regulator is
a protein inside the cell
221
In response to a specific change in the environment,
the sensor phosphorylates a region on its internal portion. The phosphate group is transferred to the response regulator, which can then turn genes on or off.
222
In induction, transcription is usually blocked by a repressor bound to the operator.
Inducer turns on transcription by binding to the repressor, altering its shape so that it can no longer bind to the operator.
223
In repression,
transcription is normally on because the repressor alone cannot bind to the operator
224
A corepressor allows repressor to
bind to the operator and block transcription.
225
Transcription is normally off because
RNA polymerase cannot bind to the promoter unless the activator is bound to the activator-binding site.
226
inducer binds to the activator,
changing its shape and allowing it to
bind to the site. RNA polymerase can then bind to the promoter and initiate transcription.
227
When glucose level is high
the unphosphorylated form of the glucose transporter component indicates
that glucose is available in the medium. This is because the phosphorylated transporter donates its phosphate group to glucose during transport into the cell.
228
When lactose is also present, the
unphosphorylated form of the glucose transporter component prevents the lactose transporter (permease) from functioning. Because lactose cannot be moved into the cell, the inducer (allolactose) cannot accumulate, so transcription of the lac operon will be blocked.
When glucose level is low, the
phosphorylated form of the transporter component indicates that not much glucose is available in the medium. This is because the phosphorylated transporter cannot donate its phosphate during glucose transport. When glucose is low, but lactose is present, the phosphorylated form of the glucose transporter component activates the enzyme that produces cAMP, which binds to the activator (CAP). The complex of
CAP and cAMP can then bind to the activator-binding site of the lac operon, allowing transcription.
