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BB1705 Biology of the Cell > Gene expression control > Flashcards

Gene expression control Flashcards

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1
Q

How can a cell control the proteins it makes?

A
  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)
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2
Q

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

A

Transcriptional control

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3
Q

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

A

RNA processing control

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4
Q

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 ?

A

RNA transport and localization control

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5
Q

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

A

Translational control

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6
Q

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

A

mRNA degredation control

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7
Q

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

A

Protein activity control

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8
Q

What are gene regulatory proteins?

A

Proteins that turn specific sets of genes on or off

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9
Q

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

A

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.

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10
Q

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 ______.

A

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.

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11
Q

Which groove in DNA is recognised by gene regulatory proteins?

A

The major groove

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12
Q

Define DNA binding domain

A

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

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13
Q

What are the types of DNA binding domain motifs?

A
  • helix-turn-helix
  • helix-loop-helix
  • zinc finger
  • leucine zipper
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14
Q

Describe the DNA binding protein motif helix-turn-helix

A
  • 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
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15
Q

What are homeotic selector genes?

A

Genes that play an essential part in orchestrating fly development

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16
Q

Define homeodomain

A

The class of proteins called the homeotic selector genes

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17
Q

Describe the DNA binding protein motif zinc fingers

A
  • It includes one or more zinc atoms as structural components
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18
Q

Describe the DNA binding motif leucine zipper

A
  • 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
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19
Q

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

A

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

20
Q

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

A
  • 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)
21
Q

What is epigenetic regulation?

A

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

22
Q

What are some examples of epigenetic mechanisms?

A

DNA methylation:

  • at CpG dinucleotides
  • of the gene promoter
23
Q

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

A

Histone acetylation activates transcription, and histone methylation silences transcription

24
Q

What is the activation domain?

A

The domain that activates transcription

25
Q

What is gene expression that is temporarily altered?

A

**Induced **expression

26
Q

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.

A

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.

27
Q

What is a** repressor**?

A

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

28
Q

What are **activator **proteins?

A

Proteins that activate genes

29
Q

What are some examples of “housekeeping” genes and proteins?

A
  • Structural proteins in chromosomes
  • RNA polymerases
  • DNA repair enzymes
  • Ribosomal proteins
  • Metabolic enzymes
30
Q

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

A

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

31
Q

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

A
  • developmental stage
  • differentiation stage
  • cell cycle stage
  • inducible expression
32
Q

What is the gene control region?

A

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

33
Q

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 _______.

A

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.

34
Q

How can gene expression be induced?

A
  • small molecules bind to specific DNA sequences in promoters
  • this activates transcription factors
  • transcription initiated
35
Q

What is an example of induced gene expression in humans?

A

The Glucocorticoid receptor protein

36
Q

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.

A

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.

37
Q

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

A

Through surface receptors which activate messengers that can activate transcription factors

38
Q

What is signal transduction?

A

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

39
Q

What are some of the post-transcriptional controls?

A
  • alternative splicing
  • alternative polyadenylation
  • tissue specific RNA editing
  • regulation of translation
40
Q

How can translation be regulated?

A
  • 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
41
Q

What’s an example of alternative polyadenylation?

A

The calcitonin gene

42
Q

What is the “untranslated region (UTR)”?

A

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

43
Q

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

A

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

44
Q

How can micro RNAs (miRNAs) control gene expression?

A

They can inhibit translation and cleave mRNAs

45
Q

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.

A

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.

46
Q

What protein facilitates the cleavage of mRNA by miRNA?

A

Argonaute

47
Q

How is a protein’s final function controlled?

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

BB1705 Biology of the Cell (11 decks)

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