The building blocks of life

1
The building blocks of life
2
The chemistry of life (cell metabolism)

• Small compounds
• O2
• CO2
• C2H5OH
• ATP
• Glucose
• etc.

• Macromolecules
• polysaccharides (large carbohydrates)
• lipids (fats)
• proteins
• nucleic acids

3
The central role of proteins in the chemistry of
life

• Proteins have a variety of functions. Structural
  proteins
• make up the physical structure of cells. Enzymes
  catalyze
• chemical reactions. Other proteins are involved
  in
• transport and storage of chemicals, and yet
  others, for
• example hormones, are involved in the regulation
  of
• biological processes. Transmembrane proteins are
  
• involved in transmission of chemical signals or
  in the
• selective transport of chemicals across cellular
  membranes.

4
A common belief

• It is generally believed that what happens in a
  cell at any
• given time is largely determined by how much of
  which
• proteins are present (expressed) at that time.

5
The building blocks of proteins

• As a first approximation, proteins can be thought
  of as
• long chains of amino acids, that is,
  polypeptides. There are
• 20 different amino acids. Each of them consists
  of a
• central carbon atom that is bonded to a carboxyl
  group, a
• hydrogen atom, an amino group, and a side chain.
  Each
• amino acid has its own characteristic side chain.

6
How proteins differ from each other

• Proteins differ by their length (typically a few
  hundred
• amino acids) and by the sequence of amino acids
  that
• make up the polypeptide chain. This sequence is
  often
• referred to as the primary structure of a
  protein. The
• function of of a protein in the chemistry of the
  cell is
• largely determined by the three-dimensional
  structure of
• the protein.

7
Abbreviations for amino acids

• Alanine A Ala
• Arginine R Arg
• Asparagine N Asn
• Aspartic acid D Asp
• Cysteine C Cys
• Glutamine Q Gln
• Glutamic acid E Glu
• Glycin G Gly
• Histidine H His
• Isoleucine I Ile

• Leucine L Leu
• Lysine K Lys
• Methionine M Met
• Phenylalanine F Phe
• Proline P Pro
• Serine S Ser
• Threonine T Thr
• Tryptophan W Trp
• Tyrosine Y Tyr
• Valine V Val

8
Characteristic properties of amino acids

• Amino acids differ in a number of physical and
  chemical
• properties. The most obvious of these properties
  is size of
• the side chain, with glycine and tryptophan being
  on
• opposite extremes of the spectrum.

9
Characteristic properties of amino acids

• Another important property is the distinction
  between
• hydrophobic and hydrophylic amino acids. Proteins
  tend to
• fold in such a way that hydrophylic amino acids
  will be
• exposed to aqueous environments, such as the
  cytoplasm,
• whereas hydrophobic amino acids tend be located
  away
• from water, for example, in the hydrophobic core
  of a
• protein, or within the bilipid layer of a cell
  membrane.
• Hydrophibicity is strongly correlated with
  polarity polar
• amino acids tend to be hydrophylic, nonpolar ones
  tend to
• be hydrophobic.

10
Peptide bonds
11
Three-dimensional structure of proteins

• The function of a protein is to a large degree
  determined
• by its 3D structure which has several levels
• Secondary structure refers to local coils and
  folds, like alpha-helices and beta-sheets (or
  pleated sheets). It results from local hydrogen
  bonds that occur at regular intervals.
• Tertiary structure of a polypeptide chain is
  superimposed on the secondary structure. It may
  result from bonding of side chains or hydrophobic
  interactions.
• Quarternary structure is the overall protein
  structure that results from the aggregation of
  polypeptide subunits.

12
The Brookhaven Protein Data Bank

• Repository of three-dimensional structures for
  proteins
• located in Brookhaven, U.S.A.
• http//www.rcsb.org/
• Data are kept in PDB file format, which is
  readable by
• RasMol.

13
Homework

• Get the RasMol viewer from www.umass.edu/microbio
  /rasmol/ and install it.
• Download HTML source file of homework template
  from my web site.
• Get .pdb file of a nice protein from Brookhaven
  protein data bank from your adopted organism.
• Open the .pdb file with RasMol, and have RasMol
  display as nice a picture of it as possible.

14
Homework

• Export the picture as a .gif file, and use the
  template to create a web page with the relevant
  info and picture of your protein.
• Send the web page and .gif file via e-mail to me
  by Thursday. Indicate whether you agree that
  your web page be posted.
• The assignment is worth two points.