Download Lecture 15, Feb 26

BIO 311C
Spring 2010
Lecture 15 – Friday 26 Feb.
1
Review
Illustration of a Polypeptide
amino acids
peptide bonds
Polypeptide (chain)
See textbook, Fig 5.21, p. 82
for a more clear illustration
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Folding and
other modifications
Functional Protein
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Structural Formula of an Amino Acid
A single amino acid that is
not chemically attached to
anything else is called a
"free amino acid".
central carbon atom
Characteristics of Free Amino Acids
A central carbon atom is attached to four chemical groups. The central carbon
is an asymmetric carbon atom unless R is identical to one of the other three
chemical groups.
Both the amino and the carboxylic acid functional group of free amino acids
are ionized at near neutral pH.
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Ways of Showing the Structural Formula of an Amino Acid
Uncharged form; does
not occur in aqueous
solutions at neutral
pH.
Charged form that
occurs in aqueous
solutions at near
neutral pH.
Detailed structure
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Abbreviated Structure
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Amino Acids Used to Construct Proteins
central carbon atom
H
+
H3N
C
COO
Twenty different kinds of amino acids are
used for constructing proteins, each with
a different "R" group.
R
Since the central carbon atom of an amino acid is asymmetrical, there are 2
enantiomers of each kind of amino acid. Cells use only the "L" enantiomer of each
kind of amino acid to construct proteins.
The R-group of a few kinds of amino acids carry an amino or a
carboxylic acid functional group. These amino acids carry three
electrical charges at pH values near 7.
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Aspartic Acid
Glycine
(shown without its
(shown without its
functional groups ionized) functional groups ionized)
Threonine
(shown without its
functional groups ionized)
How many electric charges
would this free amino acid
have in the cytoplasmic matrix
of a living cell?
How many electric charges
would this free amino acid
have in the cytoplasmic matrix
of a living cell?
How many electric charges
would this free amino acid
have in the cytoplasmic matrix
of a living cell?
How many asymmetric carbon
atoms does this free amino
acid contain?
How many asymmetric carbon
atoms does this free amino
acid contain?
How many asymmetric carbon
atoms does this free amino
acid contain?
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Formation of a Peptide Bond from Two Amino Acids
These atoms are lost as a
molecule of water during the
formation of a peptide bond.
These atoms are covalently
bonded together during
formation of a peptide bond
In most cases R1 and R2 will not be the same chemical structures.
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Dipeptide Formation From Two Amino Acids
+
H2O
aa1 + aa2
dehydration
reaction
dipeptide + H2O
Atoms of peptide bond
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A Peptide Bond Between Two Amino Acids
A peptide bond between two amino acids consists of
the four atoms shown at right. All 6 atoms shaded in
grey (above) lie in the same rigid plane, with the
double-bonded oxygen projecting in the opposite
direction from the hydrogen atom that is bonded to
the nitrogen atom.
O
C
The carboxylic acid and amino functional groups that
formed the peptide bond (see previous slide) can no
longer ionize after they have become incorporated into
a peptide bond.
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N
H
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Oligopeptides and Polypeptides
dipeptide: Two amino acids covalently bonded
together by a peptide bond:
oligopeptide:
3 - 20 amino acids
covalently bonded
together by peptide
bonds
tripeptide: Three amino acids covalently bonded
together by two peptide bonds
tetrapeptide: Four amino acids covalently bonded
together by three peptide bonds
polypeptide (also called a polypeptide chain):
More than twenty amino acids covalently bonded together by peptide bonds
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Oligopeptides and polypeptides have two distinct ends:
- an N-terminal end (also called an amino-terminal end,
- a C-terminal end (also called a carboxy-terminal end).
Example
N-terminal end
+
H3N
H
O
C
C
R1
H
H
N
H
C
R2
C
N
C-terminal end
COO -
O
A tripeptide
Can you identify the peptide bonds in this molecule?
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Hydrogen Bonding Between Two Peptide Groups
Direction of polypeptide chain
N-terminal
end
hydrogen bond
C-terminal
end
Direction of polypeptide chain
The structure imposed on portions of a polypeptide chain due to
hydrogen bonding between different peptide bonds is called the
secondary structure of the polypeptide chain.
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Multiple hydrogen bonds can form between adjacent
peptide groups along the folded polypeptide chain
Direction of polypeptide chain
N-terminal
end
additional
hydrogen bond
hydrogen bond
C-terminal
end
Direction of polypeptide chain
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A common secondary structure of polypeptide chains resembles
the shape of a stretched spring and is called the alpha-helix
conformation.
Abbreviated illustration
showing back-bone structure
and ribbon diagram of a
portion of a polypeptide chain
in an α-helix conformation.
Illustration showing all atoms of a
portion of a polypeptide chain in
an α-helix conformation. Yellow
lines represent hydrogen bonds.
This conformation is stabilized by multiple hydrogen
bonds between atoms of different peptide bonds.
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Another common secondary structure of polypeptide chains resembles
the shape of a sheet of paper folded back and forth; it is called the betasheet (or pleated sheet or beta pleated sheet) conformation.
The polypeptide chain may fold back again to
allow three (or more) regions of the polypeptide
chain to align in a thicker pleated sheet
conformation. Note the oxygen and hydrogen
atoms of peptide bonds that are projecting out
such that they are available to form additional
hydrogen bonds, which would expand the
pleated sheet. The R groups actually project at
approximately right angles to the plane of the
pleated sheet.
Illustration showing back-bone structure
and diagram of two portions of a
polypeptide chain that are aligned
together in a pleated sheet conformation.
As with the alpha-helix conformation, the pleated-sheet conformation is
stabilized by hydrogen bonding between atoms of different peptide bonds.
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Categories of R Groups
that Occur in Amino Acids
I. No R-group (glycine contains only H)
II. With R-group
A. Nonpolar R-Group
B. Polar R-Group
1. non-ionized
2. ionized
a. cationic
b. anionic
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generalized amino acid
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Leucine
Serine
an amino acid with a
nonpolar R-group
an amino acid with a polar,
non-charged R-group
R-groups are shown with a light pink background.
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Lysine
Aspartic acid
an amino acid with a
cationic R-group
an amino acid with
an anionic R-group
R-groups are shown with a light pink background.
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The Amino Acid Sequence of a Polypeptide Chain
From textbook Fig. 5.21, p. 82
Each living cell produces
several thousands of
different kinds of
polypeptide chains.
Some Features of This
Specific Polypeptide Chain
It consists of 127 amino acids.
Its N-terminal amino acid is Gly (G).
Its C-terminal amino acid is Glu (E).
Amino acid number 25 is Ala (A).
Each kind of polypeptide chain
has an exact number of amino acids.
The sequence of amino acids is exactly
the same for each copy of the same
kind of polypeptide chain.
The amino acids of a polypeptide
chain are numbered sequentially,
starting from the N-terminal (aminoterminal) end.
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Representation of a the Primary Structure of
a Portion of a Specific Polypeptide Chain
amino acids
peptide bonds
-
+
H3N
COO
Ala
A
Asp
D
Gly
G
Phe
F
Leu
L
Lys
K
Ser
S
Cys
C
Dotted line indicates
that the polypeptide
chain continues.
Dotted line indicates
that the polypeptide
chain continues.
Previously amino acids were given three-letter abbreviated names;
Now they are usually designated by one-letter abbreviated names.
The specific sequence of amino acids along a polypeptide chain, starting at the
N-terminal end, is called the primary structure of the polypeptide chain.
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In general the sequence is not a regular, repeating pattern.
It is unique to each different kind of polypeptide chain.
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Secondary Structures Contribute to the
Overall Size and Shape of a Polypeptide Chain
From Textbook Fig. 5.19, p. 81
An alpha-helix
secondary structure
A beta-sheet
secondary structure
Each alpha helix and each beta (pleated) sheet
contributes to only a portion of the overall threedimensional shape of the polypeptide chain.
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Examples of Specific R-groups
Along a Region of a Polypeptide Chain
one-letter amino acid identifier
backbone of
Polypeptide chain
R-groups of amino acids
The differing R-groups on different amino acids carry functional groups that confer
specific properties to each amino acid positioned along the polypeptide chain.
Some R groups along the polypeptide chain are nonpolar, some are polar and
uncharged, some are positively charged, and some are negatively charged.
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Kinds of Bonds that May Form Between Different R-Groups
When a Polypeptide Chain Bends and Folds in Various Ways
From textbook Fig. 5.21, p 83
Covalent bond
(Disulfide bond)
Polar bonds
Hydrogen bonds
Electrovalent (ionic)
bonds
Hydrophobic bonding
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Representations of the Conformation of a
Functional Polypeptide Chain
From Fig. 5.19, p. 81, of textbook
α helix
β sheet
disulfide
Ribbon model
Space-filling model
lysozyme
The three-dimensional shape (conformation) of a polypeptide chain is
called its tertiary structure.
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The secondary structure and tertiary structure of a polypeptide chain are
determined by its primary structure. Thus, each different polypeptide
chain with its unique sequence of amino acids also has its own unique
conformation.
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A ribbon structure of ribonuclease is shown, illustrating its native
conformation. Ribonuclease serves as a functional enzyme when in
this conformation.
Ribonuclease
A polypeptide chain that is folded into its normal, functional
conformation is said to be in its native conformation.
A polypeptide that is folded improperly so that it cannot function
is said to be to be denatured or in a denatured conformation.
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Relationship Between a Protein and a Polypeptide Chain
A polypeptide chain is a sequence of 20 or more amino acids held
together by peptide bonds.
When one or more polypeptide chains are folded in a conformation
that forms a functional unit, then the unit is called a protein (or an
active protein).
Thus, all proteins contain at least one polypeptide chain.
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Monomeric and Oligomeric Proteins
α-tubulin
lysozyme is
a monomeric protein
β-tubulin
tubulin is
a dimeric protein
A protein that consists of only one polypeptide chain is called a
monomeric protein.
Microtubules
are polymeric
proteins
A protein that consists of several (2 or a few) polypeptide chains is
called an oligomeric protein.
The three-dimensional shape of an oligomeric protein is called its
quaternary structure.
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The individual polypeptide chains of an oligomeric protein are
called subunits of the protein.
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