Carbon-based compounds
• Chapter 4~ Carbon & The Molecular Diversity of Life
Organic chemistry…
The Chemistry of CarbonForms a tetrahedral shape when bound to 4 molecules
Tetravalence- 4 e- in outer shell
Hydrocarbons• Only carbon & hydrogen
(petroleum; lipid ‘tails’)• Covalent bonding; nonpolar• High energy storage• Isomers (same molecular formula,
but different structure & properties)– structural~differing covalent
bonding arrangement– geometric~differing spatial
arrangement – enantiomers~mirror images
• pharmacological industry (thalidomide)
Prefixes
• Organic compounds are named with prefixes
• Plain hydrocarbons end with –ane – Double bonds= ene– Side groups change
names (ex: -OH = -ol)
Functional Groups
• Attachments that replace one or more of the hydrogens bonded to the carbon skeleton of the hydrocarbon
• Each has a unique property from one organic compound to another
• Hydroxyl Group – H bonded to O– alcohols– polar (oxygen)– solubility in water
• Carbonyl Group– C double bond to O– At end of H-C: aldehyde– Otherwise: ketone
• Carboxyl Group – O double bonded to C to hydroxyl– carboxylic acids (dissociation= H+)– covalent bond between O and H– Polar
• Amino Group– N to 2 H atoms– “amines”– acts as a base
• Sulfhydral Group– sulfur bonded to H– Thiols– Can cross-link with each other
• Methyl Group– C bonded to 3 H’s– Affects
shape/configuration
• Phosphate Group– phosphate ion
covalently attached by 1 O to the C skeleton
– Negatively charged
ATP= NRG
- ATP is the main energy source for cells.
- One phosphate group is cleaved off to form ADP and energy is released
Macromolecules
Chapter 5~The Structure & Function of Macromolecules
Polymers
• Covalently bonded monomers
• Condensation (dehydration) reaction– One provides a –OH while the
other provides a H to form a water molecule
• Hydrolysis– bonds between monomers are
broken by adding water (ex:digestion)
Carbohydrates• Monomer =
Monosaccharides – CH2O formula– multiple hydroxyl (-OH) groups
and 1 carbonyl (C=O) group:• aldehyde (aldose) sugar- group at end • ketone (ketose) sugar- group in center
• broken down during cellular respiration
• raw material for amino acids and fatty acids
Putting them together
• Disaccharides – glycosidic linkage
(covalent bond between 2 monosaccharides)
• Sucrose (table sugar)– most common
disaccharide
Functions of Carbohydrates
• Storage:– Starch= glucose monomers– Plants: roots/plastids – Animals: glycogen/fat
• Structure:– Cellulose~ most abundant organic
compound – Chitin~ exoskeletons; cell walls of
fungi; surgical thread
Lipids• Monomers: Triacyglycerol (triglyceride)
– Carboxyl group = fatty acid– Ester linkage: 3 fatty acids to 1 glycerol molecule
• Fats, phospholipids, steroids• Hydrophobic• Non-polar C-H bonds in fatty acid ‘tails’• Saturated vs. unsaturated fats; single vs.
double bonds
Saturated vs. Unsaturated
Phospholipids
• Two fatty acids instead of three– phosphate group attaches
to one -OH
• ‘Tails’ = hydrophobic• ‘Heads’ = hydrophilic
Phospholipids in formation
- Micelle (phospholipid droplet in water)
- Bilayer (double layer)- cell membranes
Steroids
• Lipids with 4 fused carbon rings
• Ex: cholesterol...– cell membranes– precursor for other steroids
(sex hormones)– “Good” (HDL) vs “Bad”
(LDL) cholesterol• atherosclerosis
Proteins• Importance:
– instrumental in nearly everything organisms do
– 50% dry weight of cells– most structurally sophisticated
molecules known• Monomer = amino acids (20)
– central carbon atom– carboxyl (-COOH) group– amino group (NH2)– H atom– variable group (R)
Amino Acid R- Groups
Variable (R-) group characteristics:
• R- group interactions determine shape and function– Nonpolar (hydrophobic)
• Gly, Ala, Val, Leu, Ile, Met, Phe, Trp, Pro
– Polar (hydrophilic)• Ser, Thr, Cys, Tyr, Asn, Gln
– Acids• Asp, Glu
– Bases• Lys, Arg, His
Putting them together
• Polypeptides formed by a dehydration reaction.– peptide bonds~ covalent bond of carboxyl group to
amino group
3-D Structure
• Proteins function is determined by their structural conformation
• Amino acid sequence determines how it will fold– Affinity of A.A’s for each other, etc.
• Chaperonins- proteins that assist in folding of other proteins– Segregate and protect proteins and allow them to fold
w/o any “bad influences”• Four levels of protein structure
Primary Structure• Linear structure of Amino Acids• Molecular Biology:
– each protein has a unique primary structure of amino acids
• Examples:– One amino acid substitution in hemoglobin
causes sickle-cell anemia
Secondary StructureCoils & folds caused by
hydrogen bonds • Alpha Helix:
– Coiling~ every 4th AA• fibrous proteins, keratin
• Pleated Sheet:– Parallel sheets w/ H bonding
between them• globular proteins, spider silk
Tertiary Structure• Protein takes on irregular
contortions from R group bonding– Hydrogen bonds between
polar side groups– Hydrophobic molecules
undergo van der Waals interactions
– Disulfide bridges form between cystine –SH groups
– Ionic bonds between + and -
Quaternary Structure• 2 or more polypeptide chains
aggregated into 1 macromolecule– Collagen (connective tissue
that makes up 40% of body structure)
– Hemoglobin (Oxygen binding protein in red blood cells)
* 3-D structure of proteins discovered w/ X-ray crystallography and nuclear magnetic resonance (NMR)
Denaturation
• If protein shape is changed, it cannot function properly– Heat, pH change,
chemical treatment, etc.• Sometimes proteins can
be “renatured” if environment is restored to normal (rare)
Nucleic Acids
• 2 types:– Deoxyribonucleic acid
(DNA)– Ribonucleic acid (RNA)
• Storage and transmittance of genetic information
• DNA RNA protein
• Monomers= nucleotides
• Each nucleotide is composed of:– nitrogenous base– pentose sugar– phosphate group
“Polynucleotides”
• Joined by phosphodiester linkages– covalent bonds
between phosphate groups
Nitrogenous bases• Purines always pair
w/ Pyrimidines
• DNA- - A & T- G & C
• RNA-- A & U - G & C
DNA
• In nucleus• Codes for proteins (like
blueprints)• Double helix
– 2 strands held together by H-bonds between bases
– Complimentary base pairing
• Sugar = deoxyribose• Bases- A, G, C, T
Watson and Crick
• James Watson and Francis Crick discovered the double helix structure of DNA in 1953.
RNA• Single stranded• Several types:
– Ex: mRNA, rRNA, tRNA
• Acts as messenger between DNA in nucleus and ribosomes in cytoplasm
• Sugar= ribose• Bases- A, G, C, U