Chapter 5c: The Structure and Function of Macromolecules (Proteins)

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Chapter 5cThe Structure andFunction
ofMacromolecules(Proteins)
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Polymers, Monomers, and Lipids
polymer category of biomolecules monomer
polysaccharide carbohydrates monosaccharides
polypeptides proteins amino acids
polynucleic acids RNA DNA nucleotides
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Protein Overview

• Major constituent of most cells (gt50 dry weight)
• Highly sophisticated molecules (or
  multi-molecular complexes)
• Extremely large number of unique proteins exist
• They are polymers folded into specific
  conformations (shapes)
• Conformation and functional-group chemistry
  controls function
• Made up of 20 different types of amino-acid
  monomers
• Proteins define what an organism is, what it
  looks like, how it behaves, etc. (responsible for
  most phenotype)
• You are your proteins!

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Protein Function
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Globular versus Fibrous
Fibrous protein (e.g., collagen)
Just know general shapes
Globular protein (e.g., hemoglobin)
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Enzymatic Catalysis
Globular protein
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Monomer (amino acid) Structure
R group
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Amino Acid Structure
The chemistry of R groups distinguishes amino
acids and their properties
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Amino Acid Ionization
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Amino Acid Types
Name     R-Group Properties
Glycine G Gly Hydrophobic
Alanine A Ala Hydrophobic
Valine V Val Hydrophobic
Leucine L Leu Hydrophobic
Isoleucine I Ile Hydrophobic, two chiral carbons
Proline P Pro Cyclic, not terribly hydrophobic
Phenylalanine F Phe Hydrophobic, bulky
Tyrosine Y Tyr Less hydrophobic (than Phe), bulky
Tryptophan W Trp Hydrophobic, bulky (indole ring)
Cysteine C Cys Hydrophobic, highly reactive (S-S link)
Methionine M Met Hydrophobic (start a.a.)
Serine S Ser Hydrophilic, reactive
Threonine T Thr Hydrophilic, reactive, two chiral carbons
Lysine K Lys Highly hydrophilic, positively charged
Arginine R Arg Highly hydrophilic, positively charged
Histidine H His Highly hydrophilic, positive or neutral
Aspartate D Asp Highly hydrophilic, negatively charged
Glutamate E Glu Highly hydrophilic, negatively charged
Asparagine N Asn Uncharged
Glutamine Q Gln Uncharged
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Non-Polar R groups
Know me!
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Polar R groups
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Five Categories
Note 20 (naturally translated) amino acids
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The Peptide
No need to know side chain structures
  Backbone -N-C-C-N-C-C-N-
Polypeptide linear chain of amino acids linked
by peptide bonds
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Making the Peptide Bond
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Limited Rotation
Explanation of double-bond character (resonance)
Be able to know which is the peptide bond
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Backbone Rigidity
Because of Resonance the backbone of polypeptides
has greater rigidity than otherwise might be
expected
Polypeptide backbones are more than just wet
noodles!
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Protein Depiction (4 ways)
Conformation Shape ? Function
The surface chemistry of a protein is determined
by the chemistry of exposed amino-acid R groups
The interior of proteins is held together by
R-group-to-R-group and backbone-to-backbone
interactions
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ATP Synthase
This is what you use to make the bulk of your ATP
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Pseudo 3D Image
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Conformation Shape ? Function
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Levels of Protein Structure
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Protein Primary Structure
1 structure ordered sequence of amino acids
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Protein Primary Structure
Note the Polarity of the sequence (amino ?
carboxy)
Note also the disulfide linkages (cys-cys ? S-S
bonds actually considered a component of
tertiary structure)
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Protein Secondary Structure
Be able to recognize name these
Held together by interactions (H-bonds) between
peptide backbones
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2 Structure H-Bonds
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2 to Tertiary Structure
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Protein Tertiary Structure
Tertiary structure is controlled by the
interactions between non-adjacent amino acid R
groups (note bond types)
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Protein Quaternary Structure
Quaternary structure is the interaction between
adjacent polypeptides that make up a single
protein
Note that the polypeptides reside in discrete
subunits rather than being tangled together like
spaghetti
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Protein Structure Overview
Polypeptide is not quite synonymous with
protein. The relationship is somewhat analogous
to that between a long strand of yarn and a
sweater of a particular size and shape that one
can knit from the yarn. A functional protein is
not just a polypeptide chain, but one or more
polypeptides precisely twisted, folded, and
coiled into a molecule of unique shape. It is the
amino-acid sequence of a polypeptide that
determines what three-dimensional conformation
the protein will take. (p. 70, Campbell et al.,
1999) (see p. 81 of 2005 edition)
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Sickle-Cell Disease
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Protein Denaturation
Destruction of Conformation Loss of Function
Some simple proteins can spontaneously renature
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Protein Folding
A proteins specific conformation determines how
it works. In almost every case, the function of a
protein depends on its ability to recognize and
bind to some other molecule. p. 81, Campbell
Reece (2005)
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Chaparonins
They segregate protein folding from bad
influences in the cell
Chaparonins Assist in Protein Folding
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The End