| CHEMICAL ARCHITECTURE of CELLS...
if 70% is water what's
other 30% ?
INORGANIC Elements
in cells...
95% of mass of cells is ONLY 6 ELEMENTS
- C H O N P S "
C. HOPKIN'S CaFe Mg " ?
table 2.1*
- Why only These ? covalent
bond reactivity*
-
Role of inorganics in cells
(including many metal ions):
1. they make up parts of other...
molecules,
& bone,
exoskeleton, vitamins, etc...
- 2. are dissolved in aqueous media
of the cell.
-
Dissociation of Water = pH
scale (READ*
pgs 52-548/e or 53-567/e)
1
H+ per 555 million waters = 1 x 10-7
john kyrk's animation of pH scale
Campbell -
Concept Activities
- chapter
3.3
-
Dissociation*
&
Water, Acids, Bases, pH *
Metabolome - the
complete set of small molecule metabolites
found in an organism (akin to a genome).
- estimated to be about 2,500
metabolites, 1,200 drugs, & 3,500 food
components in human body
- metabolome of plants = 50,000
metabolites
- majority of metabolome components are the...
ORGANIC
Molecules... molecules composed of C
and H
CLASSES
BIOLOGICAL ROLE
carbohydrate (CH2O)
structure &
energy molecules
fats (lipids) (CHO)
structure &
energy molecules
phospholipids
(CHO-P) membrane structure
steriods/sterols
membrane
structure - hormones
proteins
structural, enzymatic (catalytic)
 nucleic acids
informational, genetic role
Some
Basic Organic Chemistry...
ways to represent molecules graphically...
Molecular or Empirical formula vs. Structural formula
...stick and
space filling
models
fig
4.2 &
fig 4.3*
&
3D molecular models
- Hydrocarbons
- Carbon & hydrogen molecular skeletons :
- ...some examples :
chains vs. rings
fig
4.5*
- ISOMERS -
structural or
fig
4.7a*
-
...have the same
empirical formula, but different structure
- optical
fig 4.7c*
... bend plane of light is different directions (mirror images)
-
geometric
fig 4.7b*
... differ in arrangement of groups attached to C=C
-
A. CARBOHYDRATES..... have a consistent ratio of
[
CH2O
]n glucose-C6H12O6
-
MONOSACCHARIDES... the simple sugars,
-
which are the monomers that make
starch, glycogen, &
cellulose
-
(single molecules)
(polymers)
-
-
2 TYPES
of Monosaccharides:
-
aldoses [built on an aldehyde]
vs.
ketoses [built
on a ketone]
- -
names based on # C's - trioses,
pentoses, hexoses
fig
5.3*
- STRUCTURES:
linear vs. ring structure...
example:
glucose
-
ring
form*,
abbreviated ring*,
α
&
β
isomer
forms*, &
other isomers*
-
-
-
-
DISACCHARIDES...
a glucose "polymer" composed of only 2 monosaccharides
formed by
condensation rx* ---->
GLYCOSIDIC bond*
-C-O-C-
Concept Activities
- chapter
5.1 -
Polymer*s,
5.2
-
Models of Glucose *
&
Carbohydrates*
| |
|
|
|
| |
dissacharide |
bond |
polymer |
| |
maltose*
|
a-1,4
glu-glu |
---> amylose |
|
sucrose* |
a-1,2 glu-fruc |
---> sugar |
|
cellibiose* [3D]
|
ß-1,4 glu-glu |
---> cellulose |
-
POLYSACCHARIDES....
the
complex sugars.
- ... polymeric chains of monosaccharides
-
... normally form long repeats in a helix shape... (staircases)
-
- STARCH*... glucose
polymer of a-1,4glu units
- also
know as... AMYLOSE
unbranched
-
AMYLOPECTIN
branched
-
GLYCOGEN*... very
branched [branching helps solublize it]
CELLULOSE* - unbranched
glucose polymer of ß-glu
(for ex:
in leaves)
animals lack
cellulase but
symbiotic bacteria can
digest cellulose-
CHITIN* - exoskeleton
of insects &
crusteceans, adds +NH2 group
-
-
 TAKE HOME MESSAGE here.....
µ "Molecular
structure is critically important to function,
and structure
- relates
to the 'ORIENTATION'
of covalent bonds in 3D
space"
end 6
Importance of Molecular Shape to Biological Activity
2 UNIQUE properties of BIOMOLECULES gives them special FITNESS for the Living State
Configuration
- is the
spatial arrangement of atoms in a molecule...
configuration
can't be inter-converted without breaking chemical bonds
often needs an
asymmetric Carbon atom... (carbon
w 4 diff. groups attached*)
examples: STEREOISOMERS &
CHIRAL molecules
(animation)
also called enantiomers* = mirror
images
isomers with identical chemical structures, but which
rotate plane of polarized light at different angles...
levorotatory
[ L ] or
[R] = left handed -
counter
clockwise
dextrorotatory [
D] or [S] = right
handed - clockwise
figure*
medical ex: 1.Parkinson's
Disease
&
dihydroxyphenylalanine
L-DOPA
figure*
converted to dopamine - reduces symptoms
[Awakenings]
2. Ibuprofen & Albuterol
occur as R & S enantiomers
each with only one of the two stereoisomer being effective
-
C8e: fig 4.8*
-
-
-
-
-
-
-
-
Configurations -
-
good
ex:
isomers that are based upon "covalent bond" configurations
-
especially presence of double covalent bonds
C = C
-
DOUBLE
BONDS fix atoms
ABOVE & BELOW plane of molecule
removes ability of groups to
free rotate*
-
-
ex:
Configuration (structural) Isomers...
cis and trans
configurations
cis vs. trans
figure*
11-cis-retinal vs. 11-trans-retinal
retinal*
-
estradiol vs. testosterone
figure*
-
-
-
-
-
-
-
-
Conformation
-
[3D-shape]...
the surface outline or contours...
3-D orientation of a molecule, which results without breaking any
covalent bonds |
due to free rotation
[360o]
of atoms about a single chemical bond
& the weak electrostatic forces holding molecules together...figure* |
|
µ
STRUCTURE, SHAPE
and
FORM
and
BIOLOGICAL ACTIVITY... |
Molecular shape is CRUCIAL in biology,
because it determines how
biological
molecules recognize & respond to one another
with Specificity.
only molecules with complimentary shapes can
form weak bonds with each other:
ex: opiates &
endorphins -
fig 2.18(C8)* -
morphine is an opiate isolated
from opium and heroin is made from morphine. In 1975
endorphins
(signal molecules of pituitary that bind to brain receptors relieving
pain)
and opiates were shown to have
molecular shapes similar to each
other, and they can mimic them by
binding to endorphin receptors. |
-
Molecules
may have many shapes or different
isomeric forms,
 but often, only one isomer may be
biologically active
or a simple functional group
substitution can be significant...
FATS and LIPIDS...
a
TRIGLYCERIDE or
Fat or
Triacylglycerol...
a triacylglycerol is formed by condensation rx of
1
GLYCEROL
and 3 FATTY ACIDs
figure*
figure*
Properties
glycerol end of F.A. is...........HYDROPHILIC (POLAR)
hydrocarbon end of F.A. is...HYDROPHOBIC
(NON-POLAR)
figure*
SATURATED*
(solids) vs. UNSATURATED
(oils)*
fats*
figure*
fats vs. carbs*
as energy sources
a
PHOSPHOLIPID...
1 glycerol, 2 fatty acids,
PO4, & an
organic molecule
figure*
Properties
MICELLES
& BILAYERS
figure* &
figure*
CHOLESTEROLS... are lipids because
they're
insoluble in water
(13
Nobels) anabolic steroids
figure* &
in membranes*
Campbell Concept Activities -
chapter
5.3 -
Lipids*
NUCLEOTIDES...
-
are the monomers of the
nucleic acids & are composed of 3 parts...
a
nitrogenous
base*, a
ribose (5C) sugar*, a
phosphate*(-PO4)
polynucleotide building blocks*
yield a polymer of single nucleotides [ATCG (U)]
made by linking nucleotides together via
phosphodiester
bond*
RNA - ribose nucleic acid
-
sugar-phosphate backbone*
DNA - deoxy ribose nucleic acid
double helix of 2 polynucleotide chains*
Campbell Concept Activities -
chapter
5.5 -
Nucleic acids: Structure*
&
Functions*.
FUNCTIONAL GROUPS... groups of atoms
acting as a unit,- that give organic
molecules their physical properties,
their chemical
reactivity, & solubility in aqueous solutions.
most possess
electronegative atoms (N, P, O, S...
EASILY ATTRACT PROTONS)
key bonds are : ester (C-O-C=O) &
amide
(O=C-N-)
are
ionizable at physiological pH
-
-
-
-
-
Consequences
of Substitution of a H with
a
Functional Group
...Linking STRUCTURE, EMERGENT PROPERTIES, and BIOLOGICAL
ACTIVITY ?
Ethane
CH3-CH3
toxic,
flammable gas
-
Ethanol
CH3-CH2-OH ethyl
alcohol, a potable drink
-
Propionic acid
CH3-CH2-COOH
colorless, corrosive liquid with a pungent odor
-
Ethyl mercaptan
CH3-CH2-SH
"rotten eggs" -
the smell of natural gas
back to outlines
 key concepts*
- U of
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Department of Biology, University of
Miami, Coral Gables, FL 33124
Last Update -
18 September, 2008
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