Term
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Definition
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Term
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Definition
Copying of the DNA. Such as when bacteria divide they copy
their single circular chromosome so that each daughter cell will have a single copy.
This is done by enzymes in the cell called DNA polymerases |
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Term
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Definition
Making an RNA copy of a gene. Messenger RNA. This carries
the information in the DNA to the cell. The enzyme that does this is called an
RNA polymerase. |
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Term
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Definition
Converting the mRNA into protein by reading the three letters at a
time and hooking together the correct amino acids to make a protein. Ribosomes
do this. |
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Term
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Definition
The way that information is stored in DNA is in the
sequence of the nucleotides taken 3 at a time. Each 3 DNA nucleotides in
a gene code for one of the 20 amino acids. Remember that the DNA is
transcribed into mRNA and it is the mRNA code that is actually read by
ribosomes to make protein. |
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Term
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Definition
| Three letter sequence that codes for an amino acid. |
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Term
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Definition
Not all genes are active at the same time. If they were it
would constitute a tremendous waste of energy. Instead they are turned
on (transcribed) only when they are needed. |
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Term
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Definition
Genes that are not on all of the time are called inducible and they can be
turned on by inducers- molecules that turn on transcription |
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Term
| Genes that are always turned on (transcribed) are called |
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Definition
| Genes that are always turned on (transcribed) are called constitutive. |
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Term
| Central Dogma in Prokaryotes |
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Definition
A. Prokaryote
-No nucleus
-the genes are not interrupted by non coding regions
-several adjacent genes are often transcribed at the same time as
one large mRNA.
-These are translated into separate proteins. |
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Term
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Definition
Because of the bond angles formed by hydrogen bonding of the
bases, the two strands of antiparallel DNA form a right-handed
helix. |
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Term
| major groove; minor groove |
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Definition
The two sugar-phosphate
backbones form ridges in
the surface of the DNA
molecule. The space
between the ridges are
grooves. One groove is
small and is called the
Minor Groove. The other is
bigger and is called the
Major Groove. |
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Term
DNA absorbs light at a wavelength of
_____nm more than any other wavelength |
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Definition
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Term
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Definition
Single-stranded
DNA (ssDNA) absorbs more UV light
than double-stranded DNA (dsDNA) so
when dsDNA melts (denatures) you get
an increase in absorbance |
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Term
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Definition
Melting Temperature: Temperature at
which half of the hydrogen bonds between
the two strands are broken. ~85 |
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Term
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Definition
In prokaryotes, proteins
organize the chromosome
into supercoiled domains
Involved in gene regulation |
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Term
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Definition
| allows the DNA to be packed into the cell. |
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Term
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Definition
when the DNA is twisted in the opposite direction of
the helix and positive supercoiling is when the DNA is twisted in the same
direction as the helical turns. NEGATIVE supercoiling is most common in
nature. Gyrase (a form of topoisomerase) is the enzyme that does this. |
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Term
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Definition
have been discovered in extreme
thermophiles This may stabilize their DNA in hot environments. Reverse
gyrase is an enzyme that catalyzes positive supercoiling in some extreme
thermophile |
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Term
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Definition
is an enzyme that
cleaves the
phosphodiester
bond in a single
strand in the DNA
and causes the
tension to relax.
This removes the
supercoiling. |
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Term
| topoisomerase II or DNA gyrase |
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Definition
catalyzes
negative supercoiling of DNA. This enzyme is very important to the survival of
the cell. |
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Term
antibiotics that
inhibit DNA gyrase and kill bacterial cells. |
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Definition
| Naladaxic acid, novobiocin, and ciprofloxacin |
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Term
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Definition
important in determining
when genes are "turned on" and "turned off" |
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Term
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Definition
sequences can be inverted and read the same way; create the possibility for interesting structures in
DNA like hairpins and cruciform structures |
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Term
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Definition
nucleic acids that:
1. Have genes.
2. Replicate themselves.
Chromosome
Plasmid
Virus
Mitochondrion, chloroplast (eukaryotes only)
Transposable elements-can move from one place to
another
Transposons-genes with transposable elements on either
side-jumping gene |
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Term
| Nonchromosomal genetic elements |
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Definition
| A. Viruses and viroids;B. Plasmids:; C. Mitochondria and chloroplasts; D. Transposable elements (Transposons) |
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Term
only thing that is passed on to the next generation in all
organisms is |
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Definition
DNA (and in most eukaryotes-mitochondria from
your mother) |
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Term
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Definition
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Term
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Definition
With a single origin we get
"Theta replication"
because the DNA looks
like the Greek letter Theta (Circular DNA
replication) |
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Term
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Definition
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Term
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Definition
A special RNA polymerase called Primase adds a
short piece (11 ribonucleotides) of RNA to newly
exposed DNA strands. |
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Term
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Definition
adds deoxynucleotides to the
RNA primer using its free 3’-OH |
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Term
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Definition
| small pieces of the lagging strand |
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Term
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Definition
In the lagging strand, DNA
polymerase III eventually
runs into the primer from an
adjacent replicating site.
When this happens, DNA
polymerase I digests the
RNA and then fills in the
gap using the 3’ end left by
polymerase III. |
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Term
| Requirements for DNA replication |
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Definition
| 1. Template: 2. Primer 3. Primase 4. DNA polymerase III: 5. Deoxynucleotide triphosphates 6. DNA polymerase I: 7. DNA helicase 8. Single-stranded binding protein 9. DNA Ligase: |
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Term
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Definition
must have something to copy. The strand that is copied is
called the template. |
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Term
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Definition
Must have a starting place. You must have something to hook
the nucleotides to as they are brought in place. This is a short strand of
RNA. Remember that the nucleotides are added in a 5' to 3' direction. |
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Term
| Deoxynucleotide triphosphates |
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Definition
dATP,
dTTP, dCTP, dGTP. Precursors for the
growing chain. |
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Term
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Definition
When replication is
well under way this enzyme chews up the
RNA primer and replaces it with DNA. |
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Term
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Definition
This is a DNA
unwinding protein. |
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Term
| Single-stranded binding protein |
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Definition
Proteins that bind to the unwound
(ss) DNA and prevent it from re
base pairing. |
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Term
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Definition
Attaches the ends of
two DNA strands. |
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Term
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Definition
Begins at the origin of replication.
A. Origin binding protein (DnaA) binds to the origin and
then Helicase binds and separates the double strands.
B. Single stranded binding proteins bind and prevent the
strands from repairing.
C. Primase makes a short piece of RNA on the leading
strand and DNA polymerase III starts synthesizing
DNA.
D. Primase makes an RNA primer in 5' to
3' direction of the lagging strand.
E. Replication begins on the two strands
forming the replication fork |
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Term
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Definition
A. DNA Polymerase III adds DNA to the primer in the 5' to 3' direction.
B. DNA Polymerase I degrades the RNA primer and replaces it with DNA. |
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Term
| Termination (Replication) |
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Definition
A. The polymerases converge on a region of the DNA containing sequences
known as ter sites where they meet and complete the replication process.
B. The single DNA strands are joined by DNA ligase |
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Term
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Definition
| A complex of enzymes involved in replicating DNA |
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Term
The error rate in DNA replication is very low: 1 in a billion to 1 in a trillion.
This is accomplished in what 3 ways? |
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Definition
| 1. Base pairing; 2. proofreading; 3. Mismatch repair |
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Term
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Definition
DNA polymerase III reads the template nucleotides
accurately and usually inserts the correct complementary nucleotide. |
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Term
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Definition
DNA polymerase III is able to detect incorrect nucleotides that are
not complementary and remove them by chewing back the new
strand from the 3' end (3' exonuclease activity). All prokaryotes, eukaryotes and viruses have
this function. |
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Term
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Definition
by endouncleolytic proteins that are able to detect
bases that are mispaired such as A-A or A-C. These enzymes work on
DNA that has already been replicated long after the polymerase has gone
on it's way. They excise the mismatched base and replace it with
another. This is a type of endonuclease since it attacks DNA in the
middle of a strand and not at the ends. |
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Term
| RNA mediated events in the cell: |
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Definition
| Transcription and Translation |
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Term
| Transcription enzyme and product: |
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Definition
| The enzyme is protein and the product is mRNA |
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Term
| Translation enzyme and product: |
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Definition
| The enzyme is RNA and the product is protein |
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Term
| Three main types of RNA in the cell: |
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Definition
1. mRNA; messenger RNA.
2. tRNA; transfer RNA carries the amino acids-adaptor molecule.
3. rRNA; ribosomal RNA-Ribosomes are made of RNA and Protein and
the RNA is called rRNA. |
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Term
| Transcription is catalyzed by: |
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Definition
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Term
| RNAP is a ____-directed ____ polymerase |
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Definition
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Term
| Name the 5 peptide subunits of RNAP |
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Definition
α2ββ'+σ + ω; α2ββ' is called the core enzyme; The main function of
the sigma subunit is to find the proper place for the core enzyme to
begin. |
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Term
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Definition
unit of genetic expression consisting of one or more related genes and the operator
and promoter sequences that regulate their transcription |
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Term
| Who characterized the operon? |
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Definition
| Originally characterized by Jacob and Monod in 1961 |
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Term
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Definition
| Initiation:; Elongation; Termination: |
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Term
| Initiation (transcription) |
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Definition
Sigma finds the PROMOTER (a transcription on/off switch) and
the core enzyme binds to the DNA and begins transcribing (making an
RNA copy). |
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Term
| What is Sigma's function in transcription? |
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Definition
| aids in recognition of promotor and initiation site. |
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Term
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Definition
Sigma dissociates and the
core enzyme moves down the DNA,
separating the strands just long enough
to allow base pairing between the
ribonucleoside triphosphates (ATP, UTP,
CTP, GTP). Not dATP etc. Only one
strand is read by the polymerase (coding strand) |
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Term
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Definition
The polymerase reaches a
sequence in the mRNA called the
terminator and falls off the DNA. |
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Term
| What are the Two types of transcription termination? |
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Definition
| 1. Rho dependent; 2. Rho independent (intrinsic); |
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Term
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Definition
Rho is a protein that
travels behind the RNA Polymerase ON
THE NEWLY MADE RNA and if the
polymerase slows down the Rho protein
catches up to it and causes it to fall off
the DNA. Core slows down when it
encounters certain termination sequences
in the DNA called Rho utilization (rut)
sequences. |
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Term
| Rho independent (intrinsic): |
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Definition
Inverted repeats form large hairpin structures in the
newly made RNA and when these structures are followed by a string of uracils.
When the hairpin is
formed the RNA
polymerase slows down.
Because the polyU strand
is only weakly paired with
the template strand, it
dissociates from the
template leaving the
polymerase no substrate
to add new nucleotides to
thereby ending
transcription |
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Term
antibiotics that bind to and inhibit the beta
subunit of RNA polymerase. |
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Definition
| Rifamycins (Rifampicin, rifaldazine etc |
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Term
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Definition
they last a lot
longer than mRNA does
in the cell. tRNA, and rRNA are
examples |
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Term
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Definition
| 1. aa-tRNA; 2. mRNA; 3. Ribosomes; 4. Factors |
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Term
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Definition
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Term
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Definition
| carries the genetic instructions from the DNA |
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Term
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Definition
catalyze assembly of the amino acids into
peptides |
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Term
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Definition
proteins that are not part of the ribosome but are
required for proper protein synthesis. |
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Term
| What structure does the tRNA have? |
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Definition
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Term
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Definition
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Term
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Definition
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Term
| Who were awarded the Nobel Prize for the elucidation of the Genetic Code? |
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Definition
| In 1968 Marshall Nirenberg, Gobind Khorana and Robert Holley |
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Term
| Bacterial ribosome composition |
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Definition
70S composed of 30S + 50S
30S composed of 21r + 16s; 50s composed of 34r + 23s + 5s |
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Term
| There are 3 tRNA binding sites on the ribosome: |
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Definition
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Term
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Definition
Site where incoming aa-tRNA enters the
ribosome. The tRNA is carried to the A-site as part of a ternary
complex containing the aa-tRNA (1), a GTP molecule (2) and
Elongation factor Tu (3). |
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Term
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Definition
Site where the tRNA containing the growing peptide
chain is located. |
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Term
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Definition
Site where the P-site tRNA goes after it has given up its
peptide to the tRNA in the A site. tRNA that has lost its amino
acid is called deacylated tRNA. The tRNA is the E site is
deacylated tRNA. The E-site tRNA exits the ribosome as the next
aa-tRNA enters the A site to begin the next cycle. |
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Term
| Translation initiation; Formyl-Methionine-tRNA (Methionine with a formyl group on the end) |
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Definition
bound
to the P-site during initiation and is therefore always the first amino acid in every
protein in bacteria. |
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Term
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Definition
A sequence on the
mRNA called the Shine-
Dalgarno sequence is
complementary to a
sequence found in 16S
RNA and these two
sequences base pair and
bind the mRNA to the
ribosome |
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Term
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Definition
Amino acid (or peptide) is transferred to the tRNA in the A-site.
Empty (deacylated)tRNA moves to the E-site (exit).
A-site tRNA moves into the P-site and another aa-tRNA comes into the now
empty A-site. |
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Term
| What proteins are required during elongation? |
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Definition
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Term
| What protein does translocation require? |
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Definition
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Term
| What proteins assist in termination? |
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Definition
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Term
| You must have something in the ___ site to form the first peptide bond. |
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Definition
You must have something in the P site to form the first peptide bond.
The fMet-tRNA specifically goes to the P-site first. All other tRNAs go to the
A site. |
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Term
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Definition
Release factors recognize a stop codon in the A-site and the
protein synthesis machinery disassembles |
|
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Term
coupled transcription and
translation. |
|
Definition
Since there is no nucleus in prokaryotes, ribosomes can bind to the mRNA before
it is finished being transcribed |
|
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Term
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Definition
In both eukaryotes and prokaryotes a single mRNA can have several ribosomes
translating it at the same time and these mRNA/ribosome complexes are called
polysomes. |
|
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Term
| Mistranslation rate of ribosomes in bacteria? |
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Definition
|
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Term
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Definition
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Term
| What determines the destination of the protein? |
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Definition
Protein does
not contain
signal sequence: non-secreted protein. Protein contains
signal sequence: Protein
inserted
into
membrane. Sec A: Protein
secreted into
periplasm |
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