BL 424 Chapter 2: Review Composition of Cells Student learning outcomes: A*. to reinforce stating the molecular composition of cells, including monomers and their polymers (macromolecules); to describe the structure and function of carbohydrates, lipids, nucleic acids and proteins; to draw phospholipid structures and peptide bonds B**. to explain the critical importance of the structure and function of cell membranes: the role of membrane lipids as barriers, and of membrane proteins in transport; to draw concisely the fluid mosaic model of membrane structure C. to briefly explain the tools of genomics and proteomics for large-scale analyses of cell proteins. Important Figs are 2, 3*, 4, 5, 6, 7*, 8, 9, 10,11*,12, 13*,14, 15*, 22*, 23, 24, 25*, 27*, 28, 29, 31*, 32 Important Table is 1 A. Molecular Composition of cells Water is approximately 70% of the mass of cells Carbohydrates (CH2O)n provide energy, substrates for biosynthesis; simple sugars (monosaccharides) are joined in glycosidic bonds (by condensation or dehydration reactions) to form polysaccharides (Fig. 2.3) polysaccharides are storage forms of sugar, structural components or markers for cell recognition (Fig. 2.4) glycogen (and starch) are α(1->4) links of glucose cellulose is β (1->4) links of glucose some polysaccharides have branched chains Lipids* provide energy storage, structure of cell membranes and have roles in signaling Bacteria and Eukarya are similar; Archaea very different lipids fatty acids can be saturated or unsaturated fats are triacylglycerols (ester linkages of 3 fatty acids to glycerol) (Fig. 2.6) amphipathic molecules have polar and non-polar groups: part water-soluble (hydrophilic); part water-insoluble (hydrophobic)most phospholipids have glycerol, 2 fatty acids and a phosphate group: phosphatidic acid is simplest (Fig. 2.7) phosphatidyl choline has choline group on the phosphate **phosphatidyl inositol has sugar inositol on phosphate (signaling) sphingomyelin phospholipid has amino acid serine instead of glycerol glycolipids have a carbohydrate on the polar group cholesterol and steroid hormones (Fig. 2.9) have ring structures and polar OH groups Nucleic acids are informational molecules, linear polymers of nucleotides DNA vs. RNA: deoxyribose vs. ribose (Fig. 2.10) RNA includes rRNA, tRNA, mRNA Bases include purines and pyrimidines: A, G, C, T, U Synthesis involves polymerization (Fig. 2.11): formation of phosphodiester bond between nucleotides synthesis is 5’ -> 3’ (5’ phosphate to 3’ OH) Double strand DNA has hydrogen bonding between complementary bases (A-T; C-G) (Fig. 2.12) Complementary base pairing directs replication Of DNA (or RNA) Proteins are linear polymers of 20 different amino acids (aa). roles include structural, enzymatic, transport, signaling aa structure: amino end, carboxy end, side chain (FIg. 2.13) monomers are joined in peptide bond (Fig. 2.15): 1st aa is amino-terminus; last is carboxy-terminus primary sequence (the order of the amino acids) determines subsequent folding (and also directs subcellular location of protein in eukaryotic cells): secondary (α-helix, β-sheet) tertiary structures (polar, hydrophobic, S-S); quaternary structure involves multiple polypeptides: can be covalently linked (insulin) or non-covalent association (hemoglobin)B. Cell Membranes : fluid mosaic structure is critical for cells Membrane lipids: lipids are roughly 50% of mass of most membranes *phospholipid bilayer is basic structure for most living cells (Fig. 22) exceptions are Archaea which have ether-linked chains and sometimes a monolayer membrane (handout) lipid composition varies for different organelle membranes and for different organisms (Table 2.1) animal cells have glycolipids and cholesterol for membrane fluidity (Fig. 2.24) Membrane proteins - can be 25-75% of mass of membranes Fluid mosaic model of membrane structure* (Fig. 2.25*) Proteins can be integral (embedded in membrane) or merely peripheral (bound to integral proteins); integral proteins include transmembrane proteins (Fig. 2.26) Proteins are anchored in membrane by lipid or carbohydrate tags proteins on exterior are often modified by carbohydrates (important for cell-cell interactions) Transport across membranes Selective permeability of membrane: permits diffusion of small uncharged molecules and steroids, but not charged or large polar molecules Proteins transport specific compounds: (Fig. 2.28) passive transport proteins can only move substrates in an energetically favorable direction channel proteins form open pores, esp. for ions (Na+); pores are regulated by extracellular signals carrier proteins selectively bind and transport small molecules, such as glucose active transport proteins use energy of ATP to drive accumulation of compounds against concentration gradient (Fig. 2.29) (ex. H+)C. Proteomics permits large-scale analysis of cell proteins Genome is the genetic constitution of a cell. Genomics is the systemic (comparative) analysis of genetic information or organisms (genomes) Proteome is all the proteins expressed in a cell Proteomics analyzes all the proteins that are expressed – by different cells, at different times Identification of all cell proteins use two-dimensional gel electrophoresis or other purification techniques Mass spectrometry uses precise mass/charge ratios of tryptic peptides from proteins combined with genomic databases to identify proteins (Fig. 2.31) Ask what peptide could have this mass by compare To database of all possible tryptic peptides Global analyses of protein localizations often use genetic fusions of test protein to green fluorescent protein (GFP), (ex. www.//yeastgfp.ucsf.edu) or specific fluorescent antibodies to detect proteins in fixed cell Detection of protein-protein interactions on a large scale involves: Purification of protein complexes, digestion and mass spectrometry To review: Key terms and all questions at end of chapter are relevant. Draw the fluid mosaic model of plasma membrane Fig. 25, and explain how molecules can move across the membrane. State how proteins are anchored in or to the membrane. Explain the effects that different fatty acid compositions (saturated,