Mbb 331 Exam 3

Front 1

Name the general transcription factors and the order of which they bind to the initiation complex in transcription by RNAPII

Back 1

TFIID, TFIIA, TFIIB, TFIIF (+ RNA pol II), TFIIE, TFIIH

Front 2

Which RNA are products of RNAPII activity?

Back 2

snRNA (small nuclear RNA) & hnRNA (mRNA precursors)

miRNA precursors

Front 3

Which inhibitor was first used to identify the activity of RNA polymerases in eukaryotes?

Back 3

α-amanitin

Front 4

What elements are apart of the core classII promoter?

Back 4

TATA box, BRE, Inr, DCE, DPE, MTE

(Upstream elements are several kb away from the initiation start site and ARE NOT apart of the core promoter elements)

Front 5

What was the experiment used to identify the RNAPII subunits?

Back 5

Co-Immunoprecipitation via epitope tagging.

The subunits have been isolated by epitope tagging one subunit of the complex. The antibody to this epitope is added to cell lysates, allowing it to bind to its epitope and any other associated proteins.

Front 6

Which transcription factors are important for promoter clearance?

Back 6

TFIIH & TFIIE

-TFIIE recruits TFIIH which phosphorylates the CTD of the RNAP, allowing the enzyme to shed the general TFs and clear the promoter

Front 7

What can gene regulation in eukaryotes be influenced by?

Back 7

- environmental conditions

- developmental stage

- tissue or cell type

Front 8

What is a transcription factor?

Back 8

A protein that binds to certain gene sequences, and affects the ability of RNA polymerase to transcribe a gene

Front 9

Do all eukaryotic gene promoters contain a TATA box?

Back 9

No, some eukaryotic promoters are TATA-less, in which TBP of TFIID is tethered to TAFs bound to the Inr

Front 10

What modification must occur to allow RNAP II to leave the promoter?

Back 10

Phosphorylation of RNAPII CTD by TFIIH

Front 11

What is the function of TFIIA?

Back 11

To bind upstream of TFIID and stabilize the interaction of TBP at the TATA box

Front 12

What else asides from promoter clearance, can phosphorylation of the RNAPII CTD allow it to do?

Back 12

RNA processing

Front 13

Describe enhancers

Back 13

Enhancers are cis DNA elements that bind specific transcription factors called activators. They are usually several kb up or downstream from the initiation start site and are orientation and position independent. Activators bound to enhancers increase gene transcription.

Front 14

True or false: The whole TFIID complex can respond to a wide variety of activators

Back 14

True

Front 15

What type of DNA is most susceptible to digestion by DNAse-I?

Back 15

"naked DNA" unbound by histones

Front 16

What are zinc finger motifs comprised of?

Back 16

An antiparallel β sheet (two Cys residues) followed by an α helix (Two His residues), linked by a zinc ion.

Zinc fingers usually occur in ~2-9 tandem repeats

Front 17

What are steroid hormone receptors?

Back 17

They can act as activators or repressors of transcription that are controlled by ligand binding. \

Eg. Thyroid hormone receptors bind to the thyroid hormone to recruit activators and increase transcription. In the absence of thyroid, the receptor acts as a repressor as it recruits co-repressors and HDAc

Front 18

What is a nucleosome

Back 18

A nucleosome is a basic unit of DNA packaging in eukaryotes. It consists of a segment of DNA (165bp) wrapped around a histone core octamer

Front 19

What is histone H1 and what is its role in DNA regulation?

Back 19

It is not a part of the core histones, but is important to induce tighter wrapping of DNA around nucleosomes, and therefore down regulation of genes

Front 20

Which regions in active genes are considered to be DNase I hypersensitive?

Back 20

Nucleosome free regions

Front 21

How to proteins that participate in transcription interact with the histone core?

Back 21

The proteins bind the acetyl groups on the histone tails via their bromodomains.

Acetylation of histones is usually correlated to gene activation, thus bromodomain proteins are usually activators of transcription

Front 22

What is the technique used to determine that a physical association exists between transcription factors, co-repressors, and histone deacetylases?

Back 22

Immunopreciptation - One component of the tertiary complex is tagged with a epitope tag, and washed with an antibody for the certain tag.

Front 23

How may methylation of histones result in the formation of heterochromatin?

Back 23

Methyl groups added to histone tails by histone methyltrasnferases amplify the positive charge which increases the interaction with DNA. The tighter the DNA- histone interaction, the more condensed DNA becomes. Chromodomains of repressor proteins can bind to these methyl group, further repressing gene expressing.

Front 24

What its the methylation state of heterochromatin?

Back 24

hypermethylated. Methylation usually corresponds to gene repression

Front 25

How does the FACT complex facilitate chromatin transcription?

Back 25

The subunits of the FACT complex Spt16 and SSRP1 disassemble the core histone by removing the H2A and H2B dimers ahead of the transcription machinery. Once RNAPII has moved through, the FACT complex uses its chaperone activity to reassemble the core nucleosome with the help of Spt6

Front 26

What is genomic importing? Give an example.

Back 26

Genomic imprinting is and example of the effects of DNA (NOT histone) methylation whereby only one copy, from either the mother or father, of specific genes are expressed

Front 27

How does formation of the 5' cap to a newly formed mRNA transcript occur?

Back 27

Immediately after the transcript emerges, guanalyl transferase adds a modified guanine residue to the 5' end in a reverse 5'-5' orientation

Front 28

What is the sequence recognized by the CPSF during 3' processing?

Back 28

CPSF (Cleavage and polyadenylation specificity factor) recognizes the AAUAAA consensus sequence as a part of the 3' processing complex

Front 29

How many polyadenylation benefit/affect an mRNA transcript?

Back 29

- contribute to mRNA stability

- contribute the translational initiation

- be required for splicing nearest the 3' end

Front 30

How are introns removed from pre-mRNA

Back 30

They are removed in a specific order, not in a linear fashion. There may be combinations are which introns are removed, but the introns are never removed at random to produce more invariants.

Front 31

What occurs during the first trasesterificatiron reaction of nuclear mRNA splicing?

Back 31

The 2'OH of the conserved A in the branch site attacks the phosphate of the conserved G in the 5' splice site. This breaks the intron-exon bond and creates a lariat structure with the 5' splice site G phosphodiester bound to the invariant A.

Front 32

True or false: U1 snRNA binding to the 5' splice site is required for spliceosome assembly and splicing

Back 32

true

Front 33

Which two snRNPs participate in the first transesterification reaction during formation of the C1 complex?

Back 33

U2 and U2 (U2/U6 catalysis activated by dissociation of U4)

Front 34

What does control of alternative splicing involve?

Back 34

- repressors, which cause exon skipping

- enhancers, which increase recognition of weak splice sites

- splicing factors which modulate spliceosome factors

Front 35

In the presence of purified polyA binding protein, eukaryotic mRNAs form _________ visible with force field electron microscopy

Back 35

circular structures

Front 36

The spliceosome cycle includes the assembly, splicing activity and disassembly of the spliceosome. Assembly begins with the binding of ___ to the splicing substrate to form a commitment complex. ___ is the next snRNP to join the complexly pairing with the branch site (requires ATP). When ___ dissociates from ___, it displaces ___ at the 5' splice site. This ATP dependent step activates the spliceosome, in which ___ brings the two exons together.

Back 36

U1, U2, U6, U4, U1, U5

Front 37

In contrast to siRNA, miRNA

Back 37

- Can reduce target mRNA translation without transcript degradation

- Are normal and naturally occurring (cis)

- Can imperfectly pair with target RNA (usually at 3' UTRs)

Front 38

True or false: Riboswitches can regulate the expression of a gene at the level of transcription or translation.

Back 38

True

Front 39

Explain the components of a riboswitch and their roles.

Back 39

Each riboswitch is made up of two components, the aptamer and the expression platform. The aptamer binds a small molecule ligand, and in response, undergoes a conformational change. The conformation change of the aptamer causing a change in the adjoining expression platform where an RBS is usually contained.

Front 40

During siRNA amplification, the si-RISC complex can recruit RNA-dependent RNA polymerases (RdRP) to the targeted DNA. The siRNA itself acts as a primer for the RdRP to transform the target into dsRNA, which itself can be acted on by ___

Back 40

Dicer

Front 41

Why has RNAi become a powerful tool for manipulating gene expression?

Back 41

- it can target specific genes for inactivation

- it exploits naturally occurring process for DNA degradation

- it can target degradation of specific mRNA

Front 42

What is the net result after the pre-initiation complex of prokaryotic translation initiation disassembles?

Back 42

An intact 70s ribosome paired at the start codon, with the initiator tRNA carry fMet in the P-site and an empty A-site

Front 43

How does the eukaryotic pre-initiation complex for translation find the appropriate start codon.

Back 43

The eukaryotic 40s ribosomal subunit binds to the 5' cap, and with the help of eIF1 and eIF1A, scans downstream to find the first favourable start codon that satisfies Kodaks rule.

Unlike prokaryotic translation, there is nonrecognition of a Shine-Dalgarno sequence

Front 44

Several eukaryotic initiation factors have similar roles to prokaryotic initiation factors. eIF1 and eIF5 together bind to the ___ and act analogous to prokaryotic ___, while eIF1A binds to the ___ and acts analogous to prokaryotic ___, thus preventing the large ribosomal subunit from binding.

Back 44

E site, IF3, A site, IF1