Biol121 Fall2013 Lecture2 Proteins

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Proteins:Cellular workhorses

Beckers Ch 3: p 41-54

8/30/13 BIOL-121, Fall 2013, "Proteins" 1

Veronica R. Moorman, Ph.D. [email protected]

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Reminder BIOL-123 labs start the week of September 9th. There are no labs next week.

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8/30/2013

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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


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. Beckers World of the Cell, 8th ed. Hardin, et al. 2012 Pearson. Fig 3-2. Beckers World of the Cell, 8th ed. Hardin, et al. 2012 Pearson.

Nine aas have nonpolar or hydrophobic R groups.

Mostly made up of carbons and hydrogens


Fig 3-2. Beckers World of the Cell, 8th ed. Hardin, et al. 2012 Pearson.

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Acidic aas are negatively charged, while basic aas are positively charged.

You should be able to identify some functional groups



true at physiological pH

The remaining aas are polar or hydrophilic due to their atoms electronegativity.

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 Beckers World of the Cell, 8th ed. Hardin, et al. 2012 Pearson.

Amino acids bind together with peptide bonds made through dehydration reactions.



You should be able to identify peptide bonds

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The sequence of amino acids in a polypeptide chain is the 1 structure.

14

Amino- (N-) terminus Carboxy- (C-) terminus

N-Ser-Gly-Tyr-Ala-Val-C

By convention: written from amino to carboxyl ends

8/30/13 BIOL-121, Fall 2013, "Proteins"

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?

Ser-Gly-Tyr-Ala-Val

+H3NAmino

end

COO-Carboxyl end

Fig 5-12. Biology, 7th ed. Campbell and Reece. 2005 Pearson.

What is the net charge (sum of all the charges) on this peptide?

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



-helices form H-bonds every 4th residue and have 5.4 /3.6 aa per turn.


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

R-groups point outwards

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-sheets can be parallel or antiparallel depending on strand end orientation.


R-groups alternate going up and down (in/out of the board plane)

H-bonding angle differs

Parallel sheet

N

N

N

C

C

C Antiparallel sheetN

N

N

C

C

C


Top views

Each type of globular protein has its own unique 3 structure.



Neither repetitive nor easily predictive


You should know which aa residues can undergo each of these interactions

London dispersion forces and

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Disulfide bridges are covalent bonds between sulfur atoms in cysteine residues.


Where is the oxidation?Where is the reduction?

oxidation

reduction

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.


Table 3-3 Beckers World of the Cell, 8th ed. Hardin, et al. 2012 Pearson


1 2 3

4

Structural classes of proteins each have their own typical properties.


Globular proteins Fibrous proteins Membrane proteins

Roughly spherical Rod-like helix(es) or -barrelChemical 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 bilayerEg. hemoglobin Eg. keratin Eg. aquaporin

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Sickle cell anemia is a disease where the protein hemoglobin clumps together.


Healthy

Disease

NewExposedHydrophobicPatch Moleculesinteract&formafiber;capacity

tocarryoxygenlower

3 4

Moleculesdonotassociate;eachcarriesoxygen

Association RedBloodCell1

Glutamate

ValineAminoAcid

RBCsgetstuckinbloodvessels

Biology, 7th ed. Campbell and Reece. 2005 Pearson.

The fibrous protein keratin has extensive quaternary structure in hair.


1

2

44

44


MTCGSGFGGRAFSCISACGPRPGRCCITAAPYRGISCYRGLTGGFGSHSVCGGFRAGSC

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Bonding interactions of keratin can change hair curliness.


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

Hydrogen bonding:

Disulfide bridges:

straighten

Straight hair

Curlyhair

Straight hair

Water

Heat

Dry

Cool

Straight hair

Curlyhair

Straight hair

straightenWater

Heat

Dry

Cool

Which is more permanent?

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 Proteins must be denatured

- SDS

- Reducing agent, denaturant, heat

Length of protein

Can also be done natively

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.

9/4/13 BIOL-121, Fall 2013, "Enzymes" 54

Hemoglobin (a2b2 tetramer)

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?

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Biol121 Fall2013 Lecture2 Proteins