3.1, 3.3-3.5 Protein functions include defense, movement, catalysis, signaling, structure, and transport.

Hydrophilic to hydrophobic: Basic, Acidic, Polar, Nonpolar Arginine, Lysine, Aspartate, Glutamine, Asparagine, Glutamate, Histidine, Serine, Threonine, Proline, Tyrosine, Tryptophan, Cysteine, Glycine, Alanine, Methionine, Phenylalanine, Leucine, Valine, Isoleucine Polymerization is endergonic (dG>0), hydrolysis favored over condensation/dehydration reactions Secondary structure describes distinctive shaped sections of proteins that are created by hydrogen bonding between carboxyl oxygen of one amino acid residue and hydrogen of amino group on another. Secondary structure results from interactions between atoms that are part of proteins peptide-bonded backbone, not between R groups. Highly stable despite weak hydrogen bonds. Depends on primary structure Tertiary structure results from interactions between R/R-groups or R-group/backbone. Contributes to distinctive 3D shape because each interaction causes backbone to bend/fold. 4 interactions particularly important: hydrogen bonding, van der Waals interactions, covalent bonds (between sulfur atoms -> disulfide bonds/bridges), ionic bonds. Depends on primary and secondary structure. Quaternary structure describes interaction between separate polypeptides via. Bonds or other interactions among Rgroups/peptide backbone. Based on primary/secondary/tertiary structure. Allosteric regulation regulatory molecule binds at a location other than active site, changes shape 6.1-6.4 Lipids are carbon-containing compounds that are found in organisms and are largely nonpolar Membrane diffusion: O2/CO2>H2O>Toluene>Glycerol/Urea>Glucose>Cl->Na+>PO43->ATP>Amino Acids/DNA/RNA 7.1 Cytoplasm is hypertonic to environment in most habitats Prokaryotic cells may also contain circular supercoiled DNA plasmids, which help cells adapt to unusual circumstances such as presence of poison in environment (extremely rare in eukaryotes) Gram-positive bacteria = extensive peptidoglycan, gram-negative have outer membrane and some peptidoglycan DNA and RNA Bacterial cells are haploid with circular double-stranded chromosome made of DNA; 1 copy of any gene Purines = Adenine and Guanine (two rings), Pyrimidines = Cytosine, Uracil, Thymine (one ring) Phosphodiester linkage is a condensation reaction that links phosphate and hydroxyl groups Polymerization catalyzed by enzymes is endergonic, additional free energy obtained by phosphorylation (addition of phosphate groups) DNA is water soluble due to hydrophilic negatively charged sugar-phosphate backbone RNA molecules alone can specify traits, RNA can be used as genetic material, RNA can be used as template for DNA synthesis ~30x more RNA than DNA. mRNA = unstable RNA (5% of RNA); tRNA (5% of RNA) and rRNA = stable RNA (90% of RNA)

Transcription RNA secondary structure is stabilized by hydrogen bonding and occurs spontaneously. Can have tertiary and quaternary structure. 1) 2) 3) 4) Sigma binds to promoter DNA helix opens Template strand threaded through channel leading to active site of RNA polymerase Ribonucleoside triphosphates (NTPs) enter a channel at bottom of enzyme and diffuse to active site, binding with a complementary base pair on template strand of DNA. 5) Exergonic reaction catalyzed by RNA polymerase occurs; exergonic because of potential energy on NTP phosphates 6) Termination occurs when termination signal is reached; as soon as termination signal code (stretch of Us) synthesized, RNA sequence folds back onto itself to form a short double helix held by complementary base pairs (hairpin) Eukaryotic transcription 1) TATA binding protein (TBP) binds to TATA box in promoter; TBP similar to sigma in prokaryotes 2) Large number of proteins bind along RNAP to promote transcription of a gene. Some bind other sections of DNA and cause DNA to loop back so that it may contact RNAP. 3) Promoter-proximal element upstream of TBP is a regulatory region similar to regulators/operators in prokaryotes 4) RNAP I = transcription of genes for two large ribosomal subunits; RNAP II = transcription of genes encoding proteins/RNAs that regulate gene expression; RNAP III for small subunit of ribosome Differences between bacteria and eukaryote transcription: 1) Eukaryotes use many basal transcription factors to initiate vs. one sigma 2) Eukaryotes have three RNA polymerases that transcribe distinct classes of RNA (RNA pol II is only class that transcribes mRNA for proteins) 3) RNA processing; transcription and translation do not occur at same site/concurrently (intron splicing by snRNPs aggregates = spliceosome, addition of 5 cap + poly(A) 3 tail) -> +stability and +translation likelihood (regulates) 4) Many eukaryotic promoters recognized by RNA pol II include TATA box located 30bp upstream of +1 Translation Protein synthesis faster in prokaryotes, starts at N-terminus of amino acid and ends at C-terminus Small ribosomal subunit holds mRNA in place while large subunit (two rRNA in E. coli) promotes peptide bonding Initiation factors mediate interaction between small ribosomal subunit and mRNA In eukaryotes, initiation factors guide mRNA to ribosome Active site of ribosome consists of rRNA, therefore ribosome = ribozyme Lac operon = negative regulation because LacI blocks transcription; Mal operon = positive regulation/activation because MalT promotes transcription. MalT and LacI are regulators that bind to operators (an example of regulatory region). MalT regulator upstream of RNA polymerase, LacI regulator anywhere overlapping with promoter region Summary of differences between bacteria/archaea/eukarya Bacteria: bacterial ribosome, bacterial RNAP, No histones/few introns/no nucleus. Archaea: archael ribosome, eukaryotic RNAP, histones present/few introns/no nucleus. Eukaryotes: eukaryotic ribosome, eukaryotic RNAP, histones present/numerous introns/nucleus