Ch 1 Text 1

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  1. What is biochemistry?
    the study of the chemistry of life processes
  2. a.       The microscope revealed what?

                                                                   i.      At the biochemical level, all organisms have many common features
    unifying feature of this diversity: cells, which resemble single-celled microscopic organisms
  3. a.       Biochemistry is what?,                                                               i.      Members of both these classes of molecules are common, with minor variations, to all living things

    1.       Ex: DNA stores genetic info in all cellular organisms and proteins are made up of the same 20 amino acids
    the study of the chemistry of life processes which entail the interplay of biological macromolecules  and metabolites (low-MW molecules like glucose) that are chemically transformed into biological processes
  4. a.       Key metabolic processes are also common to many organisms, such as the__.
    b.      These observations suggest what?
    cellular respiration (conversion of glucose and oxygen to carbon dioxide and water) and even photosynthesis in plants which resembles animals capturing energy released from glucose breakdown

    that all living things on Earth have a common ancestor and that modern organisms have evolved from this ancestor into their present forms
  5. a.       The geological and biochemical findings that support an evolutionary timeline divide the world into three domains: __
    Eukarya, Bacteria, and Archaea
  6. Eukarya
    •                                                                i.      all multicellular organisms and microscopic unicellular organisms like yeast
    • 1.       Defining characteristic: well-defined nucleus within each cell
  7. Bacteria
    •                                                                i.      unicellular organisms such as bacteria
    • 1.       Lack a nucleus; referred to as prokaryotes, which are classified as bacteria or archaea (by Carl Woese’s discovery that certain bacteria-like organisms are distinct from other bacteria)
  8. Archaea
    diverged from bacteria early in evolution
  9. a.       The unity of life at the biochemical level makes similar __ possible; but, different organisms have specific needs
    b.      Biochemistry has been advanced by our ability to study macromolecules in great detail
    chemical reactions and the associated biological macromolecules and metabolites
  10. What is a common feature? The discovery was made in what and followed by what?
    • use of DNA for storing genetic info 
    • studies of bacteria, which was followed by the discovery of the shape of DNA
  11. The shape of DNA illustrates what?
    the importance of structure and function
  12. a.       DNA is constructed from __
                                                                   i.      It is a __ made up of __different types of __and has a __ from which protrude variable substituents.
    1.       The backbone is made of __; and, the sugar is __. Each sugar is connected to __ through different linkages and is oriented in the same way, giving each DNA strand __
    • four building blocks
    • linear polymer
    • four 
    • monomers 
    • fixed backbone
    • sugar phosphate units
    • deoxyribose
    • two phosphate groups
    • directionality
  13. 1.       The bases are __
    a.       A and G are __; T and C are __
    b.      The bases are connected to the __ in the DNA backbone through bonds and are each different from one another
    A, C, G, and T.



    sugar components
  14. a.       Most DNA molecules have __strands and Watson and Crick proposed the structureà __

    • two 
    • double helix with the sugar-phosphate backbone outside and the bases inside, which form specific base pairs held together by hydrogen bonds
  15. b.      The structure has two properties of central importance to the role of DNA as the hereditary material: What are they?
                                                                   i.      First, it is compatible with any sequence of bases

                                                                   i.      Second, because of base-pairing, the sequence of bases along one strand completely determines the sequence along the other, which enables it to act as a template 

  16. 1.       The base pairs have essentially the same shape and do what?
    a.       How do they store info?                                                                                                                                       i.      This sequence also determines the __
    fit equally well into the center of the double helical structure of any sequence

    They can store information in the sequence of bases

    sequences of the RNA and protein molecules that carry out most of the activities within cells
  17. a.       The double helix can form from its __
                                                                   i.      If two complementary DNA strands are in the same vicinity, due to their mixture of sequences, what happens?
    • component strands
    • the double helix would form nearly to completion.
  18. But what forces cause the two strands of DNA to bind to each other?

    1. Several factors come into play: __(3)__
    the types of interactions and bonds in biochemical systems and the energetic favorability of the reaction, as well as the influence of the solution conditions
  19. a.       __ and __ are important for the structure and stability of biological molecules
                                                                   i.      Atoms interact with one another through chemical bonds, including the __ that define the structure of molecules and the variety of __ 
    • Covalent and noncovalent bonds
    • covalent bonds
    • noncovalent bonds
  20.                                                                i.      Covalent bonds: rank the strength in comparison to others; what is it?

    1.       C – C has bond length of __ and bond energy of __

    2.       How much energy is required to break them

    a.       More than one electron can be shared; more bonds are __ than single bonds
                                                                                                                                           i.      Adenine has __; and, the bond length is between that expected for  __ and __
    • strongest
    • sharing of electrons
    • 1.54 Angstrom
    • 355 kJ mol-1
    • A lot of energy

    more bonds are stronger than single bonds


    C –C single bond and a C = C double bond
  21.                                                                i.      Noncovalent bonds: how strong?  but important
    1.       For fundamental noncovalent bond types are __(4)__
    a.       They differ in __(3)__
                                                                                                                                           i.      These bonds are affected in vastly different ways by the __

    electrostatic interactions, hydrogen bonds, van der Waals interactions, and hydrophobic interactions

    geometry, strength, and specificity

    presence of water
  22. a.       Electrostatic Interactions: Describe it?

     The energy of an electrostatic interaction is given by __, where __
    A charged group on one molecule can attract an oppositely charged group on another molecule

    Coulomb’s law: E=kq1q2/Dr

    • where E = energy, 
    • q1 and q2 =the charges on the two atoms (in units of the electronic charge),
    • r = the distance between the two atoms (in angstroms), 
    • D =the dielectric constant (which accounts for the effects of the intervening medium), and 
    • k is a proportionality constant
  23.                                                                                                                                        i.      An attractive interaction has a __ energy; and, the electrostatic interaction between two ions bearing single opposite charges separated by 3 angstroms in water has an energy of__
    • negative
    •  5.8 kJ mol-1
  24. c. Hydrogen Bonds
    fundamentally electrostatic interactions and responsible for base pairing
  25. What is teh H bond donor?
    group that includes both the atom to which the hydrogen atom is more tightly linked and the hydrogen atom itself
  26. What is the H bond acceptor?
                                                                                                                                           i.      atom less tightly linked to the hydrogen atom
  27. Strength in comparison to other bonds? Bond lengths?
                                                                                                                                           i.      Much weaker than covalent and longer; bond lengths range from 1.5 angstroms to 2.6 angstroms
  28.                                                                                                                                        i.      The strongest hydrogen bonds have a tendency to be what shape and why? 
    approximately straight

    such that the hydrogen-bond donor, the hydrogen atom, and the hydrogen-bond acceptor lie along a straight line
  29. a.       Van der Waals Interactions
                                                                                                                                           i.      The basis of a van der Waals interaction is that the __, leading to __ that acts through __to do what?
    • distribution of electronic charge around an atom fluctuates with time
    • asymmetric electronic charge
    • electrostatic interactions 
    • induce a complementary asymmetry in the electron distribution within its neighboring atoms
  30. 1.       The atom and its neighbors then attract one another, which increases with __until they are separated by the __

    • proximity 
    • van der Waals contact distance
  31. a.       At distances shorter than the v.d.Waals contact distance, what happens and why?
    2.       Energies associated with van der Waals interactions are __
    • very strong repulsive forces become dominant because the outer electron clouds of the two atoms overlap
    • small
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Ch 1 Text 1
Test One
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