CHEM
30 B Dr. R.
Rinehart
Chapter 19
PROTEINS
Proteins are the most important molecules in living organisms, because they are involved in everything that the organism does. They are polymers of amino acids. The DNA in the cell genome is essentially a set of instructions for the assembly of the thousands of different proteins which the cell needs to function.
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PowerPoint-type presentations on amino acids and proteins
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|
A really good, well-illustrated chapter on amino acids
and proteins |
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A really great text is available online in PDF
format |
I. AMINO ACIDS [see the tables for names and structures and other factoids]
see the
chapter 19 alphabetical amino acid table
A. General structure
1. Carboxylic
acid with amino group at position #2 [“a”
to the -CO2H]
2.
Fisher projection: all are L- except glycine
3. 20
different R-groups or “side chains;”
AA’s can be grouped into four families based on polarity of
side chain
a.
Nonpolar “hydrophobic”:
GLY, ALA, VAL, LEU, ILE, PHE, PRO, MET, TRP
b.
Polar, nonionic/ “neutral”:
SER, THR, TYR, CYS, ASN, GLN
c.
Polar, cationic
(+)
[“basic”]: HIS, LYS, ARG
d.
Polar, anionic (-)
[“acidic”]: ASP, GLU
|
Chime
introduction to amino acids, by Örjan Hansson at Göteborg University http://www.lundberg.gu.se/~orjan/bmstruct/ > Amino Acids Use Netscape!!! |
| Chime
tutorial on amino acids by Timothy Driscoll, from Worth, publishers of Lehninger Principles of Biochemistry, 3/e by Nelson and Cox http://www.worthpublishers.com/lehninger3d/lold/index.html > Protein Architecture > 1. Amino Acids Use Netscape!!! |
| Chime
stuff on amino acids by Duane W. Sears at UC Santa Barbara http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/ > Amino Acids |
| A really
good amino acid subject outline and Chime structures by Gordon Rule at Carnegie Mellon University is at http://web.archive.org/web/20051202165858/stingray.bio.cmu.edu/~web/bc/Lec/Lec04/lec04.html http://web.archive.org/web/20050827014639/stingray.bio.cmu.edu/~web/bc/Lec/Lec04/lec04.PDF http://stingray.bio.cmu.edu/~web/bc/Lec/Lec04/lec04.html |
| Notes
on amino acid side chains and their properties by Richard A. Paselk at Humboldt State U http://www.humboldt.edu/~rap1/C431.F01/C431Notes/C431n12sep.htm |
B. Properties
1. ZWITTERIONS at pH 7
2. Charge
varies with pH [low pH => more (+)
; high pH => more (-)]
3. Side
chain charge can also vary with pH
4.
Each amino acid has a unique “isoelectric point” [pI], or specific pH
where it
has NO net charge
|
to see more on the effect of pH on
side-chain ionization, go to The MIT Biology Hypertext at |
| To see more on peptide bond formation, go to The MIT Biology
Hypertext at http://web.archive.org/web/20060427180128/web.mit.edu/esgbio/www/lm/proteins/peptidebond.html http://web.mit.edu/esgbio/www/lm/proteins/peptidebond.html |
| and John Kimball's Biology Pages at http://www.ultranet.com/~jkimball/BiologyPages/P/Polypeptides.html#proteins |
II. PEPTIDES
A. Contain 2 to 50 amino acids
B. Biologically active as neurotransmitters, hormones, hormone-releasing
factors
C. Examples
III. PROTEINS: contain ~50 to ~10,000 amino acids
A. Molecular weight ~5000 to 1,000,000
B. Can act as buffers
C. FUNCTIONS
1.
Catalytic: ENZYMES
2. Structural: collagen, keratin
3. Storage/nutrition: zein, gluten, ferritin, casein, ovalbumin
4. Protective: immunoglobulins
5. Regulatory: hormones: insulin, glucagon
6. Communication: neurotransmitters
7. Motion: actin/myosin; tubulin/dynein; flagellin
8. Transport: hemoglobin, transferrin
D. Classification
1.
By shape: FIBROUS vs GLOBULAR
| Clarke Earley at Kent State University has a
Chime display of collagen at http://www.personal.kent.edu/~cearley/PChem/jmol/collagen.htm http://www.personal.kent.edu/~cearley/PChem/pchem.htm > Collagen In Jmol, not Chime, so should work with any Java-enabled browser |
| Chime and non-Chime pictures of a few
globular proteins by Mark Bishop of MPC are at http://www.mpcfaculty.net/mark_bishop/proteins.htm |
2.
By composition: SIMPLE:
contain only amino acids
CONJUGATED: contain NONprotein “prosthetic groups”
glycoproteins, phosphoproteins, lipoproteins, metalloproteins, hemoproteins,
etc.
E. LEVELS OF PROTEIN STRUCTURE
|
see a brief
presentation of 1o to 4o structure from the MIT Biology
Hypertext at |
1.
Primary:
peptide backbone with specific sequence of amino acids
backbone has amide bonds at every third atom;
for a peptide/ protein with n amino acids, there are (20)n
possible sequences
2. SECONDARY:
orderly pattern of
backbone folding due to H-bonding
a. alpha- [a]- helix
|
to
see a Chime tutorial on the a-helix by F.
Reichsman at U. Mass., go to
[use Netscape
4.7x!!] http://www.umass.edu/molvis/freichsman/protarch/page_helix/menu.html |
b.
beta [b]
structures: pleated
sheets, ribbons, bends, and barrels
|
to
see a Chime tutorial on the b-sheet by F.
Reichsman at U. Mass., go to
[use Netscape
4.7x!!] |
c.
random coil: neither a
nor b
|
|
3.
TERTIARY: specific overall 3-D shape due to further folding
caused by side-chain
interactions (listed below) with water and with each other.
Of
many possible 3-D shapes, only the most stable one is usually found;
it is called the native conformation of the protein.
a. salt bridges:
ionic interactions between ㊉
and ㊀
side chains
b. hydrogen bonds:
for side chains containing –OH, -NH2, CONH2
c. hydrophobic
interactions: water avoids
contact with nonpolar R,
forcing them to ‘hide’ in the interior; their overall geometry
determines their packing pattern
d.
disulfide bridges: form when two CYS –SH groups are close
together;
-S-S- “lock” protein chains together at that point
|
To
see Chime structures of a number of proteins in their native conformations, |
4. QUATERNARY:
many proteins require multiple subunits to function;
these
subunits (single peptide chains already folded into 3o shapes) adhere
to each
other via the same types of interactions responsible for 3o
structure between
groups on the outer surface of the 3o units;
additional types of covalent bonds besides S-S may also be present
(ester, amide, aldimine)
| A
Chime tutorial covering all levels of protein structure by Timothy
Driscoll [use Netscape 4.7x!!] designed to accompany Lehninger's biochemistry text is available at http://www.worthpublishers.com/lehninger3d/lold/index.html |
| Chime
stuff on protein structure by Duane W. Sears at UC Santa Barbara
[use Netscape 4.7x!!] http://tutor.lscf.ucsb.edu/instdev/sears/biochemistry/ > Proteins |
| An
extensive discussion of the levels of protein structure by John C. Pérez
of Texas A&M's Natural Toxins Research Center at Kingsville is available at http://web.archive.org/web/20041212233704/ntri.tamuk.edu/homepage-ntri/lectures/protein/polypeptide.html http://ntri.tamuk.edu/homepage-ntri/lectures/protein/polypeptide.html |
| Notes
on levels of protein structure by
Richard A. Paselk at Humboldt State U http://www.humboldt.edu/~rap1/C431.F01/C431Notes/C431n14sep.htm http://www.humboldt.edu/~rap1/C431.F01/C431Notes/C431n17sep.htm and http://www.humboldt.edu/~rap1/C431.F01/C431Notes/C431n19sep.htm and http://www.humboldt.edu/~rap1/C431.F01/C431Notes/C431n21sep.htm |
5. what
happens at one level determines what happens at the next; ultimately,
the sequence of amino acids controls everything else; and the genetic
information in DNA determines
the sequence.
DNA à
1o à
2o à
3o à
4o à
function
| Chime
structure of ferritin from Shelley Gaudia at Lane CC is at
[use Netscape 4.7x!!] http://web.archive.org/web/20040201024554/staff.lanecc.edu/~gaudia/ferritin.pdb http://staff.lanecc.edu/~gaudia/ferritin.pdb |
| Fibronectin
Chime tutorial from Michael Ward and David Marcey at Kenyon College
[use Netscape 4.7x!!] http://biology.kenyon.edu/BMB/Chime/Fibronectin/fibro.htm |
| Hemoglobin
Chime tutorial by Lisa Natzke at Kenyon College
[use Netscape 4.7x!!] http://biology.kenyon.edu/BMB/Chime/Lisa/HEMEMAST.HTM |
F. Reactions of proteins
1. Hydrolysis: catalyzed by acid, base, or enzymes
2. DENATURATION:
loss of biological function associated with changes in 2o/3o/4o
structure
caused by:
extremes of temperature
extremes of pH
mechanical agitation
organic solvents
detergents
exposure to surfaces
heavy metal ions [Pb2+, Hg+, Hg2+, ….]
H-bond disruptors [urea, guanidinium chloride]
reduction
of S-S bonds
denaturation
is USUALLY irreversible
http://www.lundberg.gu.se/~orjan/bmstruct/ |
http://www.wellesley.edu/Chemistry/chem227/protstruct/prtnstrc.htm |
http://www.bio.cmu.edu/courses/03231/ProtStruc/ProtStruc.htm |
| Voet, Voet, Pratt:
Fundamentals of Biochemistry: Life at the Molecular Level, 2nd Edition
http://bcs.wiley.com/he-bcs/Books?action=resource&bcsId=2261&itemId=0471214957&resourceId=5420 animations and other goodies |
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© Ronald W. Rinehart, 2002-2007