II. Lecture Section 2
A. CELL SPECIALIZATION: Regulation of Transcription (Chapter 4, 6, 7)
1. Review of Chromosomal, Gene and RNA Architecture
a. Structure of the nucleosome core particle reveals how DNA is packaged
1. Heterochromatin is highly organized and resistant to gene expression
2. Nucleosomes are usually packed together into compact chromatin
b. Chromosomal gene arrangements
1. Chromosomes contain long strings of genes
2. Genes can reside on either strand
c. Single gene components
1. Coding sequences are exons, noncoding are introns
2. Signals in DNA tell RNA polymerase where to start- stop
d. Nuclear RNA, mRNA and Protein
1. The 5’ cap, intron-exon structure and the 3’ polyadenylation site
2. nRNA splicing produces mRNA in eukaryotes
e. Other RNA molecules
1. The translational apparatus
2. RNA regulator molecules work in the nucleus and in the cytosol
f. Fast review of transcription
1. Portions of DNA sequence are transcribed into RNA
2. Transcription produces RNA complementary to one strand of DNA and
cells produce several types of RNA
2. Cell-Specific Regulation of Transcription in Eukaryotes
a. Nucleosome and histone modification regulates chromatin structure
1. DNA can be wrapped and unwrapped spontaneously and with ATP
2. Histones are covalently modified to control gene accessibility
3. The “Histone Code” hypothesis, code-readers and code-writers
b. Direct DNA methylation regulates promoter availability
1. Usually shuts down a promoter
c. Epigenetic modification can be copied and inherited
1. Changes to chromatin structure can be directly inherited
2. Add unique features to eukaryotic chromosome function
d. Transcription factors regulate promoter activation
1. Transcription initiation in eukaryotes requires many proteins
2. RNA polymerase II requires general transcription factors
e. Specialized transcriptional activities
1. Noncoding RNAs are synthesized and processed in the nucleus
2. Regulatory RNA are transcribed by specific RNA Pol enzymes
B. CELL SPECIALIZATION: RNA and Protein Regulation (Chapter 4, 6, 7, 10)
1. nRNA to (x)RNA to protein (review)
a. Selective removal of introns and splicing of exons makes mRNA out of nRNA
b. The genetic code translates nucleic acids into amino acids
c. The complex ribosome (rRNA) uses the mRNA template and tRNA codons to
translate peptides from the mRNA sequence
2. Cell-Specific Regulation of mRNA Production
a. Co/post-transcriptional RNA modification can effect amount and type of
protein expressed
1. 5’ capping and 3’ polyadenylation determine how nRNA is handled
2. Splicing different mRNAs from the same nRNA using different exons
allows cells to choose the protein they will make
b. Selective degradation of RNA
1.Prevention of export of incomplete or intronic RNA from the nucleus
2.Prevention of translation of damaged or unwanted RNA in the cytosol
3. Cell-Specific Regulation of Peptide and Protein Production
a. Regulation of translation
1. 5’ and 3’ untranslated regions of mRNAs control their translation
2. Global regulation of translations by initiation factor phosphorylation
3. Small noncoding RNA transcripts regulate many animal and plant genes
4. RNA interference is a cell defense mechanism
b. Co-/Post-translational protein regulation
1. Folding and membrane insertion
2. Covalent modifications
3. Polymer assembly
4. Proteolytic modifications
C. Protein Structure and Function (Chapter 3, 6, 16)
1. Protein Biochemistry Dictates Their Functional Activities
a. Final amino acid position results from the conformation of lowest energy
1. Driven by the polar aqueous and non-polar membrane phases
2. Self- and regulated- assembly of large structures
3. Modularity of structure is common: Protein domains and families
b. The sequence and chemistry of amino acid side chains gives the protein its
shape and the shape gives the protein its function
1. Basic protein characteristic, such as binding selectivity, chemical and
enzymatic reactivity and protein conformation, are the result
2. Regulation of Protein Structure and Function is One of the Most Fundamental Means
by which Cells Control Their Activities
a. Cells can control protein activity directly by mechanisms that target the protein
itself
1. Allosteric: Proteins with two or more binding sites, wherein activity
away from the active site will regulate activity at the active site
2. Cells can start and stop a protein’s activity by changing its structure
through the addition of a covalent subgroup
3. Cells can start and stop a protein’s activity by proteolytic cleavage
4. Some regulatory mechanisms involve multiple strategies
b. Cells can control protein activity indirectly by altering the other molecules that
share their environment
1. Cells can start and stop a protein’s activity by regulating the presence of
a critical binding partner
2. Cells can start and stop a protein’s activity by blocking its binding site
3. Cells can start and stop a protein’s activity by regulating the enzymes
that make active polymers from inactive subunits
4. Cells can start and stop a protein’s activity by regulating the scaffolded
interaction of the subunits of protein machines