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Proteins
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3.5 What Are Proteins?
– Proteins are molecules composed of chains of amino
acids
– Proteins have a variety of functions
– Enzymes are proteins that promote specific
chemical reactions
– Structural proteins (e.g., elastin) provide support
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Table 3-3
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Proteins
 Most structurally & functionally diverse group
 Function: involved in almost everything







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enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
 signals (insulin & other hormones)
 receptors
defense (antibodies)
movement (actin & myosin)
storage (bean seed proteins)
 play a role in cell membrane function
 receptor proteins: recognize and bind to
substances wanting to enter membrane
 transport proteins: help transport substances
across cell membrane
 build
muscles
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Figure 3-17 Structural proteins
Hair
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Horn
Silk
3.5 What Are Proteins?
 Proteins are molecules composed of chains of amino acids
(continued)
– Proteins are polymers of amino acids joined by peptide bonds
– All amino acids have a similar structure
– All contain amino and carboxyl groups
– All have a variable “R” group
– Some R groups are hydrophobic
– Some are hydrophilic
– Cysteine R groups can form disulfide bonds
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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)
Oh, I get it!
amino = NH2
acid = COOH
Figure 3-18 Amino acid structure
variable
group (R)
amino
group
carboxylic
acid group
hydrogen
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3 - Proteins (Honors)
 contain C, H, O, and N (nitrogen)
 amino acids (monomer) bonded together
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3.5 What Are Proteins?
 Amino acids are joined by dehydration synthesis
– An amino group reacts with a carboxyl group, and
water is lost
– The covalent bond resulting after the water is lost is a
peptide bond, and the resulting chain of two amino
acids is called a peptide
– Long chains of amino acids are known as
polypeptides, or just proteins
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Figure 3-20 Protein synthesis
amino acid
amino
group
dehydration
amino acid synthesis
carboxylic amino
acid group group
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peptide
peptide
bond
water
Building Proteins
dehydration synthesis / condensation rxn:
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http://www.wisc-online.com/objects/index_tj.asp?objID=AP13304
Proteins
 Structure

H2O
monomer = amino acids
 20 different amino acids

polymer = polypeptide
 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
Figure 3-19 Amino acid diversity
glutamic acid (glu)
aspartic acid (asp)
Hydrophilic functional groups
phenylalanine (phe)
leucine (leu)
Hydrophobic functional groups
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cysteine (cys)
Sulfur-containing
functional group
3.5 What Are Proteins?
 A protein can have as many as four levels of
structure
– Primary structure is the sequence of amino acids
linked together in a protein
– Secondary structure is a helix, or a pleated sheet
– Tertiary structure refers to complex foldings of the
protein chain held together by disulfide bridges,
hydrophobic/hydrophilic interactions, and other bonds
– Quaternary structure occurs where multiple protein
chains are linked together
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Animation: Protein Structure
Figure 3-21 The four levels of protein structure
Primary structure:
Secondary structure:
The sequence of amino
acids linked by peptide
bonds
Usually maintained by
hydrogen bonds, which
shape this helix
leu
val
heme group
lys
lys
gly
his
hydrogen
ala bond
lys
val
Quaternary structure:
Tertiary structure:
lys
helix
pro
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Folding of the helix results
from hydrogen bonds with
surrounding water molecules
and disulfide bridges between
cysteine amino acids
Individual polypeptides are
linked to one another by
hydrogen bonds or disulfide
bridges
Figure 3-22 The pleated sheet and the structure of silk protein
hydrogen
bond
stack of pleated sheets
Pleated sheet
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Structure of silk
disordered
segment
strand
of silk
Building proteins
 Peptide bonds
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
 Order of amino acids in chain
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
Secondary (2°) structure
 “Local folding”
folding along short sections of polypeptide
 interactions between
adjacent amino acids

 H bonds
 weak bonds
between R groups

forms sections of
3-D structure
 -helix
 -pleated sheet
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Secondary (2°) structure
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Sulfur containing amino acids
 Form disulfide bridges


covalent cross links betweens sulfhydryls
stabilizes 3-D structure
H-S – S-H
You wondered
why perms
smell like
rotten eggs?
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Tertiary (3°) structure
 “Whole molecule folding”

interactions between distant amino acids
 hydrophobic interactions
 cytoplasm is
water-based
 nonpolar amino
acids cluster away
from water
 H bonds & ionic bonds
 disulfide bridges
 covalent bonds between
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sulfurs in sulfhydryls (S–H)
 anchors 3-D shape
Quaternary (4°) structure
 More than one polypeptide chain bonded
together

only then does polypeptide become
functional protein
 hydrophobic interactions
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
3.5 What Are Proteins?
 The functions of proteins are related to their threedimensional structures
– Precise positioning of amino acid R groups leads to
bonds that determine secondary and tertiary structure
– Disruption of secondary and tertiary bonds leads to
denatured proteins and loss of function
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Protein denaturation
 Unfolding a protein

In Biology,
size doesn’t matter,
SHAPE matters!
conditions that disrupt H bonds, ionic
bonds, disulfide bridges
 temperature
 pH
 salinity

alter 2° & 3° structure
 alter 3-D shape

destroys functionality
 some proteins can return to their functional shape
after denaturation, many cannot
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Denatured protein
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Sickle cell anemia
I’m
hydrophilic!
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Just 1
out of 146
amino acids!
But I’m
hydrophobic!