What distinguishes living organisms?

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What distinguishes living organisms? 1.
Structurally complicated and highly organized
a. intricate internal structures b. many
kinds of complicated molecules proteins, DNA,
RNA, starches, and lipids etc. (inanimate objects
sand clay are mixtures of simple compounds) 2)
Living organisms a. extract b. transform
ENERGY c. store d. use
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Living things can extract energy from the
environment Chemical Chemoautotrophs or
lithoautotrophs H2S ? 2H S? 2e- 2NH3
4O2 ? 2HNO3 2H2O 4FeCO3 O2 6H2O ?
4Fe(OH)3 4CO2 or Sunlight Photoautotrophs nC
O2 nH2O ? (CH2O) nO2 Energy is needed to
build and maintain structures a) mechanical
energy - muscles b) chemical energy -
electric eel c) osmotic energy - plant
turger d) light energy -bioluminescence
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3) Most characteristic attribute of living
things is self-replication and self assembly it
is the quintessence of the living state 1 single
bacteria ? 109 in 24 hr inanimate matter does not
do this also the near-perfect fidelity of this
process is awesome! A crystal at equilibrium
grows but life at equilibrium is death! Life is
a set of relationships characterizing the nature,
function and interaction of biomolecules.
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Philosophers thought life contained a vital
force or vitalism but this has been rejected by
modern science. Important insights and
practical applications in medicine, agriculture,
nutrition and industry have come from
Biochemistry but ultimately biochemistry is
still concerned with the WONDER OF LIFE
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A Brief History of Biochemistry Early 19th
Century World made of either "living matter"
(organic) or "non-living matter"
(inorganic).(Vitalism) 1828 Friedrich Wohler
accomplished the synthesis of Urea from inorganic
matter. 1897 Edvard and Hans Buchner showed dead
cell extracts can perform reactions of living
cells. The molecules responsible for performing
these reactions are called enzymes Late 1800's
Emil Fischer suggested key/lock
picture. Substrate º Key, Enzyme º Lock Early
1900's Field of biochemistry emerges Structure
and function of enzymes Elucidating enzymatic
pathways 1944 Genes composed of DNA 1953 Watson
and Crick determine the structure of
DNA Biological function linked to the information
in genes
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Double helix slide
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Phylogenetic Tree of Showing Three domains of
Organisms
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How did organisms evolve?

• Blind watchmaker principle, small mutations arise
  at random.
• 1. Evolution is not directed
• 2. Evolution requires in-built sloppiness
• 3. Evolution is constrained by the past
• 4. Evolution is ongoing

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CAN you name a few of the recent
discoveries? Range of Life- Hot springs
-subduction zones -artic tundra- Antarctic dry
fields - from animal intestines to college
dormitories. These are all equal to specific
biochemical adaptations. Is Life Unique to
Earth?
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• Tools of the trade
• 3D models space filling or stick models
• H - white
• C - black
• N - blue
• O- red
• P - yellow
• S - yellow
• Stick or skeletal models show molecular frame
  work but not atomic radii
• I suggest that you get a model set to help with
  steriochemistry and structure.

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• Physical Units of Space, Time, and Energy.
• LENGTH You must know this and be comfortable
  using them.
• Length is very important!!
• C - C bond is 1.54 Å 1 mm
  10-3 m
• Hemoglobin 65Å 1 mm
  10-6 m
• Ribosomes 300Å 1 nm
  10-9 m
• Viruses 100 - 1000Å
• Cells 7 mm or 7 x 104 Å
• 1 Å 10 Å 100 Å
  1000 Å 104 Å 105 Å
• 10-10 m 10-9 m 10-8 m
  10-7 m 10-6 m 10-5 m
• Limit of a light microscope 2000 Å or 0.2mm
• 1 Å ? 104 Å knowledge comes from X-ray
  crystallography, electron microscope or atomic
  force microscope

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• Life is in constant flux
• Enzyme catalyzed reactions- Substrates ? Products
  10-3 sec - milli sec
• Unwinding of DNA 10-6 sec - micro sec
• 10-15 s 10-12 s 10-9 s 10-8
  s 10-6 s 10-3 s 10 s 103s
• femto pico nano
  micro milli sec
• femto fs excitation of chlorophyll
• pico ps charge separation in photosynthesis
• nano ns hinge protein action
• 10-8 10 ns fluorescence lifetime
• micro ms DNA unwind
• milli ms enzymatic reactions
• 103 generation of bacteria
• 2.3 x 109 sec average human life span

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Energy Ultimate source of energy is the sun E
hn 57 Kcal/mol of photons green light or 238
KJ/mol 1 cal 4.184 joules 0.239 cal 1 J You
must know how to convert between the two. ATP
energy carrier, for hydrolysis to ADP Pi 7.3
kcal/mole or 30.5 KJ/mol While vibrational
energy infrared) 0.6 kcal/mol or 2.5 KJ/mol C
- C bond 83 Kcal/mol or 346 KJ/mol the
framework of a carbon skeleton is thermally
stable but non-covalent bonds are only a few
kcal/mol or 10-20 KJ/mole
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Thermal Noncovalent ATP Green
C-C glucose
bond light
bond 1
10 100
1000 Kcal/mol KJ/mol 1 10
100
1000 Biomolecule shapes and interactions are
mediated by 4 types of non-covalent bonds.
These bonds are responsible for the overall
shape and interaction among biomolecules and can
be modified by thermal energy. Boil an egg, fry
a steak or get a sunburn.
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1) Electrostatic interactions by
coulombs law F kq1q2 q are
charges r2D
r is radius D dielectric of the
media, a shielding of charge. And k 8.99
x109Jm/C2 D 1 in a vacuum D 2-3 in grease D
80 in water Responsible for ionic bonds, salt
linkages or ion pairs, optimal electrostatic
attraction is 2.8Å
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2) Hydrogen bonds O-H
N N-H O
2.88 Å 3.04 Å
H bond donor or an H bond acceptor
N H O
C 3-7 kcal/mol or 12-28 kJ/mol very strong angle
dependence
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. 3) van der Waals attraction Non-spe
cific attractions 3-4 Å in distance
(dipole-dipole attractions) Contact
Distance Å H 1.2
1.0 kcal/mol C 2.0 4.1
kJ/mol N 1.5 weak
interactions O 1.4 important when many
atoms S 1.85 come in
contact P 1.9 Can only happen if shapes of
molecules match
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• Steric complementarity
• Occurs when large numbers of atoms are in contact
• Specificity
• When there is a large affinity for a unique
  molecule to bind to another
• a) antibodies
• b) enzyme substrate
• c) restriction enzymes

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Dielectric effect D hexane 1.9 benze
ne 2.3 diethyl ether 4.3 CHCl3 5.1 acet
one 21.4 Ethanol 24 methanol 33 H2O 8
0 HCN 116 H2O is an excellent solvent and
dissolves a large array of polar
molecules. However, it also weakens ionic and
hydrogen bonds Therefore, biological systems
sometimes exclude H2O to form maximal strength
bonds!!
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4 Hydrophobic interactions Non-polar groups
cluster together DG DH - TDS The most
important parameter for determining a
biomolecules shape. . Entropy order-disorder.
Nature prefers to maximize entropy maximum
disorder. How can structures form if they are
unstable? Are they unstable? Structures are
driven by the nature of water interactions
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