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Chem 191: Biochemistry
Lecture 9 – Proteins
I.
Introduction
A.
Protein means “first in importance”
II.
The Amino Acids
A.
Polymers of amino acids
B.
Only 20 are commonly found in proteins
C.
They are α-amino acids
Figure 19.1 - General Structure of α-amino acids
1.
2.
D.
They contain a carboxylic acid group.
The carbon adjacent to the carboxylic acid group is called the α(alpha)carbon.
3.
Attached to the α-carbon is an amino group.
Characteristic side chains.
1.
In addition to the carboxylic acid and amino groups, there is also an Rgroup attached to the α-carbon.
2.
Each amino acid has its own name
a.
They also have a three-letter and a one-letter abreviation
Table 19.1 - The Common Amino Acids
b.
c.
3.
The R-group is referred to as the amino acid sidechain.
Each of the 20 commonly occurring amino acids has a different
sidechain.
d.
Each amino acid sidechain has its own set of chemical and
physical properties.
Physical properties
a.
Non polar sidechains:
i.
Glycine
ii.
Alanine
iii.
Valine
iv.
Leucine
v.
Isoleucine
vi.
Proline
vii.
Phenylanine
viii. Methioine
b.
Polar but not charged at pH7:
i.
Serine
ii.
Threonine
iii.
Tyrosine
iv.
Tryptophan
v.
Asparagine
vi.
Glutamine
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Chem191
Lecture 9
c.
E.
F.
Proteins
vii.
Cysteine
Charged at pH7:
i.
Aspartic Acid (-)
ii.
Glutamic Acid (-)
iii.
Lysine (+)
iv.
Arginine (+)
v.
Histidine (0/+)
Abbreviations
Stereochemistery
1.
With the exception of glycine, the α-carbon atom is chiral
2.
All of the common amino acids used to make proteins have the Lconfiguration.
a.
These are absolute configurations analogous to L-glyceraldehyde.
i.
Using a Fisher-like projection, place the carboxylic acid
group at the top and the R-group at the bottom.
ii.
The L-configuration places the amino group on the left and
the hydrogen on the right.
III.
Zwitterions
A.
The carboxylic acid group is a stronger acid than water and the amino group is a
stronger base than water, therefore at pH 7 both are in their ionic form (-COOand -NH3+)
1.
This form is called the zwitterion which means “between ions”
2.
The zwitterion has a net charge of 0
a.
At lower pH values the carbolylate group becomes protonated and
the amino acid has a net charge of +1.
b.
At higher pH values the amino group becomes unprotonated and
the amino acid has a net charge of -1.
c.
There is no pH value for which both the carboxyl group and the
amino group are uncharged state.
3.
The isoelectric point is the pH value where the net charge on a molecule
is 0
IV.
Reactions of Amino Acids
A.
Oxidation of cysteine to form disulfide bonds (cystine)
1.
Two cysteine sidechain thiol groups (-SH) react to form a disulfide bond
(-S-S-)
a.
This is an oxidation reaction.
b.
This is an important reaction in proteins
2.
The two cysteines linked together by the disulfide bond are called cystine
Peptide formation
B.
Peptide bond formation
1.
As you learned in Chapter 16, amines and carboxylic acid can react to
form amides.
a.
When amino acids do this it is called a peptide bond.
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Chem191
Lecture 9
2.
C.
D.
E.
Proteins
When this reaction is done in a test tube acid chorides or and acid
anhydrides are used instead of the carboxylic acid.
a.
This is done to make the reaction more favorable.
3.
It is instructive, however, to write the reaction using the carboxylic acid
and the amine.
Forming peptides
1.
When two amino acids are bonded together by a peptide bond it is called a
dipeptide.
a.
Alanylglycine
2.
When several amino acids are bonded together by peptide bonds they are
called an oligopeptide.
3.
When many amino acids are bonded together by peptide bonds
polypeptides
a.
Your book suggests that the terms polypeptide and protein are
interchangeable.
i.
I prefer to use the term polypeptide to refer to a long chain
of amino acids connected by peptide bonds and to reserver
the term protein to refer to polypeptides that form a well
defined 3-dimensional structure and have a well-defined
function.
1.
This distinction may become clearer to you when
we discuss enzymes in the next chapter and when
we discuss how proteins fold later in this chapter.
4.
When the peptide bond forms, a carboxyl group and amino group
The N and C terminus of
Amino acid residues
V.
Important Peptides
A.
Peptide hormones
1.
Met and Leu enkephalin
2.
Oxytocin (9 aa)
a.
CYLQNCPLGNH2
b.
Smooth muscles of uterus to contract
c.
Stimulates milk ejection
3.
Vasopressin (9 aa)
a.
Raises blood pressure
b.
Antidiuretic hormone
c.
CYFQNCPRGNH2.
4.
ACTH (adrenocorticotropic hormone) from pituitary (39 aa)
5.
Insulin
6.
Human growth hormone
7.
somatostatin
VI.
Characteristics of Proteins
A.
Size
1.
6000 u to several million u
B.
Classification
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Chem191
Lecture 9
1.
2.
VII.
Proteins
Shape
a.
Fibrous proteins
b.
Globular proteins
Structure
a.
Simple
b.
Conjugated
i.
Prosthetic groups
The Primary structure of Proteins
A.
The primary structure is defined by a protein’s amino acid sequence
1.
With the exception of disulfide bonds between cyteine sidechains, this
defines all the covalent bonds in a protein
VIII. The Secondary Structure of Proteins
A.
The protein backbone can form local periodic structures.
B.
The two most common ones are the α-helix and the β-sheet
1.
Both these structure lead to hydrogen bond formation between the peptide
carbonyl oxygen and the peptide nitrogen.
IX.
The Tertiary Structure of Proteins
A.
Defines the arrangement of the elements of secondary structure.
1.
The α-helices and β-sheets are connected by loops
B.
Stabilized primarily by interactions between the sidechains; these interactions
include:
1.
Disulfide bonds
2.
Salt bridges
3.
Hydrogen bonds
4.
Hydrophobic interactions
X.
The Quaternary Structure of Proteins
A.
Proteins can assemble into bigger proteins.
1.
The proteins making up the bigger protein are called subunits.
XI.
Protein Hydrolysis and Denaturation
A.
Hydrolysis
1.
Heat
2.
Denaturants
a.
Alcohol
b.
Soaps
c.
Heavy metals Ag+, Hg+2, Pb+2
3.
pH
4