Ch. 15 Genes and How They Work

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Who studied Neurospora crassa by creating DNA mutations and seeing if their defective enzymes were inherited?

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Beadle & Tatum

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What is the type of mutation if a mutated gene is necessary to make a required compound and therefore, would not grow in minimal media?

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Nutritional mutation

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78 Terms

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Who studied Neurospora crassa by creating DNA mutations and seeing if their defective enzymes were inherited?

Beadle & Tatum

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What is the type of mutation if a mutated gene is necessary to make a required compound and therefore, would not grow in minimal media?

Nutritional mutation

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What is the theory called that one gene is responsible for one enzyme?

One gene/one-enzyme hypothesis

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What is the theory described by Francis Crick that information only flows from DNA→RNA→protein?

Central Dogma

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What are the 2 exceptions to the central dogma?

  1. Retroviruses (use reverse transcriptase. RNA→DNA→RNA→protein)

  2. Prions (protein→protein)

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  1. mRNA produced from transcription used to direct synthesis of polypeptides

  2. Takes place at ribosome

  3. Requires several kinds of RNA

Translation

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  1. DNA-directed synthesis of RNA

  2. Only one strand (template strand) of DNA is used

  3. T in DNA replaced by U in RNA

Transcription

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Who wanted to prove that codons are blocks of 3 DNA nucleotides which each code for an amino acid?

Crick and Brenner

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Code is ____________________, meaning that some amino acids are specified by more than one codon (64 codons, only 20 amino acids). Not uniform

Degenerate

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True or false: Code is not universal

False (it is)

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Which type of transcription has only one RNA polymerase, which does not need a primer and adds free RNA nucleotides to the 3’ end?

Prokaryotic transcription

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What is the template by which the RNA sequence is made?

DNA template strand

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What strand has the same nucleotide sequence as the RNA sequence (except U instead of T)?

DNA coding strand

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What is the first base to be transcribed into RNA, numbered +1, called?

Start site

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What is closer to the 5’ end of the coding strand than the start site, numbered -1,-2, -3, etc?

Upstream

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What is closer to the 3’ end of the coding strand than the start site, numbered +1,+2, +3, etc?

Downstream

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What two things are necessary in order to properly initiate RNA synthesis?

Core enzyme + sigma factor

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What is the enzyme that drives RNA synthesis?

Core enzyme

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What helps RNA polymerase recognize the beginning of genes?

Sigma factor

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What are the 3 basic steps of prokaryotic transcription?

  1. Initiation

  2. Elongation

  3. Termination

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What is a part of prokaryotic initiation of transcription that is a short sequence upstream of start site that forms a recognition and binding site for the RNA polymerase?

Promoter (TTGACA -35 sequence; TATAAT -10 sequence)

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One of the conserved sequences within the promoter that indicates site of initiation and direction of transcription

Asymmetrical

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First step in prokaryotic initiation of transcription?

-35 sequence binds to sigma subunit

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Second step in prokaryotic initiation of transcription?

DNA helix unwinds at -10 sequence

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Third step in prokaryotic initiation of transcription?

RNA polymerase binds to the unwound DNA. RNA transcription begins at the start site. Sigma factor released

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What is the unwound section of DNA template, where RNA transcription occurs called?

Transcription bubble

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The step in prokaryotic transcription where strand grows in 5’→3’ direction as nucleotides are added onto 3’ end. Transcription bubble passes and the now-transcribed DNA is rewound as it leaves bubble.

Prokaryotic Elongation

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The step in prokaryotic transcription where specific ______________ sequences are used. RNA transcript is released. RNA polymerase releases DNA. DNA rewinds back into helix

Prokaryotic Termination

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With the termination sequences, a series of complementary base pairs will bind to each other to form a __________________

Hairpin

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When a single transcription unit encodes multiple enzymes for a particular pathway, which allows them to be regulated together

Operon genes

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In eukaryotic transcription, ___ ___ ___ ____________________ transcribes rRNA

RNA polymerase I

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In eukaryotic transcription, ___ ___ ___ ____________________ transcribes mRNA

RNA polymerase II

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In eukaryotic transcription, ___ ___ ___ ____________________ transcribes tRNA and many other small RNAs

RNA polymerase III

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How is eukaryotic transcription initiation different from prokaryotic?

Transcription factors

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In eukaryotic transcription initiation, what gets the RNA polymerase II enzyme to a promoter and to initiate gene expression and interacts with RNA polymerase to form initiation complex at promoter?

Transcription factors 2

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How is eukaryotic transcription termination different from prokaryotic?

Termination sites not as well defined and RNA transcript is modified after transcription

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In eukaryotes, the primary transcript must be modified to become ___________ ______

mature mRNA

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What are the 3 ways that eukaryotic pre-mRNA are modified to produce mature mRNA?

  1. Addition of a 5’ cap

  2. Addition of a 3’ poly-A tail

  3. Removal of non-coding sequences

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The non-coding sequences are called what?

Introns

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The sequences that will be translated are called what?

Exons

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What is a complex of snRNA and proteins that recognizes the intron-exon boundaries?

snRNPs (Small ribonucleoprotein particles)

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What is a key sequence within an intron that plays a crucial role in RNA splicing that the snRNPs bind to?

Branch site

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What is the organelle responsible for removing introns made up of a cluster of snRNPs with other proteins?

Spliceosome

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The result of the 5’ end of an intron being cut and attached to branch site

Lariat (lasso)

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What is it called when a single primary transcript is spliced into different mature mRNAs that include different sets of exons during splicing?

Alternative splicing

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What carries amino acids to the ribosome for incorporation into a polypeptide (protein)?

tRNA

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An adapter protein must interact with what two things?

mRNA and amino aicds

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Amino aicds ← → _________________ __________

Acceptor stem

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mRNA← → _______________ __________

Anticodon loop

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Each tRNA must be _____________ with the correct amino aicd on the acceptor stem

Charged

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What adds amino acids to the acceptor stem of tRNA in the tRNA charging reaction?

Aminoacyl-tRNA synthetases

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Aminoacyl-tRNA synthetases produce what?

Charged tRNA 1

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What are the 3 steps in the tRNA charging reaction?

  1. Amino acid is activated. ATP provides energy to bring amino acid to enzyme

  2. tRNA binds to enzyme

  3. Amino acid attaches to tRNA. Charged tRNA is then released

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________________ _____ has an amino acid added using the energy from ATP. Can undergo peptide bond formation at ribosome without additional energy

Charged tRNA 2

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What are the 2 primary functions of the ribosome?

  1. Decode the mRNA code

  2. Form peptide bonds

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What is the enzymatic component of the large subunit of ribosome?

Peptidyl transferase

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Which tRNA binding site binds the tRNA that carried the last amino acid?

E site

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Which tRNA binding site binds the tRNA attached to the growing peptide chain?

P site

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Which tRNA binding site binds the tRNA carrying the next amino acid?

A site

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What is the main step in initiation of prokaryotic translation?

Recognition of the start codon (AUG-methionine)

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Large subunit now added. Initiator tRNA bound to P site. A site is empty

Initiation of prokaryotic translation

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What are the differences between initiation of prokaryotic vs eukaryotic translation?

In eukaryotes, initiating amino acid is methionine (not fMet). More complicated initiation complex. Lack of an RBS-small subunit recognizes and binds to 5’ cap of mRNA

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The elongation factor binds to a charged tRNA and brings it to empty A site

1st step in prokaryotic elongation of translation

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Peptidyl transferase forms peptide bond. Growing chain cut off P site tRNA and stuck on amino acid of A site tRNA

2nd step in prokaryotic elongation of translation

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Translocation of ribosome. tRNA with amino acid chain moved to P site

3rd step in prokaryotic elongation of translation

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Addition of successive amino acids occurs as a cycle

4th step in prokaryotic elongation of translation

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What allows less stringent pairing between the 3’ base of the codon and the 5’ base of the anticodon?

Wobble pairing

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Stop codons are recognized by release factors which release the polypeptide from the ribosome

Termination of prokaryotic translation

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In eukaryotes, translation may occur in the _______________ or at the _________ _________________ _________________

Cytoplasm; rough endoplasmic reticulum

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Intracellular, cytoplasmic proteins

Cytoplasm

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Intramembrane proteins or secreted proteins→ protein trafficking pathway

RER

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In order to target protein translation to the RER, what must happen?

The signal sequence at beginning of polypeptide binds to a signal recognition particle

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What mutation alters a single base?

Point mutation

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What mutation substitutes one base for another?

Base substitution

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A type of base substitution where the same amino acid was inserted?

Silent mutation

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A type of base substitution that changes the amino acid inserted?

Missense mutation

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What mutation changes to stop codon?

Nonsense mutations

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What mutation is an addition or deletion of a single base?

Frameshift mutation