Term
| DNA is __________ to mRNA which is __________ to a protein. This is the concept behind the __________ __________. |
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Definition
1) Transcription
2) Translation |
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Term
| __________ __________ species the amino acid sequence of a polypeptide chain. |
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Definition
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Term
| __________ consist of one or more polypeptide chains. |
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Definition
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Term
| __________ are built from amino acids hooked together by peptide bonds. |
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Definition
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Term
| The sequence of __________ __________ in a polypeptide is what gives a protein its unique shape and properties. |
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Definition
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Term
| All amino acids (except __________) have the same basic structure. |
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Definition
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Term
| All amino acids have a central carbon atom, known as the __________ __________; attached to it are an __________ group, a __________ group, a side chain and an __________ atom. |
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Definition
1) Alpha carbon
2) Amino
3) Carboxyl
4) Hydrogen |
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Term
| What are the two acidic amino acids? |
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Definition
1) Aspartic acid (Asp)
2) Glutamic acid (Glu) |
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Term
| What are the three basic amino acids? |
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Definition
1) Lysine (Lys)
2) Arginine (Arg)
3) Histidine (His) |
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Term
| How many neutral, nonpolar amino acids are there? Name the amino acids. |
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Definition
1) There are nine neutral, nonpolar amino acids
2) Tryptophan (Trp)
3) Phenylalanine (Phe)
4) Glycine (Gly)
5) Alanine (Ala)
6) Valine (Val)
7) Leucine (Leu)
8) Isoleucine (Ile)
9) Methionine (Met)
10) Proline (Cyclic structure) |
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Term
| How many neutral, polar amino acids are there? Name the amino acids. |
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Definition
1) There are six neutral, polar amino acids.
2) Tryosine (Tyr)
3) Serine (Ser)
4) Threonine (Thr)
5) Asparagine (Asn)
6) Glutamine (Gln)
7) Cysteine (Cys) |
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Term
__________ __________ are formed when the amino group of one amino acid is joined to the COOH group of another amino acid.
__________-__________ is defined as the number one amino acid and the __________ __________ as the last amino acid. |
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Definition
1) Peptide bonds
2) N-terminus
3) COOH terminus |
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Term
Proteins have __________ of organization:
1) __________ is the amino acid sequence
2) __________ is the folding pattern of a polypeptide chain; alpha-helix, beta-sheet, etc.
3) __________ is the 3-D structure of the protein; it reveals how the helices and pleats fold up
These three levels involve only one __________ chain
4) __________ in this level proteins may be __________ meaning there is more than one polypeptide chain. The structure refers to how the various polypeptides fit together. |
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Definition
1) Four
2) Primary
3) Secondary
4) Tertiary
5) Polypeptide
6) Quarternary
7) Multimeric |
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Term
| Which level of protein organization involves the amino acid sequence? |
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Definition
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Term
| Which level of protein organization involves the folding pattern of polypeptide chains? How many folding patterns are there and how are they created? |
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Definition
1) Secondary
2) There are two chains: alpha-helix and beta-sheet
3) They are created by intra-polypeptide hydrogen-bonding |
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Term
| Which level of protein organization involves the 3-D structure of the protein? |
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Definition
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Term
| Which level of protein organization involves proteins that are multimeric? |
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Definition
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Term
| Which level of protein organization refers to how the various polypeptides fit together? |
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Definition
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Term
| __________ is when there is more than one polypeptide chain present. |
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Definition
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Term
The linear nucleotide sequence information of a gene is directly related to the __________ __________ sequence information of the coded protein.
The N-terminal part of a protein is coded by the __________-__________ part of the gene (__________-end of the gene) and the C-terminus of the protein is coded by the end nearest the __________ __________ (__________-end of the gene). |
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Definition
1) Amino acid
2) Promoter-proximal
3) 5'
4) Transcription terminus
5) 3' |
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Term
| The process of formation of RNA from a DNA template is called __________. |
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Definition
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Term
| Only __________ strand of DNA duplex is transcribed for any one gene, otherwise one could get two different __________ from one gene but there would be __________-__________ __________ problem. |
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Definition
1) One
2) Proteins
3) RNA-RNA hybridization |
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Term
| The DNA sequence where RNA polymerase binds and starts __________ is called a __________. |
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Definition
1) Transcription
2) Promoter |
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Term
The conversion of RNA information into a protein is called __________.
In __________, the transcript is used directly without modifications.
In __________, extensive modification of the original transcript occurs. |
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Definition
1) Translation
2) Prokaryotes
3) Eukaryotes |
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Term
| Each gene usually has two parts involved in transcription - the __________ __________ and __________-__________ __________. |
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Definition
1) Regulatory sequences
2) Protein-coding sequences |
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Term
| Transcription is always in the __________ -> __________ direction. RNA synthesis requires an enzyme (__________ __________) four __________, __________ (element), and __________ __________ template. |
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Definition
1) 5' -> 3'
2) RNA polymerase
3) rNTPs
4) Mg++
5) DS DNA |
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Term
| The __________ __________ reaction is very similar to the DNA synthesis reaction catalyzed by a DNA polymerase. |
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Definition
|
|
Term
| There are four main classes of RNA in an eukaryotic cell. What are they? Which is the only unstable RNA? |
|
Definition
1) mRNA
2) rRNA
3) tRNA
4) Small nuclear RNA (snRNA)
5) Messenger RNA (mRNA) |
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Term
| Only __________ information is converted into proteins. |
|
Definition
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Term
| In bacteria, only one __________ __________ exists and it makes all three kinds of bacterial RNA (bacteria don't have __________ since they don't have nuclei). |
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Definition
1) RNA polymerase
2) snRNA |
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Term
| In eukaryotes, __________ __________ __________ makes rRNA, __________ __________ __________ makes mRNA and some snRNAsm and __________ __________ __________ makes tRNA, 5s RNA, and some snRNA. |
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Definition
1) RNA polymerase I
2) RNA polymerase II
3) RNA polymerase III |
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Term
Which RNA polymerase is responsible for producing rRNA?
Which is is responsible for producing mRNA and some snRNA?
Which is responsible for producing tRNA, 5s rRNa, and some snRNA? |
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Definition
1) RNA Polymerase I
2) RNA Polymerase II
3) RNA Polymerase III |
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Term
In prokaryotes, the __________ is located near the start of the protein-coding sequences (upstream from the gene).
Sometimes, there is a long __________-__________ __________ sequence before the start of protein-coding information. After the end of the protein-coding sequence, there is a __________ __________ sequence (downstream from the gene). |
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Definition
1) Promoter
2) 5'-leader RNA
3) Transcription terminator |
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Term
| Two sequences are important in the bacterial promoter. They are called __________ and __________ sequences. |
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Definition
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|
Term
| E. coli RNA polymerase exists in two forms: the __________ __________ and the __________. |
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Definition
1) Core polymerase
2) Holoenzyme |
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Term
The -35 and -10 sequences in the __________ of bacteria (E. coli) are recognized by the __________ factor of the bacterial RNA polymerase __________.
The enzyme first binds loosely to the promoter making an unstable __________ __________.
It is followed by the melting of bases from -10 to past +1 resulting in a very stable __________ __________ |
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Definition
1) Promoter
2) Sigma
3) Holoenzyme
4) Closed complex
5) Open complex |
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Term
Different __________ have sequences with varying degrees of homology to the consensus sequences. The higher the __________ of the consensus sequences, the greater the affinity the __________ __________ has for the promoter, and the greater the rate of __________.
The less the __________, the weaker the binding of __________ __________ and the lower the __________ level. |
|
Definition
1) Promoters
2) Homology
3) RNA polymerase
4) Transcription
5) Homology
6) RNA polymerase
7) Transcription |
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Term
The normal sigma factor in bacteria is __________.
There are other sigma factors in E. coli which are use under special conditions. |
|
Definition
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Term
| As the __________ __________ starts to make the RNA chain, the __________ subunit is released and only the core enzyme remains attached to the DNA template. |
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Definition
1) RNA polymerase
2) Sigma |
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Term
| __________ __________ are very processive. This is important because once they are detached from DNA, the core polymerase is incapable of restarting __________ __________. |
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Definition
1) RNA polymerases
2) RNA synthesis |
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Term
Termination of transcription occurs at sites called __________ __________.
There are __________ mechanisms in E. coli. What are the names of the mechanisms? |
|
Definition
1) Transcription terminators
2) Two
3) Rho protein-independent
4) Rho protein-dependent |
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Term
| What are the two transcription terminator mechanisms in E. coli? |
|
Definition
1) Rho protein-independent
2) Rho protein-depdendent |
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Term
| In the E. coli Rho protein-independent mechanism, no __________ protein is needed. __________ requires a special sequence that can make a strong __________ followed by a bunch of A's in the template DNA. |
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Definition
1) Termination
2) Termination
3) Hairpin |
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Term
| In the E. coli Rho protein-dependent mechanism, no __________ sequence or string of A's is needed. Instead, there is a rho protein0binding site. The __________-__________ binds to this sequence in the newly made RNA chain, climbs up the RNA and melts the __________-__________ __________ (in a helicase-like action using ATP breakdown energy) resulting in the release of the newly synthesized RNA chain. |
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Definition
1) Hairpin
2) Rho-protein
3) DNA-RNA hybrid |
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Term
__________ can occur in both promote and termination sequences
A mutation in the promoter sequence that creates a stronger promote is called an __________-__________ mutation.
A mutation that makes a promoter weaker is called a __________-__________ mutation.
Mutations can create a new __________ sequence in the middle of a gene. These cause a shorter __________ chain that codes for only part of the protein product.
When a mutation weakens or eliminates a terminator sequence, a transcript longer than the __________ __________ RNA is synthesized. |
|
Definition
1) Mutations
2) Up-promoter
3) Down-promoter
4) Terminator
5) RNA
6) Wild type |
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Term
__________ leads to the formation of a precursors of mRNA.
Regulation of the process is complex, resulting in many regulatory elements both __________ and __________.
There are positive regulatory elements (__________) and negative regulatory elements (__________). |
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Definition
1) Transcription
2) Upstream
3) Downstream
4) Enhancers
5) Silencers |
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|
Term
| What are the three regulatory elements that were discovered through the analysis of upstream regulatory elements? |
|
Definition
1) TATA Box (5' TATAA 3') at -30 nt
2) CAAT Box (5' GGCCAATCT 3') at -80 nt
3) GC Boxes (5' GCGCGC 3') at -100 nt |
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Term
| Transcription can occur in the absence of an __________ but it is weak. |
|
Definition
|
|
Term
| What specific factors does RNA Polymerase II need to initiate transcription? |
|
Definition
| 1) Transcription Factors (TFs); specificallt TF II. TF I and TF III are for RNA Polymerase I and III respectively |
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Term
Steps in the production of mature __________ are very different in prokaryotes and eukaryotes.
In prokaryotes, the original transcript is used as __________ and mRNA begins to be copied into _________ before the __________ process is completed.
In eukaryotes, the original transcript undergoes extensive __________-__________ processing before becoming mature mRNA. |
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Definition
1) mRNA
2) mRNA
3) Proteins
4) Transcription
5) Post-transcriptional |
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Term
| Transcription and __________ __________ occur at the same time. |
|
Definition
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Term
Most eukaryotic genes have non-coding sequences (__________) interspersed with the protein-coding sequence.
Precursor RNA is incapable of producing a functional protein; non-coding sequences (__________) must be spliced out before mRNA is mature enough to produce a functional protein. |
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Definition
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Term
The average protein-coding portion of a gene (__________) is much smaller than the non-coding stretches (__________).
As a result, most of the gene does not code for __________. |
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Definition
1) Exon
2) Intron
3) Protein |
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Term
The __________-end of a prokaryotic mRNA has three __________ derived from the first nucleotide of the RNA chain.
In eukaryotes, the 5'-end is modified by the addition of a __________ __________.
When the RNA chain grows to 20-40 nucleotides, the cap is added by a __________ __________.
The formation of the cap involves the non-templated addition of a methylated __________ in an unusual 5' -> 5' linkage.
Usually the __________ sugars of the first two nucleotides of the RNA chain are also methylated.
__________ is essential for high efficiency of binding of ribosomes to the mRNA. |
|
Definition
1) 5'
2) Phosphates
3) Methylated cap
4) Capping enzyme
5) Guanine
6) Ribose
7) Capping |
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Term
The __________-end of the mRNA contains a tail of 50-200 __________ residues, a poly (A) tail. This is a non-templated reaction in which an enzyme called __________ __________ __________ adds the tail.
Most, but not all eukaryotic __________ contain such a tail.
There appears to be no specific __________ __________ site in eukaryotes. As a result, __________ continues past the end of the protein-coding region.
There is a __________ __________ __________ site [AAUAAA], usually located several hundred nucleotides after the end of the coding sequence. By the action of a complex of proteins, the transcript is cleaved 10-30 nucleotides downstream from the __________ __________ __________.
__________ __________ __________ enzyme adds A-resides to the __________-end of the cleaved RNA. |
|
Definition
1) 3'
2) Adenine
3) Poly (A) polymerase
4) mRNAs
5) Transcription termination
6) Transcription
7) Poly (A) addition
8) Poly (A) site
9) Poly (A) polymerase
10) 3' |
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Term
| The poly (A) tail is though to protect mRNA from degradation from the __________-end by __________-__________ (the __________-end is already protected by the methylated-G cap-structure) |
|
Definition
1) 3'
2) Ribo-exonucleases
3) 5' |
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|
Term
| Precursor RNAs often contain long non-coding sequences (__________) interspersed with the protein-coding sequences. |
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Definition
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|
Term
Intron splicing occurs from the pre-mRNA molecule as it is being __________.
The __________-end cap is added first. All introns are removed before the release of the __________ from the transcription complex.
During splicing of __________, proteins are recruited to the __________-__________ __________ that later help in the export of the mature mRNA from the __________ to the __________. |
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Definition
1) Transcribed
2) 5'
3) mRNA
4) Introns
5) Intron-exon junctions
6) Nucleus
7) Cytoplasm |
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Term
In general, __________ genes do not contain introns.
However, some genes of __________ __________ have been shown to contain introns. |
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Definition
1) Prokaryotic
2) Phage T4 |
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Term
| Introns are looped out with the aid of __________. The loop is then removed by __________ __________. Adjacent __________ are joined together to make a contiguous molecule. |
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Definition
1) snRNA
2) Nuclease cleavage
3) Exons |
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Term
Introns tend to begin with __________ and end with __________.
__________ nucleotides specify the 5'-junction and __________ nucleotides specify the 3'-junction.
Step I is a cut at the __________-end of the intron and its joining to the __________-part of the intron.
Exon I becomes separated; this looped intron structure has been named __________ __________ __________.
A 2' -> 5' linkage is involved in connecting the __________ to the A-residue. The next step is cleavage at the __________-end of exon two and joining the __________-end to exon one (occurs in one step).
The __________ __________ is then linearized and degraded; all of these processes occur in the __________. |
|
Definition
1) 5' GU
2) AG 3'
3) 7+
4) 10+
5) 5'
6) 3'
7) RNA lariat structure
8) G
9) 5'
10) 3'
11) Lariat RNA
12) Nucleus |
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Term
__________, which contain small nuclear RNAs each associated with 6-10 proteins produce small nuclear RNA-protein particles (__________; usually called snurps).
__________ in some cases can occur without spliceosomes; some introns are in fact self-splicing __________. |
|
Definition
1) Spliceosomes
2) snRNPs
3) Splicing
4) Ribozymes |
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Term
| Mutations in __________ usually have no effect on the __________ as long as they do not interfere with splicing. |
|
Definition
|
|
Term
| In humans, 96% of sequences within genes are __________ and only 4% is __________-__________ information. |
|
Definition
1) Introns
2) Protein-coding |
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Term
| __________ is translated in the 5' -> 3' direction, and __________ is synthesized in the __________ -> __________ direction. |
|
Definition
1) mRNA
2) Protein
3) NH2 -> COOH |
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Term
Amino acids do not directly interact with the codons in __________.
Instead, they are brought together by small RNA molecules, the __________ molecules. |
|
Definition
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Term
Since the __________ __________ do not directly interact with mRNA, synthesis of a correct protein requires that the __________ with the right anticodon bring the correct amino acid to the __________.
The attachment of an amino acid to its tRNA is done by an enzyme called __________-__________ __________ __________.
The carboxyl end of the amino acid is attached to the 3'-__________ of the ribose of the __________ of CCA tRNA stem. |
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Definition
1) Amino acids
2) tRNA
3) Ribosomes
4) Amino-acyl tRNA synthetase
5) OH
6) Adenine |
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|
Term
| The __________ __________ are responsible for accurate protein synthesis by attaching the right amino acids to their correct tRNAs. |
|
Definition
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|
Term
| If there is a __________ __________ in the middle of a mRNA, __________ are recruited and the mRNA is degraded, a process called __________-__________ __________. |
|
Definition
1) Nonsense codon
2) Nucleases
3) Nonsense-mediated decay |
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Term
The process of __________ begins with a small subunit of ribosome binding to the mRNA.
In prokaryotes, the start codon __________ is indicated by the presence of a short sequence before it (the __________-__________ ___________) which hybridizes to the __________ in the small subunit of ribosome. |
|
Definition
1) Initiation
2) AUG
3) Shine-Dalgarno Sequence
4) rRNA |
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|
Term
Since bacteria make mRNA with information for several proteins (__________ __________), there can be several start __________ codons in a single mRNA.
In eukaryotes, usually the first __________ codon nearest to the __________-cap in the mRNA are used.
There are no internal __________ codons that specif start of other protein chains. |
|
Definition
1) Polycistronic mRNA
2) AUG
3) AUG
4) 5'
5) AUG |
|
|
Term
| Initiation in both prokaryotes and eukaryotes require protein factors called __________ __________. |
|
Definition
|
|
Term
| A complex of the small subunit of rubosomes bound to the mRNA along with several initiation factors and the first tRNA + met creates an __________ __________. |
|
Definition
|
|
Term
In bacteria, the first __________ is loaded into the ribosome by a special tRNA, called __________ tRNA, which uses a modified form of methionine, __________-__________ (a mimic of dipeptide).
Eukaryotes don't use __________-__________ to start a new chain and don't have __________ tRNA. |
|
Definition
1) Methionine
2) fmet
3) Formyl-methionine
4) Formyl-methionine
5) fmet |
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|
Term
It is only during the initiation step that a tRNA bound to a single amino acid can go into the __________-__________ of a ribosome (normally, this is reserved for a __________ to which is bound a growing peptide).
In bacteria, this initiation assembly occurs at the __________ start codon next to a __________-__________ sequence.
In eukaryotes, it occurs at the __________ and then the initiation complex moves downstream until it finds an __________ start codon.
The next step is the recruitment of the large subunit of the __________.
Now a second charged tRNA can bring amino acid number two to the __________-__________ in the ribosome. |
|
Definition
1) P-site
2) tRNA
3) AUG
4) Shine0Dalgarno
5) Cap
6) AUG
7) Ribosome
8) A-site |
|
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Term
Once both sites of the ribosome are filled (the __________ and __________ sites), a __________ __________ can form and create a dipeptide.
This requires more protein factors, such as __________ __________ (EF) and GTP (a source of energy).
Once the peptide bond has been formed, the ribosomes translocate so that the tRNA number two is now in the __________-__________.
Now amino acid number three is brought to the vacated __________-__________ and the peptide bond formation and translocation steps are repeated.
The empty tRNA is pushed into the __________-__________ (exit slot) of the ribosome upon translocation and ejected. |
|
Definition
1) P
2) A
3) Peptide bond
4) Elongation factors
5) P-site
6) A-site
7) E-site |
|
|
Term
| A single mRNA that has many ribosomes simultaneously translating it is called a __________. |
|
Definition
|
|
Term
__________ is a two-step elongation cycle that is repeated (codon by codon) until the __________-__________ is occupied by a __________ __________ (UAG, UAA, or UGA).
Normally in a cell there are no __________ capable of recognizing a nonsense codon. Instead, there are protein factors (called __________ __________) that recognize the nonsense codons and bind into the __________-__________ of the ribosome.
This causes the release of the __________ from the ribosome and breakup of the ribosome into the two subunits and release of protein factors. |
|
Definition
1) Termination
2) A-site
3) Nonsense codon
4) tRNAs
5) Release factors
6) A-site
7) mRNA |
|
|
Term
Each mature __________ has a characteristic 3-D shape that is coded in its amino acid sequence.
Two main ways of folding are the __________ __________ and __________ __________ created by intra strand hydrogen bonding.
In addition to the hydrogen bonds, covalent bonds may be formed between __________ atoms of __________. |
|
Definition
1) Protein
2) Alpha helix
3) Beta sheets
4) Sulfur
5) Cysteines |
|
|
Term
Larger proteins have a difficult time folding due to hydrophobic areas of proteins aggregating abnormally. Such proteins need the help of proteins called __________.
The __________ proteins bind to __________ areas of proteins and keep them from aggregating abnormally.
The most complex proteins are trapped inside hollow tube-like protein complexes called __________. |
|
Definition
1) Chaperones
2) Chaperone
3) Hydrophobic
4) Chaperonins |
|
|
Term
| The genetic code is composed of a __________ __________. |
|
Definition
|
|
Term
| Three __________ specify one amino acid |
|
Definition
|
|
Term
| What are the seven properties of the genetic code? |
|
Definition
1) Contains a triplet code
2) Is comma-free
3) Is non-overlapping between codons
4) Is universal among organisms
5) Degenerate: there are multiple codons for one amino acid
6) There are specific start and stop signals
7) Codon-anticodon interactions involve Watson-Crick base pairing |
|
|
Term
| What is the start codon? What are the stop codons? |
|
Definition
1) The start codon is AUG (methionine)
2) The stop codons are UAA, UAG, and UGA |
|
|
Term
| __________ __________ allows a G to pair with either C or U during the codon-anticodon base pairing. |
|
Definition
|
|
Term
| __________ are small RNA molecules that bring amino acids to the ribosomes during protein synthesis. |
|
Definition
|
|
Term
| Suppression of nonsense codons can sometimes occur due to the creation of mutant __________ that have an __________ sequence complementary to a nonsense codon. |
|
Definition
|
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