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Proteins
AP Biology
Proteins
Diverse group
Made of Amino Acids
AP Biology
2008-2009
Proteins
 Most structurally & functionally diverse group
 Function: involved in almost everything

Enzymes (pepsin, DNA polymerase)

Structural Support (keratin, collagen)

Transport of substances (hemoglobin, aquaporin)

Hormones (insulin & other hormones)

Defense (antibodies)

Contraction and Movement (actin & myosin)

Storage (bean seed proteins)
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Proteins
 Structure

H2O
monomer = Amino Acid
 20 different amino acids

polymer = Chains of AA
 protein can be one or more polypeptide
chains folded & bonded together
 large & complex molecules
 complex 3-D shape
hemoglobin
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Rubisco
growth
hormones
Amino acids
 Structure
central carbon
 amino group
 carboxyl group (acid)
 R group (side chain)

H O
H
| ||
—C— C—OH
—N—
|
H
R
 variable group
 different for each amino acid
 confers unique chemical
properties to each amino acid
 like 20 different letters of an
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alphabet
 can make many words (proteins)
Effect of different R groups:
Nonpolar amino acids
 nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?
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Effect of different R groups:
Polar amino acids
 polar or charged & hydrophilic
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Why are these polar & hydrophillic?
Ionizing in cellular waters
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H+ donors
Ionizing in cellular waters
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H+ acceptors
Sulfur containing amino acids
 Form Disulfide bonds


covalent cross links betweens sulfhydryls
stabilizes 3-D structure
H-S – S-H
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Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Fig. 7.12 (TEArt)
ss
Light chain
a chain b chain
s s
s s
s s
s s
ss
ss
Constant region
Variable region
S S Disulfide bond
ss
ss
ss s
s
ss
ss
s s
s s
s s
s s
ss
s
s
ss ss
Light chain
a chain
Heavy
chains
s s
s s
s
s
b-2
microglobulin
a chain
b chain
s
s
ss
ss
s s
s s
MHC-I
MHC-II
Plasma
membrane
T Receptor
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B Receptor
Building proteins
 Peptide Bond
covalent bond between NH2 (amine) of
one amino acid & COOH (carboxyl) of
another
 C–N bond

H2O
dehydration synthesis
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peptide
bond
Building proteins
 Polypeptide chains have direction
N-terminus = NH2 end
 C-terminus = COOH end
 repeated sequence (N-C-C) is the
polypeptide backbone

 can only grow in one direction
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Protein structure & function
 Function depends on structure

3-D structure
 twisted, folded, coiled into unique shape
pepsin
hemoglobin
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collagen
Primary (1°) structure
 Chain of Amino Acids
amino acid sequence
determined by gene (DNA)
 slight change in amino acid
sequence can affect protein’s
structure & its function

 even just one amino acid change
can make all the difference!
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lysozyme: enzyme
in tears & mucus
that kills bacteria
Sickle cell anemia
I’m
hydrophilic!
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But I’m
hydrophobic!
Secondary (2°) structure
folding along short sections of polypeptide
 interactions between
adjacent amino acids

 Hydrogen Bonds
 weak bonds
between R groups

forms sections of
3-D structure
 Alpha Helix
 B Pleated Sheet
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Secondary (2°) structure
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Tertiary (3°) structure
 interactions between distant amino acids
 Hydrophobic Interactions
 cytoplasm is
water-based
 nonpolar amino
acids cluster away
from water
 H-Bonds
 Disulfide Bonds
 covalent bonds between
sulfurs in sulfhydryls (S–H)
 anchors 3-D shape
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Quaternary (4°) structure
 Consists of the interactions of two or more
polypeptide chains

only then does polypeptide become
functional protein
AP Biology = skin & tendons
collagen
hemoglobin
Protein structure (review)
R groups
hydrophobic interactions
disulfide bridges
(H & ionic bonds)
3°
multiple
polypeptides
hydrophobic
interactions
1°
amino acid
sequence
peptide bonds
determined
by DNA
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4°
2°
R groups
H bonds
Fig. 5-21d
Abdominal glands of the
spider secrete silk fibers
made of a structural protein
containing b pleated sheets.
The radiating strands, made
of dry silk fibers, maintain
the shape of the web.
The spiral strands (capture
strands) are elastic, stretching
in response to wind, rain,
and the touch of insects.
AP Biology
2008-2009
Protein Folding in the Cell
 It is hard to predict a protein’s structure
from its primary structure
 Most proteins probably go through several
states on their way to a stable structure
 Chaperonins are protein molecules that
assist the proper folding of other proteins
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Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-24
Polypeptide
Correctly
folded
protein
Cap
Hollow
cylinder
Chaperonin
(fully assembled)
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Steps of Chaperonin 2
Action:
1 An unfolded polypeptide enters the
cylinder from one end.
The cap attaches, causing the 3 The cap comes
cylinder to change shape in
off, and the properly
such a way that it creates a
folded protein is
hydrophilic environment for
released.
the folding of the polypeptide.
Protein denaturation
 Unfolding a protein

alter 3-D shape

some proteins can return to their functional
shape after denaturation, many cannot
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Let’s build some
Proteins!
AP Biology
2008-2009