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II.  Regulation of Transcription Initiation

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II.  Regulation of Transcription Initiation

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Selective degradation = the process by which the length of time each protein functions in the cell is strictly regulated

To mark a specific protein for destruction - cell adds molecules of ubiquitin (small protein)

Proteasomes = giant protein complexes which then recognize the ubiquitin tagged proteins and degrade them

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IVA.  Protein Processing and Degradation

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IVA.  Protein Processing and Degradation

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Final chances for controlling gene expression happen after translation occurs

Regulatory proteins activated or inactivated by reversible addition of phosphate groups

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Life span of the mRNA molecules in the cytoplasm is also important in determining the pattern of protein synthesis in a cell

mRNA degradation in prokaryotes = short life span quickly degraded by enzymes within few minutes of synthesis

mRNA degradation in eukaryotes = long life span - can survive for hours, days, or even weeks

Nucleotide sequences, often in the UTR, affect how long an mRNA remains intact

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RNA processing in nucleus - allows regulation of gene expression

Alternative RNA splicing = different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

Allows the "repertoire" of eukaryotic genome to expand

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Distal control elements (called enhancers) may be thousands of nucleotides upstream or downstream of the gene or even within an intron.

Enhancers = distal control elements upstream or downstream of a gene or even within an intron that can, in eukaryotes, control the rate of transcription

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IIB.  Transcription Factors (general and specific) 

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IIB.  Transcription Factors (general and specific) 

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Transcription factors required for eukaryotic RUNA polymerase to initiate transcription

General transcription factors = essential for all protein-coding genes - bind to TATA box to initiate transcription

Specific transcription factors = in eukaryotes - high levels of transcription of particular genes that is controlled depends on control elements with set of proteins (specific transcription factors)

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Control elements = segments of noncoding DNA that serve as binding sites for the proteins called transcription factors, which in turn regulate transcription

Control elements are extremely important for the precise regulation of gene expression seen in different cell types

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IB.  DNA Methylation (Epigenetic Inheritance)

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IB.  DNA Methylation (Epigenetic Inheritance)

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Sets of enzymes have the ability to methylate certain bases in the DNA itself. Long stretches of inactive DNA are generally more methylated than regions of actively transcribed DNA. Removal of the methyl groups can turn on some genes

DNA methylation is essential in some organisms and cases for long-term inactivation of genes for cell differentiation in embryonic stage

Epigenetic inheritance = inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence (methylation is one such mechanism)

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Histone Acetylation = acetyl groups are attached to lysines in histone tails

Histone Deacetylation = removal of acetyl groups

When lysines are acetylated, the histone tails do not bind to neighboring nucleosomes. When binding does not occur, chromatin has a looser structure. This gives transcription proteins easier access to genes in acetylated regions.

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II. Regulation of Transcription Initiation

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II. Regulation of Transcription Initiation

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Differential Gene Expression is what causes specialized cells to express specific genes - even though all cells have the same genome. Differential gene expression can be controlled by several stages in eukaryotic cells. The function of a cell is determined by the appropriate set of genes that are being expressed.