Cell Biology Exam 1 Study guide Intro to Cells 1 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 cells 2 What is the cell theory Cell Theory all living things are formed by the division of existing cells 3 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 I 1 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 organization a primary amino acid sequence b secondary hydrogen bonds between polypeptide backbone groups c d quaternary is the binding of two or more polypeptides to form a single complex tertiary the final 3D conformation of single polypeptide 3 What are covalent bonds both polar and nonpolar What is a dipole covalent bonds 90 kcal mol in water or vacuum a electrons are shared b 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 atoms a b ionic bonds muted in water i e biological systems Hydrogen bonds 1 kcal mol in water electronegative atom Van der Waals interactions 0 1 kcal mol in water c a weak bond between an electronegative atom and a hydrogen bound to another d e fluctuations in the electron cloud surrounding an atom creates a transient dipole 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 network 5 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 Intrinsically disordered sequences correspond to unstructured regions of some proteins Chaperones are proteins that improve the efficiency of protein folding in cells 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 II 1 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 proteins o positive regulation of allosteric proteins o protein phosphorylation o other covalent modifications of proteins o binding of GTP o binding and hydrolysis of ATP 7 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 proteins 9 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 chromosomes 1 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 acids o 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 Heterochromatin most condensed induced by tail modifications including methylation of lysine 9 on the histone H3 tail gene poor regions centromeres and telomeres genes are not expressed vs euchromatin less condensed gene rich regions 3 How are the following terms