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Isaak: Biochemistry MBS > Lecture 5: Regulation of Gene Expression > Flashcards

Lecture 5: Regulation of Gene Expression Flashcards

1
Q

Constitutive Genes

A

Aka “housekeeping genes.”

Genes expressed in all cells because they provide basic functions needed for sustenance of all cells.

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2
Q

Global Regulatory Mechanism

A

Not specific for a given gene, but affect the expression of many genes.

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3
Q

Nucleosome

A

A complex of an octomer of histones with wound DNA.

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4
Q

Heterochromatin

A

Transcriptionally inactive and not accessible to limiting amounts of DNase I.

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5
Q

Euchromatin

A

Transcriptionally active and accessible to limiting amounts of DNase I.

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6
Q

Hypersensitive Sites

A

Sections of chromatin (usually in control regions) that are very sensitive to DNase I.

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7
Q

Locus Control Region

A

Appears to regulate chromatin organization over chromosomal domains.

Is where sensitivity to DNase I begins along the gene.

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8
Q

SWI-SNF

A

Protein complexes that can alter chromatin structure.

“Pushin’ nucleosomes around.”

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9
Q

Where can SWI-SNF complexes be found?

A

Globally.

However, it is thought that some complexes may target specific genes.

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10
Q

Histone Acetylation

A

Occurs on LYSINE residues, which leads to unfolding of chromatin.

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11
Q

What enzyme is responsible for acetylation of lysine residues on chromatin?

A

Histone Acetyltransferase (HAT)

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12
Q

HAT

A

Histone Acetyltransferase; a transcriptional “activator.”

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13
Q

HDAC

A

Histone Deacetylase; a transcriptional “repressor.”

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14
Q

What is the role of methylation on promoter regions?

A

More methylation is associated with diminished gene expression.

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15
Q

Hypermethylation

A

Diminished gene expression.

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16
Q

Hypomethylation

A

Increased gene activity.

17
Q

CpG Methylation

A

A key mediator of X-inactivation and other epigenetic effects.

18
Q

What is the significance of understanding CpG?

A

It provides a mechanism for producing heritable changes in gene expression that does not depend on DNA sequence changes.

19
Q

DNA Methyltransferase

A

Adds a methyl group to the fifth carbon of atom of some, but not all cytosine residues in CpG dinucleotides.

20
Q

Why are CpG sequences hotspots for mutations?

A

Deamination of 5-methyl cytosine produces thymine, which is not “noted” by repair machinery.

21
Q

CpG Island

A

They are long stretches of CpG-rich DNA in the promoter regions of genes that are actively transcribed in all cell types.

22
Q

What % of human genes have a CpG island near their promoter?

A

50%

23
Q

True or False?

CpG islands are almost always methylated, regardless of gene activity.

A

False.

They almost always LACK methylation, regardless of gene activity.

24
Q

Inducible Gene Expression

A

Gene expression that is influenced by various signals (developmental, nutritional, hormonal) or short transcription factors that interact with promoter or enhancer elements.

25
Q

Steroid Hormone

A

Derived from cholesterol; includes estrogen, testosterone, and progesterone.

Soluble in lipid membranes.

26
Q

How do steroid hormones exert their effects?

A

Bind to intracellular steroid receptor, which is usually a site-specific DNA binding molecule which binds to response (or enhancer) elements.

27
Q

Intracellular Steroid Receptor

A

Binds steroids in the cytoplasm and goes to the nucleus.

28
Q

Response (enhancer) Elemetns

A

Binding sites on DNA for the hormone-steroid receptor.

29
Q

What is a way to detect those mRNAs that have aberrant expression?

A

DNA Microarrays.

30
Q

DNA Microarray: Preparation

A
  1. Glass slides prepared with DNA of interest after it has been denatured to ssDNA ready for hybridization.
31
Q

DNA Microarray: RNA Isolation

A
  1. Must have two cell types to compare. Therefore, mRNA is converted into cDNA. The cDNA from that given cell type is colored with a fluorescent probe.
32
Q

DNA Microarray: Hybridization

A
  1. The cDNAs are pooled and hybridized to the DNA on the microarrays. Microscopes are used to measure amount of hybridization based on colors.
33
Q

After a microarray has been run, how can one tell if there are abnormal levels of mRNA?

A

The spot will not be a blend of two colors, but will be one of the primary colors.

34
Q

What is RNA-Seq?

A

Relatively new method used to determine the composition and quantity of RNA present in a cell; relies on NGS and is replacing DNA microarray.

35
Q

RNA interference (RNAi) via small interfering RNA (siRNA)

A

Targeted destruction of a particular mRNA via complementarity to double stranded RNA activators.

36
Q

RISC

A

RNA-induced silencing complex.

37
Q

What is the normal function of the siRNA pathway?

A

Antiviral?

Isaak: Biochemistry MBS (11 decks)

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