Organic Molecules

Carbon: The Backbone of Life cells are 70–95% water Remainder is carbon-based compounds Carbon accounts for the diversity of molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Organic chemistry is the study of carbon compounds Organic compounds range from simple molecules to colossal ones Simple: CO2: 3 atoms Complex: proteins: 1000’s of atoms Most organic compounds contain: hydrogen atoms in addition to carbon atoms Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Some question molecules present in early earth’s atmosphere EXPERIMENT 1953 Stanley Miller “Atmosphere” CH4 Water vapor Electrode NH3 H2 Condenser Cooled water containing organic molecules Cold water Figure 4.2 Can organic molecules form under conditions believed to simulate those on the early Earth? Some question molecules present in early earth’s atmosphere H2O “sea” Sample for chemical analysis

Formation of bonds with carbon electron configuration 4 electrons Tends to share electrons COVALENT BONDS Double Single Acts as an intersection Branches in many directions

Versatility of carbon Acts as an intersection Branches in many directions Up to 4 tetravalence

4 major components of organic molecules Fig. 4-4 Elements most frequently partnered with Hydrogen (valence = 1) Oxygen (valence = 2) Nitrogen (valence = 3) Carbon (valence = 4) H O N C Figure 4.4 Valences of the major elements of organic molecules 4 major components of organic molecules

Molecular diversity in carbon chains (skeletons) Straight branched rings

Hydrocarbons organic molecules consist of only carbon and hydrogen Covalent bonds Nonpolar/hydrophobic Many organic molecules, such as fats, have hydrocarbon components Hydrocarbons can undergo reactions that release a large amount of energy

Fat droplets (stained red) Fig. 4-6 Fat droplets (stained red) Figure 4.6 The role of hydrocarbons in fats 100 µm (a) Mammalian adipose cells (b) A fat molecule

C6 H12 O6 Isomers compounds with: same number of atoms of the same elements different structures Different properties C6 H12 O6

3 types of Isomers Structural isomers Geometric isomers Enantiomers Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

May also differ in the location of their double bonds Structural isomers have different covalent arrangements of their atoms # of possibilities increase as carbon skeleton increases C5 H12 – 3 forms C8 H18 – 18 forms C20 H42 – 366,319 forms May also differ in the location of their double bonds

Structural isomers same number of atoms of the same elements different covalent arrangements different structures

Geometric isomers have SAME covalent partnership of their atoms Differ in SPATIAL ARRANGMENT around a double bonded Carbon Inflexible double bonds (single bonds rotate more freely)

Enantiomers Are mirror images Middle carbon is an asymmetrical, Attached to 4 different atoms

Enantiomers Left handed and right handed Distinguishable by shape One is biologically active other is inactive

Enantiomers are important in the pharmaceutical industry Two enantiomers of a drug may have different effects Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

Effective Enantiomer Ineffective Enantiomer Drug Condition Pain; Fig. 4-8 Effective Enantiomer Ineffective Enantiomer Drug Condition Pain; inflammation Ibuprofen S-Ibuprofen R-Ibuprofen Figure 4.8 The pharmacological importance of enantiomers Albuterol Asthma R-Albuterol S-Albuterol

Thalidomide 1953-1962 dysmelia, morning sickness, teratogen Lupus HIV Chron’s racemizing

A small number of chemical groups are key to the functioning of biological molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Distinctive properties of organic molecules depend on: carbon skeleton molecular components attached to it A number of characteristic groups are often attached to skeletons of organic molecules Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

The Chemical Groups Most Important in the Processes of Life Functional groups are the components of organic molecules most commonly involved in chemical reactions number and arrangement of functional groups give each molecule its unique properties Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Functional Groups 24

Hydroxyl Polar Forms H bonds with water…helps dissolve organic compounds

Carbonyl Found in sugars

Carboxyl -COOH Organic ACID Is polar

Amino NH2 Acts as BASE

Sulfhydryl -SH Found in cysteine 2 can from bridges Stabilize proteins (tertiary) Break and reform bridges

Phosphates OPO3 -2 P Phospholipids (cell membrane) Potential to react with water releasing energy P

Methyl Addition affects gene expression Male v. female

Ch 5

Monomers and Polymers Condensation hydrolysis

4 Categories Carbohydrates Lipids (not considered polymer) Proteins Nucleic Acids

1. Carbohydrates Elements Present? Function? Building blocks:

Glucose Hexose sugar

Alpha & Beta Glucose Functional groups?

Kind of Isomer? structural Major nutrients respiration

5-carbons sugar has the formula: C5H10O5

The synthesis and breakdown of polymers

Dissacharides

Table sugar Covalent bonds Glycosidic linkages Milk sugar Malt sugar beer malt

Table sugar Enzyme: sucrase Milk sugar Enzyme: lactase Malt sugar maltase Enzyme: All digested in small intestine

Storage polysaccharides

Starch and cellulose structures Structural polysaccharide

The arrangement of cellulose in plant cell walls fiber Provides strength

fiber

Cellulose digestion: termite and Trichonympha

Cellulose digestion: cow R rumen R reticulum O omasum A abomasum fistulated cow

Chitin, a structural polysaccharide: exoskeleton and surgical thread Does contain some nitrogen

Chitin- Exoskeleton

Chitin- Exoskeleton

fungus

2. Lipids Not true polymers Not large enough to be considered macromolecule Hydrocarbon chains Hydrophobic- nonpolar

Ester bond between alcohol (glycerol) and acid (fatty acid) Lipids Elements Present? Function? Building blocks: Ester bond between alcohol (glycerol) and acid (fatty acid)

possess both hydrophobic and hydrophilic parts Functional groups? Amphipathic: possess both hydrophobic and hydrophilic parts

Saturated fatty acid single

unsaturated fatty acid double

Examples of saturated and unsaturated fats and fatty acids

Purpose of lipids?

The structure of a phospholipid amphipathic

Two structures formed by self-assembly of phospholipids in aqueous environments   

Cholesterol, a steroid lipid Amphipathic Maintain membrane fluidity

Signaling molecule

3. Proteins Elements Present? Function? Building blocks:

The 20 amino acids of proteins: polar and electrically charged

The 20 amino acids of proteins: nonpolar

Proteins.. Enzymes, Antibodies

Proteins..Spider silk: a secondary structural protein

Silk drawn from the spinnerets at the rear of a spider

Proteins….hemoglobin, insulin

Protein… Hair, Albumin

Protein Functions

Making a polypeptide chain

the four levels of protein structure

primary structure of a protein Peptide bonds Due to genetic code

Sickle Cell- association with primary structure

A single amino acid substitution in a protein causes sickle-cell disease

secondary structure of a protein H bonds Weak bond slightly - charge atom attracted to slightly + charge H Usually O &N

Interactions contributing to the tertiary structure of a protein NONPOLAR Weak bond slightly - charge atom attracted to slightly + charge H Usually O &N Covalent bond cysteine Attraction of opposite charged ions

The quaternary structure of proteins Fibrous: Insoluble Structural, support, protection Ex:skin, hair, nuclear membrane, red blood cell collagen, elastin, keratin etc.   Globular: Water soluble Catalytic Ex: insulin, myoglobin, hemoglobin,&immunoglobulins

the four levels of protein structure 4 levels of protein structure video

Denaturation and renaturation of a protein denaturing a protein

chaperonin in action

4. Nucleic Acids Elements Present? Function? Building blocks:

Nucleic Acids

The components of nucleic acids

James Watson and Francis Crick

X-ray crystallography

Rosalind Franklin

DNA RNA protein: a diagrammatic overview of information flow in a cell

Polypeptide Sequence as Evidence for Evolutionary Relationships