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Chapter 8 Flashcards

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1
Q

Gene expression

A

the means by which genetic information can be interpreted as phenotype

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2
Q

What is the general scheme of gene expression?

A

DNA –> RNA –> Protein

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3
Q

The central dogma maintains that genetic information flows into two distinct stages. They are:

A

transcription and translation

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4
Q

transcript

A

the product of transcription; a molecule of messenger RNA (mRNA) in prokaryotes, a molecule of RNA that undergoes processing to become an mRNA in eukaryotes

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5
Q

translation

A

process in which a mRNA sequence is decoded in mRNA into a sequence of amino acids (polypeptides)

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6
Q

polypeptides

A

a sequence of amino acids

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7
Q

Where does translation take place?

A

in ribosome

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8
Q

What are ribosomes composed of?

A

proteins and ribosomal RNA (rRNA)

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9
Q

genetic code

A

specific sequence of three nucleotides that codes for an amino acid

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10
Q

Transfer RNA (tRNA)

A

small RNA adapter molecules that place specific amino acids as the correct position in a growing polypeptide chain

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11
Q

How does the language of nucleotides differ from the language of proteins?

A

The language of nucleotides is written in four nucleotides and the language of proteins is written in amino acids, which are composed of three nucleotides

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12
Q

codon

A

nucleotide triplet ex) AUG

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13
Q

missense mutations

A

change a codon for one amino acid into a codon that specifies a different amino acid

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14
Q

what is proflavin?

A

an intercalating mutagen that insert itself between the paired bases stacked in the center of the DNA molecules which causes insertions or deletions of a single base pair

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15
Q

intragenic suppression

A

the restoration of gene function by one mutation canceling another in the same gene

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16
Q

reading frame

A

the sequential partitioning of nucleotides into groups of three to generate the correct order of amino acids in the resulting polypeptide chain

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17
Q

frame-shift mutations

A

changes that alter the grouping of nucleotides into codons; shift the reading frame for all codons beyond the point of insertion or deletion, almost always abolishing the function of polypeptide product

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18
Q

degenerate

A

two or more nucleotide triplets specify most of the 20 amino acids

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19
Q

messenger RNA (mRNA)

A

RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. It arises in the nucleus from the transcription of DNA sequence information and then moves to the cytoplasm, where they determine the proper order of amino acids during protein synthesis

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20
Q

template strand

A

template for mRNA; also called antisense strand or the non-coding strand

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21
Q

RNA-like strand

A

has the same polarity and sequence as the RNA strand

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22
Q

stop codons

A

three stop codons that terminate translation. The three different triplets are:

  • UAA
  • UAG
  • UGA
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23
Q

nonsense mutation

A

changes a codon that signifies an amino acid (a sense codon) into one that does not (nonsense codon)

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24
Q

What are the main characteristics of the genetic code?

A
  1. triplet codons
  2. nonoverlapping
  3. Includes three stop, or nonsense codons: UAG, UAA, and UGA
  4. the code is degenerate
  5. reading frame where methionine or AUG serves as the initiation code
  6. corresponding polarities of codons and amino acids (moves in a 5’ to 3’ direction along an mRNA)
  7. Mutations can change the message encoded in a sequence
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25
initiation code
AUG, which specifies the amino acid methionine which marks where in an mRNA the code for a particular polypeptide begins
26
wobble
the nucleotide in the last position that occurs at the anticodon that keeps the genetic code degenerative; the flexibility in base pairing between the 3' nucleotide in the codon and the 5' nucleotide in the anticodon
27
What are the three successive phases of transcription?
initiation, elongation and termination
28
What enzyme catalyzes (causes) transcription?
RNA polymerase
29
Promoters
DNA sequences near the beginning of genes that signal RNA polymerase where to begin transcription
30
RNA polymerase
- catalyzes transcription - adds nucleotides to the growing RNA polymer in the 5' to 3' direction using ribonucleotide triphosphates (ATP, CTP, GTP and UTP)
31
terminators
tells RNA polymerase where to stop transcription
32
How is transcription initiated in bacteria?
Transcription can be initiated by alternative sigma factors
33
RNA polymerase II (pol II)
transcribes genes that encode proteins
34
reverse transcription
construct a double strand of DNA from an RNA template
35
The result of transcription is a single strand of RNA known as _______
primary transcript
36
How do prokaryotes and eukaryotic organisms differ in terms of products of RNA?
In prokaryotic organisms,the RNA produced by transcription is the actual messenger RNA that guides protein synthesis. In eukaryotic organisms, most primary transcripts undergo RNA processing in the nucleus before migrating to the cytoplasm to direct protein synthesis.
37
methylated cap
a methylated guanine ( a methyl group added to a backwards G) at the 5' end of a eukaryotic mRNA that is not encoded directly by the gene
38
poly-A tail
3' end of the eukaryotic mRNA that consists of 100-200 A (adenine)
39
what enzyme adds methyl groups to the backwards G in the methylated cap?
methyl transferases
40
What is the two-step process involved in the addition of the tail to the 3' end of the mRNA?
1) RIBONUCLEAS cleaves the primary transcript to form a new 3' end; cleavage depends on the sequence AAUAA 2) Enzyme poly-A POLYMERASE adds As onto the 3' end exposed by cleavage
41
What two things are critical for the efficient translation of the mRNA into protein?
methylated caps and poly-A tails
42
What does the interaction of the proteins cause the mRNA molecule to do?
Shapes the mRNA molecule into a circle
43
How does the circular shape of mRNA molecules effect the mRNA?
It enhances the initial step of translation and stabilizes the mRNA in the cytoplasm by increasing the length of time it can serve as a messenger
44
exons
sequences found in both a gene's DNA and the mature messenger RNA (expressed regions)
45
introns
sequences found in the DNA of then gene but not in the mature mRNA (intervening regions). They interrupt, or separate, the exon sequences that actually end up in the mature mRNA
46
Where are 5' and 3' untranslated regions (5' to 3' UTRs) located? What is its function?
It is located right after the methylated cap and just before the poly-A tail. It is not translated by play an important role in regulating the efficiency of translation
47
How are introns removed from the primary transcript?
RNA splicing
48
What is RNA splicing?
the process that deletes introns and joins together successive exons to form a mature mRNA consisting only of exons
49
What are the three types of short sequences within the primary transcript that help ensure the specificity of splicing? What do they do?
1. splice donors 2. splice acceptors 3. branch sites These sites make it possible to sever the connections between an intron and the exons that precede and follow it and then join the formerly distant exons
50
What is the mechanism of splicing?
It involves two sequential cuts in the primary transcript. 1. First cut is at the splice-donor site at the 5' end of the intron--> new 5' end of the intron attaches via a phosphodiester bond, to a A at the branch site located within the intron forming a lariat structure. 2. The second cut is at the splice-acceptor site, at the 3' end of the intron which removes the intron The intron is then discarded and degraded
51
spliceosome
intranuclear machine that ensures that all of the splicing reactions take place in concert
52
What does the spliceosome consist of?
It consists of four subunits known as small nuclear ribonucleoproteins, or snRNPs
53
RNA molecules that can act as enymes and catalyze a specific biochemical reaction. An example is rRNA that joins amino acids together.
ribozymes
54
What is the function of transfer RNA (tRNA)?
tRNAs serve as adapter molecules that mediate the transfer of information from nucleic acid to protein
55
What is the structure of tRNA?
tRNA are short, single-stranded RNA molecules that carries one particular amino acid for each of the common 20 amino acid it carries Structure is considered in three levels: - primary structure: nucleotide sequence of a tRNA - secondary structure: short complementary regions within a tRNA's single strand that creates a cloverleaf shape tertiary structure: folding in three-dimensional space that creates a compact letter L
56
anticodon
at one end of the L; three nucleotides complementary to an mRNA codon specifying the amino acid carried by the tRNA; it is always available for base pairing with its complementary mRNA codon
57
What enzyme connects tRNA to the amino acid that corresponds to the anticodon?
aminoacyl-tRNA synthetases (able to read language of nucleic acid and protein)
58
charged tRNA
a tRNA covalently bonded to its amino acid; contains substantial energy that is later used to to drive peptide bond formation
59
What are the various ways in which ribosomes facilitate polypeptide synthesis?
1. recognize mRNA features that signal the start of translation 2. help ensure the accurate interpretation of the genetic code by stabilizing the interaction between tRNAs and mRNAs 3. ribosome supply the enzymatic activity that links the amino acids in a growing polypetide chain 4. by moving 5' to 3' along an mRNA molecule, they expose the mRNA codons in sequence, ensuring the linear addition of amino acids 5. ribosomes help end polypeptide synthesis by dissociating both from the mRNA direction polypeptide construction and from the polypeptide product itself
60
What are the ribosomal subunits found in E.coli?
Ribosomal subunits called the 30S subunit and the 50S subunit. - Before translation, they two subunits exists as separate entities in the cytoplasm - Soon after translation is initiated they come together to reconstitute a complete ribosome
61
What is the function of the 30S subunit?
part of the ribosome that initially binds to mRNA
62
What is the function of the larger 50S subunit?
It contributes an enzyme known as peptidyl transferase
63
What does the enzyme peptidyl transferase do?
catalyzes formation of the peptide bonds joining adjacent amino acids
64
What are the three distinct tRNA binding areas?
1. aminoacyl (or A) site 2. peptidyl (or P) site 3. exit (or E) site
65
What are the three phases of translation?
1. initiation 2. elongation 3. termination
66
What structure recognizes the initiating code?
Special initiating tRNAs carrying a modified form of methionine called formylmethionine (fMet) recognizes the initiation codon
67
larger polypeptide made before it is cleaved into smaller polypeptides
polyprotein
68
posttranslational modifications
enzymatic addition of chemical constituents, such as phosphate groups, carbohydrates, fatty acids, or even smaller peptides to specific amino acids that may modify a polypeptide after translation
69
How do prokaryotes and eukaryotes differ in terms of coupling of transcription and translation?
Prokaryotes have no nuclear membrane so transcription and translation coupling is possible. In eukaryotes, there is a nuclear membrane and so transcription and translation are not coupled.
70
In eukaryotes, what are the two situations that affect promoters from being recognized by RNA polymerase?
1. Stability of RNA polymerase interaction with the promoter is often affected by enhancer sequences located far from the promoter 2. Eukaryotic chromosomes are tightly wound around histone proteins in chromatin. In order for a promoter to be recognized by RNA polymerase, it has to unwind from chromatin
71
Where does translation begin in prokaryotes?
In prokaryotes, translation begins at a ribosome binding site on the mRNA, defined by a short, characteristic sequence of nucleotides called a Shine-Dalgarno box adjacent to an initiating AUG codon.
72
Polycistronic
they contain the information or several genes (sometimes referred to as cistrons), each of which can be translted independently starting at its own ribosome binding site
73
How does translation begin in eukaryotes?
Small ribosomal subunits first bind to the methylated cap at the 5' end of the mature mRNA and then migrates through the 5' UTR to the initiation site
74
monocistronic
mRNA that contains the information for translation for only a single kind of polypeptide.
75
How do initiation tRNAs differ in prokaryotes and eukaryotes?
In prokaryotes, tRNA carries a modified form of methionine known as N-formylmethionine. Eukaryotes carries an unmodified methionine.
76
Silent mutations
mutations that change the third nucleotide of a codon, bt do not alter the amino acid composition of the encoded polypetide.
77
Missense mutations
mutations that change a codon into a mutant codon that specifies a different amino acid Conservative-- if the substituted amino acid has chemical properties similar to the one it replaces, it may have little or no effect on protein function Nonconservative-- cause substitution of an amino acid with very different properties that have more noticeable consequences
78
Frameshift mutations
results from the insertion or deletion of nucleotides within the coding sequence that can cause unrelated amino acids or premature stop codons to appear in place of amino acids critical in protein activity, destroying or diminishing polypeptide function

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