CHEMISTRY Organic and Inorganic Molecules.ppt

The Chemistry of Life

1. CHEMISTRY OF LIFE
(INORGANIC MOLECULE)

2. INORGANIC MOLECULE
•Usually contains charged ions
•Often associated with non-living things
•Include:
–Water
–Gases: oxygen and carbon dioxide
–Acids and bases
–salts

3. Water
•Constitute 70-90% of the living material
•Life on earth is totally dependent on water
•Chemical reactions that characterize life
all take place in a water medium
•A high percentage of living things is found
in aquatic habitats

4. Water is the solvent of life
•Versatile solvent
•It can dissolve many kinds of substances
–Polarity
–Forms H-bond with other substances

5. Solubility of Salt in Water
•Negative oxygen regions of water are
attracted to sodium cations
•Positive hydrogen regions of water
cling to chloride ions
•Several water molecules are attracted to
each of the ions.
•A "tug-of-war" occurs for the positive and
negative ions between the other ions in
the crystal and the water molecules.
http://www.elmhurst.edu/~chm/vchembook/171solublesalts.html

6. •Once the ions are
released from the
crystals, the ions are
completely
surrounded by water
molecules.
•Whether the crystal
dissolves is
determined by which
attractive force is
stronger.

7. •Precipitates form
–If the internal ionic
forces in the crystal
are the strongest,
the crystal does not
dissolve.
•Crystal will dissolve
–If the attractions for
the ions by the
polar water
molecules are the
strongest.
 

8. •Substance will dissolve in
water if their molecules can
form weak bonds with water
molecules.

9. Properties of Water
1.High surface tension
–Ability of water molecules to cling
together (cohesion) due to formation of
hydrogen bonds between them.

10. A.Beading of rain water on
the surface of a waxy
surface, such as a leaf.
–Water adheres weakly
to wax and strongly to
itself, so water clusters
into drops.

11. B.Formation of
 
drops 
occurs
when a mass of liquid is
stretched.
–water adhering to the faucet
gaining mass until it is stretched
to a point where the surface
tension can no longer bind it to
the faucet
– water separates and surface
tension forms the drop into a
sphere.

12. C.Floatation of objects
denser than water occurs
when the object is
nonwettable and its weight
is small enough to be
borne by the forces arising
from surface tension.
– water stridersuse surface
tension to walk on the
surface of a pond

13. 2. Capillarity
•ability of a liquid to flow against gravity where liquid
spontaneously rise in a narrow space
e.g.- thin tube,
- porous material such as paper
- non-porous material such as liquified carbon
fiber, or in a cell.

14. Capillary water flow in a brick that is in
contact with water at the bottom.

15. • Capillarity occurs because of inter-molecular
attractive forces between the liquid and solid
surrounding surface;
•If the diameter of the tube is sufficiently small,
then the combination of
 
surface tension 
(which is
caused by
 
cohesion 
within the liquid) and force
of
 
adhesion 
between the liquid and container act
to lift the liquid.
 

16. RECALL
•Kinetic Energy
–Energy in motion
–The faster the molecule moves, the greater its kinetic
energy
•Heat
–A measure of the total quantity of kinetic energy due
to molecular motion in a body of matter.
•Temperature
–Measure the intensity of heat due to the average
kinetic energy of molecules.

17. 3. High Specific Heat
•The amount of heat (in calories) needed to raise
the temperature of a substance by 1
o
C
–Water – 1 calorie per gram
–Alcohol – 0.6 cal/g
–Salt – 0.2 cal/g
•A measure of how well a substance resist
changing its temperature when it absorbs or
release heat.

18. •Importance:
a.It enables water to absorb much heat
energy without a large increase in
temperature.
b.It enables living organisms to release
much heat energy without very large
drop in temperature

19. 4. High Heat of Vaporization
•Heat required to convert liquid to vapor at
constant temperature
•Only 1 gram of water needs to be evaporated to
cool 539g of the body of living organisms by 1
o
C
•Importance:
–Water can moderate high temperature
–Cooling effect on organism

20. 5. High Heat of Fusion
•The energy that must be removed from the
molecules of a liquid before it becomes a crystal.
•Importance:
–Water can moderate low temperature
–Protects organisms from the damaging effect
of freezing.

21. Carbon dioxide
•2 atoms of oxygen are covalently bonded to 1
atom of carbon
•It is inorganic even if it has Carbon because it is
simpler than most organic compounds
•A raw material for photosynthesis
•A by-product in the breaking down of complex
organic compounds together with water
•The beginning and end of the very complex
carbon cycle in nature

22. Oxygen
•Constitute 21% of the earth’s atmosphere
•A necessary material for the maintenance
of life of most living organisms
–Anaerobic bacteria – can live without
oxygen

23. Acids
•substance that release hydrogen ions (H
+
) into
solution
•solution with a pH lower than 7
•solution where in hydrogen (H
+
) concentration
exceeds the hydroxide (OH
-
) ion concentration
•Characterized by sour taste, litmus paper turn
red
•HCl, H
2
SO
4

24. Base (Alkali)
•Substance that release hydroxide (OH
-
) into a
solution
•Capable of combining with and neutralizing
hydrogen ions producing a solution with a pH
higher than 7.
•A solution wherein OH
-
ion concentration is higher
than the H
+
ion concentration
•Characteristics:
–Bitter taste, slippery to touch, litmus paper
turns blue
•NaOH

25. pH Scale
•A shorthand method of describing the
concentration of hydrogen ions in any solution.

27. •Maintenance of a nearly pH in
living systems (with some
exception) is essential.
Otherwise , impaired
functioning or even death may
occur.

28. Buffer
•Substances that minimize changes in the
concentration of H
+
and OH
-
in a solution.
•Carbonic acid, H
2
CO
3

29. Life on Earth
is
Carbon based.

30. ORGANIC MOLECULES
•Compounds containing carbon and hydrogen
•Form large- complex molecules, macromolecules
•Macromolecules
–Polymers, chainlike molecules consisting of
many similar or identical building blocks linked
by covalent bonds.
–Monomers, small molecules serves as the
repeating units of polymers

31. Synthesis
&
Breakdown
of
Polymers
http://kentsimmons.uwinnipeg.ca/cm1504/carbohydrates.htm

32. Main Classes of Organic Molecules
1.Carbohydrates
2.Lipids
3.Proteins
4.Nucleic acids

33. CARBOHYDRATES
•consists only of
 
carbon,
 
hydrogen, and
 
oxygen, with a hydrogen:oxygen
 atom ratio
of 2:1 (as in
 water)
•CH
2O – general formula
•Saccharide its synonym
•made up of the so called "sugars and starches“
•main source of energy in the body

34. Classes of Carbohydrates
1.Monosaccharides
–Single sugars
–Simplest carbohydrates or simple sugars
2.Disaccharides
–Double sugars
–Two monosaccharides joined by
condensation
3.Polysaccharides
–Macromolecules, polymers of many sugars

35. Monosaccharide
•open-chain or ring forms of 3 to 8 carbon atoms
http://kentsimmons.uwinnipeg.ca/cm1504/carbohydrates.htm

36. Carbonyl group
•Consists of a carbon atom joined to an oxygen
atom by a double bond.
•Types:

37. Structure and Classification of
Monosaccharides
•Location of carbonyl group:
1.Ketoses (Ketone sugars)
2.Aldoses (Aldehyde sugars)
•Length of Carbon skeletons: (3-7 carbon long)
1.Triose – 3-carbon sugar
2.Pentose – 5-carbon sugar
3.Hexose – 6-carbon sugar
•Spatial arrangement of sugar structural
components around asymmetric carbon

39. Important
Monosaccharides
1.Glucose - Blood sugar or dextrose
•most common type of monosaccharide
2.Fructose – fruit sugar
3.Galactose – milk sugar
Importance of Monosaccharides:
1.Major energy source for the cells
2.Raw material for the synthesis of other types of small
organic molecules,e.g, amino acids and fatty acids
3.Monomers into disaccharides and polysaccharides

40. Disaccharides
•Two monosaccharides joined by glycosidic
linkage (covalent bond) by dehydration reaction.
•Examples:
1.Sucrose – table sugar: glucose + fructose
2.Maltose – malt sugar: glucose + glucose
3.Lactose – milk sugar: glucose + galactose

42. Polysaccharides
•Polymers with a few hundred to a few
thousand monosaccharides joined by
glycosidic bond.
•Storage of energy
•Structural roles

43. Storage Polysaccharides
•Starch – energy storage in plants
–Polymer of glucose monomers
•Types of starch:
1.Amylose
•simplest form of starch, unbranched
2.Amylopectin
•Branched, complex form of starch
3.Glycogen
•branched chain molecule used to store glucose in
animals

45. Structural Polysaccharides
•Cellulose
–Major component of the tough walls that
enclose plant cells.
–Most abundant organic compound on earth
–Polymer of glucose
–Man cannot digest it and not a nutrient , and
are eliminated with the feces, however, an
important part of a healthful diet.
–Marked as “insoluble fiber” in food packages

47. • Chitin
–an important structural material in the
outer coverings (exoskeleton) of insects,
crabs, and lobsters
–Used to make a strong and flexible surgical
thread that decomposes after the wound
or incision heals
–Pure chitin is leathery, but are made very
hard when impregnated with calcium
carbonate.
–Glucose monomer has nitrogen-
containing appendage.

48. Exoskeleton Surgical thread

49. L I P I D S
•Composed of carbon, hydrogen, and oxygen with
no definite ratio
•Building blocks:
–Fatty acids a
–Glycerol
•Functions:
–energy storage,
–structural components of
 cell membranes,
–important signaling molecules
•Have little or no affinity to water

50. Structure of Fat (triglycerol)
•1 glycerol + 3 fatty acids = FAT molecule
•Ester linkage – bond that connects fatty acid with glycerol
http://www.odec.ca/projects/2004/thog4n0/public_html/chemfat.html

51. Types of Lipids
1.Simple lipids
–3 fatty acids bonded to glycerol
–Also called as triglycerides e.g. oil and fats
–Include:
•Stearin – derived from animal fats and from
palm plants; used to manufacture soaps and
candles
•Palmitin, Olein, Waxes

52. Fats
•Store large amount of energy
•Types of fats:
1.Saturated fats
–No double bonds between carbon atoms
composing the chain, then as many hydrogen
atoms are bonded to the carbon skeleton,
“saturated with hydrogen”.
–Animal fats: lard and butter
–Solid at room temperature
–Contributor to cardiovascular disease,
atherosclerosis.

53. 2. Unsaturated Fats (oils)
•Has one or more double bonds, formed by the
removal of hydrogen atoms from the carbon
skeleton.
•liquids because the double bonds create angles
in the carbon skeleton of the fatty acids that
make them “kinky” and prevent them from
packing together to solidify at room temperature.
•Plants and fish oils: corn oil, cod liver oil

54. http://kentsimmons.uwinnipeg.ca/cm1504/lipids.htm

55. “Hydrogenated Vegetable oils”
•Unsaturated fats synthetically converted to
saturated fats by adding hydrogen
•Prevent lipids from separating out in liquid
(oil) form.
•Peanut butter, margarine

56. 2. Compound Lipids
•Lipids in combination with other compounds
•Lipoproteins – with protein
•Glycolipids – with carbohydrates
•Phospholipids – with phosphoric acid

57. Phospholipids
•Structurally similar to fats but they have only two fatty acid tails
• ambivalent
behavior
toward water
• major
component of
cell
membranes
http://www.biology.lsu.edu/introbio/summer/Summer2004/1201/RF/Chapter%205%20review.htm

58. 2 strucutres formed by self-aasembly of
phospholipids in aqueos solution
•Micelle - electrically
charged particle
formed by an
aggregate of ions or
molecules in soaps,
detergents, and
other suspensions
•B – cell surface

59. 3. Steroids
•Composed of four fused rings of carbon atoms
with functional groups attached.
•Cholesterol and certain hormones
•Cholesterol
–Common component of animal cell
membranes
–Precursor for the synthesis of other steroids,
e.g. vertebrate sex hormone
–High level in the blood contributes to
atherosclerosis

60. •Steroids vary in the
functional group
attached to their four
interconnected rings.

61. P R O T E I N S
•Body building materials of the living organism
•One or more polypeptides folded and coiled into specific
conformation.
•Polypeptides
–polymers formed from linking various amino acids
•Peptide bond - link amino acids
•Amino acid
–Building blocks of protein
–20 amino acids
–Possessing both carboxyl and amino groups

62. General structure of Amino acid
•Alpha (α) carbon
–Asymmetric carbon at the center
–4 partners:
1.Amino group
2.Carboxyl group
3.Hydrogen atom
4.R group
– side chain
–Differs with each amino acid
–Determines the unique characteristic of amino acid.

63. Making a
Polypeptide chain
Dehydration reaction
–Forms the peptide
bond linking
carboxyl group of
one amino acid to
another amino acid
http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm

64. Four Levels of Protein Structure
1.Primary structure
–Unique sequence of amino
acids in a polypeptide
2.Secondary structure
–Folding and coiling due to H
bond formation between
carboxyl and amino groups of
non-adjacent amino acid. R
groups are NOT.

65. –Types of secondary structure:
1.α helix – coiling that are held together by
hydrogen bond between every fourth
amino acid
2.β helix – two or more regions of the
polypeptide chain lie parallel to each
other.

66. http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm
Secondary
Structure

67. 3.Tertiary structure
•Overall conformation
(shape) of a polypeptide
•Stabilized by bonds
formed between amino
acid R group
•Forms many shapes, such
as globular compact
proteins and fibrous
elongated proteins

68. 4.Quaternary structure
–Association between two or more
polypeptides that make up a protein.
–R- group interactions, H bonds, ionic
interactions
–assembled after synthesis

69. 4 Levels of Protein Structure
http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm

70. http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm

71. Factors that Determine Protein
Conformation
•Physical and chemical condition of the protein
environment
–pH, salt concentration, temperature
–Alters the normal conformation of the protein
•Denaturation
–loss of three dimensional shape of protein
–a loss of the proteins function
–If the denatured protein is allowed to cool it will
sometimes refold back into it’s original conformation,
Renaturation.

73. Protein Functions
Type of
Protein
Function Examples
EnzymaticSelective acceleration
of chemical reactions
Digestive enzymes catalyze the
hydrolysis of the polymers in food.
StructuralSupport Silk fibers – make cocoons and webs
(insects and spiders)
Collagen & elastin – fibrous
framework in connective tissue
Keratin – hair, horn, feathers
StorageStorage of amino
acids
Ovalbumin – egg white, used as an
amino acid source for the developing
embryo.
Casein – milk, major source of amino
acids for baby mammals

74. Type Function Examples
TransportTransport of other
substances
Hemoglobin – iron-containing protein
of vertebrate blood, transport oxygen
from lungs to other parts of the body.
Transport molecules across cell
membranes
HormoneCoordination of an
organisms activities
Insulin – regulate concentration of
sugar in the blood of vertebrates.
ReceptorResponse of cell to
chemical stimuli
Receptors built into the membrane of
a nerve cell detect chemical signals
released by other nerve cells.
DefenseProtection against
disease
Antibodies combat bacteria and
viruses
Contractile
and motor
Movement Actin and Myosin – muscle
movement.

75. NUCLEIC ACID
•Informational polymers (polynucleotide)
•Store and transmit hereditary information
•Composed of CHON and phosphorus
•Nucleotides – building blocks
–Components:
1.pentose sugar
2.phosphate group
3.nucleotide base

76. Nucleotide structure
http://www.buzzle.com/articles/nucleotide-structure.html

77. Types of Nucleic Acids
1.RNA – ribonucleic acid
–Important in protein synthesis
2.DNA – deoxyribonucleic acid
–Genetic material an organism
inherit from their parents.

78. Pentose sugar
-the sugars found in nucleic acid thus give them their names;
- RNA contain ribose, DNA contain deoxyribose.

79. Nitrogenous Bases
1.Pyrimidines
2.Purines
DNA
–C, T, A, G
RNA
–C, U, A, G

80. Phosphodiester bond
•Bond that link nucleotides
•the bond is formed
between the 3' -OH group
and the 5' phosphate
group
http://www.uic.edu/classes/bios/bios100/lectures/chemistry.htm

81. Polynucleotide

82. Complementary Base Pairing
•DNA
–Double stranded structure
–Base pairing:
•A – T – double bond
•G – C – triple bond
–H – bond – stabilize the DNA
•RNA
–Single stranded
•A – U
•G - C

83. http://academic.brooklyn.cuny.edu/biology/bio4fv/page/molecular%20biology/dna-structure.html

84. DNA STRAND