Term
| Within each cell the genetic information flows from ... |
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Definition
|
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Term
| The information carried within the DNA dictates the end product... |
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Definition
| (protein) that will be synthesized. This information is the genetic code |
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Term
| Conversion of DNA encoded information to RNA is called ... |
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Definition
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Term
| The information from a mRNA is then translated to an _______ in the corresponding______, which are the functional units of cells. |
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Definition
| amino acid sequence, protein |
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Term
| Scientists needed to figure out how 4 nucleotides code for ________. Therefore a 3 letter codon .... |
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Definition
20 amino acids
is the reasonable explanation. |
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Term
| In the 1950s and 1960s, Charles Yanofsky studied the gene tryptophan synthetase, which synthesizes Tryptophan (Trp)... |
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Definition
| ...and allows bacteria to grow in Trp free medium. |
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Term
| He made several substitution mutants (______) which required Trp in the medium in order to grow. |
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Definition
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Term
| Using genetic recombinations, Yanofsky... |
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Definition
| ...made a map of the various mutations. |
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Term
| Using technology available in the 1950s Yanofsky sequenced the mutant proteins being synthesized to correlate the mutation in the DNA sequence ... |
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Definition
| with the corresponding change in the amino acid sequence. |
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Term
The interpretations of Yanofsky's experiments
The changes were _____
Each mutation resulted in only one....
Each nucleotide was part of only one codon: the genetic code was.... |
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Definition
Colinear
Amino Acid Chain
Non-overlapping |
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Term
Different _______ in the same position (based on his power of resolution) could result in different amino acids in the product:
–The nucleotide sequence determines the ....
•Recombination between two different mutants in the same position resulted in _______:
–
One codon consists of ... |
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Definition
Point mutations, amino acid sequence
wild-type E.Coli
more than one nucleotide. |
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Term
| Evidence that a codon is a triple nucleotide experiment performed by |
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Definition
| Francis Crick and Sydney Brenner |
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Term
They generated mutations in bacteriophage T4 rIIB gene using the mutagen
Repeated exposure to a mutagen caused a reversal of mutant to _______. |
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Definition
proflavin
wild type phage. |
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Term
| Determined that proflavin causes _______ or insertions (________). |
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Definition
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Term
Crick and Brenner showed that ______ were caused by second mutations: restoration of gene function by canceling the action of the X ______ ____
•
By characterizing the change with each mutation, they deduced that three nucleotides ________ ______. |
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Definition
revertants
first mutations
represented a codon. |
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Term
| Frameshift mutations How T4 rIIB gene does is. Molecules of _____ can insert between ____ _____ ______ |
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Definition
| proflavin, two base pairs |
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Term
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Definition
| 2 Mutations takes it from wildtype to revertant. Crossing the recombinants with the wild type makes two recombinants. |
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Term
| Different sets of mutations generate either a..... |
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Definition
| mutant or a normal phenotype. |
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Term
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Definition
| 3 mutations of the same sign. Single base pairs, all positive or all negative. |
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Term
| A single based insertion or deletion makes... |
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Definition
| some frameshift mutations. |
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Term
Most amino acids must be _____ by multiple codons
There are potentially ____, and only _____ |
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Definition
| encoded, 64 codons, amino acids |
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Term
If each amino acid is encoded by only one codon, there would be 44 codons which would ______.
This would imply that more than 50% of the time, a frame shift_____ that would be a ‘nonsense’ codon.
Conclusion: |
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Definition
not code for any amino acid.
would result in a codon
the genetic code is degenerate. |
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Term
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Definition
| Two or more nucleotide triplets specify most of the 20 amino acids. |
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Term
Discovery of mRNA as an ______helped crack the genetic code.
Scientists developed cell extracts which when mixed with mRNA, could synthesize ________ ____ ___: in vitro translation.
•
Scientists were also able to synthesize short segments of mRNA of ______. |
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Definition
intermediate molecule
polypeptide chains
defined sequence |
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Term
| How geneticists used synthetic mRNA to limit the coding possibilities |
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Definition
| Synthetic mRNA were placed in an in vitro translational system, plus radioactive amino acids, then they analyzed the radioactive amino acids synthesized. |
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Term
| By 1965 it was known that polypeptide chains were synthesized on ________, and that different tRNA molecules carry the appropriate _______ to the ________ depending on the genetic ____ on the ______. |
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Definition
ribosomes,
amino acid, ribosome
genetic codon, mRNA |
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Term
| Using radiolabeled ________, and defined _____sequences, it was determined which _______corresponded to which ________ |
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Definition
amino acids, mRNA
codon, amino acid |
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Term
| Nirenburg and Leder added _______of known sequence, in combination with ____ charged with a ______, the amino acid bearing tRNA formed a complex with the _____ that could be trapped on a _____. |
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Definition
trinucleotides
tRNAs, radioactive amino acid
ribosome, filter. |
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Term
All living beings use the same genetic code.
Genetic code evolved early in life, and has remained constant over billions of years because of the ________ for change.
Some exceptions exist: in some ciliates, there is only ______ codon. |
|
Definition
| lack of tolerance, one nonsense codon. |
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Term
In eukaryotic _________, there are some changes: e.g.: in yeast, CUA codes for Thr instead of Leu.
The impact of this change in these organisms/organelles may not be as drastic, since there are very few ____ encoded by these systems, allowing evolution of the genetic code |
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Definition
|
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Term
| Process by which the genetic information is conveyed from a double stranded DNA molecule to a single stranded RNA molecule. |
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Definition
|
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Term
| Only one strand of DNA serves as a template: this is the ________. The complementary strand has a sequence identical to the ________ (except for a U in place of a T), and is called the __________ |
|
Definition
transcribed or anti-sense strand
RNA strand
sense strand, or the RNA-like strand. |
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Term
Salient Features of Transcription
RNA polymerase: catalyzes the ___ at a time, extending the RNA strand being synthesized in the ____ direction. |
|
Definition
addition of one ribonucleotide
5’ to 3’ |
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Term
| Promoter: ______ near the _____ of a gene. These signal the RNA polymerase to ... |
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Definition
DNA Sequences, beginning
begin transcription |
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Term
| Terminators: sequences within the______ ___ , which signal the ______ to stop transcription |
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Definition
| RNA products, RNA polymerase |
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Term
Steps of transription
Initiation: |
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Definition
Binding of RNA polymerase to double stranded DNA
Start of transcription by adding the first two ribonucleotides. |
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Term
Steps of transcription
Elongation: |
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Definition
Formation of transcription bubble.
The progression of the complex gradually in the 3’ direction to elongate the initiated RNA chain.
Rapid process: up to 40 nucleotides per second.
–
On the same gene there are several RNA strands being transcribed in a staggered fashion. |
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Term
Steps of transcription
Termination: |
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Definition
| Terminator sequences signal stop of transcription. |
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Term
| Promoter sequences facilitate the binding of the _____ to the _______ |
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Definition
| RNA polymerase, DNA to be transcribed |
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Term
| Promoters of different genes have distinct sequences, although most have characteristic short sequences of____ bases at a position between _____nucleotides upstream (called ________ in eukaryotes, ______ in prokaryotes). |
|
Definition
6 to 10, 10 to 30
TATA box and CCAAT box
Pribnow box |
|
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Term
Prokaryotic RNA polymerase is a complex _______ ______ consisting of five subunits: abb'sigma
This complex is called the _____. |
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Definition
| multimeric enzyme. holoenzyme. |
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Term
| The sigma subunit is involved only in the _________, after which it is ____ from the complex. |
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Definition
|
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Term
Eukaryotes have three types of RNA polymerases: I, II and III, each with a distinct function. RNA polymerase II ________.
Eukaryotic transcription requires additional protein factors to form a functional transcriptional complex. |
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Definition
|
|
Term
Terminator sequences
In prokaryotes there are two types:
–
Extrinsic: Rho dependent terminator: _________________. |
|
Definition
| require a protein factor called Rho. |
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Term
Rho protein trails the _____ until it reaches a _____, when Rho catches up with the polymerase.
Rho protein pulls off RNA from ______. |
|
Definition
RNA polymerase, C rich region
transcription bubble |
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Term
Terminator sequence
Intrinsic: Rho independent terminator: contain a ______ followed by six or more ________.
Causes the formation of a double stranded RNA called a_______. |
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Definition
G-C rich region, A-T sequences
hiarpin loop |
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Term
...Intristic
_______the movement of the RNA polymerase along the DNA molecule, and causes termination at the ______ region. |
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Definition
| Retards, A-T rich region. |
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Term
| In eukaryotes, the transcript ends at various sites beyond the _____ end of the RNA (_______), and is later precisely ___ during RNA processing. |
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Definition
| final 3’, AAUAAA sequence, cut |
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Term
In prokaryotes, no RNA processing is necessary: the _____ is usually the mRNA.
In eukaryotes, the ______ is called , and needs to be processed and transported to the _____ for translation to occur. |
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Definition
nascent RNA
nascent RNA pre-mRNA
cytoplasm |
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Term
The processing steps for RNA processing and transporting are:
–_____ |
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Definition
1. Addition of a 5’ 7-methyl guanosine cap.
2.Addition of a poly-A tail at the 3’ end.
3. RNA splicing to remove intervening sequences. |
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Term
Capping
•
When the RNA chain is about 30 nucleotides long, the ___ ends are modified by the addition of a ___ group in the opposite orientation: involves a ______linkage. |
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Definition
| 5’, guanine, 5-5 triphosphate |
|
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Term
...Capping
________then add methyl groups in the 7 position to that and________
The caps are recognized by the translation machinery.
They protect the growing RNA chain from ... |
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Definition
Methyl transferases, a couple more nucleotides.
degradation by nucleases |
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Term
Capping
•
When the RNA chain is about 30 nucleotides long, the ___ ends are modified by the addition of a ___ group in the opposite orientation: involves a ______linkage. |
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Definition
| 5’, guanine, 5-5 triphosphate |
|
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Term
...Capping
________then add methyl groups in the 7 position to that and________
The caps are recognized by the translation machinery.
They protect the growing RNA chain from ... |
|
Definition
Methyl transferases, a couple more nucleotides.
degradation by nucleases |
|
|
Term
Polyadenylation
•
In eukaryotes, nascent RNA is _____ downstream from the ____ conserved sequence. |
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Definition
|
|
Term
Polyadenylation
The enzyme _____adds adenine ribonucleotide tracks up to 200 bases long at the.... |
|
Definition
| poly(A) polymerase, 3’ end of the RNA |
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Term
Polyadenylation
The poly(A) tail enhances the ____ of eukaryotic mRNA and regulates its transport to the _____ ____. |
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Definition
| stability, cytoplasmic compartment |
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Term
RNA splicing
•
The mechanism by which introns (____) are removed.
•
Exons (___) are retained in the mature ______. |
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Definition
intervening sequences
expressing sequences
mRNA molecules |
|
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Term
Exon and intron lengths and numbers vary in various genes: extreme example is _____gene:
–
Gene size: 2500 Kb
–
mRNA size: 14kb
–
Exons: 79 |
|
Definition
|
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Term
|
Definition
| introns from a primary transcript. |
|
|
Term
Mechanisms of splicing
There is an intranuclear protein/RNA complex called the ____ that ensures proper splicing. |
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Definition
|
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Term
Three types of short sequences dictate the precise cutting of the intron/exon boundaries.
First one–
_______: at 3’ end of exon, and 5’ end of intron: Pu-Pu- G-U
– |
|
Definition
|
|
Term
Other two types of short sequences that dictate the precise cutting of the intron/exon boundaries:
______: 3’ end of intron. Pyr-Pyr---A-G-exon
–
_____: within the intron, about 30 nucleotides upstream of the splice acceptor, has an AT rich region with at least one A. |
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Definition
Splice Acceptor
Branch site |
|
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Term
Two sequential cuts: _____ site is cleaved, attaches to the branch site to form a ________, then the________ site is cleaved.
The intron ____, the two exons are ____. |
|
Definition
splice donor, lariat or loop structure
splice acceptor
degrades, ligated |
|
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Term
|
Definition
|
|
Term
Alternative Splicing
The same RNA can produce different protein sequences by splicing at _____. |
|
Definition
|
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Term
Trans- Splicing
•
In rare instances,___ from two different genes may be joined to form a ______ with sequences derived from two different genes: may even be from _______. |
|
Definition
exons
hybrid protein molecule
different chromosomes |
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|
Term
Translation: Assembly of _____ on a _____
•Living cells devote more energy to the synthesis of _____than to any other aspect of metabolism. |
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Definition
| polypeptides, ribosome, proteins |
|
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Term
About _____ of the dry mass of a cell consists of molecules that directly participate in protein synthesis
This reflects the importance of protein synthesis to the existence of the organism. |
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Definition
|
|
Term
Components of translation
mRNA:
–
Eukaryotes: made in the ____, transported to the _____.
–
Prokaryotes: transcription and translation occur _______. |
|
Definition
nucleus, cytoplasm.
Concurrently |
|
|
Term
Components of translation
tRNA: Adaptor molecules that mediate the transfer of information from ... |
|
Definition
|
|
Term
Components of translation
Ribosomes: manufacturing units of a cell; located in the ____ Contain ____and ____. |
|
Definition
| Cytoplasm, ribosomal RNA, proteins |
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|
Term
Components of translation
____: required for the attachment of amino acids to the correct tRNA molecule, and for ______ formation between amino acids. |
|
Definition
|
|
Term
Components of translation
Proteins: soluble factors necessary for proper.... |
|
Definition
| initiation, elongation and termination of translation |
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|
Term
tRNA
small single stranded RNA molecules of _____nucleotides in length, about 4S (________) in size.
•
In addition to A, G, C and U, tRNAs have modified bases produced by....
•
Each tRNA molecule is a____ structure, which looks like an ____ in three dimensions. |
|
Definition
70-95 , Svedberg units
...chemical alteration of the 4 primary nucleotides
clover leaf, L-shape |
|
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Term
tRNA
At the base of the L, three nucleotides form the ______.
•
The sequence of the anti codon dictates the ... The anti codon sequence is to the codon for that amino acid.
For example: GCA is a codon for alanine: the anticodon then is CGU, but in the.... |
|
Definition
Anti-codon
amino acid that binds to it
complementary
3’ to 5’ direction. |
|
|
Term
tRNA
There is at least one tRNA molecule for each amino acid: at least 20 tRNA molecules, but since there is more than one codon for some amino acids, there ...
•
The amino acid is carried at the ... |
|
Definition
more tRNA molecules.
3’ hydroxyl end of the tRNA molecule |
|
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Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
tRNA enzymes
Aminoacyl-tRNA synthetases ... to its respective amino acid.
–
There is at least one _______ for each amino acid. |
|
Definition
-catalyze the attachment of a tRNA molecule
-amino acyl tRNA synthetase |
|
|
Term
tRNA enzymes
The attachment of the amino acid ____ the tRNA molecule.
The reaction requires energy and is catalyzed in two steps by the same enzyme:
Amino Acid + ATP -->
Aminoacid~AMP + tRNA -->
The attachment of the aminoacid is at its______ . |
|
Definition
-activates/ charges
--> Amino acid~amp + PPi
-->AA~tRNA
carboxyl terminal |
|
|
Term
| tRNA enzymes _______: catalyzes the sequential transfer of amino acids to the growing chain. |
|
Definition
|
|
Term
Ribosomes They are the sites of _____ synthesis
•
They recognize features that signal the |
|
Definition
polypeptide
start of translation |
|
|
Term
Ribosomes
They ensure the accurate interpretation of the genetic code by...
They supply the enzymatic activity ... |
|
Definition
stabilizing the interaction between tRNA and the mRNA.
...that covalently links the amino acids in the polypeptide chain. |
|
|
Term
Ribosomes
...by sliding along the mRNA molecule. |
|
Definition
| They facilitate the linear reading of the genetic code |
|
|
Term
Ribosomal subunits
two subunits: large and small.
–
Prokaryotes:
–
eukaryotes: |
|
Definition
:50S + 30S = 70S
60S + 40S = 80S. |
|
|
Term
Ribosome structure
Prokaryotes: the large subunit contains one .... The small subunit contains two ... |
|
Definition
ribosomal RNA molecule, 23S, and about 31 different proteins
RNA molecules: 16S and 5S, and 21 different proteins. |
|
|
Term
Ribosomal structure
Eukaryotes: the large subunit contains three ... The small subunit consists of the... |
|
Definition
rRNA molecules: 28S, 5.8S and 5S, and 45 ribosomal proteins
18S rRNA and 33 different proteins. |
|
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Term
|
Definition
| Notice visuals, and where things are. |
|
|
Term
| Different parts of the ribosome |
|
Definition
| Peptidyl(P) site to the left, Aminoacyl (A) site to the right, Peptidal transferase on top. |
|
|
Term
| Ribosome synthesis; Where does rRNA syntehesis and ribosomal assembly occur in eukaryotes? |
|
Definition
|
|
Term
Ribosomal synthesis
•
Multiple copies of rRNA encoding genes are present in all organisms.
•
In humans, the short arms of the acrocentric chromosomes all contain ... |
|
Definition
•
Multiple copies of rRNA encoding genes are present in all organisms.
•
In humans, the short arms of the acrocentric chromosomes all contain genes for rRNA. |
|
|
Term
Before translation begins, the two ribosomal subunits exist as...
•
Soon after the start of translation, they come together. |
|
Definition
| separate entities in the cytoplasm. |
|
|
Term
Three steps of translation:
–
Initiation:
– |
|
Definition
| -sets the stage for polypeptide synthesis. |
|
|
Term
Translation
Elongation: causes the sequential addition of_____ to the polypeptide chain in a _____ as determined by the _____. |
|
Definition
amino acids
colinear fashion
sequence of mRNA |
|
|
Term
|
Definition
| Brings the polypeptide synthesis to a halt. |
|
|
Term
Initiation
The initiation codon is an ____, and is towards the _ end of the _ molecule that is being translated. It determines the ______. |
|
Definition
|
|
Term
Initiation
In prokaryotes, there is a conserved region about _____upstream from the initiating ___: this region contains a 6-nucleotide sequence (____). |
|
Definition
7 nucleotides, AUG
Shine-Dalgarno box: AGGAGG |
|
|
Term
Initiation
Initiation
The Shine-Dalgarno sequence is complementary to a region at the ____ rRNA of the small subunit; base pairing between these complementary sequences stabilizes the... |
|
Definition
3’ end of the 16
binding of the small ribosomal subunit to the mRNA for proper assembly. |
|
|
Term
Initiation
In prokaryotes, the first AUG... carrying a modified methionine: _____. ... to complete the initiation process. |
|
Definition
...is recognized by a special tRNA (tRNAfMet)
formyl methionine
The large subunit of the ribosome now attaches to the small subunit, |
|
|
Term
Initiation
In eukaryotes, the small ribosomal unit binds first to the ... at the...
It then migrates to the initiation site, usually the first .... direction.
In eukaryotes, the methione.... |
|
Definition
methylated cap (7-methyl guanosine)
5’ end of the mRNA.
AUG it encounters as it scans the mRNA in the 5’ to 3’
need not be modified |
|
|
Term
Elongation 1
At the start of elongation, the mRNA is bound to the _____, with the initiating tRNA in the ____, and the _____ free for binding to the next tRNA. |
|
Definition
| complete two subunit ribosome, P site, A site |
|
|
Term
Elongation 2
The ribosome moves along the mRNA in a _______, in a _____process, recognizing each ______. |
|
Definition
| 5’ to 3’ direction, step-wise, subsequent codon |
|
|
Term
Elongation 3
________ enzyme then catalyzes the formation of a peptide bond between the free _____of the amino acid at the ____, and the ____of the amino acid at the_____, which is actually _____to the tRNA. |
|
Definition
| The peptidyl transferase, N terminal,A site, Carboxyl end, P site, connected |
|
|
Term
Elongation 4
This disconnects the tRNA____from the amino acid, and the tRNA at the A
site now carries ______, with a free_________ and the Carboxyl terminal of the second _____connected to its _____ |
|
Definition
| fMet, two amino acids, N terminal, aa, tRNA |
|
|
Term
Termination 1
When the ribosome encounters a stop codon, there is no ....of the ribosome, instead a _____binds to it. |
|
Definition
tRNA available to bind to the A site
release factor |
|
|
Term
Termination 2
The details are not very clear, but once the release factor binds,________, releasing the large and small subunits, and the tRNA carrying the ____ is also released, freeing up the ______. |
|
Definition
the ribosome unit falls apart
polypeptide
polypeptide product |
|
|
Term
|
Definition
| is a non-Watson-Crick base pairing between two nucleotides in RNA molecules. The four main wobble base pairs are guanine-uracil, inosine-uracil, inosine-adenine, and inosine-cytosine |
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|
