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Biology Book Notes 1.

1 Roots of Biology 1) Life unified by common theme a) Organism must be distinct in some way from its environment (lipid bilayer) b) Store information in a stable way and use this information to determine its characteristic features (nucleic acid, DNA) c) Reliably/faithfully replicate and pass information from one generation to the next d) Require a source of energy from their surroundings to grow and reproduce 2) Constructed from common molecular building blocks a) Nucleic acids i) Constructed from nucleotides (1) Guanosine (G) (2) Adenosine (A) (3) Thymidine (T) (4) Cytidine (C) b) Proteins i) Constructed from amino acids c) Lipids i) Joined multiple fatty acid molecules d) Carbohydrates i) Constructed from simple sugar molecules

1.2 The Genome 1) Transmission and maintenance of the genome is essential for life a) DNA must be copied in its entirety without any mistakes b) Elaborate mechanisms in place to ensure that replication and segregation are extremely accurate 2) Genome composed of genes and intergenic regions a) Gene: a region of DNA that controls a discrete, hereditary characteristic (usually specifies the production of a functional product) b) Coding and regulatory regions ( c) Definition of gene is not as straightforward as we thought it was before 3) Genome physically organized into chromosomes a) Individual genes arranged in a linear array with intergenic DNA spacers (segements of DNA between the genes themselves) called chromosomes i) Some organisms have multiple, independent, linear chromosomes ii) Others have single, circular chromosomes b) Eukaryotic

i) Chromosomes are DNA wrapped tightly around packing proteins called histones ii) Space efficient, but need special mechanism to open/unravel iii) Some cells have plasmids extra-chromosomal pieces of DNA that sometimes carry important genetic information 4) Gene number and arrangement vary Greatly among organisms a) Governing processes comes from more than just the gene; comes from combination of gene number, production of multiple gene products from a single gene, and regulatory activity of intergenic regions 5) Molecular conservation a) Commonalities in genome sequence from different organisms 1.3 Gene Expression 1. Transcription, first step in gene expression for production of non-coding RNA and proteins a. RNA polymerase b. Stop start point specified by sequences within DNA template c. Non-coding and coding RNA 2. Translation of RNA sequence to make functional proteins a. Read three nucleotides at a time to specify which of 20 different amino acids should be used (codons) b. tRNA in ribosome read codons and grow protein chain (see p.13 diagram) c. post-translational processing (different proteins of product may be removed and additional moieties may be added) 3. Functional repertoire of cell is much more complex than just genome 4. Gene Regulation a. Ex. Liver cell will express a diff set of genes than a nerve cell

1.4 Cellular Infrastructure and Gene Expression 1. Eukaryotes contain genome in internal membrane-bound structure called the nucleus 2. Eukaryotic cells feature membrane-bound compartments with specialized functions a. Mitochondria: Powerhouses, deriving chemical energy from food b. Chloroplasts: plant cells, harvest energy from sunlight for the production of sugar within cell c. Both above contain unique DNA inside organelles that encode components for their function d. May have originated as endosymbionts, organelles living within another cell that became dependent on host for existence e. E.R. and Golgi Apparatus for production of proteins 3. Why Compartmentalization? a. Facilitate chemical reactions

i. Localizing various components together, effective cellular concentrations are increased and reactions proceed more efficiently b. In general, cellular efficiency increases c. Helps maintain fidelity/regulate gene expression since DNA contained in nucleus and cannot exit without having met certain criteria d. Helps send protein to different locations accurately, ex. Some proteins cannot have passage without certain criteria met 1.5 Expression of the Genome 1. Output of genome dictated by interplay of genes a. Phenotype, genotype b. Haploid, diploid, tetraploid (ploidy has back-up copy) 2. Deciphering natural function of genese a. Compare wild-type (normal) genes with mutant ones, forward genetics b. Two different version of genes are called alleles 3. Mutations a. Recessive mutation, for diploid one copy of gene mutant, other wild type, but wild type compensates and phenotype of mutant gene product is masked b. Dominant mutation, same, phenotype is not masked (wild type cannot compensate) c. Missense mutation: point mutation leads to incorporation of wrong amino acid d. Nonsense mutation: premature termination of amino acid change e. Silent mutation: does not affect the translated protein 4. Disease and mutations a. Somatic Cells: transmit genetic information to daughter cell in same organism b. Germline cells: involved in production of progeny and transmit genetic information from one generation to the next c. Monogenic: diseases that are a consequence of variation in a single gene d. Polygenic: diseases that are a consequence of variation in multiple genes e. Penetrance of a given mutation is percentage of individuals carrying mutant genotype that exhibit mutant phenotype 1.6 Evolution of Genome and the Tree of Life 1. Organisms grouped into three domains of life based on sequence comparison a. Phylogenetic tree (branched model grouped on extent of relatedness) b. Bacterial c. Archaeal d. Eukaryotic 2. Model Organisms a. Organisms that have features of agricultural or medical importance, yet are easy to manipulate under laboratory conditions b.