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Life, Chemistry and Water. JBS Haldane – What is Life?.

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jbs haldane what is life
JBS Haldane – What is Life?
  • I am not going to answer this question. In fact, I doubt if it will ever be possible to give a full answer, because we know what it feels like to be alive, just as we know what redness, or pain, or effort are. So we cannot describe them in terms of anything else.
jbs haldane what is life1
JBS Haldane – What is Life?
  • …life consists of chemical processes.     This pattern has special properties. It begets a similar pattern, as a flame does, but it regulates itself as a flame does not …. So when we have said that life is a pattern of chemical processes, we have said something true and important.     But to suppose that one can describe life fully on these lines is to attempt to reduce it to mechanism, which I believe to be impossible. On the other hand, to say that life does not consist of chemical processes is to my mind as futile and untrue as to say that poetry does not consist of words.
overarching theme of biology
Overarching theme of biology
  • At the molecular level, biology is based on three dimensional interactions of complementary surfaces
  • Structure dictates function
example
Example
  • There is a human version of the D crystallin protein that is known to be involved in cataract formation in the eye. Cataracts form when several proteins in the eye bond to one another and become a very large insoluble multi-protein complex.
example1
Example
  • There is a point mutation that occurs in some children that changes the arginine normally found at position 14 to a cysteine causing them to develop cataracts. The overall 3-D structure of the protein remains the same despite this substitution.
  • Structure
25 key elements in living organisms
25 Key Elements in Living Organisms
  • 96% of the weight of living organisms = carbon, hydrogen, oxygen, and nitrogen
  • 4% = calcium, phosphorus, potassium, sulfur, sodium, chlorine, and magnesium
  • 0.01% = nine trace elementsvital to biological functions
atoms and molecules
Atoms and Molecules
  • Atoms
    • Smallest units of elements
  • Molecules
    • Formed from atoms
    • Combined in fixed numbers and ratios
  • Compounds
    • Molecules with different component atoms
think pair share
Think/Pair/Share
  • What are the characteristics of the particles that compose atoms?
atomic structure
Atomic Structure
  • Atomic nucleus contains protons and neutrons
  • Electrons travel around nucleus in orbitals
atomic nucleus
Atomic Nucleus
  • Protons
    • Positively charged
  • Atomic number
    • Number of protons in an element
  • Neutrons
    • Uncharged
atomic mass
Atomic Mass
  • Atomic mass = mass of protons + neutrons (electrons have insignificant mass)
    • Proton = 1 dalton = 1.66 X 10-24 grams
    • Neutron = 1 dalton
isotopes
Isotopes
  • Atoms of an element with differing numbers of neutrons
  • Differ in physical but not chemical properties

Fig. 2-4, p. 24

slide17

Isotopes of carbon

12C

6 protons

6 neutrons

atomic number = 6

mass number = 12

13C

6 protons

7 neutrons

atomic number = 6

mass number = 13

14C

6 protons

8 neutrons

atomic number = 6

mass number = 14

Fig. 2-4b, p. 24

radiocarbon dating
Radiocarbon dating
  • The Dating Game
radioisotopes
Radioisotopes
  • Some isotope nuclei are unstable and break down (decay)
    • Release particles of matter and energy (radioactivity)
  • Radioisotopes decay at a steady rate
    • Used to estimate the age of organic material, rocks, fossils
    • Used as tracers to label molecules in chemical reactions
medically useful radioisotopes
Medically useful radioisotopes
  • Iodine-123
    • Tracer
    • Absorbed by the thyroid gland and used to produce thyroxine
    • Location in body readily detected
  • Short half-lives
  • Non-toxic
medically useful radioisotopes1
Medically useful radioisotopes
  • Idodine-131
    • Used therapeutically to treat thyroid cancer and hyperthyroidishm
electrons
Electrons
  • Electron are negatively charged
  • Number of electrons = number of protons
  • Electron mass = 1/1800 dalton
electron orbitals
Electron Orbitals
  • Electrons are found in regions of space called energy levels (shells)
  • Within each energy level, electrons are grouped into electron orbitals
electron orbitals1
Electron orbitals

Animation: The shell model of electron distribution

orbitals
Orbitals
  • s orbitals are spherical
  • p orbitals are propeller or dumbbell shaped
  • Each orbital can hold only 2 electrons
    • An atom with more than 2 electrons has more than 1 orbital
slide27
Atoms with progressively more electrons have orbitals within electron shells that are at greater and greater distances from the center of the nucleus
    • 1st shell - 1 spherical orbital (1s) - holds 2 electrons
    • 2nd shell - 1 spherical orbital (2s) and 3 dumbbell-shaped orbitals (2p) – can hold 4 pairs of electrons
nitrogen example
Nitrogen example
  • A nitrogen atom has seven protons and seven electrons
  • 2 electrons fill 1st shell
  • 5 electrons in 2nd shell
    • 2 fill 2s orbital
    • 1 each in the 3p orbitals
  • Outer 2nd shell is not full
    • Electrons in the outer shell that are available to combine with other atoms are called the valence electrons
periodic table1
Periodic table
  • Organized by atomic number
  • Rows correspond to number of electron shells
  • Columns, from left to right, indicate the numbers of electrons in the outer shell
  • Similarities of elements within a column occur because they have the same number of electrons in their outer shells, and therefore they have similar chemical bonding properties
electron orbitals2
Electron Orbitals

Fig. 2-6, p. 27

chon shells
CHON shells

Animation: Predicting the number of bonds of elements

valence electrons
Valence Electrons
  • If outermost energy level filled, atoms are stable and unreactive
  • Atoms tend to lose, gain, or share electrons to fill the outermost energy level
  • Leads to chemical bonds and forces that hold atoms together in a molecule
atomic bonds
Atomic Bonds
  • Covalent Bonds
  • Noncovalent Bonds
    • Ionic
    • Hydrogen
    • Van der Waals
bond types
Bond types

Animation: How atoms bond

slide39
Ions
  • Charged atoms
    • Cation: Positively charged ion
    • Anion: Negatively charged ion
  • Ionic Bond
    • Forms between atoms that gain or lose valence electrons completely
slide40
Ions
  • One atom loses an electron and becomes positively charged
    • Na+ :11 protons + 10 electrons
  • One atom gains an electron and becomes negatively charged
    • Cl– :17 protons + 18 electrons
ionic interactions
Ionic interactions
  • Result from the attraction of a positively charged ion (cation) with a negatively charged ion (anion)
  • Ions surrounded by hydration shell
ionic bond
Ionic Bond

Fig. 2-7, p. 28

ionic bond1
Ionic Bond
  • Exerts attractive force over greater distance than other bonds
  • Attractive force extends in all directions
  • Varies in strength depending on presence of other charged substances
covalent bonds
Covalent bonds
  • Pairs of electrons shared between atoms
  • Stable under most conditions
  • Bond energy C-C 83kcal/mole; double bond about twice as much energy needed to break the bonds
covalent bond
Covalent Bond
  • Two atoms share a pair of electrons
  • Shared orbitals occur at discrete angles and directions
covalent bonds1
Covalent Bonds

Fig. 2-8, p. 30

unequal electron sharing
Unequal Electron Sharing
  • Electronegativity
    • Measure of atom’s attractions for electrons shared in a chemical bond
  • Nonpolar covalent bond
    • Electrons shared equally
  • Polar covalent bond
    • Electrons shared unequally
unequal electron sharing1
Unequal Electron Sharing
  • Water is a polar molecule

Fig. 2-9, p. 30

polar molecules
Polar Molecules
  • Tend to associate with other polar molecules and to exclude nonpolar molecules
  • Polar molecules that associate readily with water are hydrophilic(“water preferring”)
  • Nonpolar molecules excluded by water are hydrophobic(“water avoiding”)
hydrogen bonds
Hydrogen bonds
  • Form between a covalently bonded H atom (partial +ve) and a covalently bonded N or O (partial –ve charge)
hydrogen bond
Hydrogen Bond
  • Unequal electron sharing between a hydrogen atom and another atom (oxygen, nitrogen, sulfur)
    • Hydrogen gets partial positive charge, other atom gets partial negative charge
    • Charges attract to form hydrogen bond
hydrogen bond1
Hydrogen Bond
  • Weak bond, useful in stabilizing large biological molecules such as proteins
van der waals
Van der Waals
  • Transient, weak, nonspecific attractive force
  • Both polar and nonpolar molecules
  • Random fluctuations in the distribution of electrons
van der waals forces
Van der Waals Forces
  • Natural changes in electron density of molecules
  • Regions of positive and negative charge
    • Cause molecules to stick together briefly
  • Weaker than hydrogen bonds
    • Help stabilize large biological molecules such as proteins
van der waals forces1
Van der Waals Forces
  • Gecko toes:

Fig. 2-11, p. 32

hydrophobic effect
Hydrophobic effect
  • Nonpolar molecules aggregate in water
  • Water molecules form “cages” around hydrocarbons
molecular complementarity
Molecular complementarity
  • Shape specifies function
  • Affinity
    • Number and strength of noncovalent interactions
  • Specificity