8/30/2013

Proteins:
Cellular workhorses
Becker’s Ch 3: p 41-54

Veronica R. Moorman, Ph.D. moormanr@sas.upenn.edu

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Announcements

• Reminder – BIOL-123 labs start the week of

September 9th. There are no labs next week.

• If you still do not have access to our

Blackboard site (or are having other
problems), please e-mail me and I should be
able to help.

moormanr@sas.upenn.edu

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Proteins outline

• Functional groups of the various amino acids

• Peptide bonds
• Four levels of protein structure
• Connections between proteins and chemistry
• Classes of proteins by shape and by function
• The relationship of protein structure to sickle cell anemia
and hair curliness

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Proteins are a large class of

macromolecules present in all cells.

Fig 2-29. Molecular Biology of the Cell, 5th ed. Hardin, et al. © 2008 Garland Science.

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Proteins are built from 20 amino acid (aa)

building block monomers.

Fig 3-1. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson. Fig 3-2. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

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Nine aas have nonpolar or hydrophobic

R groups.

Fig 3-2. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

• Mostly made up of carbons and hydrogens

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Acidic aas are negatively charged, while

basic aas are positively charged.
true at physiological pH

Fig 3-2. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

You should be able to identify some functional groups

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The remaining aas are polar or hydrophilic

due to their atoms’ electronegativity.

Fig 3-2. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

You should be able to identify some functional groups

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You do not need to

memorize, but do
need to be able to
recognize properties
based on the
structures from the
previous pages

Table 3-2 Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

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Amino acids bind together with peptide

bonds made through dehydration reactions.

You should be able to

identify peptide bonds
Fig 3-3. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

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The sequence of amino acids in a

polypeptide chain is the 1° structure.
Where are the peptide bonds?
How many aa residues are there?
What amino acids are they?
What functional groups do you see?
What types of interactions can they
undergo?

+H N
3
Amino
end
Amino- (N-) terminus Carboxy- (C-) terminus

By convention: written from amino to carboxyl ends

N-Ser-Gly-Tyr-Ala-Val-C
Ser-Gly-Tyr-Ala-Val What is the net charge (sum of all
the charges) on this peptide? COO-
Carboxyl end
Fig 5-12. Biology, 7th ed. Campbell and Reece. © 2005 Pearson.

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Proteins are not just the polypeptide chain;

they are the specific folded shape.

Fig 3-8. Molecular Biology of the Cell, 5th ed. Hardin, et al. © 2008 Garland Science.

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2° structure is the patterned H-bonding

between backbone functional groups.
• Many weak bonds together are strong
• Regular shapes, mainly:
– ‐helix
– -sheet

Fig 3-8. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

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-helices form H-bonds every 4th residue

and have 5.4 Å/3.6 aa per turn.

R-groups point
outwards

Fig 4-4. Lehninger Principles of Biochemistry 6th ed. Nelson and Cox. 2013 W.H. Freeman.

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-sheets can be parallel or antiparallel

depending on strand end orientation.
Parallel sheet
• R-groups alternate going up
N C and down (in/out of the
board plane)
N C • H-bonding angle differs

C Top views
N Antiparallel sheet

N C

C N

N C
Fig 4-6. Lehninger Principles of Biochemistry 6th ed. Nelson and Cox. 2013 W.H. Freeman.

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Each type of globular protein has its own

unique 3° structure.
• Neither repetitive nor easily predictive

London dispersion forces and

Fig 3-12. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

You should know which aa residues can

undergo each of these interactions
Fig 3-5. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

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Disulfide bridges are covalent bonds

between sulfur atoms in cysteine residues.

oxidation
Where is the oxidation?
Where is the reduction?
reduction

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The 4° structure involves subunit

interactions and assembly.
• Term applies only to multimeric proteins
– Has more than one polypeptide chain
• Same chemical interactions as with tertiary structure

Fig 3-11. Life, 10th ed. Sadava, et al. © 2014 W.H. Freeman.

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Proteins have primary (1°), secondary (2°),

tertiary (3°) (and quaternary (4°)) structure.
2°
1°
3°

4°

Fig 3-6. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

Table 3-3 Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson

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Structural classes of proteins each have

their own typical properties.

Globular proteins Fibrous proteins Membrane proteins

Roughly spherical Rod-like ‐helix(es) or -barrel

Chemical functions Structural functions Signaling or transport
Fold/function in water Not soluble in water Fold/function in membrane
Hydrophobic core No core (little 3 ° structure) Hydrophobics in bilayer
Eg. hemoglobin Eg. keratin Eg. aquaporin

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Sickle cell anemia is a disease where the

protein hemoglobin clumps together.
Molecules do not 
associate; each 
carries oxygen

Healthy 

Glutamate
New Exposed  Molecules interact & 
Hydrophobic Patch
form a fiber; capacity 
to carry oxygen lower

Disease RBCs get 
stuck in 
blood 
Valine vessels
Amino Acid 1 ° 3 ° 4 ° Association Red Blood Cell
Biology, 7th ed. Campbell and Reece. © 2005 Pearson.

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The fibrous protein keratin has extensive

quaternary structure in hair.
1°
MTCGSGFGGRAFSCISACGPRPGRCCITAAPYRGISCYRGLTGGFGSHSVCGGFRAGSC…
2°

4°
4°

4° 4°

Fig 3-10. Becker’s World of the Cell, 8th ed. Hardin, et al. © 2012 Pearson.

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Bonding interactions of keratin can change

hair curliness.
Disulfide bridges:
Straight Curly Straight
hair hair hair

straighten

Hydrogen bonding: Which is more permanent?

Straight
Straight Curly hair
hair hair

Water straighten Dry

Water Dry
Heat Cool
Heat Cool

Box 4-2. Lehninger Principles of Biochemistry 6th ed. Nelson and Cox. 2013 W.H. Freeman.
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Column chromatography separates

proteins using a solid, porous matrix.

• Separation by
– Charge
– Size
– Affinity
– Hydrophobicity

Fig 3-16. Lehninger Principles of Biochemistry 6th ed. Nelson and Cox © 2013 W.H. Freeman.

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SDS-PAGE (gel electrophoresis) also

separates proteins based on peptide length.
• Proteins must be made negatively charged - SDS
• Proteins must be denatured - Reducing agent, denaturant, heat
– Can also be done “natively”

Length of
protein
Fig 3-18. Lehninger Principles of Biochemistry 6th ed. Nelson and Cox. © 2013 W.H. Freeman.

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Proteins can also be classified by their

overall function.
• Enzymes – catalysts
• Structural proteins - physical support and shape
• Motility proteins - contraction and movement
• Regulatory proteins – control/coordinate cell function
• Transport proteins - move substances in/out of cells
• Hormonal proteins - communication between cells
• Receptor proteins - enables response to chemical stimuli
• Defensive proteins - protect against disease
• Storage proteins - reservoirs of amino acids

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Question for the weekend:

Myoglobin is an oxygen-binding protein found in the muscle tissues of vertebrates. It
is evolutionarily related to hemoglobin, which is the oxygen-binding protein found in
red blood cells. Myoglobin exists as a monomer in solution. Hemoglobin is a
tetrameric protein consisting of two a and two b subunits. The structures of the
individual a and b subunits of hemoglobin are remarkably similar to that of the single
subunit that makes up myoglobin. However, at a number of positions hydrophilic
residues in myoglobin have been replaced by hydrophobic residues in the a and b
subunits of hemoglobin.

Myoglobin
(monomer) A. How can this observation be reconciled with the
generalization that hydrophobic residues fold
into the interior of soluble proteins?

B. On the basis of your considerations, what can you

say about the types of interactions determining
quaternary structure in hemoglobin?
Hemoglobin (a2b2 tetramer)

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