Ocean County College BIOL 161 Lectures Chemistry of Life … ...Better known as … BIOCHEMISTRY! BIOL161_03
FUNCTIONAL GROUP STRUCTURAL FORMULA EXAMPLES COMPOUNDS Hydroxyl - OH Ethanol Carbohydrates, proteins, nucleic acids, lipids Carbonyl - C = 0 Acetaldehyde Carbohydrates, nucleic acids Carboxyl OH - C = 0 Acetic Acid Proteins, lipids Amino H - N H Alanine Proteins, nucleic acids Sulfhydryl - S - H Cysteine Proteins Phosphate O - - O – P – O O Glycerol Phosphate Nucleic acids Methyl H - C – H H Alanine Proteins Primary Functional Chemical Groups (click on 'Examples' for more information)
A pain in the -anes...
1 - Methane
2 - Ethane
3 - Propane
4 - Butane
5 - Pentane
6 - Hexane
7 - Heptane
8 - Octane
9 - Nonane
10 - Decane
Saturated C4 hydrocarbons ball-and-stick.png Ball-and-stick models of butane (top left), isobutane (top right), cyclobutane (middle left), methylcyclopropane (middle right) and bicyclo[1.1.0.]butane (bottom). Created using Accelrys DS Visualizer Pro 1.6 and GIMP.
Ribose (5 carbon) H OH H OH OH H CH 2 OH H O
2-Deoxyribose (5 carbon) Ribose has OH group! H OH H H OH H CH 2 OH H O
Glucose (6 carbon) H OH O CH 2 OH H OH H H OH H OH
Galactose (6 carbon) O CH 2 OH H OH H H OH OH H OH H
Fructose (6-carbon; 5 member ring) H OH OH H H CH 2 OH CH 2 OH OH O
Sucrose H 2 O O
Maltose H 2 O O
Nucleotides, RNA and DNA
Base + Sugar = Nucleoside
Each nucleotide consists of:
Pentose sugar (Ribose or Deoxyribose)
Purines (Adenine & Guanine)
Pyrimidines (Cytosine, Thymine & Uracil)
Glycosidic Bond Phosphate Nitrogenous Base Ribose or Deoxyribose H OH H OH H CH OH H O
Amino acids have an alkaline amino group ( -NH 2 ) and an acidic carboxyl group ( -COOH )
There are twenty (20) naturally occurring amino acids – each with a different “ -R ” group.
C C N H R OH O H H
Hydrophobic amino acids Aliphatic Alanine; ALA; A Isoleucine; ILE; I Leucine; LEU; L Valine; VAL; V
Hydrophobic amino acids Aromatic Phenylalanine; PHE; F Tyrosine; TYR; Y Tryptophan; TRP; W
Neutral amino acids Polar -R group Asparagine; ASN; N Methionine; MET; M Threonine; THR; T Serine; SER; S Cysteine; CYS; C Glutamine; GLN; Q
Acidic Amino Acids Aspartate; ASP; D (Aspartic Acid) Glutamate; GLU; E (Glutamic Acid)
Basic Amino Acids Arginine; ARG; R Histidine; HIS; H Lysine; LYS; K
Unique Amino Acids Glycine; GLY; G Proline; PRO; P
The Peptide Bond
Note the C-O-N-C- sequence between each amino acid.
Peptide bonds are formed by condensation
And, broken by hydrolysis .
In the lab this is done by placing the peptide in a 6N HCl solution at 100 ° C for 12 hrs.
They are tough bonds!
Fred Sanger and Insulin
Dr. Sanger is one of four people to have been awarded two Nobel Prizes and the only person to receive two prizes in Chemistry!
His discoveries in protein chemistry allowed him to sequence porcine insulin and deduce its structure.
Later, working with RNA – he was the first person to sequence an entire genome (granted a virus; but he did it by hand!).
Secondary structure describes the way the chain folds.
Alpha ( α )- helix
Beta ( β )- sheet
Zig zagging elements
Most proteins are a combination of both!
α -helices can 'twist' in either direction
Right-handed twist on the left
Left-handed twist on the right
β -sheet structure
The dotted lines are hydrogen bonds which bind the strands together, making this a strong flat fibrous protein.
In silk, these sheets stack together like a pile of corrugated iron.
Poly - Proline
This graphic illustrates a peptide with repeating Proline amino acids.
When three such strands wrap around each other like rope they make a strong fibrous protein, similar to those found in Collagen .
Speaking of Collagen …
Collagen is made from three strands consisting mainly of Glycine and Proline...
repeatedly wrapped into a rope, the whole forming a helix.
Electron micrographs of collagen fibres from (a) a bird's neck and (b) a rat's tail.
Three dimensional structure
the shapes which form when the secondary spirals of the protein chain further fold up on themselves.
any final alterations in the protein required for biological activity
Chains may bind together or other inorganic substances may be incorporated into the molecule.
In both hemoglobin and myoglobin, there is an Iron (Fe) ion at the center and carries oxygen (O).
A similar porphyrin ring, with magnesium (Mg) at its center is the essential part of a Chlorophyll molecule, and required for photosynthesis!
like Collagen, Silk, Keratin (hair) and Chitin (insect exoskeleton) tend to be insoluble and strong and so they have a structural role for support or protection.
What is their predominant secondary structure?
The most common group are enzymes, which control the reactions in living cells. They tend to be soluble and, due to their globular shape include an active site.
An enzyme found in tears and mucus which acts as a strong anti-bacterial agent because it digests bacteria cell walls.
It has 129 amino acids folded in both alpha helices and anti-parallel hairpins.
Can you see the active site?
A protein digesting enzyme in your stomach.
Only the carbon backbone is shown so the secondary structure can be seen.
Some parts are twisted into an alpha helix. Other parts ( in bold ) are the straight beta sheets.
Spot the active site!
Subtilisin is a bacterial enzyme, shown here binding with its substrate.
The substrate is a short polysaccharide made from six sugar molecules, which is part of the bacterial cell wall.
The substrate (in bold) is wedged into its active site and held in place by the hydrogen bonds (shown as dotted lines).
This is the ‘ enzyme- substrate complex ’ which forms for a brief moment during any enzyme controlled reaction.
Structure of Fatty Acids
The long hydrocarbon chain (or, tail) is hydrophobic .
The head of the molecule is a carboxyl group which is hydrophilic .
Fatty acids are the main component of soap, where their tails are soluble in oily dirt and their heads are soluble in water to emulsify and wash away the oily dirt.
Types of fatty acids
Saturated, mono-unsaturated and polyunsaturated fats refer to the number of hydrogens attached to the fatty acid tail!
The 'kinks' in the tail (caused by C=C bonds) cause the molecules to have large spaces in between the tails, and causes the fats to be liquid at room temp.
What about “trans”-fatty acids??
Cis & Trans orientation; note position of H.
Naturally-occurring unsaturated vegetable oils have almost all cis bonds, but using oil for frying causes some of the cis bonds to convert to trans bonds.