Gene expression control

Question 1

How can a cell control the proteins it makes?

Answer 1

1. Controlling when and how often a given gene is transcribed (transcriptional control)
2. Controlling the splicing and processing of RNA transcripts (RNA processing control)
3. Selecting which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localized (RNA transport and localization control)
4. Selecting which mRNAs in the cytoplasm are translated by ribosomes (translational control)
5. Selectively destabilizing certain mRNA molecules in the cytoplasm (mRNA degradation control)
6. Selectively activating, inactivating, degrading, or locating specific protein molecules after they have been made (protein activity control)

Question 2

What type of control controls when and how often a given gene is transcribed?

Answer 2

Transcriptional control

Question 3

What type of control controls the splicing and processing of RNA transcripts?

Answer 3

RNA processing control

Question 4

What type of control selects which completed mRNAs are exported from the nucleus to the cytosol and determines where in the cytosol they are localized ?

Answer 4

RNA transport and localization control

Question 5

What type of control selects which mRNAs in the cytoplasm are translated by ribosomes?

Answer 5

Translational control

Question 6

What type of control selectively destabilises certain mRNA molecules in the cytoplasm?

Answer 6

mRNA degredation control

Question 7

What type of control selectively activates, inactivates, degrades, or locates specific protein molecules after they have been made?

Answer 7

Protein activity control

Question 8

What are gene regulatory proteins?

Answer 8

Proteins that turn specific sets of genes on or off

Question 9

The ______** of the double helix is studded with DNA sequence _________ that ____ _________ proteins can recognize without having to ____ **the double helix.

Answer 9

The **outside **of the double helix is studded with DNA sequence **information **that **gene regulatory **proteins can recognize without having to **open **the double helix.

Question 10

The edge of each base pair is exposed at the ______ of the _______ _____, presenting a distinctive pattern of hydrogen bond _______, hydrogen bond _________, and _________ patches for proteins to recognize in both the major and minor ______.

Answer 10

The edge of each base pair is exposed at the surface of the double helix, presenting a distinctive pattern of hydrogen bond donors, hydrogen bond acceptors, and hydrophobic patches for proteins to recognize in both the major and minor groove.

Question 11

Which groove in DNA is recognised by gene regulatory proteins?

Answer 11

The major groove

Question 12

Define DNA binding domain

Answer 12

An independently folded protein domain that contains at least one motif that recognizes double- or single-stranded DNA.

Question 13

What are the types of DNA binding domain motifs?

Answer 13

• helix-turn-helix
• helix-loop-helix
• zinc finger
• leucine zipper

Question 14

Describe the DNA binding protein motif helix-turn-helix

Answer 14

• It is constructed from two alpha helices connected by a short extended chain of amino acids, which constitutes the “turn”
• The two helices are held at a fixed angle
• The more C-terminal helix is called the recognition helix because it fits into the major groove of DNA

Question 15

What are homeotic selector genes?

Answer 15

Genes that play an essential part in orchestrating fly development

Question 16

Define homeodomain

Answer 16

The class of proteins called the homeotic selector genes

Question 17

Describe the DNA binding protein motif zinc fingers

Answer 17

• It includes one or more zinc atoms as structural components

Question 18

Describe the DNA binding motif leucine zipper

Answer 18

• Two alpha helices are joined together to form a short coiled-coil
• The helices are held together by interactions between hydrophobic amino acid side chains (often on leucines) that extend from one side of each helix

Question 19

Heterodimerization is an example of ___________ ________, in which combinations of different proteins, rather than individual proteins, control a cell process

Answer 19

Heterodimerization is an example of combinatorial control, in which combinations of different proteins, rather than individual proteins, control a cell process

Question 20

Describe the DNA binding motif helix-loop-helix (HLH)

Answer 20

• Consists of a short alpha helix connected by a loop to a second, longer alpha helix
• this two-helix structure binds both to DNA and to the HLH motif of a second HLH protein
• The second HLH protein can be the same (creating a homodimer) or different (creating a heterodimer)

Question 21

What is epigenetic regulation?

Answer 21

Regulation by epigenetic changes that can modify the activation of certain genes, but not the sequence of DNA

Question 22

What are some examples of epigenetic mechanisms?

Answer 22

DNA methylation:

• at CpG dinucleotides
• of the gene promoter

Question 23

What are the two ways histones can be modfied to make changes in transcription?

Answer 23

Histone acetylation activates transcription, and histone methylation silences transcription

Question 24

What is the activation domain?

Answer 24

The domain that activates transcription

Question 25

What is gene expression that is temporarily altered?

Answer 25

**Induced **expression

Question 26

The extent of the differences in ____ \_\_\_\_\_\_\_\_\_ between different cell types may be roughly gauged by comparing the _______ composition of cells in the liver, heart, brain and so on using the technique of \_\_\_-\_\_\_\_\_\_\_\_\_\_ gel electrophoresis.

Answer 26

The extent of the differences in **gene expression** between different cell types may be roughly gauged by comparing the **protein **composition of cells in the liver, heart, brain and so on using the technique of **two-dimensional** gel electrophoresis.

Question 27

What is a** repressor**?

Answer 27

A protein, when in its active form, switches genes off

Question 28

What are **activator **proteins?

Answer 28

Proteins that activate genes

Question 29

What are some examples of "**housekeeping**" genes and proteins?

Answer 29

* Structural proteins in chromosomes * RNA polymerases * DNA repair enzymes * Ribosomal proteins * Metabolic enzymes

Question 30

Some genes are needed in only ______ tissues, therefore a more specific technique is needed to detect them called ____ \_\_\_\_\_\_\_\_\_\_\_\_.

Answer 30

Some genes are needed in only **certain** tissues, therefore a more specific technique is needed to detect them called **mass spectrometry**.

Question 31

Some genes will only be expressed at certain stages of a cell's life. What are some of these stages?

Answer 31

* **developmental** stage * **differentiation** stage * **cell cycle** stage * inducible expression

Question 32

What is the **gene control region?**

Answer 32

The whole expanse of DNA involved in **regulating** and **initiating transcription** of a gene.

Question 33

The term **gene control region **is often used to describe the whole expanse of DNA involved _________ and ________ transcription of a \_\_\_\_, including the \_\_\_\_\_\_\_\_, where general transcription factors and the polymerase assemble, and all of the \_\_\_\_\_\_\_\_ \_\_\_\_\_\_\_\_\_\_** **to which gene regulatory proteins bind to control the rate of the assembly process at the \_\_\_\_\_\_\_.

Answer 33

The term **gene control region **is often used to describe the whole expanse of DNA involved **regulating** and **initiating** transcription of a **gene**, including the **promoter**, where general transcription factors and the polymerase assemble, and all of the **regulatory sequences **to which gene regulatory proteins bind to control the rate of the assembly process at the **promoter**.

Question 34

How can gene expression be induced?

Answer 34

* small molecules bind to specific DNA sequences in promoters * this activates transcription factors * transcription initiated

Question 35

What is an example of induced gene expression in humans?

Answer 35

The **Glucocorticoid receptor protein**

Question 36

In response to \_\_\_\_\_\_\_\_\_\_\_, liver cells increase the expression of many different genes, one of which encodes the enzyme _______ \_\_\_\_\_\_\_\_\_\_\_\_\_. These genes are all regulated by the binding of the _____________ \_\_\_\_\_\_\_\_-\_\_\_\_\_\_\_\_complex to a regulatory sequence in the DNA of each gene. When the hormone is no longer present, the ___________ of the genes drop to its normal level.

Answer 36

In response to **glucocorticoids**, liver cells increase the expression of many different genes, one of which encodes the enzyme **tyrosine aminotransferase**. These genes are all regulated by the binding of the **glucocorticoid hormone**-**receptor** complex to a regulatory sequence in the DNA of each gene. When the hormone is no longer present, the **expression** of the genes drop to its normal level.

Question 37

Some molecules are too big to pass through the plasma membrane, how can they affect gene expression?

Answer 37

Through **surface receptors** which activate **messengers** that can activate transcription factors

Question 38

What is **signal transduction**?

Answer 38

The conversion of a signal outside the cell to a functional change inside the cell

Question 39

What are some of the post-transcriptional controls?

Answer 39

* alternative splicing * alternative polyadenylation * tissue specific RNA editing * regulation of translation

Question 40

How can translation be regulated?

Answer 40

* cis-acting regulatory sequences present in untranslated regions (**UTRs**) of mRNA: * targeted by trans-acting **RNA binding proteins **to promote or regulate longetivity of mRNA * targeted by **micro RNA (miRNA) **to inhibit translation or degrade RNA

Question 41

What's an example of **alternative polyadenylation**?

Answer 41

The calcitonin gene

Question 42

What is the "**untranslated region (UTR)**"?

Answer 42

The three prime untranslated region (3'-UTR) is the section of messenger RNA (mRNA) that immediately follows the translation **termination** codon

Question 43

What's an example of translation regulation in response to external stimuli?

Answer 43

iron / IRE-BP / IRE in **ferritin** and TfR mRNA

Question 44

How can **micro RNAs (miRNAs)** control gene expression?

Answer 44

They can **inhibit translation** and **cleave mRNAs**

Question 45

Once made, miRNAs base-pair with specific _____ and regulate their stability and their translation. The miRNA _________ are synthesised by RNA polymerase _ and are capped and \_\_\_\_\_\_\_\_\_\_\_\_\_. They are then processed and assembled with \_\_\_\_\_\_\_ to form a RISC (\_\_\_**-**\_\_\_\_\_\_\_\_ _________ \_\_\_\_\_\_\_). The RISC then seeks out complementary mRNA sequences and targets the __ end of the UTRs.

Answer 45

Once made, miRNAs base-pair with specific **mRNAs **and regulate their stability and their translation. The miRNA **precursors **are synthesised by RNA polymerase **II **and are capped and **polyadenylated**. They are then processed and assembled with **proteins **to form a RISC (**RNA-induced silencing complex**). The RISC then seeks out complementary mRNA sequences and targets the **3'** end of the UTRs.

Question 46

What protein facilitates the cleavage of mRNA by miRNA?

Answer 46

Argonaute

Question 47

How is a protein's final function controlled?

Answer 47

* cleavage (e.g. proinsulin → insulin) * presence of inhibitors of protein activity * other functional modifications (glycolysation, phosphorylation) * control of protein degredation