Chapter 6

True/false: Genes can be expressed with different efficiences.
True False

How do uracil and thymine differentiate?

How does DNA and RNA differ in structure?

RNA is mainly single stranded and will not form any other structure.
True False

RNA can unwind the DNA helix.
True False

RNA uses incoming nucleotides called ____ _____.

What is a transcriptional unit?

How many genes will a transcript code for in eukaryotes?

How many genes will a transcript code for in prokaryotes?

In bacteria, what signals for initiation of transcription?

In bacterial transcription, what signals elongation?

In baterial transcription, what is the process of termination?

Two important characteristics of ter sequences?

In the bacterial promoter, what is found at the -10 sequence?
At the -35 sequence?

How long is the bacterial promoter?

RNA is synthesized in the ___ to ___ direction.

What is the start site for transcription?

Eukaryotic transcription differs by the use of 3 RNA polymerases. Name them.

RNA polymerase _ transcribes the 45s precursor rRNA which is made into subunits : ___,___,___. they code for what kind of genes?

This polymerase transcribes all-protein coding genes, snoRNA, miRNA, siRNA and most snRNA genes.

RNA polymerase III codes for what type of genes?

Mitochondrial RNA polymerase is similar to ______ RNA polymerase which are both similar to _____ RNA polymerase.

Not all RNA polymerases are composed of subunits.
True False

Transcription in eukaryotes cells the involvement of proteins call ____ _____ ____

The are 3 groups of GTF's what are they?

There are _ TFIIs

In eukaryotes, RNA polymerase __ transcribes most genes.

TFIID has __ major subunits. Name them. (found in eukaryotes)

TFIIH has _ subunits. Its role it to...

Which Transcription factor has helicase as a subunit? What kind of cell is it found in?

how far is the TATTA box from the transcriptional start point in eukaryotic cells?

the 5' methyl cap is added during the ____ phase

The 5' methyl cap and associated proteins (CBC) function to;

Human genes have an average of _ exons and _ introns

(Most/some)_____ hnRNAs can be spliced in a variety of ways by _____________

Alternative splicing produces __ which produces___

When does RNA splicing occur?

RNA splicing occurs at ____ _____ located at the ______ of introns and exons

3 important consensus sequences invloved in RNA splicing..

the branch point site in an intron forms?

Name the snRNAs involved in splicing

snRNA leaves the nucleus to combine with ____ and returns to the nucleus as a ____

The U1 snRNP forms base pairs with the ___ splice junction and the BBP(_____)

The U2 snRNP _____ BBP and U2AF and forms ____ pairs with the ___ ____ consensus sequence

What snRNPs come into the scence as a triplet?

The triplet snRNP complex acts to?

RNA-RNA rearangments occur that break apart __/__ and allow __ to displace U1 at the 5' splice junction to form an active site for the second ____ ____ which completes the splice

pre-mRNA is another word for ___

____ is a formed snRNP complex. Utilizes branch point "_" to cut the hnRNA at the __ splice site

the 5' cut (RNA splicing) becomes covelently linked to ____ forming a loop called a ____

exons (post splicing) are _____ linked. The excised ____ RNA will be degraded/recycled in the ____ and the snRNPs will be degraded/recycled

____ proteins associated with the tail of RNA polymerase are also required in addition to snRNPs

True/false: Introns are only removed via snRNPs
True False

Self-splicing introns. Group I utilizes ___ ___ _ nucleotide to initiate the splicing process.
Group II utilizes an "_" nucleotide that is apart of the intron itself.

introns are degraded by ___

Describe the last event of hnRNA modification

termination is signaled by RNA nucleotide sequence ______, of which 10-30 nucleotides upstream cleavage occurs after DNA polymerase has transcribed exposing a ___ group. The DNA polymerase continues to transcribe, transcribing ter sequences rich in __ or __. This has loose ___ for the polymerase and it falls off.

this enzyme adds the 3' poly-A tail

____ and ___ proteins recognize the RNA sequence AAUAAA (poly- A site) and bind to it leaving the RNA polymerase ___.

Poly-A polymerase (PAP) adds _ A at a time

Unlike RNA polymerase, this enzyme in mRNA 3' processing DOES NOT require a template

The poly-A tail is about ____ A's long.

The 5' cap is added after or before the poly-A tail

mRNA are ____ exported. A mature mRNA is ready and signaled by a variet of ___

______ complexes are bound to the introns to help identify them for destruction by ___

mRNA is exported out the nucleus through a ___ ____ ____ with the ___ end going first

True/false: Many mRNA proteins dissociate before and after exiting the nucleus
True False

a protein call _____ nids to the mRNA to signal for export from the nucleus

In eukaryotes, a exported mRNA will form a ____ shape due to protein interactions

the most abundant non-coding RNAs are _____

Eukaryotic rRNAs are synthesized via RNA polymerase _

RNA polymerase ___ transcribes hnRNA

in Eukaryotes, RNA polymerase _ transcribes the important ___ precursor ____

Human cells have ~ ___ copies of rRNA genes distibuted in groups on 5 different haploid (therefore, on _ chromosomes in diploid cells)chromosomes; name them

45s Precursor rRNA is a ____ RNA transcript synthesized by RNA polymerase __

45s precursor rRNA is degraded in _ rRNA molecules; __,__ and __

45s precursor rRNA goes through ___ ___ having degraded regions of the nucleotide sequence

2 types of 45s precursor modifications

What enzymes are responsible for modifications of precursor rRNA? Where do the modifications occur?

5s rRNA is produced by which enzyme?

As prophase proceeds, the nucleolus ____ and no ___ precursor is made. The ___ precursor becomes active in euchromatin

____ ____ consists of __ loops thats project into the nucleolus. They organize info like formation of the nucleolus

telomerase is made in/out of the nucleus

An immature large RNA subunit and a immature small RNA subunit are exported to the ____ for final assembly. The assembled ribosome consists of the ___ subunit and the smaller ____ subunit

the number of possible codons is _x_x_ = 64. but there are only _ types of amino acids. Therefore, the genetic code is ____

The start codon is ___

the 3' end of tRNA is common to all tRNAs. The common sequence is ___

the __ end on tRNA is covalently linked to an amino acid

the shape of a tRNA resembles a ___

the tRNA precursor is synthsized by RNA polymerase ___

tRNA goes through _ significant alterations

The alterations of tRNA include;

___ ____ attach the correct amino acods to the appropriate tRNAs

a _ step process links an amino acid to a tRNA

Step 1 of linking an amino acid to a tRNA invloves the amino acid reacting with ___ to produce a ____ amino acid releasing __

Step 2 of linking an amino acid to a tRNA involves the _____ amino acid reacting with ____ to produce an ______ tRNA and releases AMP

Like DNA polymerase tRNA is a ____ ____ enzyme due to its editing site

tRNA synthesase has 2 catalytic sites called the ____ site and the ____ site

In eukaryotes the TATA box is located at the ___ region and is recognized by the ___ protein

The GTF (Eukaryotes) ____ recognized the transcription start point

TFIIE has the function to ____

the tRNA precursor is a (functional/non-functional)_______ molecule

A growing amino acid chain grows from the ___ to the ___ end

A tRNA that has contributed its amino acid and has already dissociated is termed ____ tRNA

To form a peptide bond (incoming tRNA) ____ end reacts with the ____ end of the growing chain

The prokaryotic ribosome is named ____ and consists of 2 subunits ___ and ____; .The eukaryotic enzyme is called ___ and consists of 2 subunits ___ and ____

the prokaryotic 70s ribosome adds ____ amino acids per second. the eukaryotic 80s ribosome adds __ amino acids per second.

____ proteins play important roles in all 3 phases of translation

The elongation phase of translation involves ___ steps

formation of a peptide bond is catalyzed by _____ (this enzyme is the ____ rRNA molecule acting as the ____ in the large RSU)

_____ of the large RSU changes the relative position of the tRNAs. Shifts in the 5' to 3' direction

_____ of the small RSU for a distance of _ nucleotides

During elongation, translation factors hydrolyze ___ to provide energy

In prokaryotic translation ___ causes step 4 ( translocation of the small RSU)

the ____ phase established the correct reading frame for translation

In bacteria, a special initiator _____ carries _______

the original methionine is removed by _____

the initiator tRNA starts translation by binding to the ___ site of the ribosome

Initiator tRNA moves along the RNA in the __ to __ direction searching for the first ___

In bacterial translation, no 5' cap is present. Each bacterial mRNA has a _________ located several nucleotides upstream from a ______. This is called a ____

Bacterial mRNAs are usually ______. While Eukaryotic mRNAs are typically _____

Binding of the ___ factor to the _ site signals termination. Breaks the last peptide bond via ___

In bacteria trancription and translation are ___

A ____ is a eukaryotic mRNA that is translated simutaneously by many ____

This ____ inhibitor blocks binding of aminoacyl-tRNA to the A-site of the ribosome. Another inhibitor _____ blocks mRNA synthesis by binding preferentially to RNA polymerase II

In translation, some proteins begin folding during ____

Proteins with hydrophobic regions may ___ out of solution and form ____. Proper folding involved proteins called ___

In eukaryotes there are 2 major families of molecular chaperones the ____ family and the ___family known as ____

The ____ enzyme digests incompletely folded proteins. The proteins are tagged with ______ chain and are digested into ____ ____

A protein that is to be ubiquitied will give off a _____ signal for the _____ ligase to add ubiquiton to. The activation of the signal involves a ____ ____ in normal proteins.

There are __ destabilizing amino acids at the amino end

The only kind of proteins resistant to proteases

the most important step in regulation of gene expression