Cell Biology Exam #1 Study guideIntro to Cells1. What technological development and subsequent observations led to the birth of cell biology? - Better glass lenses lead to the development of the microscope.– Hooke (1665) – dead cork cells• Birth of Cell Biology– Schleiden (1838) – plants are made of cells– Schwann (1839) – animals are made of cells2. What is the cell theory?• Cell Theory – all living things are formed by the division of existing cells3. What are the average sizes of prokaryotic and eukaryotic cells and organelles? 4. What are the resolution limits of the different types of microscopy?5. Compare and contrast bright field light microscopy, differential interference contrast light microscopy, fluorescence microcopy, confocal fluorescence microscopy, transmission electron microscopy, and scanning electron microscopy. 6. What do images produced by the different types of microscopy look like? (Check out the relevant figures in your book).7. What are the differences and similarities between prokaryotic and eukaryotic cells? 8. What are the main organelles and cell parts found in a eukaryotic cell? Proteins I1. Be familiar with the general structure of amino acids, peptide bonds and polypeptide chains (or proteins). While I don’t expect you to memorize the amino acid side chains, I do expect you to be able to tell if they are nonpolar, acidic, basic, or uncharged polar if the structure is provided.2. What are the four levels of structural organization of a protein and what characterizes each level?- 4 levels of protein structural organizationa. primary – amino acid sequenceb. secondary- hydrogen bonds between polypeptide backbone groups c. tertiary- the final 3D conformation of single polypeptide d. quaternary-is the binding of two or more polypeptides to form a single complex3. What are covalent bonds (both polar and nonpolar)? What is a dipole?covalent bonds (90 kcal/mol in water or vacuum)a. electrons are sharedb. electron sharing is unequal in a polar covalent bond Polar covalent bonds create dipoles within a molecule due to unequal electron distribution.4. What are the 4 types of non-covalent bonds/forces relevant to cells? Be able to describe them.- Electrostatic attractions (3 kcal/mol in water) -forces that attract oppositely charged atomsa. ionic bonds b. muted in water (i.e. biological systems) - Hydrogen bonds (1 kcal/mol in water)c. a weak bond between an electronegative atom and a hydrogen bound to another electronegative atom.- Van der Waals interactions (0.1 kcal/mol in water)d. fluctuations in the electron cloud surrounding an atom creates a transient dipolee. this dipole induces an opposing dipole in a nearby atom generating an attraction - Hydrophobic forces (not really a bond)f. exclusion of non-polar surfaces from the hydrogen-bonded water network5. How do proteins fold?6. What are  helices and  sheets? How are they formed?7. What are a protein domains, chaperones, intrinsically disordered sequences, disulfide bonds, and protein families? - Chaperones are proteins that improve the efficiency of protein folding in cells- Intrinsically disordered sequences correspond to unstructured regions of some proteins.- Protein domains are regions of a polypeptide chain that fold independently into a stable structure. Protein domains can be combined to create proteins with new functions.- Disulfide bonds are covalent bonds between cysteines that act as “atomic staples” to stabilize extracellular proteins.- Members of protein families have similar 3D structures (and often similar aa sequences).8. How do X-ray crystallography and nuclear magnetic resonance spectroscopy work?- X-ray crystallography is used to determine the 3D structures of proteins.- Nuclear magnetic resonance (NMR) spectroscopy is used to determine the 3D structure of small proteins.Proteins II1. What are binding sites, active sites, ligands, substrates, active sites, catalysts, and enzymes?- Ligand: anything bound by a protein - Binding site: are of a protein that interacts with a ligand- Enzymes: speed up the rate of a reaction and are not altered by the reaction (proteins that act as catalysts) - Substrates: are ligands, substrate is altered upon binding so that the desired reaction is favored - Active site: is binding site 2. What does lysozyme do?Lysozymes cleave polysaccharide chains found in bacterial cell walls. 3. What do small molecules covalently attached to protein often do?Increase protein functionality, used for functions amino acids cannot perform, (Fe binds oxygen in hemoglobin, metals near active sites make transient bonds with the substrate 4. How does feedback inhibition work? Feedback inhibition occurs when a product of pathway inhibits an enzyme that acts earlier in the pathway. 5. What is an allosteric protein? Allosteric proteins undergo conformational changes upon ligand binding which alters their activity. 6. What are some of the ways protein activity is modulated in a cell? - Amount of protein- Location of protein - Modification of protein activity (by modifying the protein’s shape)o feedback inhibition of allosteric proteinso positive regulation of allosteric proteinso protein phosphorylationo other covalent modifications of proteinso binding of GTPo binding and hydrolysis of ATP7. What do conformational changes have to do with protein activity?8. What are kinases, phosphatases, and GTPases (GTP binding proteins)? How do these regulate protein activity?- kinase – attaches phosphates to serine, threonine or tyrosine side groups on a target protein- phosphatase – removes phosphates from a target protein- Binding GTP activates GTP-binding proteins9. What are antibodies and antigens? - Antibodies are useful tools for studying proteins- Antibodies recognize specific antigens.10. How are antibodies used during immunoprecipation and as molecular tags?- Antibodies can be used for immunoprecipitation.DNA and chromosomes1. Be familiar with the general structure of nucleotides, phosphodiester bonds, and nucleic acids. - Nucleotides are composed of a base, sugar and a phosphate group- Nucleotides are linked via phosphodiester bonds to form nucleic acidso Phosphodiester bonds form via condensation reactions 2. Compare and contrast: Purines vs pyrimidines, ribose vs deoxyribose, RNA vs DNA, heterochromatin vs euchromatin.- Purines( G/A) vs pyrimidines (T/C)- Ribose : sugar in RNA vs deoxyribose: sugar in DNA- RNA vs DNA-