Ch 4 Molecular Basis of Living Organisms

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Ch 4 Molecular Basis of Living Organisms
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• After water, cells consists mostly of
  carbon-based compounds organic molecules
• Examples
• Carbohydrates, lipids, proteins, nucleic acids
  (DNA, RNA)

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Carbon Bonds

• Four valence electrons--gt allows 4 covalent
  single bonds
• Or 2 double bonds
• Consequence
• Potential to form complex molecules

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LE 4-3
Molecular Formula
Structural Formula
Ball-and-Stick Model
Space-Filling Model
Methane
Ethane
Ethene (ethylene)
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Shape of carbon complex

• Tetrahedron
• When C bonded to 4 other groups
• Groups can rotate around single bonds
• Linear/Flat/Planar
• When C is double bonded to another C
• Unable to rotate

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Common Carbon Bonding Partners in Biological
Molecules

• Hydrogen
• Oxygen
• Nitrogen

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Molecular Diversity of Organic Molecules

• Due in part to
• Formation of carbon chain
• Differences in length and organization of chain

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LE 4-5
Ethane
Propane
Length
2-methylpropane (commonly called isobutane)
Butane
Branching
1-Butene
2-Butene
Double bonds
Note molecular abbreviation
Cyclohexane
Benzene
Rings
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Isomers

• Compounds with same molecular formula but
  different structures/ properties
• Structural isomers
• different covalent arrangements of atoms
• Geometric isomers
• same covalent arrangementsdifferent spatial
  arrangements
• Enantiomers
• mirror images of each other

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LE 4-7
Structural isomer
Structural isomers differ in covalent partners,
as shown in this example of two isomers of
pentane.
Geometric
cis isomer The two Xs are on the same side.
trans isomer The two Xs are on opposite sides.
Geometric isomers differ in arrangement about a
double bond. In these diagrams, X represents an
atom or group of atoms attached to a
double-bonded carbon.
Enantiomers Stereoisomers Mirror images
L isomer
D isomer
Enantiomers differ in spatial arrangement around
an asymmetric carbon, resulting in molecules that
are mirror images, like left and right hands. The
two isomers are designated the L and D isomers
from the Latin for left and right (levo and
dextro). Enantiomers cannot be superimposed on
each other.
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LE 4-8
Enantiomers
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Functional Groups

• Molecules attached to carbon chains that are
  involved in reactions
• Determine distinctive properties of organic
  molecule

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LE 4-9
Estradiol
Female lion
Testosterone
Male lion
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• The six functional groups that are most important
  in the biological chemistry
• Hydroxyl group
• Carbonyl group
• Carboxyl group
• Amino group
• Phosphate group
• Sulfhydryl group

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LE 4-10aa
STRUCTURE
Ethanol, the alcohol present in alcoholic
beverages
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
polar as a result of the electronegative oxygen
atom drawing electrons toward itself.
Alcohols (their specific names usually end in -ol)
Attracts water molecules, helping dissolve
organic compounds such as sugars
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LE 4-10ab
Acetone, the simplest ketone
EXAMPLE
STRUCTURE
Acetone, the simplest ketone
Propanal, an aldehyde
NAME OF COMPOUNDS
Ketones if the carbonyl group is within a carbon
skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is at the end of
the carbon skeleton
A ketone and an aldehyde may be structural
isomers with different properties, as is the
case for acetone and propanal.
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LE 4-10ac
EXAMPLE
STRUCTURE
Acetic acid, which gives vinegar its sour taste
FUNCTIONAL PROPERTIES
NAME OF COMPOUNDS
Has acidic properties because it is a source of
hydrogen ions.
Carboxylic acids, or organic acids
The covalent bond between oxygen and hydrogen is
so polar that hydrogen ions (H) tend
to dissociate reversibly for example,
Acetic acid
Acetate ion
In cells, found in the ionic form, which is
called a carboxylate group.
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LE 4-10ba
EXAMPLE
STRUCTURE
Glycine
Because it also has a carboxyl group, glycine is
both an amine and a carboxylic acid compounds
with both groups are called amino acids.
FUNCTIONAL PROPERTIES
NAME OF COMPOUNDS
Acts as a base can pick up a proton from the
surrounding solution
Amine
(nonionized)
(ionized)
Ionized, with a charge of 1, under cellular
conditions
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LE 4-10bc
EXAMPLE
STRUCTURE
Glycerol phosphate
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Makes the molecule of which it is a part an anion
(negatively charged ion).
Organic phosphates
Can transfer energy between organic
molecules.





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LE 4-10bb
EXAMPLE
STRUCTURE
(may be written HS)
Ethanethiol
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can interact to help
stabilize protein Structure.
Thiols
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LE 4-10bc
Cccccccccc ccccccc ccc
PO4_
COOH
Questions?
OH
SH
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Ch 5 Overview The Molecules of Life

• Within cells
• small organic molecules bond together to form
  larger molecules
• Macromolecules
• large molecules composed of thousands of
  covalently connected atoms

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What is the structure of most organic
macromolecules?

• Polymer
• long molecule consisting of similar building
  blocks called monomers
• Three of the four classes of lifes organic
  molecules are polymers
• Carbohydrates
• Proteins
• Nucleic acids

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LE 5-2
Short polymer
Unlinked monomer
Dehydration removes a water molecule, forming a
new bond
Longer polymer
Dehydration reaction in the synthesis of a polymer
Hydrolysis adds a water molecule, breaking a bond
Hydrolysis of a polymer
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The Synthesis and Breakdown of Polymers

• Synthesis (Construction)
• Monomers link together through
• dehydration reactions (aka condensation rxn)
• Breakdown
• Polymers disassemble into monomers by
• hydrolysis (reverse of dehydration)

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Carbohydrates Functions Fuel Construction
and support

• Structure
• Simple sugars monosaccharides
• Formula (CH2O)n
• Polymers
• Disaccharides (relatively short)
• Polysaccharides (long)

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Monosaccharides
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LE 5-3
Triose sugars (C3H6O3)
Pentose sugars (C5H10O5)
Hexose sugars (C5H12O6)
Aldoses
Glyceraldehyde
Ribose
Galactose
Glucose
Ketoses
Dihydroxyacetone
Ribulose
Fructose
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• Monosaccharides
• Functions
• major fuel for cells
• raw material for building larger molecules
• Structures
• linear ---gt ring

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LE 5-4
Glucose
Linear and ring forms
Abbreviated ring structure
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• Disaccharide
• forms by a dehydration reaction between two
  monosaccharides
• Nomenclature of bond
• glycosidic linkage

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LE 5-5
Disaccharide formation
Dehydration reaction in the synthesis of maltose
14 glycosidic linkage
Glucose
Glucose
Maltose
Dehydration reaction in the synthesis of sucrose
12 glycosidic linkage
Glucose
Fructose
Sucrose
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Polysaccharides
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Storage Polysaccharides

• Fuel storage molecule in plants
• Polymer of glucose--gtStarch
• ?-glycosidic linkage
• Stored in chloroplasts and other plastids

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LE 5-7
What kind of isomer is this?
??Glucose
? Glucose
??and ? glucose ring structures
Geometric
Starch 14 linkage of ? glucose monomers.
Cellulose 14 linkage of ? glucose monomers.
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LE 5-6a
Chloroplast
Starch
1 µm
Amylose
Amylopectin
Starch a plant polysaccharide
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• Glycogen
• storage polysaccharide of glucose in ANIMALS
• Stored in liver and muscle

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LE 5-6b
Mitochondria
Glycogen granules
0.5 µm
Glycogen
Glycogen an animal polysaccharide
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Structural Polysaccharides

• Cellulose found in plant cell walls
• Polymer of glucose
• ?-glycosidic linkages

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LE 5-7
??Glucose
? Glucose
??and ? glucose ring structures
alpha
Starch
Starch 14 linkage of ? glucose monomers.
beta
Cellulose
Cellulose 14 linkage of ? glucose monomers.
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Structural difference of glucose isomers

• Polymers of alpha glucose
• helical
• Polymers with beta glucose
• Straight
• Pack together well in microfibrils
• Stabilized by H-bonds
• Strong

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LE 5-8
Cellulose microfibrils in a plant cell wall
Cell walls
Microfibril
0.5 µm
Plant cells
Cellulose molecules
b Glucose monomer
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Many animals -unable to breakdown
cellulose -lack hydrolytic enzymes -insoluble
fiber results

• Some bacteria
• Possess enzymes to breakdown cellulose
• Live in symbiotic relationship in guts of animals
  (from cow to termite)

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• Chitin
• structural polysaccharide
• in the exoskeleton of arthropods
• cell walls of many fungi
• used as surgical thread!

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Assignment Due Friday
1. Bring to class a substance made of or
containing a carbohydrate.
2. Identify the carbohydrate and do research on
its structure, function and uses. Find reliable
sources on Google and various science databases
like PubMed. Provide a short typed description
properly citations.