Regulation of gene expression

Question 1

Why is it important to have regulation of gene expression?

Answer 1

Gene regulation regulates cellular regulations/functions.

Question 2

What is the overall process of regulation of gene expression?

Answer 2

DNA gene is TRANSCRIBED into primary RNA transcript. This undergoes POSTTRANSCRIPTIONAL MODIFICATION OF mRNA into a STABLE mRNA. Then, it gets TRANSLATED into a prot. The prot gets MODIFIED so it is active and functional. It will get TRANSPORTED to where its needed. After, the prot. gets DEGRADEDinto aas that are used for the prot. made (regulated step).

Question 3

Why is overall regulation of gene expression essential ?

Answer 3

A fraction of genes are expressed at any given time. One part of the gene is active and the other, nope. The level of the final product, functional protein, depends on regulation at multiple levels (of gene expression). Its ultimate function (amount of action in cell) is the result of the amount of genes expressed overall (the ones induced and repressed)

Question 4

What does mRNA stability mean?

Answer 4

It means that the mRNA can be either degraded or maintained.

Question 5

What are the 2 classes of genes?

Answer 5

• housekeeping gene (required for the maintenance of basic cellular function; constantly expressed in ALL cells, all the time, they need to be regulated, because they TRANSCRIBE a lot) ex. Transcription factors, Repressors, translation factors, RNA binding prot., ribosomal prot….
• Regulated gene (the rest of the genes, depends on the cell env., cell life… basically, the signals it received and how it responded to it.)

Question 6

What is negative regulation?

Answer 6

When the REPRESSOR binds to the DNA sequence, it INHIBITS TRANSCRIPTION by stoping access of RNA pol to promoter + assembly/activity of transcription complex.
So, when the repressor receives a molecular signal (hormone, covalent mod., allosteric regulator, interacting prot…), it makes it dissociate or associate to the DNA sequence, depending if it was bound or not initially.

-repressors have binding sites close to promoter, called operators.

Question 7

What is positive regulation?

Answer 7

It is an ACTIVATOR that will facilitate DNA transcription by aiding in RNA pol and promoter to INTERACT.
So, when the activator receives a molecular signal (hormone, covalent mod., allosteric regulator, interacting prot…), it makes it dissociate or associate to the DNA sequence, depending if it was bound or not initially. When not bound, translation is stopped.

-activator binding sites are close to promoter, while enhancers (eukaryotes) have distant binding sites

Question 8

In which direction is DNA transcripted (on strand)?

Answer 8

from 5’ to 3’

Question 9

Does the activator and repressor bind on the same site on the DNA sequence?

Answer 9

Nope. These regulatory sequences are located before promoter (activator binding site) and after promoter (repressor binding site).

Question 10

Can promoters be common for multiple gene sequences?

Answer 10

Yes. We can replicated many DNA in bacteria, because it can multiply multiple genes with ONE common promoter.

Question 11

How can the regulatory proteins interact with the nucleotides on the DNA sequence?

Answer 11

The aa on the proteins (like transcription factors) can form H-bonds with specific nucleotides on the DNA sequence. So depending on sequence, this can be read and recognized or not. (DNA binding sequences in transcription factors = Asn, Gln, Glu, Lys, Arg.)

Question 12

In procaryotes, what are some common types of DNA binding motifs? + characteristics?

Answer 12

• Helix-turn helix domain (20 aa long, with 2 alpha segments: one aa segment acts as ‘recognition helix’)
• Zinc finger domain (30 aa long; loops are coordinated by Zn2+; DNA binding is weaker, so prots have MANY Zn fingers within the domain- to stabilize their interaction with DNA; can also act as RNA-binding motif (read RNA))

-Homeodomain (found in Eukaryotes; 60 aa long; similar to helix-turn-helinx domains)
These are general domains on the transcription factors that interact with DNA: they have diff. Characteristics and thus, recognize different stuff.

Question 13

Except for these common DNA binding motifs in procaryotes, what does the rest of the protein do?

Answer 13

The rest part of the domains interact with other proteins (some prots are already on DNA and will affect gene expression: Co activators and corepressors–Interact with other Transcription Factors and co-regulators OR non DNA binding prots, (regulatory prots have prot interaction domains)

Question 14

What is the importance of having DNA binding motifs?

Answer 14

Since regularoty proteins are bound to it, it regulates gene expression; Also, Approx. 1557 Tfs regulate about 20 000 genes, because they can be put together in diff. Combinations.

Question 15

What are some regulating characteristics unique to eukaryotic systems ?(4)

Answer 15

• Access to promoters is restricted by chromatin structure (DNA + histones = chromatin. Histones package tightly DNA, but they also regulate gene expression; how tightly DNA should be or how loose it should be)
• Genes are regulated by Positive regulation ( is most common)
• Regulatory prots are usually multimeric (come in group)
• Transcription and translation are seperated by nucleus (procaryotes don’t have nuclei, so that’s why only in Eukaryotes)

Question 16

How does chromatin limit access to promoter? How can it be changed to accessible?

Answer 16

-Chromatin = DNA + histones (H1, H2A, H2B, H3, H4–fragments from nulcease-mediated degradation).

• Heterochromatin (tightly bound DNA around histones, no transcription) and euchromatin: loosely bound, so transcription occurs.
• Transcriptionnaly active chromatin– Deficient in H1
• Transcriptionnally active chromatin – varients of histones; a region may be enriched with H3.3 and H2AZ.

-Histone modifications (Replacement/removal/ bringing varients… ) use SWI/SNF enzymes; chromatin is modified when modification of histones occur: it regulates transcription.

Question 17

What are covalent modifications of histones used for ?

What enzymes modify histones?

Answer 17

• Covalent modifications are used for RECOGNITION BY ENZ. THAT MAKE CHROMATIN to make chromatin more accessible for transcription machinery.
• Histones are covalently modified: methylation (Lys and Arg), phosphorylation (Ser, Thr), acetylation (Lys), ubiquitination and sumoylation (Lys).

-Acetylation of N-ends of histones make histones less attracted to chromatin, so chromatin can be transcribed.
(HAT enz acetylates, while HDAC removes acetylation)
(SWI/SNF (eukaryotes) create small chromatin fragments + help binding of TF to initiate transcription.

Question 18

In procaryotes, what are some protein-protein interaction domains?

Answer 18

• Leucine zipper (Leu occurs at the 7th position in this domain; partially interacts with DNA (Lys/Arg))
• basic Helix-loop-helix (- also in eukaryote, One Leu residue; partially interacts with DNA (Lys/Arg)

Both help to dimerize proteins and activation of transcription processes.

Question 19

What is the most crucial interaction that affects transcription?

Answer 19

RNA polymerase and promoter interaction

Question 20

What is a specificity factor?

Answer 20

It is something that recognizes and binds to the promoter (TATA binding prot)

Question 21

What does the changes in chromatin structure do to transcription?

Answer 21

It activated transcription.

Question 22

What happens it DNA/chromatin is methylated on it’s Cytosine residue of the CpG sequence?

Answer 22

It inhibits transcription

Question 23

How are eukaryotic promoters regulated?

Answer 23

• specific = decreases chances of random function to occur.
• the promoter (tata box) needs enhancers or UAS to start whole process.
• successful RNA Pol II to promoter interaction needs: basal transcription factors, DNA-binding transactivators and coactivators.

Question 24

Successful RNA Pol II to promoter interaction needs: basal transcription factors, DNA-binding transactivators and coactivators. What are these?

Answer 24

btf: they are required at the promoter site to form the pre-initiation complex

D-bt: they are sensitive to signal molecules; they are enhancers and UAS that help activators bind. They interact with HAT or SWI/SNF enz. to remoel chromatin+ make promoter available + make Pol II and its TFs stable for transcription.

c: are mediators and TFIID; they allow communication between DNA-binding transactivators and the Pol II complex and the TFs)

Question 25

How do repressors act upon transcription?

Answer 25

It signals to the UAS/enhancers and to mediators and to the DNA-binding transactivators (stop interacting with histones/chromatins) = prevent formation of pre-ini. complex.

Question 26

In eukaryotic gene expression start, how do all the complexes assemble on the DNA strand?

Answer 26

1-enhancer binds to DNA+ activator too
2-mediator come in
3- TATA binding prot and TFIIB bind to the promoter sequence
4-all the other TFs bind to the promoter and form the pre-ini. complex!

Question 27

Transactivators have transactivation domains. What are these? (2)

Answer 27

These are domains that activate the mediators;

• SP1 prot– has Gln-rich residues (the most common type of activator proteins have GLn-rich domains)
• CTF1– Proline-rich domain

Question 28

How does inter and intracellular signals alter eukaryotic gene expression?

Answer 28

Some intracellular receptors can receive intracellular signals, which make a hormone-receptor complex. This complex binds to HREs, which are highly specific DNA sequences and can increase or decrease gene expr.

Question 29

What are the 3 components of a nuclear receptor?

Answer 29

• DNA recognition domain (with zinc finger)
• Protein-protein interaction domain (transcription activation)
• Hormone/signal binding domain

Question 30

Eukaryotic mRNAs are under translational repression, Why?

Answer 30

When in need of a prot production, a (long) translationally repressed mRNA in the cytoplasm can be activated for translation without delay!

Question 31

What are three examples of stuff binds/gets modified and stops transcription?

Answer 31

• the binding of transitional repressors at the 3’ UTR
• the binding of prots such as 4E-BPS, which stops the interaction between Elf4E and Elf4G at the initiation complex
• the phosphorylation by PK of initiation factors at the promoter

Question 32

What is splicing? What is alternative splicing?

Answer 32

S: removal on introns from the mRNA strand to make a prot.
AS: process can create a range of unique proteins by varying the exon composition of the same mRNA. Exons can be extended or skipped, or introns can be retained.

Question 33

What are microRNA’s ?

Answer 33

-They prevent RNA translation;
We never want dsRNA, so we have si-RNA that degraes it
We want to be protected against RNA invader, so we have st-RNA.