Download Lecture #5 - Suraj @ LUMS

Biochemistry:
Revision
A. Inorganic Compounds: Compounds without
carbon.
B. Organic Compounds: Compounds synthesized by
cells and containing carbon (except for CO and
CO2).
•
Diverse group: Several million organic compounds are
known and more are identified every day.
•
Common: After water, organic compounds are the
most common substances in cells.
1.
Over 98% of the dry weight of living cells is made up of organic
compounds.
2.
Less than 2% of the dry weight of living cells is made up of
inorganic compounds.
Carbon:
unique element for basic building block of
molecules of life
•
Carbon has 4 valence electrons: Can form four
covalent bonds
1.
2.
3.
•
Can form single , double, triple bonds.
Can form large, complex, branching molecules and
rings.
Carbon atoms easily bond to C, N, O, H, P, S.
Huge variety of molecules can be formed based
on simple bonding rules of basic chemistry
Organic Compounds are Carbon Based
Carbon Can Form 4 Covalent Bonds
Different Carbon Skeletons of Organic Compounds
Diversity of Organic Compounds
Hydrocarbons:
Organic molecules that contain C and H only.
Good fuels, but not biologically important.
Undergo combustion (burn in presence of oxygen).
In general they are chemically stable.
Nonpolar: Do not dissolve in water (Hydrophobic).
Examples:
(1C) Methane:
(2C) Ethane:
(3C) Propane:
(4C) Butane:
(5C) Pentane:
(6C) Hexane:
(7C) Heptane:
(8C) Octane:
CH4 (Natural gas).
CH3CH3
CH3CH2CH3 (Gas grills).
CH3CH2CH2CH3 (Lighters).
CH3CH2CH2CH2CH3
CH3CH2CH2CH2CH2CH3
CH3CH2CH2CH2CH2CH2CH3
CH3CH2CH2CH2CH2CH2CH2CH3
Isomers:
Compounds with same chemical formula but
different structure (arrangement of atoms)
•
Isomers have different physical and chemical
properties
Structural Isomers: Differ in bonding arrangements
Butane (C4H10)
CH3--CH2--CH2--CH3
Isobutane (C4H10)
CH3
|
CH3---CH---CH3
Number of possible isomers increases with increasing
number of carbon atoms.
Functional groups
•
•
•
Play pivotal role in chemical & physical properties of
organic molecules.
Compounds that are made up solely of carbon and
hydrogen are not very reactive.
Functional groups:
One or more H atoms of the carbon skeleton may be
replaced by a functional group.
Groups of atoms that have unique chemical and
physical properties.
Usually a part of molecule that is chemically active.
Similar activity from one molecule to another.
Together with size and shape, determine unique bonding
and chemical activity of organic molecules.
Functional Groups :
Determine Chemical & Physical Properties of
Organic Molecules
Four Important Functional Groups:
1.
Hydroxyl (-OH)
2.
Carbonyl (=C=O)
3.
Carboxyl (-COOH)
4.
Amino (-NH2)
Notice that all four functional groups are polar.
1. Hydroxyl Group (-OH)
•
Is a polar group: Polar covalent bond between O and H.
•
Can form hydrogen bonds with other polar groups.
•
Generally makes molecule water soluble.
Example:
Alcohols: Organic molecules with a simple hydroxyl group:
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Methanol (wood alcohol, toxic)
•
Ethanol (drinking alcohol)
•
Propanol (rubbing alcohol)
2. Carbonyl Group (=CO)
• Is a polar group: O can be involved in H-bonding.
• Generally makes molecule water soluble.
• Aldehydes: Carbonyl is located at end of molecule
• Ketone: Carbonyl is located in middle of molecule
Examples:
• Sugars (Aldehydes or ketones)
• Formaldehyde (Aldehyde)
• Acetone (Ketone)
3. Carboxyl Group (-COOH)
• Is a polar group
• Generally makes molecule water soluble
• Acidic because it can donate H+ in solution
Example:
Carboxylic acids: Organic acids, can increase acidity of a
solution:
• Acetic acid: Sour taste of vinegar.
• Ascorbic acid (Vitamin C): Found in fruits and vegetables.
• Amino acids: Building blocks of proteins.
D. Amino Group (-NH2)
•
•
•
•
Is a polar group
Generally makes molecule water soluble
Weak base because N can accept a H+
Amine -general term given to compound with (-NH2)
Example:
Amino acids: Building blocks of proteins.
The Macromolecules of Life:
Carbohydrates, Proteins, Lipids, and Nucleic Acids
Most Biological Macromolecules are Polymers
Polymer: Large molecule consisting of many
identical or similar “subunits” linked through
covalent bonds.
Monomer: “Subunit” or building block of a
polymer.
Macromolecule: Large organic polymer. Most
macromolecules are constructed from about 70
simple monomers.
Only about 70 monomers are used by all living things on
earth to construct a huge variety of molecules
Structural variation of macromolecules is the basis for
the enormous diversity of life on earth.
Macromolecule
Monomers or Subunits
1.
Carbohydrates
20-30 monosaccharides
2.
Proteins
20 amino acids
3.
Nucleic acids (DNA/RNA)
4 nucleotides (A,G,C,T/U).
4.
Lipids (fats and oils)
20 different fatty acids and
glycerol.
Making and Breaking Polymers
•
There are two main chemical mechanisms in
the production and break down of
macromolecules.
1.
2.
•
Condensation
Hydrolysis
In the cell these mechanisms are regulated by
enzymes.
Making Polymers
Condensation or Dehydration Synthesis reactions:
The equivalent of a water molecule is removed.
General Reaction:
X - OH + HO - Y --------> X - O - Y + H2O
Monomer 1 Monomer 2
Dimer
Water
(Unlinked)
(or Polymer)
(or Polymer)
Synthetic process in which a monomer is covalently linked to
another monomer.
Anabolic Reactions: Used by cells to make large molecules
from smaller ones.
1.
2.
Require energy (endergonic)
Require catalysis by enzymes
Condensation Synthesis: Monomers are
Linked and Water is Removed
Breaking Polymers
•
•
•
Hydrolysis Reactions:
Degradation of polymers into component monomers.
Involves breaking covalent bonds between subunits.
Covalent bonds are broken by adding water.
General Reaction:
X - O - Y + H2O ----------> X - OH + HO - Y
Polymer
Water
Monomer 1 Monomer 2
(or Dimer)
Catabolic Reactions: Used by cells to break large molecules
into smaller ones
1.
Release energy (exergonic)
2.
Reactions catalyzed by enzymes
Hydrolysis: Polymers are Broken Down as
Water is Added
Hydrolysis
Making and Breaking Polymers
Examples:
Dehydration Synthesis (Condensation):
Enzyme
Glucose + Fructose ---------> Sucrose
(Monomer) (Monomer)
(Dimer)
+
H2O
Water
Hydrolysis:
Sucrose
(Dimer)
+
Enzyme
H2O ---------> Glucose + Fructose
Water
(Monomer) (Monomer)
Synthesis and Hydrolysis of Sucrose
Carbohydrates:
Molecules that store energy and are used as
building materials
• General Formula: (CH2O)n
• Simple sugars and their polymers. Three types of
carbohydrates:
A. Monosaccharides
B. Disaccharides
C. Polysaccharides
• Diverse group includes sugars, starches, cellulose.
• Biological Functions:
• Fuels, energy storage
• Structural component (cell walls)
• DNA/RNA component
A. Monosaccharides:
“Mono” single & “sacchar” sugar
Preferred source of chemical energy for cells (glucose)
Can be synthesized by plants from light, H2O and CO2.
Store energy in chemical bonds.
Carbon skeletons used to synthesize other molecules.
Characteristics:
1. May have 3-8 carbons. -OH on each carbon; one with C=0
2. Names end in -ose. Based on number of carbons:
5 carbon sugar: pentose
6 carbon sugar: hexose.
3. Can exist in linear or ring forms
4. Isomers: Many molecules with the same molecular formula, but
different atomic arrangement. Example: Glucose and fructose are
both C6H12O6. Fructose is sweeter than glucose.
Monosaccharides Can Have 3 to 8 Carbons
Both -OH and =CO Functional Groups
Linear and Ring Forms of Glucose
B. Disaccharides:
–
“Di” double & “sacchar” sugar
• Covalent bond formed by condensation reaction between 2
monosaccharides.
Examples:
1. Maltose: Glucose + Glucose.
• Energy storage in seeds.
• Used to make beer.
2. Lactose: Glucose + Galactose.
• Found in milk.
• Lactose intolerance is common among adults.
• May cause gas, cramping, bloating, diarrhea, etc.
3. Sucrose: Glucose + Fructose.
• Most common disaccharide (table sugar).
• Found in plant sap.
Maltose and Sucrose are Disaccharides
C. Polysaccharides:
“Poly” many (8 to 1000)
Functions: Storage of chemical energy and structure.
Storage polysaccharides: Cells can store simple sugars
in polysacharides and hydrolyze them when needed.
1. Starch: Glucose polymer (Helical)
Form of glucose storage in plants (amylose)
Stored in plant cell organelles called plastids
2. Glycogen: Glucose polymer (Branched)
Form of glucose storage in animals (muscle and liver
cells)
Three Different Polysaccharides of Glucose