I. Exam Section I
A. Fundamental Cell Theory and Taxonomy (Chapter 1)
1. What is life? What are Cells?
a. The definition of ‘alive’
b. What ‘organisms’ do not fit the definition?
2. How Do We Classify Living Organisms?
a. The Domains and Kingdoms of life
b. Phylogeny to the Genus/Species level
3. The Universal Features of Cells
a. Basic Features of All Cells
b. Differences between Eukaryotes and Prokaryotes
B. The Age of Genomic Taxonomy (Chapter 1, 4, 7)
1. The Existing Genomes in the World Today
a. The number of bases and the complexity of their organization vary far more
than the number of genes
b. The conservation of critical functions and the base sequence of the genes that
code for them show that all cells are related evolutionarily
c. These close structure and function relationships allow us to gain information
about ourselves from a wide variety of organisms
2. Mechanisms of Genomic Change
a. Generation of new genes
1. New genes are generated from preexisting genes, no new synthesis
2. Mutation - Accidents/mistakes followed by non-random survival
3. Gene duplication provides an important source of genetic novelty
4. DNA Shuffling - Reassortment during homologous recombination
5. Horizontal transfer - between organisms, in the lab and in nature
6. Transposable elements
b. Disruption or loss of existing genes
1. Mutation - Accidents/mistakes followed by non-random survival
2. DNA Shuffling - Reassortment during homologous recombination
3. Transposable elements
c. Size of a genome reflects the relative DNA addition and DNA loss
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3. Gene families
a. Gene duplications give rise to families of related genes in a single cell
b. More than 200 gene families are common to all three domains
c. The function of a gene can often be deducted from its sequence
C. Introduction to Multicellularity (Chapter 19)
1. Regulation of Organism Size by Cell Number
a. Size of cells is relatively common across species
b. Number of cells determines size of organism
c. Cell number is a balance between cell division and cell death
2. Regulation of Extracellular Structure
a. Functions of the Extracellular Matrix
b. Variations in the Structure of ECM
c. Specialized Connective Tissues
d. Degradation is as important as deposition for maintenance
3. Regulation of Cell Adhesion
a. Most cells must adhere to survive
b. Cell-matrix adhesion
c. Cell-cell adhesion
4. Regulation of the Internal Aqueous Environment
a. Universal nature of the aqueous environment
b. Variability in homeostatic regulation
5. Regulation of Organism Function by Intercellular Communication
a. Evolution of cell sensing and cell communication
b. Contact-dependent signaling
c. Soluble- molecule signaling
d. Structure of signaling systems in multicellular organisms
6. Regulation of Organism Function by Cell Specialization
a. Anatomical organization in multicellular organisms
b. Epithelial vs. mesenchymal cell morphologies
c. Variability of cellular phenotype
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D. 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
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E. 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
F. Mutation and Repair (Chapter 5, 4)
1. Background on DNA mutations
a. Mutation rates are extremely low but are an essential component of
evolutionary change
b. The most common source of DNA mutation is error during replication
c. Environmental damage to the DNA is independent of DNA mutation but can
also be the underlying cause
2. Common types and mechanisms of DNA mutations (p. 263-265)
a. The alteration of a single base pair (point mutation) can result from chemical
damage followed by copying error
1. DNA damage leading to structural distortion of the base pair chemistry
2. DNA base pair changes (mutations) that result from structural distortion
can include transitions and transversions
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3. Potential outcomes in protein expression and phenotype
4. Several DNA repair systems can remove these mutations
b. The insertion or deletion of a single base pair (point mutation) during DNA
replication
1. Error in reading of template and/or addition of base to daughter strand
by DNA Polymerase
2. Frame shift mutation is the result
3. Potential outcomes in protein expression and phenotype
4. Several DNA repair systems can remove these mutations
c. Single-stranded and double-stranded breaks can result from electrophilic attack
from reactive oxygen species
1. ROS are generated by either endogenous metabolic processes or
exogenous ionizing radiation (like gamma and X-rays)
2. DNA mutation is the insertion or deletion of significant amounts of
DNA, including chromosomal deletions, additions
3. Potential outcomes range from gene shuffling in or across
chromosomes, gene inactivation, altered gene regulation, gene
duplication
4. DNA repair system that can remove these mutations include
Nonhomologous End-Joining and Homologous End-Joining
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