Chapter 2 Reading Questions 1. List the four major groups of biomolecules and briefly describe their structures and functions. Carbohydrates o Body uses these groups for energy and as the building blocks of cellular components. o Primarily carbon, hydrogen and oxygen. Ratio: CH2O Lipids o Body uses these groups for energy and as the building blocks of cellular components. o Mostly Carbon and Hydrogen Proteins o Body uses these groups for energy and as the building blocks of cellular components. o Contain nitrogen, inaddition to carbon, hydrogen, and oxygen o Building blocks of proteins: amino acids: contain sulfur Nucleotides o Includes DNA,RNA,ATP, and cyclic AMP o DNA+ RNA: genetic matical o ATP: carry energy o cAMP: regulate metabolism o Contain nitrogen, inaddition to carbon, hydrogen, and oxygen 2. List and describe the four important roles electrons play in physiology. (Fig. 2.5 Review: Atoms and Molecules) Covalent bonds: determines an element’s ability to bind with other elements. Strong covalent bonds create molecules Ions: electrical charge. Ions are basis for electrical signaling in the body High energy electrons: electrons in certain atoms can capture energy from their environment and transfer it to other atoms. Allows the energy to be used for synthesis, movement, and other life processes. Released energy may also be emitted as radiation Free radicals: unstable molecules with an unpaired electron; they are thought to contribute to aging and to the development of certain diseases, such as some cancers 3. Using the electron dot models of hydrogen and oxygen, draw how covalent bonds form to make a water (H2O) molecule. (Fig. 2.6b) 4. What are the properties of a polar molecule? Give at least one example. (Fig. 2.6b) Regions of partial positive and negative charge when one or more atoms in the molecule have a strong attraction for electrons H2O 5. What are the properties of a nonpolar molecule? Give at least one example. (Fig. 2.6a) Whose shared electrons are distributed so evenly that there are no regions of partial positive or negative charge CO2 6. Using NaCl as an example, draw how an ionic bond is formed. (Fig. 2.6c) Na donates e- to Cl, making Na+, Cl- 7. Cations have a positive charge; anions have a negative charge. 8. How are hydrogen bonds formed? Draw an example. (Fig. 2.6d) The oppositely charged regions in polar molecules are attracted to each other. 9. What property of water is a result of hydrogen bonding? Surface tension 10. Describe van der Waals forces. Weak, nonspecific attractions between the nucleus of any atom and the electrons of nearby atoms. The two atoms move closer together until they are so close that their elections begin to repel one another. V weak 11. Contrast hydrophilic interactions and hydrophobic interactions. (Fig. 2.8 Review: Molecular Interactions) Hydrophilic: molecules that have polar regions or ionic bonds readily interact with the polar regions of water. This enables them to dissolve easily in water. Molecules that dissolve readily in water are said to be hydrophilic. Hydrophobic: even distribution of electrons and no positive or negative poles, nonpolar molecules have n regions of partial charge, and therefore tend to repel water molecules. 12. Give some examples of molecular shapes and the bonds that give rise to them. (Figs. 2.3, 2.4, 2.5, 2.8c) Secondary structures o The covalent bond angles between amino acids create the spiral of the alpha helix or the zigzag shape of Beta strands. o Adjacent beta strands associate into sheet-like structures that are destabilized by H bonding Tertiary structure: created through spontaneous folding as the result of covalent bonds and noncovalent interactions; glovbular proteins; 3d shape of a protein Fibrous proteins may be Beta strands or long chains of alpha helices, ex collagen, keratin 13. A(n) acid is a molecule that contributes H+ to a solution; a(n) base is a molecule that decreases the [H+] of a solution. 14. Define pH and write the equation for determining the pH of a solution. pH: the concentration of H+ in body fluids pH= -log[H+] 15. How do buffers in the body help maintain normal pH? Buffers contain anions that have strong attraction for H+ molecules. When free H+ is added to a buffer soln, the buffer’s anions bond to the H+ and minimize any change in pH. 16. List and briefly describe the seven broad categories of soluble proteins. Enzymes: biological catalysts that speed up chemical rxn’s; important role in metabolism Membrane transporters: proteins that may form channels in the cell membrane, or may bind to molecules and carry them through the membrane Signal molecules: some proteins and smaller peptides act as hormones and other signal molecules Receptors: proteins that bind signal molecules and initiate cellular responses Binding proteins: found mostly in the extracellular fluid; bind and transport molecules throughout the body; example: hemoglobin Immunoglobulins: aka antibodies, help protect the body from foreign invaders and substances Regulatory proteins: turn cell processes on and off or up and down 17. Describe the induced-fit model of protein-ligand binding and use it to explain how proteins exhibit specificity in their ligand binding. (Fig. 2.10) The induced-fit model of protein-ligand activity: the activity site changes shape to fit either substrate or product molecules. Some proteins are very specific. Specificity: the ability of a protein to bind to a certain ligand or a group of related ligands 18. Define affinity The degree to which a protein is attracted to its ligand 19. Write the equation for the equilibrium constant. Define all the terms in the equation. Keq= [PL]/[P][L] o PL: protein-ligand complex o P: protein o L: ligand 20. Describe how equilibrium is a dynamic state. (Fig. 2.11) Equilibrium is a dynamic state, In the living body, concentrations of protein or ligand change constantly through synthesis, breakdown, or movement from one compartment to another. 21. Define the law of mass action For a reaction at equilibrium, the ratio of substrates to products is always the same 22. Define the term dissociation constant and write the equation for it The dissociation constant is the reciprocal of the equilibrium constant. A large Kd indicates low binding affinity of the protein for the ligand and more P and L remaining in the unbound state. Kd= [P][L]/[PL] 23. How does the dissociation constant relate to competition between ligands for binding to a particular protein? If one protein binds to several related ligands, a comparison of their Kd values can tell us which ligand is more likely to bind to the protein 24. What are agonists? Molecules that combine with a receptor and mimic a response 25. Define the term isoform and describe how isoforms can have an effect on protein binding. (Fig. 2.3) Isoform: closely related proteins whose function is similar but whose affinity for ligands differs. 26. Describe protein activation. What role do cofactors play in activation? Some proteins are inactive when they are synthesized in the cell. In order to become active, enzymes must chop off one or more portions of the molecule. They undergo proteolytic activation. The activation of some proteins requires the presence of a cofactor, an ion or a small organic functional group. 27. Identify the basic mechanisms by which a modulator can affect protein interactions. 2 basic mechanism by which modulation takes place (either OR) o 1: the modulator changes the protein’s ability to bind the ligand o 2: the modulator changes the protein’s activity or its ability to create a response 28. Briefly describe the actions of the following modulators. (Tbl. 2.3) chemical modulators: molecultes that bind covalently or noncovalently to proteins and alter their binding ability or other activity. These chemical modulators mau activate or enchance ligand binding, decrease binding ability, or completely inactivate the protein so that it is unable to bind any ligand. Antagonists: aka inhibitors, are chemical modulators that bind to a protein and decrease its activity. competitive inhibitors (Fig. 2.12d): reversible antagonists that compete with the customary ligand for the binding site irreversible antagonists: bind tightly to the protein and cannot be displaced by competition allosteric modulators (Fig. 2.12c, e): bind reversibly to a protein at a regulatory site away from the binding site, and by doing so change the change of the binding site covalent modulators: atoms or functional groups that bind covalently to proteins and alter the proteins’ properties. May either increase or decrease a protein’s binding ability or its activity. One ex. Phosphate group 29. Describe how temperature and pH affect protein structure and function. (Fig. 2.13a) Temperate and pH changes, can disrupt the noncovalent bonds holding the protein in its tertiary conformation. The protein loses its shape and activity. Protein loses conformation: denatured. 30. Define and distinguish between the processes of up-regulation and down-regulation. (Fig. 2.13b) Up-regulation: increase in protein number or binding affinity that increases the response of the target cell Down-regulation: decrease in protein number or binding affinity that lessens response 31. Define saturation and describe how proteins can reach the point of saturation. (Fig. 2.13c) Saturation: all active sites on a given amount of protein are filled with substrate and reaction rate is maximal.
