Ch. 15 Genes and How They Work

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

Beadle & Tatum

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

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

One gene/one-enzyme hypothesis

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

Central Dogma

What are the 2 exceptions to the central dogma?

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

2. Prions (protein→protein)

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

2. Takes place at ribosome

3. Requires several kinds of RNA

Translation

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

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

Crick and Brenner

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

Degenerate

True or false: Code is not universal

False (it is)

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

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

DNA template strand

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

DNA coding strand

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

Start site

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

Upstream

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

Downstream

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

Core enzyme + sigma factor

What is the enzyme that drives RNA synthesis?

Core enzyme

What helps RNA polymerase recognize the beginning of genes?

Sigma factor

What are the 3 basic steps of prokaryotic transcription?

1. Initiation

2. Elongation

3. Termination

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)

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

Asymmetrical

First step in prokaryotic initiation of transcription?

-35 sequence binds to sigma subunit

Second step in prokaryotic initiation of transcription?

DNA helix unwinds at -10 sequence

Third step in prokaryotic initiation of transcription?

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

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

Transcription bubble

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

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

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

Hairpin

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

Operon genes

In eukaryotic transcription, ___ ___ ___ ____________________ transcribes rRNA

RNA polymerase I

In eukaryotic transcription, ___ ___ ___ ____________________ transcribes mRNA

RNA polymerase II

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

RNA polymerase III

How is eukaryotic transcription initiation different from prokaryotic?

Transcription factors

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

How is eukaryotic transcription termination different from prokaryotic?

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

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

mature mRNA

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

The non-coding sequences are called what?

Introns

The sequences that will be translated are called what?

Exons

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

snRNPs (Small ribonucleoprotein particles)

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

Branch site

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

Spliceosome

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

Lariat (lasso)

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

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

tRNA

An adapter protein must interact with what two things?

mRNA and amino aicds

Amino aicds ← → _________________ __________

Acceptor stem

mRNA← → _______________ __________

Anticodon loop

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

Charged

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

Aminoacyl-tRNA synthetases

Aminoacyl-tRNA synthetases produce what?

Charged tRNA 1

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

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

Charged tRNA 2

What are the 2 primary functions of the ribosome?

1. Decode the mRNA code

2. Form peptide bonds

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

Peptidyl transferase

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

E site

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

P site

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

A site

What is the main step in initiation of prokaryotic translation?

Recognition of the start codon (AUG-methionine)

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

Initiation of prokaryotic translation

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

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

1st step in prokaryotic elongation of translation

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

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

3rd step in prokaryotic elongation of translation

Addition of successive amino acids occurs as a cycle

4th step in prokaryotic elongation of translation

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

Wobble pairing

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

Termination of prokaryotic translation

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

Cytoplasm; rough endoplasmic reticulum

Intracellular, cytoplasmic proteins

Cytoplasm

Intramembrane proteins or secreted proteins→ protein trafficking pathway

RER

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

What mutation alters a single base?

Point mutation

What mutation substitutes one base for another?

Base substitution

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

Silent mutation

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

Missense mutation

What mutation changes to stop codon?

Nonsense mutations

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

Frameshift mutation